bioRxiv Channel: California Institute of Technology https://biorxiv.org This feed contains articles for bioRxiv Channel "California Institute of Technology" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Designing Robustness to Temperature in a Feedforward Loop Circuit ]]> https://biorxiv.org/content/10.1101/000091v1?rss=1 Shaunak Sen Jongmin Kim Richard M. Murray 2013-11-07 doi:10.1101/000091 Cold Spring Harbor Laboratory Press 2013-11-07 <![CDATA[ Design and implementation of a synthetic biomolecular concentration tracker ]]> https://biorxiv.org/content/10.1101/000448v1?rss=1 Victoria Hsiao Emmanuel LC de los Santos Weston R Whitaker John E Dueber Richard M Murray 2013-11-15 doi:10.1101/000448 Cold Spring Harbor Laboratory Press 2013-11-15 <![CDATA[ Resource usage and gene circuit performance characterization in a cell-free ?breadboard? ]]> https://biorxiv.org/content/10.1101/000885v1?rss=1 Dan Siegal-Gaskins Zoltan A. Tuza Jongmin Kim Vincent Noireaux Richard M. Murray 2013-11-25 doi:10.1101/000885 Cold Spring Harbor Laboratory Press 2013-11-25 <![CDATA[ p97-dependent retrotranslocation and proteolytic processing govern formation of active Nrf1 upon proteasome inhibition ]]> https://biorxiv.org/content/10.1101/001602v1?rss=1 Senthil K Radhakrishnan Willem den Besten Raymond J Deshaies 2013-12-29 doi:10.1101/001602 Cold Spring Harbor Laboratory Press 2013-12-29 <![CDATA[ Population diversification in a yeast metabolic program promotes anticipation of environmental shifts ]]> https://biorxiv.org/content/10.1101/002907v1?rss=1 Ophelia S Venturelli Ignacio Zuleta Richard M Murray Hana El-Samad 2014-02-21 doi:10.1101/002907 Cold Spring Harbor Laboratory Press 2014-02-21 <![CDATA[ Rapidly characterizing the fast dynamics of RNA genetic circuitry with cell-free transcription-translation (TX-TL) systems ]]> https://biorxiv.org/content/10.1101/003335v1?rss=1 Melissa K Takahashi James Chappell Clarmyra A Hayes Zachary Z Sun Vipul Singhal Kevin J Spring Shaima Al-Khabouri Christopher P Fall Vincent Noireaux Richard M Murray Julius B Lucks 2014-03-17 doi:10.1101/003335 Cold Spring Harbor Laboratory Press 2014-03-17 <![CDATA[ Comparison of the theoretical and real-world evolutionary potential of a genetic circuit. ]]> https://biorxiv.org/content/10.1101/003772v1?rss=1 Manuel Razo-Mejia James Boedicker Daniel Jones Alexander de Luna Justin Block Kinney Rob Phillips 2014-04-02 doi:10.1101/003772 Cold Spring Harbor Laboratory Press 2014-04-02 <![CDATA[ An analytical approach to bistable biological circuit discrimination using real algebraic geometry ]]> https://biorxiv.org/content/10.1101/008581v1?rss=1 Dan Siegal-Gaskins Elisa Franco Tiffany Zhou Richard M Murray 2014-08-30 doi:10.1101/008581 Cold Spring Harbor Laboratory Press 2014-08-30 <![CDATA[ Synthetic logic circuits using RNA aptamer against T7 RNA polymerase ]]> https://biorxiv.org/content/10.1101/008771v1?rss=1 Jongmin Kim Juan F Quijano Enoch Yeung Richard M Murray 2014-09-04 doi:10.1101/008771 Cold Spring Harbor Laboratory Press 2014-09-04 <![CDATA[ Engineering Transcriptional Regulator Effector Specificity using Computational Design and In Vitro Rapid Prototyping: Developing a Vanillin Sensor ]]> https://biorxiv.org/content/10.1101/015438v1?rss=1 Emmanuel Lorenzo Cornejo de los Santos Joseph T Meyerowitz Stephen L Mayo Richard M Murray 2015-02-19 doi:10.1101/015438 Cold Spring