bioRxiv Channel: Northeastern University https://biorxiv.org This feed contains articles for bioRxiv Channel "Northeastern University" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Emergence of structural and dynamical properties of ecological mutualistic networks ]]> https://biorxiv.org/content/10.1101/001818v1?rss=1 Samir Suweis Filippo Simini Jayanth Banavar Amos Maritan 2014-01-14 doi:10.1101/001818 Cold Spring Harbor Laboratory Press 2014-01-14 <![CDATA[ Post-transcriptional regulation across human tissues ]]> https://biorxiv.org/content/10.1101/020206v1?rss=1 Alexander Franks Edoardo Airoldi Nikolai Slavov 2015-05-31 doi:10.1101/020206 Cold Spring Harbor Laboratory Press 2015-05-31 <![CDATA[ Extent of EMT promotes invasive, contact-induced sliding on progressively narrower fiber-like tracks ]]> https://biorxiv.org/content/10.1101/044800v1?rss=1 Daniel F Milano Senthil K Muthuswamy Anand R Asthagiri 2016-03-19 doi:10.1101/044800 Cold Spring Harbor Laboratory Press 2016-03-19 <![CDATA[ System-wide quantitative proteomics of the metabolic syndrome in mice: genotypic and dietary effects ]]> https://biorxiv.org/content/10.1101/051508v1?rss=1 Camille Terfve Eduard Sabido Yibo Wu Emanuel Goncalves Meena Choi Stefania Vaga Olga Vitek Julio Saez-Rodriguez Ruedi Aebersold 2016-05-03 doi:10.1101/051508 Cold Spring Harbor Laboratory Press 2016-05-03 <![CDATA[ Not just methods: User expertise explains the variability of outcomes of genome-wide studies ]]> https://biorxiv.org/content/10.1101/055046v1?rss=1 Kathleen E Lotterhos Olivier Francois Michael G.B. Blum 2016-05-24 doi:10.1101/055046 Cold Spring Harbor Laboratory Press 2016-05-24 <![CDATA[ MINOTAUR: A platform for the analysis and visualization of multivariate results from genome scans with R Shiny ]]> https://biorxiv.org/content/10.1101/062158v1?rss=1 Robert Verity Caitlin Collins Daren C. Card Sara M Schaal Liuyang Wang Kathleen Lotterhos 2016-07-05 doi:10.1101/062158 Cold Spring Harbor Laboratory Press 2016-07-05 <![CDATA[ Projected spread of Zika virus in the Americas ]]> https://biorxiv.org/content/10.1101/066456v1?rss=1 Qian Zhang Kaiyuan Sun Matteo Chinazzi Ana Pastore-Piontti Natalie E Dean Diana P Rojas Stefano Merler Dina Mistry Piero Poletti Luca Rossi Margaret Bray M. Elizabeth Halloran Ira M Longini Alessandro Vespignani 2016-07-28 doi:10.1101/066456 Cold Spring Harbor Laboratory Press 2016-07-28 <![CDATA[ A Novel Clustering Method for Patient Stratification ]]> https://biorxiv.org/content/10.1101/073189v1?rss=1 Hongfu Liu Rui Zhao Hongsheng Fang Feixiong Cheng Yun Fu Yang-Yu Liu 2016-09-03 doi:10.1101/073189 Cold Spring Harbor Laboratory Press 2016-09-03 <![CDATA[ Visual crowding is a combination of an increase of positional uncertainty, source confusion, and featural averaging ]]> https://biorxiv.org/content/10.1101/088898v1?rss=1 Harrison, W. J. Bex, P. J. 2016-11-21 doi:10.1101/088898 Cold Spring Harbor Laboratory Press 2016-11-21 <![CDATA[ Age-dependence and aging-dependence: The case of neuronal loss and lifespan in a C. elegans model of Parkinson’s disease ]]> https://biorxiv.org/content/10.1101/098038v1?rss=1 Apfeld, J. Fontana, W. 2017-01-04 doi:10.1101/098038 Cold Spring Harbor Laboratory Press 2017-01-04 <![CDATA[ Evidence for a Large-Scale Brain System Supporting Allostasis and Interoception in Humans ]]> https://biorxiv.org/content/10.1101/098970v1?rss=1 Kleckner, I. Zhang, J. Touroutoglou, A. Chanes, L. Xia, C. Simmons, W. K. Quigley, K. Dickerson, B. Barrett, L. 2017-01-10 doi:10.1101/098970 Cold Spring Harbor Laboratory Press 2017-01-10 <![CDATA[ From affect to control: Functional specialization of the insula in motivation and regulation ]]> https://biorxiv.org/content/10.1101/102368v1?rss=1 Wager, T. D. Barrett, L. F. 2017-01-24 doi:10.1101/102368 Cold Spring Harbor Laboratory Press 2017-01-24 <![CDATA[ Mass-spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation ]]> https://biorxiv.org/content/10.1101/102681v1?rss=1 Budnik, B. Levy, E. Slavov, N. 2017-01-24 doi:10.1101/102681 Cold Spring Harbor Laboratory Press 2017-01-24 <![CDATA[ Alternative REST Splicing Underappreciated ]]> https://biorxiv.org/content/10.1101/119552v1?rss=1 Chen, G.-L. Miller, G. M. 2017-03-22 doi:10.1101/119552 Cold Spring Harbor Laboratory Press 2017-03-22 <![CDATA[ A personalized, multi-omics approach identifies genes involved in cardiac hypertrophy and heart failure ]]> https://biorxiv.org/content/10.1101/120329v1?rss=1 Santolini, M. Romay, M. C. Yukhtman, C. L. Rau, C. D. Ren, S. Saucerman, J. J. Wang, J. J. Weiss, J. N. Wang, Y. Lusis, A. J. Karma, A. 2017-03-24 doi:10.1101/120329 Cold Spring Harbor Laboratory Press 2017-03-24 <![CDATA[ Pervasive Discordance Between mRNA And Protein Expression During Embryonic Stem Cell Differentiation ]]> https://biorxiv.org/content/10.1101/123497v1?rss=1 van den Berg, P. Budnik, B. Slavov, N. Semrau, S. 2017-04-03 doi:10.1101/123497 Cold Spring Harbor Laboratory Press 2017-04-03 <![CDATA[ Unexpected sequences and structures of mtDNA required for efficient transcription from the first heavy-strand promoter ]]> https://biorxiv.org/content/10.1101/129908v1?rss=1 Uchida, A. Murugesapillai, D. Wang, Y. Lodeiro, M. F. Prabhakar, S. Arnold, J. Maher, L. J. Williams, M. C. Cameron, C. E. 2017-04-24 doi:10.1101/129908 Cold Spring Harbor Laboratory Press 2017-04-24 <![CDATA[ Mitochondrial pseudogenes suggest repeated inter-species hybridization in hominid evolution. ]]> https://biorxiv.org/content/10.1101/134502v1?rss=1 Popadin, K. Gunbin, K. Peshkin, L. Annis, S. Kraytsberg, G. Markuzon, N. Ackermann, R. R. Khrapko, K. 2017-05-09 doi:10.1101/134502 Cold Spring Harbor Laboratory Press 2017-05-09 <![CDATA[ Role Of Chymotrypsin-Like Elastase 1 In Lung Physiology And in α1-Antitrypsin Deficiency ]]> https://biorxiv.org/content/10.1101/138776v1?rss=1 Joshi, R. Heinz, A. Fan, Q. Guo, S. Monia, B. Schmelzer, C. E. H. Weiss, A. S. Batie, M. Parameswaran, H. Varisco, B. M. 2017-05-16 doi:10.1101/138776 Cold Spring Harbor Laboratory Press 2017-05-16 <![CDATA[ Network integration of multi-tumour omics data suggests novel targeting strategies ]]> https://biorxiv.org/content/10.1101/146209v1?rss=1 Faria do Valle, I. Menichetti, G. Simonetti, G. Bruno, S. Zironi, I. Fernandes Durso, D. Mombach, J. C. M. Martinelli, G. Castellani, G. Remondini, D. 2017-06-05 doi:10.1101/146209 Cold Spring Harbor Laboratory Press 2017-06-05 <![CDATA[ Tolloid cleavage activates latent GDF8 by priming the pro-complex for dissociation ]]> https://biorxiv.org/content/10.1101/154823v1?rss=1 Le, V. Q. Iacob, R. E. Tian, Y. McConaughy, W. Su, Y. Zhao, B. Engen, J. R. Pirruccello-Straub, M. Springer, T. A. 2017-06-23 doi:10.1101/154823 Cold Spring Harbor Laboratory Press 2017-06-23 <![CDATA[ Human activities influence the direction and magnitude of local biodiversity change over time ]]> https://biorxiv.org/content/10.1101/162362v1?rss=1 Dunic, J. C. Elahi, R. Hensel, M. J. S. Kearns, P. J. O'Connor, M. I. Acuna, D. Honig, A. Wilson, A. R. Byrnes, J. E. K. 2017-07-12 doi:10.1101/162362 Cold Spring Harbor Laboratory Press 2017-07-12 <![CDATA[ Sensory discrimination by isolated feeding tentacles in Sanderia malayensis ]]> https://biorxiv.org/content/10.1101/162867v1?rss=1 Mori, K. Sullivan, M. Ayers, J. 2017-07-12 doi:10.1101/162867 Cold Spring Harbor Laboratory Press 2017-07-12 <![CDATA[ Determining whether a class of random graphs is consistent with an observed contact network ]]> https://biorxiv.org/content/10.1101/168047v1?rss=1 Nath, M. Ren, Y. Khorramzadeh, Y. Eubank, S. 2017-07-27 doi:10.1101/168047 Cold Spring Harbor Laboratory Press 2017-07-27 <![CDATA[ Quantifying homologous proteins and proteoforms ]]> https://biorxiv.org/content/10.1101/168765v1?rss=1 Malioutov, D. Chen, T. Jaffe, J. Airoldi, E. Carr, S. Budnik, B. Slavov, N. 2017-07-26 doi:10.1101/168765 Cold Spring Harbor Laboratory Press 2017-07-26 <![CDATA[ Preliminary results of models to predict areas in the Americas with increased likelihood of Zika virus transmission in 2017. ]]> https://biorxiv.org/content/10.1101/187591v1?rss=1 Asher, J. Barker, C. Chen, G. Cummings, D. Chinazzi, M. Daniel-Wayman, S. Fischer, M. Ferguson, N. Follman, D. Halloran, M. E. Johansson, M. Kugeler, K. Kwan, J. Lessler, J. Longini, I. M. Merler, S. Monaghan, A. Pastore y Piontti, A. Perkins, A. Prevots, D. R. Reiner, R. Rossi, L. Rodriguez-Barraquer, I. Siraj, A. S. Sun, K. Vespignani, A. Zhang, Q. 2017-09-18 doi:10.1101/187591 Cold Spring Harbor Laboratory Press 2017-09-18 <![CDATA[ Symbiodinium functional diversity and clade specificity under global change stressors ]]> https://biorxiv.org/content/10.1101/190413v1?rss=1 Davies, S. W. Ries, J. B. Marchetti, A. Granzotti, R. Castillo, K. D. 2017-09-18 doi:10.1101/190413 Cold Spring Harbor Laboratory Press 2017-09-18 <![CDATA[ Simulations for Designing and Interpreting Intervention Trials in Infectious Diseases ]]> https://biorxiv.org/content/10.1101/198051v1?rss=1 Halloran, M. E. Auranen, K. Baird, S. Basta, N. E. Bellan, S. Brookmeyer, R. Cooper, B. DeGruttola, V. Hughes, J. Lessler, J. Lofgren, E. T. Longini, I. Onnela, J.-P. Ozler, B. Seage, G. Smith, T. A. Vespignani, A. Vynnycky, E. Lipsitch, M. 2017-10-06 doi:10.1101/198051 Cold Spring Harbor Laboratory Press 2017-10-06 <![CDATA[ Asymmetric migration decreases stability but increases resilience in a heterogeneous metacommunity ]]> https://biorxiv.org/content/10.1101/201723v1?rss=1 Limdi, A. Perez-Escudero, A. Li, A. Gore, J. 2017-10-11 doi:10.1101/201723 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ Natural hybridization reveals incompatible alleles that cause melanoma in swordtail fish ]]> https://biorxiv.org/content/10.1101/2019.12.12.874586v1?rss=1 Powell, D. L. Garcia, M. Keegan, M. Reilly, P. Du, K. Diaz-Loyo, A. P. Banerjee, S. Blakkan, D. Reich, D. E. Andolfatto, P. Rosenthal, G. G. Schartl, M. Schumer, M. 2019-12-13 doi:10.1101/2019.12.12.874586 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ Delicate balances in cancer chemotherapy: modeling immune recruitment and emergence of systemic drug resistance ]]> https://biorxiv.org/content/10.1101/2019.12.12.874891v1?rss=1 Tran, A. P. Al-Radhawi, M. A. Kareva, I. Wu, J. Waxman, D. J. Sontag, E. D. 2019-12-13 doi:10.1101/2019.12.12.874891 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ Global broadcasting of local fractal fluctuations in a bodywide distributed system supports perception via effortful touch ]]> https://biorxiv.org/content/10.1101/2019.12.15.876961v1?rss=1 Mangalam, M. Carver, N. S. Kelty-Stephen, D. G. 2019-12-15 doi:10.1101/2019.12.15.876961 Cold Spring Harbor Laboratory Press 2019-12-15 <![CDATA[ FoodMine: Exploring Food Contents in Scientific Literature ]]> https://biorxiv.org/content/10.1101/2019.12.17.880062v1?rss=1 Hooton, F. Menichetti, G. Barabasi, A.-L. 2019-12-18 doi:10.1101/2019.12.17.880062 Cold Spring Harbor Laboratory Press 2019-12-18 <![CDATA[ Offline tDCS modulates prefrontal cortical-subcortical cerebellar fear pathways in delayed fear extinction ]]> https://biorxiv.org/content/10.1101/2019.12.18.880658v1?rss=1 Avila, A. G. Guiomar, R. Valerio, D. Goncalves, O. F. Almeida, J. 2019-12-19 doi:10.1101/2019.12.18.880658 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ A mathematical model exhibiting the effect of DNA methylation on the stability boundary in cell-fate networks ]]> https://biorxiv.org/content/10.1101/2019.12.19.883280v1?rss=1 Chen, T. Ali Al-Radhawi, M. Sontag, E. 2019-12-20 doi:10.1101/2019.12.19.883280 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ Self-regulation of single-stranded DNA wrapping dynamics by E. coli SSB promotes both stable binding and rapid dissociation ]]> https://biorxiv.org/content/10.1101/2019.12.20.885368v1?rss=1 Naufer, M. N. Morse, M. Möller, G. B. McIsaac, J. Rouzina, I. Beuning, P. J. Williams, M. 2019-12-21 doi:10.1101/2019.12.20.885368 Cold Spring Harbor Laboratory Press 2019-12-21 <![CDATA[ Validation of a Mathematical Model of Cancer Incorporating Spontaneous and Induced Evolution to Drug Resistance ]]> https://biorxiv.org/content/10.1101/2019.12.27.889444v1?rss=1 Gevertz, J. L. Greene, J. M. Sontag, E. D. 2019-12-28 doi:10.1101/2019.12.27.889444 Cold Spring Harbor Laboratory Press 2019-12-28 <![CDATA[ The Ortholog Conjecture Revisited: the Value of Orthologs and Paralogs in Function Prediction ]]> https://biorxiv.org/content/10.1101/2019.12.27.889691v1?rss=1 Stamboulian, M. Guerrero, R. F. Hahn, M. W. Radivojac, P. 2019-12-28 doi:10.1101/2019.12.27.889691 Cold Spring Harbor Laboratory Press 2019-12-28 <![CDATA[ General DNA methylation patterns and environmentally-induced differential methylation in the eastern oyster (Crassostrea virginica) ]]> https://biorxiv.org/content/10.1101/2020.01.07.897934v1?rss=1 Venkataraman, Y. R. Downey-Wall, A. Ries, J. Westfield, I. White, S. J. Roberts, S. Lotterhos, K. E. 2020-01-08 doi:10.1101/2020.01.07.897934 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Machine learning and dengue forecasting: Comparing random forests and artificial neural networks for predicting dengue burdens at the national sub-national scale in Colombia ]]> https://biorxiv.org/content/10.1101/2020.01.14.906297v1?rss=1 Zhao, N. Charland, K. Carabali, M. Nsoesie, E. Maher-Giroux, M. Rees, E. Yuan, M. Garcia Balaguera, C. Jaramillo Ramirez, G. Zinszer, K. 2020-01-14 doi:10.1101/2020.01.14.906297 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Atf-6 regulates lifespan through ER-mitochondrial calcium homeostasis ]]> https://biorxiv.org/content/10.1101/2020.01.14.906693v1?rss=1 Burkewitz, K. Dutta, S. Kelley, C. A. Steinbaugh, M. Cram, E. J. Mair, W. B. 2020-01-15 doi:10.1101/2020.01.14.906693 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Fluorescence Labeling of Circulating Tumor Cells with Folate Receptor Targeted Molecular Probes for Diffuse In Vivo Flow Cytometry ]]> https://biorxiv.org/content/10.1101/2020.01.22.913137v1?rss=1 Patil, R. A. Srinivasarao, M. Amiji, M. Low, P. S. Niedre, M. 2020-01-23 doi:10.1101/2020.01.22.913137 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Two dominant brain states reflect optimal and suboptimal attention ]]> https://biorxiv.org/content/10.1101/2020.01.31.928523v1?rss=1 Yamashita, A. Rothlein, D. Kucyi, A. Valera, E. M. Esterman, M. 2020-01-31 doi:10.1101/2020.01.31.928523 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ The SensorOverlord predicts the accuracy of measurements with ratiometric biosensors ]]> https://biorxiv.org/content/10.1101/2020.01.31.928895v1?rss=1 Stanley, J. A. Johnsen, S. B. Apfeld, J. 2020-02-01 doi:10.1101/2020.01.31.928895 Cold Spring Harbor Laboratory Press 2020-02-01 <![CDATA[ Gα/GSA-1 works upstream of PKA/KIN-1 to regulate calcium signaling and contractility in the Caenorhabditis elegans spermatheca ]]> https://biorxiv.org/content/10.1101/2020.02.03.932871v1?rss=1 Castaneda, P. G. Cecchetelli, A. D. Pettit, H. N. Cram, E. J. 2020-02-04 doi:10.1101/2020.02.03.932871 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Distinct error rates for reference and non-reference genotypes estimated by pedigree analysis ]]> https://biorxiv.org/content/10.1101/2020.02.06.937649v1?rss=1 Wang, R. J. Radivojac, P. Hahn, M. W. 2020-02-06 doi:10.1101/2020.02.06.937649 Cold Spring Harbor Laboratory Press 2020-02-06 <![CDATA[ Transcranial Photobiomodulation with Near-Infrared Light from Childhood to Elderliness: Simulation of Dosimetry ]]> https://biorxiv.org/content/10.1101/2020.02.06.937821v1?rss=1 Yuan, Y. Cassano, P. Pias, M. Fang, Q. 2020-02-07 doi:10.1101/2020.02.06.937821 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Improving model-based fNIRS analysis using mesh-based anatomical and light-transport models ]]> https://biorxiv.org/content/10.1101/2020.02.07.939447v1?rss=1 Tran, A. P. Yan, S. Fang, Q. 2020-02-09 doi:10.1101/2020.02.07.939447 Cold Spring Harbor Laboratory Press 2020-02-09 <![CDATA[ Integrating multimodal data sets into a mathematical framework to describe and predict therapeutic resistance in cancer ]]> https://biorxiv.org/content/10.1101/2020.02.11.943738v1?rss=1 Johnson, K. E. Howard, G. R. Morgan, D. Brenner, E. Gardner, A. L. Durrett, R. E. Mo, W. Al'Khafaji, A. M. Sontag, E. Jarrett, A. M. Yankeelov, T. E. Brock, A. 2020-02-12 doi:10.1101/2020.02.11.943738 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Brain activation and connectivity in anorexia nervosa and body dysmorphic disorder when viewing bodies: relationships to clinical symptoms and perception of appearance ]]> https://biorxiv.org/content/10.1101/2020.02.12.934083v1?rss=1 Moody, T. D. Morfini, F. Cheng, G. Sheen, C. L. Kerr, W. Strober, M. Feusner, J. D. 2020-02-13 doi:10.1101/2020.02.12.934083 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Accelerating Monte Carlo modeling of structured-light based diffuse optical imaging via "photon sharing" ]]> https://biorxiv.org/content/10.1101/2020.02.16.951590v1?rss=1 Yan, S. Yao, R. Intes, X. Fang, Q. 2020-02-17 doi:10.1101/2020.02.16.951590 Cold Spring Harbor Laboratory Press 2020-02-17 <![CDATA[ C. elegans processes sensory information to choose between freeloading and self-defense strategies ]]> https://biorxiv.org/content/10.1101/2020.02.24.963637v1?rss=1 Schiffer, J. Servello, F. Heath, W. Amrit, F. R. G. Stumbur, S. Johnsen, S. B. Stanley, J. A. Tam, H. Brennan, S. McGowan, N. Vogelaar, A. Xu, Y. Serkin, W. Ghazi, A. Apfeld, J. 2020-02-25 doi:10.1101/2020.02.24.963637 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Controlled neighbor exchanges drive glassy behavior, intermittency and cell streaming in epithelial tissues ]]> https://biorxiv.org/content/10.1101/2020.02.28.970541v1?rss=1 Das, A. Sastry, S. Bi, D. 2020-02-28 doi:10.1101/2020.02.28.970541 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ Resting-State Connectivity of Auditory and Reward Systems in Alzheimer's Disease and Mild Cognitive Impairment ]]> https://biorxiv.org/content/10.1101/2020.03.11.986125v1?rss=1 Wang, D. Belden, A. Geddes, M. R. Hanser, S. Loui, P. 2020-03-11 doi:10.1101/2020.03.11.986125 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Antibiotic hypersensitivity signatures identify targets for attack in the Acinetobacter baumannii cell envelope ]]> https://biorxiv.org/content/10.1101/2020.03.11.987479v1?rss=1 Geisinger, E. Mortman, N. J. Dai, Y. Cokol, M. Syal, S. Farinha, A. Fisher, D. Tang, A. Lazinski, D. W. Wood, S. Anthony, J. Opijnen, T. Isberg, R. R. 2020-03-12 doi:10.1101/2020.03.11.987479 Cold Spring Harbor Laboratory Press 2020-03-12 <![CDATA[ Exploring Chromosomal Structural Heterogeneity AcrossMultiple Cell Lines ]]> https://biorxiv.org/content/10.1101/2020.03.21.001917v1?rss=1 Cheng, R. R. Contessoto, V. Aiden, E. L. Wolynes, P. G. Di Pierro, M. Onuchic, J. N. 2020-03-22 doi:10.1101/2020.03.21.001917 Cold Spring Harbor Laboratory Press 2020-03-22 <![CDATA[ Addition of Multiple Introns to a Cas9 Gene Results in Dramatic Improvement in Efficiency for Generation of Gene Knockouts in Plants ]]> https://biorxiv.org/content/10.1101/2020.04.03.023036v1?rss=1 Grützner, R. Martin, P. Horn, C. Mortensen, S. Cram, E. J. Lee-Parsons, C. W. T. Stuttmann, J. Marillonnet, S. 2020-04-04 doi:10.1101/2020.04.03.023036 Cold Spring Harbor Laboratory Press 2020-04-04 <![CDATA[ Rapid Assessment of T-Cell Receptor Specificity of the Immune Repertoire ]]> https://biorxiv.org/content/10.1101/2020.04.06.028415v1?rss=1 Lin, X. George, J. T. Schafer, N. P. Clementi, C. Onuchic, J. N. Levine, H. 2020-04-07 doi:10.1101/2020.04.06.028415 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Phenotypic switching and adaptive strategies of cancer cells in response to stress: insights from live cell imaging and mathematical modeling ]]> https://biorxiv.org/content/10.1101/2020.04.06.028472v1?rss=1 Nam, A. Mohanty, A. Bhattacharya, S. Kotnala, S. Achuthan, S. Hari, K. Nathan, A. Rangarajan, G. Massarelli, E. Levine, H. Jolly, M. K. Kulkarni, P. Salgia, R. 2020-04-07 doi:10.1101/2020.04.06.028472 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Distributed implementation of Boolean functions by transcriptional synthetic circuits ]]> https://biorxiv.org/content/10.1101/2020.04.21.053231v1?rss=1 Ali Al-Radhawi, M. Tran, A. P. Ernst, E. Chen, T. Voigt, C. Sontag, E. 2020-04-22 doi:10.1101/2020.04.21.053231 Cold Spring Harbor Laboratory Press 2020-04-22 <![CDATA[ RADSex: a computational workflow to study sex determination using Restriction Site-Associated DNA Sequencing data ]]> https://biorxiv.org/content/10.1101/2020.04.22.054866v1?rss=1 Feron, R. Pan, Q. Wen, M. Imarazene, B. Jouanno, E. Anderson, J. Herpin, A. Journot, L. Parrinello, H. Klopp, C. Kottler, V. A. Roco, A. S. Du, K. Kneitz, S. Adolfi, M. Wilson, C. A. McCluskey, B. Amores, A. Desvignes, T. Goetz, F. W. Takanashi, A. Kawaguchi, M. Detrich, H. W. Oliveira, M. Nobrega, R. Sakamoto, T. Nakamoto, M. Wargelius, A. Karlsen, O. Wang, Z. Stöck, M. Waterhouse, R. M. Braasch, I. Postlethwait, J. H. Schartl, M. Guiguen, Y. 2020-04-23 doi:10.1101/2020.04.22.054866 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ New Music System Reveals Spectral Contribution to Statistical Learning ]]> https://biorxiv.org/content/10.1101/2020.04.29.068163v1?rss=1 Loui, P. 2020-04-30 doi:10.1101/2020.04.29.068163 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Epigenetic feedback and stochastic partitioning during cell division can drive resistance to EMT ]]> https://biorxiv.org/content/10.1101/2020.04.29.068239v1?rss=1 Jia, W. Tripathi, S. Chakraborty, P. Chedere, A. Rangarajan, A. Levine, H. Jolly, M. K. 2020-05-01 doi:10.1101/2020.04.29.068239 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ Evolution leads to emergence: An analysis of protein interactomes across the tree of life ]]> https://biorxiv.org/content/10.1101/2020.05.03.074419v1?rss=1 Hoel, E. Klein, B. Swain, A. Griebenow, R. Levin, M. 2020-05-03 doi:10.1101/2020.05.03.074419 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ Crystal Structure of the Werner's Syndrome Helicase ]]> https://biorxiv.org/content/10.1101/2020.05.04.075176v1?rss=1 Newman, J. A. Gavard, A. E. Lieb, S. Ravichandran, M. C. Hauer, K. Werni, P. Geist, L. Boettcher, J. Engen, J. R. Rumpel, K. Samwer, M. Petronczki, M. Gileadi, O. 2020-05-05 doi:10.1101/2020.05.04.075176 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Uncovering the genetic blueprint of the C. elegans nervous system ]]> https://biorxiv.org/content/10.1101/2020.05.04.076315v1?rss=1 Kovacs, I. A. Barabasi, D. L. Barabasi, A.-L. 2020-05-05 doi:10.1101/2020.05.04.076315 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Spiny mice (Acomys) exhibit attenuated hallmarks of aging and rapid cell turnover after UV exposure in the skin epidermis ]]> https://biorxiv.org/content/10.1101/2020.05.07.083287v1?rss=1 Wong, W. Kim, A. Seifert, A. W. Maden, M. Crane, J. D. 2020-05-10 doi:10.1101/2020.05.07.083287 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Proteomic Analysis Uncovers Measles Virus Protein C Interaction with p65/iASPP/p53 Protein Complex ]]> https://biorxiv.org/content/10.1101/2020.05.08.084418v1?rss=1 Meignie, A. Combredet, C. Santolini, M. Kovacs, I. A. Douche, T. Giai Gianetto, Q. Eun, H. Matondo, M. Jacob, Y. Grailhe, R. Tangy, F. Komarova, A. V. 2020-05-09 doi:10.1101/2020.05.08.084418 Cold Spring Harbor Laboratory Press 2020-05-09 <![CDATA[ TAZ inhibits GR and coordinates hepatic glucose homeostasis in normal physiologic states ]]> https://biorxiv.org/content/10.1101/2020.05.12.091264v1?rss=1 Xu, S. Liu, Y. Hu, R. Wang, M. Stohr, O. Xiong, Y. Chen, L. Kang, H. Zheng, L. Cai, S. He, L. Wang, C. Copps, K. D. White, M. Miao, J. 2020-05-14 doi:10.1101/2020.05.12.091264 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Multifractal signatures of perceptual processing on anatomical sleeves of the human body ]]> https://biorxiv.org/content/10.1101/2020.05.12.091702v1?rss=1 Mangalam, M. Carver, N. S. Kelty-Stephen, D. G. 2020-05-14 doi:10.1101/2020.05.12.091702 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ BAP31 regulated polarization of macrophages through C/EBP β in cutaneous wound healing ]]> https://biorxiv.org/content/10.1101/2020.05.14.095554v1?rss=1 Yuan, Q. Zhao, B. Cao, Y. Yan, J.-c. Sun, L.-j. Liu, X. Xu, Y. Wang, X.-y. Wang, B. 2020-05-15 doi:10.1101/2020.05.14.095554 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Hypothetical control of postural sway ]]> https://biorxiv.org/content/10.1101/2020.05.19.104760v1?rss=1 Mangalam, M. Kelty-Stephen, D. G. 2020-05-22 doi:10.1101/2020.05.19.104760 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Towards complete and error-free genome assemblies of all vertebrate species ]]> https://biorxiv.org/content/10.1101/2020.05.22.110833v1?rss=1 Rhie, A. McCarthy, S. A. Fedrigo, O. Damas, J. Formenti, G. Koren, S. Uliano-Silva, M. Chow, W. Fungtammasan, A. Gedman, G. L. Cantin, L. J. Thibaud-Nissen, F. Haggerty, L. Lee, C. Ko, B. J. Kim, J. Bista, I. Smith, M. Haase, B. Mountcastle, J. Winkler, S. Paez, S. Howard, J. Vernes, S. C. Lama, T. M. Grutzner, F. C. Warren, W. C. Balakrishnan, C. Burt, D. George, J. M. Biegler, M. Iorns, D. Digby, A. Eason, D. Edwards, T. Wilkinson, M. Turner, G. F. Meyer, A. Kautt, A. F. Franchini, P. Detrich, H. W. Svardal, H. Wagner, M. Naylor, G. J. P. Pippel, M 2020-05-23 doi:10.1101/2020.05.22.110833 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ What is an adaptive pattern of brain activity for a child? It depends on their environment ]]> https://biorxiv.org/content/10.1101/2020.05.29.124297v1?rss=1 Ellwood-Lowe, M. E. Whitfield-Gabrieli, S. Bunge, S. A. 2020-05-31 doi:10.1101/2020.05.29.124297 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Ocean acidification induces subtle shifts in gene expression and DNA methylation in mantle tissue of the Eastern oyster (Crassostrea virginica) ]]> https://biorxiv.org/content/10.1101/2020.06.05.136424v1?rss=1 Downey-Wall, A. Cameron, L. Ford, B. McNally, E. Venkataraman, Y. Roberts, S. Ries, J. Lotterhos, K. 2020-06-06 doi:10.1101/2020.06.05.136424 Cold Spring Harbor Laboratory Press 2020-06-06 <![CDATA[ Postural instability recruits shorter-timescale processes into the non-Gaussian cascade processes ]]> https://biorxiv.org/content/10.1101/2020.06.05.136895v1?rss=1 Furmanek, M. P. Mangalam, M. Kelty-Stephen, D. G. Juras, G. 2020-06-08 doi:10.1101/2020.06.05.136895 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ Reproductive Barriers as a Byproduct of Gene Network Evolution ]]> https://biorxiv.org/content/10.1101/2020.06.12.147322v1?rss=1 Yang, C.-H. Scarpino, S. V. 2020-06-13 doi:10.1101/2020.06.12.147322 Cold Spring Harbor Laboratory Press 2020-06-13 <![CDATA[ Negative interplay between biofilm formation and competence in the environmental strains of Bacillus subtilis ]]> https://biorxiv.org/content/10.1101/2020.06.15.153833v1?rss=1 She, Q. Hunter, E. Qin, Y. Nicolau, S. Zalis, E. A. Wang, H. Chen, Y. Chai, Y. 2020-06-16 doi:10.1101/2020.06.15.153833 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ The SPIRE1 actin nucleator coordinates actin/myosin functions in the regulation of mitochondrial motility ]]> https://biorxiv.org/content/10.1101/2020.06.19.161109v1?rss=1 Straub, F. Welz, T. Alberico, H. Brandao, R. O. Huber, A. Samol-Wolf, A. Brakebusch, C. Woods, D. Kollmar, M. Martin-Gonzalez, J. Kerkhoff, E. 2020-06-20 doi:10.1101/2020.06.19.161109 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Exposure duration modulates the response of Caribbean corals to global change stressors ]]> https://biorxiv.org/content/10.1101/2020.06.19.161711v1?rss=1 Aichelman, H. E. Bove, C. B. Castillo, K. D. Boulton, J. M. Knowlton, A. C. Nieves, O. C. Ries, J. B. Davies, S. W. 2020-06-20 doi:10.1101/2020.06.19.161711 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Universal features of epidemic models under social distancing guidelines ]]> https://biorxiv.org/content/10.1101/2020.06.21.163931v1?rss=1 Sadeghi, M. Greene, J. Sontag, E. 2020-06-22 doi:10.1101/2020.06.21.163931 Cold Spring Harbor Laboratory Press 2020-06-22 <![CDATA[ Ultra-compact Dual-band Smart NEMS Magnetoelectric Antennas for Simultaneous Wireless Energy Harvesting and Magnetic Field Sensing ]]> https://biorxiv.org/content/10.1101/2020.06.22.165894v1?rss=1 Zaeimbashi, M. Nasrollahpour, M. Khalifa, A. Romano, A. Liang, X. Chen, H. Sun, N. Matyushov, A. Lin, H. Dong, C. Xu, Z. Mittal, A. Martos-Repath, I. Jha, G. Mirchandani, N. Das, D. Onabajo, M. Shrivastava, A. Cash, S. Sun, N. 2020-06-23 doi:10.1101/2020.06.22.165894 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ 3D Visualization of Macromolecule Synthesis ]]> https://biorxiv.org/content/10.1101/2020.06.24.169300v1?rss=1 Duerr, T. J. Comellas, E. Jeon, E. K. Farkas, J. E. Joetzjer, M. Garnier, J. Shefelbine, S. J. Monaghan, J. R. 2020-06-26 doi:10.1101/2020.06.24.169300 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Dopamine-related striatal neurophysiology is associated with specialization of frontostriatal reward circuitry through adolescence ]]> https://biorxiv.org/content/10.1101/2020.06.24.169847v1?rss=1 Parr, A. C. Calabro, F. J. Larsen, B. Tervo-Clemmens, B. Foran, W. Olafsson, V. Luna, B. 2020-06-25 doi:10.1101/2020.06.24.169847 Cold Spring Harbor Laboratory Press 2020-06-25 <![CDATA[ Stiffening of the Extracellular Matrix is a Sufficient Condition for AirwayHyperreactivity. ]]> https://biorxiv.org/content/10.1101/2020.06.27.175687v1?rss=1 Jamieson, R. R. Stasiak, S. E. Polio, S. R. Ruberti, J. W. Parameswaran, H. 2020-06-29 doi:10.1101/2020.06.27.175687 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Resilience and evolvability of protein-protein interaction networks ]]> https://biorxiv.org/content/10.1101/2020.07.02.184325v1?rss=1 Klein, B. Holmer, L. Smith, K. M. Johnson, M. M. Swain, A. Stolp, L. Teufel, A. I. Kleppe, A. 2020-07-02 doi:10.1101/2020.07.02.184325 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Primary human colonic mucosal barrier crosstalk with super oxygen-sensitive Faecalibacterium prausnitzii in continuous culture ]]> https://biorxiv.org/content/10.1101/2020.07.02.185082v1?rss=1 Zhang, J. Huang, Y. Yoon, J.-Y. Kemmitt, J. Wright, C. Schneider, K. Sphabmixay, P. Hernandez-Gordillo, V. Holcomb, S. J. Bhushan, B. M. Rohatgi, G. Benton, K. Carpenter, D. Kester, J. Eng, G. Breault, D. T. Yilmaz, O. Taketani, M. Voigt, K. A. Carrier, R. L. Trumper, D. L. Griffith, L. G. 2020-07-03 doi:10.1101/2020.07.02.185082 Cold Spring Harbor Laboratory Press 2020-07-03 <![CDATA[ FLN-1/Filamin is required to anchor the actomyosin cytoskeleton and for global organization of sub-cellular organelles in a contractile tissue ]]> https://biorxiv.org/content/10.1101/2020.07.03.186965v1?rss=1 Kelley, C. A. Triplett, O. Mallick, S. Burkewitz, K. Mair, W. B. Cram, E. J. 2020-07-04 doi:10.1101/2020.07.03.186965 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Combinatorial transcriptional profiling of mouse and human enteric neurons identifies shared and disparate subtypes in situ. ]]> https://biorxiv.org/content/10.1101/2020.07.03.187211v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@1b41277org.highwire.dtl.DTLVardef@12856feorg.highwire.dtl.DTLVardef@1674dadorg.highwire.dtl.DTLVardef@11ca1c8_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG ]]> May-Zhang, A. A. Tycksen, E. Southard-Smith, A. N. Deal, K. K. Benthal, J. T. Buehler, D. P. Adam, M. Simmons, A. J. Monaghan, J. R. Matlock, B. K. Flaherty, D. K. Potter, S. Lau, K. S. Southard-Smith, E. M. 2020-07-04 doi:10.1101/2020.07.03.187211 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Cognitive Benefits of Exercise Interventions: An fMRI Activation Likelihood Estimation Meta-Analysis ]]> https://biorxiv.org/content/10.1101/2020.07.04.187401v1?rss=1 Yu, Q. Herold, F. Becker, B. KluGah-Brown, B. Zhang, Y. Perrey, S. Veronese, N. Muller, N. G. Zou, L. Kramer, A. F. 2020-07-06 doi:10.1101/2020.07.04.187401 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ A DNA-based optical nanosensor for in vivo imaging of acetylcholine in the peripheral nervous system ]]> https://biorxiv.org/content/10.1101/2020.07.06.189696v1?rss=1 Xia, J. Yang, H. Mu, M. Micovic, N. Poskanzer, K. E. Monaghan, J. R. Clark, H. A. 2020-07-06 doi:10.1101/2020.07.06.189696 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ Extracting neural signals from semi-immobilized animals with deformable non-negative matrix factorization ]]> https://biorxiv.org/content/10.1101/2020.07.07.192120v1?rss=1 Nejatbakhsh, A. Varol, E. Yemini, E. Venkatachalam, V. Lin, A. Samuel, A. D. T. Paninski, L. 2020-07-10 doi:10.1101/2020.07.07.192120 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ The heat shock transcription factor HSF-1 protects Caenorhabditis elegans from peroxide stress ]]> https://biorxiv.org/content/10.1101/2020.07.13.200634v1?rss=1 Servello, F. A. Apfeld, J. 2020-07-14 doi:10.1101/2020.07.13.200634 Cold Spring Harbor Laboratory Press 2020-07-14 <![CDATA[ Raf promotes dimerization of the Ras G-domain with increased allosteric connections ]]> https://biorxiv.org/content/10.1101/2020.07.15.205070v1?rss=1 Packer, M. Parker, J. A. Chung, J. K. Li, Z. Lee, Y. K. Cookis, T. Guterres, H. Alvarez, S. Hossain, M. A. Donnelly, D. P. Agar, J. N. Makowski, L. Buck, M. Groves, J. T. Mattos, C. 2020-07-15 doi:10.1101/2020.07.15.205070 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ Visual effort moderates postural cascade dynamics ]]> https://biorxiv.org/content/10.1101/2020.07.17.209486v1?rss=1 Mangalam, M. Lee, I.-C. Newell, K. M. Kelty-Stephen, D. G. 2020-07-19 doi:10.1101/2020.07.17.209486 Cold Spring Harbor Laboratory Press 2020-07-19 <![CDATA[ Visual effort moderates a self-correcting nonlinear postural control policy ]]> https://biorxiv.org/content/10.1101/2020.07.17.209502v1?rss=1 Kelty-Stephen, D. G. Lee, I.-C. Carver, N. S. Newell, K. M. Mangalam, M. 2020-07-19 doi:10.1101/2020.07.17.209502 Cold Spring Harbor Laboratory Press 2020-07-19 <![CDATA[ Proprioceptive afferents differentially contribute to effortful perception of object heaviness and mass distribution ]]> https://biorxiv.org/content/10.1101/2020.07.18.210401v1?rss=1 Mangalam, M. Desai, N. P. Singh, T. 2020-07-19 doi:10.1101/2020.07.18.210401 Cold Spring Harbor Laboratory Press 2020-07-19 <![CDATA[ Statistical classification of dynamic bacterial growth with sub-inhibitory concentrations of nanoparticles and its implications for disease treatment ]]> https://biorxiv.org/content/10.1101/2020.07.19.210930v1?rss=1 Jones, A.-A. D. Medina-Cruz, D. Kim, N. Y. Mi, G. Bartomeu Garcia, C. Baranda-Pellejero, L. Bassous, N. Webster, T. J. 2020-07-19 doi:10.1101/2020.07.19.210930 Cold Spring Harbor Laboratory Press 2020-07-19 <![CDATA[ Magnetic Temporal Interference For Noninvasive, High-resolution, and Localized Deep Brain Stimulation: Concept Validation ]]> https://biorxiv.org/content/10.1101/2020.07.20.212845v1?rss=1 Zaeimbashi, M. Khalifa, A. Dong, C. Wei, Y. Cash, S. Sun, N. 2020-07-21 doi:10.1101/2020.07.20.212845 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Retinal optic flow during natural locomotion ]]> https://biorxiv.org/content/10.1101/2020.07.23.217893v1?rss=1 Matthis, J. S. Muller, K. S. Bonnen, K. L. Hayhoe, M. M. 2020-07-24 doi:10.1101/2020.07.23.217893 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ The genetic architecture of the sexually selected sword ornament and its evolution in hybrid populations ]]> https://biorxiv.org/content/10.1101/2020.07.23.218164v1?rss=1 Powell, D. L. Payne, C. Keegan, M. Banerjee, S. M. Cui, R. Andolfatto, P. Schumer, M. Rosenthal, G. G. 2020-07-24 doi:10.1101/2020.07.23.218164 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ A mitochondrial mutational signature of temperature and longevity in ectothermic and endothermic vertebrates. ]]> https://biorxiv.org/content/10.1101/2020.07.25.221184v1?rss=1 G substitutions on a heavy chain (hereafter AH>GH) of mtDNA in aged mammals, interpreting it as a hallmark of age-related oxidative damage. In this study, we hypothesized that the occurrence of AH>GH substitutions may depend on the level of aerobic metabolism, which can be inferred from an organisms body temperature. To test this hypothesis, we used body temperature in endotherms and environmental temperature in ectotherms as proxies for metabolic rate and reconstructed mtDNA mutational spectra for 1350 vertebrate species. Our results showed that temperature was associated with increased rates of AH>GH and asymmetry of AH>GH in different species of ray-finned fishes and within geographically distinct clades of European anchovy. Analysis of nucleotide composition in the most neutral synonymous sites of fishes revealed that warm-water species were expectedly more A-poor and G-rich compared to cold-water species. Finally, we extended our analyses to all vertebrates and observed higher AH>GH and increased asymmetry of AH>GH in warm-blooded (mammals and birds) compared to cold-blooded (Actinopterygii, amphibia, reptilia) vertebrate classes. Overall, our findings suggest that temperature, through its influence on metabolism and oxidative damage, shapes the mutational properties and nucleotide content of the mtDNA in all vertebrates. ]]> Mikhailova, A. G. Shamanskiy, V. Mihailova, A. A. Ushakova, K. Tretiakov, E. Oreshkov, S. Knorre, D. Polishchuk, L. Lawless, D. Mazunin, I. Kunz, W. Tanaka, M. Fleischmann, Z. Aidlen, D. Makeev, V. Kuptsov, A. Fellay, J. S. Khrapko, K. Gunbin, K. Popadin, K. 2020-07-26 doi:10.1101/2020.07.25.221184 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ Regular Tai Chi Practice Is Associated with Improved Memory as well as Structural and Functional Integrity of the Hippocampal Formation in the Elderly ]]> https://biorxiv.org/content/10.1101/2020.07.26.222190v1?rss=1 Yue, C. Yu, Q. Zhang, Y. Herold, F. Mei, J. Kong, Z. Perrey, S. Liu, J. Muller, N. G. Zhang, Z. Tao, Y. Kramer, A. Becker, B. Zou, L. 2020-07-27 doi:10.1101/2020.07.26.222190 Cold Spring Harbor Laboratory Press 2020-07-27 <![CDATA[ Crystal structure reveals the full Ras:Raf interface and advances mechanistic understanding of Raf activation ]]> https://biorxiv.org/content/10.1101/2020.07.28.225938v1?rss=1 Cookis, T. Mattos, C. 2020-07-29 doi:10.1101/2020.07.28.225938 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ singlecellVR: interactive visualization of single-cell data in virtual reality ]]> https://biorxiv.org/content/10.1101/2020.07.30.229534v1?rss=1 Stein, D. F. Chen, H. Vinyard, M. E. Pinello, L. 2020-07-30 doi:10.1101/2020.07.30.229534 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ Control of aperture closure during reach-to-grasp movements in immersive haptic-free virtual reality ]]> https://biorxiv.org/content/10.1101/2020.08.01.232470v1?rss=1 Mangalam, M. Yarossi, M. Furmanek, M. P. Tunik, E. 2020-08-04 doi:10.1101/2020.08.01.232470 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Greater TMS-evoked frontoparietal effective connectivity is correlated with better cognitive performance ]]> https://biorxiv.org/content/10.1101/2020.08.03.234518v1?rss=1 Morris, T. P. Redondo-Camos, M. Cattaneo, G. Macia, D. Solana_Sanchez, J. Espana-Irla, G. Delgado-Galen, S. Alviarez-Schulze, V. Pachon Garcia, C. Santarnecchi, E. Tadayon, E. Ozdemir, R. Tormos-Munoz, J. M. Bartres-Faz, D. Pascual-Leone, A. Shafi, M. 2020-08-04 doi:10.1101/2020.08.03.234518 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ msiPL: Non-linear Manifold and Peak Learning of Mass Spectrometry Imaging Data Using Artificial Neural Networks ]]> https://biorxiv.org/content/10.1101/2020.08.13.250142v1?rss=1 Abdelmoula, W. M. Lopez, B. G.-C. Randall, E. C. Kapur, T. Sarkaria, J. N. White, F. M. Agar, J. N. Wells, W. M. Agar, N. Y. R. 2020-08-14 doi:10.1101/2020.08.13.250142 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Effects of SARS-CoV-2 Mutations on Protein Structures and Intraviral Protein-Protein Interactions ]]> https://biorxiv.org/content/10.1101/2020.08.15.241349v1?rss=1 Wu, S. Tian, C. Liu, P. Guo, D. Zheng, W. Huang, X. Zhang, Y. Liu, L. 2020-08-16 doi:10.1101/2020.08.15.241349 Cold Spring Harbor Laboratory Press 2020-08-16 <![CDATA[ Multifractality in postural sway supports quiet eye training in aiming tasks: A study of golf putting ]]> https://biorxiv.org/content/10.1101/2020.08.19.258053v1?rss=1 Jacobson, N. Berleman-Paul, Q. Mangalam, M. Kelty-Stephen, D. G. 2020-08-20 doi:10.1101/2020.08.19.258053 Cold Spring Harbor Laboratory Press 2020-08-20 <![CDATA[ A simple, high-throughput method of protein and label removal from extracellular vesicle samples ]]> https://biorxiv.org/content/10.1101/2020.08.20.260307v1?rss=1 Welsh, J. A. Killingswroth, B. Kepley, J. Traynor, T. McKinnon, K. Savage, J. Appel, D. Aldape, K. Camphausen, K. Berzofsky, J. A. Ivanov, A. R. Ghiran, I. H. Jones, J. C. 2020-08-21 doi:10.1101/2020.08.20.260307 Cold Spring Harbor Laboratory Press 2020-08-21 <![CDATA[ Optimizing accuracy and depth of protein quantification in experiments using isobaric carriers ]]> https://biorxiv.org/content/10.1101/2020.08.24.264994v1?rss=1 Specht, H. Slavov, N. 2020-08-24 doi:10.1101/2020.08.24.264994 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ PFRED: A computational platform for siRNA and antisense oligonucleotides design. ]]> https://biorxiv.org/content/10.1101/2020.08.25.265983v1?rss=1 Sciabola, S. Xi, H. Cruz, D. Cao, Q. Lawrence, C. Zhang, T. Rotstein, S. Hughes, J. D. Caffrey, D. R. Stanton, R. V. 2020-08-25 doi:10.1101/2020.08.25.265983 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ Gene expression profiles of inflammatory breast cancer reveal high heterogeneity across the epithelial-hybrid-mesenchymal spectrum ]]> https://biorxiv.org/content/10.1101/2020.08.27.267609v1?rss=1 Chakraborty, P. George, J. T. Woodward, W. Levine, H. Jolly, M. K. 2020-08-27 doi:10.1101/2020.08.27.267609 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ Predicting the Health Impact of Dietary Polyphenols Using a Network Medicine Framework ]]> https://biorxiv.org/content/10.1101/2020.08.27.270173v1?rss=1 do Valle, I. F. Roweth, H. G. Malloy, M. W. Moco, S. Barron, D. Battinelli, E. Loscalzo, J. Barabasi, A.-L. 2020-08-28 doi:10.1101/2020.08.27.270173 Cold Spring Harbor Laboratory Press 2020-08-28 <![CDATA[ De novo genome assembly of the Tobacco Hornworm moth (Manduca sexta) ]]> https://biorxiv.org/content/10.1101/2020.08.29.270983v1?rss=1 14 Mb. We annotated the assembly by lifting over existing annotations and supplementing with additional supporting RNA-based data for a total of 25,256 genes. The new reference assembly is accessible in annotated form for public use. We demonstrate that improved continuity of the M. sexta genome improves resequencing studies and benefits future research on M. sexta as a model organism. ]]> Gershman, A. Romer, T. G. Fan, Y. Razaghi, R. Smith, W. A. Timp, W. 2020-08-31 doi:10.1101/2020.08.29.270983 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Deep learning and alignment of spatially-resolved whole transcriptomes of single cells in the mouse brain with Tangram ]]> https://biorxiv.org/content/10.1101/2020.08.29.272831v1?rss=1 Biancalani, T. Scalia, G. Buffoni, L. Avasthi, R. Lu, Z. Sanger, A. Tokcan, N. Vanderburg, C. R. Segerstolpe, A. Zhang, M. Avraham-Davidi, I. Vickovic, S. Nitzan, M. Ma, S. Buenrostro, J. D. Brown, N. B. Fanelli, D. Zhuang, X. Macosko, E. Regev, A. 2020-08-30 doi:10.1101/2020.08.29.272831 Cold Spring Harbor Laboratory Press 2020-08-30 <![CDATA[ Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon-anticodon pairing ]]> https://biorxiv.org/content/10.1101/2020.09.01.277525v1?rss=1 Hoffer, E. D. Hong, S. Maehigashi, T. Gonzalez, R. L. Whitford, P. Dunham, C. M. 2020-09-01 doi:10.1101/2020.09.01.277525 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Time scales of mixing in an imperforate scleractinian coelenteron ]]> https://biorxiv.org/content/10.1101/2020.09.03.281709v1?rss=1 Williams, S. D. Patterson, M. R. 2020-09-04 doi:10.1101/2020.09.03.281709 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ Natural sensory context drives diverse brain-wide activity during C. elegans mating ]]> https://biorxiv.org/content/10.1101/2020.09.09.289454v1?rss=1 Susoy, V. Hung, W. Witvliet, D. Whitener, J. E. Wu, M. Graham, B. J. Zhen, M. Venkatachalam, V. Samuel, A. D. T. 2020-09-10 doi:10.1101/2020.09.09.289454 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Improved Prediction of Smoking Status via Isoform-Aware RNA-seq Deep Learning Models ]]> https://biorxiv.org/content/10.1101/2020.09.09.290395v1?rss=1 Wang, Z. Masoomi, A. Xu, Z. Boueiz, A. Lee, S. Zhao, T. Cho, M. Hersh, C. P. Silverman, E. K. Dy, J. Castaldi, P. 2020-09-13 doi:10.1101/2020.09.09.290395 Cold Spring Harbor Laboratory Press 2020-09-13 <![CDATA[ Proteomics of autophagy deficient macrophages reveals enhanced antimicrobial immunity via the oxidative stress response ]]> https://biorxiv.org/content/10.1101/2020.09.10.291344v1?rss=1 Maculins, T. Verschueren, E. Hinkle, T. Chang, P. Chalouni, C. Lim, J. Katakam, A. K. Kunz, R. C. Erickson, B. K. Huang, T. Choi, M. Tsai, T.-H. Vitek, O. Reichelt, M. Rohde, J. R. Dikic, I. Kirkpatrick, D. S. Murthy, A. 2020-09-12 doi:10.1101/2020.09.10.291344 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ A non-canonical EZH2 function sensitizes solid tumors to genotoxic stress ]]> https://biorxiv.org/content/10.1101/2020.09.11.291534v1?rss=1 LIAO, Y. Chen, C.-H. Shah, N. Xiao, T. Feit, A. Yang, M. Cai, C. Gao, S. Xue, P. Liu, Z. Xu, H. Lee, J. Li, W. Mei, S. Pierre, R. S. Shu, S. Fei, T. Duarte, M. Zhao, J. Bradner, J. E. Polyak, K. Kantoff, P. W. Long, H. Balk, S. W. Liu, S. X. Brown, M. Xu, K. 2020-09-11 doi:10.1101/2020.09.11.291534 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ Assessing and Predicting Efficacy of Dance Intervention for Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2020.09.14.297325v1?rss=1 Krotinger, A. Loui, P. 2020-09-15 doi:10.1101/2020.09.14.297325 Cold Spring Harbor Laboratory Press 2020-09-15 <![CDATA[ Essential gene analysis in Acinetobacter baumannii by high-density transposon mutagenesis and CRISPR interference ]]> https://biorxiv.org/content/10.1101/2020.09.15.299016v1?rss=1 Bai, J. Dai, Y. Farinha, A. Tang, A. Y. Syal, S. Vargas-Cuebas, G. Surujon, D. Isberg, R. R. van Opijnen, T. Geisinger, E. 2020-09-16 doi:10.1101/2020.09.15.299016 Cold Spring Harbor Laboratory Press 2020-09-16 <![CDATA[ Innervated adrenomedullary microphysiological system to model prenatal nicotine and opioid exposure ]]> https://biorxiv.org/content/10.1101/2020.09.22.308973v1?rss=1 Soucy, J. R. Burchett, G. Brady, R. Breault, D. T. Koppes, A. N. Koppes, R. A. 2020-09-22 doi:10.1101/2020.09.22.308973 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Robust Self-Regeneratable Stiff Living Materials ]]> https://biorxiv.org/content/10.1101/2020.09.24.311589v1?rss=1 Manjula-Basavanna, A. Duraj-Thatte, A. Joshi, N. S. 2020-09-25 doi:10.1101/2020.09.24.311589 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Insights into the diversity and survival strategies of soil bacterial isolates from the Atacama Desert ]]> https://biorxiv.org/content/10.1101/2020.09.24.312199v1?rss=1 Reverdy, A. Hathaway, D. Jha, J. Sullivan, J. Michaels, G. Diaz Mac-Adoo, D. Riquelme, C. Chai, Y. Godoy, V. G. 2020-09-24 doi:10.1101/2020.09.24.312199 Cold Spring Harbor Laboratory Press 2020-09-24 <![CDATA[ A hybrid mesh and voxel based Monte Carlo algorithm for accurate and efficient photon transport modeling in complex bio-tissues ]]> https://biorxiv.org/content/10.1101/2020.10.01.322982v1?rss=1 Yan, S. Fang, Q. 2020-10-03 doi:10.1101/2020.10.01.322982 Cold Spring Harbor Laboratory Press 2020-10-03 <![CDATA[ Oxygen-generating cryogels restore T cell-mediated cytotoxicity in hypoxic tumors ]]> https://biorxiv.org/content/10.1101/2020.10.08.329805v1?rss=1 Colombani, T. Eggermont, L. J. Hatfield, S. M. Rezaeeyazdi, M. Memic, A. Sitkovsky, M. V. Bencherif, S. A. 2020-10-09 doi:10.1101/2020.10.08.329805 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Light transport modeling in highly complex tissues using implicit mesh-based Monte Carlo algorithm ]]> https://biorxiv.org/content/10.1101/2020.10.11.335232v1?rss=1 Yan, S. Yuan, Y. Fang, Q. 2020-10-12 doi:10.1101/2020.10.11.335232 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ Naegleria fowleri: protein structures to facilitate drug discovery for the deadly, pathogenic free-living amoeba ]]> https://biorxiv.org/content/10.1101/2020.10.20.327296v1?rss=1 Barret, K. Tillery, L. Goldstein, J. Lassner, J. W. Osterhout, B. Tran`, N. L. Xu, L. Young, R. Craig, J. Chun, I. Dranow, D. M. Abendroth, J. Delker, S. L. Davies, D. R. Mayclin, S. J. Calhoun, B. Bolejack, M. J. Staker, B. Subramanian, S. Phan, I. Q. Lorimer, D. D. Myler, P. J. Edwards, T. E. Kyle, D. E. Rice, C. A. Morris, J. Leahy, J. W. Manetsch, R. Barrett, L. K. Van Voorhis, W. 2020-10-20 doi:10.1101/2020.10.20.327296 Cold Spring Harbor Laboratory Press 2020-10-20 <![CDATA[ Multifractality distinguishes reactive from proactive cascades in postural control ]]> https://biorxiv.org/content/10.1101/2020.10.21.349589v1?rss=1 Kelty-Stephen, D. Furmanek, M. P. Mangalam, M. 2020-10-22 doi:10.1101/2020.10.21.349589 Cold Spring Harbor Laboratory Press 2020-10-22 <![CDATA[ Protein hyperacylation links mitochondrial dysfunction with nuclear organization ]]> https://biorxiv.org/content/10.1101/2020.10.23.350892v1?rss=1 Smestad, J. A. McCauley, M. Amato, M. Xiong, Y. Liu, J. Sin, Y.-C. Ellingson, J. Chen, Y. Al Khazal, F. Wilbanks, B. Lee, J.-H. Ordog, T. Rouzina, I. Williams, M. C. Locasale, J. Maher, L. J. 2020-10-23 doi:10.1101/2020.10.23.350892 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ A two-hit adversity model in developing rats reveals sex-specific impacts on prefrontal cortex structure and behavior ]]> https://biorxiv.org/content/10.1101/2020.10.23.352161v1?rss=1 Gildawie, K. R. Ryll, L. M. Hexter, J. C. Peterzell, S. Valentine, A. A. Brenhouse, H. C. 2020-10-25 doi:10.1101/2020.10.23.352161 Cold Spring Harbor Laboratory Press 2020-10-25 <![CDATA[ A computational neural model for mapping degenerate neural architectures ]]> https://biorxiv.org/content/10.1101/2020.11.13.382192v1?rss=1 Khan, Z. Wang, Y. Sennesh, E. Z. Dy, J. Ostadabbas, S. van de Meent, J.-W. Hutchinson, J. B. Satpute, A. B. 2020-11-16 doi:10.1101/2020.11.13.382192 Cold Spring Harbor Laboratory Press 2020-11-16 <![CDATA[ Bell-shaped dose response for a system with no IFFLs ]]> https://biorxiv.org/content/10.1101/2020.11.17.387605v1?rss=1 Sontag, E. 2020-11-20 doi:10.1101/2020.11.17.387605 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Modeling Side-Stream Enhanced Biological Phosphorus Removal (S2EBPR) System Using Agent-based Model with Adaptive Maintenance, Decay and TCA Metabolism ]]> https://biorxiv.org/content/10.1101/2020.11.18.387589v1?rss=1 Li, G. Tooker, N. B. Wang, D. Srinivasan, V. Barnard, J. L. Russel, A. Takacs, I. Bott, C. Dobrowski, P. Onnis-Hayden, A. Gu, A. Z. 2020-11-18 doi:10.1101/2020.11.18.387589 Cold Spring Harbor Laboratory Press 2020-11-18 <![CDATA[ Hybrid Living Capsules Autonomously Produced by Engineered Bacteria ]]> https://biorxiv.org/content/10.1101/2020.11.23.394965v1?rss=1 Birnbaum, D. P. Manula-Basavanna, A. Kan, A. Joshi, N. S. 2020-11-24 doi:10.1101/2020.11.23.394965 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ Ultra-high field (7T) functional magnetic resonance imaging in amyotrophic lateral sclerosis ]]> https://biorxiv.org/content/10.1101/2020.12.02.408278v1?rss=1 Barry, R. Babu, S. Anteraper, S. Triantafyllou, C. Keil, B. Rowe, O. Rangaprakash, D. Paganoni, S. Lawson, R. Dheel, C. Cernasov, P. Rosen, B. Ratai, E.-M. Atassi, N. 2020-12-03 doi:10.1101/2020.12.02.408278 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Confocal imaging capacity on a widefield microscope using a spatial light modulator ]]> https://biorxiv.org/content/10.1101/2020.12.03.409581v1?rss=1 Wang, Y. L. Grooms, N. W. F. Civale, S. C. Chung, S. H. 2020-12-03 doi:10.1101/2020.12.03.409581 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Machine Learning-based Biomarkers Identification and Validation from Toxicogenomics - Bridging to Regulatory Relevant Phenotypic Endpoints ]]> https://biorxiv.org/content/10.1101/2020.12.18.423486v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@11bc876org.highwire.dtl.DTLVardef@105ebc2org.highwire.dtl.DTLVardef@1b91a63org.highwire.dtl.DTLVardef@1738486_HPS_FORMAT_FIGEXP M_FIG TOC Art C_FIG ]]> Rahman, S. M. Lan, J. Kaeli, D. Dy, J. Alshawabkeh, A. Gu, A. Z. 2020-12-21 doi:10.1101/2020.12.18.423486 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ Machine Leaning-based Determination of Sampling Depth for Complex Environmental Systems: Case Study with Single-Cell Raman Spectroscopy Data in EBPR Systems ]]> https://biorxiv.org/content/10.1101/2020.12.18.423496v1?rss=1 View larger version (56K): org.highwire.dtl.DTLVardef@1261a6eorg.highwire.dtl.DTLVardef@91369aorg.highwire.dtl.DTLVardef@197f64dorg.highwire.dtl.DTLVardef@1ab3c19_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Li, G. Wu, C. Wang, D. Srinivasan, V. Kaeli, D. R. Dy, J. G. Gu, A. Z. 2020-12-21 doi:10.1101/2020.12.18.423496 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ Stable Polymer Bilayers for Protein Channel Recordings at High Guanidinium Chloride Concentrations ]]> https://biorxiv.org/content/10.1101/2020.12.29.424722v1?rss=1 Yu, L. Kang, X. Alibakhshi, M. A. Pavlenok, M. Niederweis, M. E. Wanunu, M. 2020-12-30 doi:10.1101/2020.12.29.424722 Cold Spring Harbor Laboratory Press 2020-12-30 <![CDATA[ Bottom-up inputs are required for the establishment of top-down connectivity onto cortical layer 1 neurogliaform cells ]]> https://biorxiv.org/content/10.1101/2021.01.08.425944v1?rss=1 Ibrahim, L. A. Huang, S. Otero, M. F. Sherer, M. Vemuri, S. Xu, Q. Machold, R. Rudy, B. Fishell, G. 2021-01-09 doi:10.1101/2021.01.08.425944 Cold Spring Harbor Laboratory Press 2021-01-09 <![CDATA[ Combined Enhanced Biological Phosphorus Removal (EBPR) and Nitrite Accumulation for Treating High-strength Wastewater ]]> https://biorxiv.org/content/10.1101/2021.01.16.426983v1?rss=1 Yuan, Z. Kang, D. Li, G. Lee, J. Han, I. Wang, D. Zheng, P. Reid, M. C. Gu, A. Z. 2021-01-19 doi:10.1101/2021.01.16.426983 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ Sterically-Confined Rearrangements of SARS-CoV-2 Spike Protein Control Cell Invasion ]]> https://biorxiv.org/content/10.1101/2021.01.18.427189v1?rss=1 Dodero Rojas, E. Onuchic, J. N. Whitford, P. 2021-01-19 doi:10.1101/2021.01.18.427189 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ Bacterial galactosemia is caused by cytoplasmic interference of an essential cell wall biosynthesis glycosyltransferase ]]> https://biorxiv.org/content/10.1101/2021.01.22.426804v1?rss=1 Habib, C. Mueller, A. Liu, M. Zhu, J. Schneider, T. Garner, E. Sun, Y. Chai, Y. 2021-01-22 doi:10.1101/2021.01.22.426804 Cold Spring Harbor Laboratory Press 2021-01-22 <![CDATA[ PIP2 regulation of TRPC5 channel activation and desensitization ]]> https://biorxiv.org/content/10.1101/2021.01.25.428089v1?rss=1 Ningoo, M. Plant, L. D. Greka, A. Logothetis, D. E. 2021-01-26 doi:10.1101/2021.01.25.428089 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Generalizable prediction of stimulus-independent, task-unrelated thought from functional brain networks ]]> https://biorxiv.org/content/10.1101/2021.01.25.428126v1?rss=1 Kucyi, A. Esterman, M. Capella, J. Green, A. Uchida, M. Biederman, J. Gabrieli, J. D. E. Valera, E. M. Whitfield-Gabrieli, S. 2021-01-26 doi:10.1101/2021.01.25.428126 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Resting State Functional Connectivity Predicts Future Changes in Sedentary Behavior ]]> https://biorxiv.org/content/10.1101/2021.01.26.428161v1?rss=1 Morris, T. P. Kucyi, A. Arnold Anteraper, S. Geddes, M. R. Nieto-Castanon, A. Burzynska, A. Gothe, N. Fanning, J. Salerno, E. Whitfield-Gabrieli, S. Hillman, C. H. McAuley, E. Kramer, A. F. 2021-01-27 doi:10.1101/2021.01.26.428161 Cold Spring Harbor Laboratory Press 2021-01-27 <![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[ Electrical Unfolding of Cytochrome c During Translocation Through a Nanopore Constriction ]]> https://biorxiv.org/content/10.1101/2021.02.10.430607v1?rss=1 Tripathi, P. Benabbas, A. Mehrafrooz, B. Yamazaki, H. Aksimentiev, A. Champion, P. Wanunu, M. 2021-02-11 doi:10.1101/2021.02.10.430607 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ FRET-based screening in HEK293T identifies p38 MAPK and PKC inhibition as therapeutic targets for α-synuclein aggregation ]]> https://biorxiv.org/content/10.1101/2021.02.16.431382v1?rss=1 Svanbergsson, A. Ek, F. Martinsson, I. Rodo, J. Liu, D. Brandi, E. Haikal, C. Torres-Garcia, L. Li, W. Gouras, G. Olsson, R. Bjorklund, T. Li, J.