Harbor Laboratory Press 2015-02-19 <![CDATA[ Prototyping 1,4-butanediol (BDO) biosynthesis pathway in a cell-free transcription-translation (TX-TL) system ]]> https://biorxiv.org/content/10.1101/017814v1?rss=1 Yong Y Wu Stephanie Culler Julia Khandurina Stephen Van Dien Richard M Murray 2015-04-09 doi:10.1101/017814 Cold Spring Harbor Laboratory Press 2015-04-09 <![CDATA[ Characterizing and Prototyping Genetic Networks with Cell-Free Transcription-Translation Reactions ]]> https://biorxiv.org/content/10.1101/019620v1?rss=1 Melissa K Takahashi Clarmyra A. Hayes James Chappell Zachary Z. Sun Richard M Murray Vincent Noireaux Julius B. Lucks 2015-05-21 doi:10.1101/019620 Cold Spring Harbor Laboratory Press 2015-05-21 <![CDATA[ Protein degradation in a TX-TL cell-free expression system using ClpXP protease ]]> https://biorxiv.org/content/10.1101/019695v1?rss=1 Zachary Sun Jongmin Kim Vipul Singhal Richard M Murray 2015-05-22 doi:10.1101/019695 Cold Spring Harbor Laboratory Press 2015-05-22 <![CDATA[ Design Space Exploration of the Violacein Pathway in Escherichia coli Based Transcription Translation Cell-Free System (TX-TL) ]]> https://biorxiv.org/content/10.1101/027656v1?rss=1 Phuc H.B. Nguyen Yong Wu Shaobin Guo Richard M Murray 2015-09-27 doi:10.1101/027656 Cold Spring Harbor Laboratory Press 2015-09-27 <![CDATA[ Generalized Regressive Motion: a Visual Cue to Collision ]]> https://biorxiv.org/content/10.1101/029819v1?rss=1 Krzysztof Chalupka Michael Dickinson Pietro Perona 2015-10-26 doi:10.1101/029819 Cold Spring Harbor Laboratory Press 2015-10-26 <![CDATA[ A population-based temporal logic gate for timing and recording chemical events ]]> https://biorxiv.org/content/10.1101/029967v1?rss=1 Victoria Hsiao Yutaka Hori Paul Rothemund Richard Murray 2015-10-27 doi:10.1101/029967 Cold Spring Harbor Laboratory Press 2015-10-27 <![CDATA[ DataJoint: managing big scientific data using MATLAB or Python ]]> https://biorxiv.org/content/10.1101/031658v1?rss=1 Dimitri Yatsenko Jacob Reimer Alexander S Ecker Edgar Y Walker Fabian Sinz Philipp Berens Andreas Hoenselaar Ronald James Cotton Athanassios S. Siapas Andreas S. Tolias 2015-11-14 doi:10.1101/031658 Cold Spring Harbor Laboratory Press 2015-11-14 <![CDATA[ Intracranial Markers of Conscious Face Perception in Humans ]]> https://biorxiv.org/content/10.1101/037234v1?rss=1 Fabiano Baroni Jochem van Kempen Hiroto Kawasaki Christopher K. Kovach Hiroyuki Oya Matthew A. Howard Ralph Adolphs Naotsugu Tsuchiya 2016-02-01 doi:10.1101/037234 Cold Spring Harbor Laboratory Press 2016-02-01 <![CDATA[ A Genetically Encoded Reporter for Diffusion Weighted Magnetic Resonance Imaging ]]> https://biorxiv.org/content/10.1101/037515v1?rss=1 Arnab Mukherjee Di Wu Hunter C. Davis Mikhail G. Shapiro 2016-01-25 doi:10.1101/037515 Cold Spring Harbor Laboratory Press 2016-01-25 <![CDATA[ Contents of Consciousness Investigated as Integrated Information in Direct Human Brain Recordings ]]> https://biorxiv.org/content/10.1101/039032v1?rss=1 Andrew M. Haun Masafumi Oizumi Christopher K Kovach Hiroto Kawasaki Hiroyuki Oya Matthew A Howard Ralph Adolphs Naotsugu Tsuchiya 2016-02-15 doi:10.1101/039032 Cold Spring Harbor Laboratory Press 2016-02-15 <![CDATA[ Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly ]]> https://biorxiv.org/content/10.1101/040741v1?rss=1 John M A Grime James F Dama Barbie K Ganser-Pornillos Cora L Woodward Grant J Jensen Mark J Yeager Gregory Voth 2016-02-23 doi:10.1101/040741 Cold Spring Harbor Laboratory Press 2016-02-23 <![CDATA[ Sporulation, bacterial cell envelopes, and the origin of life ]]> https://biorxiv.org/content/10.1101/041624v1?rss=1 Elitza I Tocheva Davi R Ortega Grant J Jensen 2016-02-29 doi:10.1101/041624 Cold Spring Harbor Laboratory Press 2016-02-29 <![CDATA[ Rational design and whole-genome predictions of single guide RNAs for efficient CRISPR/Cas9-mediated genome editing in Ciona ]]> https://biorxiv.org/content/10.1101/041632v1?rss=1 Shashank Gandhi Lionel Christiaen Alberto Stolfi 2016-02-28 doi:10.1101/041632 Cold Spring Harbor Laboratory Press 2016-02-28 <![CDATA[ Divergence of gene regulatory network linkages during specification of ectoderm and mesoderm in early development of sea urchins ]]> https://biorxiv.org/content/10.1101/044149v1?rss=1 Eric M Erkenbrack Eric H Davidson 2016-03-16 doi:10.1101/044149 Cold Spring Harbor Laboratory Press 2016-03-16 <![CDATA[ Modeling multi-particle complexes in stochastic chemical systems ]]> https://biorxiv.org/content/10.1101/045435v1?rss=1 Muir J Morrison Justin B Kinney 2016-03-23 doi:10.1101/045435 Cold Spring Harbor Laboratory Press 2016-03-23 <![CDATA[ A new computational model captures fundamental architectural features of diverse biological networks ]]> https://biorxiv.org/content/10.1101/046813v1?rss=1 Bader Al-Anzi Noah Olsman Christopher Ormerod Sherif Gerges Georgios Piliouras John Ormerod Kai Zinn 2016-04-02 doi:10.1101/046813 Cold Spring Harbor Laboratory Press 2016-04-02 <![CDATA[ Neighborhood regulation by lncRNA promoters, transcription, and splicing ]]> https://biorxiv.org/content/10.1101/050948v1?rss=1 Jesse M Engreitz Jenna E Haines Glen Munson Jenny Chen Elizabeth M Perez Michael Kane Patrick E McDonel Mitchell Guttman Eric S Lander 2016-04-29 doi:10.1101/050948 Cold Spring Harbor Laboratory Press 2016-04-29 <![CDATA[ MPAthic: quantitative modeling of sequence-function relationships for massively parallel assays ]]> https://biorxiv.org/content/10.1101/054676v1?rss=1 William T. Ireland Justin B. Kinney 2016-05-21 doi:10.1101/054676 Cold Spring Harbor Laboratory Press 2016-05-21 <![CDATA[ iSUMO - integrative prediction of functionally relevant SUMOylated proteins ]]> https://biorxiv.org/content/10.1101/056564v1?rss=1 Xiaotong Yao Rebecca Bish Christine Vogel 2016-06-01 doi:10.1101/056564 Cold Spring Harbor Laboratory Press 2016-06-01 <![CDATA[ Binding of synGAP to PDZ Domains of PSD-95 is Regulated by Phosphorylation and Shapes the Composition of the Postsynaptic Density ]]> https://biorxiv.org/content/10.1101/058016v1?rss=1 Ward G Walkup Tara L Mastro Leslie T Schenker Jost Vielmetter Rebecca Hu Ariella Iancu Meera Reghunathan Barry D Bannon Mary B Kennedy 2016-06-09 doi:10.1101/058016 Cold Spring Harbor Laboratory Press 2016-06-09 <![CDATA[ The role of single occupancy effects on integrase dynamics in a cell-free system ]]> https://biorxiv.org/content/10.1101/059675v1?rss=1 Georgios Artavanis Victoria Hsiao Clarmyra A Hayes Richard M Murray 2016-06-18 doi:10.1101/059675 Cold Spring Harbor Laboratory Press 2016-06-18 <![CDATA[ Enhancer sharing promotes neighborhoods of transcriptional regulation across eukaryotes ]]> https://biorxiv.org/content/10.1101/061218v1?rss=1 Porfirio Quintero-Cadena Paul Sternberg 2016-06-28 doi:10.1101/061218 Cold Spring