-Y. 2021-02-16 doi:10.1101/2021.02.16.431382 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Engineering the Immune Adaptor Protein STING as a Biologic ]]> https://biorxiv.org/content/10.1101/2021.02.18.431824v1?rss=1 Sun, X. Ni, Y. He, Y. Yang, M. Tani, T. Kitajima, S. Barbie, D. A. Li, J. 2021-02-18 doi:10.1101/2021.02.18.431824 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Chemoenzymatic labeling of DNA methylation patterns for single-molecule epigenetic mapping ]]> https://biorxiv.org/content/10.1101/2021.02.24.432628v1?rss=1 Gabrieli, T. Michaeli, Y. Avraham, S. Torchinsky, D. Juhasz, M. Coruh, C. Arbib, N. Zhou, Z. S. Law, J. A. Weinhold, E. Ebenstein, Y. 2021-02-24 doi:10.1101/2021.02.24.432628 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ Bi-phasic dynamics of the mitochondrial DNA mutation m.3243A>G in blood: An unbiased, mutation level-dependent model implies positive selection in the germline. ]]> https://biorxiv.org/content/10.1101/2021.02.26.433045v1?rss=1 G) is the most common pathogenic mtDNA variant responsible for disease in humans. It is widely accepted that m.3243A>G levels decrease in blood with age, and an age correction representing [~]2% annual decline is often applied to account for this change in mutation level. Here we report that recent data indicate the dynamics of m.3243A>G are more complex and depend on the mutation level in blood in a bi-phasic way. Consequently, the traditional 2% correction, which is adequate on average, creates opposite predictive biases at high and low mutation levels. Unbiased age correction is needed to circumvent these drawbacks of the standard model. We propose to eliminate both biases by using an approach where age correction depends on mutation level in a biphasic way to account for the dynamics of m.3243A>G in blood. The utility of this approach was further tested in estimating germline selection of m.3243A>G. The biphasic approach permitted us to uncover patterns consistent with the possibility of positive selection for m.3243A>G. Germline selection of m.3243A>G shows an arching profile by which selection is positive at intermediate mutant fractions and declines at high and low mutant fractions. We conclude that use of this biphasic approach will greatly improve the accuracy of modelling changes in mtDNA mutation frequencies in the germline and in somatic cells during aging. ]]> Fleishmann, Z. Pickett, S. J. Franco, M. Aidlen, D. Khrapko, M. Stein, D. Markuzon, N. Popadin, K. Braverman, M. Woods, D. C. Tilly, J. L. Turnbull, D. Khrapko, K. 2021-02-26 doi:10.1101/2021.02.26.433045 G in blood: An unbiased, mutation level-dependent model implies positive selection in the germline.]]> Cold Spring Harbor Laboratory Press 2021-02-26 <![CDATA[ Abnormal function in dentate nuclei precedes the onset of psychosis: a resting-state fMRI study in high-risk individuals ]]> https://biorxiv.org/content/10.1101/2021.02.28.433240v1?rss=1 Arnold Anteraper, S. Guell, X. Collin, G. Qi, Z. Ren, J. Nair, A. Seidman, L. J. Keshavan, M. S. Zhang, T. Tang, Y. Li, H. McCarley, R. W. Niznikiewicz, M. A. Shenton, M. E. Stone, W. S. Wang, J. Whitfield-Gabrieli, S. 2021-03-02 doi:10.1101/2021.02.28.433240 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ FAM57B is a modulator of ceramide synthesis that regulates sphingolipid homeostasis and synaptic composition in the developing brain ]]> https://biorxiv.org/content/10.1101/2021.03.02.433619v1?rss=1 Tomasello, D. L. Kim, J. L. Khodour, Y. McCammon, J. M. Mitalipova, M. Jaenisch, R. Futerman, A. H. Sive, H. 2021-03-02 doi:10.1101/2021.03.02.433619 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ 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[ Refining Convergent Rate Analysis with Topology in Mammalian Longevity and Marine Transitions ]]> https://biorxiv.org/content/10.1101/2021.03.06.434197v1?rss=1 Treaster, S. Daane, J. M. Harris, M. 2021-03-08 doi:10.1101/2021.03.06.434197 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Beyond residence time: quantifying factors that drive the spatially explicit filtration services of a 'pristine' oyster population ]]> https://biorxiv.org/content/10.1101/2021.03.10.434772v1?rss=1 Gray, M. W. Pinton, D. Canestrelli, A. Marcum, P. Dix, N. Kimbro, D. Grizzle, R. 2021-03-11 doi:10.1101/2021.03.10.434772 Cold Spring Harbor Laboratory Press 2021-03-11 <![CDATA[ Design and proof-of-concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain ]]> https://biorxiv.org/content/10.1101/2021.03.15.435496v1?rss=1 Staquicini, D. I. Tang, F. H. F. Markosian, C. Yao, V. J. Staquicini, F. I. Dodero Rojas, E. Contessoto, V. G. Davis, D. O'Brien, P. Habib, N. Smith, T. L. Bruiners, N. Sidman, R. L. Gennaro, M. L. Lattime, E. C. Libutti, S. K. Whitford, P. C. Burley, S. K. Onuchic, J. N. Arap, W. Pasqualini, R. 2021-03-16 doi:10.1101/2021.03.15.435496 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Amotosalen is a bacterial multidrug efflux pump substrate potentially affecting its pathogen inactivation activity ]]> https://biorxiv.org/content/10.1101/2021.03.15.435562v1?rss=1 Green, A. B. Zulauf, K. E. Truelson, K. A. Chiaraviglio, L. Cui, M. Zhang, Z. Ware, M. P. Flegel, W. A. Haspel, R. L. Yu, E. W. Kirby, J. E. 2021-03-16 doi:10.1101/2021.03.15.435562 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ The interplay of chromatin phase separation and lamina interactions in nuclear organisation ]]> https://biorxiv.org/content/10.1101/2021.03.16.435657v1?rss=1 Laghmach, R. Di Pierro, M. Potoyan, D. A. 2021-03-17 doi:10.1101/2021.03.16.435657 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Binary Interactome Models of Inner- Versus Outer-Complexome Organization ]]> https://biorxiv.org/content/10.1101/2021.03.16.435663v1?rss=1 Lambourne, L. Yadav, A. Wang, Y. Desbuleux, A. Kim, D.-K. Cafarelli, T. Pons, C. Kovacs, I. A. Jailkhani, N. Schlabach, S. De Ridder, D. Luck, K. Bian, W. Shen, Y. Mee, M. Jacob, Y. Lemmens, I. Rolland, T. Tavernier, J. Spirohn, K. Zhong, Q. Aloy, P. Hao, T. Charloteaux, B. Roth, F. P. Hill, D. E. Calderwood, M. A. Twizere, J.-C. Vidal, M. 2021-03-17 doi:10.1101/2021.03.16.435663 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Insular cortex corticotropin-releasing factor integrates stress signaling with social decision making. ]]> https://biorxiv.org/content/10.1101/2021.03.23.436680v1?rss=1 Rieger, N. S. Varela, J. A. Ng, A. J. Granata, L. Djerdjaj, A. Brenhouse, H. C. Christianson, J. P. 2021-03-23 doi:10.1101/2021.03.23.436680 Cold Spring Harbor Laboratory Press 2021-03-23 <![CDATA[ Derivation of stationary distributions of biochemical reaction networks via structure transformation ]]> https://biorxiv.org/content/10.1101/2021.03.23.436681v1?rss=1 Hong, H. Kim, J. Al-Radhawi, M. A. Sontag, E. D. Kim, J. K. 2021-03-24 doi:10.1101/2021.03.23.436681 Cold Spring Harbor Laboratory Press 2021-03-24 <![CDATA[ Evolutionary differences in the ACE2 reveals the molecular origins of COVID-19 susceptibility ]]> https://biorxiv.org/content/10.1101/2021.03.25.437113v1?rss=1 Cheng, R. R. Dodero-Rojas, E. Di Pierro, M. Onuchic, J. N. 2021-03-26 doi:10.1101/2021.03.25.437113 Cold Spring Harbor Laboratory Press 2021-03-26 <![CDATA[ Development and Validation of Fluorescently Labeled, Functional Type I Collagen Molecules ]]> https://biorxiv.org/content/10.1101/2021.03.26.437209v1?rss=1 Siadat, S. M. Susilo, M. E. Paten, J. A. Silverman, A. A. DiMarzio, C. A. Ruberti, J. W. 2021-03-26 doi:10.1101/2021.03.26.437209 Cold Spring Harbor Laboratory Press 2021-03-26 <![CDATA[ Perceiving and remembering speech depend on nonlinearity in movements producing and exploring speech ]]> https://biorxiv.org/content/10.1101/2021.03.28.437328v1?rss=1 Bloomfield, L. Lane, E. Mangalam, M. Kelty-Stephen, D. 2021-03-29 doi:10.1101/2021.03.28.437328 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ A Chemical-Enhanced System for CRISPR-Based Nucleic Acid Detection ]]> https://biorxiv.org/content/10.1101/2021.03.28.437376v1?rss=1 Li, Z. Zhao, W. Ma, S. Li, Z. Yao, Y. Fei, T. 2021-03-28 doi:10.1101/2021.03.28.437376 Cold Spring Harbor Laboratory Press 2021-03-28 <![CDATA[ Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases ]]> https://biorxiv.org/content/10.1101/2021.03.29.437539v1?rss=1 Trigg, S. A. Venkataraman, Y. R. Gavery, M. Roberts, S. B. Bhattacharya, D. Downey-Wall, A. Eirin-Lopez, J. M. Johnson, K. M. Lotterhos, K. E. Puritz, J. B. Putnam, H. M. 2021-03-30 doi:10.1101/2021.03.29.437539 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ A constitutively expressed fluorescence ubiquitin cell cycle indicator (FUCCI) in axolotls for studying tissue regeneration ]]> https://biorxiv.org/content/10.1101/2021.03.30.437716v1?rss=1 Duerr, T. J. Jeon, E. K. Wells, K. M. Villanueva, A. Seifert, A. W. McCusker, C. D. Monaghan, J. R. 2021-03-30 doi:10.1101/2021.03.30.437716 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ Designing, optimizing, and assessing modular functional near-infrared brain imaging probes using an automated software workflow ]]> https://biorxiv.org/content/10.1101/2021.04.06.438705v1?rss=1 Vanegas, M. Mireles Nunez, M. Fang, Q. 2021-04-06 doi:10.1101/2021.04.06.438705 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Immunosuppression broadens evolutionary pathways to treatment failure during Acinetobacter baumannii pneumonia ]]> https://biorxiv.org/content/10.1101/2021.04.07.438861v1?rss=1 Huo, W. Busch, L. M. Hamami, E. Hernandez-Bird, J. Marshall, C. W. Geisinger, E. Cooper, V. S. van Opijnen, T. Rosch, J. Isberg, R. R. 2021-04-09 doi:10.1101/2021.04.07.438861 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ The Population Genetics of Gene Regulatory Networks ]]> https://biorxiv.org/content/10.1101/2021.04.11.439376v1?rss=1 Yang, C.-H. Scarpino, S. V. 2021-04-11 doi:10.1101/2021.04.11.439376 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Longitudinal characterization of neuroanatomical changes in the Fischer 344 rat brain during normal aging and between sexes ]]> https://biorxiv.org/content/10.1101/2021.04.12.439510v1?rss=1 Fowler, C. F. Goerzen, D. A. Madularu, D. Devenyi, G. A. Near, J. Chakravarty, M. 2021-04-13 doi:10.1101/2021.04.12.439510 Cold Spring Harbor Laboratory Press 2021-04-13 <![CDATA[ Programmable Microbial Ink for 3D Printing of Living Materials Produced from Genetically Engineered Protein Nanofibers ]]> https://biorxiv.org/content/10.1101/2021.04.19.440538v1?rss=1 Duraj-Thatte, A. M. Manjula Basavanna, A. Rutledge, J. Xia, J. Hassan, S. Sourlis, A. Rubio, A. G. Lesha, A. Zenkl, M. Kan, A. Weitz, D. Zhang, Y. S. Joshi, N. S. 2021-04-20 doi:10.1101/2021.04.19.440538 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ The dynamics of subunit rotation in a eukaryotic ribosome ]]> https://biorxiv.org/content/10.1101/2021.04.19.440545v1?rss=1 Freitas, F. C. Fuchs, G. Oliveira, R. J. d. Whitford, P. C. 2021-04-20 doi:10.1101/2021.04.19.440545 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Multidose evaluation of 6,710 drug repurposing library identifies potent SARS-CoV-2 infection inhibitors In Vitro and In Vivo. ]]> https://biorxiv.org/content/10.1101/2021.04.20.440626v1?rss=1 12 scaffold classes and 813 host targets with micromolar to low nanomolar activities. From these classes, representatives were extensively evaluated for mechanism of action in stable and primary human cell models, and additionally against Beta and Delta SARS-CoV-2 variants and MERS-CoV. One promising candidate, obatoclax, significantly reduced SARS-CoV-2 viral lung load in mice. Ultimately, this work establishes a rigorous approach for future pharmacological and computational identification of novel host factor dependencies and treatments for viral diseases. ]]> Patten, J. Keiser, P. T. Gysi, D. M. Menichetti, G. Mori, H. Donahue, C. J. Gan, X. do Valle, I. F. Geoghegan-Barek, K. Anantpadma, M. Berrigan, J. L. Jalloh, S. C. Ayazika, K. T. Wagner, F. Zitnik, M. Ayehunie, S. Anderson, D. Loscalzo, J. Gummuluru, S. Namchuk, M. N. Barabasi, A.-L. Davey, R. A. 2021-04-20 doi:10.1101/2021.04.20.440626 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ CMOS electrochemical imaging arrays for thedetection and classification of microorganisms ]]> https://biorxiv.org/content/10.1101/2021.04.21.440070v1?rss=1 Arcadia, C. E. Hu, K. Epstein, S. Wanunu, M. Adler, A. Rosenstein, J. K. 2021-04-22 doi:10.1101/2021.04.21.440070 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Droplet sample preparation for single-cell proteomics applied to the cell cycle ]]> https://biorxiv.org/content/10.1101/2021.04.24.441211v1?rss=1 Leduc, A. Huffman, R. G. Slavov, N. 2021-04-26 doi:10.1101/2021.04.24.441211 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Cluster Size Distribution of Cells Disseminating from a Primary Tumor ]]> https://biorxiv.org/content/10.1101/2021.04.29.441921v1?rss=1 min, {Gamma} > 1), when the cells are hybrid in nature, the mean cluster size, [Formula], where min increases with increase in {Gamma}. For {Gamma} [≤] 0, [Formula], the cells behave as completely mesenchymal. In presence of spectrum of hybrid states with different degree of EMT-ness (motility) in primary tumor, the cells which are relatively more mesenchymal (higher ) in nature, form larger clusters, whereas the smaller clusters are relatively more epithelial (lower ). Moreover, the heterogeneity in is comparatively higher for smaller clusters with respect to that for larger clusters. We also observe that more extended cell shapes promote the formation of smaller clusters. Overall, this study establishes a framework which connects the nature and size of migrating clusters disseminating from a primary tumor with the phenotypic composition of the tumor, and can lead to the better understanding of metastasis. Author summaryIn the process of metastasis, tumor cells disseminate from the primary tumor either as single cells or multicellular clusters. These clusters are potential contributor to the initiation of secondary tumor in distant organs. Our computational model captures the size distribution of migrating clusters depending on the adhesion and motility of the cells (which determine the degree of their EMT nature). Furthermore, we investigate the effect of heterogeneity of cell types in the primary tumor on the resultant heterogeneity of cell types in clusters of different sizes. We believe that the understanding the formation and nature of these clusters, dangerous actors in the deadly aspect of cancer progression, will be useful for improving prognostic methods and eventually better treatments. ]]> Mukherjee, M. Levine, H. 2021-04-29 doi:10.1101/2021.04.29.441921 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Morphine exposure bidirectionally alters c-Fos expression in a sex-, age-, and brain region-specific manner during adolescence ]]> https://biorxiv.org/content/10.1101/2021.04.29.441958v1?rss=1 Figueroa, C. Yang, H. DiSpirito, J. Bourgeois, J. R. Kalyanasundaram, G. Doshi, I. Bilbo, S. D. Kopec, A. M. 2021-04-30 doi:10.1101/2021.04.29.441958 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ METTL8 is required for 3-methylcytosine modification in human mitochondrial tRNAs ]]> https://biorxiv.org/content/10.1101/2021.05.02.442361v1?rss=1 Lentini, J. Bargabos, R. Chen, C. Fu, D. 2021-05-03 doi:10.1101/2021.05.02.442361 Cold Spring Harbor Laboratory Press 2021-05-03 <![CDATA[ Digital 3D Brain MRI Arterial Territories Atlas ]]> https://biorxiv.org/content/10.1101/2021.05.03.442478v1?rss=1 Liu, C.-F. Hsu, J. Xu, X. Kim, N. G. Sheppard, S. Meier, E. Miller, M. Hillis, A. E. Faria, A. V. 2021-05-04 doi:10.1101/2021.05.03.442478 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ massNet: integrated processing and classification of spatially resolved mass spectrometry data using deep learning for rapid tumor delineation ]]> https://biorxiv.org/content/10.1101/2021.05.06.442938v1?rss=1 Abdelmoula, W. M. Stopka, S. Randall, E. C. Regan, M. Agar, J. N. Sarkaria, J. N. Wells, W. M. Kapur, T. Agar, N. Y. R. 2021-05-07 doi:10.1101/2021.05.06.442938 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ Spatial-temporal targeted and non-targeted surveys to assess microbiological composition of drinking water in Puerto Rico following Hurricane Maria. ]]> https://biorxiv.org/content/10.1101/2021.05.07.442998v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@100c1e9org.highwire.dtl.DTLVardef@bae402org.highwire.dtl.DTLVardef@1cf41bborg.highwire.dtl.DTLVardef@1e46105_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sevillano, M. C. Vosloo, S. Cotto, I. Dai, Z. Jiang, T. Santiago Santana, J. M. Padilla, I. Y. Rosario-Pabon, Z. Velez Vega, C. Cordero, J. F. Alshawabkeh, A. Gu, A. Z. Pinto, A. J. 2021-05-07 doi:10.1101/2021.05.07.442998 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ Automated, high-accuracy, remote measurement of heart rate ]]> https://biorxiv.org/content/10.1101/2021.05.13.443967v1?rss=1 Yang, Y. Zhang, H. Lian, C. Zhao, Y. Xin, L. Li, L. 2021-05-14 doi:10.1101/2021.05.13.443967 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ "How do we do this at a distance?!" A descriptive study of remote undergraduate research programs during COVID-19 ]]> https://biorxiv.org/content/10.1101/2021.05.17.443632v1?rss=1 Erickson, O. A. Cole, R. B. Isaacs, J. M. Alvarez-Clare, S. Arnold, J. Augustus-Wallace, A. Ayoob, J. C. Berkowitz, A. Branchaw, J. L. Burgio, K. R. Cannon, C. H. Ceballos, R. M. Cohen, C. S. Coller, H. Disney, J. Doze, V. A. Eggers, M. J. Farina, S. Ferguson, E. L. Gray, J. J. Greenberg, J. T. Hoffman, A. Jensen-Ryan, D. Kao, R. M. Keene, A. C. Kowalko, J. E. Lopez, S. A. Mathis, C. Minkara, M. Murren, C. J. Ondrechen, M. J. Ordonez, P. Osano, A. Padilla-Crespo, E. Palchoudhury, S. Qin, H. Ramirez-Lugo, J. Reithel, J. Shaw, C. A. Smith, A. Smith, R. Su 2021-05-17 doi:10.1101/2021.05.17.443632 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ A proteomics sample metadata representation for multiomics integration, and big data analysis. ]]> https://biorxiv.org/content/10.1101/2021.05.21.445143v1?rss=1 Dai, C. Fullgrabe, A. Pfeuffer, J. Solovyeva, E. Deng, J. Moreno, P. Kamatchinathan, S. Jaiswal Kundu, D. George, N. Fexova, S. Gruning, B. Foll, M. C. Griss, J. Vaudel, M. Audain, E. Locard-Paulet, M. Turewicz, M. Eisenacher, M. Uszkoreit, J. Van Den Bossche, T. Schwammle, V. Webel, H. Schulze, S. Bouyssie, D. Jayaram, S. Kumar Duggineni, V. Samaras, P. Wilhelm, M. Choi, M. Wang, M. Kohlbacher, O. Brazma, A. Papatheodorou, I. Bandeira, N. W. Deutsch, E. Vizcaino, J. A. Bai, M. Levitsky, L. Sachsenberg, T. Perez-Riverol, Y. 2021-05-23 doi:10.1101/2021.05.21.445143 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ A connectomic study of a petascale fragment of human cerebral cortex ]]> https://biorxiv.org/content/10.1101/2021.05.29.446289v1?rss=1 Shapson-Coe, A. Januszewski, M. Berger, D. R. Pope, A. Wu, Y. Blakely, T. Schalek, R. L. Li, P. Wang, S. Maitlin-Shepard, J. Karlupia, N. Dorkenwald, S. Sjostedt, E. Leavitt, L. Lee, D. Bailey, L. Fitzmaurice, A. Kar, R. Field, B. Wu, H. Wagner-Carena, J. Aley, D. Lau, J. Lin, Z. Wei, D. Pfister, H. Peleg, A. Jain, V. Lichtman, J. W. 2021-05-30 doi:10.1101/2021.05.29.446289 Cold Spring Harbor Laboratory Press 2021-05-30 <![CDATA[ Cysteine dependence in Lactobacillus iners constitutes a novel therapeutic target to modify the vaginal microbiota ]]> https://biorxiv.org/content/10.1101/2021.06.12.448098v1?rss=1 Bloom, S. M. Mafunda, N. A. Woolston, B. M. Hayward, M. R. Frempong, J. F. Abai, A. B. Xu, J. Mitchell, A. J. Westergaard, X. Hussain, F. A. Xulu, N. Dong, M. Dong, K. L. Gumbi, T. Ceasar, X. Rice, J. K. Choksi, N. Ismail, N. Ndung'u, T. Ghebremichael, M. S. Balskus, E. P. Mitchell, C. M. Kwon, D. S. 2021-06-12 doi:10.1101/2021.06.12.448098 Cold Spring Harbor Laboratory Press 2021-06-12 <![CDATA[ Profiling the in vitro and in vivo activity of streptothricin-F against carbapenem-resistant Enterobacterales: a historic scaffold with a novel mechanism of action ]]> https://biorxiv.org/content/10.1101/2021.06.14.448463v1?rss=1 10-fold in vitro selectivity of S-F compared with S-D on LLC-PK1 and J774 cell lines. In vivo, delayed renal toxicity occurred at >10-fold higher doses of S-F compared with S-D. Substantial treatment effect of S-F in the murine thigh model was observed against the otherwise pandrug-resistant, NDM-1-expressing Klebsiella pneumoniae Nevada strain at dosing levels without observable or minimal toxicity. Resistance mutations obtained in single ribosomal operon E. coli identify novel interactions with 16S rRNA helix 34, i.e., C1504A and A1196G/C conferred high level resistance to nourseothricin. Based on promising, unique activity, we suggest that the streptothricin scaffold deserves further pre-clinical exploration as a potential therapeutic for the treatment of CRE and potentially other multidrug-resistant, gram-negative pathogens. IMPORTANCEStreptothricins are a historic class of antibiotics discovered by Waksman and colleagues in the 1940s. Toxicities associated with the streptothricin natural product mixture, also known as nourseothricin, discouraged further development. However, we found that a component of nourseothricin, streptothricin-F, retained potent activity against contemporary carbapenem-resistant Enterobacterales with significant selectivity in in vitro and in vivo assays. This included demonstration of rapid bactericidal activity in vitro and substantial therapeutic effect in the murine thigh model against a pandrug-resistant Klebsiella pneumoniae isolate at non-toxic concentrations. Through resistance mutation analysis, we identified helix 34 of 16S rRNA in the prokaryotic ribosome, and specifically bases C1054 and A1196, as critical for streptothricins activity. The mechanism of action is distinct from other known translation inhibitors. Based on promising and unique activity, we believe the streptothricin scaffold deserves further pre-clinical exploration as a potential therapeutic for the treatment of CRE and potentially other multidrug-resistant, Gram-negative pathogens. ]]> Smith, K. P. Kang, Y.-S. Green, A. B. Dowgiallo, M. G. Miller, B. C. Chiaraviglio, L. Truelson, K. A. Zulauf, K. E. Rodriguez, S. Manetsch, R. Kirby, J. E. 2021-06-15 doi:10.1101/2021.06.14.448463 Cold Spring Harbor Laboratory Press 2021-06-15 <![CDATA[ Spatial structure, phase, and the contrast of natural images ]]> https://biorxiv.org/content/10.1101/2021.06.16.448761v1?rss=1 Rideaux, R. West, R. K. Bex, P. J. Mattingley, J. B. Harrison, W. J. 2021-06-17 doi:10.1101/2021.06.16.448761 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Single domain antibodies against enteric pathogen virulence factors are active as curli fiber fusions on probiotic E. coli Nissle 1917 ]]> https://biorxiv.org/content/10.1101/2021.06.18.448998v1?rss=1 Gelfat, I. Aqeel, Y. Tremblay, J. M. Jaskiewicz, J. Shrestha, A. Lee, J. N. Hu, S. Qian, X. Magoun, L. Sheoran, A. Bedenice, D. Giem, C. Manjula-Basavanna, A. Osbourne, M. S. Tzipori, S. Shoemaker, C. B. Leong, J. M. Joshi, N. S. 2021-06-18 doi:10.1101/2021.06.18.448998 Cold Spring Harbor Laboratory Press 2021-06-18 <![CDATA[ Immunosuppressive traits of the hybrid epithelial/mesenchymal phenotype ]]> https://biorxiv.org/content/10.1101/2021.06.21.449285v1?rss=1 Sahoo, S. Nayak, S. P. Hari, K. Mandal, S. Kishore, A. Levine, H. Jolly, M. K. 2021-06-22 doi:10.1101/2021.06.21.449285 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Voltage-driven polyelectrolyte complexation inside a nanopore ]]> https://biorxiv.org/content/10.1101/2021.06.21.449295v1?rss=1 Muthukumar, M. Tripathi, P. Jeon, B.-j. 2021-06-22 doi:10.1101/2021.06.21.449295 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Classical swine fever virus NS5A inhibits NF-κB signaling by targeting NEMO ]]> https://biorxiv.org/content/10.1101/2021.06.21.449351v1?rss=1 Li, J. Yu, H. Jiang, W. Ma, P. Feng, Z. Lu, Y. Tu, C. Sun, J. 2021-06-22 doi:10.1101/2021.06.21.449351 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Regulation of GTPase function by autophosphorylation ]]> https://biorxiv.org/content/10.1101/2021.06.23.449327v1?rss=1 Johnson, C. W. Seo, H.-S. Terrell, E. M. KleinJan, F. Gebregiworgis, T. Gasmi-Seabrook, G. M. C. Geffken, E. A. Lakhani, J. Song, K. Popow, O. Paulo, J. A. Liu, A. Mattos, C. Marshall, C. B. Ikura, M. Morrison, D. K. Dhe-Paganon, S. Haigis, K. M. 2021-06-23 doi:10.1101/2021.06.23.449327 Cold Spring Harbor Laboratory Press 2021-06-23 <![CDATA[ Protein crosslinking as a therapeutic strategy for SOD1-related ALS ]]> https://biorxiv.org/content/10.1101/2021.06.23.449516v1?rss=1 Hossain, M. A. Sarin, R. Donnelly, D. P. Miller, B. C. Salisbury, J. P. Conway, J. B. Watson, S. Winters, J. N. Alam, N. Sivasankar, D. Ponmudiyan, A. C. Gawde, T. Kannapadi, S. Auclair, J. R. Makowski, L. Ringe, D. Ondrechen, M. J. Chen, Y. Manetsch, R. Agar, J. N. 2021-06-23 doi:10.1101/2021.06.23.449516 Cold Spring Harbor Laboratory Press 2021-06-23 <![CDATA[ Protection of the prodomain 1-helix correlates with latency in the transforming growth factor- family ]]> https://biorxiv.org/content/10.1101/2021.06.24.449816v1?rss=1 Le, V. Q. Zhao, B. Iacob, R. E. Tian, Y. Toohey, C. Engen, J. R. Springer, T. A. 2021-06-25 doi:10.1101/2021.06.24.449816 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Diffuse ions coordinate dynamics in a ribonucleoprotein assembly ]]> https://biorxiv.org/content/10.1101/2021.06.25.448160v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@14f36caorg.highwire.dtl.DTLVardef@1963073org.highwire.dtl.DTLVardef@146fbf8org.highwire.dtl.DTLVardef@14860ab_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Wang, A. Levi, M. Mohanty, U. Whitford, P. C. 2021-06-26 doi:10.1101/2021.06.25.448160 Cold Spring Harbor Laboratory Press 2021-06-26 <![CDATA[ Cerebello-cerebral Functional Connectivity Networks in Major Depressive Disorder: A CAN-BIND-1 Study Report ]]> https://biorxiv.org/content/10.1101/2021.06.25.449819v1?rss=1 Anteraper, S. A. Guell, X. Lee, Y. J. Raya, J. Demchenko, I. Churchill, N. W. Frey, B. N. Hassel, S. Lam, R. W. MacQueen, G. M. Milev, R. Schweizer, T. A. Strother, S. C. Whitfield-Gabrieli, S. Kennedy, S. H. Bhat, V. The CAN-BIND Investigator Team, 2021-06-28 doi:10.1101/2021.06.25.449819 Cold Spring Harbor Laboratory Press 2021-06-28 <![CDATA[ MCX Cloud - a modern, scalable, high-performance and in-browser Monte Carlo simulation platform with cloud computing ]]> https://biorxiv.org/content/10.1101/2021.06.28.450034v1?rss=1 Fang, Q. Yan, S. 2021-06-29 doi:10.1101/2021.06.28.450034 Cold Spring Harbor Laboratory Press 2021-06-29 <![CDATA[ Using diffusion MRI data acquired with ultra-high gradients to improve tractography in routine-quality data ]]> https://biorxiv.org/content/10.1101/2021.06.28.450265v1?rss=1 Maffei, C. Lee, C. Planich, M. Ramprasad, M. Ravi, N. Trainor, D. Urban, Z. Kim, M. Jones, R. Henin, A. Hofmann, S. Pizzagalli, D. Auerbach, R. Gabrieli, J. Whitfield-Gabrieli, S. Greve, D. Haber, S. Yendiki, A. 2021-06-30 doi:10.1101/2021.06.28.450265 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ Design, synthesis, and characterization of mG2P026 as a high contrast PET imaging ligand for metabotropic glutamate receptor 2 ]]> https://biorxiv.org/content/10.1101/2021.06.29.450249v1?rss=1 5%, non-decay corrected), high molar activity (> 180 GBq/mol), and excellent chemical and radiochemical purities (> 98%). Preliminary characterization of [18F]8 and [18F]9 in rats confirmed their excellent brain permeability with [18F]9 showing better brain heterogeneity and favorable binding kinetics. Pretreatment with different classes of PAMs enhanced the radioactivity uptake for both [18F]8 and [18F]9 at the regions of interest by 20.3-40.9% and 16.7-81.6%, respectively, due to their pharmacological effects. Further evaluation of [18F]9 in a nonhuman primate confirmed its superior brain heterogeneity in mapping mGlu2 receptors and its higher specific binding than [18F]6. Pretreatment with 0.5 mg/kg BINA led (2) to an enhanced brain uptake of [18F]9 by 3% in high tracer uptake regions that was consistent with the rat studies. Therefore, [18F]9 has the potential to be translated for human studies. ]]> Yuan, G. Dhaynaut, M. Guehl, N. J. Afshar, S. Huynh, D. Moon, S.-H. Iyengar, S. Kang, H. J. Ondrechen, M. J. El Fakhri, G. Normandin, M. D. Brownell, A.-L. 2021-07-01 doi:10.1101/2021.06.29.450249 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ Synthesis and characterization of 5-(2-fluoro-4-pyridine-7-carboxamide as a PET imaging ligand for metabotropic glutamate receptor 2 ]]> https://biorxiv.org/content/10.1101/2021.06.29.450413v1?rss=1 99%). PET imaging of [11C]13 in rats demonstrated its superior brain heterogeneity, particularly in the regions of striatum, thalamus, hippocampus, and cortex. Accumulation of [11C]13 in these regions of interest (ROIs) was reduced with pretreatment of mGluR2 NAMs, VU6001966 (9) and MNI-137 (26), the extent of which revealed a time-dependent drug effect of the blocking agents. In a nonhuman primate, [11C]13 selectively accumulated in mGluR2-rich regions, especially in different cortical areas, putamen, thalamus, and hippocampus, and resulted in high-contrast brain images. The regional total volume of distribution (VT) estimates of [11C]13 decreased by 14% after the pretreatment with 9. Therefore, [11C]13 is a potential candidate for translational PET imaging studies of mGluR2 function. ]]> Yuan, G. Dhaynaut, M. Lan, Y. Guehl, N. J. Huynh, D. Iyengar, S. Afshar, S. Wang, H. Moon, S.-H. Ondrechen, M. J. Wang, C. Shoup, T. El Fakhri, G. Normandin, M. D. Brownell, A.-L. 2021-06-30 doi:10.1101/2021.06.29.450413 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ Parametric modulators of sex-biased conditioned fear responding ]]> https://biorxiv.org/content/10.1101/2021.06.30.450556v1?rss=1 Mitchell, J. R. Trettel, S. G. Li, A. J. Wasielewski, S. Huckleberry, K. A. Fanikos, M. Golden, E. Shansky, R. M. 2021-06-30 doi:10.1101/2021.06.30.450556 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ High-density transposon mutagenesis in Mycobacterium abscessus identifies an essential penicillin-binding lipo-protein (PBP-lipo) involved in septal peptidoglycan synthesis and antibiotic sensitivity ]]> https://biorxiv.org/content/10.1101/2021.07.01.450732v1?rss=1 Akusobi, C. Benghomari, B. S. Wolf, I. D. Singhvi, S. Zhu, J. Ioerger, T. R. Rubin, E. J. 2021-07-01 doi:10.1101/2021.07.01.450732 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ Music-Based Intervention Connects Auditory and Reward Systems ]]> https://biorxiv.org/content/10.1101/2021.07.02.450867v1?rss=1 Quinci, M. Belden, A. Goutama, V. Gong, D. Hanser, S. Donovan, N. J. Geddes, M. Loui, P. 2021-07-03 doi:10.1101/2021.07.02.450867 Cold Spring Harbor Laboratory Press 2021-07-03 <![CDATA[ HAPPILEE: The Harvard Automated Processing Pipeline In Low Electrode Electroencephalography, a standardized software for low density EEG and ERP data ]]> https://biorxiv.org/content/10.1101/2021.07.02.450940v1?rss=1 Lopez, K. L. Monachino, A. D. Morales, S. Leach, S. Bowers, M. Gabard-Durnam, L. J. 2021-07-04 doi:10.1101/2021.07.02.450940 Cold Spring Harbor Laboratory Press 2021-07-04 <![CDATA[ The HAPPE plus Event-Related (HAPPE+ER) Software: A Standardized Processing Pipeline for Event-Related Potential Analyses ]]> https://biorxiv.org/content/10.1101/2021.07.02.450946v1?rss=1 Monachino, A. D. Lopez, K. L. Pierce, L. J. Gabard-durnam, l. J. 2021-07-04 doi:10.1101/2021.07.02.450946 Cold Spring Harbor Laboratory Press 2021-07-04 <![CDATA[ CAT, AGTR2, L-SIGN and DC-SIGN are potential receptors for the entry of SARS-CoV-2 into human cells ]]> https://biorxiv.org/content/10.1101/2021.07.07.451411v1?rss=1 Guo, D. Guo, R. Li, Z. Zhang, Y. Zheng, W. Huang, X. Aziz, T. Zhang, Y. Liu, L. 2021-07-07 doi:10.1101/2021.07.07.451411 Cold Spring Harbor Laboratory Press 2021-07-07 <![CDATA[ Evaluating de novo assembly and binning strategies for time-series drinking water metagenomes. ]]> https://biorxiv.org/content/10.1101/2021.07.11.451960v1?rss=1 Vosloo, S. Huo, L. Anderson, C. L. Rivera, M. S. Dai, Z. Pinto, A. J. 2021-07-12 doi:10.1101/2021.07.11.451960 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Global change differentially modulates coral physiology and suggests future shifts in Caribbean reef assemblages ]]> https://biorxiv.org/content/10.1101/2021.07.13.452173v1?rss=1 Bove, C. B. Davies, S. W. Ries, J. B. Umbanhowar, J. Thomasson, B. C. Farquhar, E. B. McCoppin, J. A. Castillo, K. D. 2021-07-14 doi:10.1101/2021.07.13.452173 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ Allosteric control of Ubp6 and the proteasome via a bidirectional switch ]]> https://biorxiv.org/content/10.1101/2021.07.16.452743v1?rss=1 Hung, K. Y. S. Klumpe, S. Eisele, M. R. Elsasser, S. Tian, G. Sun, S. Moroco, J. A. Cheng, T. C. Joshi, T. Seibel, T. Van Dalen, D. Feng, X.-H. Lu, Y. Ovaa, H. Engen, J. R. Lee, B.-H. Rudack, T. Sakata, E. Finley, D. 2021-07-17 doi:10.1101/2021.07.16.452743 Cold Spring Harbor Laboratory Press 2021-07-17 <![CDATA[ Natural interploidy hybridization among the key taxa involved in the origin of horticultural chrysanthemums ]]> https://biorxiv.org/content/10.1101/2021.07.29.454281v1?rss=1 Qi, S. Twyford, A. D. Ding, J. Borrell, J. S. Ma, Y. Wang, N. 2021-07-29 doi:10.1101/2021.07.29.454281 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Brain structure and function predict adherence to an exercise intervention in older adults ]]> https://biorxiv.org/content/10.1101/2021.07.30.454451v1?rss=1 Morris, T. P. Burzynska, A. Voss, M. Fanning, J. Salerno, E. A. Prakash, R. Gothe, N. P. Whitfield-Gabrieli, S. Hillman, C. H. McAuley, E. Kramer, A. F. 2021-08-01 doi:10.1101/2021.07.30.454451 Cold Spring Harbor Laboratory Press 2021-08-01 <![CDATA[ Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: A case study of an urothelial cancer cohort analyzed in the Galaxy framework ]]> https://biorxiv.org/content/10.1101/2021.08.09.455649v1?rss=1 Föll, M. C. Volkmann, V. Enderle-Ammour, K. Wilhelm, K. Guo, D. Vitek, O. Bronsert, P. G. C. Schilling, O. 2021-08-10 doi:10.1101/2021.08.09.455649 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ SMOG 2 and OpenSMOG: Extending the limits of structure-based models ]]> https://biorxiv.org/content/10.1101/2021.08.15.456423v1?rss=1 Oliveira, A. B. Contessoto, V. Hassan, A. Byju, S. Wang, A. Wang, Y. Dodero Rojas, E. G. Mohanty, U. Noel, J. Onuchic, J. N. Whitford, P. C. 2021-08-16 doi:10.1101/2021.08.15.456423 Cold Spring Harbor Laboratory Press 2021-08-16 <![CDATA[ AMPing up the search: An in silico approach to identifying Antimicrobial Peptides (AMPs) with potential anti-biofilm activity ]]> https://biorxiv.org/content/10.1101/2021.08.16.456477v1?rss=1 Mhade, S. Panse, S. Tendulkar, G. Awate, R. Kadam, S. Kaushik, K. 2021-08-17 doi:10.1101/2021.08.16.456477 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Microbial dark carbon fixation fueled by nitrate enrichment ]]> https://biorxiv.org/content/10.1101/2021.08.24.457596v1?rss=1 Vineis, J. H. Bulseco, A. N. Bowen, J. L. 2021-08-27 doi:10.1101/2021.08.24.457596 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Local mechanical stimuli shape tissue growth in vertebrate joint morphogenesis ]]> https://biorxiv.org/content/10.1101/2021.08.28.458034v1?rss=1 Comellas, E. Farkas, J. E. Kleinberg, G. Lloyd, K. Mueller, T. Duerr, T. J. Munoz, J. J. Monaghan, J. R. Shefelbine, S. J. 2021-08-28 doi:10.1101/2021.08.28.458034 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Apropos of Universal Epitope Discovery for COVID-19 Vaccines: A Framework for Targeted Phage Display-Based Delivery and Integration of New Evaluation Tools ]]> https://biorxiv.org/content/10.1101/2021.08.30.458222v1?rss=1 Markosian, C. Staquicini, D. I. Dogra, P. Dodero-Rojas, E. Tang, F. H. F. Smith, T. L. Contessoto, V. G. Libutti, S. K. Wang, Z. Cristini, V. Whitford, P. C. Burley, S. K. Onuchic, J. N. Pasqualini, R. Arap, W. 2021-08-31 doi:10.1101/2021.08.30.458222 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ Efficient ancestry and mutation simulation with msprime 1.0 ]]> https://biorxiv.org/content/10.1101/2021.08.31.457499v1?rss=1 Baumdicker, F. Bisschop, G. Goldstein, D. Gower, G. Ragsdale, A. P. Tsambos, G. Zhu, S. Eldon, B. Ellerman, C. E. Galloway, J. G. Gladstein, A. L. Gorjanc, G. Guo, B. Jeffery, B. Kretzschmar, W. W. Lohse, K. Matschiner, M. Nelson, D. Pope, N. S. Quinto-Cortes, C. D. Rodrigues, M. F. Saunack, K. Sellinger, T. Thornton, K. van Kemenade, H. Wohns, A. W. Wong, Y. Gravel, S. Kern, A. D. Koskela, J. Ralph, P. L. Kelleher, J. 2021-09-01 doi:10.1101/2021.08.31.457499 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Functional connectivity gradients as a common neural architecture for predictive processing in the human brain ]]> https://biorxiv.org/content/10.1101/2021.09.01.456844v1?rss=1 Katsumi, Y. Kamona, N. Zhang, J. Bunce, J. G. Hutchinson, J. B. Yarossi, M. Tunik, E. Quigley, K. S. Dickerson, B. C. Feldman Barrett, L. 2021-09-01 doi:10.1101/2021.09.01.456844 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Nanobody-Functionalized Cellulose for Capturing and Containing SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2021.09.01.458653v1?rss=1 Sun, X. Yang, S. Al-Dossary, A. Broitman, S. Ni, Y. Yang, M. Li, J. 2021-09-02 doi:10.1101/2021.09.01.458653 Cold Spring Harbor Laboratory Press 2021-09-02 <![CDATA[ Modeling CRISPR-Cas13d on-target and off-target effects using machine learning approaches ]]> https://biorxiv.org/content/10.1101/2021.09.02.458773v1?rss=1 Cheng, X. Li, Z. Shan, R. Li, Z. Chao, L. Peng, J. Fei, T. Li, W. 2021-09-04 doi:10.1101/2021.09.02.458773 Cold Spring Harbor Laboratory Press 2021-09-04 <![CDATA[ Genome-wide transcriptional profiling uncovers a similar oligodendrocyte-related transcriptional response to acute and chronic alcohol drinking in the amygdala ]]> https://biorxiv.org/content/10.1101/2021.09.07.459347v1?rss=1 Narendra, S. Klengel, C. Hamzeh, B. Patel, D. Otten, J. Lardenoije, R. Newman, E. L. Miczek, K. A. Klengel, T. Ressler, K. J. Suh, J. 2021-09-09 doi:10.1101/2021.09.07.459347 Cold Spring Harbor Laboratory Press 2021-09-09 <![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[ Mechanical Causation of Biological Structure: Productive Pulls Produce Persistent Filaments in a Human Fibroblast Model of Matrix Development ]]> https://biorxiv.org/content/10.1101/2021.09.10.459665v1?rss=1 Silverman, A. A. Siadat, S. M. Olszewski, J. D. Ruberti, J. W. 2021-09-11 doi:10.1101/2021.09.10.459665 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ Full-length NLRP3 forms oligomeric cages to mediate NLRP3 sensing and activation ]]> https://biorxiv.org/content/10.1101/2021.09.12.459968v1?rss=1 Andreeva, L. David, L. Rawson, S. Shen, C. Pasricha, T. Pelegrin, P. Wu, H. 2021-09-12 doi:10.1101/2021.09.12.459968 Cold Spring Harbor Laboratory Press 2021-09-12 <![CDATA[ Seeing the Forest for the trees: Assessing genetic offset predictions with Gradient Forest ]]> https://biorxiv.org/content/10.1101/2021.09.20.461151v1?rss=1 Laruson, A. J. Fitzpatrick, M. C. Keller, S. R. Haller, B. C. Lotterhos, K. E. 2021-09-23 doi:10.1101/2021.09.20.461151 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Assessment of community efforts to advance computational prediction of protein-protein interactions ]]> https://biorxiv.org/content/10.1101/2021.09.22.461292v1?rss=1 Wang, X.-W. Madeddu, L. Spirohn, K. Martini, L. Fazzone, A. Becchetti, L. Wytock, T. P. Kovacs, I. A. Balogh, O. M. Benczik, B. Petervari, M. Agg, B. Ferdinandy, P. Vulliard, L. Menche, J. Colonnese, S. Petti, M. Scarano, G. Cuomo, F. Hao, T. Laval, F. Willems, L. Twizere, J.-C. Calderwood, M. Petrillo, E. Barabasi, A.-L. Silverman, E. K. Loscalzo, J. Velardi, P. Liu, Y.-Y. 2021-09-23 doi:10.1101/2021.09.22.461292 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ A new class of cell wall-recycling L,D-carboxypeptidase determines β-lactam susceptibility and morphogenesis in Acinetobacter baumannii ]]> https://biorxiv.org/content/10.1101/2021.09.22.461454v1?rss=1 Dai, Y. Pinedo, V. Tang, A. Y. Cava, F. Geisinger, E. 2021-09-23 doi:10.1101/2021.09.22.461454 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Modulation of sensory perception by hydrogen peroxide enables Caenorhabditis elegans to find a niche that provides both food and protection from hydrogen peroxide ]]> https://biorxiv.org/content/10.1101/2021.09.23.461430v1?rss=1 Schiffer, J. A. Stumbur, S. V. Seyedolmohadesin, M. Xu, Y. Serkin, W. T. McGowan, N. G. Banjo, O. Torkashvand, M. Lin, A. Hosea, C. N. Assie, A. Samuel, B. S. O'Donnell, M. P. Venkatachalam, V. Apfeld, J. 2021-09-24 doi:10.1101/2021.09.23.461430 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Control of subunit stoichiometry in single-chain MspA nanopores ]]> https://biorxiv.org/content/10.1101/2021.09.25.461773v1?rss=1 Pavlenok, M. Yu, L. Herrmann, D. Wanunu, M. Niederweis, M. 2021-09-25 doi:10.1101/2021.09.25.461773 Cold Spring Harbor Laboratory Press 2021-09-25 <![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[ Unidirectional Single-File Transport of Full-Length Proteins Through a Nanopore ]]> https://biorxiv.org/content/10.1101/2021.09.28.462155v1?rss=1 Yu, L. Kang, X. Li, F. Mehrafrooz, B. Makhamreh, A. Fallahi, A. Aksimentiev, A. Chen, M. Wanunu, M. 2021-09-28 doi:10.1101/2021.09.28.462155 Cold Spring Harbor Laboratory Press 2021-09-28 <![CDATA[ Stimulating music supports attention in listeners with attentional difficulties ]]> https://biorxiv.org/content/10.1101/2021.10.01.462777v1?rss=1 Woods, K. J. Sempaio, G. James, T. Przysinda, E. Hewett, A. Spencer, A. E. Morillon, B. Loui, P. 2021-10-03 doi:10.1101/2021.10.01.462777 Cold Spring Harbor Laboratory Press 2021-10-03 <![CDATA[ Age-related change in task-evoked amygdala-prefrontal circuitry: a multiverse approach with an accelerated longitudinal cohort aged 4-22 years ]]> https://biorxiv.org/content/10.1101/2021.10.08.463601v1?rss=1 Bloom, P. A. VanTieghem, M. Gabard-Durnam, L. Gee, D. G. Flannery, J. Caldera, C. Goff, B. Telzer, E. H. Humphreys, K. L. Fareri, D. S. Shapiro, M. Algharazi, S. Bolger, N. Aly, M. Tottenham, N. 2021-10-09 doi:10.1101/2021.10.08.463601 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ Nuclear DNA-encoded fragments of mitochondrial DNA (mtDNA) confound analysis of selection of mtDNA mutations in human primordial germ cells. ]]> https://biorxiv.org/content/10.1101/2021.10.18.464832v1?rss=1 Franco, M. Fleischmann, Z. Annis, S. Khrapko, K. Tilly, J. L. Woods, D. C. Popadin, K. Orseshkov, S. 2021-10-19 doi:10.1101/2021.10.18.464832 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Translocation of polyubiquitinated protein substrates by the hexameric Cdc48 ATPase ]]> https://biorxiv.org/content/10.1101/2021.10.21.465358v1?rss=1 Ji, Z. Li, H. Peterle, D. Paulo, J. A. Ficarro, S. B. Wales, T. E. Marto, J. Gygi, S. Engen, J. R. Rapoport, T. A. 2021-10-21 doi:10.1101/2021.10.21.465358 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ SPARClink: an interactive tool to visualize the impact of the SPARC program ]]> https://biorxiv.org/content/10.1101/2021.10.22.465507v1?rss=1 Soundarajan, S. Kuruppu, S. Singh, A. Kim, J. Achalla, M. 2021-10-25 doi:10.1101/2021.10.22.465507 Cold Spring Harbor Laboratory Press 2021-10-25 <![CDATA[ ProS-GNN: Predicting effects of mutations on protein stability using graph neural networks ]]> https://biorxiv.org/content/10.1101/2021.10.25.465658v1?rss=1 Wang, S. Tang, H. Shan, P. Zuo, L. 2021-10-26 doi:10.1101/2021.10.25.465658 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Increasing the throughput of sensitive proteomics by plexDIA ]]> https://biorxiv.org/content/10.1101/2021.11.03.467007v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@144bba6org.highwire.dtl.DTLVardef@17bbf20org.highwire.dtl.DTLVardef@140f497org.highwire.dtl.DTLVardef@179faa9_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Derks, J. Leduc, A. Huffman, R. G. Specht, H. Ralser, M. Demichev, V. Slavov, N. 2021-11-04 doi:10.1101/2021.11.03.467007 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct, long-read sequencing ]]> https://biorxiv.org/content/10.1101/2021.11.03.467190v1?rss=1 Tavakoli, S. Nabizadehmashhadtoroghi, M. Makhamreh, A. Gamper, H. Rezapour, N. Hou, Y.-M. Wanunu, M. Rouhanifard, S. H. 2021-11-04 doi:10.1101/2021.11.03.467190 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Interneuron Control of C. elegans Developmental Decision-making ]]> https://biorxiv.org/content/10.1101/2021.11.07.467589v1?rss=1 Chai, C. M. Torkashvand, M. Seyedolmohadesin, M. Park, H. Venkatachalam, V. Sternberg, P. W. 2021-11-08 doi:10.1101/2021.11.07.467589 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ Photoimmunotherapy retains its anti-tumor efficacy with increasing stromal content in heterotypic pancreatic cancer spheroids ]]> https://biorxiv.org/content/10.1101/2021.11.09.467929v1?rss=1 Saad, M. A. Zhung, W. Stanley, M. E. Formica, S. Garcia, S. G. Obaid, G. Hasan, T. 2021-11-10 doi:10.1101/2021.11.09.467929 Cold Spring Harbor Laboratory Press 2021-11-10 <![CDATA[ A synthetic distributed genetic multi-bit counter ]]> https://biorxiv.org/content/10.1101/2021.11.10.468063v1?rss=1 View larger version (65K): org.highwire.dtl.DTLVardef@19a5330org.highwire.dtl.DTLVardef@cbb5c2org.highwire.dtl.DTLVardef@a0b5borg.highwire.dtl.DTLVardef@16f9d07_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chen, T. Ali Al-Radhawi, M. Voigt, C. Sontag, E. 2021-11-11 doi:10.1101/2021.11.10.468063 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Lactate production can function to increase human epithelial cell iron concentration ]]> https://biorxiv.org/content/10.1101/2021.11.11.468295v1?rss=1 Ghio, C. Soukup, J. M. Dailey, L. A. Ghio, A. Schreinemachers, D. M. Koppes, R. A. Koppes, A. N. 2021-11-12 doi:10.1101/2021.11.11.468295 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ Three-dimensional Cancer Cell Migration Directed by Dual Mechanochemical Guidance ]]> https://biorxiv.org/content/10.1101/2021.11.11.468299v1?rss=1 Esfahani, P. Levine, H. Mukherjee, M. Sun, B. 2021-11-12 doi:10.1101/2021.11.11.468299 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ Active Segregation Dynamics in the Living Cell ]]> https://biorxiv.org/content/10.1101/2021.11.20.469404v1?rss=1 Bansal, A. Das, A. Rao, M. 2021-11-20 doi:10.1101/2021.11.20.469404 Cold Spring Harbor Laboratory Press 2021-11-20 <![CDATA[ Noise in a metabolic pathway leads to persister formation in Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2021.11.26.470138v1?rss=1 Quigley, J. Lewis, K. 2021-11-26 doi:10.1101/2021.11.26.470138 Cold Spring Harbor Laboratory Press 2021-11-26 <![CDATA[ NRF2-dependent epigenetic regulation can promote the hybrid epithelial/mesenchymal phenotype ]]> https://biorxiv.org/content/10.1101/2021.12.02.470615v1?rss=1 Jia, W. Jolly, M. K. Levine, H. 2021-12-03 doi:10.1101/2021.12.02.470615 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ Mitochondrial mutational spectrum is associated with mammalian longevity: a novel signature of oxidative damage. ]]> https://biorxiv.org/content/10.1101/2021.12.03.460832v1?rss=1 GH substitutions (H - heavy chain notation) is twice higher in species with high versus low generation length making their mtDNA more AH poor and GH rich. Considering that AH>GH substitutions are also sensitive to the time spent single stranded (TSSS) during asynchroniuos mtDNA replication we demonstrated that AH>GH substitution rate is a function of both species-specific generation length and position specific TSSS. We propose that AH>GH is a mitochondria-specific signature of oxidative damage associated with both aging and TSSS. ]]> Mikhailova, A. G. Mikhailova, A. A. Ushakova, K. Tretiakov, E. Shamanskiy, V. A. Iurchenko, A. Zazhytska, M. Kozenkova, E. Zdobnov, E. M. Makeev, V. Yurov, V. Tanaka, M. Gostimskaya, I. Fleischmann, Z. M. Annis, S. Franco, M. Wasko, K. Kunz, W. Knorre, D. Mazunin, I. Nikolaev, S. Fellay, J. Reymond, A. Khrapko, K. Gunbin, K. Popadin, K. 2021-12-07 doi:10.1101/2021.12.03.460832 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ A family of fitness landscapes modeled through gene regulatory networks ]]> https://biorxiv.org/content/10.1101/2021.12.03.471063v1?rss=1 Yang, C.-H. Scarpino, S. V. 2021-12-03 doi:10.1101/2021.12.03.471063 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ Immobilization of C. elegans on cultivation plates by thermoelectric cooling for high-throughput subcellular-resolution microscopy ]]> https://biorxiv.org/content/10.1101/2021.12.09.471981v1?rss=1 98%, significantly increasing experimental speed. By obviating individual animal manipulation, our approach could also empower automated imaging of large C. elegans populations within standard experimental setups and workflows. ]]> Wang, Y. L. Jaklitsch, E. L. Grooms, N. W. F. Schulting, L. G. Chung, S. H. 2021-12-09 doi:10.1101/2021.12.09.471981 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Dopamine and GPCR-mediated modulation of DN1 clock neurons gates the circadian timing of sleep ]]> https://biorxiv.org/content/10.1101/2021.12.16.472997v1?rss=1 Schlichting, M. Richhariya, S. Herndon, N. Ma, D. Xin, J. Lenh, W. Abruzzi, K. Rosbash, M. 2021-12-17 doi:10.1101/2021.12.16.472997 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ Quantifying the patterns of metabolic plasticity and heterogeneity along the epithelial-hybrid-mesenchymal spectrum in cancer ]]> https://biorxiv.org/content/10.1101/2021.12.18.473275v1?rss=1 Muralidharan, S. Sahoo, S. Saha, A. Chandran, S. Majumdar, S. S. Levine, H. Jolly, M. K. 2021-12-21 doi:10.1101/2021.12.18.473275 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ MIAAIM: Multi-omics image integration and tissue state mapping using topological data analysis and cobordism learning ]]> https://biorxiv.org/content/10.1101/2021.12.20.472858v1?rss=1 Hess, J. M. Ilies, I. Schapiro, D. Iskra, J. J. Abdelmoula, W. M. Regan, M. S. Theocharidis, G. Wu, C. L. Veves, A. Agar, N. Y. R. Sluder, A. E. Poznansky, M. C. Reeves, P. M. Sirbulescu, R. F. 2021-12-21 doi:10.1101/2021.12.20.472858 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Virtually the same? Evaluating the effectiveness of remote undergraduate research experiences ]]> https://biorxiv.org/content/10.1101/2022.01.03.474815v1?rss=1 Hess, R. A. Erickson, O. A. Cole, R. B. Isaacs, J. M. Alvarez-Clare, S. Arnold, J. Augustus-Wallace, A. C. Ayoob, J. C. Berkowitz, A. Branchaw, J. L. Burgio, K. R. Cannon, C. H. Ceballos, R. M. Cohen, C. S. Coller, H. Disney, J. Doze, V. A. Eggers, M. J. Ferguson, E. L. Gray, J. J. Greenberg, J. T. Hoffmann, A. Jensen-Ryan, D. Kao, R. M. Keene, A. C. Kowalko, J. Lopez, S. A. Mathis, C. Minkara, M. Murren, C. J. Ondrechen, M. J. Ordonez, P. Osano, A. Padilla-Crespo, E. Palchoudhury, S. Qin, H. Ramirez-Lugo, J. Reithel, J. Shaw, C. A. Smith, A. Smith, R. J 2022-01-05 doi:10.1101/2022.01.03.474815 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ Magnetic Temporal Interference for Noninvasive Focal Brain Stimulation ]]> https://biorxiv.org/content/10.1101/2022.01.10.475762v1?rss=1 Khalifa, A. Abrishami, S. M. Zaeimbashi, M. Tang, A. D. Coughlin, B. Rodger, J. Sun, N. Cash, S. S. 2022-01-12 doi:10.1101/2022.01.10.475762 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ BlenderPhotonics - a versatile environment for 3-D complex bio-tissue modeling and light transport simulations based on Blender ]]> https://biorxiv.org/content/10.1101/2022.01.12.476124v1?rss=1 Zhang, Y. Fang, Q. 2022-01-14 doi:10.1101/2022.01.12.476124 Cold Spring Harbor Laboratory Press 2022-01-14 <![CDATA[ Von Willebrand factor A1 domain affinity for GPIbα and stability are differentially regulated by its O-glycosylated N-linker and C-linker ]]> https://biorxiv.org/content/10.1101/2022.01.13.476208v1?rss=1 Iacob, R. Bonazza, K. Hudson, N. Li, J. Lu, C. Engen, J. R. Springer, T. A. 2022-01-13 doi:10.1101/2022.01.13.476208 Cold Spring Harbor Laboratory Press 2022-01-13 <![CDATA[ Transverse and axial resolution of femtosecond laser ablation ]]> https://biorxiv.org/content/10.1101/2022.01.13.476227v1?rss=1 Wang, Y. L. Grooms, N. W. F. Chung, S. H. 2022-01-15 doi:10.1101/2022.01.13.476227 Cold Spring Harbor Laboratory Press 2022-01-15 <![CDATA[ Graphics processing unit-accelerated Monte Carlo simulation of polarized light in complex three-dimensional media ]]> https://biorxiv.org/content/10.1101/2022.01.13.476270v1?rss=1 Yan, S. Jacques, S. L. Ramella-Roman, J. C. Fang, Q. 2022-01-15 doi:10.1101/2022.01.13.476270 Cold Spring Harbor Laboratory Press 2022-01-15 <![CDATA[ Framework for Denoising Monte Carlo Photon Transport Simulations Using Deep Learning ]]> https://biorxiv.org/content/10.1101/2022.01.19.477008v1?rss=1 Raayai Ardakani, M. Yu, L. Kaeli, D. R. Fang, Q. 2022-01-22 doi:10.1101/2022.01.19.477008 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ Found in translation: Microproteins are a new class of potential host cell impurity in mAb drug products ]]> https://biorxiv.org/content/10.1101/2022.01.20.475618v1?rss=1 Castro-Rivadeneyra, M. Tzani, I. Kelly, P. Strasser, L. Guapo, F. Tierney, C. Zhang, L. Clynes, M. Karger, B. L. Barron, N. Bones, J. Clarke, C. 2022-01-22 doi:10.1101/2022.01.20.475618 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ Genomics-based annotations help unveil the molecular composition of edible plants ]]> https://biorxiv.org/content/10.1101/2022.01.24.477528v1?rss=1 Ofaim, S. Menichetti, G. Sebek, M. Barabasi, A. L. 2022-01-25 doi:10.1101/2022.01.24.477528 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues ]]> https://biorxiv.org/content/10.1101/2022.02.01.478655v1?rss=1 Contessoto, V. G. Dudchenko, O. Aiden, E. L. Wolynes, P. G. Onuchic, J. N. Di Pierro, M. 2022-02-03 doi:10.1101/2022.02.01.478655 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ A natural fusion of flavodiiron, rubredoxin, and NADH:rubredoxin oxidoreductase domains is the highly efficient water-forming oxidase of T. vaginalis ]]> https://biorxiv.org/content/10.1101/2022.02.02.478753v1?rss=1 Abdulaziz, E. N. Bell, T. A. Rashid, B. Heacock, M. L. Skinner, O. S. Yaseen, M. A. Chao, L. H. Mootha, V. K. Pierik, A. J. Cracan, V. 2022-02-02 doi:10.1101/2022.02.02.478753 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ Comparative miRNA Transcriptomics of Mouse and Macaque Reveals Cytoskeleton is An Inhibitor for C. neoformans Invasion into Brain ]]> https://biorxiv.org/content/10.1101/2022.02.14.480319v1?rss=1 Li, H. Han, X. Du, W. Meng, Y. Li, Y. Sun, T. Liang, Q. Li, C. Suo, C. Gao, X. Qiu, Y. Tian, W. An, M. Zhang, H. Fu, Y. Li, X. Lan, T. Yang, S. Zhang, Z. Geng, W. Ding, C. Shang, H. 2022-02-14 doi:10.1101/2022.02.14.480319 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ Shaping the Genome via Lengthwise Compaction, Phase Separation, and Lamina Adhesion ]]> https://biorxiv.org/content/10.1101/2022.02.28.482402v1?rss=1 Brahmachari, S. Contessoto, V. Di Pierro, M. Onuchic, J. N. 2022-03-02 doi:10.1101/2022.02.28.482402 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Blinding efficacy and adverse events following repeated transcranial alternating current, direct current, and random noise stimulation. ]]> https://biorxiv.org/content/10.1101/2022.03.04.482999v1?rss=1 Sheffield, J. G. Rampersad, S. Brem, A.