Harbor Laboratory Press 2016-06-28 <![CDATA[ Low activity microstates during sleep ]]> https://biorxiv.org/content/10.1101/067892v1?rss=1 Hiroyuki Miyawaki Yazan Billeh Kamran Diba 2016-08-04 doi:10.1101/067892 Cold Spring Harbor Laboratory Press 2016-08-04 <![CDATA[ The Effect of Compositional Context on Synthetic Gene Net-works ]]> https://biorxiv.org/content/10.1101/083329v1?rss=1 Yeung, E. Dy, A. J. Martin, K. B. Ng, A. H. Del Vecchio, D. Beck, J. L. Collins, J. J. Murray, R. M. 2016-10-25 doi:10.1101/083329 Cold Spring Harbor Laboratory Press 2016-10-25 <![CDATA[ Structure of the Legionella Dot/Icm type IV secretion system in situ by electron cryotomography ]]> https://biorxiv.org/content/10.1101/085977v1?rss=1 Ghosal, D. Chang, Y.-W. Jeong, K. C. Vogel, J. P. Jensen, G. J. 2016-11-07 doi:10.1101/085977 Cold Spring Harbor Laboratory Press 2016-11-07 <![CDATA[ Novel computational method for predicting polytherapy switching strategies to overcome tumor heterogeneity and evolution ]]> https://biorxiv.org/content/10.1101/086553v1?rss=1 Jonsson, V. D. Blakely, C. M. Lin, L. Asthana, S. Olivas, V. Gubens, M. A. Matni, N. Bastian, B. C. Taylor, B. S. Doyle, J. C. Bivona, T. G. 2016-11-08 doi:10.1101/086553 Cold Spring Harbor Laboratory Press 2016-11-08 <![CDATA[ A Bayesian approach to inferring chemical signal timing and amplitude in a temporal logic gate using the cell population distributional response ]]> https://biorxiv.org/content/10.1101/087379v1?rss=1 Baetica, A.-A. Catanach, T. A. Hsiao, V. Murray, R. Beck, J. 2016-11-14 doi:10.1101/087379 Cold Spring Harbor Laboratory Press 2016-11-14 <![CDATA[ Cobalt enrichment in anaerobic microbial cocultures revealed by synchrotron X-ray fluorescence imaging ]]> https://biorxiv.org/content/10.1101/087585v1?rss=1 Glass, J. B. Chen, S. Dawson, K. S. Horton, D. R. Vogt, S. Ingall, E. D. Twining, B. S. Orphan, V. J. 2016-11-14 doi:10.1101/087585 Cold Spring Harbor Laboratory Press 2016-11-14 <![CDATA[ Engineered reciprocal chromosome translocations drive high threshold, reversible population replacement in Drosophila ]]> https://biorxiv.org/content/10.1101/088393v1?rss=1 Buchman, A. B. Ivy, T. Marshall, J. M. Akbari, O. Hay, B. A. 2016-11-17 doi:10.1101/088393 Cold Spring Harbor Laboratory Press 2016-11-17 <![CDATA[ FlyLimbTracker: an active contour based approach for leg segment tracking in unmarked, freely behaving Drosophila ]]> https://biorxiv.org/content/10.1101/089714v1?rss=1 Uhlmann, V. Ramdya, P. Delgado-Gonzalo, R. Benton, R. Unser, M. 2016-11-26 doi:10.1101/089714 Cold Spring Harbor Laboratory Press 2016-11-26 <![CDATA[ Prototyping a valinomycin biosynthesis pathway within a cell-free transcription-translation (TX-TL) system ]]> https://biorxiv.org/content/10.1101/091520v1?rss=1 Zhou, T. 2016-12-04 doi:10.1101/091520 Cold Spring Harbor Laboratory Press 2016-12-04 <![CDATA[ Decoding sequence-level information to predict membrane protein expression ]]> https://biorxiv.org/content/10.1101/098673v1?rss=1 Saladi, S. M. Muller, A. Javed, N. Clemons, W. M. 2017-01-05 doi:10.1101/098673 Cold Spring Harbor Laboratory Press 2017-01-05 <![CDATA[ Multiplexed dynamic imaging of genomic loci in single cells by combined CRISPR imaging and DNA sequential FISH ]]> https://biorxiv.org/content/10.1101/101477v1?rss=1 Takei, Y. Shah, S. Harvey, S. Qi, L. S. Cai, L. 2017-01-18 doi:10.1101/101477 Cold Spring Harbor Laboratory Press 2017-01-18 <![CDATA[ Monod-Wyman-Changeux Analysis of Ligand-Gated Ion Channel Mutants ]]> https://biorxiv.org/content/10.1101/102194v1?rss=1 Einav, T. Phillips, R. 2017-01-22 doi:10.1101/102194 Cold Spring Harbor Laboratory Press 2017-01-22 <![CDATA[ The ultrastructure of Shewanella oneidensis MR-1 nanowires revealed by electron cryo-tomography ]]> https://biorxiv.org/content/10.1101/103242v1?rss=1 Subramanian, P. Pirbadian, S. El-Naggar, M. Y. Jensen, G. J. 2017-01-28 doi:10.1101/103242 Cold Spring Harbor Laboratory Press 2017-01-28 <![CDATA[ The 4D Nucleome Project ]]> https://biorxiv.org/content/10.1101/103499v1?rss=1 Dekker, J. Belmont, A. S. Guttman, M. Leshyk, V. O. Lis, J. T. Lomvardas, S. Mirny, L. A. O'Shea, C. C. Park, P. J. Ren, B. Ritland, J. C. Shendure, J. Zhong, S. The 4D Nucleome Network, 2017-01-26 doi:10.1101/103499 Cold Spring Harbor Laboratory Press 2017-01-26 <![CDATA[ Expressing Biologically Active Membrane Proteins in a Cell-Free Transcription-Translation Platform ]]> https://biorxiv.org/content/10.1101/104455v1?rss=1 Guo, S. Vaish, A. Chen, Q. Murray, R. M. 2017-01-30 doi:10.1101/104455 Cold Spring Harbor Laboratory Press 2017-01-30 <![CDATA[ SUPERMAN prevents stamen formation and promotes stem cell termination in the fourth whorl of the Arabidopsis flower ]]> https://biorxiv.org/content/10.1101/107722v1?rss=1 Prunet, N. Yang, W. Das, P. Meyerowitz, E. M. Jack, T. P. 2017-02-10 doi:10.1101/107722 Cold Spring Harbor Laboratory Press 2017-02-10 <![CDATA[ Uncharacterized bacterial structures revealed by electron cryotomography ]]> https://biorxiv.org/content/10.1101/108191v1?rss=1 Dobro, M. J. Oikonomou, C. M. Piper, A. Cohen, J. Guo, K. Jensen, T. Tadayon, J. Donermeyer, J. Park, Y. Solis, B. A. Kjaer, A. Jewett, A. I. McDowall, A. W. Chen, S. Chang, Y.-W. Shi, J. Subramanian, P. Iancu, C. V. Li, Z. Briegel, A. Tocheva, E. I. Pilhofer, M. Jensen, G. J. 2017-02-13 doi:10.1101/108191 Cold Spring Harbor Laboratory Press 2017-02-13 <![CDATA[ Structure of the archaellar motor and associated cytoplasmic cone in Thermococcus kodakaraensis ]]> https://biorxiv.org/content/10.1101/108209v1?rss=1 Briegel, A. Oikonomou, C. M. Chang, Y.-W. Kjaer, A. Huang, A. N. Kim, K. W. Ghosal, D. Gunsalus, R. P. Jensen, G. J. 2017-02-13 doi:10.1101/108209 Cold Spring Harbor Laboratory Press 2017-02-13 <![CDATA[ In vivo structures of an intact type VI secretion system revealed by electron cryotomography ]]> https://biorxiv.org/content/10.1101/108233v1?rss=1 Chang, Y.-W. Rettberg, L. A. Jensen, G. J. 2017-02-14 doi:10.1101/108233 Cold Spring Harbor Laboratory Press 2017-02-14 <![CDATA[ Model-based spike sorting with a mixture of drifting t-distributions ]]> https://biorxiv.org/content/10.1101/109850v1?rss=1 Shan, K. Q. Lubenov, E. V. Siapas, A. G. 2017-02-20 doi:10.1101/109850 Cold Spring Harbor Laboratory Press 2017-02-20 <![CDATA[ Repressing Integrase attachment site operation with CRISPR-Cas9 in E. coli ]]> https://biorxiv.org/content/10.1101/110254v1?rss=1 Shur, A. Murray, R. M. 2017-02-21 doi:10.1101/110254 Cold Spring Harbor Laboratory Press 2017-02-21 <![CDATA[ Engineering pulsatile communication in bacterial consortia ]]> https://biorxiv.org/content/10.1101/111906v1?rss=1 Parkin, J. Hsiao, V. Murray, R. M. 2017-02-26 doi:10.1101/111906 Cold Spring Harbor Laboratory Press 2017-02-26 <![CDATA[ Finding analytic stationary solutions to the chemical master equation by gluing state spaces at one or two states recursively ]]> https://biorxiv.org/content/10.1101/113340v1?rss=1 Meng, X. F. Baetica, A.