-K. Mansfield, K. Orhan, U. Dillard, M. McKanna, J. Plessow, F. Thompson, T. Santarnecchi, E. Pascual-Leone, A. Pavel, M. Mathan, S. Cohen Kadosh, R. 2022-03-07 doi:10.1101/2022.03.04.482999 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Stimulus-dependent depth constancy during head tilt ]]> https://biorxiv.org/content/10.1101/2022.03.04.483050v1?rss=1 0.05), despite that IPDs and the axis of disparity were differentially affected by the tilts. However, for random dot stimuli, stereoacuity decreased with increasing orientation difference between the head and monitor (H and M: p<0.05; B: p>0.05]. Head tilt decreases IPD and rotates the axis of interocular disparity, however, these manipulations affect stereoacuity when measured with noise stimuli but not with sparse stimuli. The results are consistent with a vestibular input to stereoscopic disparity processing that can be detected by sparse stimuli but is masked by dense stimuli. The results have implications for natural vision and for clinical screening in patients with abnormal head posture. Significance statementDepth perception is a critical feature of human vision and it is thought that the ability to perceive stereoscopic depth is bound to an essentially eye-fixed, horizontal disparity of each image that rapidly deteriorates away from that limited horizontal axis. In a set of head tilt experiments, we varied the orientations of stereoscopic images and demonstrate that stereoacuity remains constant when deploying sparse narrow-band stimuli, and only worsens when using fine-detailed noise stimuli that mask off-axis disparities. These results shine new light upon the debate of neuroplasticity of stereo vision. Moreover, the results are consequential for diagnosis and treatment in people with atypical head- and eye alignment, such as for patients with torticollis or strabismus. ]]> Skerswetat, J. Caoli, A. Bex, P. J. 2022-03-04 doi:10.1101/2022.03.04.483050 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Automated classification of estrous stage in rodents using deep learning ]]> https://biorxiv.org/content/10.1101/2022.03.09.483678v1?rss=1 Wolcott, N. Sit, K. Raimondi, G. Hodges, T. Shansky, R. Galea, L. Ostroff, L. Goard, M. 2022-03-12 doi:10.1101/2022.03.09.483678 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ A Microengineered Brain-Chip to Model Neuroinflammation in Humans ]]> https://biorxiv.org/content/10.1101/2022.03.11.484005v1?rss=1 Pediaditakis, I. Kodella, K. R. Manatakis, D. V. Le, C. Y. Barthakur, S. Sorets, A. Gravanis, A. Ewart, L. Rubin, L. L. Manolakos, E. S. Hinojosa, C. D. Karalis, K. 2022-03-14 doi:10.1101/2022.03.11.484005 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Prioritized single-cell proteomics reveals molecular and functional polarization across primary macrophages ]]> https://biorxiv.org/content/10.1101/2022.03.16.484655v1?rss=1 View larger version (19K): org.highwire.dtl.DTLVardef@c44f04org.highwire.dtl.DTLVardef@1fb3e8org.highwire.dtl.DTLVardef@15c456eorg.highwire.dtl.DTLVardef@d271e0_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Huffman, R. G. Leduc, A. Wichmann, C. di Gioia, M. Borriello, F. Specht, H. Derks, J. Khan, S. Emmott, E. Petelski, A. A. Perlman, D. H. Cox, J. Zanoni, I. Slavov, N. 2022-03-18 doi:10.1101/2022.03.16.484655 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ Evidence-based calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for clinical use of PP3/BP4 criteria ]]> https://biorxiv.org/content/10.1101/2022.03.17.484479v1?rss=1 Pejaver, V. Byrne, A. B. Feng, B.-J. Pagel, K. A. Mooney, S. D. Karchin, R. O'Donnell-Luria, A. Harrison, S. M. Tavtigian, S. V. Greenblatt, M. S. Biesecker, L. G. Radivojac, P. Brenner, S. E. ClinGen Sequence Variant Interpretation Working Group, 2022-03-19 doi:10.1101/2022.03.17.484479 Cold Spring Harbor Laboratory Press 2022-03-19 <![CDATA[ Neuronal temperature perception induces specific defenses that enable C. elegans to cope with the enhanced reactivity of hydrogen peroxide at high temperature ]]> https://biorxiv.org/content/10.1101/2022.03.21.485202v1?rss=1 Servello, F. A. Fernandes, R. Eder, M. Harris, N. Martin, O. M. Oswal, N. Lindberg, A. Derosiers, N. Sengupta, P. Stroustrup, N. Apfeld, J. 2022-03-23 doi:10.1101/2022.03.21.485202 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ Identifying competition phenotypes in synthetic biochemical circuits ]]> https://biorxiv.org/content/10.1101/2022.03.22.485420v1?rss=1 Ali Al-Radhawi, M. Del Vecchio, D. Sontag, E. 2022-03-23 doi:10.1101/2022.03.22.485420 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ Signal and Measurement Considerations for Human Translation of Diffuse in vivo Flow Cytometry ]]> https://biorxiv.org/content/10.1101/2022.03.23.485369v1?rss=1 Ivich, F. Pace, J. Williams, A. Shumel, M. Fang, Q. Niedre, M. 2022-03-23 doi:10.1101/2022.03.23.485369 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ Suboptimal foraging decisions and involvement of the ventral tegmental area in human opioid addiction ]]> https://biorxiv.org/content/10.1101/2022.03.24.485654v1?rss=1 Raio, C. M. Biernacki, K. Kapoor, A. Wengler, K. Bonagura, D. Xue, J. Constantino, S. M. Horga, G. Konova, A. B. 2022-03-27 doi:10.1101/2022.03.24.485654 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Actin turnover required for adhesion-independent bleb migration ]]> https://biorxiv.org/content/10.1101/2022.04.01.486735v1?rss=1 Copos, C. Strychalski, W. 2022-04-01 doi:10.1101/2022.04.01.486735 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ Active emulsions in living cell membranes driven by contractile stresses and transbilayer coupling ]]> https://biorxiv.org/content/10.1101/2022.04.02.486649v1?rss=1 Saha, S. Das, A. Patra, C. Anilkumar, A. A. Sil, P. Mayor, S. Rao, M. 2022-04-04 doi:10.1101/2022.04.02.486649 Cold Spring Harbor Laboratory Press 2022-04-04 <![CDATA[ Thermal Effects on Neurons During Stimulation of the Brain ]]> https://biorxiv.org/content/10.1101/2022.04.02.486840v1?rss=1 Kim, T. Kadji, H. Whalen, A. Ashourvan, A. Freeman, E. Fried, S. Tadigadapa, S. Schiff, S. J. 2022-04-03 doi:10.1101/2022.04.02.486840 Cold Spring Harbor Laboratory Press 2022-04-03 <![CDATA[ Human statistical learning dynamically shapes the hippocampal processing of temporal associations ]]> https://biorxiv.org/content/10.1101/2022.04.04.487009v1?rss=1 Tang, W. Christiansen, M. H. Qi, Z. 2022-04-05 doi:10.1101/2022.04.04.487009 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ BCG vaccination of Diversity Outbred mice induces cross-reactive antibodies to SARS-CoV-2 spike protein ]]> https://biorxiv.org/content/10.1101/2022.04.18.488640v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@1ff9d16org.highwire.dtl.DTLVardef@a2302dorg.highwire.dtl.DTLVardef@8ee2borg.highwire.dtl.DTLVardef@4c7b55_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Specht, A. G. Kurtz, S. L. Elkins, K. L. Specht, H. Beamer, G. 2022-04-19 doi:10.1101/2022.04.18.488640 Cold Spring Harbor Laboratory Press 2022-04-19 <![CDATA[ The field of protein function prediction as viewed by different domain scientists ]]> https://biorxiv.org/content/10.1101/2022.04.18.488641v1?rss=1 Ramola, R. Friedberg, I. Radivojac, P. 2022-04-18 doi:10.1101/2022.04.18.488641 Cold Spring Harbor Laboratory Press 2022-04-18 <![CDATA[ Two interdigitated fine-scale channels for encoding motion and stereopsis within the human magnocellular stream ]]> https://biorxiv.org/content/10.1101/2022.04.20.488911v1?rss=1 Kennedy, B. Bex, P. Hunter, D. G. Nasr, S. 2022-04-20 doi:10.1101/2022.04.20.488911 Cold Spring Harbor Laboratory Press 2022-04-20 <![CDATA[ Regenerating axolotl retinas regrow diverse cell types with modulation by Notch signaling and reconnect to the brain ]]> https://biorxiv.org/content/10.1101/2022.04.28.489898v1?rss=1 Yandulskaya, A. S. Miller, M. N. Ansaripour, R. Carrier, R. L. Monaghan, J. R. 2022-04-29 doi:10.1101/2022.04.28.489898 Cold Spring Harbor Laboratory Press 2022-04-29 <![CDATA[ Compressive stress drives adhesion-dependent unjamming transitions in breast cancer cell migration ]]> https://biorxiv.org/content/10.1101/2022.04.30.490153v1?rss=1 Cai, G. S. Nguyen, A. Bashirzadeh, Y. Lin, S.-S. Bi, D. Liu, A. P. 2022-05-01 doi:10.1101/2022.04.30.490153 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ NetAct: a computational platform to construct core transcription factor regulatory networks using gene activity ]]> https://biorxiv.org/content/10.1101/2022.05.06.487898v1?rss=1 Su, K. Katebi, A. R. Kohar, V. R. Clauss, B. Gordin, D. Qin, Z. Karuturi, R. K. M. Li, S. Lu, M. 2022-05-07 doi:10.1101/2022.05.06.487898 Cold Spring Harbor Laboratory Press 2022-05-07 <![CDATA[ Messenger-RNA Modification Standards and Machine Learning Models Facilitate Absolute Site-Specific Pseudouridine Quantification ]]> https://biorxiv.org/content/10.1101/2022.05.06.490948v1?rss=1 Makhamreh, A. Tavakoli, S. Gamper, H. Nabizadehmashhadtoroghi, M. Fallahi, A. Hou, Y.-M. Rouhanifard, S. H. Wanunu, M. 2022-05-06 doi:10.1101/2022.05.06.490948 Cold Spring Harbor Laboratory Press 2022-05-06 <![CDATA[ Small-angle x-ray microdiffraction from fibrils embedded in tissue thin sections ]]> https://biorxiv.org/content/10.1101/2022.05.10.491381v1?rss=1 Nepal, P. Bashit, A. A. Yang, L. Makowski, L. 2022-05-11 doi:10.1101/2022.05.10.491381 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Near-Infrared Diffuse In Vivo Flow Cytometry ]]> https://biorxiv.org/content/10.1101/2022.05.11.491330v1?rss=1 Pace, J. Ivich, F. Marple, E. Niedre, M. 2022-05-11 doi:10.1101/2022.05.11.491330 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Intrinsic RNA targeting constrains the utility of CRISPR-Cas13 systems ]]> https://biorxiv.org/content/10.1101/2022.05.14.491940v1?rss=1 Li, Z. Li, Z. Cheng, X. Wang, X. Ma, S. Wang, S. Lu, Z. Zhang, H. Zhao, W. Chen, Z. Yao, Y. Chao, L. Li, W. Fei, T. 2022-05-14 doi:10.1101/2022.05.14.491940 Cold Spring Harbor Laboratory Press 2022-05-14 <![CDATA[ Peripheral sensory neuron CB2 cannabinoid receptors are necessary for both CB2-mediated antinociceptive efficacy and sparing of morphine tolerance in a mouse model of neuropathic pain ]]> https://biorxiv.org/content/10.1101/2022.05.16.492135v1?rss=1 Carey, L. M. Xu, Z. Rajic, G. Makriyannis, A. Romero, J. Hillard, C. Mackie, K. Hohmann, A. G. 2022-05-16 doi:10.1101/2022.05.16.492135 Cold Spring Harbor Laboratory Press 2022-05-16 <![CDATA[ Neuroanatomical and Functional Consequences of Oxytocin Treatment at Birth ]]> https://biorxiv.org/content/10.1101/2022.05.21.492438v1?rss=1 Kenkel, W. Ortiz, R. Yee, J. R. Perkeybile, A. M. Kulkarni, P. Carter, C. S. Ferris, C. F. 2022-05-23 doi:10.1101/2022.05.21.492438 Cold Spring Harbor Laboratory Press 2022-05-23 <![CDATA[ Full-duplex acoustic interaction system for cognitive experiments with cetaceans ]]> https://biorxiv.org/content/10.1101/2022.05.27.493738v1?rss=1 Rychen, J. Semoroz, J. Eckerle, A. Hahnloser, R. Kleinberger, R. 2022-05-29 doi:10.1101/2022.05.27.493738 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ Functional imaging and quantification of multi-neuronal olfactory responses in C. elegans ]]> https://biorxiv.org/content/10.1101/2022.05.27.493772v1?rss=1 Lin, A. Qin, S. Casademunt, H. Wu, M. Hung, W. Cain, G. Tan, N. Valenzuela, R. Lesanpezeshki, L. Pehlevan, C. Venkatachalam, V. Zhen, M. Samuel, A. 2022-05-29 doi:10.1101/2022.05.27.493772 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ Lamellar Thickness Measurements in Normal and Osteogenesis Imperfecta Human Bone, with development of a method of automated thickness averaging to simplify quantitation. ]]> https://biorxiv.org/content/10.1101/2022.05.30.493917v1?rss=1 Chow, J. Ryan, N. Shefelbine, S. J. Shapiro, F. 2022-05-31 doi:10.1101/2022.05.30.493917 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Within-species control reveals novel immune response genes in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2022.05.31.494203v1?rss=1 Ranawade, A. V. Levine, E. Hartman, E. 2022-05-31 doi:10.1101/2022.05.31.494203 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Effects of Reduced Achilles Subtendons Relative Displacement on Healthy Elderly Walking: A Simulation Study ]]> https://biorxiv.org/content/10.1101/2022.06.01.494269v1?rss=1 Khosrotabar, M. Aftabi, H. Karimpour, M. Ahmadabadi, M. N. 2022-06-01 doi:10.1101/2022.06.01.494269 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ Galaxy Training: A Powerful Framework for Teaching! ]]> https://biorxiv.org/content/10.1101/2022.06.02.494505v1?rss=1 Hiltemann, S. Rasche, H. Gladman, S. Hotz, H.-R. Lariviere, D. Blankenberg, D. Jagtap, P. D. Wollmann, T. Bretaudeau, A. Goue, N. Griffin, T. J. Royaux, C. Le Bras, Y. Mehta, S. Syme, A. E. Coppens, F. Droesbeke, B. Soranzo, N. Bacon, W. Psomopoulos, F. E. Gallardo-Alba, C. Davis, J. Föll, M. C. Fahrner, M. Doyle, M. A. Serrano-Solano, B. Fouilloux, A. C. van Heusden, P. Maier, W. Clements, D. Heyl, F. Grüning, B. A. Batut, B. Galaxy Training Network, 2022-06-03 doi:10.1101/2022.06.02.494505 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Minimal frustration underlies the usefulness of incomplete and inexact regulatory network models in biology ]]> https://biorxiv.org/content/10.1101/2022.06.07.495167v1?rss=1 Tripathi, S. Kessler, D. A. Levine, H. 2022-06-09 doi:10.1101/2022.06.07.495167 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Genomics of cold adaptations in the Antarctic notothenioid fish radiation. ]]> https://biorxiv.org/content/10.1101/2022.06.08.494096v1?rss=1 Bista, I. Wood, J. M. D. Desvignes, T. McCarthy, S. A. Matschiner, M. Ning, Z. Tracey, A. Torrance, J. Sims, Y. Chow, W. Smith, M. Oliver, K. Haggerty, L. Salzburger, W. Postlethwait, J. H. Howe, K. Clark, M. S. Detrich, W. H. Cheng, C.- H. C. Miska, E. A. Durbin, R. 2022-06-09 doi:10.1101/2022.06.08.494096 Cold Spring Harbor Laboratory Press 2022-06-09 <![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[ A Mechanistic Study on the Cellular Uptake, Intracellular Trafficking, and Antisense Gene Regulation of Bottlebrush Polymer-Conjugated Oligonucleotides ]]> https://biorxiv.org/content/10.1101/2022.06.15.496353v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@56e08eorg.highwire.dtl.DTLVardef@1b09510org.highwire.dtl.DTLVardef@a785corg.highwire.dtl.DTLVardef@1641874_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Zhang, L. Wang, Y. Chen, P. Wang, D. Zhang, Z. Ruimeng, W. Kang, X. Fang, Y. Lu, H. Cai, J. Ren, M. Dong, S. Zhang, K. 2022-06-17 doi:10.1101/2022.06.15.496353 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Generating New Musical Preferences from Hierarchical Mapping of Predictions to Reward ]]> https://biorxiv.org/content/10.1101/2022.06.17.496615v1?rss=1 Kathios, N. Sachs, M. E. Zhang, E. Ou, Y. Loui, P. 2022-06-18 doi:10.1101/2022.06.17.496615 Cold Spring Harbor Laboratory Press 2022-06-18 <![CDATA[ Sparse-spectral microendoscopy for real-time visualization of tumor cell phenotype and microenvironment spatial heterogeneity in vivo ]]> https://biorxiv.org/content/10.1101/2022.06.17.496624v1?rss=1 Spring, B. Q. Palanisami, A. Saad, M. A. Kercher, E. M. Lang, R. T. Harman, R. C. Sutin, J. Mai, Z. Hasan, T. 2022-06-18 doi:10.1101/2022.06.17.496624 Cold Spring Harbor Laboratory Press 2022-06-18 <![CDATA[ Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species ]]> https://biorxiv.org/content/10.1101/2022.06.18.496602v1?rss=1 Klughammer, J. Romanovskaia, D. Nemc, A. Posautz, A. Seid, C. Schuster, L. C. Keinath, M. C. Lugo Ramos, J. S. Kosack, L. Evankow, A. Prinz, D. Kirchberger, S. Erguner, B. Datlinger, P. Fortelny, N. Schmidl, C. Farlik, M. Skjaerven, K. Bergthaler, A. Liedvogel, M. Thaller, D. Burger, P. A. Hermann, M. Distel, M. Distel, D. L. Kubber-Heiss, A. Bock, C. 2022-06-20 doi:10.1101/2022.06.18.496602 Cold Spring Harbor Laboratory Press 2022-06-20 <![CDATA[ Inflammatory mediators act at renal pericytes to elicit contraction of vasa recta and reduce pericyte density along this medullary vascular network ]]> https://biorxiv.org/content/10.1101/2022.06.21.496998v1?rss=1 Lilley, R. J. Taylor, K. Wildman, S. S. P. Peppiatt-Wildman, C. M. 2022-06-21 doi:10.1101/2022.06.21.496998 Cold Spring Harbor Laboratory Press 2022-06-21 <![CDATA[ Ratchet, swivel, tilt and roll: A complete description of subunit rotation in the ribosome ]]> https://biorxiv.org/content/10.1101/2022.06.22.497108v1?rss=1 Hassan, A. Byju, S. Freitas, F. C. Roc, C. Pender, N. Nguyen, K. Kimbrough, E. M. Mattingly, J. Gonzalez, R. L. Oliveira, R. J. d. Dunham, C. M. Whitford, P. C. 2022-06-22 doi:10.1101/2022.06.22.497108 Cold Spring Harbor Laboratory Press 2022-06-22 <![CDATA[ A Long-Circulating Vector for Aptamers Based upon Polyphosphodiester-Backboned Molecular Brushes ]]> https://biorxiv.org/content/10.1101/2022.06.30.498214v1?rss=1 Wang, Y. Wang, D. Lin, J. Lyu, Z. Chen, P. Sun, T. Xue, C. Mojtabavi, M. Vedadghavami, A. Zhang, Z. Wang, R. Zhang, L. Park, C. Heo, G. S. Liu, Y. Dong, S. Zhang, K. 2022-07-02 doi:10.1101/2022.06.30.498214 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Cortical Parvalbumin-positive Interneuron Development and Function are Altered in the APC Conditional Knockout Mouse Model of Infantile Spasm Syndrome ]]> https://biorxiv.org/content/10.1101/2022.07.06.499046v1?rss=1 Ryner, R. F. Derera, I. Armbruster, M. Kansara, A. Sommer, M. Pirone, A. Noubary, F. Jacob, M. Dulla, C. 2022-07-06 doi:10.1101/2022.07.06.499046 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ Modbamtools: Analysis of single-molecule epigenetic data for long-range profiling, heterogeneity, and clustering ]]> https://biorxiv.org/content/10.1101/2022.07.07.499188v1?rss=1 Razaghi, R. Hook, P. W. Ou, S. Schatz, M. Hansen, K. D. Jain, M. Timp, W. 2022-07-08 doi:10.1101/2022.07.07.499188 Cold Spring Harbor Laboratory Press 2022-07-08 <![CDATA[ A Draft Human Pangenome Reference ]]> https://biorxiv.org/content/10.1101/2022.07.09.499321v1?rss=1 Liao, W.-W. Asri, M. Ebler, J. Doerr, D. Haukness, M. Hickey, G. Lu, S. Lucas, J. K. Monlong, J. Abel, H. J. Buonaiuto, S. Chang, X. H. Cheng, H. Chu, J. Colonna, V. Eizenga, J. M. Feng, X. Fischer, C. Fulton, R. S. Garg, S. Groza, C. Guarracino, A. Harvey, W. T. Heumos, S. Howe, K. Jain, M. Lu, T.-Y. Markello, C. Martin, F. J. Mitchell, M. W. Munson, K. M. Mwaniki, M. N. Novak, A. M. Olsen, H. E. Pesout, T. Porubsky, D. Prins, P. Sibbesen, J. A. Tomlinson, C. Villani, F. Vollger, M. R. Human Pangenome Reference Consortium, Bourque, G. Chaisson, M. 2022-07-09 doi:10.1101/2022.07.09.499321 Cold Spring Harbor Laboratory Press 2022-07-09 <![CDATA[ Infiltration of Tumor Spheroids by Activated Immune Cells ]]> https://biorxiv.org/content/10.1101/2022.07.11.499636v1?rss=1 Mukherjee, M. Chepizhko, O. Lionetti, M. C. Zapperi, S. La Porta, C. A. M. Levine, H. 2022-07-13 doi:10.1101/2022.07.11.499636 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ The fidelity of genetic information transfer with aging segregates according to biological processes ]]> https://biorxiv.org/content/10.1101/2022.07.18.500243v1?rss=1 Sivakumar, S. LeFebre, R. Menichetti, G. Mugler, A. Ambrosio, F. 2022-07-20 doi:10.1101/2022.07.18.500243 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Versatile Multiple Object Tracking in Sparse 2D/3D Videos Via Diffeomorphic Image Registration ]]> https://biorxiv.org/content/10.1101/2022.07.18.500485v1?rss=1 Yu, J. Nejatbakhsh, A. Torkashvand, M. Gangadharan, S. Seyedolmohadesin, M. Kim, J. Paninski, L. Venkatachalam, V. 2022-07-20 doi:10.1101/2022.07.18.500485 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ A Quantitative Evaluation of Topological Motifs and Their Coupling in Gene Circuit State Distributions ]]> https://biorxiv.org/content/10.1101/2022.07.19.500691v1?rss=1 Clauss, B. Lu, M. 2022-07-20 doi:10.1101/2022.07.19.500691 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Mapping the unicellular transcriptome of the ascending thoracic aorta to changes in mechanosensing and mechanoadaptation during aging ]]> https://biorxiv.org/content/10.1101/2022.07.21.501037v1?rss=1 Farra, Y. M. Rivera, C. Silvestro, M. Matz, J. Pratama, Y. Kumari, P. Vlahos, J. Ramkhelawon, B. Bellini, C. 2022-07-22 doi:10.1101/2022.07.21.501037 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ M2M-InvNet: TMS Induced Electric Field Reconstruction from Muscle Responses Using a Convolutional Network and Variational Inference ]]> https://biorxiv.org/content/10.1101/2022.07.22.501062v1?rss=1 Akbar, M. N. 2022-07-23 doi:10.1101/2022.07.22.501062 Cold Spring Harbor Laboratory Press 2022-07-23 <![CDATA[ Pattern formation and bistability in a synthetic intercellular genetic toggle ]]> https://biorxiv.org/content/10.1101/2022.08.02.502488v1?rss=1 Magalhaes, B. d. F. Fan, G. Sontag, E. Josic, K. Bennett, M. R. 2022-08-02 doi:10.1101/2022.08.02.502488 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ SUMOylation of NaV1.2 channels regulates the velocity of backpropagating action potentials in cortical pyramidal neurons ]]> https://biorxiv.org/content/10.1101/2022.08.02.502500v1?rss=1 Kotler, O. Khrapunsky, Y. Shvartsman, A. Dai, H. Plant, L. D. Goldstein, S. A. N. Fleidervish, I. 2022-08-03 doi:10.1101/2022.08.02.502500 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Does the paradigm of genotype-environment associations need to be re-assessed? The paradox of adaptive phenotypic clines with non-clinal patterns in causal alleles ]]> https://biorxiv.org/content/10.1101/2022.08.03.502621v1?rss=1 Lotterhos, K. E. 2022-08-05 doi:10.1101/2022.08.03.502621 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Optimal Cancer Evasion in a Dynamic Immune Microenvironment ]]> https://biorxiv.org/content/10.1101/2022.08.03.502723v1?rss=1 George, J. T. Levine, H. 2022-08-05 doi:10.1101/2022.08.03.502723 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Modulation of cannabinoid receptor signaling by endocannabinoids ]]> https://biorxiv.org/content/10.1101/2022.08.06.502185v1?rss=1 Krishna Kumar, K. Robertson, M. J. Thadhani, E. Wang, H. Suomivuori, C.-M. Powers, A. S. Ji, L. Nikas, S. P. Gerasi, M. Vemuri, K. Dror, R. Inoue, A. Makriyannis, A. Skiniotis, G. Kobilka, B. K. 2022-08-07 doi:10.1101/2022.08.06.502185 Cold Spring Harbor Laboratory Press 2022-08-07 <![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[ High-Voltage Biomolecular Sensing Using a Bacteriophage Portal Protein Covalently Immobilized Within a Solid-State Nanopore ]]> https://biorxiv.org/content/10.1101/2022.08.07.503088v1?rss=1 Mojtabavi, M. Greive, S. Antson, A. Wanunu, M. 2022-08-07 doi:10.1101/2022.08.07.503088 Cold Spring Harbor Laboratory Press 2022-08-07 <![CDATA[ A Data-Driven Optimization Method for Coarse-Graining Gene Regulatory Networks ]]> https://biorxiv.org/content/10.1101/2022.08.10.503498v1?rss=1 Caranica, C. Lu, M. 2022-08-13 doi:10.1101/2022.08.10.503498 Cold Spring Harbor Laboratory Press 2022-08-13 <![CDATA[ Chromosome-level genome of the three-spot damselfish, Dascyllus trimaculatus ]]> https://biorxiv.org/content/10.1101/2022.08.16.504202v1?rss=1 Roberts, M. B. Schultz, D. T. Gatins, R. Escalona, M. Bernardi, G. 2022-08-18 doi:10.1101/2022.08.16.504202 Cold Spring Harbor Laboratory Press 2022-08-18 <![CDATA[ Targeting default mode network connectivity with mindfulness-based fMRI neurofeedback: A pilot study among adolescents with affective disorder history ]]> https://biorxiv.org/content/10.1101/2022.08.22.504796v1?rss=1 Zhang, J. Raya, J. Morfini, F. Urban, Z. Pagliaccio, D. Yendiki, A. Auerbach, R. P. Bauer, C. C. C. Whitfield-Gabrieli, S. 2022-08-25 doi:10.1101/2022.08.22.504796 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ The butterfly effect: mutational bias of SARS-CoV-2 affects its pattern of molecular evolution on synonymous and nonsynonymous levels ]]> https://biorxiv.org/content/10.1101/2022.08.22.504819v1?rss=1 U and G>U biased. This bias forces the SARS-CoV-2 genome to become increasingly U-rich unless selection cancels it. We analysed the consequences of this bias on the composition of the most neutral (four-fold degenerate synonymous substitutions) and the least neutral positions (nonsynonymous substitutions). The neutral nucleotide composition is already highly saturated by U and, according to our model, it is at equilibrium, suggesting that in the future, we dont expect any more increase in U. However, nonsynonymous changes continue slowly evolve towards equilibrium substituting CG-rich amino-acids ("losers") with U-rich ones ("gainers"). This process is universal for all genes of SARS-CoV-2 as well as for other coronaviridae species. In line with the direction mutation pressure hypothesis, we show that viral-specific amino acid content is associated with the viral-specific mutational spectrum due to the accumulation of effectively neutral slightly deleterious variants (losers to gainers) during the molecular evolution. The tuning of a protein space by the mutational process is expected to be typical for species with relaxed purifying selection, suggesting that the purging of slightly-deleterious variants in the SARS-CoV-2 population is not very effective, probably due to the fast expansion of the viral population during the pandemic. Understanding the mutational process can help to design more robust vaccines, based on gainer-rich motifs, close to the mutation-selection equilibrium. ]]> Voronka, A. Efimenko, B. Oreshkov, S. Franco, M. Fleischmann, Z. Yurov, V. Trufanova, A. Timonina, V. Ree, N. Penfrat, E. Junier, T. Agranovsky, A. Khrapko, K. Gunbin, K. Fellay, J. Popadin, K. 2022-08-22 doi:10.1101/2022.08.22.504819 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ Epigenetic memory acquired during long-term EMTinduction governs the recovery to the epithelial state ]]> https://biorxiv.org/content/10.1101/2022.08.23.504814v1?rss=1 Jain, P. Corbo, S. Mohammad, K. George, J. T. Levine, H. Toneff, M. J. Jolly, M. K. 2022-08-25 doi:10.1101/2022.08.23.504814 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ A second unveiling: haplotig masking of the eastern oyster genome improves population-level inference ]]> https://biorxiv.org/content/10.1101/2022.08.29.505626v1?rss=1 Puritz, J. B. Guo, X. Hare, M. P. He, Y. Hillier, L. Liu, M. Lotterhos, K. E. Minx, P. Modak, T. Proestou, D. Rice, E. S. Tomlison, C. Warren, W. C. Witkop, E. Zhao, H. Gomez-Chiarri, M. 2022-08-29 doi:10.1101/2022.08.29.505626 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Nucleotide and structural polymorphisms of the eastern oyster genome paint a mosaic of divergence, selection, and human impacts ]]> https://biorxiv.org/content/10.1101/2022.08.29.505629v1?rss=1 Puritz, J. B. Zhao, H. Guo, X. Hare, M. P. He, Y. LaPeyre, J. Lotterhos, K. E. Lundgren, K. M. Modak, T. Proestou, D. A. Rawson, P. Fernandez Robledo, J. A. Witkop, E. Weedop, K. B. Gomez-Chiarri, M. 2022-09-01 doi:10.1101/2022.08.29.505629 Cold Spring Harbor Laboratory Press 2022-09-01 <![CDATA[ Structural Reorganization and Relaxation Dynamics of Axially Stressed Chromosomes ]]> https://biorxiv.org/content/10.1101/2022.09.03.506488v1?rss=1 Ruben, B. S. Brahmachari, S. Contessoto, V. G. Cheng, R. R. Oliveira Junior, A. B. Di Pierro, M. Onuchic, J. N. 2022-09-04 doi:10.1101/2022.09.03.506488 Cold Spring Harbor Laboratory Press 2022-09-04 <![CDATA[ Bridging global actin network patterns to local molecular dynamics: a combined modeling and machine learning framework ]]> https://biorxiv.org/content/10.1101/2022.09.06.506753v1?rss=1 Rostami, M. W. Bannish, B. E. Gasior, K. Pinals, R. L. Copos, C. Dawes, A. T. 2022-09-07 doi:10.1101/2022.09.06.506753 Cold Spring Harbor Laboratory Press 2022-09-07 <![CDATA[ Behavior shapes retinal motion statistics during natural locomotion ]]> https://biorxiv.org/content/10.1101/2022.09.06.506797v1?rss=1 Muller, K. S. Matthis, J. Bonnen, K. Cormack, L. K. Huk, A. Hayhoe, M. 2022-09-08 doi:10.1101/2022.09.06.506797 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Microglia protect fungi against copper starvation and promote brain infection ]]> https://biorxiv.org/content/10.1101/2022.09.07.506901v1?rss=1 Mohamed, S. H. Fu, M. S. Hain, S. Alselami, A. Vanhoffelen, E. Li, Y. Bojang, E. Lukande, R. Ballou, E. R. May, R. C. Ding, C. Vande Velde, G. Drummond, R. A. 2022-09-07 doi:10.1101/2022.09.07.506901 Cold Spring Harbor Laboratory Press 2022-09-07 <![CDATA[ Sounding the alarm: sex differences in rat ultrasonic vocalizations during Pavlovian fear conditioning and extinction ]]> https://biorxiv.org/content/10.1101/2022.09.13.507801v1?rss=1 Laine, M. A. Mitchell, J. R. Rhyner, J. Clark, R. Kannan, A. Keith, J. Pikus, M. Bergeron, E. Ravaglia, I. Ulgenturk, E. Shinde, A. Shansky, R. M. 2022-09-16 doi:10.1101/2022.09.13.507801 Cold Spring Harbor Laboratory Press 2022-09-16 <![CDATA[ Synthesis of Long RNA with a Site-Specific Modification by Enzymatic Splint Ligation ]]> https://biorxiv.org/content/10.1101/2022.09.17.508400v1?rss=1 Gamper, H. McCormick, C. Tavakoli, S. Wanunu, M. Rouhanifard, S. H. Hou, Y.-M. 2022-09-18 doi:10.1101/2022.09.17.508400 Cold Spring Harbor Laboratory Press 2022-09-18 <![CDATA[ Expression of thioredoxin-1 in the ASJ neuron corresponds with and enhances intrinsic regenerative capacity under lesion conditioning in C. elegans ]]> https://biorxiv.org/content/10.1101/2022.09.19.508543v1?rss=1 Grooms, N. W. F. W. F. Fitzgerald, M. Q. Schulting, L. G. Urena, S. E. Chung, S. H. 2022-09-19 doi:10.1101/2022.09.19.508543 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Resolving chaperone-assisted protein folding on the ribosome at the peptide level ]]> https://biorxiv.org/content/10.1101/2022.09.23.509153v1?rss=1 Wales, T. E. Pajak, A. Roeselova, A. Shivakumaraswamy, S. Howell, S. Hartl, F.-U. Engen, J. R. Balchin, D. 2022-09-23 doi:10.1101/2022.09.23.509153 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ MSstatsPTM: Statistical relative quantification of post-translational modifications in bottom-up mass spectrometry-based proteomics ]]> https://biorxiv.org/content/10.1101/2022.09.24.509068v1?rss=1 Kohler, D. Tsai, T.-H. Verschueren, E. Huang, T. Hinkle, T. Phu, L. Choi, M. Vitek, O. 2022-09-26 doi:10.1101/2022.09.24.509068 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Increase the flow rate and improve hydrogen deuterium exchange mass spectrometry ]]> https://biorxiv.org/content/10.1101/2022.09.25.509411v1?rss=1 Peterle, D. DePice, D. Wales, T. E. Engen, J. R. 2022-09-27 doi:10.1101/2022.09.25.509411 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Cortical somatostatin interneuron subtypes form cell-type specific circuits ]]> https://biorxiv.org/content/10.1101/2022.09.29.510081v1?rss=1 Wu, J. S. Sevier, E. Saldi, G.-A. Yu, S. Abbott, L. Choi, D. H. Sherer, M. Qiu, Y. Shinde, A. Rizzo, D. Xu, Q. Barrera, I. Kumar, V. Marrero, G. Pörnneke, A. Huang, S. Rudy, B. Stafford, D. A. Macosko, E. Chen, F. Fishell, G. 2022-09-29 doi:10.1101/2022.09.29.510081 Cold Spring Harbor Laboratory Press 2022-09-29 <![CDATA[ Targeting Fusobacterium nucleatum through Chemical Modifications of Host-Derived Transfer RNA Fragments ]]> https://biorxiv.org/content/10.1101/2022.09.29.510195v1?rss=1 Yang, M. Dong, P.-T. Cen, L. Shi, W. He, X. Li, J. 2022-09-30 doi:10.1101/2022.09.29.510195 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Protein Language Model Predicts Mutation Pathogenicity and Clinical Prognosis ]]> https://biorxiv.org/content/10.1101/2022.09.30.510294v1?rss=1 Liu, X. Yang, X. Ouyang, L. Guo, G. Su, J. Xi, R. Yuan, K. Yuan, F. 2022-10-03 doi:10.1101/2022.09.30.510294 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ Vascular tortuosity quantification as an outcome metric of the oxygen-induced retinopathy model of ischemic retinopathy ]]> https://biorxiv.org/content/10.1101/2022.10.02.510568v1?rss=1 Marra, K. V. Chen, J. S. Robles-Holmes, H. K. Miller, J. Wei, G. Ideguchi, Y. Ly, K. B. Prenner, S. Erdogmus, D. Ferrara, N. Campbell, J. P. Friedlander, M. Nudleman, E. 2022-10-04 doi:10.1101/2022.10.02.510568 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ Serotonin signaling in the enteric nervous system and connection to autism spectrum disorder: a translational mathematical model ]]> https://biorxiv.org/content/10.1101/2022.10.11.511819v1?rss=1 Kareva, I. 2022-10-14 doi:10.1101/2022.10.11.511819 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ Extracellular vesicles from non-neuroendocrine SCLC cells promote adhesion and survival of neuroendocrine SCLC cells ]]> https://biorxiv.org/content/10.1101/2022.10.12.511984v1?rss=1 Jimenez, L. Stolzenbach, V. Ozawa, P. M. M. Ramirez-Solano, M. A. Liu, Q. Sage, J. Weaver, A. 2022-10-13 doi:10.1101/2022.10.12.511984 Cold Spring Harbor Laboratory Press 2022-10-13 <![CDATA[ The mitochondrial component of human infertility- an increased mtDNA content and an excess of ultra-rare mtDNA variants in aneuploid versus euploid embryos. ]]> https://biorxiv.org/content/10.1101/2022.10.14.512116v1?rss=1 Ri, M. T. Ree, N. Oreshkov, S. Tofilo, M. Kirillova, A. Zvereva, I. Gunbin, K. Yurov, V. Salumets, A. Woods, D. C. Tilly, J. L. Khrapko, K. Fellay, J. Mazunin, I. Popadin, K. 2022-10-18 doi:10.1101/2022.10.14.512116 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ An Associative Memory Hamiltonian Model for DNA and Nucleosomes ]]> https://biorxiv.org/content/10.1101/2022.10.15.512163v1?rss=1 Lu, W. Onuchic, J. N. Di Pierro, M. 2022-10-18 doi:10.1101/2022.10.15.512163 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Genome-wide phage susceptibility analysis in Acinetobacter baumannii reveals capsule modulation as a central determinant of phage defense ]]> https://biorxiv.org/content/10.1101/2022.10.17.512463v1?rss=1 Bai, J. Raustad, N. Denoncourt, J. van Opijnen, T. Geisinger, E. 2022-10-17 doi:10.1101/2022.10.17.512463 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Neural predictors of subjective fear depend on the situation ]]> https://biorxiv.org/content/10.1101/2022.10.20.513114v1?rss=1 Wang, Y. Kragel, P. A. Satpute, A. B. 2022-10-21 doi:10.1101/2022.10.20.513114 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ USP10 strikes down Wnt/β-catenin signaling by dual-wielding deubiquitinase activity and phase transition potential ]]> https://biorxiv.org/content/10.1101/2022.10.31.514466v1?rss=1 Wang, Y. Mao, A. Liu, J. Li, P. Zheng, S. Tong, T. Li, Z. Zhang, H. Ma, L. Lin, J. Pang, Z. Han, Q. Li, F. Zhang, X. Chen, M. He, X. Zhang, X. Fei, T. Liu, B. Gao, D. Cao, L. Wang, Q. Li, Y. Sheng, R. 2022-11-01 doi:10.1101/2022.10.31.514466 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Targeting AAV vectors to the CNS via de novo engineered capsid-receptor interactions ]]> https://biorxiv.org/content/10.1101/2022.10.31.514553v1?rss=1 Huang, Q. Chen, A. T. Chan, K. Y. Sorensen, H. Barry, A. J. Azari, B. Beddow, T. Zheng, Q. Zhao, B. Tobey, I. G. Eid, F.-E. Chan, Y. A. Deverman, B. E. 2022-11-01 doi:10.1101/2022.10.31.514553 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Strategies for increasing the depth and throughput of protein analysis by plexDIA ]]> https://biorxiv.org/content/10.1101/2022.11.05.515287v1?rss=1 View larger version (18K): org.highwire.dtl.DTLVardef@14d73f5org.highwire.dtl.DTLVardef@1f7f008org.highwire.dtl.DTLVardef@afd392org.highwire.dtl.DTLVardef@16b20da_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Derks, J. Slavov, N. 2022-11-05 doi:10.1101/2022.11.05.515287 Cold Spring Harbor Laboratory Press 2022-11-05 <![CDATA[ Neural Entrainment to Musical Pulse In Naturalistic Music Is Preserved In Aging: Implications for Music-Based Interventions ]]> https://biorxiv.org/content/10.1101/2022.11.05.515314v1?rss=1 Tichko, P. Page, N. Kim, J. C. Large, E. Loui, P. 2022-11-06 doi:10.1101/2022.11.05.515314 Cold Spring Harbor Laboratory Press 2022-11-06 <![CDATA[ DNA-enhanced CuAAC ligand enables live-cell detection of intracellular biomolecules ]]> https://biorxiv.org/content/10.1101/2022.11.10.515969v1?rss=1 Nian, K. Liu, Y. Brigandi, L. Rouhanifard, S. H. 2022-11-10 doi:10.1101/2022.11.10.515969 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ Paired aptamer capture and FISH detection of individual virions enables cell-free determination of infectious titer ]]> https://biorxiv.org/content/10.1101/2022.11.13.516306v1?rss=1 Liu, Y. Potts, J. L. Nian, K. McCormick, C. A. Fanari, O. Rouhanifard, S. H. 2022-11-13 doi:10.1101/2022.11.13.516306 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Cultivation and Fluorescent in situ hybridization suggest that some shipworm species acquire endosymbiotic bacteria through indirect horizontal transmission ]]> https://biorxiv.org/content/10.1101/2022.11.13.516348v1?rss=1 Speare, L. Distel, D. L. 2022-11-15 doi:10.1101/2022.11.13.516348 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ The Alternate Ligand Jagged Enhances the Robustness of Notch Signaling Patterns ]]> https://biorxiv.org/content/10.1101/2022.11.16.516674v1?rss=1 Mukherjee, M. Levine, H. 2022-11-17 doi:10.1101/2022.11.16.516674 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Dynamics of alpha suppression index both modality specific and general attention processes ]]> https://biorxiv.org/content/10.1101/2022.11.16.516776v1?rss=1 Clements, G. M. Gyurkovics, M. Low, K. A. Kramer, A. F. Beck, D. M. Fabiani, M. Gratton, G. 2022-11-16 doi:10.1101/2022.11.16.516776 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ A compact breast shape acquisition system for improving diffuse optical tomography image reconstructions ]]> https://biorxiv.org/content/10.1101/2022.11.20.517255v1?rss=1 Vanegas, M. Nunez, M. M. Xu, E. Yan, S. Fang, Q. 2022-11-20 doi:10.1101/2022.11.20.517255 Cold Spring Harbor Laboratory Press 2022-11-20 <![CDATA[ Effect of depth on crowding investigated with a multi-depth plane display ]]> https://biorxiv.org/content/10.1101/2022.11.23.517719v1?rss=1 Smithers, S. P. Shao, Y. Altham, J. Bex, P. J. 2022-11-28 doi:10.1101/2022.11.23.517719 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ Despite impaired binocular function, binocular disparity integration across the visual field is spared in normal aging and glaucoma ]]> https://biorxiv.org/content/10.1101/2022.11.28.518250v1?rss=1 Maiello, G. Kwon, M. 2022-11-30 doi:10.1101/2022.11.28.518250 Cold Spring Harbor Laboratory Press 2022-11-30 <![CDATA[ Rethinking bacterial relationships in light of their molecular abilities ]]> https://biorxiv.org/content/10.1101/2022.11.28.518265v1?rss=1 Mahlich, Y. Zhu, C. Chung, H. Velaga, P. K. de Paolis Kaluza, M. C. Radivojac, P. Friedberg, I. Bromberg, Y. 2022-11-29 doi:10.1101/2022.11.28.518265 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ Neural mechanisms of parasite-induced summiting behavior in 'zombie' Drosophila ]]> https://biorxiv.org/content/10.1101/2022.12.01.518723v1?rss=1 Elya, C. Lavrentovich, D. Lee, E. Pasadyn, C. Duval, J. Basak, M. Saykina, V. de Bivort, B. L. 2022-12-01 doi:10.1101/2022.12.01.518723 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ The complete sequence of a human Y chromosome ]]> https://biorxiv.org/content/10.1101/2022.12.01.518724v1?rss=1 Rhie, A. Nurk, S. Cechova, M. Hoyt, S. J. Taylor, D. J. Altemose, N. Hook, P. W. Koren, S. Rautiainen, M. Alexandrov, I. A. Allen, J. Asri, M. Bzikadze, A. V. Chen, N.-C. Chin, C.-S. Diekhans, M. Flicek, P. Formenti, G. Fungtammasan, A. Garcia Giron, C. Garrison, E. Gershman, A. Gerton, J. Grady, P. G. Guarracino, A. Haggerty, L. Halabian, R. Hansen, N. F. Harris, R. Hartley, G. A. Harvey, W. T. Haukness, M. Heinz, J. Hourlier, T. Hubley, R. M. Hunt, S. E. Hwang, S. Jain, M. Kesharwani, R. K. Lewis, A. P. Li, H. Logsdon, G. A. Lucas, J. K. Makalowski, 2022-12-01 doi:10.1101/2022.12.01.518724 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Estimating Nutrient Concentration in Food Using Untargeted Metabolomics ]]> https://biorxiv.org/content/10.1101/2022.12.02.518912v1?rss=1 Sebek, M. L. Menichetti, G. Barabasi, A.-L. 2022-12-02 doi:10.1101/2022.12.02.518912 Cold Spring Harbor Laboratory Press 2022-12-02 <![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[ Layer-dependent activity in the human superior colliculus during working memory ]]> https://biorxiv.org/content/10.1101/2022.12.06.518975v1?rss=1 Chen, D. Kragel, P. A. Wager, T. D. Wald, L. L. Bianciardi, M. Satpute, A. B. Quigley, K. S. Barrett, L. F. Katsumi, Y. Theriault, J. E. 2022-12-06 doi:10.1101/2022.12.06.518975 Cold Spring Harbor Laboratory Press 2022-12-06 <![CDATA[ RecA balances genomic stability and evolution using many successive mismatch tolerant homology tests ]]> https://biorxiv.org/content/10.1101/2022.12.09.519633v1?rss=1 PRENTISS, M. Wang, D. Fu, J. Prevost, C. Godoy, V. Kleckner, N. E. Danilowicz, C. 2022-12-10 doi:10.1101/2022.12.09.519633 Cold Spring Harbor Laboratory Press 2022-12-10 <![CDATA[ The role of human superior colliculus in affective experiences during visual and somatosensory stimulation ]]> https://biorxiv.org/content/10.1101/2022.12.09.519812v1?rss=1 Chen, D. Kragel, P. A. Savoca, P. W. Wald, L. L. Bianciardi, M. Wager, T. D. Quigley, K. S. Satpute, A. B. Barrett, L. F. Theriault, J. E. 2022-12-11 doi:10.1101/2022.12.09.519812 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Ocean currents drive the worldwide colonization of the most widespread marine plant, eelgrass (Zostera marina) ]]> https://biorxiv.org/content/10.1101/2022.12.10.519859v1?rss=1 Yu, L. Khachaturyan, M. Matschiner, M. Healey, A. Bauer, D. Cameron, B. Cusson, M. Duffy, J. E. Fodrie, F. J. Gill, D. Grimwood, J. Hori, M. Hovel, K. Hughes, A. R. Jahnke, M. Jenkins, J. Keymanesh, K. Kruschel, C. Mamidi, S. Moksnes, P.-O. Nakaoka, M. Pennacchio, C. Reiss, K. Rossi, F. Ruesink, J. L. Schultz, S. Talbot, S. Unsworth, R. Schmutz, J. Dagan, T. Stachowicz, J. J. Van de Peer, Y. Olsen, J. L. Reusch, T. B. H. 2022-12-10 doi:10.1101/2022.12.10.519859 Cold Spring Harbor Laboratory Press 2022-12-10 <![CDATA[ Who bears the load? IOP-induced collagen fiber recruitment over the corneoscleral shell ]]> https://biorxiv.org/content/10.1101/2022.12.10.519931v1?rss=1 Foong, T. Y. Hua, Y. Amini, R. Sigal, I. A. 2022-12-13 doi:10.1101/2022.12.10.519931 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Reanalysis of mtDNA mutations of human primordial germ cells (PGCs) reveals significant contamination with NUMTs, and challenges predominantly purifying selection in late PGCs ]]> https://biorxiv.org/content/10.1101/2022.12.12.520138v1?rss=1 Fleischmann, Z. Cote-LHeureux, A. Franco, M. Oreshkov, S. Annis, S. Khrapko, M. Aidlen, D. Popadin, K. Woods, D. C. Tilly, J. L. Khrapko, K. 2022-12-14 doi:10.1101/2022.12.12.520138 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ 7-Tesla evidence for columnar and rostral--caudal organization of the human periaqueductal grey response in the absence of threat: a working memory study ]]> https://biorxiv.org/content/10.1101/2022.12.21.521479v1?rss=1 Fischbach, A. K. Satpute, A. B. Quigley, K. S. Kragel, P. A. Bianciardi, M. Wald, L. L. Wager, T. D. Feldman Barrett, L. Theriault, J. E. 2022-12-22 doi:10.1101/2022.12.21.521479 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Directed Biosynthesis of Mitragynine Stereoisomers ]]> https://biorxiv.org/content/10.1101/2022.12.22.521574v1?rss=1 Schotte, C. Jiang, Y. Grzech, D. Dang, T. Laforest, L. Leon, F. Mottinelli, M. Nadakuduti, S. S. McCurdy, C. R. O'Connor, S. E. 2022-12-22 doi:10.1101/2022.12.22.521574 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ FunGeneTyper: An Expandable Deep Learning-based Framework for Ultra-accurate Classification and Discovery of Functional Protein-Coding Genes ]]> https://biorxiv.org/content/10.1101/2022.12.28.522150v1?rss=1 0.99) and fine-grained classification and discovery of antibiotic resistance genes (ARGs) and virulence factor or toxin genes. Specifically, this new framework achieves superior performance in discovering new ARGs from human gut (accuracy: 0.8512; and F1-score: 0.6948), wastewater (0.7273; 0.6072), and soil (0.8269; 0.5445) samples, beating the state-of-the-art bioinformatics tools and protein sequence-based (F1-score: 0.0556-0.5065) and domain-based (F1-score: 0.2630-0.5224) alignment approaches. We empowered the generalized application of the framework by implementing a lightweight, privacy-preserving and plug-and-play neural network module shareable among global developers and users. The FunGeneTyper* is released to promote the monitoring of key functional genes and discovery of precious enzymatic resources from diverse microbiomes. ]]> Zhang, G. Wang, H. Zhang, L. Zhang, Z. Guo, G. Yang, J. Yuan, F. Ju, F. 2022-12-30 doi:10.1101/2022.12.28.522150 Cold Spring Harbor Laboratory Press 2022-12-30 <![CDATA[ Distinct spatial patterns of neural and physiology-related activity in the human periaqueductal grey during anticipatory social stress. ]]> https://biorxiv.org/content/10.1101/2022.12.29.522243v1?rss=1 Theriault, J. E. Fischbach, A. K. Kragel, P. A. Wager, T. D. Wald, L. L. Bianciardi, M. Quigley, K. S. Barrett, L. F. Satpute, A. B. 2022-12-29 doi:10.1101/2022.12.29.522243 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ Interplay between acetylation and ubiquitination of imitation switch chromatin remodeler Isw1 confers multidrug resistance in Cryptococcus neoformans ]]> https://biorxiv.org/content/10.1101/2022.12.30.522307v1?rss=1 Meng, Y. Li, Z. Jiang, T. Sun, T. Li, Y. Gao, X. Li, H. Suo, C. Li, C. Yang, S. Lan, T. Liao, G. Liu, T.-B. Wang, P. Ding, C. 2022-12-30 doi:10.1101/2022.12.30.522307 Cold Spring Harbor Laboratory Press 2022-12-30 <![CDATA[ Auditory and Reward Connectivity in Young and Older Adults During Music Listening and Rest ]]> https://biorxiv.org/content/10.1101/2023.01.01.522417v1?rss=1 Belden, A. Quinci, M. A. Geddes, M. R. Hanser, S. B. Donovan, N. J. Loui, P. 2023-01-02 doi:10.1101/2023.01.01.522417 Cold Spring Harbor Laboratory Press 2023-01-02 <![CDATA[ Periplasmic stress contributes to a tradeoff between protein secretion and cell growth in E. Coli Nissile ]]> https://biorxiv.org/content/10.1101/2023.01.09.523330v1?rss=1 Emani, S. S. Kan, A. S. Storms, T. Bonanno, S. Law, J. Ray, S. Joshi, N. S. 2023-01-10 doi:10.1101/2023.01.09.523330 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Hypoxia-inducing cryogels uncover key cancer-immune cell interactions in an oxygen-deficient tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2023.01.10.523477v1?rss=1 Colombani, T. Rogers, Z. Bhatt, K. Sinoimeri, J. Gerbereux, L. Hamrangsekachaee, M. Bencherif, S. A. 2023-01-10 doi:10.1101/2023.01.10.523477 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation ]]> https://biorxiv.org/content/10.1101/2023.01.12.523790v1?rss=1 Kolmogorov, M. Billingsley, K. J. Mastoras, M. Meredith, M. Monlong, J. Lorig-Roach, R. Asri, M. Alvarez Jerez, P. Malik, L. Dewan, R. Reed, X. Genner, R. M. Daida, K. Behera, S. Shafin, K. Pesout, T. Prabakaran, J. Carnevali, P. North American Brain Expression Consortium (NABEC), Yang, J. Rhie, A. Scholz, S. W. Traynor, B. J. Miga, K. H. Jain, M. Timp, W. Phillippy, A. M. Chaisson, M. Sedlazeck, F. J. Blauwendraat, C. Paten, B. 2023-01-15 doi:10.1101/2023.01.12.523790 Cold Spring Harbor Laboratory Press 2023-01-15 <![CDATA[ Real-time feedback reduces participant motion during task-based fMRI ]]> https://biorxiv.org/content/10.1101/2023.01.12.523791v1?rss=1 Rogers, C. S. Jones, M. S. McConkey, S. McLaughlin, D. J. Peelle, J. E. 2023-01-13 doi:10.1101/2023.01.12.523791 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Oxycodone self-administration and reinstatement in male and female squirrel monkeys: Effects of alternative reinforcer availability ]]> https://biorxiv.org/content/10.1101/2023.01.12.523850v1?rss=1 Moura, F. B. Booth, R. Kohut, S. 2023-01-16 doi:10.1101/2023.01.12.523850 Cold Spring Harbor Laboratory Press 2023-01-16 <![CDATA[ Oxygen-induced chromophore degradation in the photoswitchable red fluorescent protein rsCherry ]]> https://biorxiv.org/content/10.1101/2023.01.13.523900v1?rss=1 Bui, T. Y. H. De Zitter, E. Moeyaert, B. Pecqueur, L. Srinivasu, B. Y. Economou, A. Fontecave, M. Van Meervelt, L. Dedecker, P. Pedre, B. 2023-01-13 doi:10.1101/2023.01.13.523900 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Role of Complementarity-Determining Regions 1 and 3 in Pathologic Amyloid Formation by Human Immunoglobulin κ1 Light Chains ]]> https://biorxiv.org/content/10.1101/2023.02.01.526662v1?rss=1 Klimtchuk, E. S. Peterle, D. Bullitt, E. A. Connors, L. H. Engen, J. R. Gursky, O. 2023-02-03 doi:10.1101/2023.02.01.526662 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Data-Driven Optimization of DIA Mass-Spectrometry by DO-MS ]]> https://biorxiv.org/content/10.1101/2023.02.02.526809v1?rss=1 View larger version (13K): org.highwire.dtl.DTLVardef@1334corg.highwire.dtl.DTLVardef@cec8bcorg.highwire.dtl.DTLVardef@1dcc07eorg.highwire.dtl.DTLVardef@1e1abd2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Wallmann, G. Leduc, A. Slavov, N. 2023-02-03 doi:10.1101/2023.02.02.526809 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Low dimensionality of phenotypic space as an emergent property of coordinated teams in biological regulatory networks ]]> https://biorxiv.org/content/10.1101/2023.02.03.526930v1?rss=1 Hari, K. Harlapur, P. Saxena, A. Girish, A. Levine, H. Jolly, M. K. 2023-02-03 doi:10.1101/2023.02.03.526930 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Assembly and operation of a cooling stage to immobilize C. elegans on their culture plates ]]> https://biorxiv.org/content/10.1101/2023.02.03.526998v1?rss=1 Wang, Y. L. Grooms, N. W. F. Ma, C. Chung, S. H. 2023-02-04 doi:10.1101/2023.02.03.526998 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ How useful is genomic data for predicting maladaptation to future climate? ]]> https://biorxiv.org/content/10.1101/2023.02.10.528022v1?rss=1 Lind, B. M. Candido-Ribeiro, R. Singh, P. Lu, M. Obreht Vidakovic, D. Booker, T. R. Whitlock, M. C. Yeaman, S. Isabel, N. Aitken, S. N. 2023-02-13 doi:10.1101/2023.02.10.528022 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ Cardinal v3 - a versatile open source software for mass spectrometry imaging analysis ]]> https://biorxiv.org/content/10.1101/2023.02.20.529280v1?rss=1 Bemis, K. A. Foell, M. C. Guo, D. Lakkimsetty, S. S. Vitek, O. 2023-02-21 doi:10.1101/2023.02.20.529280 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Phased nanopore assembly with Shasta and modular graph phasing with GFAse ]]> https://biorxiv.org/content/10.1101/2023.02.21.529152v1?rss=1 Lorig-Roach, R. Meredith, M. Monlong, J. Jain, M. Olsen, H. McNulty, B. Porubsky, D. Montague, T. G. Lucas, J. Condon, C. Eizenga, J. Juul, S. McKenzie, S. Simmonds, S. Park, J. Asri, M. Koren, S. Eichler, E. Axel, R. Martin, B. Carnevali, P. Miga, K. Paten, B. 2023-02-22 doi:10.1101/2023.02.21.529152 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ Machined silicon traps for capturing novel bacterial communities and strains in-situ ]]> https://biorxiv.org/content/10.1101/2023.02.21.529475v1?rss=1 Romero Santiveri, C. Vineis, J. H. Martins, S. Calaza, C. Gaspar, J. Bowen, J. L. Goluch, E. D. 2023-02-22 doi:10.1101/2023.02.21.529475 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ Can deep learning predict human intelligence from structural brain MRI? ]]> https://biorxiv.org/content/10.1101/2023.02.24.529924v1?rss=1 Hussain, M. A. LaMay, D. Grant, E. Ou, Y. 2023-02-27 doi:10.1101/2023.02.24.529924 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ AIM (Angular Indication Measurement) paradigm: Adaptive, self-administered, and generalizable vision assessment used to measure visual acuity ]]> https://biorxiv.org/content/10.1101/2023.02.25.529586v1?rss=1 2 adaptive steps for AIM-VA. AIM-VAs ability to detect defocus was comparable with that of an ETDRS letter chart and showed greater sensitivity to astigmatic blur, and AIM-VAs repeatability is comparable with ETDRS when using 2 or more adaptive steps. AIMs self-administered orientation judgment approach is generalizable to interrogate other visual functions, e.g., contrast, color, motion, stereo-vision. ]]> Skerswetat, J. He, J. Shah, J. B. Aycardi, N. Bex, P. J. 2023-02-27 doi:10.1101/2023.02.25.529586 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Continuous, long-term crawling behavior characterized by a robotic transport system ]]> https://biorxiv.org/content/10.1101/2023.02.27.530235v1?rss=1 Yu, J. Dancausse, S. Paz, M. Faderin, T. Gaviria, M. Shomar, J. W. Zucker, D. Venkatachalam, V. Klein, M. 2023-02-28 doi:10.1101/2023.02.27.530235 Cold Spring Harbor Laboratory Press 2023-02-28 <![CDATA[ Structure-based discovery of cannabinoid-1 receptor agonists with reduced side effects ]]> https://biorxiv.org/content/10.1101/2023.02.27.530254v1?rss=1 Tummino, T. A. Iliopoulos-Tsoutsouvas, C. Braz, J. M. O'Brien, E. S. Stein, R. M. Craik, V. Tran, N. K. Ganapathy, S. Shiimura, Y. Tong, F. Ho, T. C. Radchenko, D. S. Moroz, Y. S. Liu, F. Rosado, S. R. Bhardwaj, K. Benitez, J. Liu, Y. Kandasamy, H. Normand, C. Semache, M. Sabbagh, L. Glenn, I. Irwin, J. J. Kumar, K. K. Makriyannis, A. Basbaum, A. I. Shoichet, B. K. 2023-03-03 doi:10.1101/2023.02.27.530254 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Fine-tuning GPCR-mediated neuromodulation by biasing signaling through different G-protein subunits ]]> https://biorxiv.org/content/10.1101/2023.03.03.529094v1?rss=1 Park, J.-C. Luebbers, A. Dao, M. Semeano, A. Papakonstantinou, M. P. Broselid, S. Yano, H. Martemyanov, K. Garcia-Marcos, M. 2023-03-04 doi:10.1101/2023.03.03.529094 Cold Spring Harbor Laboratory Press 2023-03-04 <![CDATA[ AspFlex: molecular tools to study gene expression and regulation in Acinetobacter baumannii ]]> https://biorxiv.org/content/10.1101/2023.03.17.533205v1?rss=1 Brychcy, M. Kokodynski, A. Lloyd, D. E. Godoy, V. G. 2023-03-18 doi:10.1101/2023.03.17.533205 Cold Spring Harbor Laboratory Press 2023-03-18 <![CDATA[ Personal interests amplify engagement of language regions in the brains of children with and without autism ]]> https://biorxiv.org/content/10.1101/2023.03.21.533695v1?rss=1 D'Mello, A. M. Olson, H. A. Johnson, K. T. Nishith, S. Frosch, I. R. Gabrieli, J. D. E. 2023-03-23 doi:10.1101/2023.03.21.533695 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Modeling the role of immune cell conversion in the tumor-immune microenviroment ]]> https://biorxiv.org/content/10.1101/2023.03.22.533789v1?rss=1 Moffett, A. S. Deng, Y. Levine, H. 2023-03-24 doi:10.1101/2023.03.22.533789 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Age-related variability in network engagement during music listening ]]> https://biorxiv.org/content/10.1101/2023.03.24.534123v1?rss=1 Faber, S. E. Belden, A. G. Loui, P. McIntosh, A. R. 2023-03-25 doi:10.1101/2023.03.24.534123 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Turing pattern prediction in three-dimensional domains: the role of initial conditions and growth ]]> https://biorxiv.org/content/10.1101/2023.03.29.534782v1?rss=1 Ben Tahar, S. Munoz, J. J. Shefelbine, S. J. Comellas, E. 2023-03-30 doi:10.1101/2023.03.29.534782 Cold Spring Harbor Laboratory Press 2023-03-30 <![CDATA[ Transposon-sequencing across multiple Mycobacterium abscessus isolates reveals significant functional genomic diversity among strains ]]> https://biorxiv.org/content/10.1101/2023.03.29.534805v1?rss=1 Akusobi, C. Benghomari, B. S. Choudhery, S. Singhvi, S. Hicks, A. L. Ioerger, T. R. Rubin, E. J. 2023-03-29 doi:10.1101/2023.03.29.534805 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ SEQUENCE VS. STRUCTURE: DELVING DEEP INTO DATA DRIVEN PROTEIN FUNCTION PREDICTION ]]> https://biorxiv.org/content/10.1101/2023.04.02.534383v1?rss=1 Tian, X. Wang, Z. Yang, K. K. Su, J. Du, H. Zheng, Q. Guo, G. Yang, M. Yang, F. Yuan, F. 2023-04-04 doi:10.1101/2023.04.02.534383 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ Multicellular, IVT-derived, unmodified human transcriptome for nanopore direct RNA analysis ]]> https://biorxiv.org/content/10.1101/2023.04.06.535889v1?rss=1 McCormick, C. A. Akeson, S. Tavakoli, S. Bloch, D. Klink, I. N. Jain, M. Rouhanifard, S. H. 2023-04-07 doi:10.1101/2023.04.06.535889 Cold Spring Harbor Laboratory Press 2023-04-07 <![CDATA[ CB1R blockade unmasks TRPV1-mediated contextual fear generalization in female, but not male rats ]]> https://biorxiv.org/content/10.1101/2023.04.12.536625v1?rss=1 Huckleberry, K. A. Calitri, R. Li, A. J. Mejdell, M. Singh, A. Bhutani, V. Laine, M. A. Nastase, A. S. Morena, M. Hill, M. Shansky, R. M. 2023-04-12 doi:10.1101/2023.04.12.536625 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ The 'Stem' and the 'Workers' of the mtDNA population of the cell. Evidence from mutational analysis. ]]> https://biorxiv.org/content/10.1101/2023.04.14.536897v1?rss=1 Cote-L'Heureux, A. Franco, M. Maithania, Y. N. K. Popadin, K. Woods, D. C. Tilly, J. Khrapko, K. 2023-04-15 doi:10.1101/2023.04.14.536897 Cold Spring Harbor Laboratory Press 2023-04-15 <![CDATA[ Inferring control objectives in a virtual balancing task in humans and monkeys ]]> https://biorxiv.org/content/10.1101/2023.05.02.539055v1?rss=1 Sadeghi, M. Sharif Razavian, R. Bazzi, S. Chowdhury, R. H. Batista, A. P. Loughlin, P. J. Sternad, D. 2023-05-02 doi:10.1101/2023.05.02.539055 Cold Spring Harbor Laboratory Press 2023-05-02 <![CDATA[ HIF-stabilizing Biomaterials: from Hypoxia-mimicking to Hypoxia-inducing ]]> https://biorxiv.org/content/10.1101/2023.05.04.539396v1?rss=1 1 day) hypoxic conditions. We also aim to highlight the advantages and limitations of these emerging biomaterials for biomedical applications, with an emphasis on cancer research. ]]> Colombani, T. Bhatt, K. Epel, B. Kotecha, M. Bencherif, S. A. 2023-05-05 doi:10.1101/2023.05.04.539396 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ Levy movements and a slowly decaying memory allow efficient collective learning in groups of interacting foragers ]]> https://biorxiv.org/content/10.1101/2023.05.08.539904v1?rss=1 Falcon-Cortes, A. Boyer, D. Aldana, M. Ramos-Fernandez, G. 2023-05-09 doi:10.1101/2023.05.08.539904 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ A new antibiotic from an uncultured bacterium binds to an immutable target ]]> https://biorxiv.org/content/10.1101/2023.05.15.540765v1?rss=1 Shukla, R. Peoples, A. J. Ludwig, K. C. Maity, S. Derks, M. G. N. Krueger, A. M. de Benedetti, S. Vermeulen, B. J. A. Honorato, R. V. Grein, F. Lavore, F. Bonvin, A. M. J. J. Kubitscheck, U. Breukink, E. Achorn, C. Nitti, A. Schwalen, C. J. Spoering, A. L. Ling, L. L. Hughes, D. Lelli, M. Roos, W. H. Lewis, K. Schneider, T. Weingarth, M. 2023-05-15 doi:10.1101/2023.05.15.540765 Cold Spring Harbor Laboratory Press 2023-05-15 <![CDATA[ Engineered bacteria titrate hydrogen sulfide and induce concentration-dependent effects on host in a gut microphysiological system ]]> https://biorxiv.org/content/10.1101/2023.05.16.538950v1?rss=1 Hayes, J. A. Lunger, A. W. Sharma, A. S. Fernez, M. T. Koppes, R. A. Koppes, A. N. Woolston, B. M. 2023-05-16 doi:10.1101/2023.05.16.538950 Cold Spring Harbor Laboratory Press 2023-05-16 <![CDATA[ Novel mechanism of MYC deregulation in Multiple Myeloma ]]> https://biorxiv.org/content/10.1101/2023.05.19.541506v1?rss=1 Rahmat, M. Clement, K. Alberge, J.-B. Sklavenitis-Pistofidis, R. Kodgule, R. Fulco, C. Heilpern-Mallory, D. Nilsson, K. Dorfman, D. Engreitz, J. Getz, G. Pinello, L. Ryan, R. Ghobrial, I. M. 2023-05-22 doi:10.1101/2023.05.19.541506 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Structure of mitoribosome reveals mechanism of mRNA binding, tRNA interactions with L1 stalk, roles of cofactors and rRNA modifications ]]> https://biorxiv.org/content/10.1101/2023.05.24.542018v1?rss=1 Singh, V. Itoh, Y. Del'Olio, S. Hassan, A. Naschberger, A. Flygaard, R. K. Nobe, Y. Izumikawa, K. Aibara, S. Andrell, J. Whitford, P. Barrientos, A. Taoka, M. Amunts, A. 2023-05-24 doi:10.1101/2023.05.24.542018 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Modeling kidney development, disease, and plasticity with clonal expandable nephron progenitor cells and nephron organoids ]]> https://biorxiv.org/content/10.1101/2023.05.25.542343v1?rss=1 Huang, B. Zeng, Z. Li, H. Li, Z. Chen, X. Guo, J. Zhang, C. C. Schreiber, M. E. Vonk, A. Xiang, T. Patel, T. Li, Y. Parvez, R. Der, B. Chen, J. H. Liu, Z. Thornton, M. E. Grubbs, B. H. Diao, Y. Dou, Y. Gnedeva, K. Lindstrom, N. O. Ying, Q.-L. Pastor-Soler, N. M. Fei, T. Hallows, K. R. McMahon, A. P. Li, Z. 2023-05-25 doi:10.1101/2023.05.25.542343 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Identification of post-transcriptional modifications in nucleic acid sequences using propose-designed molecular beacons ]]> https://biorxiv.org/content/10.1101/2023.05.25.542360v1?rss=1 Sahu, P. Pereira, G. Wang, J. Dokholyan, N. Szeliski, K. tran, V. Korneck, M. Tigges, J. Jones, J. Ghiran, I. 2023-05-25 doi:10.1101/2023.05.25.542360 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Allosteric site variants affect GTP hydrolysis on RAS ]]> https://biorxiv.org/content/10.1101/2023.05.29.542740v1?rss=1 Johnson, C. W. Fetics, S. K. Davis, K. P. Rodrigues, J. A. Mattos, C. 2023-05-29 doi:10.1101/2023.05.29.542740 Cold Spring Harbor Laboratory Press 2023-05-29 <![CDATA[ Conformational heterogeneity of the BTK PHTH domain drives multiple regulatory states ]]> https://biorxiv.org/content/10.1101/2023.06.02.543453v1?rss=1 Lin, D. Y.-w. Kueffer, L. E. Juneja, P. Wales, T. E. Engen, J. R. Andreotti, A. H. 2023-06-03 doi:10.1101/2023.06.02.543453 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ A Pumpless, High-Throughput Microphysiological SystemConfirms Enteric Innervation of Duodenal Epithelium Strengthensthe Barrier Function ]]> https://biorxiv.org/content/10.1101/2023.06.03.543561v1?rss=1 Nichols, K. Snyder, J. Koppes, R. Koppes, A. 2023-06-04 doi:10.1101/2023.06.03.543561 Cold Spring Harbor Laboratory Press 2023-06-04 <![CDATA[ A deep learning-based drug repurposing screening and validation for anti-SARS-CoV-2 compounds by targeting the cell entry mechanism ]]> https://biorxiv.org/content/10.1101/2023.06.03.543589v1?rss=1 Yao, Y. Zhang, Y. Li, Z. Chen, Z. Wang, X. Li, Z. Yu, L. Cheng, X. Li, W. Jiang, W.-J. Wu, H.-J. Feng, Z. Sun, J. Fei, T. 2023-06-05 doi:10.1101/2023.06.03.543589 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Diversity at single nucleotide to pangenome scales among sulfur cycling bacteria in salt marshes ]]> https://biorxiv.org/content/10.1101/2023.06.08.544202v1?rss=1 Perez Castro, S. Peredo, E. L. Mason, O. Vineis, J. H. Bowen, J. L. Mortazavi, B. Ganesh, A. Ruff, S. E. Paul, B. G. Giblin, A. Cardon, Z. 2023-06-10 doi:10.1101/2023.06.08.544202 Cold Spring Harbor Laboratory Press 2023-06-10 <![CDATA[ A subtle structural modification of a synthetic cannabinoid receptor agonist drastically increases its efficacy at the CB1 receptor ]]> https://biorxiv.org/content/10.1101/2023.06.10.544442v1?rss=1 Yano, H. Chitsazi, R. Lucaj, C. Tran, P. Hoffman, A. F. Baumann, M. H. Lupica, C. R. Shi, L. 2023-06-12 doi:10.1101/2023.06.10.544442 Cold Spring Harbor Laboratory Press 2023-06-12 <![CDATA[ Comparing kinetic proofreading and kinetic segregation for T cell receptor activation ]]> https://biorxiv.org/content/10.1101/2023.06.11.544497v1?rss=1 Moffett, A. S. Ganzinger, K. A. Eckford, A. 2023-06-11 doi:10.1101/2023.06.11.544497 Cold Spring Harbor Laboratory Press 2023-06-11 <![CDATA[ Predicting the impact of rare variants on RNA splicing in CAGI6 ]]> https://biorxiv.org/content/10.1101/2023.06.20.545093v1?rss=1 Lord, J. Jaramillo Oquendo, C. Wai, H. A. Douglas, A. G. L. Bunyan, D. J. Wang, Y. Hu, Z. Zeng, Z. Danis, D. Katsonis, P. Williams, A. Lichtarge, O. Chang, Y. Bagnall, R. D. Mount, S. M. Matthiasardottir, B. Lin, C. van Overeem Hansen, T. Leman, R. Martins, A. Houdayer, C. Krieger, S. Bakolitsa, C. Peng, Y. Kamandula, A. Radivojac, P. Baralle, D. 2023-06-22 doi:10.1101/2023.06.20.545093 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Rapid Prototyping of Thermoplastic Microfluidic 3D Cell Culture Devices by Creating Regional Hydrophilicity Discrepancy ]]> https://biorxiv.org/content/10.1101/2023.06.23.546122v1?rss=1 Bai, H. Olson, K. N. P. Pan, M. Marshall, T. Singh, H. Ma, J. Gilbride, P. Yuan, Y.-C. Si, L. Maharjan, S. Huang, D. Qian, X. Livermore, C. Zhang, Y. S. Xie, X. 2023-06-26 doi:10.1101/2023.06.23.546122 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Lysine vitcylation is a novel vitamin C-derived protein modification that enhances STAT1-mediated immune response ]]> https://biorxiv.org/content/10.1101/2023.06.27.546774v1?rss=1 He, X. Wei, Y. Wu, J. Wang, Q. Bergholz, J. S. Gu, H. Zou, J. Lin, S. Wang, W. Xie, S. Jiang, T. Lee, J. Asara, J. M. Zhang, K. Cantley, L. C. Zhao, J. J. 2023-06-27 doi:10.1101/2023.06.27.546774 Cold Spring Harbor Laboratory Press 2023-06-27 <![CDATA[ Real-time targeted illumination in widefield microscopy achieves confocal quality neuronal images ]]> https://biorxiv.org/content/10.1101/2023.07.09.548132v1?rss=1 Wang, Y. L. Fan, J. Chung, S. H. 2023-07-10 doi:10.1101/2023.07.09.548132 Cold Spring Harbor Laboratory Press 2023-07-10 <![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[ Cortical and subcortical mapping of the allostatic-interoceptive system in the human brain: replication and extension with 7 Tesla fMRI ]]> https://biorxiv.org/content/10.1101/2023.07.20.548178v1?rss=1 Zhang, J. Chen, D. Srirangarajan, T. Theriault, J. Kragel, P. A. Hartley, L. Lee, K. M. McVeigh, K. Wager, T. Wald, L. L. Satpute, A. B. Quigley, K. S. Whitfield-Gabrieli, S. Barrett, L. F. Bianciardi, M. 2023-07-24 doi:10.1101/2023.07.20.548178 Cold Spring Harbor Laboratory Press 2023-07-24 <![CDATA[ Matrix stiffness modulates 3D spheroid sorting and burst-like collective migration ]]> https://biorxiv.org/content/10.1101/2023.07.23.549940v1?rss=1 Cai, G. Li, X. Lin, S.-S. Chen, S. J. Koning, K. Bi, D. Liu, A. P. 2023-07-25 doi:10.1101/2023.07.23.549940 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML ]]> https://biorxiv.org/content/10.1101/2023.07.29.551111v1?rss=1 Katebi, A. R. Chen, X. Li, S. Lu, M. 2023-07-31 doi:10.1101/2023.07.29.551111 Cold Spring Harbor Laboratory Press 2023-07-31 <![CDATA[ Comprehensive genome editing confers "off-the-shelf" CAR-T cells superior efficacy against solid tumors ]]> https://biorxiv.org/content/10.1101/2023.08.03.551705v1?rss=1 Murray, R. Navarrete, N. R. R. Desai, K. Chowdhury, M. R. Chilakapati, S. R. Chong, B. Messana, A. Sobon, H. Rocha, J. Musenge, F. Camblin, A. Ciaramella, G. Sitkovsky, M. Maldini, C. Hatfield, S. 2023-08-04 doi:10.1101/2023.08.03.551705 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ RACER-m Leverages Structural Features for Sparse T Cell Specificity Prediction ]]> https://biorxiv.org/content/10.1101/2023.08.06.552190v1?rss=1 Wang, A. T. Lin, X. Chau, K. N. Onuchic, J. N. Levine, H. George, J. T. 2023-08-07 doi:10.1101/2023.08.06.552190 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Graph Theoretical Network Structures Underlie Age-Related Differences in the Functional Connectome During Rest and Music Listening ]]> https://biorxiv.org/content/10.1101/2023.08.08.552499v1?rss=1 Belden, A. Loui, P. 2023-08-12 doi:10.1101/2023.08.08.552499 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ An adult clock component links circadian rhythms to pancreatic β-cell maturation ]]> https://biorxiv.org/content/10.1101/2023.08.11.552890v1?rss=1 Montalvo, A. P. Gruskin, Z. L. Leduc, A. Liu, M. Gao, Z. Ahn, J. H. Straubhaar, J. R. Slavov, N. Alvarez-Dominguez, J. R. 2023-08-12 doi:10.1101/2023.08.11.552890 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ Integrating Gaze, image analysis, and body tracking: Foothold selection during locomotion. ]]> https://biorxiv.org/content/10.1101/2023.08.18.553818v1?rss=1 Muller, K. S. Panfili, D. Matthis, J. Bonnen, K. Hayhoe, M. 2023-08-18 doi:10.1101/2023.08.18.553818 Cold Spring Harbor Laboratory Press 2023-08-18 <![CDATA[ Longevity Bottlenecks ]]> https://biorxiv.org/content/10.1101/2023.08.18.553936v1?rss=1 Florea, M. Hamalainen, M. Seebold, P. Cheng, N. Murray, P. Colville, A. J. Zheng, S. Ingham, D. Kantelal, R. De Sicilia, R. 2023-08-21 doi:10.1101/2023.08.18.553936 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ TESOGENASE, An Engineered Nuclease Editor for Enhanced Targeted Genome Integration ]]> https://biorxiv.org/content/10.1101/2023.08.28.553855v1?rss=1 4Kb transgene knock-in in primary cells. We further demonstrated that enGager mediated enhancement for genome integration is ssDNA, but less dsDNA dependent. Using one of the mini-enGagers, we demonstrated large chimeric antigen receptor (CAR) transgene integration in primary T cells with exceptional efficiency and anti-tumor function. These tripartite editors with ssDNA optimized genome engineering system (TESOGENASETM) add a set of novel endonuclease editors into the gene-editing toolbox for potential cell and gene therapeutic development based on ssDNA mediated non-viral genome engineering. HighlightO_LIA reporter Knock-in screening establishes enGager system to identify TESOGENASE editor to improving ssDNA mediated genome integration C_LIO_LIMini-TESOGENASEs developed by fusing Cas9 nuclease with novel ssDNA binding motifs C_LIO_LImRNA mini-TESOGENASEs enhance targeted genome integration via various non-viral delivery approaches C_LIO_LIEfficient functional CAR-T cell engineering by mini-TESOGENASE C_LI ]]> Nam, H. Xie, K. Majumdar, I. Yang, S. Starzyk, J. Lee, D. Shan, R. Li, J. Wu, H. 2023-08-29 doi:10.1101/2023.08.28.553855 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Local read haplotagging enables accurate long-read small variant calling ]]> https://biorxiv.org/content/10.1101/2023.09.07.556731v1?rss=1 Kolesnikov, A. Cook, D. E. Nattestad, M. Ashley, E. A. Gorzynski, J. Goenka, S. D. Jain, M. McNulty, B. Miga, K. H. Paten, B. Chang, P.-C. Carroll, A. Shafin, K. 2023-09-12 doi:10.1101/2023.09.07.556731 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Programmed Cell Death Modifies Neural Circuits and Tunes Intrinsic Behavior ]]> https://biorxiv.org/content/10.1101/2023.09.11.557249v1?rss=1 Kochersberger, A. Torkashvand, M. M. Lee, D. Baskoylu, S. Sengupta, T. Koonce, N. Emerson, C. Patel, N. V. Colon-Ramos, D. Flavell, S. W. Horvitz, H. R. Venkatachalam, V. Hammarlund, M. 2023-09-14 doi:10.1101/2023.09.11.557249 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ In vivo Imaging using Surface Enhanced Spatially Offset Raman Spectroscopy (SESORS): Balancing Sampling Frequency to Improve Overall Image Acquisition ]]> https://biorxiv.org/content/10.1101/2023.09.17.558110v1?rss=1 Nicolson, F. Andreiuk, B. Lee, E. O'Donnell, B. Whitley, A. Riepl, N. Burkhart, D. Cameron, A. Protti, A. Rudder, S. Yang, J. Mabbott, S. Haigis, K. M. 2023-09-18 doi:10.1101/2023.09.17.558110 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ An Information-Theoretic Approach to Reward Rate Optimization in the Tradeoff Between Controlled and Automatic Processing in Neural Network Architectures ]]> https://biorxiv.org/content/10.1101/2023.09.18.558214v1?rss=1 Petri, G. Musslick, S. Cohen, J. D. 2023-09-18 doi:10.1101/2023.09.18.558214 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ Ventromedial Frontoinsular Connectivity is Associated with Long-term Smoking Behavior Change in Aging ]]> https://biorxiv.org/content/10.1101/2023.09.18.558264v1?rss=1 Thovinakere, N. Noriega de la Colina, A. Ai, M. Walker, C. Baracchini, G. Tremblay-Mercier, J. Villeneuve, S. Spreng, N. Geddes, M. The PREVENT-AD Research Group, 2023-09-18 doi:10.1101/2023.09.18.558264 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ A computational account of real-world attentional allocation based on visual gain fields ]]> https://biorxiv.org/content/10.1101/2023.09.18.558354v1?rss=1 Harrison, W. J. Stead, I. Wallis, T. S. A. Bex, P. J. Mattingley, J. B. 2023-09-18 doi:10.1101/2023.09.18.558354 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ 4D Mesoscale liquid model of nucleus resolves chromatin's radial organization ]]> https://biorxiv.org/content/10.1101/2023.09.21.558819v1?rss=1 Laghmach, R. Di Pierro, M. Potoyan, D. 2023-09-23 doi:10.1101/2023.09.21.558819 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ Mechanical imbalance between normal and cancer cells drives epithelial defence against cancer ]]> https://biorxiv.org/content/10.1101/2023.09.27.559723v1?rss=1 Gupta, P. Kayal, S. Pothapragada, S. P. Senapati, H. K. Devendran, P. Bi, D. Das, T. 2023-09-29 doi:10.1101/2023.09.27.559723 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Microbially Driven Reversible Actuation and Color Changing Materials ]]> https://biorxiv.org/content/10.1101/2023.09.29.560148v1?rss=1 Kuang, H. Y. Bonanno, S. Chang, W.-T. Bower, D. Q. Pratt, V. M. Zerkowski, J. Scaperdas, N. Young, L. A. Wilson, D. J. Deravi, L. F. Joshi, N. S. 2023-10-01 doi:10.1101/2023.09.29.560148 Cold Spring Harbor Laboratory Press 2023-10-01 <![CDATA[ BBQ methods: Streamlined workflows for Bacterial Burden Quantification in infected cells by confocal microscopy ]]> https://biorxiv.org/content/10.1101/2023.10.01.560379v1?rss=1 Augenstreich, J. Shuster, M. J. Lyu, Z. Fan, Y. Ling, J. Briken, V. 2023-10-02 doi:10.1101/2023.10.01.560379 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Controlling pericellular oxygen tension in cell culture reveals distinct breast cancer responses to low oxygen tensions ]]> https://biorxiv.org/content/10.1101/2023.10.02.560369v1?rss=1 Rogers, Z. J. Colombani, T. C. Khan, S. Bhatt, K. Nukovic, A. Zhou, G. Woolston, B. M. Taylor, C. T. Gilkes, D. M. Slavov, N. Bencherif, S. A. 2023-10-03 doi:10.1101/2023.10.02.560369 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Identification of Determinants that Allow Maintenance of High-Level Fluoroquinolone Resistance in Acinetobacter baumannii ]]> https://biorxiv.org/content/10.1101/2023.10.03.560562v1?rss=1 Hamami, E. Huo, W. Castaneda, A. Bai, J. Syal, S. Ortiz-Martinez, J. C. van Opijnen, T. Geisinger, E. Isberg, R. R. 2023-10-03 doi:10.1101/2023.10.03.560562 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Characterization of Gαs and Gαolf activation by catechol and non-catechol dopamine D1 receptor agonists ]]> https://biorxiv.org/content/10.1101/2023.10.03.560682v1?rss=1 Nguyen, A. M. Semeano, A. Quach, V. Inoue, A. Nichols, D. E. Yano, H. 2023-10-05 doi:10.1101/2023.10.03.560682 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Traumatic brain injury disrupts state-dependent functional cortical connectivity in a mouse model ]]> https://biorxiv.org/content/10.1101/2023.10.06.560776v1?rss=1 Bottom-Tanzer, S. Corella, S. Meyer, J. Sommer, M. Bolanos, L. Murphy, T. Quinones, S. Heiney, S. Shtrahman, M. Whalen, M. Oren, R. Higley, M. J. Cardin, J. A. Noubary, F. Armbruster, M. Dulla, C. 2023-10-06 doi:10.1101/2023.10.06.560776 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Neuroinflammation increases oxygen extraction in a mouse model of Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2023.10.16.562353v1?rss=1 Liu, C. Cardenas-Rivera, A. Teitelbaum, S. Birmingham, A. Alfadhel, M. Yaseen, M. A. 2023-10-19 doi:10.1101/2023.10.16.562353 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Biochemical and functional characterization of the p.A165T missense variant of mitochondrial amidoxime-reducing component 1 in HepG2 cells ]]> https://biorxiv.org/content/10.1101/2023.10.18.562989v1?rss=1 Hou, W. Watson, C. Cecconie, T. Bolaki, M. N. Brady, J. J. Lu, Q. Gatto, G. J. Day, T. A. 2023-10-19 doi:10.1101/2023.10.18.562989 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Power and reproducibility in the external validation of brain-phenotype predictions ]]> https://biorxiv.org/content/10.1101/2023.10.25.563971v1?rss=1 Rosenblatt, M. Tejavibulya, L. Camp, C. C. Jiang, R. Westwater, M. L. Noble, S. Scheinost, D. 2023-10-30 doi:10.1101/2023.10.25.563971 Cold Spring Harbor Laboratory Press 2023-10-30 <![CDATA[ Transcriptomic network analysis of brain and bone reveals shared molecular mechanisms underlyingAlzheimer's Disease and related dementias and Osteoporosis ]]> https://biorxiv.org/content/10.1101/2023.10.26.559969v1?rss=1 Nagarajan, A. Laird, J. Ugochukwu, O. Reppe, S. Gautvik, K. Ross, R. D. Bennett, D. A. Rosen, C. J. Kiel, D. P. Higginbotham, L. A. Seyfried, N. Lary, C. W. 2023-10-28 doi:10.1101/2023.10.26.559969 Cold Spring Harbor Laboratory Press 2023-10-28 <![CDATA[ Expression of Filaments of the Geobacter Extracellular Cytochrome OmcS in Shewanella oneidensis ]]> https://biorxiv.org/content/10.1101/2023.10.26.564108v1?rss=1 Lin, T. Ding, W. Zhang, D. Yang, Y. Li, F. Xu, D. Lovley, D. R. Song, H. 2023-10-26 doi:10.1101/2023.10.26.564108 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ Drug-Target-Interaction Prediction with Contrastive and Siamese Transformers. ]]> https://biorxiv.org/content/10.1101/2023.10.26.564262v1?rss=1 Ikechukwu, D. Kumar, A. 2023-10-31 doi:10.1101/2023.10.26.564262 Cold Spring Harbor Laboratory Press 2023-10-31 <![CDATA[ Regulation of chromatin transcription dynamics by DNA supercoiling ]]> https://biorxiv.org/content/10.1101/2023.11.06.565891v1?rss=1 Brahmachari, S. Tripathi, S. Onuchic, J. N. Levine, H. 2023-11-06 doi:10.1101/2023.11.06.565891 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ A high-density diffuse optical tomography dataset of naturalistic viewing ]]> https://biorxiv.org/content/10.1101/2023.11.07.565473v1?rss=1 Sherafati, A. Bajracharya, A. Jones, M. Speh, E. Munsi, M. Lin, C.-H. P. Fishell, A. K. Hershey, T. Eggebrecht, A. T. Culver, J. P. Peelle, J. E. 2023-11-11 doi:10.1101/2023.11.07.565473 Cold Spring Harbor Laboratory Press 2023-11-11 <![CDATA[ Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific ]]> https://biorxiv.org/content/10.1101/2023.11.08.566026v1?rss=1 Gatins, R. Arias, C. F. Sanchez, C. Bernardi, G. De Leon, L. F. 2023-11-10 doi:10.1101/2023.11.08.566026 Cold Spring Harbor Laboratory Press 2023-11-10 <![CDATA[ MITF regulates IDH1 and NNT and drives a transcriptional program protecting cutaneous melanoma from reactive oxygen species ]]> https://biorxiv.org/content/10.1101/2023.11.10.564582v1?rss=1 Roider, E. Lakatos, A. I. T. McConnell, A. M. Wang, P. Mueller, A. Kawakami, A. Tsoi, J. Szabolcs, B. L. Ascsillan, A. A. Suita, Y. Igras, V. Lo, J. A. Hsiao, J. J. Lapides, R. Pal, D. M. P. Lengyel, A. S. Navarini, A. Okazaki, A. Iliopoulos, O. Nemeth, I. Graeber, T. G. Zon, L. Giese, R. W. Kemeny, L. V. Fisher, D. E. 2023-11-14 doi:10.1101/2023.11.10.564582 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ Testing of putative antiseizure drugs in a preclinical Dravet syndrome zebrafish model ]]> https://biorxiv.org/content/10.1101/2023.11.11.566723v1?rss=1 Whyte-Fagundes, P. Vance, A. Carroll, A. Figueroa, F. Manukyan, C. Baraban, S. C. 2023-11-15 doi:10.1101/2023.11.11.566723 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Targeted micro-fiber arrays for measuring and manipulating localized multi-scale neural dynamics over large, deep brain volumes during behavior ]]> https://biorxiv.org/content/10.1101/2023.11.17.567425v1?rss=1 Vu, M.-A. T. Brown, E. H. Wen, M. J. Noggle, C. A. Zhang, Z. Monk, K. J. Bouabid, S. Mroz, L. Graham, B. M. Zhuo, Y. Li, Y. Otchy, T. M. Tian, L. Davison, I. G. Boas, D. A. Howe, M. W. 2023-11-17 doi:10.1101/2023.11.17.567425 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ A novel, wave-shaped profile of germline selection of pathogenic mtDNA mutations is discovered by bypassing a classical statistical bias. ]]> https://biorxiv.org/content/10.1101/2023.11.21.568140v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@1142cc0org.highwire.dtl.DTLVardef@186002aorg.highwire.dtl.DTLVardef@74d176org.highwire.dtl.DTLVardef@163ca6c_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO (Graphic Summary) Pathogenic mtDNA mutations that cause a host of devastating inherited diseases are usually thought to follow an intriguing inheritance trend: Mothers with low levels of mutation (called mother heteroplasmy, Hm) tend to bear children with higher child heteroplasmy (Hch) then their own which constitutes positive Heteroplasmy Shift (HS=Hch-Hm). In contrast, mothers with high heteroplasmy Hm bear children with lower heteroplasmy Hc (negative HS). C_FIG ]]> Cote-LHeureux, A. Fleischmann, Z. Franco, M. Chen, Z. Khrapko, M. Vyshedskiy, B. Braverman, M. Popadin, K. Pickett, S. Woods, D. C. Tilly, J. Turnbull, D. Khrapko, K. 2023-11-22 doi:10.1101/2023.11.21.568140 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Discovery of a novel MarR-type transcriptional regulator that controls cell death in Bacillus subtilis biofilms ]]> https://biorxiv.org/content/10.1101/2023.11.22.568295v1?rss=1 McClennen, G. Angelini, L. L. Fox, G. Godoy, V. Chai, Y. 2023-11-23 doi:10.1101/2023.11.22.568295 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP ]]> https://biorxiv.org/content/10.1101/2023.11.27.568927v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@c82330org.highwire.dtl.DTLVardef@17e5f2forg.highwire.dtl.DTLVardef@19b200borg.highwire.dtl.DTLVardef@154e336_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Leduc, A. Koury, L. Cantlon, J. Slavov, N. 2023-11-28 doi:10.1101/2023.11.27.568927 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ Engineered Bacillus subtilis as oral probiotics to target circulating lactic acid ]]> https://biorxiv.org/content/10.1101/2023.11.30.569300v1?rss=1 Yang, M. Hutchinson, N. Yin, J. Guan, M. Wang, Z. Chen, P. Yang, S. Crane, J. D. Zhang, K. Li, J. 2023-12-01 doi:10.1101/2023.11.30.569300 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Biolearn, an open-source library for biomarkers of aging ]]> https://biorxiv.org/content/10.1101/2023.12.02.569722v1?rss=1 Ying, K. Paulson, S. Perez-Guevara, M. Emamifar, M. Casas Martinez, M. Kwon, D. Poganik, J. R. Moqri, M. Gladyshev, V. N. 2023-12-04 doi:10.1101/2023.12.02.569722 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ Higher-order connectomics of human brain function reveals local topological signatures of task decoding, individual identification, and behavior ]]> https://biorxiv.org/content/10.1101/2023.12.04.569913v1?rss=1 Santoro, A. Battiston, F. Lucas, M. Petri, G. Amico, E. 2023-12-05 doi:10.1101/2023.12.04.569913 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Unravelling the Mitochondrial Mutational Landscape in Chordates: damage-induced versus replication-induced signatures, their Etiologies, and dynamics ]]> https://biorxiv.org/content/10.1101/2023.12.08.570826v1?rss=1 T mutations (about 30%); and (iii) asymmetrical, heavy-strand-specific A>G mutations, influenced by metabolic and age-specific factors (about 20%). We propose that both asymmetrical signatures are driven by single-strand specific damage coupled with inefficient base excision repair on the lagging (heavy) strand of mtDNA. Understanding the detailed mechanisms of this damage is crucial for developing strategies to reduce somatic mtDNA mutational load, which is vital for combating age-related diseases. ]]> Iliushchenko, D. Efimenko, B. Mikhailova, A. G. Shamanskiy, V. Saparbaev, M. Mazunin, I. Knorre, D. Kunz, W. Denisov, S. Khrapko, K. Fellay, J. Gunbin, K. Popadin, K. 2023-12-11 doi:10.1101/2023.12.08.570826 Cold Spring Harbor Laboratory Press 2023-12-11 <![CDATA[ Post-Transcriptional Methylation of Mitochondrial-tRNA Differentially Contributes to Mitochondrial Pathology ]]> https://biorxiv.org/content/10.1101/2023.12.09.569632v1?rss=1 Maharjan, S. Gamper, H. Yamaki, Y. Henley, R. Y. Sheng, N. Suzuki, T. Suzuki, T. Piccirilli, J. A. Wanunu, M. Seifert, E. Wallace, D. C. Hou, Y.-M. 2023-12-10 doi:10.1101/2023.12.09.569632 Cold Spring Harbor Laboratory Press 2023-12-10 <![CDATA[ Breakage fusion bridge cycles drive high oncogene copy number, but not intratumoral genetic heterogeneity or rapid cancer genome change ]]> https://biorxiv.org/content/10.1101/2023.12.12.571349v1?rss=1 93%) and recall (92%) in detecting BFB amplifications in cancer cell lines, PDX models and primary tumors. OM-based comparisons demonstrated that short-read BFB detection using our AmpliconSuite (AS) toolkit also achieved high precision, albeit with reduced sensitivity. We detected 371 BFB events using whole genome sequences from 2,557 primary tumors and cancer lines. BFB amplifications were preferentially found in cervical, head and neck, lung, and esophageal cancers, but rarely in brain cancers. BFB amplified genes show lower variance of gene expression, with fewer options for regulatory rewiring relative to ecDNA amplified genes. BFB positive (BFB (+)) tumors showed reduced heterogeneity of amplicon structures, and delayed onset of resistance, relative to ecDNA(+) tumors. EcDNA and BFB amplifications represent contrasting mechanisms to increase the copy numbers of oncogene with markedly different characteristics that suggest different routes for intervention. ]]> Dehkordi, S. R. Wong, I. T.-L. Ni, J. Luebeck, J. Zhu, K. Prasad, G. Krockenberger, L. Xu, G. Chowdhury, B. Rajkumar, U. Caplin, A. Muliaditan, D. Coruh, C. Jin, Q. Turner, K. Teo, S. X. Pang, A. W. C. Alexandrov, L. Chua, C. E. L. Furnari, F. Paulson, T. Law, J. Chang, H. Yue, F. DasGupta, R. Zhao, J. Mischel, P. S. Bafna, V. 2023-12-13 doi:10.1101/2023.12.12.571349 Cold Spring Harbor Laboratory Press 2023-12-13 <![CDATA[ Electro-Osmotic Flow Generation via a Sticky Ion Action ]]> https://biorxiv.org/content/10.1101/2023.12.14.571673v1?rss=1 Mehrafrooz, B. Yu, L. Siwy, Z. S. Wanunu, M. Aksimentiev, A. S. 2023-12-15 doi:10.1101/2023.12.14.571673 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ Implementation of an enriched membrane protein carrier channel for enhanced detection of membrane proteins in mass spectrometry-based thermal stability assays ]]> https://biorxiv.org/content/10.1101/2023.12.17.571949v1?rss=1 Phaneuf, C. G. Ivanov, A. R. 2023-12-17 doi:10.1101/2023.12.17.571949 Cold Spring Harbor Laboratory Press 2023-12-17 <![CDATA[ Impact of the clinically approved BTK inhibitors on the conformation of full-length BTK and analysis of the development of BTK resistance mutations in chronic lymphocytic leukemia. ]]> https://biorxiv.org/content/10.1101/2023.12.18.572223v1?rss=1 Joseph, R. E. Wales, T. E. Jayne, S. Britton, R. G. Fulton, D. B. Engen, J. R. Dyer, M. J. S. Andreotti, A. 2023-12-18 doi:10.1101/2023.12.18.572223 Cold Spring Harbor Laboratory Press 2023-12-18 <![CDATA[ Dynamics of single-cell protein covariation during epithelial-mesenchymal transition ]]> https://biorxiv.org/content/10.1101/2023.12.21.572913v1?rss=1 View larger version (78K): org.highwire.dtl.DTLVardef@84ba15org.highwire.dtl.DTLVardef@1d4c753org.highwire.dtl.DTLVardef@6a4210org.highwire.dtl.DTLVardef@174fa1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Khan, S. Conover, R. Asthagiri, A. R. Slavov, N. 2023-12-23 doi:10.1101/2023.12.21.572913 Cold Spring Harbor Laboratory Press 2023-12-23 <![CDATA[ Homological landscape of human brain functional sub-circuits ]]> https://biorxiv.org/content/10.1101/2023.12.22.573062v1?rss=1 Duong-Tran, D. Kaufmann, R. Chen, J. Wang, X. Garai, S. Xu, F. Bao, J. Amico, E. Kaplan, A. D. Petri, G. Goni, J. Zhao, Y. Shen, L. 2023-12-23 doi:10.1101/2023.12.22.573062 Cold Spring Harbor Laboratory Press 2023-12-23 <![CDATA[ FANCJ promotes PARP1 activity during DNA replication that is essential in BRCA1 deficient cells ]]> https://biorxiv.org/content/10.1101/2024.01.04.574095v1?rss=1 Cong, K. MacGilvary, N. Lee, S. MacLeod, S. Calvo, J. Peng, M. Nedergaard Kousholt, A. Day, T. Cantor, S. 2024-01-04 doi:10.1101/2024.01.04.574095 Cold Spring Harbor Laboratory Press 2024-01-04 <![CDATA[ Identification of essential genes that support fitness of Acinetobacter baumannii efflux pump overproducers in the presence of fluoroquinolone ]]> https://biorxiv.org/content/10.1101/2024.01.04.574119v1?rss=1 Hamami, E. Huo, W. Neal, K. Neisewander, I. Geisinger, E. Isberg, R. R. 2024-01-05 doi:10.1101/2024.01.04.574119 Cold Spring Harbor Laboratory Press 2024-01-05 <![CDATA[ Negative allosteric modulation of cannabinoid CB1 receptor signaling suppresses opioid-mediated tolerance and withdrawal without blocking opioid antinociception ]]> https://biorxiv.org/content/10.1101/2024.01.06.574477v1?rss=1 Iyer, V. Saberi, S. A. Pacheco, R. Fender Sizemore, E. Stockman, S. Kulkarni, A. Cantwell, L. Thakur, G. A. Hohmann, A. G. 2024-01-06 doi:10.1101/2024.01.06.574477 Cold Spring Harbor Laboratory Press 2024-01-06 <![CDATA[ Linkers in bitopic agonists shape bias profile among transducers for the dopamine D2 and D3 receptors ]]> https://biorxiv.org/content/10.1101/2024.01.07.574547v1?rss=1 Semeano, A. Garland, R. Bonifazi, A. Lee, K. H. Famiglietti, J. Zhang, W. Jo, Y. J. Battiti, F. O. Shi, L. Newman, A. H. Yano, H. 2024-01-08 doi:10.1101/2024.01.07.574547 Cold Spring Harbor Laboratory Press 2024-01-08 <![CDATA[ Metatranscriptomic analysis reveals synergistic activities of comammox and anammox bacteria in full-scale attached growth nitrogen removal system. ]]> https://biorxiv.org/content/10.1101/2024.01.08.574720v1?rss=1 Johnston, J. Vilardi, K. Cotto, I. Sudarshan, A. Bian, K. Klaus, S. Bachmann, M. Parsons, M. Wilson, C. Bott, C. Pinto, A. 2024-01-09 doi:10.1101/2024.01.08.574720 Cold Spring Harbor Laboratory Press 2024-01-09 <![CDATA[ Prevotella are major contributors of sialidases in the human vaginal microbiome. ]]> https://biorxiv.org/content/10.1101/2024.01.09.574895v1?rss=1 Pelayo, P. Hussain, F. A. Werlang, C. A. Wu, C. Woolston, B. M. Ribbeck, K. Kwon, D. S. Balskus, E. P. 2024-01-09 doi:10.1101/2024.01.09.574895 Cold Spring Harbor Laboratory Press 2024-01-09 <![CDATA[ Normalized level set model for segmentation of low-contrast objects in 2- and 3- dimensional images ]]> https://biorxiv.org/content/10.1101/2024.01.12.574651v1?rss=1 Baig, M. M. J. Wang, Y. L. Chung, S. H. Stepanyants, A. 2024-01-15 doi:10.1101/2024.01.12.574651 Cold Spring Harbor Laboratory Press 2024-01-15 <![CDATA[ Negative allosteric modulation of CB1 cannabinoid receptor signaling decreases intravenous morphine self-administration and relapse in mice ]]> https://biorxiv.org/content/10.1101/2024.01.16.575900v1?rss=1 Oliva, I. Kazi, F. A. Cantwell, L. N. Thakur, G. A. Crystal, J. D. Hohmann, A. G. 2024-01-20 doi:10.1101/2024.01.16.575900 Cold Spring Harbor Laboratory Press 2024-01-20 <![CDATA[ Brain-phenotype predictions can survive across diverse real-world data ]]> https://biorxiv.org/content/10.1101/2024.01.23.576916v1?rss=1 Adkinson, B. D. Rosenblatt, M. Dadashkarimi, J. Tejavibulya, L. Jiang, R. Noble, S. Scheinost, D. 2024-01-24 doi:10.1101/2024.01.23.576916 Cold Spring Harbor Laboratory Press 2024-01-24 <![CDATA[ Revealing brain network dynamics during the emotional state of suspense using topological data analysis ]]> https://biorxiv.org/content/10.1101/2024.01.29.577820v1?rss=1 Olave Herrera, A. A. Perea, J. A. Gomez, F. 2024-01-30 doi:10.1101/2024.01.29.577820 Cold Spring Harbor Laboratory Press 2024-01-30 <![CDATA[ Multiplexed Short-wave Infrared Imaging Highlights Anatomical Structures in Mice ]]> https://biorxiv.org/content/10.1101/2024.01.29.577849v1?rss=1 Zhong, X. Patel, A. Sun, Y. Saeboe, A. M. Dennis, A. M. 2024-01-30 doi:10.1101/2024.01.29.577849 Cold Spring Harbor Laboratory Press 2024-01-30 <![CDATA[ The limits of predicting maladaptation to future environments with genomic data ]]> https://biorxiv.org/content/10.1101/2024.01.30.577973v1?rss=1 Lind, B. M. Lotterhos, K. E. 2024-01-31 doi:10.1101/2024.01.30.577973 Cold Spring Harbor Laboratory Press 2024-01-31 <![CDATA[ Chronic Pod-Mod E-Cigarette Aerosol Exposure Induces Aortic Dysfunction in Hypercholesterolemic Mice: Role of Oxidative Stress and Inflammation ]]> https://biorxiv.org/content/10.1101/2024.01.30.578110v1?rss=1 Farra, Y. M. Matz, J. Wilker, H. Kim, H. Rivera, C. F. Vlahos, J. Ramkhelawon, B. Oakes, J. Bellini, C. 2024-02-02 doi:10.1101/2024.01.30.578110 Cold Spring Harbor Laboratory Press 2024-02-02 <![CDATA[ Mechanically Tunable, Compostable, Healable and Scalable Engineered Living Materials ]]> https://biorxiv.org/content/10.1101/2024.01.31.578234v1?rss=1 Manjula-Basavanna, A. Joshi, N. Duraj-Thatte, A. 2024-02-02 doi:10.1101/2024.01.31.578234 Cold Spring Harbor Laboratory Press 2024-02-02 <![CDATA[ The Origin and Evolution of Orphan Genes: A Case Study in Tea Plant Family ]]> https://biorxiv.org/content/10.1101/2024.02.01.578514v1?rss=1 Cheng, L. Hao, Y. Han, Q. Qiao, Z. Li, M. Liu, D. Yin, H. Li, T. Long, W. Luo, S. Gao, Y. Zhang, Z. Yu, H. Sun, X. ZHAO, Y. 2024-02-06 doi:10.1101/2024.02.01.578514 Cold Spring Harbor Laboratory Press 2024-02-06 <![CDATA[ Whole-Genome Sequencing of Three Extremophile Bacillus subtilis StrainsIsolated from the Atacama Desert ]]> https://biorxiv.org/content/10.1101/2024.02.11.578748v1?rss=1 Cavanaugh, N. T. Kumar, G. Couto Frignani, M. Thewedros, N. Twahirwa, M. Riquelme, C. Hudson, A. Chai, Y. Godoy, V. 2024-02-12 doi:10.1101/2024.02.11.578748 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ Whole-Genome Sequencing of a Janthinobacterium sp. Isolated from the Patagonian Desert ]]> https://biorxiv.org/content/10.1101/2024.02.11.579814v1?rss=1 Cavanaugh, N. T. Kumar, G. Reverdy Pearson, A. Colbert, J. Riquelme, C. Hudson, A. O. Chai, Y. Godoy, V. 2024-02-12 doi:10.1101/2024.02.11.579814 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ Using high-resolution functional MRI to differentiate impacts of strabismic and anisometropic amblyopia on evoked ocular dominance activity in humans ]]> https://biorxiv.org/content/10.1101/2024.02.11.579855v1?rss=1 Nasr, S. Skerswetat, J. Gaier, E. D. Malladi, S. N. Kennedy, B. Tootell, R. B. Bex, P. Hunter, D. G. 2024-02-13 doi:10.1101/2024.02.11.579855 Cold Spring Harbor Laboratory Press 2024-02-13 <![CDATA[ Characterizing directional dynamics of semantic prediction based on inter-regional temporal generalization ]]> https://biorxiv.org/content/10.1101/2024.02.13.580183v1?rss=1 Mamashli, F. Khan, S. Hatamimajoumerd, E. Jas, M. Uluc, I. Lankinen, K. Obleser, J. Friederici, A. D. Maess, B. Ahveninen, J. 2024-02-14 doi:10.1101/2024.02.13.580183 Cold Spring Harbor Laboratory Press 2024-02-14 <![CDATA[ Oxygen carrying nanoemulsions and respiratory hyperoxia eliminate tumor hypoxia-induced suppression and improve cancer immunotherapy ]]> https://biorxiv.org/content/10.1101/2024.02.17.580835v1?rss=1 Halpin-Veszeleiova, K. Mallouh, M. Apro, A. Romero, N. Bahr, C. Shin, M. Ward, K. Rosenberg, L. Sitkovsky, M. Spiess, B. Hatfield, S. M. 2024-02-21 doi:10.1101/2024.02.17.580835 Cold Spring Harbor Laboratory Press 2024-02-21 <![CDATA[ Human Foot Force Informs Balance Control Strategies when Standing on a Narrow Beam ]]> https://biorxiv.org/content/10.1101/2024.02.27.582256v1?rss=1 Shiozawa, K. Russo, M. Lee, J. Hogan, N. Sternad, D. 2024-03-01 doi:10.1101/2024.02.27.582256 Cold Spring Harbor Laboratory Press 2024-03-01 <![CDATA[ Assessing methylation detection for primary human tissue using Nanopore sequencing ]]> https://biorxiv.org/content/10.1101/2024.02.29.581569v1?rss=1 Genner, R. Akeson, S. Meredith, M. Jerez, P. A. Malik, L. Baker, B. Miano-Burkhardt, A. Team, C.-l.-r. Paten, B. Billingsley, K. J. Blauwendraat, C. Jain, M. 2024-03-01 doi:10.1101/2024.02.29.581569 Cold Spring Harbor Laboratory Press 2024-03-01 <![CDATA[ Unlocking Herbal Potentials: Novel Shikimate Kinase Inhibitors in the Fight Against Antibiotic Resistance ]]> https://biorxiv.org/content/10.1101/2024.03.02.583126v1?rss=1 Nirgudkar, S. Chai, Y. 2024-03-03 doi:10.1101/2024.03.02.583126 Cold Spring Harbor Laboratory Press 2024-03-03 <![CDATA[ Cannabinoid CB2 receptors in primary sensory neurons are implicated in CB2 agonist-mediated suppression of paclitaxel-induced neuropathic nociception and sexually-dimorphic sparing of morphine tolerance ]]> https://biorxiv.org/content/10.1101/2024.03.05.583426v1?rss=1 Guenther, K. G. Lin, X. Xu, Z. Makriyannis, A. Romero, J. Hillard, C. Mackie, K. Hohmann, A. G. 2024-03-10 doi:10.1101/2024.03.05.583426 Cold Spring Harbor Laboratory Press 2024-03-10 <![CDATA[ CB1 Cannabinoid Receptor Agonists Induce Acute Respiratory Depression in Awake Mice ]]> https://biorxiv.org/content/10.1101/2024.03.12.584260v1?rss=1 Watkins, J. M. Aradi, P. Hahn, R. Makriyannis, A. Mackie, K. Katona, I. Hohmann, A. G. 2024-03-13 doi:10.1101/2024.03.12.584260 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ WISH-BONE: Whole-mount In Situ Histology, to label osteocyte mRNA and protein in 3D adult mouse bones ]]> https://biorxiv.org/content/10.1101/2024.03.14.585053v1?rss=1 Meslier, Q. A. Duerr, T. J. Nguyen, B. Monaghan, J. R. Shefelbine, S. J. 2024-03-15 doi:10.1101/2024.03.14.585053 Cold Spring Harbor Laboratory Press 2024-03-15 <![CDATA[ Evaluating a Novel High-Density EEG Sensor Net Structure for Improving Inclusivity in Infants with Curly or Tightly Coiled Hair ]]> https://biorxiv.org/content/10.1101/2024.03.18.584988v1?rss=1 Mlandu, N. McCormick, S. A. Davel, L. Zieff, M. R. Bradford, L. Herr, D. Jacobs, C. A. Khumalo, A. Knipe, C. Madi, Z. Mazubane, T. Methola, B. Mhlakwaphalwa, T. Miles, M. Goolam Nabi, Z. Negota, R. Nkubungu, K. Pan, T. Samuels, R. Williams, S. Williams, S. R. Avery, T. Foster, G. Donald, K. A. Gabard-Durnam, L. J. 2024-03-18 doi:10.1101/2024.03.18.584988 Cold Spring Harbor Laboratory Press 2024-03-18 <![CDATA[ The origin and evolution of cultivated rice and genomic signatures of heterosis for yield traits in super-hybrid rice ]]> https://biorxiv.org/content/10.1101/2024.03.19.585738v1?rss=1 Liu, D. Yin, H. Li, T. Wang, L. Lu, S. Yu, H. Sun, X. Zhang, T. Zhao, Q. ZHAO, Y. 2024-03-19 doi:10.1101/2024.03.19.585738 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ Sensory integration of food availability and population density during the diapause exit decision involves insulin-like signaling in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2024.03.20.586022v1?rss=1 Zhang, M. G. Seyedolmohadesin, M. Mercado, S. H. Park, H. Finnen, N. Schroeder, F. C. Venkatachalam, V. Sternberg, P. W. 2024-03-25 doi:10.1101/2024.03.20.586022 Cold Spring Harbor Laboratory Press 2024-03-25 <![CDATA[ Screening and characterization of 133 physiologically-relevant environmental chemicals for reproductive toxicity ]]> https://biorxiv.org/content/10.1101/2024.03.22.584808v1?rss=1 Ulaganathan, G. Jiang, H. Canio, N. Oke, A. Armstrong, S. S. Abrahamsson, D. Varshavsky, J. R. Lam, J. Cooper, C. Robinson, J. F. Fung, J. Woodruff, T. J. Allard, P. 2024-03-27 doi:10.1101/2024.03.22.584808 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Elucidating Microbial Iron Corrosion Mechanisms with a Hydrogenase-Deficient Strain of Desulfovibrio vulgaris ]]> https://biorxiv.org/content/10.1101/2024.03.24.586472v1?rss=1 Wang, D. Ueki, T. Ma, P. Xu, D. Lovley, D. R. 2024-03-24 doi:10.1101/2024.03.24.586472 Cold Spring Harbor Laboratory Press 2024-03-24 <![CDATA[ Locus Coeruleus Contrast and Diffusivity: Effects of Age and Relations to Memory ]]> https://biorxiv.org/content/10.1101/2024.03.25.586618v1?rss=1 Bennett, I. J. Langley, J. Sun, A. Solis, K. Seitz, A. R. Hu, X. P. 2024-03-29 doi:10.1101/2024.03.25.586618 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Effects of early life adversity and adolescent basolateral amygdala inhibition on corticolimbic connectivity and anxiety behaviors ]]> https://biorxiv.org/content/10.1101/2024.03.26.586708v1?rss=1 Cody, C. R. Artur de la Villarmois, E. Auger, M. Miguelez Fernandez, A. Lardizaball, J. McKnight, C. Tseng, K. Brenhouse, H. C. 2024-03-29 doi:10.1101/2024.03.26.586708 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ An adverse rearing environment alters maternal responsiveness to infant ultrasonic vocalizations ]]> https://biorxiv.org/content/10.1101/2024.03.26.586776v1?rss=1 Rekapalli, A. Roman, I. Brenhouse, H. C. Cody, C. R. 2024-03-29 doi:10.1101/2024.03.26.586776 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess neuronal epitranscriptome plasticity ]]> https://biorxiv.org/content/10.1101/2024.03.26.586895v1?rss=1 Fanari, O. Tavakoli, S. Akeson, S. Makhamreh, A. Nian, K. McCormick, C. A. Qiu, Y. Bloch, D. Jain, M. Wanunu, M. Rouhanifard, S. H. 2024-03-29 doi:10.1101/2024.03.26.586895 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Outer membrane vesicles can contribute to cellulose degradation in Teredinibacter turnerae, a cultivable intracellular endosymbiont of shipworms ]]> https://biorxiv.org/content/10.1101/2024.03.27.587001v1?rss=1 Gasser, M. T. Liu, A. Altamia, M. A. Bresinger, B. Brewer, S. L. Flatau, R. Hancock, E. Preheim, S. P. Filone, C. M. Distel, D. L. 2024-03-27 doi:10.1101/2024.03.27.587001 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ DNA methylation modulates transcriptional noise in response to elevated pCO2 in the eastern oyster (Crassostrea virginica) ]]> https://biorxiv.org/content/10.1101/2024.04.04.588108v1?rss=1 Venkataraman, Y. R. Huffmyer, A. S. White, S. J. Downey-Wall, A. Ashey, J. Becker, D. M. Bengtsson, Z. Putnam, H. M. Strand, E. Rodriguez-Casariego, J. A. Wanamaker, S. A. Lotterhos, K. E. Roberts, S. 2024-04-08 doi:10.1101/2024.04.04.588108 Cold Spring Harbor Laboratory Press 2024-04-08 <![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[ Connectome caricatures: removing large-amplitude co-activation patterns in resting-state fMRI emphasizes individual differences ]]> https://biorxiv.org/content/10.1101/2024.04.08.588578v1?rss=1 Rodriguez, R. X. Noble, S. Camp, C. C. Scheinost, D. 2024-04-11 doi:10.1101/2024.04.08.588578 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ Development of a recombineering system for the acetogen Eubacterium limosum with Cas9 counterselection for markerless genome engineering ]]> https://biorxiv.org/content/10.1101/2024.04.09.588731v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@1366103org.highwire.dtl.DTLVardef@11b1f0borg.highwire.dtl.DTLVardef@1931600org.highwire.dtl.DTLVardef@1896e4c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sanford, P. A. Woolston, B. M. 2024-04-12 doi:10.1101/2024.04.09.588731 Cold Spring Harbor Laboratory Press 2024-04-12 <![CDATA[ The landscape of regional missense mutational intolerance quantified from 125,748 exomes ]]> https://biorxiv.org/content/10.1101/2024.04.11.588920v1?rss=1 Chao, K. R. Wang, L. Panchal, R. Liao, C. Abderrazzaq, H. Ye, R. Schultz, P. Compitello, J. Grant, R. H. Kosmicki, J. A. Weisburd, B. Phu, W. Wilson, M. W. Laricchia, K. M. Goodrich, J. K. Goldstein, D. Goldstein, J. I. Vittal, C. Poterba, T. Baxter, S. Watts, N. A. Solomonson, M. gnomAD consortium, Tiao, G. Rehm, H. L. Neale, B. M. Talkowski, M. E. MacArthur, D. G. O'Donnell-Luria, A. Karczewski, K. J. Radivojac, P. Daly, M. J. Samocha, K. E. 2024-04-13 doi:10.1101/2024.04.11.588920 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ Medium Composition Affects Microbial Corrosion Rates ]]> https://biorxiv.org/content/10.1101/2024.04.11.589044v1?rss=1 Wang, D. Ueki, T. Ma, P. Xu, D. Lovley, D. 2024-04-11 doi:10.1101/2024.04.11.589044 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ Atp1a2 and Kcnj9 are candidate genes underlying oxycodone behavioral sensitivity and withdrawal in C57BL/6 substrains ]]> https://biorxiv.org/content/10.1101/2024.04.16.589731v1?rss=1 Goldberg, L. R. Baskin, B. M. Adla, Y. Beierle, J. A. Kelliher, J. C. Yao, E. J. Kirkpatrick, S. L. Reed, E. R. Jenkins, D. F. Luong, A. M. Luttik, K. P. Scotellaro, J. A. Drescher, T. A. Crotts, S. B. Yazdani, N. Ferris, M. T. R. Johnson, W. E. Mulligan, M. K. Bryant, C. D. 2024-04-17 doi:10.1101/2024.04.16.589731 Cold Spring Harbor Laboratory Press 2024-04-17 <![CDATA[ Nuclear size-regulated emergence of topological packing order on growing human lung alveolospheres ]]> https://biorxiv.org/content/10.1101/2024.04.17.589951v1?rss=1 Tang, W. Huang, J. Pegoraro, A. F. Zhang, J. H. Tang, Y. Bi, D. Kotton, D. N. Guo, M. 2024-04-20 doi:10.1101/2024.04.17.589951 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Profiling the LAM family of contact site tethers provides insights into their regulation and function ]]> https://biorxiv.org/content/10.1101/2024.04.18.590074v1?rss=1 Fenech, E. J. Kupervaser, M. Boshnakovska, A. Ravid, S. Gomes Castro, I. Asraf, Y. Callegari, S. Lenz, C. Rehling, P. Schuldiner, M. 2024-04-18 doi:10.1101/2024.04.18.590074 Cold Spring Harbor Laboratory Press 2024-04-18 <![CDATA[ Regulation of Chromatin Modifications through Coordination of Nucleus Size and Epithelial Cell Morphology Heterogeneity ]]> https://biorxiv.org/content/10.1101/2024.04.18.590164v1?rss=1 Bermudez, A. Latham, Z. Ma, A. Bi, D. Hu, J. Lin, N. 2024-04-22 doi:10.1101/2024.04.18.590164 Cold Spring Harbor Laboratory Press 2024-04-22 <![CDATA[ CRISPR screens reveal convergent targeting strategies against evolutionarily distinct chemoresistance in cancer ]]> https://biorxiv.org/content/10.1101/2024.04.24.591030v1?rss=1 Zhong, C. Jiang, W.-J. Yao, Y. Li, Z. Li, Y. Wang, S. Wang, X. Zhu, W. Wu, S. Wang, J. Fan, S. Ma, S. Liu, Y. Zhang, H. Zhao, W. Zhao, L. Feng, Y. Li, Z. Guo, R. Yu, L. Pei, F. Hu, J. Feng, X. Yang, Z. Yang, Z. Yang, X. Hou, Y. Zhang, D. Xu, D. Sheng, R. Li, Y. Liu, L. Wu, H.-J. Huang, J. Fei, T. 2024-04-27 doi:10.1101/2024.04.24.591030 Cold Spring Harbor Laboratory Press 2024-04-27 <![CDATA[ Topology-Driven Negative Sampling Enhances Generalizability in Protein-Protein Interaction Prediction ]]> https://biorxiv.org/content/10.1101/2024.04.27.591478v1?rss=1 Chatterjee, A. Ravandi, B. Philip, N. H. Abdelmessih, M. Mowrey, W. R. Ricchiuto, P. Liang, Y. Ding, W. Mobarec, J. C. Eliassi-Rad, T. 2024-04-29 doi:10.1101/2024.04.27.591478 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ Mathematical model of intestinal lipolysis of a long-chain triglyceride ]]> https://biorxiv.org/content/10.1101/2024.05.01.592066v1?rss=1 Rezhdo, O. West, R. Kim, M. Ng, B. Saphier, S. Carrier, R. L. 2024-05-04 doi:10.1101/2024.05.01.592066 Cold Spring Harbor Laboratory Press 2024-05-04 <![CDATA[ Negative Selection Allows DNA Mismatch Repair-Deficient Mouse Fibroblasts In Vitro to Tolerate High Levels of Somatic Mutations ]]> https://biorxiv.org/content/10.1101/2024.05.04.592535v1?rss=1 Zhang, L. Lee, M. Hao, X. Ehlert, J. Chi, Z. Jin, B. Maslov, A. Y. Barabasi, A.-L. Hoeijmakers, J. H. J. Edelmann, W. Vijg, J. Dong, X. 2024-05-07 doi:10.1101/2024.05.04.592535 Cold Spring Harbor Laboratory Press 2024-05-07 <![CDATA[ Helping behavior is associated with increased affiliative behavior, activation of the prosocial brain network and elevated oxytocin receptor expression in the nucleus accumbens ]]> https://biorxiv.org/content/10.1101/2024.05.06.592793v1?rss=1 Hazani, R. Breton, J. M. Trachtenberg, E. Kantor, B. Maman, A. Bigelman, E. Cole, S. Weller, A. Ben-Ami Bartal, I. 2024-05-07 doi:10.1101/2024.05.06.592793 Cold Spring Harbor Laboratory Press 2024-05-07 <![CDATA[ Mismatch between pollen and pistil size causes asymmetric mechanical reproductive isolation across Phlox species ]]> https://biorxiv.org/content/10.1101/2024.05.08.593106v1?rss=1 Feller, A. F. Burgin, G. Lewis, N. Prabhu, R. Hopkins, R. 2024-05-10 doi:10.1101/2024.05.08.593106 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ mRNA psi profiling using nanopore DRS reveals cell-type-specific pseudouridylation ]]> https://biorxiv.org/content/10.1101/2024.05.08.593203v1?rss=1 McCormick, C. A. Qiu, Y. Fanari, O. Liu, Y. Bloch, D. Klink, I. N. Meseonznik, M. Jain, M. Wanunu, M. Rouhanifard, S. H. 2024-05-10 doi:10.1101/2024.05.08.593203 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ A Novel Regulation on the Developmental Checkpoint Protein Sda that Controls Sporulation and Biofilm Formation in Bacillus subtilis ]]> https://biorxiv.org/content/10.1101/2024.05.13.593929v1?rss=1 Chai, Y. He, Y. Qin, Y. Greenwich, J. Balaban, S. Darcera, M. V. L. Gozzi, K. 2024-05-15 doi:10.1101/2024.05.13.593929 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Evaluation of enzyme activity predictions for variants of unknown significance in Arylsulfatase A ]]> https://biorxiv.org/content/10.1101/2024.05.16.594558v1?rss=1 Jain, S. Trinidad, M. Nguyen, T. B. Jones, K. Diaz Neto, S. Ge, F. Glagovsky, A. Jones, C. Moran, G. Wang, B. Rahimi, K. Zeynep Calici, S. Cedillo, L. R. Berardelli, S. Ozden, B. Chen, K. Katsonis, P. Williams, A. Lichtarge, O. Rana, S. Pradhan, S. Srinivasan, R. Sajeed, R. Joshi, D. Faraggi, E. Jernigan, R. Kloczkowski, A. Xu, J. Song, Z. Ozkan, S. Padilla, N. de la Cruz, X. Acuna-Hidalgo, R. Grafmuller, A. Jimenez Barron, L. T. Manfredi, M. Savojardo, C. Babbi, G. Martelli, P. L. Casadio, R. Sun, Y. Zhu, S. Shen, Y. Pucci, F. Rooman, M. Cia, G. R 2024-05-19 doi:10.1101/2024.05.16.594558 Cold Spring Harbor Laboratory Press 2024-05-19 <![CDATA[ Analyzing high-throughput assay data to advance the rapid screening of environmental chemicals for human reproductive toxicity ]]> https://biorxiv.org/content/10.1101/2024.05.21.595187v1?rss=1 Varshavsky, J. R. Lam, J. Cooper, C. Allard, P. Fung, J. Oke, A. Kumar, R. Robinson, J. Woodruff, T. 2024-05-22 doi:10.1101/2024.05.21.595187 Cold Spring Harbor Laboratory Press 2024-05-22 <![CDATA[ Spatial Profiling of Metals through Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging ]]> https://biorxiv.org/content/10.1101/2024.05.22.594980v1?rss=1 Stopka, S. Bodineau, C. Baquer, G. Lin, J.-R. Hossain, M. A. Regan, M. S. Ruiz, D. F. Fletcher, S.-M. Pourquie, O. Lutsenko, S. Payne, C. Agar, J. N. Mazitschek, R. McDannold, N. Sorger, P. K. Santagata, S. Agar, N. 2024-05-23 doi:10.1101/2024.05.22.594980 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ Single-cell proteomics reveals decreased abundance of proteostasis and meiosis proteins in advanced maternal age oocytes ]]> https://biorxiv.org/content/10.1101/2024.05.23.595547v1?rss=1 GALATIDOU, S. PETELSKI, A. A. PUJOL, A. LATTES, K. LATORRACA, L. B. FAIR, T. POPOVIC, M. VASSENA, R. SLAVOV, N. BARRAGAN, M. 2024-05-24 doi:10.1101/2024.05.23.595547 Cold Spring Harbor Laboratory Press 2024-05-24 <![CDATA[ Machine Learning Models for Cardiovascular Disease Prediction: A Comparative Study ]]> https://biorxiv.org/content/10.1101/2024.05.27.596092v1?rss=1 Yan, C. Xing, Y. Liu, S. Gao, E. Wang, J. 2024-06-01 doi:10.1101/2024.05.27.596092 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Integrative epigenetics and transcriptomics identify aging genes in human blood ]]> https://biorxiv.org/content/10.1101/2024.05.30.596713v1?rss=1 Moqri, M. Poganik, J. R. Herzog, C. Ying, K. Chen, Q. Emamifar, M. Tyshkovskiy, A. Alec, E. W. Mur, J. Matei-Dediu, B. Goeminne, L. Mitchell, W. McCartney, D. L. Marioni, R. L. Lasky-Su, J. A. Snyder, M. Gladyshev, V. N. 2024-06-03 doi:10.1101/2024.05.30.596713 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Pulse Instabilities Can Shape Virus-Immune Co-evolution ]]> https://biorxiv.org/content/10.1101/2024.05.31.596810v1?rss=1 Kessler, D. A. Levine, H. 2024-06-03 doi:10.1101/2024.05.31.596810 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Amygdala circuit mechanisms underlying alcohol seeking ]]> https://biorxiv.org/content/10.1101/2024.06.03.596970v1?rss=1 Suh, J. Pasqualini, A. L. Zambrano, M. A. RESSLER, K. J. 2024-06-03 doi:10.1101/2024.06.03.596970 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Model supports asymmetric regulation across the intercellular junction for collective cell polarization ]]> https://biorxiv.org/content/10.1101/2024.06.03.597091v1?rss=1 Levandosky, K. Copos, C. 2024-06-03 doi:10.1101/2024.06.03.597091 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Decreased scene-selective activity within the posterior intraparietal cortex in amblyopic adults ]]> https://biorxiv.org/content/10.1101/2024.06.05.597579v1?rss=1 Malladi, S. N. Skerswetat, J. Tootell, R. B. Gaier, E. D. Bex, P. Hunter, D. G. Nasr, S. 2024-06-08 doi:10.1101/2024.06.05.597579 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Critical assessment of missense variant effect predictors on disease-relevant variant data ]]> https://biorxiv.org/content/10.1101/2024.06.06.597828v1?rss=1 Rastogi, R. Chung, R. Li, S. Li, C. Lee, K. Woo, J. Kim, D.-W. Keum, C. Babbi, G. Martelli, P. L. Savojardo, C. Casadio, R. Chennen, K. Weber, T. Poch, O. Ancien, F. Cia, G. Pucci, F. Raimondi, D. Vranken, W. Rooman, M. Marquet, C. Olenyi, T. Rost, B. Andreoletti, G. Kamandula, A. Peng, Y. Bakolitsa, C. Mort, M. Cooper, D. N. Bergquist, T. Pejaver, V. Liu, X. Radivojac, P. Brenner, S. E. Ioannidis, N. M. 2024-06-08 doi:10.1101/2024.06.06.597828 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Network connectivity differences in music listening among older adults following a music-based intervention ]]> https://biorxiv.org/content/10.1101/2024.06.13.598944v1?rss=1 Faber, S. Belden, A. McIntosh, R. Loui, P. 2024-06-14 doi:10.1101/2024.06.13.598944 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ A phosphorylation signal activates genome-wide transcriptional control by BfmR, the global regulator of Acinetobacter resistance and virulence. ]]> https://biorxiv.org/content/10.1101/2024.06.16.599214v1?rss=1 1000 genes, its direct regulon is undefined. Moreover, how phosphorylation controls the regulator is unclear. Here, we address these problems by combining mutagenesis, ChIP-seq, and in vitro phosphorylation to study the functions of phospho-BfmR. We show that phosphorylation is required for BfmR-mediated gene regulation, antibiotic resistance, and sepsis development in vivo. Consistent with activating the protein, phosphorylation induces dimerization and target DNA affinity. Integrated analysis of genome-wide binding and transcriptional profiles of BfmR led to additional key findings: (1) Phosphorylation dramatically expands the number of genomic sites BfmR binds; (2) DNA recognition involves a direct repeat motif widespread across promoters; (3) BfmR directly regulates 303 genes as activator (eg, capsule, peptidoglycan, and outer membrane biogenesis) or repressor (pilus biogenesis); (4) BfmR controls several non-coding sRNAs. These studies reveal the centrality of a phosphorylation signal in driving A. baumannii disease and disentangle the extensive pathogenic gene-regulatory network under its control. ]]> Raustad, N. Dai, Y. Iinishi, A. Mohapatra, A. Soo, M. W. Hay, E. Hernandez, G. M. Geisinger, E. 2024-06-17 doi:10.1101/2024.06.16.599214 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Single-nucleus proteomics identifies regulators of protein transport ]]> https://biorxiv.org/content/10.1101/2024.06.17.599449v1?rss=1 Derks, J. Jonson, T. Leduc, A. Khan, S. Koury, L. Rafiee, M.-R. Slavov, N. 2024-06-18 doi:10.1101/2024.06.17.599449 Cold Spring Harbor Laboratory Press 2024-06-18 <![CDATA[ DeEPsnap: human essential gene prediction by integrating multi-omics data ]]> https://biorxiv.org/content/10.1101/2024.06.20.599958v1?rss=1 Zhang, X. Xiao, W. Cochran, B. H. Xiao, W. 2024-06-22 doi:10.1101/2024.06.20.599958 Cold Spring Harbor Laboratory Press 2024-06-22 <![CDATA[ The DivisionCounter, a method for counting large ranges of cell divisions in vivo, reveals cell dynamics of leukemic cell killing via CAR-T therapy ]]> https://biorxiv.org/content/10.1101/2024.06.24.600543v1?rss=1 Hustin, L. S. Conrad, C. Liu, C. Fuentealba, J. Menegatti, S. Shneer, S. Battistella, A. Tabarin, F. Weber, T. S. Amigorena, S. Duffy, K. R. Perie, L. 2024-06-28 doi:10.1101/2024.06.24.600543 Cold Spring Harbor Laboratory Press 2024-06-28 <![CDATA[ Creating a genetic toolbox for the carbon-fixing, nitrogen-fixing and dehalogenating bacterium Xanthobacter autotrophicus ]]> https://biorxiv.org/content/10.1101/2024.06.26.600795v1?rss=1 Van Voorhis, A. F. Sherbo, R. S. 2024-06-27 doi:10.1101/2024.06.26.600795 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ Dynamic functional connectivity correlates of trait mindfulness in early adolescence ]]> https://biorxiv.org/content/10.1101/2024.07.01.601544v1?rss=1 Treves, I. N. Marusak, H. A. Decker, A. Kucyi, A. Hubbard, N. A. Bauer, C. C. C. Leonard, J. Grotzinger, H. Giebler, M. A. Camacho Torres, Y. Imhof, A. Romeo, R. Calhoun, V. Gabrieli, J. D. E. 2024-07-04 doi:10.1101/2024.07.01.601544 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ Spectrotemporal profiling of ultrasonic vocalizations during neonatal opioid withdrawal reveals a kappa opioid receptor component in female mice ]]> https://biorxiv.org/content/10.1101/2024.07.02.601766v1?rss=1 Wingfield, K. K. Misic, T. Jain, K. McDermott, C. S. Abney, N. M. Richardson, K. T. Rubman, M. B. Beierle, J. A. Miracle, S. A. Sandago, E. J. Baskin, B. M. Borrelli, K. N. Yao, E. J. Wachman, E. M. Bryant, C. D. 2024-07-04 doi:10.1101/2024.07.02.601766 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ CPIExtract: A software package to collect and harmonize small molecule and protein interactions ]]> https://biorxiv.org/content/10.1101/2024.07.03.601957v1?rss=1 Piras, A. Chenghao, S. Sebek, M. L. Ispirova, G. Menichetti, G. 2024-07-05 doi:10.1101/2024.07.03.601957 Cold Spring Harbor Laboratory Press 2024-07-05 <![CDATA[ Distinct modes of holobiont specialization among cryptic coral lineages ]]> https://biorxiv.org/content/10.1101/2024.07.05.598868v1?rss=1 Grupstra, C. G. B. Meyer-Kaiser, K. S. Bennett, M.-J. Andres, M. O. Juszkiewicz, D. J. Fifer, J. E. Da-Anoy, J. P. Gomez-Campo, K. Martinez-Rugerio, I. Aichelman, H. E. Huzar, A. K. Hughes, A. M. Rivera, H. E. Davies, S. W. 2024-07-06 doi:10.1101/2024.07.05.598868 Cold Spring Harbor Laboratory Press 2024-07-06 <![CDATA[ Identification of P-type ATPase as a bacterial transporter for host-derived small RNA ]]> https://biorxiv.org/content/10.1101/2024.07.05.602285v1?rss=1 Dong, P.-T. Yang, M. Cen, L. Zhou, P. Xu, D. Xiong, P. Wu, C. Li, J. He, X. 2024-07-07 doi:10.1101/2024.07.05.602285 Cold Spring Harbor Laboratory Press 2024-07-07 <![CDATA[ Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y ]]> https://biorxiv.org/content/10.1101/2024.07.08.602613v1?rss=1 Rengarajan, S. Derks, J. Bellott, D. W. Slavov, N. Page, D. C. 2024-07-10 doi:10.1101/2024.07.08.602613 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ 3D Brain Vascular Niche Model Captures Invasive Behavior and Gene Signatures of Glioblastoma ]]> https://biorxiv.org/content/10.1101/2024.07.09.601756v1?rss=1 Lee, V. K. Tejero, R. Silvia, N. Sattiraju, A. Ramakrishnan, A. Shen, L. Wojcinski, A. Kesari, S. Friedel, R. H. Zou, H. Dai, G. 2024-07-13 doi:10.1101/2024.07.09.601756 Cold Spring Harbor Laboratory Press 2024-07-13 <![CDATA[ Limiting the impact of protein leakage in single-cell proteomics ]]> https://biorxiv.org/content/10.1101/2024.07.26.605378v1?rss=1 Leduc, A. Xu, Y. Shipkovenska, G. Dou, Z. Slavov, N. 2024-07-27 doi:10.1101/2024.07.26.605378 Cold Spring Harbor Laboratory Press 2024-07-27 <![CDATA[ Closing the genome of Teredinibacter turnerae T7902 by long-read nanopore sequencing ]]> https://biorxiv.org/content/10.1101/2024.07.30.605897v1?rss=1 Gasser, M. T. Liu, A. Flatau, R. Altamia, M. A. Filone, C. M. Distel, D. L. 2024-07-30 doi:10.1101/2024.07.30.605897 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ Retinoic acid breakdown is required for proximodistal positional identity during amphibian limb regeneration ]]> https://biorxiv.org/content/10.1101/2024.08.07.607055v1?rss=1 Duerr, T. J. Miller, M. Kumar, S. Bakr, D. Griffiths, J. R. Gautham, A. K. Douglas, D. Voss, S. R. Monaghan, J. R. 2024-08-09 doi:10.1101/2024.08.07.607055 Cold Spring Harbor Laboratory Press 2024-08-09 <![CDATA[ Thermoneutral Housing has Limited Effects on Social Isolation-Induced Bone Loss in Male C57BL/6J Mice ]]> https://biorxiv.org/content/10.1101/2024.08.09.607315v1?rss=1 Mountain, R. Peters, R. Langlais, A. Stohn, J. P. Lary, C. Motyl, K. J. 2024-08-09 doi:10.1101/2024.08.09.607315 Cold Spring Harbor Laboratory Press 2024-08-09 <![CDATA[ Complete genome sequences of two new strains of the shipworm endosymbiont, Teredinibacter turnerae ]]> https://biorxiv.org/content/10.1101/2024.08.13.607755v1?rss=1 Gasser, M. T. Flatau, R. Altamia, M. A. Filone, C. M. Distel, D. L. 2024-08-16 doi:10.1101/2024.08.13.607755 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ Galvanotactic directionality of cell groups depends on group size ]]> https://biorxiv.org/content/10.1101/2024.08.13.607794v1?rss=1 Copos, C. sun, y. Zhu, K. Zhang, Y. Reid, B. Draper, B. W. Lin, F. Yue, H. Bernadskaya, Y. Zhao, M. Mogilner, A. 2024-08-13 doi:10.1101/2024.08.13.607794 Cold Spring Harbor Laboratory Press 2024-08-13 <![CDATA[ Behavioral and neural correlates of diverse conditioned fear responses in male and female rats ]]> https://biorxiv.org/content/10.1101/2024.08.20.608817v1?rss=1 Mitchell, J. Vincelette, L. Tuberman, S. Sheppard, V. Bergeron, E. Calitri, R. Clark, R. Cody, C. R. Kannan, A. Keith, J. Parakoyi, A. Pikus, M. Vance, V. Ziane, L. Brenhouse, H. Laine, M. Shansky, B. 2024-08-21 doi:10.1101/2024.08.20.608817 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ Revisiting equivalent optical properties for cerebrospinal fluid to improve diffusion-based modeling accuracy in the brain ]]> https://biorxiv.org/content/10.1101/2024.08.20.608859v1?rss=1 Lewis, A. Fang, Q. 2024-08-21 doi:10.1101/2024.08.20.608859 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ Evolutionary mismatch between nuclear and mitochondrial genomes does not promote reversion mutations in mtDNA. ]]> https://biorxiv.org/content/10.1101/2024.08.21.609033v1?rss=1 Franco, M. Popadin, K. Woods, D. C. Khrapko, K. 2024-08-23 doi:10.1101/2024.08.21.609033 Cold Spring Harbor Laboratory Press 2024-08-23 <![CDATA[ A genetically encoded fluorescent reporter for polyamines ]]> https://biorxiv.org/content/10.1101/2024.08.24.609500v1?rss=1 Sharma, P. Kim, C. Y. Keys, H. R. Imada, S. Joseph, A. B. Ferro, L. Kunchok, T. Anderson, R. Yilmaz, O. H. Weng, J.-K. Jain, A. 2024-08-26 doi:10.1101/2024.08.24.609500 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Alternate RNA decoding results in stable and abundant proteins in mammals ]]> https://biorxiv.org/content/10.1101/2024.08.26.609665v1?rss=1 Tsour, S. Machne, R. Leduc, A. Widmer, S. Slavov, N. 2024-08-26 doi:10.1101/2024.08.26.609665 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Proteome asymmetry in mouse and human embryos before fate specification ]]> https://biorxiv.org/content/10.1101/2024.08.26.609777v1?rss=1 Iwamoto-Stohl, L. K. Petelski, A. A. Meglicki, M. Fu, A. Khan, S. Specht, H. Huffman, G. Derks, J. Jorgensen, V. Weatherbee, B. A. Weberling, A. Gantner, C. W. Mandelbaum, R. S. Paulson, R. J. Lam, L. Ahmady, A. Vasquez, E. S. Slavov, N. Zernicka-Goetz, M. 2024-08-26 doi:10.1101/2024.08.26.609777 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ High-throughput Image-based Clustering of CAR-T/Tumor Cocultures for Rapid and Facile Hit Identification ]]> https://biorxiv.org/content/10.1101/2024.08.28.609577v1?rss=1 Xu, Z. Liu, X. Madden-Hennessey, K. Urbani, J. Nikkhoi, S. K. Ramasubramanian, A. G. Venugopal, K. Zhao, Q. L. Smith, E. Fu, Y. 2024-08-28 doi:10.1101/2024.08.28.609577 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ The Balanced Mind and its Intrinsic Neural Timescales in Advanced Meditators ]]> https://biorxiv.org/content/10.1101/2024.08.29.609126v1?rss=1 Malipeddi, S. Sasidharan, A. Venugopal, R. Ventura, B. Bauer, C. C. P.N., R. Mehrotra, S. John, J. P. Kutty, B. M. Northoff, G. 2024-08-30 doi:10.1101/2024.08.29.609126 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Aerosol delivery of immunotherapy and Hesperetin-loaded nanoparticles increases survival in a murine lung cancer model ]]> https://biorxiv.org/content/10.1101/2024.08.30.609714v1?rss=1 Yasmin-Karim, S. Richards, G. Fam, A. Ogurek, A.-M. Sridhar, S. Makrigiorgos, G. M. 2024-08-30 doi:10.1101/2024.08.30.609714 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Creating anatomically-derived, standardized, customizable, and three-dimensional printable head caps for functional neuroimaging ]]> https://biorxiv.org/content/10.1101/2024.08.30.610386v1?rss=1 McCann, A. Xu, E. Yen, F.-Y. Joseph, N. Fang, Q. 2024-08-30 doi:10.1101/2024.08.30.610386 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Dissecting reversible and irreversible single cell state transitions from gene regulatory networks ]]> https://biorxiv.org/content/10.1101/2024.08.30.610498v1?rss=1 Ramirez, D. Lu, M. 2024-09-01 doi:10.1101/2024.08.30.610498 Cold Spring Harbor Laboratory Press 2024-09-01 <![CDATA[ Validation studies and multi-omics analysis of Zhx2 as a candidate quantitative trait gene underlying brain oxycodone metabolite (oxymorphone) levels and behavior ]]> https://biorxiv.org/content/10.1101/2024.08.30.610534v1?rss=1 Lynch, W. B. Miracle, S. A. Goldstein, S. I. Beierle, J. A. Bhandari, R. Gerhardt, E. T. Farnan, A. Nguyen, B.-M. Wingfield, K. K. Kazerani, I. Saavedra, G. A. Averin, O. Baskin, B. M. Ferris, M. T. Reilly, C. A. Emili, A. Bryant, C. D. 2024-09-01 doi:10.1101/2024.08.30.610534 Cold Spring Harbor Laboratory Press 2024-09-01 <![CDATA[ Chronic mitochondrial fragmentation elicits a neuroprotective Warburg-like effect in Drosophila neurons ]]> https://biorxiv.org/content/10.1101/2024.08.30.610549v1?rss=1 Richhariya, S. Shin, D. Schlichting, M. Rosbash, M. 2024-09-01 doi:10.1101/2024.08.30.610549 Cold Spring Harbor Laboratory Press 2024-09-01 <![CDATA[ Mitochondrial direct repeat reduction as a strategy for enhancing human longevity: the case of the common repeat ]]> https://biorxiv.org/content/10.1101/2024.09.02.610808v1?rss=1 Shamanskiy, V. A. Gunbin, K. V. Tretiakov, E. O. Mazunin, I. O. Skripskaya, V. Mihailova, A. A. Mikhailova, A. G. Ree, N. Timonina, V. Knorre, D. Kunz, W. S. Okada, Y. Fiorell, N. Reymond, A. Bazykin, G. A. Fellay, J. Tanaka, M. Khrapko, K. Popadin, K. 2024-09-03 doi:10.1101/2024.09.02.610808 Cold Spring Harbor Laboratory Press 2024-09-03 <![CDATA[ Olfactory Mucosa-Derived Mesenchymal Stem Cells Differentiate Towards a Schwann Cell-Like Phenotype Towards Sourcing for Peripheral Nerve Regeneration ]]> https://biorxiv.org/content/10.1101/2024.09.03.611001v1?rss=1 Neuman, K. Koppes, A. N. Koppes, R. A. 2024-09-06 doi:10.1101/2024.09.03.611001 Cold Spring Harbor Laboratory Press 2024-09-06 <![CDATA[ Tensions on the actin cytoskeleton and apical cell junctions in the C. elegans spermatheca are influenced by spermathecal anatomy, ovulation state and activation of myosin ]]> https://biorxiv.org/content/10.1101/2024.09.03.611016v1?rss=1 Sadeghian, F. Grooms, N. W. F. Chung, S. H. Cram, E. J. 2024-09-05 doi:10.1101/2024.09.03.611016 Cold Spring Harbor Laboratory Press 2024-09-05 <![CDATA[ Understanding therapeutic tolerance through a mathematical model of drug-induced resistance ]]> https://biorxiv.org/content/10.1101/2024.09.04.611211v1?rss=1 Sontag, E. D. Gevertz, J. L. Greene, J. Comandante-Lou, N. Prosperi, S. 2024-09-07 doi:10.1101/2024.09.04.611211 Cold Spring Harbor Laboratory Press 2024-09-07 <![CDATA[ NetMedPy: A Python package for Large-Scale Network Medicine Screening ]]> https://biorxiv.org/content/10.1101/2024.09.05.611537v1?rss=1 Aldana, A. Sebek, M. Ispirova, G. Dorantes-Gilardi, R. Barabasi, A.-L. Loscalzo, J. Menichetti, G. 2024-09-08 doi:10.1101/2024.09.05.611537 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ Associations on the Fly, a new feature aiming to facilitate exploration of the Open Targets Platform evidence ]]> https://biorxiv.org/content/10.1101/2024.09.10.612089v1?rss=1 20 diverse sources to provide target-disease associations, covering evidence derived from genetic associations, somatic mutations, known drugs, differential expression, animal models, pathways and systems biology. An in-house target identification scoring framework weighs the evidence from each data source and type, contributing to an overall score for each of the 7.8M target-disease associations. However, the previous infrastructure did not allow user-led dynamic adjustments in the contribution of different evidence types for target prioritisation, a limitation frequently raised by our user community. Furthermore, the previous Platform user interface did not support navigation and exploration of the underlying target-disease evidence on the same page, occasionally making the user journey counterintuitive. ResultsHere, we describe "Associations on the Fly" (AOTF), a new Platform feature - developed as part of a wider product refactoring project - to enable formulation of more flexible and impactful therapeutic hypotheses through dynamic adjustment of the weight of contributing evidence from each source, altering the prioritisation of targets. Availability and implementationAll Open Targets code is available as open source: [https://github.com/opentargets]. This tool was implemented using React v18 and its code is accessible here: [https://github.com/opentargets/ot-ui-apps]. The tools described in the paper are accessible through the Open Targets Platform web interface [https://platform.opentargets.org/] and GraphQL API (https://platform-docs.opentargets.org/data-access/graphql-api). Data is available for download here: [https://platform.opentargets.org/downloads] and from the EMBL-EBI FTP: [https://ftp.ebi.ac.uk/pub/databases/opentargets/platform/]. Supplementary informationAdditional information on this tool can be found on the Platform documentation pages [https://platform-docs.opentargets.org/web-interface, https://platform-docs.opentargets.org/web-interface/associations-on-the-fly, https://platform-docs.opentargets.org/target-prioritisation] and training video [https://youtu.be/2A9bksboAag]. ContactAnnalisa Buniello, EMBL-EBI, buniello@ebi.ac.uk ]]> Cruz-Castillo, C. Fumis, L. Mehta, C. Martinez-Osorio, R. E. Roldan-Romero, J. M. Cornu, H. Uniyal, P. Solano-Roman, A. Carmona, M. Ochoa, D. McDonagh, E. M. Buniello, A. 2024-09-14 doi:10.1101/2024.09.10.612089 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ Mindfulness-based Neurofeedback: A Systematic Review of EEG and fMRI studies ]]> https://biorxiv.org/content/10.1101/2024.09.12.612669v1?rss=1 Treves, I. N. Greene, K. D. Bajwa, Z. Wool, E. Kim, N. Bauer, C. C. Bloom, P. A. Pagliaccio, D. Zhang, J. Whitfield-Gabrieli, S. Auerbach, R. P. 2024-09-15 doi:10.1101/2024.09.12.612669 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Capturing sclera anisotropy using direct collagen fiber models. Linking microstructure to macroscopic mechanical properties. ]]> https://biorxiv.org/content/10.1101/2024.09.12.612702v1?rss=1 0.89). Through an inverse-fitting process we determined model characteristics, including specimen-specific fiber mechanical properties to match equibiaxial loading. Interestingly, the equibiaxial properties also reproduced all the non-equibiaxial behaviors. These results indicate that the direct fiber modeling method naturally accounted for tissue anisotropy within its fiber structure. Direct fiber modeling is therefore a promising approach to understand how macroscopic behavior arises from microstructure. ]]> Ji, F. Islam, M. R. Sebastian, F. Schilpp, H. Wang, B. Hua, Y. Amini, R. Sigal, I. A. 2024-09-17 doi:10.1101/2024.09.12.612702 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ Structural and immunological characterization of the H3 influenza hemagglutinin during antigenic drift ]]> https://biorxiv.org/content/10.1101/2024.09.13.612776v1?rss=1 de Paiva Froes Rocha, R. Tomris, I. Bowman, C. A. Stevens, E. Kantorow, J. Peng, W. Oeverdieck, S. Ferguson, J. A. Jung, D. D. Herfst, S. Snijder, J. Chakraborty, S. Torrents de la Pena, A. Berndsen, Z. T. de Vries, R. P. Ward, A. B. 2024-09-19 doi:10.1101/2024.09.13.612776 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Calibration of additional computational tools expands ClinGen recommendation options for variant classification with PP3/BP4 criteria ]]> https://biorxiv.org/content/10.1101/2024.09.17.611902v1?rss=1 Bergquist, T. Stenton, S. L. Nadeau, E. A. W. Byrne, A. B. Greenblatt, M. S. Harrison, S. M. Tavtigian, S. V. O'Donnell-Luria, A. Biesecker, L. G. Radivojac, P. Brenner, S. E. Pejaver, V. ClinGen Sequence Variant Interpretation Working Group, 2024-09-21 doi:10.1101/2024.09.17.611902 Cold Spring Harbor Laboratory Press 2024-09-21 <![CDATA[ A Strategic Blend of Stabilizing Polymers to Control Particle Surface Charge for Enhanced Mucus Transport and Cell Binding ]]> https://biorxiv.org/content/10.1101/2024.09.17.613453v1?rss=1 Stevens, C. A. Sevarika, B. Wilson, B. K. Wang, C.-M. Carcamo-Oyarce, G. Degen, G. Kassis, T. Lehr, C. M. Carrier, R. Ribbeck, K. Prud'homme, R. K. 2024-09-19 doi:10.1101/2024.09.17.613453 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair for somatic benchmarks ]]> https://biorxiv.org/content/10.1101/2024.09.18.613544v1?rss=1 McDaniel, J. H. Patel, V. Olson, N. D. He, H.-J. He, Z. Schmitt, A. Sikkink, K. Sedlazeck, F. Doddapaneni, H. Jhangiani, S. N. Muzny, D. M. Gingras, M.-C. Mehta, H. Paulin, L. F. Hastie, A. R. Yu, H.-C. Weigman, V. Rojas, A. Kennedy, K. Remington, J. Gonzalez, I. Sudkamp, M. Wiseman, K. Lajoie, B. Levy, S. Jain, M. Akeson, S. Narzisi, G. Steinsnyder, Z. Reeves, C. Shelton, J. Kingan, S. B. Lambert, C. Bayabyan, P. Wenger, A. M. McLaughlin, I. J. Adamson, A. Kingsley, C. Wescott, M. Kim, Y. Paten, B. Park, J. Violich, I. Miga, K. H. Gardner, J. McNul 2024-09-22 doi:10.1101/2024.09.18.613544 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Human Mesofluidic Intestinal Model for Studying Transport of Drug Carriers and Bacteria Through a Live Mucosal Barrier ]]> https://biorxiv.org/content/10.1101/2024.09.18.613692v1?rss=1 Wang, C.-M. Oberoi, H. S. Law, D. Li, Y. Kassis, T. Griffith, L. G. Breault, D. T. Carrier, R. L. 2024-09-22 doi:10.1101/2024.09.18.613692 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Building plumbing influences the microdiversity and community assembly of the drinking water microbiome. ]]> https://biorxiv.org/content/10.1101/2024.09.23.614467v1?rss=1 He, H. Huo, L. Oosthuizen-Vosloo, S. Pieper, K. Stubbins, A. Yoon, B. Pinto, A. 2024-09-23 doi:10.1101/2024.09.23.614467 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ Higher-order and distributed synergistic functional interactions encode information gain in goal-directed learning ]]> https://biorxiv.org/content/10.1101/2024.09.23.614484v1?rss=1 Combrisson, E. Basanisi, R. Neri, M. Auzias, G. Petri, G. Marinazzo, D. Panzeri, S. Brovelli, A. 2024-09-24 doi:10.1101/2024.09.23.614484 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ 3D spatial distribution of Sost mRNA and Sclerostin expression in response to in vivo mechanical loading ]]> https://biorxiv.org/content/10.1101/2024.09.23.614612v1?rss=1 Meslier, Q. A. Hoffman, J. Oehrlein, R. Kurczy, D. Monaghan, J. R. Shefelbine, S. J. 2024-09-25 doi:10.1101/2024.09.23.614612 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ Which perceptual categories do observers experience during multistable perception? ]]> https://biorxiv.org/content/10.1101/2024.09.24.614648v1?rss=1 Skerswetat, J. Bex, P. J. 2024-09-24 doi:10.1101/2024.09.24.614648 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Novel color vision assessment tool: AIM Color Detection and Discrimination ]]> https://biorxiv.org/content/10.1101/2024.09.26.615300v1?rss=1 He, J. Skerswetat, J. Bex, P. J. 2024-09-27 doi:10.1101/2024.09.26.615300 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Neuronal activity regulating the dauer entry decision in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2024.09.30.615551v1?rss=1 Prakash, S. J. Seyedolmohadesin, M. Zhang, M. G. Cohen, S. M. Gharib, S. Venkatachalam, V. Sternberg, P. W. 2024-10-01 doi:10.1101/2024.09.30.615551 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Multiple transcription factors regulate the expression of genes for error prone DNA polymerases in Acinetobacter baumannii ]]> https://biorxiv.org/content/10.1101/2024.09.30.615892v1?rss=1 View larger version (17K): org.highwire.dtl.DTLVardef@502a49org.highwire.dtl.DTLVardef@10844bcorg.highwire.dtl.DTLVardef@1d8be41org.highwire.dtl.DTLVardef@b2a68e_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG ]]> Nguyen, B. H. Ching, C. Macguire, A. Casula, P. Newman, C. Finley, F. Godoy, V. 2024-10-01 doi:10.1101/2024.09.30.615892 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ The Plasmodium falciparum NCR1 membrane protein is a novel antimalarial target that exports cholesterol to maintain membrane homeostasis ]]> https://biorxiv.org/content/10.1101/2024.09.30.615907v1?rss=1 Zhang, Z. Lyu, M. Han, X. Bandara, S. Cui, M. Istvan, E. S. Geng, X. Tringides, M. Gregor, W. Miyagi, M. Oberstaller, J. Adams, J. H. Zhang, Y. Nieman, M. von Lintig, J. Goldberg, D. Yu, E. W. 2024-09-30 doi:10.1101/2024.09.30.615907 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Making Aptamers More Antibody-like: Targeting AXL in Vivo Using a Bottlebrush Polymer-Conjugated Aptamer ]]> https://biorxiv.org/content/10.1101/2024.10.02.616316v1?rss=1 Sun, T. Lin, J. Xue, C. Wang, Y. Chen, P. Wei, Y. Xu, G. Sidonia, A. Nenopoulos, C. Tashkandi, H. Zhang, K. 2024-10-03 doi:10.1101/2024.10.02.616316 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Bottlebrush polymers with sequence-controlled backbones for enhanced oligonucleotide delivery ]]> https://biorxiv.org/content/10.1101/2024.10.03.616318v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@1a332e7org.highwire.dtl.DTLVardef@1630ab1org.highwire.dtl.DTLVardef@15306dforg.highwire.dtl.DTLVardef@1e83f0e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Wei, Y. Chen, P. Li, D. Lin, J. Sun, T. Wang, Y. Yang, S. Nenopoulos, C. Oetheimer, C. Li, Y. Xue, C. Mona, M. Zhang, K. 2024-10-03 doi:10.1101/2024.10.03.616318 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Growth-coupled microbial biosynthesis of the animal pigment xanthommatin ]]> https://biorxiv.org/content/10.1101/2024.10.04.616593v1?rss=1 Bushin, L. B. Alter, T. B. Alvan-Vargas, M. V. G. Dürr, L. Olson, E. C. Avila, M. J. Puiggene, O. Kim, T. Deravi, L. F. Feist, A. M. Nikel, P. I. Moore, B. S. 2024-10-06 doi:10.1101/2024.10.04.616593 Cold Spring Harbor Laboratory Press 2024-10-06 <![CDATA[ Inferring post-transcriptional regulation within and across cell types in human testis ]]> https://biorxiv.org/content/10.1101/2024.10.08.617313v1?rss=1 Khan, S. Elcheikhali, M. Leduc, A. Huffman, R. G. Derks, J. Franks, A. Slavov, N. 2024-10-13 doi:10.1101/2024.10.08.617313 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ Assessment of high-efficacy agonism in synthetic cannabinoid receptor agonists containing l-tert-leucinate ]]> https://biorxiv.org/content/10.1101/2024.10.11.617959v1?rss=1 Lucaj, C. Pitha, C. Davis, J. Yano, H. 2024-10-15 doi:10.1101/2024.10.11.617959 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ On the analysis of functional PET (fPET)-FDG: baseline mischaracterization can introduce artifactual metabolic (de)activations ]]> https://biorxiv.org/content/10.1101/2024.10.17.618550v1?rss=1 Coursey, S. E. Mandeville, J. Reed, M. B. Hartung, G. A. Garimella, A. Sari, H. Lanzenberger, R. Price, J. C. Polimeni, J. R. Greve, D. N. Hahn, A. Chen, J. E. 2024-10-21 doi:10.1101/2024.10.17.618550 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ Wnt specifically induces FZD5/8 endocytosis and degradation and the involvement of RSPO-ZNRF3/RNF43 and DVL ]]> https://biorxiv.org/content/10.1101/2024.10.18.619000v1?rss=1 Luo, D. Zheng, J. Lv, S. Sheng, R. Chen, M. He, X. Zhang, X. 2024-10-19 doi:10.1101/2024.10.18.619000 Cold Spring Harbor Laboratory Press 2024-10-19 <![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[ Dissociable Default Mode Network Connectivity Patterns Underlie Distinct Symptoms in Psychosis Risk ]]> https://biorxiv.org/content/10.1101/2024.10.25.620271v1?rss=1 Ajunwa, C. C. Zhang, J. Collin, G. Keshavan, M. S. Tang, Y. Zhang, T. Li, H. Shenton, M. E. Stone, W. S. Wang, J. Niznikiewicz, M. Whitfield-Gabrieli, S. 2024-10-25 doi:10.1101/2024.10.25.620271 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Shared and unique lifetime stressor characteristics and brain networks predict adolescent anxiety and depression ]]> https://biorxiv.org/content/10.1101/2024.10.25.620373v1?rss=1 Qu, Y. Chopra, S. Qu, S. Cocuzza, C. V. Labache, L. Bauer, C. C. C. Morfini, F. Whitfield-Gabrieli, S. Slavich, G. M. Joormann, J. Holmes, A. J. 2024-10-26 doi:10.1101/2024.10.25.620373 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ Borrelia burgdorferi loses essential genetic elements and cell proliferative potential during stationary phase in culture but not in the tick vector. ]]> https://biorxiv.org/content/10.1101/2024.10.28.620338v1?rss=1 Zhang, J. Takacs, C. N. McCausland, J. W. Mueller, E. Buron, J. Thappeta, Y. Wachter, J. Rosa, P. A. Jacobs-Wagner, C. 2024-10-28 doi:10.1101/2024.10.28.620338 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Discovery and isolation of novel capsaicinoids and their TRPV1-related activity ]]> https://biorxiv.org/content/10.1101/2024.10.29.620944v1?rss=1 View larger version (17K): org.highwire.dtl.DTLVardef@1d56d02org.highwire.dtl.DTLVardef@e7a66dorg.highwire.dtl.DTLVardef@5f409forg.highwire.dtl.DTLVardef@18b88f7_HPS_FORMAT_FIGEXP M_FIG C_FIG Created in BioRender. Smith, J. (2025) https://BioRender.com/a61h668 HighlightsO_LI5 novel capsaicinoids (vanilloids) and 13 other capsaicinoids were isolated from chilis. C_LIO_LIThe slightest deviation in the capsaicin structure results in decreased TRPV1 activity. C_LIO_LIA single hydroxylation can reduce potency to TRPV1 100-fold. C_LIO_LINon-pungent vanilloids modulate capsaicin-TRPV1 activity. C_LI ]]> Smith, J. Stillerov, V. T. Dracinsky, M. Gaustad, H. L. A. Lorenzi, Q. Smrckova, H. Reinardt, J. K. Lienard, M. A. Bednarova, L. Sacha, P. Pluskal, T. 2024-11-03 doi:10.1101/2024.10.29.620944 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ NuclampFISH enables cell sorting based on nuclear RNA expression for chromatin analysis ]]> https://biorxiv.org/content/10.1101/2024.10.30.619948v1?rss=1 Liu, Y. Qiu, Y. Nian, K. Rouhanifard, S. H. 2024-11-01 doi:10.1101/2024.10.30.619948 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Detecting Special Genes in Marine Symbionts: A Phylogeny-Deviation Approach Identifies Recombination-Enhancing Variants ]]> https://biorxiv.org/content/10.1101/2024.10.31.621220v1?rss=1 Zhou, X. Li, W. Xie, S. Xia, K. Xiao, M. Yang, X. Li, Z. 2024-11-03 doi:10.1101/2024.10.31.621220 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ An SH3-binding allosteric modulator stabilizes the global conformation of the AML-associated Src-family kinase, Hck ]]> https://biorxiv.org/content/10.1101/2024.11.05.622136v1?rss=1 Selzer, A. M. Gerlach, G. Gonzalez-Areizaga, G. Wales, T. E. Cui, S. Y. Iyer, P. Engen, J. R. Camacho, C. Ishima, R. Smithgall, T. E. 2024-11-08 doi:10.1101/2024.11.05.622136 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ The acoustic properties, syllable structure, and syllable sequences of ultrasonic vocalizations (USVs) during neonatal opioid withdrawal in FVB/N mouse substrains ]]> https://biorxiv.org/content/10.1101/2024.11.06.622304v1?rss=1 Wingfield, K. K. Misic, T. Miracle, S. A. McDermott, C. S. Jain, K. Abney, N. M. Richardson, K. T. Rubman, M. B. Beierle, J. A. Wachman, E. M. Bryant, C. D. 2024-11-07 doi:10.1101/2024.11.06.622304 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ Co-Therapy with S1P and Heparan Sulfate Derivatives to Restore Endothelial Glycocalyx and Combat Pro-Atherosclerotic Endothelial Dysfunction ]]> https://biorxiv.org/content/10.1101/2024.11.06.622347v1?rss=1 Mitra, R. Pentland, K. Kolev, S. Eden, M. J. Levine, E. Oakes, J. M. Ebong, E. E. 2024-11-08 doi:10.1101/2024.11.06.622347 Cold Spring Harbor Laboratory Press 2024-11-08 <![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[ Clair3-RNA: A deep learning-based small variant caller for long-read RNA sequencing data ]]> https://biorxiv.org/content/10.1101/2024.11.17.624050v1?rss=1 Zheng, Z. Yu, X. Chen, L. Lee, Y.-L. Xin, C. Wong, A. O. K. Jain, M. Kesharwani, R. K. Sedlazeck, F. J. Luo, R. 2024-11-18 doi:10.1101/2024.11.17.624050 Cold Spring Harbor Laboratory Press 2024-11-18 <![CDATA[ Molecular Polymorphism of tau aggregates in Pick's disease ]]> https://biorxiv.org/content/10.1101/2024.11.19.624253v1?rss=1 Liu, J. Stewart, T. C. Hyman, B. T. Burghammer, M. Cotte, M. Makowski, L. 2024-11-19 doi:10.1101/2024.11.19.624253 Cold Spring Harbor Laboratory Press 2024-11-19 <![CDATA[ Representation Learning of Human Disease Mechanisms for a Foundation Model in Rare and Common Diseases ]]> https://biorxiv.org/content/10.1101/2024.11.19.624381v1?rss=1 Ravandi, B. Mowrey, W. R. Chatterjee, A. Ricchiuto, P. Haddadi, P. Abdelmessih, M. Ding, W. Lambden, S. Ughetto, M. Barrett, I. Diethe, T. Del Angel, G. Eliassi-Rad, T. 2024-11-21 doi:10.1101/2024.11.19.624381 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Cumulative dose responses for adapting biological systems ]]> https://biorxiv.org/content/10.1101/2024.11.22.624851v1?rss=1 Gupta, A. Sontag, E. D. 2024-11-25 doi:10.1101/2024.11.22.624851 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ A multi-level formalism to capture the characteristics of hybrid phenotypes in Epithelial-Mesenchymal Plasticity ]]> https://biorxiv.org/content/10.1101/2024.11.26.625479v1?rss=1 Hari, K. Tripathi, S. Anand, V. Jolly, M. K. Levine, H. 2024-12-02 doi:10.1101/2024.11.26.625479 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ The emergence and loss of cyclic peptides in Nicotiana illuminate dynamics and mechanisms of plant metabolic evolution ]]> https://biorxiv.org/content/10.1101/2024.11.29.626059v1?rss=1 Suh, E. M. Reinhardt, J. K. Weng, J.-K. 2024-12-01 doi:10.1101/2024.11.29.626059 Cold Spring Harbor Laboratory Press 2024-12-01 <![CDATA[ Anapc5 and Anapc7 as genetic modifiers of KIF18A function in fertility and mitotic progression ]]> https://biorxiv.org/content/10.1101/2024.12.03.626395v1?rss=1 Nesbit, C. Martin, W. Czechanski, A. Byers, C. Raghupathy, N. Ferraj, A. Stumpff, J. Reinholdt, L. G. 2024-12-04 doi:10.1101/2024.12.03.626395 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ Rates of evolution differ between cell types identified by single-cell RNAseq in threespine stickleback ]]> https://biorxiv.org/content/10.1101/2024.12.06.627160v1?rss=1 Rodgers, M. L. Subramanian, S. Fuess, L. E. He, W. Scarpino, S. V. Roth-Monzon, A. Jeffries, D. Seignon, M. Milligan-McClellan, K. Carrier, R. Steinel, N. C. Bolnick, D. I. 2024-12-09 doi:10.1101/2024.12.06.627160 Cold Spring Harbor Laboratory Press 2024-12-09 <![CDATA[ The Role of BAZ2-dependent Chromatin Remodeling in Suppressing G4 DNA Structures and Associated Genomic Instability ]]> https://biorxiv.org/content/10.1101/2024.12.10.627505v1?rss=1 Vandeuren, A. L. O'Dare, K. Wilson, R. H. C. van Eijk, P. Julio, L. R. Macleod, S. G. Chee, E. Salpukas, A. Kriz, E. M. Lantz, G. A. Gordon, S. J. V. Elsässer, S. J. Reed, S. H. Day, T. A. 2024-12-11 doi:10.1101/2024.12.10.627505 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ Modular environmental pleiotropy of genes involved in local adaptation to climate despite physical linkage ]]> https://biorxiv.org/content/10.1101/202481v1?rss=1 Lotterhos, K. Hodgins, K. Yeaman, S. Degner, J. Aitken, S. 2017-10-13 doi:10.1101/202481 Cold Spring Harbor Laboratory Press 2017-10-13 <![CDATA[ Selective attention modulates surface filling-in ]]> https://biorxiv.org/content/10.1101/221150v1?rss=1 Harrison, W. J. Ayeni, A. J. Bex, P. J. 2017-11-17 doi:10.1101/221150 Cold Spring Harbor Laboratory Press 2017-11-17 <![CDATA[ Controllability in an islet specific regulatory network identifies the transcriptional factor NFATC4, which regulates Type 2 Diabetes associated genes ]]> https://biorxiv.org/content/10.1101/226456v1?rss=1 Sharma, A. Halu, A. Decano, J. L. Menche, J. Liu, Y.-Y. Prasad, R. B. Fadista, J. Santolini, M. Padi, M. Weiss, S. T. Vidal, M. Silverman, E. K. Aikawa, M. Barabasi, A.-L. Groop, L. Loscalzo, J. 2017-11-29 doi:10.1101/226456 Cold Spring Harbor Laboratory Press 2017-11-29 <![CDATA[ A Multi-Species Functional Embedding Integrating Sequence and Network Structure ]]> https://biorxiv.org/content/10.1101/229211v1?rss=1 Leiserson, M. Fan, J. Cannistra, A. Fried, I. Lim, T. Schaffner, T. Crovella, M. Hescott, B. 2017-12-04 doi:10.1101/229211 Cold Spring Harbor Laboratory Press 2017-12-04 <![CDATA[ Mitochondrial heteroplasmy is responsible for Atovaquone drug resistance in Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/232033v1?rss=1 95% Y268S copies under in vitro ATO selection. Further we uncovered high mitochondrial diversity in a global collection of 1279 genomes in which heteroplasmic polymorphisms were >3-fold more prevalent than homoplasmic SNPs. Moreover, significantly higher mitochondrial genome copy number was found in Asia (e.g., Cambodia) versus Africa (e.g., Ghana). Similarly, ATO drug selections in vitro induced >3-fold mitochondrial copy number increases in ATO resistant lines. Hidden mitochondrial diversity is a previously unknown mechanism of antimalarial drug resistance and characterization of mitochondrial heteroplasmy will be of paramount importance in combatting resistance to antimalarials targeting the electron transport chain. ]]> Siegel, S. V. Rivero, A. V. Adapa, S. R. Wang, C. Manetsch, R. Jiang, R. H. Kyle, D. E. 2017-12-10 doi:10.1101/232033 Cold Spring Harbor Laboratory Press 2017-12-10 <![CDATA[ Three-Dimensional Binocular Eye-Hand Coordination in Normal Vision and with Simulated Visual Impairment ]]> https://biorxiv.org/content/10.1101/232488v1?rss=1 Maiello, G. Kwon, M. Bex, P. J. 2017-12-13 doi:10.1101/232488 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ A mathematical approach to differentiate spontaneous and induced evolution to drug resistance during cancer treatment ]]> https://biorxiv.org/content/10.1101/235150v1?rss=1 Greene, J. M. Gevertz, J. L. Sontag, E. D. 2017-12-15 doi:10.1101/235150 Cold Spring Harbor Laboratory Press 2017-12-15 <![CDATA[ Macrophage resilience and control of intracellular bacteria requires sst1-dependent integration of c-Myc, stress response and type I IFN pathways ]]> https://biorxiv.org/content/10.1101/238873v1?rss=1 Bhattacharya, B. Chatterjee, S. Berland, R. Pichugin, A. Ivanov, A. Connor, J. H. Yan, B.-S. Kobzik, L. Kramnik, I. 2017-12-22 doi:10.1101/238873 Cold Spring Harbor Laboratory Press 2017-12-22 <![CDATA[ Beyond the ribosome: proteome-wide secretability studies using SECRiFY ]]> https://biorxiv.org/content/10.1101/241349v1?rss=1 105 protein fragments by two yeast species, S. cerevisiae and P. pastoris, using custom fragment libraries, surface display and a sequencing-based readout. Screening human proteome fragments with a median size of 50 - 100 amino acids, we generated datasets that enable datamining into protein features underlying secretability, revealing a striking role for intrinsic disorder and chain flexibility. SECRiFY is the first methodology that generates sufficient amounts of annotated data for advanced machine learning methods to deduce secretability predictors. The finding that secretability is indeed a learnable feature of protein sequences is of significant impact in the broad area of recombinant protein expression and de novo protein design. ]]> Boone, M. Ramasamy, P. Maddelein, D. Turan, D. Martens, L. Vandermarliere, E. Vranken, W. Callewaert, N. 2018-01-14 doi:10.1101/241349 Cold Spring Harbor Laboratory Press 2018-01-14 <![CDATA[ NanoAmpli-Seq: A workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform ]]> https://biorxiv.org/content/10.1101/244517v1?rss=1 Calus, S. T. Ijaz, U. Z. Pinto, A. J. 2018-01-07 doi:10.1101/244517 Cold Spring Harbor Laboratory Press 2018-01-07 <![CDATA[ Reducing False Positives in CRISPR/Cas9 Screens from Copy Number Variations ]]> https://biorxiv.org/content/10.1101/247031v1?rss=1 Wu, A. Xiao, T. Fei, T. Liu, S. X. Li, W. 2018-01-11 doi:10.1101/247031 Cold Spring Harbor Laboratory Press 2018-01-11 <![CDATA[ Passive Audio Vocal Capture and Measurement in the Evaluation of Selective Mutism ]]> https://biorxiv.org/content/10.1101/250308v1?rss=1 Xu, H. Stroud, J. Jozanovic, R. Clucas, J. Son, J. Koo, B. Schwarz, J. Klein, A. Busman, R. Milham, M. P. 2018-01-18 doi:10.1101/250308 Cold Spring Harbor Laboratory Press 2018-01-18 <![CDATA[ Preserved functional connectivity in the default mode and salience networks is associated with youthful memory in superaging ]]> https://biorxiv.org/content/10.1101/254193v1?rss=1 Zhang, J. Andreano, J. Dickerson, B. C. Touroutoglou, A. Barrett, L. F. 2018-01-29 doi:10.1101/254193 Cold Spring Harbor Laboratory Press 2018-01-29 <![CDATA[ Limb bone scaling in hopping diprotodonts and quadrupedal artiodactyls ]]> https://biorxiv.org/content/10.1101/256768v1?rss=1 Doube, M. Felder, A. A. Chua, M. Y. Lodhia, K. Kłosowski, M. M. Hutchinson, J. R. Shefelbine, S. J. 2018-01-30 doi:10.1101/256768 Cold Spring Harbor Laboratory Press 2018-01-30 <![CDATA[ Neuregulin-1 exerts molecular control over axolotl lung regeneration through ErbB family receptors ]]> https://biorxiv.org/content/10.1101/258517v1?rss=1 Jensen, T. B. Giunta, P. Schulz, N. G. Kyeremateng, Y. Wong, H. Adesina, A. Monaghan, J. R. 2018-02-01 doi:10.1101/258517 Cold Spring Harbor Laboratory Press 2018-02-01 <![CDATA[ IFIT3 and IFIT2/3 promote IFIT1-mediated translation inhibition by enhancing binding to non-self RNA. ]]> https://biorxiv.org/content/10.1101/261776v1?rss=1 Fleith, R. C. Mears, H. V. Emmott, E. Graham, S. C. Mansur, D. S. Sweeney, T. R. 2018-02-08 doi:10.1101/261776 Cold Spring Harbor Laboratory Press 2018-02-08 <![CDATA[ Open Community Challenge Reveals Molecular Network Modules with Key Roles in Diseases ]]> https://biorxiv.org/content/10.1101/265553v1?rss=1 Choobdar, S. Ahsen, M. E. Crawford, J. Tomasoni, M. Lamparter, D. Lin, J. Hescott, B. Hu, X. Mercer, J. Natoli, T. Narayan, R. The DREAM Module Identification Challenge Consortium, Subramanian, A. Stolovitzky, G. Kutalik, Z. Lage, K. Slonim, D. K. Saez-Rodriguez, J. Cowen, L. J. Bergmann, S. Marbach, D. 2018-02-15 doi:10.1101/265553 Cold Spring Harbor Laboratory Press 2018-02-15 <![CDATA[ Targeted Drug Delivery by Radiation-Induced Tumor Vascular Modulation ]]> https://biorxiv.org/content/10.1101/268714v1?rss=1 nView larger version (84K):norg.highwire.dtl.DTLVardef@a6df8borg.highwire.dtl.DTLVardef@19e3179org.highwire.dtl.DTLVardef@c223aaorg.highwire.dtl.DTLVardef@1b3a08d_HPS_FORMAT_FIGEXP M_FIG GRAPHICAL ABSTRACTnnC_FIG ]]> Kunjachan, S. Kotb, S. Kumar, R. Pola, R. Pechar, M. Gremse, F. Taleeli, R. Trichard, F. Motto-Ros, V. Sancey, L. Detappe, A. Protti, A. Shanmugam, I. Ireland, T. Etrych, T. Sridhar, S. Tillement, O. Makrigiorgos, G. M. Berbeco, R. 2018-02-20 doi:10.1101/268714 Cold Spring Harbor Laboratory Press 2018-02-20 <![CDATA[ Serial Dependence in Position Perception Occurs at the Time of Perception ]]> https://biorxiv.org/content/10.1101/270272v1?rss=1 Manassi, M. Liberman, A. Kosovicheva, A. Zhang, K. Whitney, D. 2018-02-25 doi:10.1101/270272 Cold Spring Harbor Laboratory Press 2018-02-25 <![CDATA[ Network-based prediction of protein interactions ]]> https://biorxiv.org/content/10.1101/275529v1?rss=1 Kovacs, I. A. Luck, K. Spirohn, K. Wang, Y. Pollis, C. Schlabach, S. Bian, W. Kim, D.-K. Kishore, N. Hao, T. Calderwood, M. A. Vidal, M. Barabasi, A.-L. 2018-03-02 doi:10.1101/275529 Cold Spring Harbor Laboratory Press 2018-03-02 <![CDATA[ Prolonged lag time results in small colony variants and reflects a sub-population of persisters in vivo ]]> https://biorxiv.org/content/10.1101/279968v1?rss=1 Vulin, C. Leimer, N. Huemer, M. Ackermann, M. Zinkernagel, A. S. 2018-03-12 doi:10.1101/279968 Cold Spring Harbor Laboratory Press 2018-03-12 <![CDATA[ Variability and compensation of cardiomycoyte ionic conductances at the population level ]]> https://biorxiv.org/content/10.1101/283275v1?rss=1 Rees, C. Yang, J.-H. Santolini, M. Lusis, A. J. Weiss, J. N. Karma, A. 2018-03-15 doi:10.1101/283275 Cold Spring Harbor Laboratory Press 2018-03-15 <![CDATA[ Nearshore corals on the Mesoamerican Barrier Reef System on pace to cease growing as soon as year 2110 ]]> https://biorxiv.org/content/10.1101/298158v1?rss=1 Baumann, J. Ries, J. Rippe, J. Courtney, T. Aichelman, H. Westfield, I. Castillo, K. 2018-04-09 doi:10.1101/298158 Cold Spring Harbor Laboratory Press 2018-04-09 <![CDATA[ Quantifying the risk of local Zika virus transmission in the continental US during the 2015-2016 ZIKV epidemic ]]> https://biorxiv.org/content/10.1101/298315v1?rss=1 Sun, K. Zhang, Q. Pastore y Piontti, A. Chinazzi, M. Mistry, D. Dean, N. E. Rojas, D. P. Merler, S. Poletti, P. Rossi, L. Halloran, M. E. Longini, I. M. Vespignani, A. 2018-04-11 doi:10.1101/298315 Cold Spring Harbor Laboratory Press 2018-04-11 <![CDATA[ Glial cells in the heart? Replicating the diversity of the myocardium with low-cost 3D models ]]> https://biorxiv.org/content/10.1101/306233v1?rss=1 Soucy, J. R. Askaryan, J. Diaz, D. Koppes, A. N. Annabi, N. Koppes, R. 2018-04-23 doi:10.1101/306233 Cold Spring Harbor Laboratory Press 2018-04-23 <![CDATA[ Golgi stabilization, not its front-rear bias, is associated with EMT-enhanced fibrillar migration ]]> https://biorxiv.org/content/10.1101/308536v1?rss=1 Natividad, R. J. Lalli, M. L. Muthuswamy, S. K. Asthagiri, A. R. 2018-04-25 doi:10.1101/308536 Cold Spring Harbor Laboratory Press 2018-04-25 <![CDATA[ Adult-born neurons maintain hippocampal cholinergic inputs and support working memory during aging ]]> https://biorxiv.org/content/10.1101/311423v1?rss=1 Kirshenbaum, G. Robson, V. K. Shansky, R. M. Savage, L. M. Leonardo, E. D. Dranovsky, A. 2018-04-30 doi:10.1101/311423 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ Robust associative learning is sufficient to explain structural and dynamical properties of local cortical circuits ]]> https://biorxiv.org/content/10.1101/320432v1?rss=1 Zhang, D. Zhang, C. Stepanyants, A. 2018-05-11 doi:10.1101/320432 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Lead-DBS v2: Toward a comprehensive pipeline for deep brain stimulation imaging ]]> https://biorxiv.org/content/10.1101/322008v1?rss=1 Horn, A. Li, N. Dembek, T. A. Kappel, A. Boulay, C. Ewert, S. Tietze, A. Husch, A. Perera, T. Neumann, W.-J. Reisert, M. Si, H. Oostenveld, R. Rorden, C. Yeh, F.-C. Fang, Q. Herrington, T. M. Vorwerk, J. Kuehn, A. A. 2018-05-15 doi:10.1101/322008 Cold Spring Harbor Laboratory Press 2018-05-15 <![CDATA[ Understanding the impact of crosslinked PCL/PEG/GelMA electrospun nanofibers on bactericidal activity ]]> https://biorxiv.org/content/10.1101/322321v1?rss=1 De-Paula, M. Ghannadian, P. Afewerki, S. Marciano, F. Viana, B. Harb, S. Bassous, N. Webster, T. Lobo, A. 2018-05-15 doi:10.1101/322321 Cold Spring Harbor Laboratory Press 2018-05-15 <![CDATA[ Fusion surface structure, function, and dynamics of gamete fusogen HAP2 ]]> https://biorxiv.org/content/10.1101/324194v1?rss=1 Feng, J. Dong, X. Pinello, J. F. Zhang, J. Lu, C. Iacob, R. E. Engen, J. R. Snell, W. J. Springer, T. 2018-05-16 doi:10.1101/324194 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Mitochondrial ClpX activates an essential metabolic enzyme through partial unfolding ]]> https://biorxiv.org/content/10.1101/327056v1?rss=1 Kardon, J. R. Moroco, J. A. Engen, J. R. Baker, T. A. 2018-05-21 doi:10.1101/327056 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ Immunobiochemical reconstruction of influenza lung infection - Melanoma skin cancer interactions ]]> https://biorxiv.org/content/10.1101/331546v1?rss=1 Nikolaev, E. V. Zloza, A. Sontag, E. 2018-05-25 doi:10.1101/331546 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Predict plant-derived xenomiRs from plant miRNA sequences using random forest and one-dimensional convolutional neural network models ]]> https://biorxiv.org/content/10.1101/345249v1?rss=1 Zhao, Q. Mao, Q. Zhao, Z. Dou, T. Wang, Z. Cui, X. Liu, Y. Fan, X. 2018-06-13 doi:10.1101/345249 Cold Spring Harbor Laboratory Press 2018-06-13 <![CDATA[ Predicting perturbation patterns from the topology of biological networks ]]> https://biorxiv.org/content/10.1101/349324v1?rss=1 Santolini, M. Barabasi, A.-L. 2018-06-17 doi:10.1101/349324 Cold Spring Harbor Laboratory Press 2018-06-17 <![CDATA[ The sequences near Chi sites allow the RecBCD pathway to avoid genomic rearrangements ]]> https://biorxiv.org/content/10.1101/351395v1?rss=1 Prentiss, M. G. Godoy, V. Danilowicz, C. Prevost, C. Tashjian, T. Li, C. 2018-06-20 doi:10.1101/351395 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ Ancestral Roles of the Fam20C Family of Secreted Protein Kinases Revealed by Functional Analysis in C. elegans ]]> https://biorxiv.org/content/10.1101/363440v1?rss=1 Gerson-Gurwitz, A. Worby, C. A. Lee, K.-Y. Khaliullin, R. Bouffard, J. Cheerambathur, D. Cram, E. J. Oegema, K. Dixon, J. E. Desai, A. 2018-07-06 doi:10.1101/363440 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ Using SMOG 2 to simulate complex biomolecular assemblies ]]> https://biorxiv.org/content/10.1101/371617v1?rss=1 Levi, M. Bandarkar, P. Yang, H. Wang, A. Mohanty, U. Noel, J. K. Whitford, P. C. 2018-07-18 doi:10.1101/371617 Cold Spring Harbor Laboratory Press 2018-07-18 <![CDATA[ In vitro determination of the CB1 efficacy of illicit synthetic cannabinoids ]]> https://biorxiv.org/content/10.1101/385583v1?rss=1 Sachdev, S. Vemuri, K. Banister, S. Longworth, M. Kassiou, M. Santiago, M. J. Makriyannis, A. Connor, M. 2018-08-06 doi:10.1101/385583 Cold Spring Harbor Laboratory Press 2018-08-06 <![CDATA[ Propionic acid enhances the virulence of Crohn’s disease-associated adherent-invasive Escherichia coli ]]> https://biorxiv.org/content/10.1101/387647v1?rss=1 Ormsby, M. J. Johnson, S. A. Meikle, L. M. Goldstone, R. J. McIntosh, A. Wessel, H. M. Hulme, H. E. McConnachie, C. C. Connolly, J. P. Roe, A. J. Fitzgerald, E. Gerasimidis, K. Morrison, D. Smith, D. G. Wall, D. M. 2018-08-09 doi:10.1101/387647 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ Adaptation of proteins to the cold in Antarctic fish: A role for Methionine? ]]> https://biorxiv.org/content/10.1101/388900v1?rss=1 Berthelot, C. Clarke, J. Desvignes, T. Detrich, H. W. Flicek, P. Peck, L. S. Peters, M. Postlethwait, J. H. Clark, M. S. 2018-08-09 doi:10.1101/388900 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ A model of repetitive mild brain injury without symptoms – risk for Parkinson’s disease with aging? ]]> https://biorxiv.org/content/10.1101/390856v1?rss=1 Kulkarni, P. Morrison, T. R. Cai, X. Iriah, S. Lange, M. S. Kennedy, L. Sabrick, J. Neuroth, L. Hoffman, G. E. Ferris, C. F. Praveen Kulkanri, Thomas R Morrison, Xuezhu Cai, Sade Iriah, Mary S Lange, Laprosha Kennedy, Julia S, 2018-08-13 doi:10.1101/390856 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ Visuomotor Control of Ankle Joint using Position vs. Force ]]> https://biorxiv.org/content/10.1101/391367v1?rss=1 Farjadian, A. B. Nabian, M. Hartman, A. Yen, S.-C. Nasseroleslami, B. 2018-08-13 doi:10.1101/391367 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ 22kHz and 55kHz ultrasonic vocalizations differentially influence neural and behavioral outcomes: Implications for modeling anxiety via auditory stimuli in the rat ]]> https://biorxiv.org/content/10.1101/395772v1?rss=1 Demaestri, C. Brenhouse, H. C. Honeycutt, J. A. 2018-08-20 doi:10.1101/395772 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ DART-ID increases single-cell proteome coverage ]]> https://biorxiv.org/content/10.1101/399121v1?rss=1 Chen, A. Franks, A. Slavov, N. 2018-08-23 doi:10.1101/399121 Cold Spring Harbor Laboratory Press 2018-08-23 <![CDATA[ Parvalbumin loss following chronic sub-anesthetic NMDA antagonist treatment is age-dependent in the hippocampus: Implications for modeling NMDA hypofunction ]]> https://biorxiv.org/content/10.1101/399188v1?rss=1 Honeycutt, J. A. Chrobak, J. J. 2018-08-23 doi:10.1101/399188 Cold Spring Harbor Laboratory Press 2018-08-23 <![CDATA[ Automated sample preparation for high-throughput single-cell proteomics ]]> https://biorxiv.org/content/10.1101/399774v1?rss=1 Specht, H. Harmange, G. Perlman, D. H. Emmott, E. Niziolek, Z. Budnik, B. Slavov, N. 2018-08-25 doi:10.1101/399774 Cold Spring Harbor Laboratory Press 2018-08-25 <![CDATA[ Rapid prototyping of a multilayer microphysiological system for primary human intestinal epithelial culture ]]> https://biorxiv.org/content/10.1101/400721v1?rss=1 Hosic, S. Puzan, M. L. Lake, W. Zhou, F. Koppes, R. A. Breault, D. T. Murthy, S. K. Koppes, A. N. 2018-08-27 doi:10.1101/400721 Cold Spring Harbor Laboratory Press 2018-08-27 <![CDATA[ Extracellular matrix stiffness regulates force transmission pathways in multicellular ensembles of human airway smooth muscle cells. ]]> https://biorxiv.org/content/10.1101/402842v1?rss=1 Polio, S. R. Stasiak, S. Krishnan, R. Parameswaran, H. 2018-08-29 doi:10.1101/402842 Cold Spring Harbor Laboratory Press 2018-08-29 <![CDATA[ Integration of Molecular Interactome and Targeted Interaction Analysis to Identify a COPD Disease Network Module ]]> https://biorxiv.org/content/10.1101/408229v1?rss=1 Sharma, A. Kitsak, M. Cho, M. C. Ameli, A. Zhou, X. Jiang, Z. Crapo, J. D. Beaty, T. H. Menche, J. Bakke, P. S. Santolini, M. Silverman, E. K. 2018-09-04 doi:10.1101/408229 Cold Spring Harbor Laboratory Press 2018-09-04 <![CDATA[ CluSim: a Python package for the comparison of clusterings and dendrograms ]]> https://biorxiv.org/content/10.1101/410084v1?rss=1 Gates, A. J. Ahn, Y.-Y. 2018-09-06 doi:10.1101/410084 Cold Spring Harbor Laboratory Press 2018-09-06 <![CDATA[ New Drosophila long-term memory genes revealed by assessing computational function prediction methods. ]]> https://biorxiv.org/content/10.1101/414565v1?rss=1 Kacsoh, B. Z. Barton, S. Jiang, Y. Zhou, N. Mooney, S. D. Friedberg, I. Radivojac, P. Greene, C. S. Bosco, G. 2018-09-11 doi:10.1101/414565 Cold Spring Harbor Laboratory Press 2018-09-11 <![CDATA[ Accurate registration of 3D time-lapse microscopy images ]]> https://biorxiv.org/content/10.1101/436824v1?rss=1 Mousavi Kahaki, S. M. Wang, S.-L. Stepanyants, A. 2018-10-05 doi:10.1101/436824 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ Artificial neural network filters for enhancing 3D optical microscopy images of neurites ]]> https://biorxiv.org/content/10.1101/441071v1?rss=1 Wang, S.-L. Mousavi Kahaki, S. M. Stepanyants, A. 2018-10-11 doi:10.1101/441071 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ The RhoGAP SPV-1 regulates calcium signaling to control the contractility of the C. elegans spermatheca during embryo transits. ]]> https://biorxiv.org/content/10.1101/441386v1?rss=1 Bouffard, J. Cecchetelli, A. D. Clifford, C. Sethi, K. Zaidel-Bar, R. Cram, E. J. 2018-10-12 doi:10.1101/441386 Cold Spring Harbor Laboratory Press 2018-10-12 <![CDATA[ The landscape of intrinsic and evolved fluoroquinolone resistance in Acinetobacter baumannii includes suppression of drug-induced prophage replication ]]> https://biorxiv.org/content/10.1101/442681v1?rss=1 Geisinger, E. Vargas-Cuebas, G. Mortman, N. J. Syal, S. Wainwright, E. Lazinski, D. W. Wood, S. Zhu, Z. Anthony, J. van Opijnen, T. Isberg, R. R. 2018-10-14 doi:10.1101/442681 Cold Spring Harbor Laboratory Press 2018-10-14 <![CDATA[ In vitro model of inflammatory, hypoxia, and cancer stem cell signaling in pancreatic cancer using heterocellular 3-dimensional spheroids ]]> https://biorxiv.org/content/10.1101/454397v1?rss=1 Sursh, M. Mattheolabakis, G. Singh, A. Amiji, M. M. 2018-10-26 doi:10.1101/454397 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ Proteostasis environment shapes higher-order epistasis operating on antibiotic resistance ]]> https://biorxiv.org/content/10.1101/470971v1?rss=1 Guerrero, R. F. Scarpino, S. Rodrigues, J. V. Hartl, D. L. Ogbunugafor, C. B. 2018-11-16 doi:10.1101/470971 Cold Spring Harbor Laboratory Press 2018-11-16 <![CDATA[ Mathematical Details on a Cancer Resistance Model ]]> https://biorxiv.org/content/10.1101/475533v1?rss=1 Greene, J. Sanchez-Tapia, C. Sontag, E. 2018-11-22 doi:10.1101/475533 Cold Spring Harbor Laboratory Press 2018-11-22 <![CDATA[ Historical contingency shapes adaptive radiation in Antarctic fishes ]]> https://biorxiv.org/content/10.1101/478842v1?rss=1 250,000 loci across 46 species to examine hypotheses concerning the origin and diversification of key traits in the adaptive radiation of Antarctic notothenioid fishes. Contrary to expectations of adaptive evolution, we show that notothenioids experienced a punctuated burst of genomic diversification and evolved key skeletal modifications before the onset of polar conditions in the Southern Ocean. We show that diversifying selection in pathways associated with human skeletal dysplasias facilitates ecologically important variation in buoyancy among Antarctic notothenioid species, and demonstrate the sufficiency of altered trip11, col1a2 and col1a1 function in zebrafish (Danio rerio) to phenocopy skeletal reduction in Antarctic notothenioids. Rather than adaptation being driven by the cooling of the Antarctic (6), our results highlight the role of exaptation and historical contingency in shaping the adaptive radiation of notothenioids. Understanding the historical and environmental context for the origin of key traits in adaptive radiations provides context in forecasting the effects of climate change on the stability and evolvability of natural populations. ]]> Daane, J. M. Dornburg, A. Smits, P. MacGuigan, D. J. Hawkins, M. B. Near, T. J. Detrich, H. W. Harris, M. P. 2018-11-26 doi:10.1101/478842 Cold Spring Harbor Laboratory Press 2018-11-26 <![CDATA[ Glycolytic inhibitor 2-deoxyglucose prevents cortical hyperexcitability after traumatic brain injury ]]> https://biorxiv.org/content/10.1101/479782v1?rss=1 Koenig, J. B. Cantu, D. Low, C. Noubary, F. Croker, D. Whalen, M. Kong, D. Dulla, C. G. 2018-11-27 doi:10.1101/479782 Cold Spring Harbor Laboratory Press 2018-11-27 <![CDATA[ PTPN22 interacts with EB1 to regulate T cell receptor signaling ]]> https://biorxiv.org/content/10.1101/481507v1?rss=1 Zhang, X. Bai, B. Wang, T. Zhao, J. Zhang, N. Zhao, Y. Wang, X. Wang, B. Yu, Y. 2018-11-28 doi:10.1101/481507 Cold Spring Harbor Laboratory Press 2018-11-28 <![CDATA[ In Vivo Flow Cytometry of Extremely Rare Circulating Cells ]]> https://biorxiv.org/content/10.1101/488619v1?rss=1 Tan, X. Patil, R. Bartosik, P. Runnels, J. Lin, C. P. Niedre, M. 2018-12-07 doi:10.1101/488619 Cold Spring Harbor Laboratory Press 2018-12-07 <![CDATA[ Evolution of connections and cell types: integrating diffusion MR tractography with gene expression data highlights increased cortico-cortical projections in primates ]]> https://biorxiv.org/content/10.1101/493593v1?rss=1 Charvet, C. Palani, A. Priya Kabaria, P. Takahashi, E. 2018-12-13 doi:10.1101/493593 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ The integrated stress response mediates type I interferon driven necrosis in Mycobacterium tuberculosis granulomas ]]> https://biorxiv.org/content/10.1101/499467v1?rss=1 Bhattacharya, B. Xiao, S. Chatterjee, S. Urbanowski, M. Ordonez, A. Ihms, E. A. Agrahari, G. Lun, S. Berland, R. Pichugin, A. Gao, Y. Connor, J. Ivanov, A. Yan, B.-S. Kobzik, L. Jain, S. Bishai, W. Kramnik, I. 2018-12-19 doi:10.1101/499467 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ On the Periodic Gain of the Ribosome Flow Model ]]> https://biorxiv.org/content/10.1101/507988v1?rss=1 Sadeghi, M. Ali Al-Radhawi, M. Margaliot, M. Sontag, E. 2018-12-28 doi:10.1101/507988 Cold Spring Harbor Laboratory Press 2018-12-28 <![CDATA[ Rigid Foot Soles Improve Balance in Beam Walking ]]> https://biorxiv.org/content/10.1101/510990v1?rss=1 Huber, M. E. Chiovetto, E. Giese, M. Sternad, D. 2019-01-03 doi:10.1101/510990 Cold Spring Harbor Laboratory Press 2019-01-03 <![CDATA[ DO-MS: Data-Driven Optimization of Mass Spectrometry Methods ]]> https://biorxiv.org/content/10.1101/512152v1?rss=1 Huffman, G. Specht, H. Chen, A. T. Slavov, N. 2019-01-06 doi:10.1101/512152 Cold Spring Harbor Laboratory Press 2019-01-06 <![CDATA[ Dissecting the energetics of subunit rotation in the ribosome ]]> https://biorxiv.org/content/10.1101/514448v1?rss=1 Levi, M. Whitford, P. C. 2019-01-08 doi:10.1101/514448 Cold Spring Harbor Laboratory Press 2019-01-08 <![CDATA[ Transient Probability Distributions of Gene Regulatory Networks with Slow Promoter Kinetics ]]> https://biorxiv.org/content/10.1101/514547v1?rss=1 Ali Al-Radhawi, M. 2019-01-09 doi:10.1101/514547 Cold Spring Harbor Laboratory Press 2019-01-09 <![CDATA[ Shigella flexneri adherence factor expression in in vivo-like conditions ]]> https://biorxiv.org/content/10.1101/514679v1?rss=1 Chanin, R. B. Nickerson, K. P. Llanos-Chea, A. Sistrunk, J. R. Rasko, D. Vijaya Kumar, D. K. De La Parra, J. Auclair, J. Ding, J. Li, K. Dogiparthi, S. Kusber, B. Faherty, C. S. 2019-01-08 doi:10.1101/514679 Cold Spring Harbor Laboratory Press 2019-01-08 <![CDATA[ In Vivo Monitoring of Rare Circulating Tumor Cell and Cluster Dissemination in a Multiple Myeloma Xenograft Model ]]> https://biorxiv.org/content/10.1101/516641v1?rss=1 Patil, R. Tan, X. Bartosik, P. Detappe, A. Runnels, J. M. Ghobrial, I. M. Lin, C. P. Niedre, M. 2019-01-11 doi:10.1101/516641 Cold Spring Harbor Laboratory Press 2019-01-11 <![CDATA[ In vitro implementation of robust gene regulation in a synthetic biomolecular integral controller ]]> https://biorxiv.org/content/10.1101/525279v1?rss=1 Agrawal, D. K. Marshall, R. Noireaux, V. Sontag, E. D. 2019-01-20 doi:10.1101/525279 Cold Spring Harbor Laboratory Press 2019-01-20 <![CDATA[ Perfect adaptation of CD8+ T cell responses to constant antigen input over a wide range of affinity is overcome by costimulation ]]> https://biorxiv.org/content/10.1101/535385v1?rss=1 Trendel, N. C. Kruger, P. Nguyen, J. Gaglione, S. Dushek, O. 2019-01-30 doi:10.1101/535385 Cold Spring Harbor Laboratory Press 2019-01-30 <![CDATA[ Ordered Hexagonal Patterns via Notch-Delta Signaling ]]> https://biorxiv.org/content/10.1101/550657v1?rss=1 Kessler, D. A. Levine, H. Teomy, E. 2019-02-15 doi:10.1101/550657 Cold Spring Harbor Laboratory Press 2019-02-15 <![CDATA[ The high persister phenotype of Pseudomonas aeruginosa is associated with increased fitness and persistence in cystic fibrosis airways ]]> https://biorxiv.org/content/10.1101/561589v1?rss=1 Mojsoska, B. Cameron, D. R. Bartell, J. A. Haagensen, J. A. Sommer, L. M. Lewis, K. Molin, S. Johansen, H. K. 2019-02-27 doi:10.1101/561589 Cold Spring Harbor Laboratory Press 2019-02-27 <![CDATA[ Decreasing Serine Levels During Growth Transition Triggers Biofilm Formation in Bacillus subtilis ]]> https://biorxiv.org/content/10.1101/564526v1?rss=1 Greenwich, J. Reverdy, A. Gozzi, K. Di Cecco, G. Tashjian, T. F. Godoy-Carter, V. Chai, Y. 2019-03-01 doi:10.1101/564526 Cold Spring Harbor Laboratory Press 2019-03-01 <![CDATA[ High angular resolution diffusion MRI reveals conserved and deviant programs in the paths that guide human cortical circuitry ]]> https://biorxiv.org/content/10.1101/576967v1?rss=1 Charvet, C. J. Das, A. Song, J. W. Tindall-Burgess, D. J. Kabaria, P. Dai, G. Kane, T. Takahashi, E. 2019-03-16 doi:10.1101/576967 Cold Spring Harbor Laboratory Press 2019-03-16 <![CDATA[ Biologically inspired model of associative memory storage with noisy neurons and synapses ]]> https://biorxiv.org/content/10.1101/583922v1?rss=1 Zhang, C. Zhang, D. Stepanyants, A. 2019-03-21 doi:10.1101/583922 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Mitochondrial mutational spectrum provides an universal marker of cellular and organismal longevity ]]> https://biorxiv.org/content/10.1101/589168v1?rss=1 T substitutions, is typical only for the nuclear genome while it is extremely rare and age-independent in mtDNA. Thus it is still unclear if there is a mitochondria - specific mutational signature of the oxidative damage. Here, reconstructing mtDNA mutational spectra for human cancers originated from 21 tissues with various cell turnover rate, human oocytes fertilized at different ages, and 424 mammalian species with variable generation length which is a proxy for oocyte age, we observed that the frequency of AH>GH substitutions (H - heavy chain notation) is positively correlated with cellular and organismal longevity. Moreover, this mutational bias from AH to GH affects nucleotide content at the fourfold degenerative synonymous positions leading to a deficit of AH and excess of GH, which is especially pronounced in long-lived mammals. Taking into account additionally, that AH>GH is sensitive to time being single stranded during mtDNA asynchronous replication and A>G is associated with oxidative damage of single-stranded DNA in recent bacterial experiments we propose that AH>GH is a mutational signature of oxidative damage in mtDNA. ]]> Mikhaylova, A. G. Mikhailova, A. A. Ushakova, K. Tretyakov, E. Iurchenko, A. Zazhytska, M. Knorre, D. Zdobnov, E. Fleischmann, Z. Annis, S. Franco, M. Wasko, K. Kunz, W. Mazunin, I. Nikolaev, S. Reymond, A. Khrapko, K. Gunbin, K. Popadin, K. 2019-03-26 doi:10.1101/589168 Cold Spring Harbor Laboratory Press 2019-03-26 <![CDATA[ Ethanolamine regulates CqsR quorum-sensing signaling in Vibrio cholerae ]]> https://biorxiv.org/content/10.1101/589390v1?rss=1 Ng, W.-L. Watve, S. Barrasso, K. Jung, S. A. Davis, K. J. Hawver, L. A. Khataokar, A. Palaganas, R. G. Neiditch, M. B. Perez, L. J. 2019-03-26 doi:10.1101/589390 Cold Spring Harbor Laboratory Press 2019-03-26 <![CDATA[ Near-optimal combination of disparity across a log-polar scaled visual field ]]> https://biorxiv.org/content/10.1101/589937v1?rss=1 Maiello, G. Chessa, M. Bex, P. J. Solari, F. 2019-03-26 doi:10.1101/589937 Cold Spring Harbor Laboratory Press 2019-03-26 <![CDATA[ A Mechanism for Epithelial-Mesenchymal Heterogeneity in a Population of Cancer Cells ]]> https://biorxiv.org/content/10.1101/592691v1?rss=1 Tripathi, S. Levine, H. Jolly, M. K. 2019-03-28 doi:10.1101/592691 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ Oligotyping and Genome-Resolved Metagenomics Reveal Distinct Candidatus Accumulibacter Communities in Full-Scale Side-Stream versus Conventional Enhanced Biological Phosphorus Removal (EBPR) Configurations ]]> https://biorxiv.org/content/10.1101/596692v1?rss=1 Srinivasan, V. N. Li, G. Wang, D. Tooker, N. B. Dai, Z. Onnis-Hayden, A. Pinto, A. J. Gu, A. Z. 2019-04-03 doi:10.1101/596692 Cold Spring Harbor Laboratory Press 2019-04-03 <![CDATA[ Prospects for transcranial temporal interference stimulation in humans: a computational study ]]> https://biorxiv.org/content/10.1101/602102v1?rss=1 Rampersad, S. Roig-Solvas, B. Yarossi, M. Kulkarni, P. P. Santarnecchi, E. Dorval, A. D. Brooks, D. H. 2019-04-08 doi:10.1101/602102 Cold Spring Harbor Laboratory Press 2019-04-08 <![CDATA[ Deleterious in late life mitochondrial alleles and aging: secrets of Japanese centenarians ]]> https://biorxiv.org/content/10.1101/603282v1?rss=1 Mikhailova, A. Shamansky, V. Bazykin, G. A. Mazunin, I. Gunbin, K. Kunz, W. Reymond, A. Tanaka, M. Khrapko, K. Popadin, K. 2019-04-15 doi:10.1101/603282 Cold Spring Harbor Laboratory Press 2019-04-15 <![CDATA[ A reference map of the human protein interactome ]]> https://biorxiv.org/content/10.1101/605451v1?rss=1 Luck, K. Kim, D. K. Lambourne, L. Spirohn, K. Begg, B. E. Bian, W. Brignall, R. Cafarelli, T. Campos-Laborie, F. J. Charloteaux, B. Choi, D. Cote, A. G. Daley, M. Deimling, S. Desbuleux, A. Dricot, A. Gebbia, M. Hardy, M. F. Kishore, N. Knapp, J. J. Kovacs, I. A. Lemmens, I. Mee, M. W. Mellor, J. C. Pollis, C. Pons, C. Richardson, A. D. Schlabach, S. Teeking, B. Yadav, A. Babor, M. Balcha, D. Basha, O. Chin, S.-F. Choi, S. G. Colabella, C. Coppin, G. D'Amata, C. De Ridder, D. De Rouck, S. Duran-Frigola, M. Ennajdaoui, H. Goebels, F. Gopal, A. Haddad 2019-04-10 doi:10.1101/605451 Cold Spring Harbor Laboratory Press 2019-04-10 <![CDATA[ Google searches accurately forecast RSV hospitalizations ]]> https://biorxiv.org/content/10.1101/607119v1?rss=1 0.95) and low phase differences were seen between counts of hospitalizations and search volume in WA, MD, FL, and CT. Searching for RSV began in FL and radiated outward and three distinct transmission clusters were identified: the south and northeast, the northwest and Appalachia, and the center of the country. Calculated initiation dates for prophylaxis closely followed those calculated using traditional data sources (correlation = 0.84).nnConclusionsThis work validates searches as a proxy for RSV hospitalizations. Search query surveillance of RSV is a rapid and no-cost addition to traditional RSV hospitalization surveillance and may be useful for medical and public health decision-making. ]]> Althouse, B. M. Weinberger, D. M. Scarpino, S. V. Pitzer, V. Ayers, J. W. Wenger, E. Fung, I. C.-H. Dredze, M. Hu, H. 2019-04-26 doi:10.1101/607119 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Pericytes enable effective angiogenesis in the presence of pro inflammatory signals ]]> https://biorxiv.org/content/10.1101/608059v1?rss=1 Kang, T.-Y. Bocci, F. Jolly, M. K. Levine, H. Onuchic, J. N. Levchenko, A. 2019-04-13 doi:10.1101/608059 Cold Spring Harbor Laboratory Press 2019-04-13 <![CDATA[ Functional Territories of Human Dentate Nucleus ]]> https://biorxiv.org/content/10.1101/608620v1?rss=1 Guell, X. D'Mello, A. M. Hubbard, N. A. Romeo, R. R. Gabrieli, J. D. Whitfield-Gabrieli, S. Schmahmann, J. D. Arnold Anteraper, S. 2019-04-13 doi:10.1101/608620 Cold Spring Harbor Laboratory Press 2019-04-13 <![CDATA[ Ifit1 regulates norovirus infection and enhances the interferon response in murine macrophage-like cells. ]]> https://biorxiv.org/content/10.1101/611236v1?rss=1 Mears, H. V. Emmott, E. Chaudhry, Y. Hosmillo, M. Goodfellow, I. G. Sweeney, T. R. 2019-04-17 doi:10.1101/611236 Cold Spring Harbor Laboratory Press 2019-04-17 <![CDATA[ The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens ]]> https://biorxiv.org/content/10.1101/653105v1?rss=1 Zhou, N. Jiang, Y. Bergquist, T. R. Lee, A. J. Kacsoh, B. Z. Crocker, A. W. Lewis, K. A. Georghiou, G. Nguyen, H. N. Hamid, M. N. Davis, L. The Critical Assessment of Function Annotation, Rost, B. Brenner, S. E. Orengo, C. A. Jeffery, C. J. Bosco, G. D. Hogan, D. A. Martin, M. J. O'Donovan, C. Mooney, S. D. Greene, C. S. Radivojac, P. Friedberg, I. 2019-05-29 doi:10.1101/653105 Cold Spring Harbor Laboratory Press 2019-05-29 <![CDATA[ Microbial Nitrogen Metabolism in Chloraminated Drinking Water Reservoirs ]]> https://biorxiv.org/content/10.1101/655316v1?rss=1 Potgieter, S. C. Dai, Z. Venter, S. N. Sigudu, M. Pinto, A. J. 2019-06-13 doi:10.1101/655316 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ Assemblies of F-actin and myosin-II minifilaments: steric hindrance and stratification at the membrane cortex ]]> https://biorxiv.org/content/10.1101/656082v1?rss=1 Das, A. Bhat, A. Sknepnek, R. Koester, D. V. Mayor, S. Rao, M. 2019-05-31 doi:10.1101/656082 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Quasi-Mendelian Paternal Inheritance of mitochondrial DNA: A notorious artifact, or anticipated mtDNA behavior? ]]> https://biorxiv.org/content/10.1101/660670v1?rss=1 Annis, S. Fleischmann, Z. Khrapko, M. Franco, M. Woods, D. Kunz, W. Ellis, P. J. Khrapko, K. 2019-06-17 doi:10.1101/660670 Cold Spring Harbor Laboratory Press 2019-06-17 <![CDATA[ Visual dynamics cues in learning complex physical interactions ]]> https://biorxiv.org/content/10.1101/662353v1?rss=1 Hasson, C. J. Jalili, P. F. 2019-06-11 doi:10.1101/662353 Cold Spring Harbor Laboratory Press 2019-06-11 <![CDATA[ The unjamming transition is distinct from the epithelial-to-mesenchymal transition. ]]> https://biorxiv.org/content/10.1101/665018v1?rss=1 Mitchel, J. A. Das, A. O'Sullivan, M. J. Stancil, I. T. DeCamp, S. J. Koehler, S. Butler, J. P. Fredberg, J. J. Nieto, M. A. Bi, D. Park, J.-A. 2019-06-10 doi:10.1101/665018 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ High-throughput single-cell proteomics quantifies the emergence of macrophage heterogeneity ]]> https://biorxiv.org/content/10.1101/665307v1?rss=1 View larger version (19K): org.highwire.dtl.DTLVardef@18ead97org.highwire.dtl.DTLVardef@26b51aorg.highwire.dtl.DTLVardef@13bd6a8org.highwire.dtl.DTLVardef@189cf00_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Specht, H. Emmott, E. Koller, T. Slavov, N. 2019-06-09 doi:10.1101/665307 Cold Spring Harbor Laboratory Press 2019-06-09 <![CDATA[ Disinfectant residuals in drinking water systems select for mycobacterial populations with intrinsic antimicrobial resistance. ]]> https://biorxiv.org/content/10.1101/675561v1?rss=1 Sevillano, M. C. Dai, Z. Calus, S. T. Bautista de los Santos, Q. M. Eren, A. M. Ijaz, U. Z. van der Wielen, P. W. J. J. Pinto, A. 2019-06-20 doi:10.1101/675561 Cold Spring Harbor Laboratory Press 2019-06-20 <![CDATA[ NeuroPAL: A Neuronal Polychromatic Atlas of Landmarks for Whole-Brain Imaging in C. elegans ]]> https://biorxiv.org/content/10.1101/676312v1?rss=1 Yemini, E. Lin, A. Nejatbakhsh, A. Varol, E. Sun, R. Mena, G. E. Samuel, A. D. Paninski, L. Venkatachalam, V. Hobert, O. 2019-06-20 doi:10.1101/676312 Cold Spring Harbor Laboratory Press 2019-06-20 <![CDATA[ Reproducible microbial community dynamics of two drinking water systems treating similar source waters. ]]> https://biorxiv.org/content/10.1101/678920v1?rss=1 Potgieter, S. C. Pinto, A. J. Havenga, M. Sigudu, M. Venter, S. N. 2019-06-21 doi:10.1101/678920 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Sustained Co-evolution in a Stochastic Model of the Cancer-Immune Interaction ]]> https://biorxiv.org/content/10.1101/679746v1?rss=1 George, J. T. Levine, H. 2019-06-23 doi:10.1101/679746 Cold Spring Harbor Laboratory Press 2019-06-23 <![CDATA[ High-Resolution Tomographic Analysis of in vitro 3D Glioblastoma Tumor Model under Long-Term Drug Treatment ]]> https://biorxiv.org/content/10.1101/684019v1?rss=1 Ozturk, M. S. Lee, V. K. Zou, H. Friedel, R. H. Dai, G. Intes, X. 2019-07-11 doi:10.1101/684019 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ Channeling macrophage polarization by using a selective translation inhibitor ]]> https://biorxiv.org/content/10.1101/691808v1?rss=1 Chatterjee, S. Waligurski, E. Bhattacharya, B. Yabaji, S. M. Vallavoju, N. Roy, S. Brown, L. E. Beeler, A. B. Ivanov, A. R. Kobzik, L. Porco, J. A. Kramnik, I. 2019-07-03 doi:10.1101/691808 Cold Spring Harbor Laboratory Press 2019-07-03 <![CDATA[ Mathematical models of protease-based enzymatic biosensors ]]> https://biorxiv.org/content/10.1101/695320v1?rss=1 Agrawal, D. K. Khare, S. Sontag, E. D. 2019-07-08 doi:10.1101/695320 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ Long solids retention times and attached growth phase favor prevalence of comammox bacteria in nitrogen removal systems. ]]> https://biorxiv.org/content/10.1101/696351v1?rss=1 10 days) and/or in the attached growth phase. Using a newly designed qPCR assay targeting the amoB gene of clade A comammox bacteria in combination with quantitation of other canonical nitrifiers, we show that long solids retention time is the key process parameter associated with the prevalence and abundance of comammox bacteria. The increase in comammox bacterial abundance was not associated with concomitant decrease in the abundance of canonical nitrifiers; however, systems with comammox bacteria showed significantly better and temporally stable ammonia removal compared to systems where they were not detected. Finally, in contrast to recent studies, we do not find any significant association of comammox bacterial prevalence and abundance with dissolved oxygen concentrations in this study.nnHighlightsO_LIClade A comammox bacteria were detected in wastewater nitrogen removal systems.nC_LIO_LINew qPCR assay targeting the amoB gene of clade A comammox bacteria was developed.nC_LIO_LIComammox bacteria are prevalent in mainstream conventional and simultaneous nitrification-denitrification systems with long solids retention times (>10 days).nC_LIO_LIComammox bacteria were not detected in sidestream partial nitrification-anammox systems included in this study.nC_LInnnnO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/696351v2_ufig1.gif" ALT="Figure 1">nView larger version (28K):norg.highwire.dtl.DTLVardef@3228c9org.highwire.dtl.DTLVardef@113dfb8org.highwire.dtl.DTLVardef@1c4adaforg.highwire.dtl.DTLVardef@166f997_HPS_FORMAT_FIGEXP M_FIG GRAPHICAL ABSTRACTnnC_FIG ]]> Cotto, I. Dai, Z. Huo, L. Anderson, C. L. Vilardi, K. J. Ijaz, U. Z. Khunjar, W. Wilson, C. De Clippeleir, H. Gilmore, K. Bailey, E. Pinto, A. 2019-07-09 doi:10.1101/696351 Cold Spring Harbor Laboratory Press 2019-07-09 <![CDATA[ A computational framework for a Lyapunov-enabled analysis of biochemical reaction networks ]]> https://biorxiv.org/content/10.1101/696716v1?rss=1 Ali Al-Radhawi, M. Angeli, D. Sontag, E. 2019-07-09 doi:10.1101/696716 Cold Spring Harbor Laboratory Press 2019-07-09 <![CDATA[ Too much, too young? Altered corticolimbic axonal innervation and resting state functional connectivity suggests sex-dependent outcomes in a rat model of early life adversity ]]> https://biorxiv.org/content/10.1101/700666v1?rss=1 Honeycutt, J. A. Demaestri, C. Peterzell, S. Silveri, M. M. Cai, X. Kulkarni, P. Cunningham, M. G. Ferris, C. F. Brenhouse, H. C. 2019-07-14 doi:10.1101/700666 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability ]]> https://biorxiv.org/content/10.1101/706705v1?rss=1 Wang, R. J. Thomas, G. W. C. Raveendran, M. Harris, A. R. Doddapaneni, H. Muzny, D. M. Capitanio, J. P. Radivojac, P. Rogers, J. Hahn, M. W. 2019-07-18 doi:10.1101/706705 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ Genetic and molecular mechanism for distinct clinical phenotypes conveyed by allelic truncating mutations implicated in FBN1 ]]> https://biorxiv.org/content/10.1101/726646v1?rss=1 Wu, N. Lin, M. Liu, Z. Liu, G. Zhao, S. Li, C. Chen, W. Akdemir, Z. C. Lin, J. Song, X. Wang, S. Xu, Q. Zhao, Y. Wang, L. Zhang, Y. Yan, Z. Liu, S. Liu, J. Chen, Y. Yang, X. Sun, T. Yang, X.-Z. Niu, Y. Li, X. You, W. Qiu, B. Ding, C. Liu, P. Zhang, S. Fonseca, C. Posey, J. E. Qiu, G. Lupski, J. R. Wu, Z. Zhang, J. 2019-08-08 doi:10.1101/726646 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ Inferring reaction network structure from single-cell, multiplex data, using toric systems theory ]]> https://biorxiv.org/content/10.1101/731018v1?rss=1 Wang, S. Lin, J.-r. Sontag, E. D. Sorger, P. K. 2019-08-09 doi:10.1101/731018 Cold Spring Harbor Laboratory Press 2019-08-09 <![CDATA[ Improvising at Rest: Differentiating Jazz and Classical Music Training with Resting State Functional Connectivity ]]> https://biorxiv.org/content/10.1101/732073v1?rss=1 Belden, A. G. Zeng, H. Przysinda, E. Anteraper, S. A. Whitfield-Gabrieli, S. Loui, P. 2019-08-11 doi:10.1101/732073 Cold Spring Harbor Laboratory Press 2019-08-11 <![CDATA[ Anticipating critical transitions in epithelial-hybrid-mesenchymal cell-fate determination ]]> https://biorxiv.org/content/10.1101/733006v1?rss=1 Sarkar, S. Sinha, S. K. Levine, H. Jolly, M. K. Dutta, P. S. 2019-08-13 doi:10.1101/733006 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Intercellular communication controls agonist-induced calcium oscillations independently of gap junctions in smooth muscle cells. ]]> https://biorxiv.org/content/10.1101/734269v1?rss=1 Stasiak, S. E. Jamieson, R. R. Bouffard, J. Cram, E. J. Parameswaran, H. 2019-08-15 doi:10.1101/734269 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ SGID: a comprehensive and interactive database of the silkworm ]]> https://biorxiv.org/content/10.1101/739961v1?rss=1 Zhu, Z. Guan, Z. Liu, G. Wang, Y. Zhang, Z. 2019-08-26 doi:10.1101/739961 Cold Spring Harbor Laboratory Press 2019-08-26 <![CDATA[ An MRI-Derived Neuroanatomical Atlas of the Fischer 344 Rat Brain for Automated Anatomical Segmentation ]]> https://biorxiv.org/content/10.1101/743583v1?rss=1 Goerzen, D. Fowler, C. Devenyi, G. A. Germann, J. Madularu, D. Chakravarty, M. Near, J. 2019-08-22 doi:10.1101/743583 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Machine learning guided association of adverse drug reactions with in vitro target-based pharmacology ]]> https://biorxiv.org/content/10.1101/750950v1?rss=1 Arat, S. Ietswaart, R. Chen, A. X. Farahmand, S. Kim, B. Armstrong, D. Urban, L. 2019-08-30 doi:10.1101/750950 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ A Neural Network Based Algorithm for Dynamically Adjusting Activity Targets to Sustain Exercise Engagement Among People Using Activity Trackers ]]> https://biorxiv.org/content/10.1101/775908v1?rss=1 Mohammadi, R. Centi, A. J. Atif, M. Agboola, S. Jethwani, K. Kvedar, J. C. Kamarthi, S. 2019-09-19 doi:10.1101/775908 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ A highly prevalent and pervasive densovirus discovered among sea stars from the North American Atlantic Coast ]]> https://biorxiv.org/content/10.1101/781609v1?rss=1 Jackson, E. W. Pepe-Ranney, C. Johnson, M. R. Distel, D. L. Hewson, I. 2019-09-25 doi:10.1101/781609 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Intercellular adhesion stiffness moderates cell decoupling on stiff substrates ]]> https://biorxiv.org/content/10.1101/802520v1?rss=1 Vargas, D. A. Heck, T. Smeets, B. Ramon, H. Parameswaran, H. Van Oosterwyck, H. 2019-10-13 doi:10.1101/802520 Cold Spring Harbor Laboratory Press 2019-10-13 <![CDATA[ Niche-inspired synthetic matrices for epithelial organoid culture ]]> https://biorxiv.org/content/10.1101/806919v1?rss=1 Hernandez-Gordillo, V. Kassis, T. Lampejo, A. Choi, G. Gamboa, M. E. Gnecco, J. S. Breault, D. Carrier, R. Griffith, L. G. 2019-10-16 doi:10.1101/806919 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ RecA influences biofilm development in the opportunistic pathogen Acinetobacter baumannii ]]> https://biorxiv.org/content/10.1101/809392v1?rss=1 Ching, C. Downs, M. Muller, P. Isley, B. Fowle, W. Godoy, V. G. 2019-10-17 doi:10.1101/809392 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Drug-tolerant idling melanoma cells exhibit theory-predicted metabolic low-low phenotype ]]> https://biorxiv.org/content/10.1101/809889v1?rss=1 Jia, D. Paudel, B. Hayford, C. E. Hardeman, K. Levine, H. Onuchic, J. N. Quaranta, V. 2019-10-17 doi:10.1101/809889 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Short-term circulating tumor cell dynamics in mouse xenograft models and implications for liquid biopsy. ]]> https://biorxiv.org/content/10.1101/814368v1?rss=1 Williams, A. Fitzgerald, J. Niedre, M. 2019-10-22 doi:10.1101/814368 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ GPU-accelerated mesh-based Monte Carlo photon transport simulations ]]> https://biorxiv.org/content/10.1101/815977v1?rss=1 Fang, Q. Yan, S. 2019-10-23 doi:10.1101/815977 Cold Spring Harbor Laboratory Press 2019-10-23 <![CDATA[ Secondary metabolic symbiosis in shipworms (Teredinidae) ]]> https://biorxiv.org/content/10.1101/826933v1?rss=1 Altamia, M. A. Lin, Z. Trindade-Silva, A. E. Uy, I. D. Shipway, J. R. Veras Wilke, D. Concepcion, G. P. Distel, D. L. Schmidt, E. W. Haygood, M. G. 2019-10-31 doi:10.1101/826933 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ Disinfection exhibits systematic impacts on the drinking water microbiome. ]]> https://biorxiv.org/content/10.1101/828970v1?rss=1 Dai, Z. Sevillano, M. C. Calus, S. T. Bautista-de los Santos, Q. M. Eren, A. M. van der Wielen, P. W. J. J. Ijaz, U. Z. Pinto, A. J. 2019-11-02 doi:10.1101/828970 Cold Spring Harbor Laboratory Press 2019-11-02 <![CDATA[ Ytterbium-doped fibre femtosecond laser offers robust design with deep and precise microsurgery ]]> https://biorxiv.org/content/10.1101/829242v1?rss=1 Harreguy, M. B. Marfil, V. Gabel, C. V. Chung, S. H. Haspel, G. 2019-11-04 doi:10.1101/829242 Cold Spring Harbor Laboratory Press 2019-11-04 <![CDATA[ Caenorhabditis elegans PIEZO Channel Coordinates Multiple Reproductive Tissues to Govern Ovulation ]]> https://biorxiv.org/content/10.1101/847392v1?rss=1 Bai, X. Bouffard, J. Lord, A. Brugman, K. Sternberg, P. W. Cram, E. J. Golden, A. 2019-11-20 doi:10.1101/847392 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Redox signaling modulates Rho activity and tissue contractility in the C. elegans spermatheca ]]> https://biorxiv.org/content/10.1101/849463v1?rss=1 Kelley, C. A. De Henau, S. Bell, L. Dansen, T. B. Cram, E. J. 2019-11-20 doi:10.1101/849463 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Compact attractors of an antithetic integral feedback system have a simple structure ]]> https://biorxiv.org/content/10.1101/868000v1?rss=1 Margaliot, M. Sontag, E. D. 2019-12-08 doi:10.1101/868000 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ In situ SAXS of protein deposits in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/868273v1?rss=1 150 [A]) aggregates appear to represent A{beta} fibrils that have coalesced side-to-side with one another to create fibrillar bundles or macrofibrillar aggregates. Tau fibrils exhibit an Rxc of ~55 [A] with little sign of coalescence into larger structure. The in situ mapping of these structures revealed subtle variation in A{beta} structure across different brain areas and different cases. ]]> Makowski, L. Roig Solvas, B. Hyman, B. T. 2019-12-06 doi:10.1101/868273 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ Structure-based analysis of CysZ-mediated cellular uptake of sulfate ]]> https://biorxiv.org/content/10.1101/131318v1?rss=1 Liu, Q. Clarke, O. B. Leal Pinto, E. Kloss, B. Tabuso, S. Love, J. Punta, M. Banerjee, S. Rajashankar, K. R. Rost, B. Logothetis, D. Quick, M. Hendrickson, W. A. Mancia, F. Assur Sanghai, Z. 2017-04-26 doi:10.1101/131318 Cold Spring Harbor Laboratory Press 2017-04-26 <![CDATA[ Insights into rumen microbial biosynthetic gene cluster diversity through genome-resolved metagenomics ]]> https://biorxiv.org/content/10.1101/2020.05.19.105130v1?rss=1 Anderson, C. L. Fernando, S. C. 2020-05-20 doi:10.1101/2020.05.19.105130 Cold Spring Harbor Laboratory Press 2020-05-20 <![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[ A Mechanistic Modeling Framework Reveals the Key Principles Underlying Tumor Metabolism ]]> https://biorxiv.org/content/10.1101/2021.01.04.424598v1?rss=1 Tripathi, S. Park, J. H. Pudakalakatti, S. Bhattacharya, P. K. Kaipparettu, B. A. Levine, H. 2021-01-05 doi:10.1101/2021.01.04.424598 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ The secreted tyrosine kinase VLK is essential for normal platelet activation and thrombus formation ]]> https://biorxiv.org/content/10.1101/2021.01.24.427281v1?rss=1 Revollo, L. Merrill-Skoloff, G. De Ceunynck, K. Dilks, J. Bordoli, M. Peters, C. Noetzli, L. Ionescu, A. Rosen, V. Italiano, J. Whitman, M. Flaumenhaft, R. 2021-01-26 doi:10.1101/2021.01.24.427281 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ A theoretical approach to coupling the epithelial-mesenchymal transition (EMT) to extracellular matrix (ECM) stiffness via LOXL2 ]]> https://biorxiv.org/content/10.1101/2021.02.04.429859v1?rss=1 Deng, Y. Chakraborty, P. Jolly, M. K. Levine, H. 2021-02-05 doi:10.1101/2021.02.04.429859 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Mechanical Interplay Between Transcription Elongation and DNA Supercoiling ]]> https://biorxiv.org/content/10.1101/2021.03.04.433986v1?rss=1 Tripathi, S. Brahmachari, S. Onuchic, J. N. Levine, H. 2021-03-04 doi:10.1101/2021.03.04.433986 Cold Spring Harbor Laboratory Press 2021-03-04 <![CDATA[ Vascular and perivascular cell profiling reveals the molecular and cellular bases of blood-brain barrier heterogeneity ]]> https://biorxiv.org/content/10.1101/2021.04.26.441465v1?rss=1 Pfau, S. J. Langen, U. H. Fisher, T. M. Prakash, I. Nagpurwala, F. Lozoya, R. A. Lee, W.-C. A. Wu, Z. Gu, C. 2021-04-27 doi:10.1101/2021.04.26.441465 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ High-Stability Polyimide-based Flexible Electrodes with IrOx to Interface the Mouse Vagus Nerve ]]> https://biorxiv.org/content/10.1101/2021.05.10.442867v1?rss=1 7x. PI encapsulation had stable impedance spectra for at least 336 days for interdigitated electrodes. Stim-Stab testing using an aggressive paradigm and rigorous optical and electrical characterization, revealed that half of electrodes showed less than minor damage at the endpoints. A trend of decreasing respiratory rate with stimulation current reached statistical significance at 500 {micro}A, demonstrating efficacy for Flex electrodes. SignificanceFlex electrodes offer demonstrated efficacy, low impedance (443 {+/-} 32 {Omega} at 103 Hz), excellent bench test stability, and cost-effective fabrication. Acute devices are easy to integrate, and mechanically robust chronic devices will be investigated in vivo in future studies. These characteristics make the electrodes well-positioned to advance bioelectronics medicine research by 1) enabling reliable studies with statistically relevant populations of acute mouse models, and 2) offering the potential for a technology that can be used in chronic studies, which scales to very small nerves. ]]> Sun, T. Falcone, J. D. Crosfield, C. Lopez, M. F. Peragine, J. Modi, R. Sharma, R. Baker, B. Anderson, G. Savani, S. Li, C. Chang, E. H. Sohal, H. Rieth, L. 2021-05-11 doi:10.1101/2021.05.10.442867 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ Protein sensors of bacterial kinase activity reveal antibiotic-dependent kinase activation in single cells ]]> https://biorxiv.org/content/10.1101/2021.05.27.446034v1?rss=1 Zheng, C. R. Singh, A. Libby, A. Silver, P. A. Libby, E. A. 2021-05-27 doi:10.1101/2021.05.27.446034 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Characterization of vaginal microbial enzymes identifies amylopullulanases that support growth of Lactobacillus crispatus on glycogen ]]> https://biorxiv.org/content/10.1101/2021.07.19.452977v1?rss=1 Woolston, B. M. Jenkins, D. J. Hood-Pishchany, M. I. Rakoff-Nahoum, S. Balskus, E. P. 2021-07-19 doi:10.1101/2021.07.19.452977 Cold Spring Harbor Laboratory Press 2021-07-19 <![CDATA[ Cell wall synthesis and remodeling dynamics determine bacterial division site architecture and cell shape ]]> https://biorxiv.org/content/10.1101/2021.10.02.462887v1?rss=1 Navarro, P. P. Vettiger, A. Ananda, V. Y. Montero Llopis, P. Allolio, C. Bernhardt, T. G. Chao, L. H. 2021-10-03 doi:10.1101/2021.10.02.462887 Cold Spring Harbor Laboratory Press 2021-10-03 <![CDATA[ Ingestible capsule for detecting labile inflammatory biomarkers in situ ]]> https://biorxiv.org/content/10.1101/2022.02.16.480562v1?rss=1 Inda, M. E. Jimenez, M. Liu, Q. Phan, N. Ahn, J. Steiger, C. Wentworth, A. Riaz, A. Zirtiloglu, T. Wong, K. Ishida, K. Fabian, N. Jenkins, J. Kuosmanen, J. Madani, W. McNally, R. Lai, Y. Mimee, M. Nadeau, P. Chandrakasan, A. Hayward, A. Traverso, G. Yazicigil, R. T. Lu, T. K. 2022-02-16 doi:10.1101/2022.02.16.480562 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ Discovery of Potent Pyrazoline-Based Covalent SARS-CoV-2 Main Protease Inhibitors ]]> https://biorxiv.org/content/10.1101/2022.03.05.483025v1?rss=1 Moon, P. Boike, L. Dovala, D. Henning, N. J. Knapp, M. Spradlin, J. N. Ward, C. C. Wolleb, H. Zammit, C. M. Fuller, D. Blake, G. Murphy, J. P. Wang, F. Lu, Y. Moquin, S. A. Tandeske, L. Hesse, M. J. McKenna, J. M. Tallarico, J. Schirle, M. Toste, F. D. Nomura, D. K. 2022-03-07 doi:10.1101/2022.03.05.483025 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Mind the gap: Nodes of Ranvier are remodeled by chronic psychosocial stress and neuronal activity ]]> https://biorxiv.org/content/10.1101/2022.04.05.487090v1?rss=1 Koskinen, M.-K. Laine, M. A. Abdollahzadeh, A. Gigliotta, A. Mazzini, G. Journee, S. H. Alenius, V. Trontti, K. Tohka, J. Hyytia, P. Sierra, A. Hovatta, I. 2022-04-07 doi:10.1101/2022.04.05.487090 Cold Spring Harbor Laboratory Press 2022-04-07 <![CDATA[ Huntingtin turnover: Modulation of huntingtin degradation by cAMP-dependent protein kinase A (PKA) phosphorylation of C-HEAT domain Ser2550 ]]> https://biorxiv.org/content/10.1101/2022.05.04.490694v1?rss=1 Lee, Y. Kim, H. Barker, D. Vijayvargia, R. Atwal, R. S. Specht, H. Keshishian, H. Carr, S. A. Lee, R. Kwak, S. Hyun, K.-g. Loupe, J. MacDonald, M. E. Song, J.-J. Seong, I. 2022-05-04 doi:10.1101/2022.05.04.490694 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Broad Recognition of Mamu-Bw4 and -A-related MHC class I Ligands by Rhesus Macaque Killer-Cell Immunoglobulin-Like Receptors ]]> https://biorxiv.org/content/10.1101/2022.05.25.493479v1?rss=1 Anderson, J. L. Sandstrom, K. Nicholas, R. E. Smith, W. R. Wetzel, M. Klenchin, V. A. Evans, D. T. 2022-05-25 doi:10.1101/2022.05.25.493479 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Prefrontal cortex melanocortin 4 receptors (MC4R) mediate food intake behavior in mice ]]> https://biorxiv.org/content/10.1101/2022.06.01.494383v1?rss=1 Ross, R. A. Kim, A. Das, P. Li, Y. Choi, Y. K. Thompson, A. T. Douglas, E. Subramanian, S. Ramos, K. Callahan, K. Bolshakov, V. Y. Ressler, K. J. 2022-06-02 doi:10.1101/2022.06.01.494383 Cold Spring Harbor Laboratory Press 2022-06-02 <![CDATA[ Decoding the coupled decision-making of the epithelial-mesenchymal transition and metabolic reprogramming in cancer ]]> https://biorxiv.org/content/10.1101/2022.08.02.502548v1?rss=1 Galbraith, M. L. Levine, H. L. Onuchic, J. Jia, D. 2022-08-05 doi:10.1101/2022.08.02.502548 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Proteomic Mapping of Intercellular Synaptic Environments via Flavin-Dependent Photoredox Catalysis ]]> https://biorxiv.org/content/10.1101/2022.09.29.510150v1?rss=1 Bechtel, T. J. Bertoch, J. M. Olow, A. K. Duich, M. White, C. H. Reyes-Robles, T. Fadeyi, O. O. Oslund, R. C. 2022-09-30 doi:10.1101/2022.09.29.510150 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ An international scholastic network to generate LexA enhancer-trap lines for Drosophila ]]> https://biorxiv.org/content/10.1101/2022.11.24.517565v1?rss=1 Kim, E. S. Rajan, A. Chang, K. Gulick, C. English, E. Nakada, S. Beard, C. O'Connor, S. Mastroianni, S. Downey, E. Feigenbaum, M. Tolentino, C. Pace, A. Khan, M. Moon, S. DiPrima, J. Syed, A. Lin, F. Govindarajan, S. Abukhadra, Y. Bacon, I. Beckerle, J. Bloomfield, O. Cho, S. Esi Donkor, N. Garberg, L. Harrington, A. Hoang, M. Lawani, N. Noori, A. Park, E. Parsons, E. Oravitan, P. Chen, M. Molina, C. Richmond, C. Reddi, A. Huang, J. Shugrue, C. Coviello, R. Unver, S. Indelicarto, M. Islamovic, E. McIlroy, R. Yang, A. Hamad, M. Griffin, E. Ahmed, Z 2022-11-25 doi:10.1101/2022.11.24.517565 Cold Spring Harbor Laboratory Press 2022-11-25 <![CDATA[ DRG afferents that mediate physiologic and pathologic mechanosensation from the distal colon ]]> https://biorxiv.org/content/10.1101/2022.11.27.518103v1?rss=1 Wolfson, R. L. Abdelaziz, A. Rankin, G. Kushner, S. Qi, L. Mazor, O. Choi, S. Sharma, N. Ginty, D. D. 2022-11-28 doi:10.1101/2022.11.27.518103 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ Social Isolation Causes Cortical and Trabecular Bone Loss in Adult Male, but not Female, C57BL/6J Mice ]]> https://biorxiv.org/content/10.1101/2023.01.27.525939v1?rss=1 Mountain, R. V. Langlais, A. L. Hu, D. Baron, R. Lary, C. W. Motyl, K. J. 2023-01-28 doi:10.1101/2023.01.27.525939 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ Hypoxia-inducible factor 2 is a key determinant of manganese excess and polycythemia in SLC30A10 deficiency ]]> https://biorxiv.org/content/10.1101/2023.02.20.529270v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@c25fc8org.highwire.dtl.DTLVardef@11e70feorg.highwire.dtl.DTLVardef@18c5518org.highwire.dtl.DTLVardef@26b61f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Prajapati, M. Zhang, J. Z. Mercadante, C. J. Kowalski, H. L. Delaney, B. Anderson, J. A. Guo, S. Aghajan, M. Bartnikas, T. B. 2023-02-21 doi:10.1101/2023.02.20.529270 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Identification of a pharmaceutical biostasis inducer that slows metabolism in multiple vertebrates that do not hibernate ]]> https://biorxiv.org/content/10.1101/2023.02.27.530270v1?rss=1 Sperry, M. M. Charrez, B. Fotowat, H. Gardner, E. Pilobello, K. Izadifar, Z. Lin, T. Kuelker, A. Kaki, S. Lewandowski, M. Lightbown, S. Martinez, R. Marquez, S. Sesay, A. Shcherbina, K. Takeda, T. Andrijauskaite, K. Cisneros, E. Lopez, R. Cano, I. Maxwell, Z. Veraza, R. Bunegin, L. Percival, T. J. Yracheta, J. Pena, J. J. Wood, D. M. Homas, Z. T. Hinshaw, C. J. Cox-Hinshaw, J. Parry, O. G. Sleeter, J. J. Weitzel, E. Levin, M. Super, M. Novak, R. Ingber, D. E. 2023-02-28 doi:10.1101/2023.02.27.530270 Cold Spring Harbor Laboratory Press 2023-02-28 <![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[ FRESH™ 3D bioprinted cardiac tissue, a bioengineered platform for in-vitro toxicology and pharmacology ]]> https://biorxiv.org/content/10.1101/2023.03.13.528447v1?rss=1 600 million cells/mL, and within 14 days demonstrated reproducible calcium transients and fast conduction velocity of [~]25 cm/s. Interrogation of these cardiac tissues with the {beta}-adrenergic receptor agonist isoproterenol showed native-like positive chronotropic and inotropic responses, a combination of responses that is not typically observed in 2D monolayer models or standard 3D engineered heart tissue approaches. These results confirm that FRESH 3D bioprinted cardiac tissues represents a novel in vitro platform that enables early in vitro pharmacology and toxicology screening. ]]> Finkel, S. Sweet, S. Locke, T. Smith, S. Wang, Z. Sandini, C. Imredy, J. He, Y. Durante, M. Lagrutta, A. Feinberg, A. Lee, A. 2023-03-15 doi:10.1101/2023.03.13.528447 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Perirhinal Cortex Learns A Predictive Map of The Task Environment ]]> https://biorxiv.org/content/10.1101/2023.03.17.532214v1?rss=1 Lee, D. G. McLachlan, C. A. Nogueira, R. Kwon, O. Carey, A. House, G. Lagani, G. D. LaMay, D. Fusi, S. Chen, J. L. 2023-03-18 doi:10.1101/2023.03.17.532214 Cold Spring Harbor Laboratory Press 2023-03-18 <![CDATA[ Organization and replicon interactions within the highly segmented genome of Borrelia burgdorferi ]]> https://biorxiv.org/content/10.1101/2023.03.19.532819v1?rss=1 Ren, Z. Takacs, C. N. Brandao, H. B. Jacobs-Wagner, C. Wang, X. 2023-03-20 doi:10.1101/2023.03.19.532819 Cold Spring Harbor Laboratory Press 2023-03-20 <![CDATA[ SKOOTS: Skeleton oriented object segmentation for mitochondria ]]> https://biorxiv.org/content/10.1101/2023.05.05.539611v1?rss=1 Buswinka, C. J. Nitta, H. Osgood, R. T. Indzhykulian, A. A. 2023-05-08 doi:10.1101/2023.05.05.539611 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Skp1 proteins are structural components of the synaptonemal complex in C. elegans ]]> https://biorxiv.org/content/10.1101/2023.05.13.540652v1?rss=1 Blundon, J. Cesar, B. Bae, J. W. Cavka, I. Haversat, J. Ries, J. Koehler, S. Kim, Y. 2023-05-14 doi:10.1101/2023.05.13.540652 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Chronic stress triggers seeking of a starvation-like state in anxiety-prone female mice ]]> https://biorxiv.org/content/10.1101/2023.05.16.541013v1?rss=1 Kucukdereli, H. Pottala, T. Amsalem, O. Lim, M. Potgieter, L. Hasbrouck, A. Lutas, A. Andermann, M. L. 2023-05-17 doi:10.1101/2023.05.16.541013 Cold Spring Harbor Laboratory Press 2023-05-17 <![CDATA[ Sorgoleone degradation by sorghum-associated bacteria; an opportunity for enforcing plant growth promotion ]]> https://biorxiv.org/content/10.1101/2023.05.26.542311v1?rss=1 Oda, Y. Elmore, J. R. Nelson, W. C. Wilson, A. Farris, Y. Shrestha, R. Garcia, C. F. Pettinga, D. Ogden, A. J. Baldino, H. Alexander, W. G. Deutschbauer, A. Hurtado, C. V. McDermott, J. E. Guss, A. M. Coleman-Derr, D. McClure, R. Harwood, C. S. Egbert, R. 2023-05-26 doi:10.1101/2023.05.26.542311 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ Integrative Multi-omic Profiling of Two Human Decedents Receiving Pig Heart Xenografts Reveals Strong Perturbations in Early Immune-Cell and Cellular Metabolism Responses. ]]> https://biorxiv.org/content/10.1101/2023.06.05.543406v1?rss=1 Schmauch, E. Piening, B. D. Xia, B. Zhu, C. Stern, J. Zhang, W. Dowdell, A. Loza, B. Mohebnasab, M. Gragert, L. Khalil, K. Camellato, B. de Oliveira, M. F. O'Brien, D. Weldon, E. Lin, X. Gao, H. Kagermazova, L. Kim, J. Loupy, A. Heguy, A. Taylor, S. Zhu, F. Gao, S. Gandla, D. Reddy, K. Chang, A. Michael, B. Jiang, L. Jian, R. Narula, N. Linna-Kuosmanen, S. Kaikkonen-Maatta, M. Lorber, M. Kellis, M. Tatapudi, V. Ayares, D. Griesemer, A. Mangiola, M. Pass, H. Snyder, M. P. Boeke, J. D. Montgomery, R. A. Keating, B. J. 2023-06-08 doi:10.1101/2023.06.05.543406 Cold Spring Harbor Laboratory Press 2023-06-08 <![CDATA[ NOP16 is a histone mimetic that regulates Histone H3K27 methylation and gene repression ]]> https://biorxiv.org/content/10.1101/2023.06.13.544862v1?rss=1 Takashima, K. Lee, D.-J. Trovero, M. F. Rothi, M. H. Mistry, M. Zhang, Y. Li, Z. Davis, C. P. Li, Z. Natale, J. Schmid, E. Al Haddad, J. Hoffmann, G. B. Dietmann, S. Sui, S. H. Oshiumi, H. Lieberman, J. Greer, E. L. 2023-06-13 doi:10.1101/2023.06.13.544862 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ Functional Connectivity Development along the Sensorimotor-Association Axis Enhances the Cortical Hierarchy ]]> https://biorxiv.org/content/10.1101/2023.07.20.549090v1?rss=1 Luo, A. Sydnor, V. J. Pines, A. Larsen, B. Alexander-Bloch, A. F. Cieslak, M. Covitz, S. Chen, A. Esper, N. B. Feczko, E. Franco, A. R. Gur, R. E. Gur, R. C. Houghton, A. Hu, F. Keller, A. S. Kiar, G. Mehta, K. Salum, G. A. Tapera, T. Xu, T. Zhao, C. Fair, D. A. Salo, T. Shinohara, R. T. Milham, M. P. Satterthwaite, T. D. 2023-07-25 doi:10.1101/2023.07.20.549090 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Sex-specific adaptations to VTA circuits following subchronic stress ]]> https://biorxiv.org/content/10.1101/2023.08.02.551665v1?rss=1 Bouarab, C. Wynalda, M. Thompson, B. V. Khurana, A. Cody, C. R. Kisner, A. Polter, A. M. 2023-08-02 doi:10.1101/2023.08.02.551665 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Transcriptomic profiling of Schlemm's canal cells reveals a lymphatic-biased identity and three major cell states ]]> https://biorxiv.org/content/10.1101/2023.08.31.555823v1?rss=1 Balasubramanian, R. Kizhatil, K. Li, T. Tolman, N. Bhandari, A. Clark, G. Bupp-Chickering, V. Zhou, S. Peregrin, J. Simon, M. Montgomery, C. Qian, J. John, S. 2023-09-03 doi:10.1101/2023.08.31.555823 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ The molecular reach of antibodies determines their SARS-CoV-2 neutralisation potency ]]> https://biorxiv.org/content/10.1101/2023.09.06.556503v1?rss=1 45 patient-isolated IgG1 antibodies interacting with SARS-CoV-2 RBD surfaces. Our method reproduces the monovalent on/off-rates and enables measurements of the bivalent on-rate and the molecular reach: the maximum antigen separation that supports bivalent binding. We find large variations in these parameters across antibodies, including variations in reach (22-46 nm) that exceed the physical antibody size ([~]15 nm) due to the antigen size. The bivalent model integrates all parameters, including reach and antigen density, to predict an emergent binding potency for each antibody that matches their neutralisation potency. Indeed, antibodies with similar monovalent affinities to the same RBD-epitope but with different reaches display differences in emergent bivalent binding that match differences in their neutralisation potency. Together, our work highlights that antibodies within an isotype class binding the same antigen can display differences in molecular reach that can substantially modulate their emergent binding and functional properties. Lay SummaryAntibodies are soluble proteins that can neutralise pathogens by sticking to them. They contain two identical arms that allow them to simultaneously bind two identical antigen molecules on pathogen surfaces. Although we know that bivalent binding is important for neutralisation, we dont know how different antibodies achieve it. We developed a new model to analyse the mechanism of bivalent binding and used it to study over 45 antibodies from COVID-19 patients that bind the RBD antigen of SARS-CoV-2. Unexpectedly, we found that the molecular reach of an antibody, which is the maximum antigen separation that supports bivalent binding, varied widely between antibodies and exceeded their physical size. We show how antibody binding emerges from the interplay of multiple factors, including reach, and that this emergent binding predicts their neutralisation function. The ability to analyse and predict bivalent binding should improve our understanding and exploitation of antibodies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/556503v2_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@1674563org.highwire.dtl.DTLVardef@fc7feborg.highwire.dtl.DTLVardef@1325847org.highwire.dtl.DTLVardef@41ad51_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Huhn, A. Nissley, D. A. Wilson, D. B. Kutuzov, M. A. Donat, R. Tan, T. K. Zhang, Y. Barton, M. I. Liu, C. Dejnirattisai, W. Supasa, P. Mongkolsapaya, J. Townsend, A. James, W. S. Screaton, G. van der Merwe, P. A. Deane, C. Isaacson, S. Dushek, O. 2023-09-07 doi:10.1101/2023.09.06.556503 Cold Spring Harbor Laboratory Press 2023-09-07 <![CDATA[ Reconstruction of single cell lineage trajectories and identification of diversity in fates during the epithelial-to-mesenchymal transition ]]> https://biorxiv.org/content/10.1101/2023.09.19.558325v1?rss=1 Cheng, Y.-C. Zhang, Y. Tripathi, S. BV, H. Jolly, M. K. Schiebinger, G. Levine, H. McDonald, T. O. Michor, F. 2023-09-22 doi:10.1101/2023.09.19.558325 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Brief Apnea and Hypoventilation Reduces Seizure Duration and Shifts Seizure Location for Several Hours in a Model of Severe Traumatic Brain Injury. ]]> https://biorxiv.org/content/10.1101/2023.09.21.558686v1?rss=1 Rodriguez Lara, F. A. Sunkavalli, P. A. Mikaelian, M. A. Golemb, B. Staley, K. J. Costine-Bartell, B. A. 2023-09-22 doi:10.1101/2023.09.21.558686 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Potentiating NaV1.1 in Dravet syndrome patient iPSC-derived GABAergic neurons increases neuronal firing frequency and decreases network synchrony ]]> https://biorxiv.org/content/10.1101/2023.09.28.559990v1?rss=1 Kelley, M. R. Chipman, L. B. Asano, S. Knott, M. Howard, S. T. Berg, A. P. 2023-09-29 doi:10.1101/2023.09.28.559990 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ A Drug-Free Pathogen Capture and Neutralizing Nasal Spray to Prevent Emerging Respiratory Infections ]]> https://biorxiv.org/content/10.1101/2023.10.02.560602v1?rss=1 99.99%. In mice, PCANS showed nasal retention for at least 8 h and was safe for daily administration. A single prophylactic dose of PCANS protected mice against supra-lethal dosages of a mouse-adapted H1N1 Influenza virus (PR8), reduced lung viral titer by >99.99%, improved survival, and suppressed pathological manifestations. Together, our data suggest PCANS as a promising daily-use prophylactic approach against current and emerging respiratory infections. ]]> Joseph, J. Baby, H. M. Quintero, J. R. Kenney, D. Mebratu, Y. Bhatia, E. Shah, P. Swain, K. Kaur, S. Li, X. L. Mwangi, J. Snapper, O. Nair, R. Agus, E. Ranganathan, S. Kage, J. Gao, J. Luo, J. N. Yu, A. Douam, F. Tesfaigzi, Y. Karp, J. Joshi, N. 2023-10-03 doi:10.1101/2023.10.02.560602 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ An injectable in situ crosslinkable platform for ultra-long-acting delivery of hydrophilic therapeutics ]]> https://biorxiv.org/content/10.1101/2023.11.04.565631v1?rss=1 Lee, S. Zhao, S. Chen, X. Zhu, L. Joseph, J. Agus, E. Barooj, S. Mary, H. B. Shah, P. Slaughter, K. Cheung, K. Luo, J. N. Gao, J. Lee, D. Karp, J. Joshi, N. 2023-11-05 doi:10.1101/2023.11.04.565631 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development ]]> https://biorxiv.org/content/10.1101/2023.11.07.566024v1?rss=1 Carroll, S. H. Schafer, S. Kawasaki, K. Tsimbal, C. Jule, A. M. Hallett, S. A. Li, E. Liao, E. C. 2023-11-07 doi:10.1101/2023.11.07.566024 Cold Spring Harbor Laboratory Press 2023-11-07 <![CDATA[ GABAergic circuits reflect different requirements for emergent perception in postnatal mouse neocortex ]]> https://biorxiv.org/content/10.1101/2023.11.21.568139v1?rss=1 Ghezzi, F. Baruchin, L. J. Ha, N. T. Shah-Ostrowski, M. J. Chama, A. G. C. Stacey, J. A. Butt, S. J. B. 2023-11-21 doi:10.1101/2023.11.21.568139 Cold Spring Harbor Laboratory Press 2023-11-21 <![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[ AP-2α/AP-2β transcription factors are key regulators of epidermal homeostasis ]]> https://biorxiv.org/content/10.1101/2023.12.03.569763v1?rss=1 Zhang, H. Raymundo, J. Daly, K. E. Zhu, W. Senapati, B. Marneros, A. G. 2023-12-04 doi:10.1101/2023.12.03.569763 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ Electroadhesive hydrogel interface for prolonged mucosal theranostics ]]> https://biorxiv.org/content/10.1101/2023.12.19.572448v1?rss=1 Ying, B. Nan, K. Zhu, Q. Khuu, T. Ro, H. Qin, S. Wang, S. Jiang, K. Chen, Y. Bao, G. Jenkins, J. Pettinari, A. Kuosmanen, J. Ishida, K. Lopez, A. Li, J. Hayward, A. Langer, R. Traverso, G. 2023-12-20 doi:10.1101/2023.12.19.572448 Cold Spring Harbor Laboratory Press 2023-12-20 <![CDATA[ Synthetic integrin antibodies discovered by yeast display reveal αV subunit pairing preferences with β subunits ]]> https://biorxiv.org/content/10.1101/2024.01.26.577394v1?rss=1 {beta}3>{beta}1={beta}5. ]]> Hao, Y. Yan, J. Fraser, C. Jiang, A. Anuganti, M. Zhang, R. Lloyd, K. Jardine, J. Coppola, J. Meijers, R. Li, J. Springer, T. A. 2024-01-27 doi:10.1101/2024.01.26.577394 Cold Spring Harbor Laboratory Press 2024-01-27 <![CDATA[ A comprehensive map of transient protein-protein interactions and their structural features in the E. coli 1-carbon metabolism pathway ]]> https://biorxiv.org/content/10.1101/2024.02.17.580827v1?rss=1 Bhattacharyya, S. Ranganathan, S. Chowdhury, S. ADKAR, B. V. Khrapko, M. Shakhnovich, E. 2024-02-21 doi:10.1101/2024.02.17.580827 Cold Spring Harbor Laboratory Press 2024-02-21 <![CDATA[ Native β-barrel substrates pass through two shared intermediates during folding on the BAM complex ]]> https://biorxiv.org/content/10.1101/2024.05.09.593409v1?rss=1 Santos, T. M. A. Thomson, B. D. Marquez, M. D. Pan, L. Monfared, T. H. Kahne, D. E. 2024-05-09 doi:10.1101/2024.05.09.593409 Cold Spring Harbor Laboratory Press 2024-05-09 <![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[ Targeted Degradation of CDK9 Potently Disrupts the MYC Transcriptional Network ]]> https://biorxiv.org/content/10.1101/2024.05.14.593352v1?rss=1 Toure, M. A. Motoyama, K. Xiang, Y. Urgiles, J. Kabinger, F. Koglin, A.-S. Iyer, R. S. Gagnon, K. Kumar, A. Ojeda, S. Harrison, D. A. Rees, M. G. Roth, J. A. Ott, C. J. Schiavoni, R. Whittaker, C. A. Levine, S. S. White, F. M. Calo, E. Richters, A. Koehler, A. N. 2024-05-15 doi:10.1101/2024.05.14.593352 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ A Mechanically Resilient Soft Hydrogel Improves Drug Delivery for Treating Post-Traumatic Osteoarthritis in Physically Active Joints ]]> https://biorxiv.org/content/10.1101/2024.05.16.594611v1?rss=1 Joshi, N. Yan, J. Dang, M. Slaughter, K. Wang, Y. Wu, D. Ung, T. Pandya, V. Chen, M. X. Kaur, S. Bhagchandani, S. Alfassam, H. Joseph, J. Gao, J. Dewani, M. Yip, R. C. S. Weldon, E. Shah, P. Shukla, C. Sherman, N. Luo, J. N. Conway, T. Elickhoff, J. P. Botelho, L. Alhasan, A. Karp, J. Ermann, J. 2024-05-21 doi:10.1101/2024.05.16.594611 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Leukocytes have a heparan sulfate glycocalyx that regulates recruitment during inflammation ]]> https://biorxiv.org/content/10.1101/2024.05.21.595098v1?rss=1 Priestley, M. J. Hains, A. K. Mulholland, I. Z. Spijkers-Shaw, S. Zubkova, O. V. Dyer, D. P. Saunders, A. J. 2024-05-21 doi:10.1101/2024.05.21.595098 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Synthetic genomes unveil the effects of synonymous recoding ]]> https://biorxiv.org/content/10.1101/2024.06.16.599206v1?rss=1 Nyerges, A. Chiappino-Pepe, A. Budnik, B. Baas-Thomas, M. Flynn, R. Yan, S. Ostrov, N. Liu, M. Wang, M. Zheng, Q. Hu, F. Chen, K. Rudolph, A. Chen, D. Ahn, J. Spencer, O. Ayalavarapu, V. Tarver, A. Harmon-Smith, M. Hamilton, M. Blaby, I. Yoshikuni, Y. Hajian, B. Jin, A. Kintses, B. Szamel, M. Seregi, V. Shen, Y. Li, Z. Church, G. M. 2024-06-16 doi:10.1101/2024.06.16.599206 Cold Spring Harbor Laboratory Press 2024-06-16 <![CDATA[ Covert actions of epidural stimulation on spinal locomotor circuits ]]> https://biorxiv.org/content/10.1101/2024.06.18.599598v1?rss=1 Garcia-Ramirez, D. L. McGrath, J. R. Ha, N. T. Wheel, J. H. Atoche, S. J. Yao, L. Stachowski, N. J. Giszter, S. F. Dougherty, K. J. 2024-06-21 doi:10.1101/2024.06.18.599598 Cold Spring Harbor Laboratory Press 2024-06-21 <![CDATA[ Airway basal stem cells are necessary for the maintenance of functional intraepithelial airway macrophages. ]]> https://biorxiv.org/content/10.1101/2024.06.25.600501v1?rss=1 Kooistra, T. Saez, B. Roche, M. Egea-Zorrilla, A. Li, D. Anketell, D. Nguyen, N. Villoria, J. Gillis, J. Petri, E. Vera, L. Smith, N. P. Alladina, J. Zhang, Y. Vinarsky, V. Shivaraju, M. Sheng, S. L. Gonzalez-Celeiro, M. Mou, H. Waghray, A. Lin, B. Paksa, A. Yanger, K. Tata, P. R. Zhao, R. Causton, B. Zulueta, J. Prosper, F. Cho, J. L. Villani, A.-C. Haber, A. Rajagopal, J. Medoff, B. D. Pardo-Saganta, A. 2024-06-26 doi:10.1101/2024.06.25.600501 Cold Spring Harbor Laboratory Press 2024-06-26 <![CDATA[ Functional analysis of ESRP1/2 gene variants and CTNND1 isoforms in orofacial cleft pathogenesis ]]> https://biorxiv.org/content/10.1101/2024.07.02.601574v1?rss=1 Caetano da Silva, C. Macias Trevino, C. Mitchell, J. Murali, H. Tsimbal, C. Dalessandro, E. Carroll, S. H. Kochhar, S. Curtis, S. W. Cheng, C. H. E. Wang, F. Kutschera, E. Carstens, R. P. Xing, Y. Wang, K. Leslie, E. J. Liao, E. C. 2024-07-02 doi:10.1101/2024.07.02.601574 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Antimicrobial cetylpyridinium chloride suppresses mast cell function by targeting tyrosine phosphorylation of Syk kinase ]]> https://biorxiv.org/content/10.1101/2024.07.04.602096v1?rss=1 Obeng, B. Bennett, L. J. West, B. E. Wagner, D. J. Fleming, P. J. Tasker, M. N. Lorenger, M. K. Smith, D. R. Systuk, T. Plummer, S. M. Eom, J. Paine, M. D. Frangos, C. T. Wilczek, M. P. Shim, J. K. Maginnis, M. S. Gosse, J. A. 2024-07-08 doi:10.1101/2024.07.04.602096 Cold Spring Harbor Laboratory Press 2024-07-08 <![CDATA[ Expansion and revision of the genus Xanthobacter and proposal of Roseixanthobacter gen. nov. ]]> https://biorxiv.org/content/10.1101/2024.07.11.603134v1?rss=1 Soltysiak, M. P. M. Jalihal, A. P. Christophersen, C. E. Ory, A. L. H. Lee, A. D. Boulton, J. M. Springer, M. 2024-07-11 doi:10.1101/2024.07.11.603134 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Clarifying misconceptions of biomolecular condensate formation ]]> https://biorxiv.org/content/10.1101/2024.07.17.603945v1?rss=1 Hosamane, N. Hartman, M. Dubach, M. 2024-07-19 doi:10.1101/2024.07.17.603945 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ Imaging of developing human brains with ex vivo PSOCT and dMRI ]]> https://biorxiv.org/content/10.1101/2024.07.27.605383v1?rss=1 Wang, H. Blanke, N. Gong, D. Ortug, A. Alatorre Warren, J. L. Clickner, C. Ammon, W. Nolan, J. Cotronis, Z. van der Kouwe, A. Takahashi, E. 2024-07-29 doi:10.1101/2024.07.27.605383 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ Computational modeling of cancer cell metabolism along the catabolic-anabolic axes ]]> https://biorxiv.org/content/10.1101/2024.08.15.608169v1?rss=1 Villela-Castrejon, J. Levine, H. Onuchic, J. N. George, J. T. Jia, D. 2024-08-19 doi:10.1101/2024.08.15.608169 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ A human induced pluripotent stem (hiPS) cell model for the holistic study of epithelial to mesenchymal transitions (EMTs) ]]> https://biorxiv.org/content/10.1101/2024.08.16.608353v1?rss=1 Hookway, C. Borensztejn, A. Harris, L. K. Carlson, S. Dalgin, G. Mishra, S. Nivedita, N. Adams, E. M. Barszczewski, T. Dixon, J. C. Edmonds, J. H. Ehlers, E. A. Ferrante, A. J. Fuqua, M. A. Garrison, P. Gopalan, J. Gregor, B. W. Hedayati, M. J. Klein, K. N. Leveille, C. L. Meharry, S. L. Morris, H. S. Nadarajan, G. Oluoch, S. A. Parent, S. E. Phan, A. Roberts, B. Sanchez, E. E. Sluzewski, M. F. Snyder, L. S. Thirstrup, D. J. Thottam, J. P. Torvi, J. R. Turman, G. Viana, M. P. Wilhelm, L. Wijesooriya, C. S. Yao, J. Theriot, J. A. Rafelski, S. M. Gunawarda 2024-08-19 doi:10.1101/2024.08.16.608353 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Amputation Triggers Long-Range Epidermal Permeability Changes in Evolutionarily Distant Regenerative Organisms ]]> https://biorxiv.org/content/10.1101/2024.08.29.610385v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@81b022org.highwire.dtl.DTLVardef@52c2e9org.highwire.dtl.DTLVardef@17a5f93org.highwire.dtl.DTLVardef@118b8f6_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Dooling, K. E. Kim, R. T. Kim, E. M. Chen, E. Abouelela, A. Tajer, B. J. Lopez, N. J. Paoli, J. C. Powell, C. J. Luong, A. G. Wu, S. Y. C. Thornton, K. N. Singer, H. D. Savage, A. M. Bateman, J. DiTommaso, T. Payzin-Dogru, D. Whited, J. L. 2024-08-30 doi:10.1101/2024.08.29.610385 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Increased burden of rare risk variants across gene expression networks predisposes to sporadic Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2024.08.30.610195v1?rss=1 Eubanks, E. VanderSleen, K. Mody, J. Patel, N. Sacks, B. Darestani Farahani, M. Wang, J. Elliott, J. Jaber, N. Akcimen, F. Bandres-Ciga, S. Helweh, F. Liu, J. Archakam, S. Kimelman, R. Sharma, B. Socha, P. Guntur, A. Bartels, T. Dettmer, U. Mouradian, M. M. Bahrami, A. H. Dai, W. Baum, J. Shi, Z. Hardy, J. Kara, E. 2024-09-01 doi:10.1101/2024.08.30.610195 Cold Spring Harbor Laboratory Press 2024-09-01 <![CDATA[ Cis-regulatory elements driving motor neuron-restricted viral payload expression within the mammalian spinal cord ]]> https://biorxiv.org/content/10.1101/2024.09.02.610875v1?rss=1 Nagy, M. A. Price, S. Wang, K. Gill, S. P. Ren, E. McElrath, L. Pajak, V. Deighan, S. Liu, B. Liu, X. Diallo, A. Lo, S.-C. Kleiman, R. Henderson, C. Suh, J. Griffith, E. C. Greenberg, M. E. Hrvatin, S. 2024-09-04 doi:10.1101/2024.09.02.610875 Cold Spring Harbor Laboratory Press 2024-09-04 <![CDATA[ Intestinal helminth skews DC2 development towards regulatory phenotype to counter the anti-helminth immune response. ]]> https://biorxiv.org/content/10.1101/2024.09.11.612410v1?rss=1 Andrusaite, A. T. Ridgewell, O. J. Ahlback, A. A. Webster, H. C. Yamaguchi, H. Peel, M. Frede, A. Al-Khalidi, S. K. Farthing, A. Heawood, A. L. Smith, A. Roberts, E. W. Mowat, A. M. Maizels, R. M. M. Perona-Wright, G. Milling, S. W. 2024-09-15 doi:10.1101/2024.09.11.612410 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Identification of potent biparatopic antibodies targeting FGFR2 fusion driven cholangiocarcinoma. ]]> https://biorxiv.org/content/10.1101/2024.09.16.613045v1?rss=1 Chaturantabut, S. Oliver, S. Frederick, D. T. Kim, J. Robinson, F. P. Sinopoli, A. Song, T.-Y. Rodriguez, D. J. Chang, L. Kesar, D. He, Y. Ching, M. Dzvurumi, R. Atari, A. Tseng, Y.-Y. Bardeesy, N. Sellers, W. R. 2024-09-18 doi:10.1101/2024.09.16.613045 Cold Spring Harbor Laboratory Press 2024-09-18 <![CDATA[ Pharmacological inhibition of Fms-like kinase 3 (FLT3) promotes neuronal maturation and suppresses seizure in a mouse model ]]> https://biorxiv.org/content/10.1101/2024.10.02.616380v1?rss=1 Cruite, K. Moore, M. Gallagher, M. Coleman, E. Yin, Y. Lin, S. Shahbo, E. Lungjangwa, T. Hovestadt, V. Jaenisch, R. Maguire, J. Tang, X. 2024-10-03 doi:10.1101/2024.10.02.616380 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Self-Documenting Plasmids ]]> https://biorxiv.org/content/10.1101/2024.10.29.620927v1?rss=1 Peccoud, S. J. Hernandez, S. I. Kar, D. M. Berezin, C.-T. Peccoud, J. 2024-10-30 doi:10.1101/2024.10.29.620927 Cold Spring Harbor Laboratory Press 2024-10-30 <![CDATA[ Hunger modulates exploration through suppression of dopamine signaling in the tail of striatum ]]> https://biorxiv.org/content/10.1101/2024.11.11.622990v1?rss=1 Kamath, T. Lodder, B. Bilsel, E. Green, I. Dalangin, R. Capelli, P. Raghubardayal, M. Legister, J. Hulshof, L. G. Wallace, J. B. Tian, L. Uchida, N. Watabe-Uchida, M. Sabatini, B. L. 2024-11-11 doi:10.1101/2024.11.11.622990 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Tracing the stepwise Darwinian evolution of a plant halogenase ]]> https://biorxiv.org/content/10.1101/2024.12.09.627616v1?rss=1 Kim, C. Y. Kastner, D. W. Mitchell, A. J. Gutierrez, M. A. Yao, J. S. Neumann, E. N. Kulik, H. J. Weng, J.-K. 2024-12-11 doi:10.1101/2024.12.09.627616 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ Shear stress mediates metabolism and growth in electroactive biofilms ]]> https://biorxiv.org/content/10.1101/391029v1?rss=1 Jones, A.-A. D. Buie, C. R. 2018-08-13 doi:10.1101/391029 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ Alpha-Synuclein is a Target of Fic-mediated Adenylylation/AMPylation: Implications for Parkinson’s Disease ]]> https://biorxiv.org/content/10.1101/525659v1?rss=1 Mattoo, S. Sanyal, A. Dutta, S. Chandran, A. Koller, A. Camara, A. Watson, B. G. Sengupta, R. Ysselstein, D. Montenegro, P. Cannon, J. R. Rochet, C. 2019-01-21 doi:10.1101/525659 Cold Spring Harbor Laboratory Press 2019-01-21 <![CDATA[ Noroviruses subvert the core stress granule component G3BP1 to promote viral VPg-dependent translation. ]]> https://biorxiv.org/content/10.1101/571455v1?rss=1 Hosmillo, M. Lu, J. McAllaster, M. R. Eaglesham, J. B. Wang, X. Emmott, E. Domingues, P. Chaudhry, Y. Fitzmaurice, T. J. Tung, M. K. H. Panas, M. McInerney, G. Locker, N. Willen, C. B. Goodfellow, I. 2019-03-08 doi:10.1101/571455 Cold Spring Harbor Laboratory Press 2019-03-08 <![CDATA[ Herpes simplex virus-1 pUL56 degrades GOPC to alter the plasma membrane proteome ]]> https://biorxiv.org/content/10.1101/729343v1?rss=1 Soh, T. K. Davies, C. T. R. Muenzner, J. Connor, V. Bouton, C. R. Barrow, H. G. Smith, C. Emmott, E. Antrobus, R. Graham, S. C. Weekes, M. P. Crump, C. M. 2019-08-08 doi:10.1101/729343 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ Biomechanical Modelling of Sitting Movements for Designing Robotic Lower-Limb Prostheses and Exoskeletons with Energy Regeneration ]]> https://biorxiv.org/content/10.1101/801258v1?rss=1 Laschowski, B. Sharif Razavian, R. McPhee, J. 2019-10-10 doi:10.1101/801258 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Corollary Discharge Promotes a Sustained Motor State in a Neural Circuit for Navigation ]]> https://biorxiv.org/content/10.1101/861559v1?rss=1 Ji, N. Venkatachalam, V. Rodgers, H. Hung, W. Kawano, T. Clark, C. Lim, M. Alkema, M. J. Zhen, M. J. Samuel, A. 2019-12-03 doi:10.1101/861559 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation ]]> https://biorxiv.org/content/10.1101/2024.12.16.628723v1?rss=1 Billingsley, K. J. Meredith, M. Daida, K. Alvarez Jerez, P. Negi, S. Malik, L. Genner, R. M. Moller, A. Zheng, X. Gibson, S. B. Mastoras, M. Baker, B. Kouam, C. Paquette, K. Jarreau, P. Makarious, M. B. Moore, A. Hong, S. Vitale, D. Shah, S. Monlong, J. Pantazis, C. B. Asri, M. Shafin, K. Carnevali, P. Marenco, S. Auluck, P. Mandal, A. Miga, K. H. Rhie, A. Reed, X. Ding, J. Cookson, M. R. Nalls, M. Singleton, A. Miller, D. E. Chaisson, M. Timp, W. Gibbs, J. R. Phillippy, A. M. Kolmogorov, M. Jain, M. Sedlazeck, F. J. Paten, B. Blauwendraat, C. 2024-12-18 doi:10.1101/2024.12.16.628723 Cold Spring Harbor Laboratory Press 2024-12-18 <![CDATA[ Deaminase-mediated chromatin accessibility profiling with single-allele resolution ]]> https://biorxiv.org/content/10.1101/2024.12.17.628768v1?rss=1 Yu, T. Li, Z. Gibbs, E. Iwase, R. Francoeur, M. J. Phan, Q. v. Zhao, J. Rosin, J. Cole, P. A. Pinello, L. Sherwood, R. I. 2024-12-20 doi:10.1101/2024.12.17.628768 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ A comprehensive benchmark for multiple highly efficient base editors with broad targeting scope ]]> https://biorxiv.org/content/10.1101/2024.12.17.628899v1?rss=1 Wang, X. Cheng, X. Li, Z. Ma, S. Zhang, H. Chen, Z. Yao, Y. Li, Z. Zhong, C. Li, Y. Zhang, Y. Menon, V. Chao, L. Li, W. Fei, T. 2024-12-20 doi:10.1101/2024.12.17.628899 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Parental kynurenine 3-monooxygenase genotype in mice directs sex-specific behavioral outcomes in offspring ]]> https://biorxiv.org/content/10.1101/2024.12.18.629210v1?rss=1 Milosavljevic, S. Piroli, M. V. Sandago, E. J. Piroli, G. G. Smith, H. H. Beggiato, S. Frizzell, N. Pocivavsek, A. 2024-12-20 doi:10.1101/2024.12.18.629210 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Identifying the Brain Circuits that Regulate Pain-Induced Sleep Disturbances ]]> https://biorxiv.org/content/10.1101/2024.12.20.629596v1?rss=1 Lynch, N. De Luca, R. Spinieli, R. L. Rillosi, E. Thomas, R. C. Sailesh, S. Gangeddula, N. Lima, J. D. Bandaru, S. Arrigoni, E. Burstein, R. Thankachan, S. Kaur, S. 2024-12-20 doi:10.1101/2024.12.20.629596 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Elucidation of gene clusters underlying withanolide biosynthesis in ashwagandha through yeast metabolic engineering ]]> https://biorxiv.org/content/10.1101/2024.12.24.630284v1?rss=1 Reynolds, E. Trauger, M. Li, F.-S. Huang, J. Moss, T. Christ, B. Xu, M. Knoch, E. Weng, J.-K. 2024-12-25 doi:10.1101/2024.12.24.630284 Cold Spring Harbor Laboratory Press 2024-12-25 <![CDATA[ Real-time fMRI neurofeedback reduces default mode network and auditory cortex functional connectivity in schizophrenia ]]> https://biorxiv.org/content/10.1101/2025.01.02.631107v1?rss=1 Zhang, J. Bauer, C. C. C. Morfini, F. Lee, Y. Stone, L. Awad, A. Okano, K. Hwang, M. Shinn, A. K. Niznikiewicz, M. A. Whitfield-Gabrieli, S. 2025-01-02 doi:10.1101/2025.01.02.631107 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Mettl15-Mettl17 modulates the transition from early to late pre-mitoribosome ]]> https://biorxiv.org/content/10.1101/2024.12.18.629302v1?rss=1 Zgadzay, Y. Mirabello, C. Wanes, G. Panek, T. Chauhan, P. Nystedt, B. Zikova, A. Gahura, O. Amunts, A. 2025-01-04 doi:10.1101/2024.12.18.629302 Cold Spring Harbor Laboratory Press 2025-01-04 <![CDATA[ Spatial density and habitat associations of Atlantic Cod on the Northeastern US Continental Shelf ]]> https://biorxiv.org/content/10.1101/2025.01.08.631947v1?rss=1 Lankowicz, K. Grabowski, J. Sherwood, G. D. Kerr, L. 2025-01-10 doi:10.1101/2025.01.08.631947 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ Understanding the high-order network plasticity mechanisms of ultrasound neuromodulation ]]> https://biorxiv.org/content/10.1101/2025.01.11.632528v1?rss=1 Gatica, M. Atkinson-Clement, C. Coronel-Oliveros, C. Alkhawashki, M. Mediano, P. A. M. Tagliazucchi, E. Rosas, F. E. Kaiser, M. Petri, G. 2025-01-12 doi:10.1101/2025.01.11.632528 Cold Spring Harbor Laboratory Press 2025-01-12 <![CDATA[ Real-time fMRI neurofeedback modulates auditory cortex activity and connectivity in schizophrenia patients with auditory hallucinations: A controlled study ]]> https://biorxiv.org/content/10.1101/2025.01.13.632809v1?rss=1 Bauer, C. C. C. Zhang, J. Morfini, F. Hinds, O. Wighton, P. Lee, Y. Stone, L. Awad, A. Okano, K. Hwang, M. Hammoud, J. Nestor, P. Whitfield-Gabrieli, S. Shinn, A. K. Niznikiewicz, M. A. 2025-01-15 doi:10.1101/2025.01.13.632809 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Convergent flow-mediated mesenchymal force drives embryonic foregut constriction and splitting ]]> https://biorxiv.org/content/10.1101/2025.01.22.634318v1?rss=1 Yan, R. Hoffmann, L. A. Oikonomou, P. Li, D. Lee, C. Gill, H. K. Mongera, A. Nerurkar, N. Mahadevan, L. Tabin, C. J. 2025-01-23 doi:10.1101/2025.01.22.634318 Cold Spring Harbor Laboratory Press 2025-01-23 <![CDATA[ Pancreatic injury induces β-cell regeneration in axolotl ]]> https://biorxiv.org/content/10.1101/2025.01.23.634564v1?rss=1 Powell, C. J. Singer, H. D. Juarez, A. R. Kim, R. T. Payzin-Dogru, D. Savage, A. M. Lopez, N. J. Blair, S. J. Abouelela, A. Dittrich, A. Akeson, S. G. Jain, M. Whited, J. L. 2025-01-23 doi:10.1101/2025.01.23.634564 Cold Spring Harbor Laboratory Press 2025-01-23 <![CDATA[ Mathematical Characterization of Drug-Induced Persistence in Cancer ]]> https://biorxiv.org/content/10.1101/2025.01.21.634165v1?rss=1 Park, J. T. Levine, H. 2025-01-24 doi:10.1101/2025.01.21.634165 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ De novo Autogenic Engineered Living Functional Materials ]]> https://biorxiv.org/content/10.1101/2025.01.21.634218v1?rss=1 Hammad, H. M. Swarnadeep, S. Crater, E. R. Moore, R. B. Deshmukh, S. Manjula-Basavanna, A. Duraj-Thatte, A. M. 2025-01-24 doi:10.1101/2025.01.21.634218 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ User-Assisted Approach for Accurate Nonrigid Registration of Images and Traces ]]> https://biorxiv.org/content/10.1101/2025.01.29.635549v1?rss=1 Baig, M. M. J. Hoang, T. T. N. Chung, S. H. Stepanyants, A. 2025-02-02 doi:10.1101/2025.01.29.635549 Cold Spring Harbor Laboratory Press 2025-02-02 <![CDATA[ On-demand delivery of fibulin-1 enables repeated basement membrane stretching ]]> https://biorxiv.org/content/10.1101/2025.02.02.636120v1?rss=1 Soh, A. W. J. Arnwine, M. R. Gianakas, C. A. Clark, Z. D. Chi, Q. Cram, E. J. Hoffman, B. D. Sherwood, D. R. 2025-02-03 doi:10.1101/2025.02.02.636120 Cold Spring Harbor Laboratory Press 2025-02-03 <![CDATA[ Combined effects of mechanical loading and Piezo1 chemical activation on 22-months-old female mouse bone adaptation ]]> https://biorxiv.org/content/10.1101/2025.02.05.636720v1?rss=1 Meslier, Q. A. Oehrlein, R. Shefelbine, S. J. 2025-02-05 doi:10.1101/2025.02.05.636720 Cold Spring Harbor Laboratory Press 2025-02-05 <![CDATA[ Protein degradation and growth dependent dilution substantially shape mammalian proteomes ]]> https://biorxiv.org/content/10.1101/2025.02.10.637566v1?rss=1 Leduc, A. Slavov, N. 2025-02-12 doi:10.1101/2025.02.10.637566 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Composition and RNA binding specificity of metazoan RNase MRP ]]> https://biorxiv.org/content/10.1101/2025.02.21.639568v1?rss=1 Liu, Y. He, S. Pyo, K. Zheng, S. Chen, M. Cheloufi, S. Slavov, N. Marzluff, W. F. Murn, J. 2025-02-23 doi:10.1101/2025.02.21.639568 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ Reproducible Brain Charts: An open data resource for mapping brain development and its associations with mental health ]]> https://biorxiv.org/content/10.1101/2025.02.24.639850v1?rss=1 Shafiei, G. Esper, N. B. Hoffmann, M. S. Ai, L. Chen, A. A. Cluce, J. Covitz, S. Giavasis, S. Lane, C. Mehta, K. Moore, T. M. Salo, T. Tapera, T. M. Calkins, M. E. Colcombe, S. Davatzikos, C. Gur, R. E. Gur, R. C. Pan, P. M. Jackowski, A. P. Rokem, A. Rohde, L. A. Shinohara, R. T. Tottenham, N. Zuo, X.-N. Cieslak, M. Franco, A. R. Kiar, G. Salum, G. A. Milham, M. P. Satterthwaite, T. D. 2025-02-26 doi:10.1101/2025.02.24.639850 Cold Spring Harbor Laboratory Press 2025-02-26 <![CDATA[ Programming cellular condensates for living materials using an intrinsically disordered protein display platform ]]> https://biorxiv.org/content/10.1101/2025.03.02.640994v1?rss=1 Chang, R. Tu, H. Joshi, N. S. 2025-03-03 doi:10.1101/2025.03.02.640994 Cold Spring Harbor Laboratory Press 2025-03-03 <![CDATA[ Direct RNA sequencing of primary human T cells reveals the impact of immortalization on mRNA pseudouridine modifications. ]]> https://biorxiv.org/content/10.1101/2025.03.02.641090v1?rss=1 Fanari, O. Bloch, D. Qiu, Y. Meseonznik, M. Makhamreh, A. Wanunu, M. Rouhanifard, S. H. 2025-03-10 doi:10.1101/2025.03.02.641090 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Ion Channel Reaction Networks: Dielectric Screening and the Importance of Off-Pathway Flux ]]> https://biorxiv.org/content/10.1101/2025.03.06.637869v1?rss=1 View larger version (17K): org.highwire.dtl.DTLVardef@1144eaaorg.highwire.dtl.DTLVardef@387f8eorg.highwire.dtl.DTLVardef@13e4e01org.highwire.dtl.DTLVardef@1732864_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Weckel-Dahman, H. Daum, A. Carlsen, R. Southam, T. He, M. Swanson, J. M. 2025-03-10 doi:10.1101/2025.03.06.637869 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Emergent dynamics of cellular decision making in multi-node mutually repressive regulatory networks ]]> https://biorxiv.org/content/10.1101/2025.03.06.641782v1?rss=1 BV, H. Billakurthi, H. S. Adigwe, S. Hari, K. Levine, H. Gedeon, T. Jolly, M. K. 2025-03-11 doi:10.1101/2025.03.06.641782 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Allosteric Control and Glycan Shielding Adaptations in the SARS-CoV-2 Spike from Early to Peak Virulence ]]> https://biorxiv.org/content/10.1101/2025.03.11.642723v1?rss=1 Chakraborty, S. Nguyen, K. N. Zhao, M. Gnanakaran, S. 2025-03-12 doi:10.1101/2025.03.11.642723 Cold Spring Harbor Laboratory Press 2025-03-12 <![CDATA[ A Chlorinated Diketopiperazine Antibiotic Targets Mycobacterium Tuberculosis DNA Gyrase ]]> https://biorxiv.org/content/10.1101/2025.03.10.642354v1?rss=1 Liang, L. Quigley, J. Theriault, M. Iinishi, A. Bargabos, R. Morrissette, M. Ghiglieri, M. L. Curtis, T. Corsetti, R. Son, S. Sarkar, B. Lewis, K. 2025-03-13 doi:10.1101/2025.03.10.642354 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Overlooked features lead to divergent neurobiological interpretations of brain-based machine learning biomarkers ]]> https://biorxiv.org/content/10.1101/2025.03.12.642878v1?rss=1 Adkinson, B. D. Rosenblatt, M. Sun, H. Dadashkarimi, J. Tejavibulya, L. Horien, C. Westwater, M. L. Noble, S. Scheinost, D. 2025-03-13 doi:10.1101/2025.03.12.642878 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Combining model-based and data-driven models: an application to synthetic biology resource competition ]]> https://biorxiv.org/content/10.1101/2025.03.09.642275v1?rss=1 Darabi, A. An, Z. Al-Radhawi, M. A. Cho, W. Siami, M. Sontag, E. 2025-03-14 doi:10.1101/2025.03.09.642275 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Unveiling Interaction Signatures Across Viral Pathogens through VASCO: Viral Antigen-Antibody Structural COmplex dataset ]]> https://biorxiv.org/content/10.1101/2025.03.11.642737v1?rss=1 Wong, K. Subramanian, I. Stevens, E. Chakraborty, S. 2025-03-14 doi:10.1101/2025.03.11.642737 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Cleaved vs. Uncleaved: How Furin Cleavage Reshapes the Conformational Landscape of SARS-CoV-2 Spike ]]> https://biorxiv.org/content/10.1101/2025.03.12.642945v1?rss=1 Mani, N. Suresh, R. Chakraborty, S. 2025-03-14 doi:10.1101/2025.03.12.642945 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Phase-field Approach to Cellular Blebbing ]]> https://biorxiv.org/content/10.1101/2025.03.14.643157v1?rss=1 Ji, K. Levine, H. Karma, A. 2025-03-17 doi:10.1101/2025.03.14.643157 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ Serotonergic signaling governs C. elegans sensory response to conflicting olfactory stimuli ]]> https://biorxiv.org/content/10.1101/2025.03.19.644218v1?rss=1 Srinivasan, J. Muirhead, C. S. Guerra, S. Fox, B. W. Schroeder, F. C. 2025-03-19 doi:10.1101/2025.03.19.644218 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ Impacts of competition and phenotypic plasticity on the viability of adaptive therapy ]]> https://biorxiv.org/content/10.1101/2025.03.20.644475v1?rss=1 Vibishan, B. Jain, P. Sharma, V. Hari, K. Kadelka, C. George, J. T. Jolly, M. K. 2025-03-25 doi:10.1101/2025.03.20.644475 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ Diet induced insulin resistance is due to induction of PTEN expression ]]> https://biorxiv.org/content/10.1101/2025.03.25.645201v1?rss=1 Mukherjee, R. Pancholi, P. Sharma, M. Solomon, H. Timaul, M. Thant, C. MsGriskin, R. Hayatt, O. Markov, V. D'Allara, J. Bekker, S. Candelier, J. Vanaja, K. Rosen, N. 2025-03-26 doi:10.1101/2025.03.25.645201 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ Growth charts of infant visual neurodevelopment generalize across global contexts ]]> https://biorxiv.org/content/10.1101/2025.03.25.645314v1?rss=1 Margolis, E. T. Camp, C. Sobrino, A. C. Polanczyk, G. V. Fatori, D. Khula South Africa Team, Germina Team, LABS Team, GABA Team, 1kD EEG Working Group, 1kD Machine Learning Working Group, Cornelissen, L. Berde, C. B. Hensch, T. K. Nelson, C. A. Shephard, E. Donald, K. A. Scheinost, D. Gabard-Durnam, L. J. 2025-03-26 doi:10.1101/2025.03.25.645314 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ Integrating Interpretable Machine Learning and Multi-omics Systems Biology for Personalized Biomarker Discovery and Drug Repurposing in Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2025.03.24.644676v1?rss=1 Mottaqi, M. Zhang, P. Xie, L. 2025-03-28 doi:10.1101/2025.03.24.644676 Cold Spring Harbor Laboratory Press 2025-03-28 <![CDATA[ From Lab to Concert Hall: Effects of Live Performance on Neural Entrainment and Engagement ]]> https://biorxiv.org/content/10.1101/2025.04.03.646931v1?rss=1 Asthagiri, A. Loui, P. 2025-04-03 doi:10.1101/2025.04.03.646931 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Quantifying the influence of genetic context on duplicated mammalian genes ]]> https://biorxiv.org/content/10.1101/2025.04.03.647042v1?rss=1 Moffett, A. S. Falcon-Cortes, A. Di Pierro, M. 2025-04-04 doi:10.1101/2025.04.03.647042 Cold Spring Harbor Laboratory Press 2025-04-04 <![CDATA[ Incorporating special interests to investigate the language system in autism: A feasibility pilot fMRI study ]]> https://biorxiv.org/content/10.1101/2025.04.04.647117v1?rss=1 Olson, H. A. Johnson, K. T. Nishith, S. Gabrieli, J. D. E. D'Mello, A. M. 2025-04-05 doi:10.1101/2025.04.04.647117 Cold Spring Harbor Laboratory Press 2025-04-05 <![CDATA[ Bactofilins are essential spatial organizers of peptidoglycan insertion in the Lyme disease spirochete Borrelia burgdorferi ]]> https://biorxiv.org/content/10.1101/2025.04.09.647816v1?rss=1 Zinck, C. B. Carracoi, V. Kloos, Z. A. Wachter, J. Schwartz, C. Stewart, P. E. Jacobs-Wagner, C. Rosa, P. A. Takacs, C. N. 2025-04-09 doi:10.1101/2025.04.09.647816 Cold Spring Harbor Laboratory Press 2025-04-09 <![CDATA[ Enhanced Activity of Apramycin and Apramycin-Based Combinations Against Mycobacteroides abscessus ]]> https://biorxiv.org/content/10.1101/2025.04.09.648020v1?rss=1 Huang, Y. Trueslon, K. A. Stuart, I. A. O'Doherty, G. A. Kirby, J. E. 2025-04-09 doi:10.1101/2025.04.09.648020 Cold Spring Harbor Laboratory Press 2025-04-09 <![CDATA[ Dynamic Pathway of Guanidine-III Riboswitch Folding Revealed by Single-Molecule FRET: Mg2+-Assisted Preorganization and Ligand-Induced Kinetic Trapping ]]> https://biorxiv.org/content/10.1101/2025.04.15.648854v1?rss=1 Jiang, M. Bian, Y. Zou, L. Liu, T. Ji, Z. Ren, W. Guo, Z. Cao, Y. Jiao, Y. Pan, H. 2025-04-20 doi:10.1101/2025.04.15.648854 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ STPath: A Generative Foundation Model for Integrating Spatial Transcriptomics and Whole Slide Images ]]> https://biorxiv.org/content/10.1101/2025.04.19.649665v1?rss=1 Huang, T. Liu, T. Babadi, M. Ying, R. Jin, W. 2025-04-24 doi:10.1101/2025.04.19.649665 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Non-duality in brain and experience of advanced meditators - Key role for Intrinsic Neural Timescales ]]> https://biorxiv.org/content/10.1101/2025.04.21.649758v1?rss=1 Malipeddi, S. Sasidharan, A. Ventura, B. Venugopal, R. Bauer, C. C. Tewarie, P. K. B. Ravindra, P. N. Mehrotra, S. John, J. P. Subramaniam, B. Laureys, S. Kutty, B. M. Northoff, G. 2025-04-29 doi:10.1101/2025.04.21.649758 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Hypoxia Exacerbates Kir2.1 Channel Dysfunction in an Andersen-Tawil Syndrome Variant Through a SUMO-Dependent Mechanism ]]> https://biorxiv.org/content/10.1101/2025.04.25.650734v1?rss=1 Chandrashekar, A. Xu, Y. Ma, X. Yauch, A. K. Scholl, E. Yang, Y. Gada, K. D. Kawano, T. Cui, M. Plant, L. D. 2025-04-29 doi:10.1101/2025.04.25.650734 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Characterization of a potential antibiotic target site on the ribosome ]]> https://biorxiv.org/content/10.1101/2025.05.02.651724v1?rss=1 Golstein, M. Wang, Y. Byju, S. Mohanty, U. Whitford, P. C. 2025-05-02 doi:10.1101/2025.05.02.651724 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ Exploring C1 substrate cofeeding in Eubacterium limosum with AneVO, a low-cost anaerobic parallel bioreactor platform ]]> https://biorxiv.org/content/10.1101/2025.05.02.651948v1?rss=1 Hoyt, K. O. Zhou, G. Gasparrini, W. Sliter, P. J. Hart, D. J. Khalil, A. S. Woolston, B. M. 2025-05-02 doi:10.1101/2025.05.02.651948 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ Evaluation of Nanopore direct RNA sequencing updates for modification detection ]]> https://biorxiv.org/content/10.1101/2025.05.01.651717v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@1215534org.highwire.dtl.DTLVardef@160f38forg.highwire.dtl.DTLVardef@164a9corg.highwire.dtl.DTLVardef@17c72e5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Esfahani, N. G. Stein, A. J. Akeson, S. Tzadikario, T. Jain, M. 2025-05-04 doi:10.1101/2025.05.01.651717 Cold Spring Harbor Laboratory Press 2025-05-04 <![CDATA[ Understanding the physical processes behind DNA-DNA proximity ligation assays ]]> https://biorxiv.org/content/10.1101/2025.05.02.649190v1?rss=1 Zubillaga Herrera, B. J. Das, A. Burack, L. R. Wang, A. Di Pierro, M. 2025-05-04 doi:10.1101/2025.05.02.649190 Cold Spring Harbor Laboratory Press 2025-05-04 <![CDATA[ Multiomic clocks to predict phenotypic age in mice ]]> https://biorxiv.org/content/10.1101/2025.04.30.651114v1?rss=1 Vera, D. Griffin, P. T. Leigh, D. Kras, J. Ramos, E. Bishof, I. Butler, A. Chwalek, K. Vogel, D. Kane, A. E. Sinclair, D. A. 2025-05-06 doi:10.1101/2025.04.30.651114 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ A spatial code governs olfactory receptor choice and aligns sensory maps in the nose and brain ]]> https://biorxiv.org/content/10.1101/2025.05.02.651738v1?rss=1 Brann, D. H. Tsukahara, T. Tau, C. Kalloor, D. Lubash, R. Thamarai Kannan, L. Klimpert, N. Kollo, M. Escamilla-Del-Arenal, M. Bintu, B. Bozza, T. Datta, S. R. 2025-05-08 doi:10.1101/2025.05.02.651738 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ A Toolbox for the Personalization of Plasmonic Photothermal Therapy in Orthotopic Mouse Tumor Models ]]> https://biorxiv.org/content/10.1101/2025.05.02.651947v1?rss=1 Fernandez Esteberena, P. R. Vilches, C. Morales-Dalmau, J. Mireles, M. Martinez-Lozano, M. d. M. de Miguel, I. Casanovas, O. Quidant, R. Durduran, T. 2025-05-08 doi:10.1101/2025.05.02.651947 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ Whole-brain chemosensory responses of both C. elegans sexes ]]> https://biorxiv.org/content/10.1101/2025.05.15.654129v1?rss=1 Seyedolmohadesin, M. Fu, X. Torkashvand, M. Rasouli, S. Lang, S. Li, L. Kalinski, C. Cook, S. J. Schroeder, F. C. Yemini, E. Venkatachalam, V. 2025-05-19 doi:10.1101/2025.05.15.654129 Cold Spring Harbor Laboratory Press 2025-05-19 <![CDATA[ PSMtags improve peptide sequencing and throughput in sensitive proteomics ]]> https://biorxiv.org/content/10.1101/2025.05.22.655509v1?rss=1 Specht, H. Yeh, M. Sipe, S. Barnes-Seeman, D. Adamo, M. McDonnell, K. Agius, M. P. Friedrich, C. Pang, W. K. Huang, Y. Shiva Raju, K. Vuong, W. Lee, M. A. Yesilcimen, A. Pentelute, B. L. Slavov, N. 2025-05-27 doi:10.1101/2025.05.22.655509 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ JMod: Joint modeling of mass spectra for empowering multiplexed DIA proteomics ]]> https://biorxiv.org/content/10.1101/2025.05.22.655512v1?rss=1 McDonnell, K. Wamsley, N. Derks, J. Sipe, S. Yeh, M. Specht, H. Slavov, N. 2025-05-27 doi:10.1101/2025.05.22.655512 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Increasing mass spectrometry throughput using time-encoded sample multiplexing ]]> https://biorxiv.org/content/10.1101/2025.05.22.655515v1?rss=1 View larger version (20K): org.highwire.dtl.DTLVardef@1c1d799org.highwire.dtl.DTLVardef@1319339org.highwire.dtl.DTLVardef@1b8bf4borg.highwire.dtl.DTLVardef@16d9e9_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Derks, J. McDonnell, K. Wamsley, N. Stewart, P. Yeh, M. Specht, H. Slavov, N. 2025-05-27 doi:10.1101/2025.05.22.655515 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Obesity dysregulates feeding-evoked response dynamics in hypothalamic satiety neurons ]]> https://biorxiv.org/content/10.1101/2025.05.22.655553v1?rss=1 Porniece, M. Baker, J. Ausfahl, C. D. Zhang, S. X. Andermann, M. L. 2025-05-27 doi:10.1101/2025.05.22.655553 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Energy Constraints and Neural Strategy Transitions in Alzheimer's: A Game-Theoretic Model ]]> https://biorxiv.org/content/10.1101/2025.05.24.655918v1?rss=1 Kareva, I. Karev, G. 2025-05-28 doi:10.1101/2025.05.24.655918 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Ubiquitin-Proteasome System Dysregulation in Alzheimer's Disease Impacts Protein Abundance ]]> https://biorxiv.org/content/10.1101/2025.05.29.656728v1?rss=1 Collins, M. A. Friedrich, C. Elcheikhali, M. Stewart, P. Derks, J. Connors Stewart, T. Altig, K. Melloni, A. Petelski, A. Oakley, D. Hyman, B. Slavov, N. 2025-05-29 doi:10.1101/2025.05.29.656728 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ Could malaria mosquitoes be controlled by periodic releases of transgenic mosquitocidal Metarhizium pingshaense fungus? A mathematical modeling approach ]]> https://biorxiv.org/content/10.1101/2025.05.28.656721v1?rss=1 Pant, B. Bilgo, E. Mitra, A. Safdar, S. Diabate, A. St. Leger, R. Gumel, A. B. 2025-05-31 doi:10.1101/2025.05.28.656721 Cold Spring Harbor Laboratory Press 2025-05-31 <![CDATA[ Neural Spectral Prediction for Structure Elucidation with Tandem Mass Spectrometry ]]> https://biorxiv.org/content/10.1101/2025.05.28.656653v1?rss=1 Wang, R. Manjrekar, M. Mahjour, B. Avila-Pacheco, J. Provenzano, J. Reynolds, E. Lederbauer, M. Mashin, E. Goldman, S. L. Wang, M. Weng, J.-K. Plata, D. L. Clish, C. B. Coley, C. W. 2025-06-01 doi:10.1101/2025.05.28.656653 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Projected warming disrupts embryonic development and hatch timing in Antarctic fish ]]> https://biorxiv.org/content/10.1101/2025.05.28.656708v1?rss=1 Streeter, M. S. Le Francois, N. R. Desvignes, T. Grondin, J. Postlethwait, J. H. Detrich, H. W. Daane, J. 2025-06-01 doi:10.1101/2025.05.28.656708 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ BifurcatoR: A Framework for Revealing Clinically Actionable Signal in Variance Masquerading as Noise ]]> https://biorxiv.org/content/10.1101/2025.06.01.657083v1?rss=1 Madaj, Z. B. Ding, M. Khoo, C. K. Tokarski, E. Fagnocchi, L. PERMUTE, Li, Z. Riordan, J. Pospisilik, J. A. Nadeau, J. Lary, C. Triche, T. J. 2025-06-03 doi:10.1101/2025.06.01.657083 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ A Characterization of Axolotl Digit Regeneration: Conserved Mechanisms, Divergent Patterning, and a Critical Role for Hedgehog Signaling ]]> https://biorxiv.org/content/10.1101/2025.06.03.657663v1?rss=1 Griffiths, J. R. Miller, M. Duerr, T. J. Owen, A. E. Monaghan, J. R. 2025-06-06 doi:10.1101/2025.06.03.657663 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Investigating the repeatability and behavioral relationships of acuity, contrast sensitivity, form, and motion perception measurements using a novel tablet-based vision test tool ]]> https://biorxiv.org/content/10.1101/2025.06.09.658584v1?rss=1 Green, J. Skerswetat, J. Bex, P. J. Schmidtmann, G. 2025-06-12 doi:10.1101/2025.06.09.658584 Cold Spring Harbor Laboratory Press 2025-06-12 <![CDATA[ TRPV4 Inhibition Reduces Cartilage Growth During Axolotl Limb Regeneration ]]> https://biorxiv.org/content/10.1101/2025.06.10.658903v1?rss=1 Kondiboyina, V. Miller, M. Ritterbuck, M. Owen, A. Duerr, T. J. Monaghan, J. R. Shefelbine, S. J. 2025-06-15 doi:10.1101/2025.06.10.658903 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Population-specific brain charts reveal Chinese-Western differences in neurodevelopmental trajectories ]]> https://biorxiv.org/content/10.1101/2025.06.17.659820v1?rss=1 Sun, L. Qin, W. Liang, X. Wang, C. Men, W. Duan, Y. Fan, X.-R. Cai, Q. Qiu, S. Wang, M. Gong, Q. Tian, Y. Liang, P. Liu, Z. Zhang, X. Song, H. Ye, Z. Zhang, P. Dong, Q. Tao, S. Zhu, W. Zhang, J. Xie, F. Feng, J. Zhang, J. Liu, C. Qian, Q. Zhang, B. Meng, M. Hu, L. Gao, J.-H. Jiang, T. Zhu, X. Zhang, Y. Liu, L. Liu, H. Liao, W. Wang, D. Wang, H. Guo, T. Dai, Z. Lui, S. Xu, K. Li, L. Xie, P. Feng, C. Cui, G. Wu, J. Yin, X. Ding, G. Xian, J. Zhao, L. Lu, J. Liu, Z. Han, Y. Yuan, Z. Zhang, X. Si, T. Zhou, F. Bi, Y. Wu, D. Gao, F. Wang, 2025-06-18 doi:10.1101/2025.06.17.659820 Cold Spring Harbor Laboratory Press 2025-06-18 <![CDATA[ Beyond Reorganization: Intrinsic cortical hierarchies constrain experience-dependent plasticity in sensory-deprived humans ]]> https://biorxiv.org/content/10.1101/2025.06.19.660510v1?rss=1 Orsenigo, D. Setti, F. Pagani, M. Petri, G. Tamietto, M. Luppi, A. I. Ricciardi, E. 2025-06-21 doi:10.1101/2025.06.19.660510 Cold Spring Harbor Laboratory Press 2025-06-21 <![CDATA[ The Topological Architecture of Brain Identity ]]> https://biorxiv.org/content/10.1101/2025.06.20.660792v1?rss=1 Poetto, S. Merritt, H. Santoro, A. Rabuffo, G. Battaglia, D. A. Vaccarino, F. Saggar, M. Brovelli, A. Petri, G. 2025-06-21 doi:10.1101/2025.06.20.660792 Cold Spring Harbor Laboratory Press 2025-06-21 <![CDATA[ Climbing fibers selectively recruit disinhibitory interneurons to enhance dendritic calcium signaling in cerebellar Purkinje cells ]]> https://biorxiv.org/content/10.1101/2025.06.22.660768v1?rss=1 Santos-Valencia, F. Lackey, E. Norton, A. Asem, W. Gaynor, C. S. ediger, s. Hemelt, m. E. Nguyen, T. Lee, W.-C. A. Brunel, N. Hull, C. regehr, w. 2025-06-23 doi:10.1101/2025.06.22.660768 Cold Spring Harbor Laboratory Press 2025-06-23 <![CDATA[ Theory of Temporal Pattern Learning in Echo State Networks ]]> https://biorxiv.org/content/10.1101/2025.06.23.661158v1?rss=1 Hakim, V. Karma, A. 2025-06-25 doi:10.1101/2025.06.23.661158 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Beyond Pairwise Interactions: Charting Higher-Order Models of Brain Function ]]> https://biorxiv.org/content/10.1101/2025.06.24.661306v1?rss=1 Santoro, A. Neri, M. Poetto, S. Orsenigo, D. Diano, M. Gatica, M. Petri, G. 2025-06-25 doi:10.1101/2025.06.24.661306 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Testing Sensorimotor Timing in a Living Laboratory: Behavioral Signatures of a Neural Oscillator ]]> https://biorxiv.org/content/10.1101/2025.06.25.661347v1?rss=1 Serre, H. Harrigian, K. Park, S.-W. Sternad, D. 2025-06-25 doi:10.1101/2025.06.25.661347 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Haplotype-Resolved DNA Methylation at the APOE Locus identifies Allele-Specific Epigenetic Signatures Relevant to Alzheimer's Disease Risk ]]> https://biorxiv.org/content/10.1101/2025.07.01.662592v1?rss=1 T), {varepsilon}3 (reference), and {varepsilon}4 (rs429358(T>C)), arise from two coding variants in exon 4 and confer distinct AD risk profiles, with {varepsilon}4 increasing risk and {varepsilon}2 providing protection. The {varepsilon}3-linked APOE variant rs769455[T] has also been associated with elevated AD risk in individuals of African ancestry carrying both rs769455[T] and {varepsilon}4 alleles. These single nucleotide variants (SNVs) reside in a cytosine-phosphate-guanine (CpG) island, which is a region with a higher frequency of CpG sites compared to the rest of the genome. CpG sites are subject to 5-methylcytosine (5mC) methylation by DNA methyltransferases which add a methyl group to the fifth carbon on the cytosine residue of a CpG site. The presence of SNVs can disrupt this process, making these regions prime targets for differential methylation; however, allele-specific methylation patterns in APOE remain poorly resolved due to technical limitations of conventional bisulfite and methylation array based methods, including degraded DNA quality, sparse CpG coverage, and lack of haplotype phasing. Here, we leverage high-accuracy long-read sequencing data to generate haplotype-resolved methylation profiles of the APOE locus in 332 postmortem brain samples from two ancestrally different cohorts. This includes 201 individuals of European ancestry from the North American Brain Expression Consortium (NABEC), comprising 402 haplotypes (48 {varepsilon}2 and 58 {varepsilon}4 alleles), and 131 individuals of African and African admixed ancestry from the Human Brain Core Collection (HBCC), comprising 262 haplotypes (25 {varepsilon}2, 64 {varepsilon}4, and 7 rs769455 alleles). A linear regression analysis identified 18 novel differentially methylated CpG sites (DMCs) associated with APOE {varepsilon}2, {varepsilon}4, and rs769455 within a gene cluster spanning TOMM40, APOE, APOC1, and APOC4-APOC2. This represents the most comprehensive haplotype-resolved methylation study of APOE in human brain tissue to date. Our results uncover distinct allele-specific methylation signatures and demonstrate the power of long-read sequencing for resolving epigenetic variation relevant to AD risk. ]]> Genner, R. M. Meredith, M. Moller, A. Weller, C. Daida, K. Ayuketah, A. Jerez, P. A. Akeson, S. Malik, L. Baker, B. Kouam, C. Paquette, K. Marenco, S. Auluck, P. Mandal, A. Paten, B. Reed, X. Jain, M. Cookson, M. R. Singleton, A. B. Nalls, M. A. Blauwendraat, C. Billingsley, K. J. 2025-07-02 doi:10.1101/2025.07.01.662592 Cold Spring Harbor Laboratory Press 2025-07-02 <![CDATA[ Hybrid yak-cattle in situ conservation via interspecies somatic cell nuclear transfer at ultra-high-altitude region ]]> https://biorxiv.org/content/10.1101/2025.07.10.664179v1?rss=1 Yu, D. Nima, Q. Cao, L. Gu, S. Yin, K. Zhang, Y. Wang, J. Basang, W. Huang, Y. 2025-07-16 doi:10.1101/2025.07.10.664179 Cold Spring Harbor Laboratory Press 2025-07-16 <![CDATA[ Twice as nice: Boosts in adolescent reinforcement learning from Pavlovian bias and age-related prioritization of reward-motivated incidental memory. ]]> https://biorxiv.org/content/10.1101/2025.07.11.664442v1?rss=1 Hegefeld, H. M. Davidow, J. Y. 2025-07-17 doi:10.1101/2025.07.11.664442 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Microbial consortia in salt marsh sediments are sequentially buried over millennia and genomic complementarity analysis indicates an important role in complex carbon decomposition ]]> https://biorxiv.org/content/10.1101/2025.07.18.665577v1?rss=1 Vineis, J. H. Bulseco, A. N. Cardon, Z. G. Bowen, J. L. 2025-07-23 doi:10.1101/2025.07.18.665577 Cold Spring Harbor Laboratory Press 2025-07-23 <![CDATA[ Synaptic sign switching mediates online dopamine updates ]]> https://biorxiv.org/content/10.1101/2025.07.23.666367v1?rss=1 Li, S. Wang, W. Knipe, G. Jerng, E. Capelli, P. Zhou, C. Bilsel, E. Sabatini, B. L. 2025-07-24 doi:10.1101/2025.07.23.666367 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ Recurrent connectivity supports carbon dioxide sensitivity in Aedes aegypti mosquitoes ]]> https://biorxiv.org/content/10.1101/2025.07.29.667487v1?rss=1 Bao, J. Alford, W. Khandelwa, A. Walsh, L. Lantz, G. Poncio, S. Capdevila, L. S. Azatian, Y. DePasquale, B. Hildebrand, D. G. Younger, M. A. Lee, W.-C. A. 2025-07-30 doi:10.1101/2025.07.29.667487 Cold Spring Harbor Laboratory Press 2025-07-30 <![CDATA[ Platelets drive immune suppression and glioblastoma growth in a sex-dependent manner via PAR4 signaling ]]> https://biorxiv.org/content/10.1101/2025.08.06.668464v1?rss=1 Sloan, A. R. Bukenya, G. Aggarwal, A. Lee, J. Rosoff, D. Alban, T. Juric, I. Silver, D. J. Tacj, L. Navadgi, T. Tannish, G. Yuan, X. Coker, J. Scalise, A. Rajasekar, B. Vincenti, A. Mulkearns-Hubert, E. E. Horbinski, C. Sloan, A. E. Hubert, C. G. Luo, J. Rubin, J. B. Stavrou, E. X. Lohoff, F. W. Nieman, M. T. Sangwan, N. Chan, T. Khorana, A. A. Dhawan, A. Cameron, S. Lathia, J. 2025-08-08 doi:10.1101/2025.08.06.668464 Cold Spring Harbor Laboratory Press 2025-08-08 <![CDATA[ Bottlebrush Polymer Conjugates for Enhanced Antisense Oligonucleotide Therapy in Myotonic Dystrophy Type 1 ]]> https://biorxiv.org/content/10.1101/2025.08.06.668589v1?rss=1 View larger version (21K): org.highwire.dtl.DTLVardef@e3961corg.highwire.dtl.DTLVardef@194225dorg.highwire.dtl.DTLVardef@5c470dorg.highwire.dtl.DTLVardef@3cc46a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Li, Y. Oetheimer, C. Wang, Y. Heo, G. S. Wu, J. Chang, R. Zhang, W. Schneider, E. Chen, J. Fang, Y. Wei, Y. Nian, K. Zhang, H. Sherman, L. Liu, Y. Zhang, K. 2025-08-08 doi:10.1101/2025.08.06.668589 Cold Spring Harbor Laboratory Press 2025-08-08 <![CDATA[ GHIST 2024: The 1st Genomic History Inference Strategies Tournament ]]> https://biorxiv.org/content/10.1101/2025.08.05.668560v1?rss=1 Struck, T. J. Vaughn, A. H. Daigle, A. Ray, D. D. Noskova, E. Sequeira, J. J. Antonets, S. Alekseevskaya, E. Grigoreva, E. Raines, E. McMaster, E. S. Kovacs, T. G. L. Ragsdale, A. P. Moreno-Estrada, A. Lotterhos, K. E. Siepel, A. Gutenkunst, R. N. 2025-08-11 doi:10.1101/2025.08.05.668560 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome ]]> https://biorxiv.org/content/10.1101/2025.08.09.669508v1?rss=1 Wanes, G. Mohanty, U. Whitford, P. C. 2025-08-12 doi:10.1101/2025.08.09.669508 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Comprehensive evaluation of antibody responses to mosquitoes and mosquito-borne arboviruses using highly multiplexed serology ]]> https://biorxiv.org/content/10.1101/2025.08.15.670562v1?rss=1 Anahtar, M. Striplet, D. Philbin, E. Lacsina, J. R. Valenzuela, J. G. Johansson, M. Oliveira, F. Willen, L. Kamhawi, S. Cote-Lheureux, A. Fortune, S. M. Neafsey, D. 2025-08-15 doi:10.1101/2025.08.15.670562 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Single-Cell Characterization of Anterior Segment Development: Cell Types, Pathways, and Signals Driving Formation of the Trabecular Meshwork and Schlemm's Canal ]]> https://biorxiv.org/content/10.1101/2025.08.15.670438v1?rss=1 Balasubramanian, R. Tolman, N. Li, T. Hannan, A. Bupp-Chickering, V. Polanco, K. Bhandari, A. Zhou, S. Simon, M. Peregrin, J. Montgomery, C. Kizhatil, K. Qian, J. John, S. 2025-08-21 doi:10.1101/2025.08.15.670438 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ SEAHORSE: A Serendipity Engine Assaying Heterogeneous Omics-Related Sampling Experiments ]]> https://biorxiv.org/content/10.1101/2025.08.15.670514v1?rss=1 Quackenbush, A. Kolluri, J. Biju, R. Nhong, S. DeConti, D. Quackenbush, J. Saha, E. 2025-08-21 doi:10.1101/2025.08.15.670514 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ Connectome-based predictive modelling predicts frailty levels in older adults ]]> https://biorxiv.org/content/10.1101/2025.08.26.672253v1?rss=1 Ghaffari, A. Abouzaki, M. Romero, Y. Sun, A. Seitz, A. langley, j. Bennett, I. Hu, X. 2025-08-31 doi:10.1101/2025.08.26.672253 Cold Spring Harbor Laboratory Press 2025-08-31 <![CDATA[ A multi-frequency whole-brain neural mass model with homeostatic feedback inhibition ]]> https://biorxiv.org/content/10.1101/2025.08.26.672269v1?rss=1 Coronel-Oliveros, C. Lehue, F. Herzog, R. Mindlin, I. Gatica, M. Kowalczyk-Grebska, N. Medel, V. Cruzat, J. Gonzalez-Gomez, R. Hernandez, H. Tagliazucchi, E. Prado, P. Orio, P. Ibanez, A. 2025-08-31 doi:10.1101/2025.08.26.672269 Cold Spring Harbor Laboratory Press 2025-08-31 <![CDATA[ Improving neuroimaging headgear placement robustness using facial-landmark guided augmented reality ]]> https://biorxiv.org/content/10.1101/2025.08.29.660730v1?rss=1 Yen, F.-Y. Lin, Y.-A. Fang, Q. 2025-09-01 doi:10.1101/2025.08.29.660730 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ Systemic inflammation reduces astrocyte Ca2+ and neurovascular coupling in a mouse model of Alzheimers disease ]]> https://biorxiv.org/content/10.1101/2025.08.31.673380v1?rss=1 Liu, C. Sakha, K. A. Anton, J. Cardenas-Rivera, A. Yaseen, M. A. 2025-09-04 doi:10.1101/2025.08.31.673380 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Soil composition structures genetic variation across small spatial scales in a rare serpentine endemic plant ]]> https://biorxiv.org/content/10.1101/2025.09.01.673272v1?rss=1 Braasch, J. Harencar, J. G. Swope, S. M. 2025-09-05 doi:10.1101/2025.09.01.673272 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ Automated Quantification of Stereotypical Motor Movements in Autism Using Persistent Homology ]]> https://biorxiv.org/content/10.1101/2025.09.03.674008v1?rss=1 MBaye, A. A. Perea, J. A. Tralie, C. J. Goodwin, M. S. 2025-09-05 doi:10.1101/2025.09.03.674008 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ Gel-Amin for improving signal propagation and extracellular recordings of cardiomyocytes in a 3D Microphysiological System ]]> https://biorxiv.org/content/10.1101/2025.09.04.674300v1?rss=1 Pizzarella, D. Neuman, K. E. Burson, N. Koppes, A. N. Koppes, R. A. 2025-09-09 doi:10.1101/2025.09.04.674300 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ Endogenous suspension and reset of consciousness: 7T fMRI brain mapping of the extended cessation meditative endpoint ]]> https://biorxiv.org/content/10.1101/2025.09.06.674021v1?rss=1 Yang, W. F. Kadambi, A. Abellaneda-Perez, K. Mackin, G. Beslic, I. Potash, R. Sparby, T. Sacchet, M. D. 2025-09-11 doi:10.1101/2025.09.06.674021 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[ Sex Differences in Plasma Levels of Endocannabinoids and Related Lipids Before and After acute and repeated mTBI: an exploratory study for plasma biomarkers for mTBI ]]> https://biorxiv.org/content/10.1101/2025.09.10.675401v1?rss=1 Richter, E. Woodward, T. Kulkarni, P. Ferris, C. Bradshaw, H. B. 2025-09-15 doi:10.1101/2025.09.10.675401 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ Accounting for longitudinal peak quality metrics with MSstats+ enhances differential analysis in proteomic experiments with data-independent acquisition ]]> https://biorxiv.org/content/10.1101/2025.09.11.675573v1?rss=1 Kohler, D. Dogu, E. Bhattacharya, M. Karayel, O. Magana, M. Wu, A. Anania, V. G. Vitek, O. 2025-09-16 doi:10.1101/2025.09.11.675573 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Developmental Connectomics of the Mouse Cerebellum ]]> https://biorxiv.org/content/10.1101/2025.09.15.676403v1?rss=1 Dhanyasi, N. Meirovitch, Y. Kapoor, V. Wilson, A. M. Wang, S. Wei, D. Schalek, R. Ma, R. Wu, Y. Manthena, A. Cervantes, D. C. Lin, Z. Liu, Y. Chimaladinne, S. Morris, B. Vaddiparti, I. A. Zhu, Y. Dokiburra, S. Parampalli, R. Yang, F. Berger, D. R. Pfister, H. Murthy, V. N. Lichtman, J. W. 2025-09-16 doi:10.1101/2025.09.15.676403 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ CNS-Tau Specific Antibodies Illuminate Disease Signatures Across Tauopathies ]]> https://biorxiv.org/content/10.1101/2025.09.14.676119v1?rss=1 Liu, L. Zheng, Y. Slominski, L. Quan, Q. Saba, A. Bellier, J.-P. Yoo, H.-B. Roman, A. Hennessey, E. L. Wijethunga, S. Okyay, E. L. Miller, M. B. Yang, H.-S. Selkoe, D. J. Chhatwal, J. 2025-09-17 doi:10.1101/2025.09.14.676119 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Evidence for the Transient Presence of Atypical Astrocytes in Mice Following a Single, Closed-Head Mild Traumatic Brain Injury ]]> https://biorxiv.org/content/10.1101/2025.09.16.676600v1?rss=1 Blackman, J. B. Krauss, R. Quinones, S. Tirja, P. Sommer, M. E. Munoz-Ballester, C. Noubary, F. Armbruster, M. Robel, S. Anderson, T. Dulla, C. G. 2025-09-17 doi:10.1101/2025.09.16.676600 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Dimethylindanoylindole isomers revealed different pharmacological profiles at CB1 and CB2 cannabinoid receptors ]]> https://biorxiv.org/content/10.1101/2025.09.16.676463v1?rss=1 Oh, S. J. Guo, R. Lucaj, C. Ahmed, K. T. Dudley, G. B. Yano, H. 2025-09-18 doi:10.1101/2025.09.16.676463 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Engineering NIR probes to enhance affinity and clinical workflow compatibility for prostate cancer imaging ]]> https://biorxiv.org/content/10.1101/2025.09.16.676549v1?rss=1 Malankar, G. S. Szafran, D. A. Kumar, G. Pacce, J. Devereux, M. Tao, K. Gomes, M. Greer, W. S. Rounds, C. C. Masillati, A. M. Gergis, S. Ledvina, H. Wong, M. H. Niedre, M. J. Wang, L. G. Gibbs, S. L. 2025-09-18 doi:10.1101/2025.09.16.676549 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Vascular-Perfusable Human 3D Brain-on-Chip ]]> https://biorxiv.org/content/10.1101/2025.09.18.676925v1?rss=1 Stanton, A. E. Pinals, R. L. Choi, A. Truong, N. Kang, E. Jiang, A. Lozano Cruz, C. F. Hawkins, S. Sarcar, R. Volkova, A. King, O. Agbas, E. Nakano, M. Chiu, C.-C. Bubnys, A. Wright, S. Staab, C. Bikdash, R. Forden, E. Langer, R. Tsai, L.-H. 2025-09-19 doi:10.1101/2025.09.18.676925 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Principles of protein abundance regulation across single cells in a mammalian tissue ]]> https://biorxiv.org/content/10.1101/2025.09.17.676955v1?rss=1 Leduc, A. Shipkovenska, G. Xu, Y. Franks, A. Slavov, N. 2025-09-20 doi:10.1101/2025.09.17.676955 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Pore-Based RNA Evaluation for Control of Integrity, Sequence, and Errors - Quality Control (PRECISE-QC) ]]> https://biorxiv.org/content/10.1101/2025.09.20.677417v1?rss=1 View larger version (19K): org.highwire.dtl.DTLVardef@1163a7forg.highwire.dtl.DTLVardef@5a709corg.highwire.dtl.DTLVardef@19737e6org.highwire.dtl.DTLVardef@d71a60_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yee, Y. Boyko, D. Pandit, B. Royzen, M. Rouhanifard, S. H. Wanunu, M. 2025-09-21 doi:10.1101/2025.09.20.677417 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Cytoplasmic localization of PUS7 facilitates a pseudouridine-dependent enhancement of cellular stress tolerance ]]> https://biorxiv.org/content/10.1101/2025.09.22.675887v1?rss=1 Ruan, M. Engels, S. M. Burroughs, M. R. Li, X. Stower, R. Tzadikario, T. Powell, C. Bloch, D. Fanari, O. Akeson, S. Eyler, D. E. Weidmann, C. Rouhanifard, S. H. Jain, M. Contreras, L. M. Koutmou, K. S. 2025-09-22 doi:10.1101/2025.09.22.675887 Cold Spring Harbor Laboratory Press 2025-09-22 <![CDATA[ Effects of the Neutral CB1 Receptor Antagonist AM6527 on Spontaneous, Consummatory, and Motivated Behavior in Mice ]]> https://biorxiv.org/content/10.1101/2025.09.22.677777v1?rss=1 Ecevitoglu, A. Flanagan-Burt, Q. C. Zhang, M. Moon, B. K. Ji, L. Makriyannis, A. Suh, J. 2025-09-22 doi:10.1101/2025.09.22.677777 Cold Spring Harbor Laboratory Press 2025-09-22 <![CDATA[ Rare bioactive tau oligomers from Alzheimer brain support both templated misfolding and fibril formation ]]> https://biorxiv.org/content/10.1101/2025.09.24.678227v1?rss=1 Quittot, N. Sivasankaran, D. Boeken, D. Chen, Y. Chun, J. E. Wiedmer, A. Derosla, V. Martins, M. B. M. S. Brooks, F. A. Meisl, G. Cotton, M. W. Arumuganainar, D. G. Stewart, T. C. Melloni, A. Frosh, M. P. Oakley, D. Makowski, L. Wanunu, M. Klenerman, D. Hyman, B. 2025-09-25 doi:10.1101/2025.09.24.678227 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Stage-specific transcriptomics of a leader cell reveals cell machineries driving collective invasion ]]> https://biorxiv.org/content/10.1101/2025.09.29.679269v1?rss=1 Agarwal, P. Maimon Zielonka, I. Gingold, H. Stolzenbach, V. Anava, S. Antonova, O. Cram, E. J. Rechavi, O. Zaidel-Bar, R. 2025-10-01 doi:10.1101/2025.09.29.679269 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Multi-Scale Kinetics Modeling and Advanced Assay for mRNA-Lipid Nanoparticle Potency Assessment ]]> https://biorxiv.org/content/10.1101/2025.09.29.679406v1?rss=1 View larger version (63K): org.highwire.dtl.DTLVardef@1f3ec2borg.highwire.dtl.DTLVardef@1163893org.highwire.dtl.DTLVardef@1dc530borg.highwire.dtl.DTLVardef@1d0264a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yang, Y. Qiu, Y. Wang, K. Liu, Y. Sanyal, G. Whitford, P. C. Rouhanifard, S. H. Xie, W. 2025-10-01 doi:10.1101/2025.09.29.679406 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Rational Design of Multiclade Coronavirus Spike Immunodominant Domain Nanoparticles Elicit Broad Antibody Responses ]]> https://biorxiv.org/content/10.1101/2025.10.01.679649v1?rss=1 Dzuvor, C. K. O. Moak, S. McManus, L. R. Thomas, A. Dzordzorme, A. E. Kim, T. Joseph, J. Foley, V. Gordon, I. J. Novik, L. Holman, L. A. Dropulic, L. K. McNamara, R. P. Corbett-Helaire, K. S. 2025-10-01 doi:10.1101/2025.10.01.679649 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ GOA-1 regulates spermathecal transits ]]> https://biorxiv.org/content/10.1101/2025.09.30.679514v1?rss=1 Sadeghian, F. Cram, E. J. 2025-10-02 doi:10.1101/2025.09.30.679514 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Long-Read epigenetic clocks identify improved brain aging predictions ]]> https://biorxiv.org/content/10.1101/2025.09.30.679553v1?rss=1 Grant, S. M. Makarious, M. B. Meredith, M. Moller, A. Grant-Peters, M. Hicks, A. Mandal, A. Auluck, P. Leonard, H. Kuznetsov, N. Weller, C. Reed, X. Jain, M. Ferrucci, L. Cookson, M. R. Ryten, M. Nalls, M. A. Billingsley, K. J. 2025-10-03 doi:10.1101/2025.09.30.679553 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ The genetic architecture of trabecular bone score and association with fracture: a genome-wide association and meta-analysis ]]> https://biorxiv.org/content/10.1101/2025.10.01.678241v1?rss=1 Lu, H. Tibbitts, G. LI, G. H.-Y. Frysz, M. Lary, C. W. Trajanoska, K. Das, N. R. de Groot, L. Cheung, C.-L. van Schoor, N. M. Uitterlinden, A. G. van der Velde, N. Tobias, J. H. Rivadeneira, F. Evans, D. M. Kiel, D. P. Kemp, J. P. Medina-Gomez, C. 2025-10-03 doi:10.1101/2025.10.01.678241 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ A switch in collagen expression regulates cessation of distal tip cell migration in C. elegans ]]> https://biorxiv.org/content/10.1101/2025.10.03.680101v1?rss=1 Stolzenbach, V. Griffin, S. S. Agarwal, P. Zaidel-Bar, R. Cram, E. J. 2025-10-03 doi:10.1101/2025.10.03.680101 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Multi-team conflict resolution is ineffective for stable decision making ]]> https://biorxiv.org/content/10.1101/2025.10.06.679762v1?rss=1 Anand, V. Haldar, K. Moger, A. Gedeon, T. Hari, K. Jolly, M. K. 2025-10-07 doi:10.1101/2025.10.06.679762 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Design and fabrication of demountable 3D microphysiological systems for modeling barrier function and underlying tissue interactions ]]> https://biorxiv.org/content/10.1101/2025.10.10.681761v1?rss=1 Banerjee, S. Brady, R. Abu-Absi, L. Miller, D. Schellberg, B. Dai, G. Koppes, A. N. Koppes, R. A. 2025-10-13 doi:10.1101/2025.10.10.681761 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ The neural correlates of novel versus familiar metaphors in healthy young adults: A functional near-infrared spectroscopy study ]]> https://biorxiv.org/content/10.1101/2025.10.12.681881v1?rss=1 Schwartz, A. Gilmore, N. Meier, E. L. 2025-10-13 doi:10.1101/2025.10.12.681881 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ Examining oculomotor behavior in central vision loss with a gaze-contingent display ]]> https://biorxiv.org/content/10.1101/2025.10.12.681883v1?rss=1 Maniglia, M. Maxwell, E. Vice, J. Visscher, K. Seitz, A. 2025-10-14 doi:10.1101/2025.10.12.681883 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Random, fragile, or correlated: Mechanisms of synteny decay in mammals ]]> https://biorxiv.org/content/10.1101/2025.10.13.682123v1?rss=1 Moffett, A. S. Di Pierro, M. 2025-10-14 doi:10.1101/2025.10.13.682123 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Structures of folding intermediates on BAM show diverse substrates fold by a uniform mechanism ]]> https://biorxiv.org/content/10.1101/2025.10.16.682720v1?rss=1 Thomson, B. D. Marquez, M. D. Rawson, S. dos Santos, T. M. A. Harrison, S. C. Kahne, D. 2025-10-17 doi:10.1101/2025.10.16.682720 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Patterns of intersubject correlations parallel organizational gradients during naturalistic viewing ]]> https://biorxiv.org/content/10.1101/2025.10.19.683222v1?rss=1 Smith, M. E. Samara, A. Cabalo, D. G. Ngo, A. Shearer, H. Bernhardt, B. C. Vanderwal, T. 2025-10-20 doi:10.1101/2025.10.19.683222 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Benchmarking Perturbation Tools for the Noncoding Genome ]]> https://biorxiv.org/content/10.1101/2025.10.21.683665v1?rss=1 Zhang, H. Luo, S. Wang, X. Lin, L. Liang, R. Zhong, C. Zhang, Y. Zhao, W. Chen, Z. Liu, X. Chen, F. Sun, N. Huang, J. Fei, T. 2025-10-22 doi:10.1101/2025.10.21.683665 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ A Quasi-Stationary Distribution Bound for Fault Analysis in Gene Regulatory Networks ]]> https://biorxiv.org/content/10.1101/2025.10.21.683707v1?rss=1 Cravo, F. Fuegger, M. Nowak, T. 2025-10-22 doi:10.1101/2025.10.21.683707 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ YAP1 defines an emergent, plastic population of relapsed small cell lung cancer ]]> https://biorxiv.org/content/10.1101/2025.10.21.683746v1?rss=1 Stewart, C. A. Ramkumar, K. Wang, R. Xi, Y. Halliday, A. Diao, L. Wang, Q. Serrano, A. Groves, S. Heeke, S. Tanimoto, A. Kaiser, L. Lewis, W. Bose, M. Da Rocha, P. Karacosta, L. Quaranta, V. Wang, J. George, J. Solis Soto, L. M. Zhang, B. Heymach, J. V. Byers, L. A. Gay, C. M. 2025-10-22 doi:10.1101/2025.10.21.683746 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Exploring the functions of JAKMIP1 in neuronal IL-6/STAT3 signaling and its relevance to chromosome 15q-duplication syndrome ]]> https://biorxiv.org/content/10.1101/2025.10.21.683757v1?rss=1 Martin, J. G. Martin, E.-R. Takamura, N. Harlow, C. E. Bamford, R. A. Smith, R. G. Morgan, N. G. Inaba-Inoue, S. Mill, J. Srivastava, D. P. Dawe, H. R. Chilton, J. K. Russell, M. A. Oguro-Ando, A. 2025-10-22 doi:10.1101/2025.10.21.683757 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ The Contextual Affects of Facial Expression ]]> https://biorxiv.org/content/10.1101/2025.10.23.683775v1?rss=1 Cui, B. Bex, P. J. 2025-10-27 doi:10.1101/2025.10.23.683775 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ The Affects of Central Vision Loss on Emotion Perception ]]> https://biorxiv.org/content/10.1101/2025.10.23.683781v1?rss=1 Cui, B. Bex, P. J. 2025-10-27 doi:10.1101/2025.10.23.683781 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Are mitochondrial DNA mutations under purifying selection in somatic tissues? ]]> https://biorxiv.org/content/10.1101/2025.10.26.684677v1?rss=1 Franco, M. Bandell, J. Popadin, K. Woods, D. C. Khrapko, K. 2025-10-30 doi:10.1101/2025.10.26.684677 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Phosphorylation of a conserved intrinsically disordered region is necessary for activation of a bacterial Hanks-type Ser/Thr kinase signaling pathway ]]> https://biorxiv.org/content/10.1101/2025.11.01.686061v1?rss=1 Grunfeld, N. Levine, E. Libby, E. A. 2025-11-02 doi:10.1101/2025.11.01.686061 Cold Spring Harbor Laboratory Press 2025-11-02 <![CDATA[ Measuring Perfusion Pressure and Flow Resistance in a Microfluidic Device Using an External Optical System ]]> https://biorxiv.org/content/10.1101/2025.11.03.686291v1?rss=1 Coughlin, M. C. Floryan, M. Offeddu, G. Coughlin, M. F. 2025-11-04 doi:10.1101/2025.11.03.686291 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Circadian rhythms in sexual behavior and their influence on reproductive outcomes in mice ]]> https://biorxiv.org/content/10.1101/2025.11.05.686629v1?rss=1 Aten, S. Blake, C. Keister, E. Veith, A. Fishbein, E. Ramirez-Plascencia, O. Thompson, M. Howe, S. Pereira, S. Sela, Y. Navarro, V. Saper, C. 2025-11-06 doi:10.1101/2025.11.05.686629 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ Evaluating Field Trial Designs for Genetically Modified Mosquito Interventions: An In-Silico Simulation Approach ]]> https://biorxiv.org/content/10.1101/2025.11.05.686816v1?rss=1 Chitturi, J. Ventura, P. C. Kummer, A. G. Vasquez, C. SeRine, E. Hill, M. D. Manica, M. Poletti, P. Beier, J. C. Ejima, K. Johansson, M. Merler, S. Yu, H. Mutebi, J.-P. Litvinova, M. Wilke, A. B. B. Ajelli, M. 2025-11-06 doi:10.1101/2025.11.05.686816 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ High dynamic range shortwave infrared (SWIR) imaging of mice with an InGaAs camera ]]> https://biorxiv.org/content/10.1101/2025.11.06.687088v1?rss=1 Patel, A. Zhong, X. Moffett, M. A. Sun, Y. Dennis, A. M. 2025-11-08 doi:10.1101/2025.11.06.687088 Cold Spring Harbor Laboratory Press 2025-11-08 <![CDATA[ Dynamic interaction between stress hormones and neutrophils promotes neutrophil extracellular trap formation with behavioral consequences ]]> https://biorxiv.org/content/10.1101/2025.11.12.688017v1?rss=1 Thangamani, K. B. Prece, H. Carter, J. Douglas, O. Brengel, E. Ferris, C. Okeke, E. 2025-11-13 doi:10.1101/2025.11.12.688017 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ The neuroscience of highly stable, positive, and refined states of consciousness during jhana-type advanced concentration absorption meditation (ACAM-J) ]]> https://biorxiv.org/content/10.1101/2025.11.12.688050v1?rss=1 Yang, W. F. Potash, R. Mackin, G. Beslic, I. Bianciardi, M. Sprby, T. Sacchet, M. D. 2025-11-13 doi:10.1101/2025.11.12.688050 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ DNA adduct and mutational profiles reveal a threshold of cellular defenses against N-nitrosodimethylamine administered to mice in drinking water ]]> https://biorxiv.org/content/10.1101/2025.11.13.687536v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@1e6ae72org.highwire.dtl.DTLVardef@1c6fad6org.highwire.dtl.DTLVardef@7e3716org.highwire.dtl.DTLVardef@52a87b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gubina, N. E. Volk, L. B. Dormitzer, A. F. Michelsen, E. M. Pribyl, L. J. Corrigan, J. J. Dalvie, E. D. Armijo, A. L. Norales, M. M. Bugher, N. A. Schonvisky, K. M. Plata, D. L. Engelward, B. P. Croy, R. G. Essigmann, J. M. Fedeles, B. I. 2025-11-14 doi:10.1101/2025.11.13.687536 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Wormtrails: a python package for viewing C. elegans movement ]]> https://biorxiv.org/content/10.1101/2025.11.14.688522v1?rss=1 Ashih, C. D. Xu, Y. Apfeld, J. 2025-11-17 doi:10.1101/2025.11.14.688522 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Unconventional linkers facilitate potent stabilized coronavirus stem antibody responses following nanoparticle vaccination ]]> https://biorxiv.org/content/10.1101/2025.11.19.689216v1?rss=1 Dzuvor, C. K. O. Moak, S. P. McManus, L. R. Dzordzorme, A. E. Evanson, L. R. Kim, T. Thomas, A. Adeyemi, O. Foley, V. Limaye, A. McNamara, R. P. Corbett-Helaire, K. S. 2025-11-19 doi:10.1101/2025.11.19.689216 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ Reductive death is averted by an ancient metabolic switch. ]]> https://biorxiv.org/content/10.1101/2025.11.24.690166v1?rss=1 Ahsan, F. M. Rotti, J. F. Yerevanian, A. I. Emans, S. W. Stuhr, N. L. Aceves-Salvador, J. A. Wang, W. Baker, D. J. Pouli, D. Skinner, O. S. Blower, M. D. Soukas, A. A. 2025-11-25 doi:10.1101/2025.11.24.690166 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Paradoxical gene regulation explained by competition for genomic sites ]]> https://biorxiv.org/content/10.1101/2025.11.27.691022v1?rss=1 Jatkar, D. D. Aravind, K. M. Sontag, E. D. Del Vecchio, D. 2025-11-27 doi:10.1101/2025.11.27.691022 Cold Spring Harbor Laboratory Press 2025-11-27 <![CDATA[ Optimization of heuristic logic synthesis by iteratively reducing circuit substructures using a database of optimal implementations ]]> https://biorxiv.org/content/10.1101/2025.11.28.691216v1?rss=1 Tran, A. P. Jatkar, D. D. Ali Al-Radhawi, M. Ernst, E. A. Sontag, E. D. 2025-11-29 doi:10.1101/2025.11.28.691216 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ Ancient DNA from shells reveals delayed genomic erosion and rapid immune adaptation in the critically endangered black abalone ]]> https://biorxiv.org/content/10.64898/2025.12.01.690857v1?rss=1 Wooldridge, B. Kapp, J. D. Ford, S. M. Seligmann, W. E. Conwell, H. C. Tzadikario, T. Oppenheimer, J. Anderson, Z. G. Le Moan, A. Abadia-Cardoso, A. Raimondi, P. Shapiro, B. A. 2025-12-03 doi:10.64898/2025.12.01.690857 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ Revealing Interactions between Microbes, Metabolites, and Dietary Compounds using Genome-scale Analysis ]]> https://biorxiv.org/content/10.64898/2025.12.03.692129v1?rss=1 Wang, T. Gyori, B. Weiss, S. T. Menichetti, G. Liu, Y.-Y. 2025-12-06 doi:10.64898/2025.12.03.692129 Cold Spring Harbor Laboratory Press 2025-12-06 <![CDATA[ Microbiome-behavior coupling shapes infant adaptation to early maternal unpredictability ]]> https://biorxiv.org/content/10.64898/2025.12.03.692149v1?rss=1 Amso, D. Bottino, G. F. Forest, T. A. Bonham, K. S. Zieff, M. Patel, F. Miles, M. Herr, D. Espinoza-Heredia, C. D'Amato, C. Ren, J. Goldstone, M. Mbale, E. Alexander, D. C. Jones, D. K. Williams, S. C. Fifer, W. P. Gabard-Durnam, L. Klepac-Ceraj, V. Donald, K. A. 2025-12-08 doi:10.64898/2025.12.03.692149 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Building dynamical models of multi-step state transitions from single cell gene expression trajectories ]]> https://biorxiv.org/content/10.64898/2025.12.08.693064v1?rss=1 You, Y. Caranica, C. Lu, M. 2025-12-11 doi:10.64898/2025.12.08.693064 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Plasticity Associated with Adoption of Social Roles in Clown Anemonefish ]]> https://biorxiv.org/content/10.64898/2025.12.09.693150v1?rss=1 Vizer, L. F. Alvarado, D. Bove, C. Herrera, M. Hughes, A. Thompson, K. Bogdanowicz, S. M. Laudet, V. Davies, S. Buston, P. 2025-12-11 doi:10.64898/2025.12.09.693150 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ UV induces common cutaneous amyloid-like melanosomal protein aggregates ]]> https://biorxiv.org/content/10.64898/2025.12.17.689083v1?rss=1 Theodosakis, N. Howland, P. B. Hejna, M. Ostrowski, S. M. Cohen-Neamie, T. A. Joseph, R. A. Ji, H. Greuel, A. E. Boozer, J. R. Demian, M. Y. Asim, A. Nguyen, K. Mu, A. M. Seifert, P. Kaminiow, K. D. Zhang, Y. Fassini, A. Germana, S. Shaw, K. C. Lin, W. M. Hoang, M. P. Wu, X. Chandra, S. S. Hacohen, N. Ballabio, A. Bakshi, R. Udeshi, N. D. Horn, T. D. Ganesan, A. K. Murphy, G. F. Carr, S. A. Hyman, B. Song, J. S. Fisher, D. E. 2025-12-18 doi:10.64898/2025.12.17.689083 Cold Spring Harbor Laboratory Press 2025-12-18 <![CDATA[ Elemental Composition and Degradation Rate Impact the Biocompatibility of Copper Chalcogenide Nanocrystals ]]> https://biorxiv.org/content/10.64898/2025.12.17.695045v1?rss=1 Zhong, X. Katsarakes, G. P. Nagarkar, S. Dennis, A. M. 2025-12-20 doi:10.64898/2025.12.17.695045 Cold Spring Harbor Laboratory Press 2025-12-20 <![CDATA[ Low-temperature HILIC provides enhanced separations and stability for LC-MS-based metabolomics ]]> https://biorxiv.org/content/10.64898/2025.12.19.695573v1?rss=1 Liu, Y. Jastrab, M. L. Xiao, M. Lisci, M. Bader, T. K. Jourdain, A. A. Wales, T. E. Skinner, O. S. 2025-12-22 doi:10.64898/2025.12.19.695573 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Predicting interaction-specific protein-protein interaction perturbations by missense variants with MutPred-PPI ]]> https://biorxiv.org/content/10.64898/2025.12.20.695738v1?rss=1 Stewart, R. Laval, F. Coppin, G. Spirohn-Fitzgerald, K. Tixhon, M. Hao, T. Calderwood, M. A. Mort, M. Cooper, D. N. Vidal, M. Radivojac, P. 2025-12-23 doi:10.64898/2025.12.20.695738 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ A Foundational Generative Model for Cross-platform Unified Enhancement of Spatial Transcriptomics ]]> https://biorxiv.org/content/10.64898/2025.12.23.696267v1?rss=1 1.7 million H&E-ST pairs and >5.8 million single-cell profiles, demonstrating state-of-the-art performance across ten ST platforms, on both individual and coupled challenges. The real-world utility and generalizability were validated on a rare suprasellar tumor, papillary craniopharyngioma, and an unseen ST platform (Open-ST) for primary and metastatic head and neck squamous cell carcinoma. ]]> Wang, X. Liu, H. Que, N. Tao, C. Jiang, Y. Jiang, Y. Zhu, P. Zhu, J. Li, X. Price, S. Xu, J. Xi, J. Wang, X. Li, C. 2025-12-25 doi:10.64898/2025.12.23.696267 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ Rapid fluorescence lifetime sensor development of LifeCamp enables transient and baseline absolute calcium measurements ]]> https://biorxiv.org/content/10.64898/2025.12.23.696288v1?rss=1 Lodder, B. Raghubardayal, M. Ganesh, S. Cai, X. Stern, J. Sherman, M. Rosen, P. Kamath, T. Hartman, I. Siegel, M. Timmins, J. Adan, R. Andermann, M. L. Sabatini, B. L. 2025-12-25 doi:10.64898/2025.12.23.696288 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ tRNA isodecoder analysis using Nanopore ionic current signals and deep learning ]]> https://biorxiv.org/content/10.64898/2025.12.27.696718v1?rss=1 Akeson, S. Kakhaki, P. D. Esfahani, N. G. Reinsch, J. L. Barry, M. L. Zamecnik, M. Tzadikario, T. Abu-Shumays, R. L. Garcia, D. M. Koutmou, K. Jain, M. 2025-12-28 doi:10.64898/2025.12.27.696718 Cold Spring Harbor Laboratory Press 2025-12-28 <![CDATA[ Structural and functional evidence for ephaptic control of Purkinje cell spike timing by networks of molecular layer interneurons ]]> https://biorxiv.org/content/10.64898/2025.12.28.696768v1?rss=1 Norton, A. Lackey, E. P. Ozturk, S. Gaynor, C. S. Ediger, S. Lee, W.-C. A. Hull, C. A. Regehr, W. G. 2025-12-29 doi:10.64898/2025.12.28.696768 Cold Spring Harbor Laboratory Press 2025-12-29 <![CDATA[ Ecological Dynamics of Pro-tumor and Anti-tumor Teams in the Tumor Microenvironment ]]> https://biorxiv.org/content/10.64898/2025.12.31.697148v1?rss=1 Anand, V. Jolly, M. K. Levine, H. 2026-01-01 doi:10.64898/2025.12.31.697148 Cold Spring Harbor Laboratory Press 2026-01-01 <![CDATA[ Integrative analysis of papain-like cysteine proteases and cystatins reveals stress-dependent regulatory modules in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.64898/2025.12.31.697236v1?rss=1 Wu, S. Yi, X. Li, S. Zhao, B. 2026-01-02 doi:10.64898/2025.12.31.697236 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ Aging, matrix metalloproteinase imaging, and survival prospects in aortic aneurysm ]]> https://biorxiv.org/content/10.64898/2026.01.02.697375v1?rss=1 51-week-old (old) Apoe-/- mice. Aortic MMP activation was quantified by PET/CT using an MMP-targeted tracer, 64Cu-RYM2, at baseline and 1 week after Ang II infusion. MMP activity and expression were quantified by tissue zymography and quantitative reverse transcription polymerase chain reaction, and compared between different segments of the aorta in young and old animals, and before and after Ang II infusion. ResultsOld animals survival to 28 days was significantly lower than that of young Ang-II-infused Apoe-/- mice (P < 0.05). 64Cu-RYM2 PET/CT showed significantly higher aortic MMP activation before and 1 week after Ang-II infusion in old compared to young Apoe-/-mice. The 64Cu-RYM2 signal was significantly higher in animals that did not survive 28 days than those that did (P < 0.01). MMP activity significantly increased by 4 days after Ang-II infusion, when dissection was found in a subset of Apoe-/- mice; and was significantly higher in the dissected, compared to adjacent, apparently normal, segments of the aorta. MMP activity was also significantly higher in the ascending thoracic aorta of untreated young and old mice, as well as of Ang-II-treated Apoe-/-mice (which was associated with significantly higher Mmp2 gene expression), and of old wild-type mice. ConclusionAging is associated with increased MMP activity along the aorta and worse AA survival. MMP-targeted molecular imaging can inform the aneurysm survival prospects. Selective MMP inhibitors and tracers may help prevent and track aneurysm growth, dissection, and rupture. ]]> Ghim, M. Varli, O. Ahmad, A. Neishabouri, A. Kukreja, G. Zhang, Z. Zarnegar, S. Gangemi, N. Toczek, J. Zhang, J. Liu, C. Liu, Y. Gropler, R. Sadeghi, M. M. 2026-01-02 doi:10.64898/2026.01.02.697375 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ Can AI Conduct Autonomous Scientific Research? Case Studies on Two Real-World Tasks ]]> https://biorxiv.org/content/10.64898/2026.01.05.697809v1?rss=1 Agrawal, S. Anadkat, H. Athimoolam, K. Bhardwaj, H. Chowdhury, T. Gao, S. Kamat, P. Makwana, V. Shariff, M. Badkul, A. Xie, L. Sinitskiy, A. 2026-01-06 doi:10.64898/2026.01.05.697809 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ 3D genome architecture regulates the traffic of transcription factors throughout human chromosomes ]]> https://biorxiv.org/content/10.64898/2026.01.06.698019v1?rss=1 Das, A. Cheng, R. R. Potoyan, D. A. Di Pierro, M. 2026-01-06 doi:10.64898/2026.01.06.698019 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ Small molecule stabilization of diverse amyloidogenic immunoglobulin light chains revealed by hydrogen-deuterium exchange mass spectrometry ]]> https://biorxiv.org/content/10.64898/2026.01.07.698275v1?rss=1 Peterle, D. Yan, N. L. Klimtchuk, E. S. Wales, T. E. Gursky, O. Kelly, J. W. Engen, J. R. Morgan, G. J. 2026-01-08 doi:10.64898/2026.01.07.698275 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Positive germline selection of mtDNA mutations: evidence from the oocyte. ]]> https://biorxiv.org/content/10.64898/2025.12.31.697248v1?rss=1 View larger version (65K): org.highwire.dtl.DTLVardef@96fc4eorg.highwire.dtl.DTLVardef@8e717eorg.highwire.dtl.DTLVardef@1bd38b8org.highwire.dtl.DTLVardef@1d6cc69_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure A.C_FLOATNO Cumulative proportion curves of relevant types of mutations (color coded). The corresponding selection metrics,[S] 0.01, and Monte-Carlo p-values are shown, analyses for other thresholds: tables 2 and S1 C_FIG O_TBL View this table: org.highwire.dtl.DTLVardef@1063ef6org.highwire.dtl.DTLVardef@10fa4b2org.highwire.dtl.DTLVardef@5e13corg.highwire.dtl.DTLVardef@64afaorg.highwire.dtl.DTLVardef@12484f3_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable S1.C_FLOATNO C_TBL In Figure 1, datapoints represent clones of mutations ranked by their size and plotted vs. their cumulative contribution to the mutational pool (in reverse order). The resulting cumulative curves represent the collective expansion of clones of mutations of each type. As previously shown by direct simulations (Franco et al., 2025), the slope of the curve qualitatively depicts the relative intensity of clonal expansion. The green curve consists of synonymous (neutral) mutations and thus defines the trajectory of expansion driven by neutral genetic drift. Curves that diverge upward from the neutral green curve imply faster-than-neutral expansion, i.e., positive selection in corresponding mutation types, and those that diverge downward (grey Co1 curve) imply negative selection. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=169 SRC="FIGDIR/small/697248v1_fig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@9483a5org.highwire.dtl.DTLVardef@4efc4dorg.highwire.dtl.DTLVardef@1964229org.highwire.dtl.DTLVardef@1d1c5d9_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Cumulative proportion curves of relevant types of mutations (color coded). C_FIG To estimate selection, we first defined extent of clonal expansion,[E] t (mutant class), a measure of overall clonal expansion, i.e., the proportion of aggregate fraction of mutants of a particular class in clones that exceeded a specific size (i.e., MF). For example,[E] 0.01(coding) is the ratio of aggregate mutant fraction of all large clones (MF>0.01) of coding mutations, divided by the aggregate mutant fraction of all coding mutations.[E] t changes with t, but at each t, it permits us to compare the extent of expansion between different classes of mutations (e.g., coding vs. non-coding). Selection at the intracellular level manifests as an acceleration or deceleration of the expansion (or loss) of mutant clones relative to the expansion expected under random drift, as represented by synonymous mutations. Accordingly, a measure of clonal selection for a tested mutation class, denoted[S] t(tested), is defined as the excess clonal expansion in the tested mutations over expansion of synonymous mutations, normalized by the expansion of synonymous mutations: O_FD O_INLINEFIG[Formula 1]C_INLINEFIGM_FD(1)C_FD In Fig.1, [S]0.01 and p-values demonstrate: O_LIStrong positive selection of noncoding mutations (blue). C_LIO_LIPositive selection of coding mutations (orange). C_LIO_LIA higher positive selection in conservative (i.e., more detrimental) coding mutations (red). So, selection may be driven by the detrimental effects of mtDNA mutations. C_LIO_LINegative selection in the Co1 gene (grey). Thus, negative/purifying selection does exist, but dominates only in specific small regions (like Co1). C_LIO_LISelection in non-coding mutations starts at low mutant fractions, coding at higher mutant fractions. C_LI This confirms the prevalence of positive selection and clarifies why Arbeithuber et al. perceived selection as purifying. The authors compared coding to non-coding mutations. The latter are under stronger positive selection than coding mutations. Thus, coding mutations appear to be under relative negative selection, but only in comparison to non-synonymous mutations, not in absolute, real terms. Note that positive selection does not necessarily proceed in oocytes. Some of the mutations present in oocytes originate in primordial germ cells (PGCs), where they may also have been under selection before being passed on to oocytes. Indeed, positive selection in PGCs has been demonstrated previously (Fleischmann et al., 2024). Finally, positive selection of detrimental mutations in oocytes may seem surprising from an evolutionary perspective. A possible explanation is that the detrimental effects of mtDNA mutations usually do not show up till MF surpasses a physiological threshold. Thus, positive expansion may expose the detrimental phenotype of mutations and assist in removing carrier cells, embryos, or individuals, thus reducing burden on the mother. In line with this, purifying selection become prevalent among inherited mtDNA mutations. ]]> Franco, M. Fleischmann, Z. Annis, S. Cote-L'Heureux, A. Aidlen, D. Khrapko, M. Vyshedskiy, B. Mirzoyan, D. Bandell, J. Popadin, K. Woods, D. C. Tilly, J. L. Khrapko, K. 2026-01-09 doi:10.64898/2025.12.31.697248 Cold Spring Harbor Laboratory Press 2026-01-09 <![CDATA[ Energetic implications of fMRI-based nodal complex network metrics: a complex picture unfolds across diverse brain states ]]> https://biorxiv.org/content/10.64898/2026.01.08.694967v1?rss=1 Feng, S. Coursey, S. E. Nolin, S. A. Zurcher, N. R. Wey, H.-Y. Polimeni, J. R. Villien, M. Bhanot, A. Rosen, B. R. Hooker, J. M. Chen, J. E. 2026-01-09 doi:10.64898/2026.01.08.694967 Cold Spring Harbor Laboratory Press 2026-01-09 <![CDATA[ Pannexin-1 channel activity regulates neurogenesis and cell survival in the developing cortex ]]> https://biorxiv.org/content/10.64898/2026.01.09.697058v1?rss=1 Hylton, N. K. Kang, D. J. Decker, S. C. Exposito-Alonso, D. Cambridge, C. N. Golinski, S. R. Soriano, K. I. Neil, J. E. Talukdar, M. Andersen, R. E. Buckner, T. M. Qian, X. Doddi, A. D. Braddock, S. R. DeGennaro, E. M. Akula, S. K. Simo, S. Smith, R. S. Walsh, C. A. 2026-01-09 doi:10.64898/2026.01.09.697058 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[ Aerobic Exercise Preserves Capillary Oxygen Homeostasis and Neurovascular Function in a Mouse Model of Alzheimer's Disease ]]> https://biorxiv.org/content/10.64898/2026.01.15.699787v1?rss=1 Cardenas-Rivera, A. Erdogmus, E. Birmingham, A. Yee, E. Anton, J. Lu, Z. Li, Y. Morais, M. Loghmani, N. Liu, C. Yaseen, M. A. 2026-01-16 doi:10.64898/2026.01.15.699787 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ An integrated, scaled approach to resolve TSC2 variants of uncertain significance ]]> https://biorxiv.org/content/10.64898/2026.01.16.699909v1?rss=1 Biar, C. G. Wang, Z. R. Camp, N. D. Holmes, D. L. Wheelock, M. K. Pendyala, S. McGee, A. V. Gupta, P. McEwen, A. E. Tejura, M. Richardson, M. E. Weyandt, J. D. Coleman, T. Stewart, R. Zeiberg, D. Vandi, A. J. Dawson, S. Radivojac, P. Starita, L. M. Carvill, G. L. James, R. G. Fowler, D. M. Calhoun, J. D. 2026-01-18 doi:10.64898/2026.01.16.699909 Cold Spring Harbor Laboratory Press 2026-01-18 <![CDATA[ Hyperactivated YAP1 Drives an Invasive EMT Subtype of Cervical Squamous Cell Carcinoma ]]> https://biorxiv.org/content/10.64898/2026.01.18.700207v1?rss=1 Liu, J. Lv, X. Ruan, J. He, C. Hua, G. Chen, P. Zhao, X. Shi, D. Yang, S. Polakkottil, A. Moness, M. Carbajal, B. Kurma, G. Guda, R. Mohamed, A. Abioye, o. Sadreyev, R. davis, J. S. Wang, C. 2026-01-19 doi:10.64898/2026.01.18.700207 Cold Spring Harbor Laboratory Press 2026-01-19 <![CDATA[ Ribosomal Protein bL27 Protects Translating Ribosomes from tmRNA-SmpB ]]> https://biorxiv.org/content/10.64898/2026.01.19.700400v1?rss=1 Seerpatham, D. Wanes, G. Pathirage, C. Cabrera, M. Usoro, E. Koutmou, K. Dunham, C. Whitford, P. Keiler, K. 2026-01-19 doi:10.64898/2026.01.19.700400 Cold Spring Harbor Laboratory Press 2026-01-19 <![CDATA[ PfApiAT2 is a proline transporter essential for the transmission of Plasmodium falciparum by the mosquito vector. ]]> https://biorxiv.org/content/10.64898/2026.01.20.700404v1?rss=1 Khushu, M. Kissel, R. C. Kauffman, J. Taccheri, C. Singh, N. Summers, R. L. Plant, L. D. Wirth, D. Catteruccia, F. Bopp, S. 2026-01-20 doi:10.64898/2026.01.20.700404 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ PRISME: A MATLAB Toolbox For Large Data-Driven Multimodal Power Benchmarking ]]> https://biorxiv.org/content/10.64898/2026.01.21.700878v1?rss=1 Cravo, F. Fischbach, A. Shearer, H. Rosenblatt, M. Scheinost, D. Noble, S. 2026-01-22 doi:10.64898/2026.01.21.700878 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Extracellular vesicles facilitate the horizontal transfer of drug resistance and stem-like properties between ovarian tumor cells ]]> https://biorxiv.org/content/10.64898/2026.01.20.699925v1?rss=1 View larger version (44K): org.highwire.dtl.DTLVardef@6b4ffborg.highwire.dtl.DTLVardef@1501931org.highwire.dtl.DTLVardef@1a5f31aorg.highwire.dtl.DTLVardef@1fb475f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pooladanda, V. Xu, R. Zarella, D. Matoba, Y. Shimada, C. Kumar, S. Kim, E. Dibenedetto, P. Qin, X. Sarosiek, K. Krueger, M. Magrassi, N. Amiji, M. Azimi-Mohammadabadi, M. Winter, U. Castro, C. M. Im, H. M. Kumar, R. Wang, C. Cowdon-Dahl, K. Nephew, K. Yeku, O. Milane, L. Rueda, B. R. 2026-01-23 doi:10.64898/2026.01.20.699925 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ PRDX6 Modulates Immune Checkpoint Inhibitor Response by Antagonizing Ferroptosis Induced By HDAC Inhibitors ]]> https://biorxiv.org/content/10.64898/2026.01.21.700636v1?rss=1 Liu, Z. John, J. Johnson, N. Singh, P. Wang, Z. Sanchez, G. J. Wang, J. H. Liu, X. 2026-01-23 doi:10.64898/2026.01.21.700636 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Histology-Aware Graph for Modeling Intercellular Communication in Spatial Transcriptomics ]]> https://biorxiv.org/content/10.64898/2026.01.22.701166v1?rss=1 Wang, X. Tao, C. Jiang, Y. Liu, H. Jiang, Z. Zhu, P. Que, N. Xi, J. Price, S. Mou, Y. Li, C. 2026-01-23 doi:10.64898/2026.01.22.701166 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ The C. elegans nervous system reads the internal state of the hydrogen peroxide-detoxification machinery to trigger escape from this common reactive chemical ]]> https://biorxiv.org/content/10.64898/2026.01.22.701078v1?rss=1 Xu, Y. Gangadharan, S. Seyedolmohadesin, M. Gebeyaw, E. Fulton, A. Ashih, C. D. Duncan, M. Zelich, M. Liu, J. Torkashvand, M. Shaw, D. Gusarova, K. Macwan, M. Kelly, A. Beslic, I. Sood, A. Liu, O. Scholz, M. Venkatachalam, V. Apfeld, J. 2026-01-24 doi:10.64898/2026.01.22.701078 Cold Spring Harbor Laboratory Press 2026-01-24 <![CDATA[ A low-variance subspace underlies individual differences in resting state fMRI ]]> https://biorxiv.org/content/10.64898/2026.01.25.701594v1?rss=1 Borovykh, A. Weissenbacher, M. Noble, S. Shinn, M. 2026-01-27 doi:10.64898/2026.01.25.701594 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ An Integrated Multiphoton Imaging Workflow for Quantitative Analysis of Aortic Tissue Microstructure ]]> https://biorxiv.org/content/10.64898/2026.01.25.701601v1?rss=1 Baig, M. M. J. Vargas, A. I. Jennings, T. Amini, R. Bellini, C. 2026-01-27 doi:10.64898/2026.01.25.701601 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Traumatic Brain Injury Associated with Altered Corpus Callosum Microstructure in Females: Exploring the Roles of Menopause Timing and Hormone Therapy in UK Biobank ]]> https://biorxiv.org/content/10.64898/2026.01.26.701743v1?rss=1 Espana-Irla, G. Tinney, E. M. Perko, M. Nwakamma, M. Noble, S. Morris, T. P. 2026-01-27 doi:10.64898/2026.01.26.701743 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Dynamic conformational ensembles of soluble Tau encode neuronal toxicity prior to aggregation ]]> https://biorxiv.org/content/10.64898/2026.01.26.701882v1?rss=1 Georgescauld, F. Okekenwa, S. Boyd, T. Donahue, C. Quittot, N. Dickson, J. Fan, Z. Brady, S. Blackston, C. Hyman, B. Song, Y. 2026-01-27 doi:10.64898/2026.01.26.701882 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Circuit-Specific Resting-State fMRI Signatures for Stratifying First-Episode Major Depressive Disorder and Predicting Recurrence Risk ]]> https://biorxiv.org/content/10.64898/2026.01.26.701909v1?rss=1 Tu, Y. Hao, K. Wang, F. Qiu, S. Zhang, W. 2026-01-29 doi:10.64898/2026.01.26.701909 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ SAGA1 and SAGA2 localize the starch sheath to the pyrenoid in Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.64898/2026.01.27.702031v1?rss=1 Crans, V. L. Burton, M. I. Garde, A. Wang, L. Jonikas, M. C. 2026-01-29 doi:10.64898/2026.01.27.702031 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ Cortex-specific inversion of visual responses during sleep ]]> https://biorxiv.org/content/10.64898/2026.01.30.702868v1?rss=1 Cicero, N. G. Klimova, M. Vinke, L. Ling, S. Lewis, L. D. 2026-02-02 doi:10.64898/2026.01.30.702868 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Thermodynamic Insights into the WT and Y220C TP53 DBDs Reveals that the Oncogenic Y220C Variant is a Loss of Function Mutation for Zn2+-binding at Physiological Temperature ]]> https://biorxiv.org/content/10.64898/2026.01.31.701171v1?rss=1 Stuckey, J. I. Vivat, V. Dickson, B. M. Setser, J. W. Li, Y. Cremers, C. M. Wilson, J. E. Peterle, D. Engen, J. R. Wales, T. E. Wilcken, R. Rohan, E. B. Chenail, G. Audia, J. E. Sims, R. J. 2026-02-03 doi:10.64898/2026.01.31.701171 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Early detection of sudden transitions in Notch signalling ]]> https://biorxiv.org/content/10.64898/2026.02.01.703083v1?rss=1 Tikader, B. Sarkar, S. Sinha, S. K. Levine, H. Jolly, M. K. Dutta, P. S. 2026-02-03 doi:10.64898/2026.02.01.703083 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ eScreen: a deep learning framework for functionally decoding the regulatory genome at single-nucleotide resolution ]]> https://biorxiv.org/content/10.64898/2026.02.02.703403v1?rss=1 Luo, S. Lin, L. Zhang, H. Yang, Y. Liu, Y. Han, Y. Chen, F. Liang, R. Niang, X. Dai, J. Chen, R. Lin, H. Li, Z. Peng, Y. Fei, T. Huang, J. 2026-02-05 doi:10.64898/2026.02.02.703403 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ A biophysical framework for accurately identifying antigen single-amino acid escape variants and corresponding variant-specific compensatory TCR sequences ]]> https://biorxiv.org/content/10.64898/2026.02.02.703411v1?rss=1 Ghoreyshi, Z. S. Levine, H. Lin, X. Onuchic, J. N. George, J. T. 2026-02-05 doi:10.64898/2026.02.02.703411 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ Ribociclib as a Potential Multi-Target Inhibitor of Pro-Inflammatory Cytokines: An In Silico Investigation ]]> https://biorxiv.org/content/10.64898/2026.02.04.703909v1?rss=1 Rahman, R. Ornob, A. 2026-02-07 doi:10.64898/2026.02.04.703909 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ The Role of Retinal Flow in Walking ]]> https://biorxiv.org/content/10.64898/2026.02.05.704053v1?rss=1 Powell, N. Panfili, D. Oh, Y. Matthis, J. Hayhoe, M. 2026-02-09 doi:10.64898/2026.02.05.704053 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ How the non-motile kinesin KIF7 adapts conserved kinesin principles for itsfunction in Hedgehog signaling ]]> https://biorxiv.org/content/10.64898/2026.02.06.704517v1?rss=1 Haque, F. Srinivasu, B. Wales, T. E. Engen, J. R. Subramanian, R. 2026-02-10 doi:10.64898/2026.02.06.704517 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ When attention falters: brain, breathing, and behavioral signals of lapses in interoceptive attention ]]> https://biorxiv.org/content/10.64898/2026.02.07.704566v1?rss=1 0.75). Breathing variability and breathing-behavior coupling showed smaller but generalizable predictive value (AUCs < 0.65). Whole-brain connectivity models also predicted lapses (AUC {approx} 0.65) and incorporated regions within the DMN, dorsal, and ventral attention networks--overlapping with systems implicated in exteroceptive attention-- as well as the somatomotor network. Further, models that included brain connectivity marginally outperformed behavior-only models. Together, these findings suggest that interoceptive lapses reflect both shared mechanisms with exteroceptive attention failures and additional contributions from brain systems involved in bodily representation and sensory pathways. Although generalizability is limited by the clinical sample and absence of an exteroceptive comparison task, these results highlight candidate brain-body markers of interoceptive attention that may inform real-time monitoring during mind-body interventions and improve understanding of interoceptive disturbance in affective disorders. ]]> Treves, I. N. Shaffer, C. Decker, A. Jaffe, N. Tierney, A. O. Auerbach, R. P. Webb, C. A. 2026-02-10 doi:10.64898/2026.02.07.704566 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ Cell jamming transition is regulated by mitochondrial pyruvate transport and endocytosis ]]> https://biorxiv.org/content/10.64898/2026.02.09.704880v1?rss=1 Bermudez, A. Latham, Z. Diaz, J. Yan, W. Chen, J. Bi, D. Goldstein, A. S. Hu, J. K. Lin, N. Y. C. 2026-02-10 doi:10.64898/2026.02.09.704880 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ 4,5-dihydroxyhexanoic acid is a robust circulating and urine marker of mitochondrial disease and its severity ]]> https://biorxiv.org/content/10.64898/2026.02.10.705117v1?rss=1 90% of detected features in modern metabolomics experiments and hold immense untapped promise for new basic and biomedical research. We recently used mass spectrometry-based metabolomics to identify and validate 19 circulating blood-based biomarkers for patients with the mitochondrial DNA (mtDNA) m.3243A>G pathogenic variant, which is the most frequent cause of the mitochondrial disorder MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes). However, the most significantly changing biomarker corresponded to an "unknown" metabolite. Here, we combine cheminformatics with analytical chemistry and identify that feature as 4,5-dihydroxyhexanoic acid (4,5-DHHA), a metabolite previously associated with inherited defects of gamma-aminobutyric acid (GABA) catabolism, but with no prior links to mitochondrial respiratory chain disorders. We validate this finding in an independent MELAS cohort and further show that 4,5-DHHA levels correlate with disease severity and are elevated in patients with other forms of mitochondrial disease and sepsis. Furthermore, brain 4,5-DHHA levels were elevated in two genetic mouse models of mitochondrial disease. In vitro and tissue culture experiments indicate that 4,5-DHHA is generated when the GABA catabolite succinic semialdehyde reacts with an intermediate of the pyruvate dehydrogenase reaction and is sensitive to mitochondrial complex I function. Our work identifies 4,5-DHHA as a robust plasma and urine marker of mitochondrial dysfunction in humans and reveals new connections between the respiratory chain and GABA metabolism. Significance StatementInborn errors of the mitochondrial respiratory chain cause severe, progressive diseases, yet effective treatments and biomarkers remain limited. Modern metabolomics detects thousands of molecules in biofluids, but the vast majority are unidentified. In this study, we investigate the most significantly altered blood metabolite in patients with the most common mitochondrial disease - MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes) - and identify it as an 4,5-dihydroxyhexanoic acid (4,5-DHHA). We show that 4,5-DHHA is reproducibly elevated and correlates with severity. Levels are increased across multiple mitochondrial disorders as well as in sepsis and rise when respiratory chain function is impaired. These findings establish 4,5-DHHA as a promising biomarker of mitochondrial dysfunction and reveal a link to dysregulated GABA metabolism. ]]> Skinner, O. S. Miranda, M. Dong, F. Struhl, T. Walker, M. A. Schleifer, G. Henke, M. T. Clardy, J. Hirano, M. De Vivo, D. C. Schon, E. A. Engelstad, K. Siegmund, S. E. Laprise, C. Des Rosiers, C. Sharma, R. Mootha, V. K. 2026-02-12 doi:10.64898/2026.02.10.705117 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ A scalable approach to resolving variants of uncertain significance ]]> https://biorxiv.org/content/10.64898/2026.02.14.705848v1?rss=1 90,000 unobserved variants; 62% had enough evidence to be "preclassified" as pathogenic or benign. We validated our data, evidence and classifications using All of Us and created interactive resources to enable clinical use of the calibrated data. Thus, for 40 genes, representing 1% of the clinical genome, we resolve most existing VUS and future variants, illustrating how systematic use of scalable evidence can empower genomic medicine. ]]> Tejura, M. Chen, Y. McEwen, A. E. Stewart, R. Sverchkov, Y. Laval, F. Woo, I. Zeiberg, D. Shen, R. Fayer, S. Stone, J. Smith, N. Casadei, S. Wang, Z. R. Snyder, M. Capodanno, B. J. Gupta, P. Benazouz, M. Jain, S. Heidl, S. Muffley, L. Dong, S. Lin, K. Hitz, B. C. Gabdank, I. Da, E. Y. Best, S. Grindstaff, S. Reinhart, D. Rodriguez-Salas, L. Seid, O. Vandi, A. J. Wenman, C. Wheelock, M. K. Pendyala, S. Holmes, D. Xu, A. Hosokai, A. Tixhon, M. Reno, C. Ewald, J. D. Spirohn-Fitzgerald, K. Teelucksingh, T. Hao, T. Chen, Z. S. Haghighi, M. Hamid, A. K. 2026-02-15 doi:10.64898/2026.02.14.705848 Cold Spring Harbor Laboratory Press 2026-02-15 <![CDATA[ Proximity-Informed Graph Learning Defines Spatial Protein Communities for Tumor-Associated Proximity Antigen Discovery ]]> https://biorxiv.org/content/10.64898/2026.02.13.705629v1?rss=1 Scandore, C. Malone, C. F. May, C. K. de Regt, A. K. Guernsey, J. Ma, H. Dephoure, N. Setter, B. Howell, R. A. Johnson, K. R. Farr, C. L. Romero, S. Vignale, L. Vittum, T. Dawson, E. Habtetsion, T. Nardi, F. Woodruff, B. Mathay, M. Swanson, J. Ton, Q. Farahani, P. E. Gene, R. W. Misurelli, J. Caldwell, Z. Xu, H. Hornsby, M. Gavin, M. A. Klock, H. E. Eryilmaz, E. Holland, P. M. Lesley, S. A. Oslund, R. C. Fadeyi, O. O. 2026-02-16 doi:10.64898/2026.02.13.705629 Cold Spring Harbor Laboratory Press 2026-02-16 <![CDATA[ Ancestry-specific performance of variant effect predictors in clinical variant classification ]]> https://biorxiv.org/content/10.64898/2026.02.14.705914v1?rss=1 Hoffing, R. Zeiberg, D. Stenton, S. L. Mort, M. Cooper, D. N. Hahn, M. W. O'Donnell-Luria, A. Ward, L. D. Radivojac, P. 2026-02-17 doi:10.64898/2026.02.14.705914 Cold Spring Harbor Laboratory Press 2026-02-17 <![CDATA[ Human Cerebral Cortex Organization Characterized by Functional PET-FDG "Metabolic Connectivity" ]]> https://biorxiv.org/content/10.64898/2026.02.15.706044v1?rss=1 Du, P. Coursey, S. E. Xu, T. Jamadar, S. D. Nolin, S. A. Wan, B. Wey, H.-Y. Polimeni, J. R. Price, J. C. Liu, Q. Chen, J. E. 2026-02-17 doi:10.64898/2026.02.15.706044 Cold Spring Harbor Laboratory Press 2026-02-17 <![CDATA[ A druggable redox switch on SHP1 controls macrophage inflammation ]]> https://biorxiv.org/content/10.64898/2026.02.19.706790v1?rss=1 Ng, M. Y. Nix, M. N. Du, G. Davidek, I. Burger, N. Shin, S. Toenjes, S. Xiao, H. Wei, S. Seo, H.-S. Dhe-Paganon, S. Wales, T. E. Engen, J. Mills, E. Che, J. Zhang, T. Gray, N. Chouchani, E. 2026-02-20 doi:10.64898/2026.02.19.706790 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ In Silico Identification of Aminoadipate Semialdehyde Synthase (AASS) as a Novel Prognostic Biomarker in Triple-Negative Breast Cancer ]]> https://biorxiv.org/content/10.64898/2026.02.19.706804v1?rss=1 Majeed, M. Akram, M. Z. Tariq, H. 2026-02-20 doi:10.64898/2026.02.19.706804 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Magnesium as a Conformational Gatekeeper of KRAS: Structural Dynamics and Therapeutic Implications ]]> https://biorxiv.org/content/10.64898/2026.02.20.707046v1?rss=1 Srinivasu, B. Y. Damerla, T. S. Stec, A. Zhou, Z. Engen, J. R. Westover, K. d. Wales, T. E. 2026-02-21 doi:10.64898/2026.02.20.707046 Cold Spring Harbor Laboratory Press 2026-02-21 <![CDATA[ Rational Design Reveals Structural Plasticity of the CsgA β-Solenoid Enabling Programmable Autogenic Engineered Living Materials ]]> https://biorxiv.org/content/10.64898/2026.02.23.707537v1?rss=1 Hammad, H. Swarnadeep, S. Priode, H. Jackson, E. Kurowski, A. Moore, R. Manjula-Basavanna, A. Deshmukh, S. Duraj-Thatte, A. 2026-02-24 doi:10.64898/2026.02.23.707537 Cold Spring Harbor Laboratory Press 2026-02-24 <![CDATA[ Phenotypic and Genomic Evidence of Adaptive Tracking in Thermal Tolerance of Wild Populations of an Invasive Drosophila. ]]> https://biorxiv.org/content/10.64898/2026.02.26.708249v1?rss=1 McCabe, E. Gautier, M. Eller, K. Garvin, M. O. McCracken, A. R. Redondo, S. Bergland, A. O. Bangerter, A. Lotterhos, K. E. Nunez, J. C. B. Teets, N. M. 2026-02-27 doi:10.64898/2026.02.26.708249 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ Beyond Fixation: Persistent Genetic Variation Under Intense Selection ]]> https://biorxiv.org/content/10.64898/2026.03.02.706684v1?rss=1 Arnold, K. R. Greenspan, Z. S. Robinson, R. D. Pupo, A. Chavarin, V. V. Chang, K. S. Cannell, C. O. Qi, M. Mueller, L. D. Rose, M. R. Phillips, M. A. 2026-03-04 doi:10.64898/2026.03.02.706684 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ The complete genome of the KOLF2.1J reference iPSC line ]]> https://biorxiv.org/content/10.64898/2026.03.06.710144v1?rss=1 Alvarez Jerez, P. Rhie, A. Kim, J. Hebbar, P. Nag, S. Antipov, D. Koren, S. Lara, E. Beilina, A. Hansen, N. F. Arber, C. F. Zulueta, J. Wild-Crea, P. Patel, D. Hickey, G. Waltz, B. Malik, L. Skarnes, W. C. Reed, X. Genner, R. Daida, K. Pantazis, C. B. Grenn, F. Nalls, M. A. Billingsley, K. Fossati, V. Wray, S. Ward, M. Ryten, M. Cookson, M. R. Jain, M. Paten, B. Phillippy, A. M. Blauwendraat, C. 2026-03-09 doi:10.64898/2026.03.06.710144 Cold Spring Harbor Laboratory Press 2026-03-09 <![CDATA[ Multi-site MRI analysis of morphometric differences in brain regions in the presence of hearing loss and tinnitus across the adult lifespan ]]> https://biorxiv.org/content/10.64898/2026.03.06.710136v1?rss=1 Abraham, I. Ajmera, S. Zhang, W. Leaver, A. M. Sutton, B. P. Peelle, J. E. Husain, F. T. 2026-03-10 doi:10.64898/2026.03.06.710136 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ Evaluating the Utility of a Nanoscale Flow Cytometer for Detection of Surface Proteins on HIV and Extracellular Vesicles ]]> https://biorxiv.org/content/10.64898/2026.03.09.710614v1?rss=1 Burnie, J. Ouano, C. Costa, V. Castrosin, I. Hammond, C. Matthews, H. Tigges, J. Corbett-Helaire, K. S. 2026-03-10 doi:10.64898/2026.03.09.710614 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ Ion Channel Nano-Diagnostics for ER+ Breast Cancer ]]> https://biorxiv.org/content/10.64898/2026.03.09.710404v1?rss=1 Gkikas, M. Dadiotis, E. Zaka, M. Aly, N. Chan, K. Logothetis, D. E. 2026-03-11 doi:10.64898/2026.03.09.710404 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ MSstatsResponse: Semi-parametric statistical model enhances detection of drug-protein interactions in chemoproteomics experiments ]]> https://biorxiv.org/content/10.64898/2026.03.09.710598v1?rss=1 Szvetecz, S. Kohler, D. Federspiel, J. Field, D. S. Jean-Beltran, P. Seward, R. J. Suh, H. Xue, L. Vitek, O. 2026-03-11 doi:10.64898/2026.03.09.710598 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Decoding epitope immunodominance in HIV Env using cryoEM and machine learning ]]> https://biorxiv.org/content/10.64898/2026.03.09.710672v1?rss=1 100 Env-antibody complexes. These data informed the development of a surface-centric, machine-learning model to predict relative Antigen Surface Immunodominance (ASI model). Comparison of ASI-predicted epitope sites with the specificities of Env-induced antibodies showed that the model accurately identifies immunodominant regions and highlights the structural features driving immune bias. Notably, immunogens redesigned based on model predictions successfully redirected Ab responses toward a normally subdominant epitope, demonstrating the potential of strategies coupling targeted assembly of focused structural libraries with machine learning to uncover complex molecular patterns and enable design of more effective vaccine antigens. ]]> Schuhmacher, J. Xiao, S. Eray, E. R. Brown, S. Zambrowski, A. Jain, A. Garcia, D. M. Ozorowski, G. Zhu, W. Saam, K. Caniels, T. G. Moore, J. P. Crispin, M. Sanders, R. W. Chakraborty, S. Correia, B. E. Ward, A. B. Antanasijevic, A. 2026-03-11 doi:10.64898/2026.03.09.710672 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Legacy 4(1H)-quinolone scaffolds activity against acute and chronic Toxoplasma gondii infection ]]> https://biorxiv.org/content/10.64898/2026.03.10.710892v1?rss=1 Sleda, M. A. Diagne, K. Clifton, V. M. Baierna, B. Manetsch, R. Moreno, S. N. J. 2026-03-11 doi:10.64898/2026.03.10.710892 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Rapid and Interpretable AMR Diagnostics via Genomics and Cell Painting using Differential Geometry-based Directed-Simplicial Neural Networks on Multimodal Data ]]> https://biorxiv.org/content/10.64898/2026.03.11.711128v1?rss=1 Thakur, L. S. Mahajan, S. S. Bharj, G. Ding, M. Dekanoidze, N. Shrivastava, V. 2026-03-12 doi:10.64898/2026.03.11.711128 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ Model recapitulates regenerative limb blastema formation through local softening of the wounded epithelium ]]> https://biorxiv.org/content/10.64898/2026.03.11.711112v1?rss=1 Finkbeiner, S. Brew-Smith, A. Wang, X. Fu, D. T. Monaghan, J. R. Copos, C. 2026-03-13 doi:10.64898/2026.03.11.711112 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ SPECIES DISTRIBUTION PROJECTIONS UNDER INTERNAL CLIMATE VARIABILITY REVEAL MULTIPLE PLAUSIBLE FUTURES REQUIRING FLEXIBLE CLIMATE-READY DECISIONS ]]> https://biorxiv.org/content/10.64898/2026.03.11.711202v1?rss=1 Benavides-Martinez, I. F. Mawalagedara, R. Ray, A. Aggarwal, K. Allyn, A. Mills, K. E. Ganguly, A. R. 2026-03-13 doi:10.64898/2026.03.11.711202 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Automated culture and monitoring of a high-throughput human heart-on-a-chip ]]> https://biorxiv.org/content/10.64898/2026.03.11.711145v1?rss=1 Schellberg, B. G. Burson, N. T. Gomes, J. Dai, G. Koppes, A. N. Koppes, R. A. 2026-03-14 doi:10.64898/2026.03.11.711145 Cold Spring Harbor Laboratory Press 2026-03-14 <![CDATA[ Polypharmacology of an Optimal Kinase Library ]]> https://biorxiv.org/content/10.64898/2026.03.17.711623v1?rss=1 Mills, C. E. Hug, C. Sajeevan, K. A. Clark, N. Victor, C. Chung, M. Rawat, S. Aldridge, B. Albers, M. W. Chowdhury, R. Gyori, B. M. Sorger, P. K. 2026-03-19 doi:10.64898/2026.03.17.711623 Cold Spring Harbor Laboratory Press 2026-03-19 <![CDATA[ Library docking for Cannabinoid-2 Receptor ligands ]]> https://biorxiv.org/content/10.64898/2026.03.19.713017v1?rss=1 Rachman, M. M. Iliopoulos-Tsoutsouvas, C. Dominic Sacco, M. Xu, X. Wu, C.-G. Santos, E. Glenn, I. S. Paris, L. Cahill, M. K. Ganapathy, S. Tummino, T. A. Moroz, Y. S. Radchenko, D. S. Okorie, M. Tawfik, V. L. Irwin, J. J. Makriyannis, A. Skiniotis, G. Shoichet, B. K. 2026-03-21 doi:10.64898/2026.03.19.713017 Cold Spring Harbor Laboratory Press 2026-03-21 <![CDATA[ Inter-individual variation of cellular and gene-expression properties of the human striatum ]]> https://biorxiv.org/content/10.64898/2026.03.20.713160v1?rss=1 Burger, S. Yoo, O. Nemesh, J. Muratoglu, E. Vanderburg, C. Yuan, J. Shakir, K. Mello, C. J. Rayan, N. A. Milidantri, J. Kim, K. Drouin, S. Finn, E. Gao, H. Budnik, N. Goldman, M. Fritch, H. Genovese, G. Hogan, M. Catalini, O. Kashin, S. Rockweiler, N. Wysoker, A. Macaisa, L. Reese, L. Flowers, K. Kraft, A. W. Fleming, S. J. Coe, M. Gunaratne, R. Spina, L. Crombie, C. Mohsin, A. Kamitaki, N. Macosko, E. Z. Ichihara, K. McCarroll, S. A. 2026-03-23 doi:10.64898/2026.03.20.713160 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ A Mitochondrial Basis for Tead4 Bioavailability at the First Mammalian Cell Fate Decision ]]> https://biorxiv.org/content/10.64898/2026.03.22.713230v1?rss=1 Sheehan, H. C. Piasecki, A. Woods, D. C. Tilly, J. L. 2026-03-23 doi:10.64898/2026.03.22.713230 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ Modulating Innate Immune Responses to Curli Fibers Through Protein Engineering ]]> https://biorxiv.org/content/10.64898/2026.03.23.713613v1?rss=1 Bonanno, S. Sheta, R. Ramu, T. Verenkar, S. Kim, D. Bessette, E. Pierre, P. Joshi, N. S. 2026-03-25 doi:10.64898/2026.03.23.713613 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ A network for self-transcendence derived from patients with brain lesions ]]> https://biorxiv.org/content/10.64898/2026.03.24.713239v1?rss=1 Healey, M. R. Sanchez-Gama, Y. Ding, M. McMahon, J. T. Bourbon, C. Jesani, R. Atwood, G. D. Lord, B. T. Sanguinetti, J. Brewer, J. Vago, D. R. Siddiqi, S. H. Fabbro, F. Urgesi, C. Nielsen, J. A. Ferguson, M. A. 2026-03-27 doi:10.64898/2026.03.24.713239 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Mitochondrial subpopulations in oocytes and cumulus cells exhibit distinct age-associated changes and selective plasticity in response to NMN supplementation ]]> https://biorxiv.org/content/10.64898/2026.03.25.714214v1?rss=1 Piasecki, A. J. Sheehan, H. Ledo Hopgood, P. Tilly, J. L. Woods, D. C. 2026-03-27 doi:10.64898/2026.03.25.714214 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Mitochondria-Associated Transcription Precedes Oxidative Phosphorylation Activation During Human Pre-Implantation Embryogenesis ]]> https://biorxiv.org/content/10.64898/2026.03.25.714226v1?rss=1 Piasecki, A. J. Franco, M. Capelluto, F. Khrapko, K. Tilly, J. L. Woods, D. C. 2026-03-27 doi:10.64898/2026.03.25.714226 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Structure-Led Exploration of the Metagenome Yields Novel RNA-Guided Nucleases with Broad PAM Diversity ]]> https://biorxiv.org/content/10.64898/2026.03.27.714800v1?rss=1 de los Santos, E. L. Rieber, L. Wang, M. Catherman, S. Hatfield, S. Bowen, T. 2026-03-29 doi:10.64898/2026.03.27.714800 Cold Spring Harbor Laboratory Press 2026-03-29 <![CDATA[ The diploid reference genome of a human embryonic stem cell line ]]> https://biorxiv.org/content/10.64898/2026.03.26.714432v1?rss=1 Pacar, I. Ungaro, M. T. Chen, Y. Dallali, H. Medico, J. A. Hebbar, P. Diekhaus, M. Di Tommaso, E. Geleta, M. Chan, P. P. Lowe, T. M. Balacco, J. Jain, N. Ackerman, F. Mochi, M. Ioannidis, A. G. Sawarkar, N. Diaz, K. Krishna Sudhakar, K. Powell, J. E. Jain, M. Rosa, A. Croft, G. F. Tanzer, A. Jarvis, E. D. Formenti, G. Salama, S. R. Giunta, S. 2026-03-30 doi:10.64898/2026.03.26.714432 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ The world's first cloned golden wild yak via interspecific SCNT: 4800m donor origin and 4200m vitrified blastocyst transfer ]]> https://biorxiv.org/content/10.64898/2026.03.29.715085v1?rss=1 Yu, D. Zhang, Q. Cao, L. Gu, S. Zhang, Y. Liu, C. Yin, K. Wang, J. Pan, B. Liu, Y. Zhou, G. Lan, D. Huang, Y. Basang, W. 2026-03-31 doi:10.64898/2026.03.29.715085 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Subcellular Localization Constrains Protein Detectability and Reveals Systematic RNA-Protein Discordance Across Cancers ]]> https://biorxiv.org/content/10.64898/2026.03.30.713919v1?rss=1 Joshi, K. Kate, S. 2026-04-01 doi:10.64898/2026.03.30.713919 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Range-wide genetic population structure and environmental adaptation in the eastern oyster (Crassostrea virginica) provides insight for aquaculture ]]> https://biorxiv.org/content/10.64898/2026.03.30.715280v1?rss=1 1Mb). Our results identified genomic targets for aquaculture breeding programs aimed at climate resilience, reveal complex patterns of human impacts in managed systems, and demonstrate how seascape genomics can be used to improve aquaculture outcomes. ]]> Eppley, M. G. Bajaj, K. Rumberger, C. Leung, E. Mongillo, N. Small, J. Lotterhos, K. 2026-04-01 doi:10.64898/2026.03.30.715280 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Contrasting effects of geographic distance, environmental distance, and intraspecific diversity on the performance of a marine invertebrate in common gardens ]]> https://biorxiv.org/content/10.64898/2026.04.02.716183v1?rss=1 Bajaj, K. E. Mongillo, N. Eppley, M. G. Rumberger, C. A. Segnitz, Z. Katsuki, S. Carnegie, R. Small, J. Lotterhos, K. E. 2026-04-04 doi:10.64898/2026.04.02.716183 Cold Spring Harbor Laboratory Press 2026-04-04 <![CDATA[ Control of cell division by an Acinetobacter baumannii protein with a novel nucleotidyl-cyclase-like fold ]]> https://biorxiv.org/content/10.64898/2026.04.03.716176v1?rss=1 Farinha, A. Soo, M. W. Minasov, G. Inniss, N. L. Shuvalova, L. Dharamdasani, V. Finkler, J. Stearns, O. Shenoy, T. Kim, C. Satchell, K. J. Geisinger, E. 2026-04-04 doi:10.64898/2026.04.03.716176 Cold Spring Harbor Laboratory Press 2026-04-04 <![CDATA[ Terazosin drives sex-dependent adrenergic-bioenergetic reprogramming to restore network function in Alzheimer's disease ]]> https://biorxiv.org/content/10.64898/2026.04.02.716175v1?rss=1 Pattanashetty, S. G. Serrano, P. A. Rockwell, P. Xie, L. Figueiredo-Pereira, M. E. 2026-04-06 doi:10.64898/2026.04.02.716175 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ Bridging Higher-Order Information Theory and Neuroimaging: A Voxel-Wise O-Information Framework ]]> https://biorxiv.org/content/10.64898/2026.04.06.716652v1?rss=1 Camino-Pontes, B. Jimenez-Marin, A. Tellaetxe-Elorriaga, I. Erramuzpe Aliaga, A. Diez, I. Bonifazi, P. Gatica, M. Rosas, F. E. Marinazzo, D. Stramaglia, S. Cortes, J. 2026-04-08 doi:10.64898/2026.04.06.716652 Cold Spring Harbor Laboratory Press 2026-04-08 <![CDATA[ Calibration of in-frame indel variant effect predictors for clinical variant classification ]]> https://biorxiv.org/content/10.64898/2026.04.15.718599v1?rss=1 Abderrazzaq, H. Singh, M. Babb, L. Bergquist, T. Brenner, S. E. Pejaver, V. O'Donnell-Luria, A. Radivojac, P. ClinGen Computational Working Group, ClinGen Variant Classification Working Group, 2026-04-18 doi:10.64898/2026.04.15.718599 Cold Spring Harbor Laboratory Press 2026-04-18 <![CDATA[ 16S rRNA k-mer composition encodes microbial functional potential ]]> https://biorxiv.org/content/10.64898/2026.04.16.718937v1?rss=1 Liu, J. De Paolis Klauza, M. C. Bromberg, Y. 2026-04-18 doi:10.64898/2026.04.16.718937 Cold Spring Harbor Laboratory Press 2026-04-18