-A. Singhal, V. Murray, R. M. 2017-03-03 doi:10.1101/113340 Cold Spring Harbor Laboratory Press 2017-03-03 <![CDATA[ Population regulation in microbial consortia using dual feedback control ]]> https://biorxiv.org/content/10.1101/120253v1?rss=1 Ren, X. Baetica, A.-A. Swaminathan, A. Murray, R. M. 2017-03-24 doi:10.1101/120253 Cold Spring Harbor Laboratory Press 2017-03-24 <![CDATA[ Distinguishing Signal From Autofluorescence In Cryogenic Correlated Light And Electron Microscopy Of Mammalian Cells ]]> https://biorxiv.org/content/10.1101/120642v1?rss=1 Carter, S. D. Mageswaran, S. K. Farino, Z. J. Mamede, J. I. Oikonomou, C. M. Hope, T. J. Freyberg, Z. Jensen, G. J. 2017-03-26 doi:10.1101/120642 Cold Spring Harbor Laboratory Press 2017-03-26 <![CDATA[ Implementation and System Identification of a Phosphorylation-Based Insulator in a Cell-Free Transcription-Translation System ]]> https://biorxiv.org/content/10.1101/122606v1?rss=1 Guo, S. Yeung, E. Murray, R. M. 2017-03-30 doi:10.1101/122606 Cold Spring Harbor Laboratory Press 2017-03-30 <![CDATA[ Hypocretin underlies the evolution of sleep loss in the Mexican cavefish ]]> https://biorxiv.org/content/10.1101/122903v1?rss=1 Jaggard, J. B. Stahl, B. A. Lloyd, E. Duboue, E. R. Keene, A. C. 2017-03-31 doi:10.1101/122903 Cold Spring Harbor Laboratory Press 2017-03-31 <![CDATA[ Prototyping And Implementation Of A Novel Feedforward Loop In A Cell-Free Transcription-Translation System And Cells ]]> https://biorxiv.org/content/10.1101/123190v1?rss=1 Guo, S. Murray, R. M. 2017-04-02 doi:10.1101/123190 Cold Spring Harbor Laboratory Press 2017-04-02 <![CDATA[ FtsEX-Mediated Regulation Of Inner Membrane Fusion And Cell Separation Reveals Morphogenetic Plasticity In Caulobacter crescentus ]]> https://biorxiv.org/content/10.1101/124214v1?rss=1 Meier, E. L. Yao, Q. Daitch, A. K. Jensen, G. J. Goley, E. D. 2017-04-04 doi:10.1101/124214 Cold Spring Harbor Laboratory Press 2017-04-04 <![CDATA[ Cell type boundaries organize plant development ]]> https://biorxiv.org/content/10.1101/126466v1?rss=1 Heisler, M. G. Caggiano, M. P. Yu, X. Bhatia, N. Larsson, A. Ram, H. Ohno, C. K. Sappl, P. Meyerowitz, E. M. Jonsson, H. 2017-04-11 doi:10.1101/126466 Cold Spring Harbor Laboratory Press 2017-04-11 <![CDATA[ Challenges And Emerging Directions In Single-Cell Analysis ]]> https://biorxiv.org/content/10.1101/127761v1?rss=1 Yuan, G.-C. Cai, L. Elowitz, M. Enver, T. Fan, G. Guo, G. Irizarry, R. Kharchenko, P. Kim, J. Orkin, S. Quackenbush, J. Saadatpour, A. Schroeder, T. Shivdasani, R. Tirosh, I. 2017-04-15 doi:10.1101/127761 Cold Spring Harbor Laboratory Press 2017-04-15 <![CDATA[ Ubiquitin and ATP-dependent unfoldase activity of P97/VCP·NPLOC4·UFD1L1 is enhanced by a mutation that causes multisystem proteinopathy ]]> https://biorxiv.org/content/10.1101/129528v1?rss=1 Blythe, E. Olson, K. Chau, V. Deshaies, R. 2017-04-21 doi:10.1101/129528 Cold Spring Harbor Laboratory Press 2017-04-21 <![CDATA[ Optimal Sensory Coding By Populations Of ON And OFF Neurons ]]> https://biorxiv.org/content/10.1101/131946v1?rss=1 Gjorgjieva, J. Meister, M. Sompolinsky, H. 2017-04-28 doi:10.1101/131946 Cold Spring Harbor Laboratory Press 2017-04-28 <![CDATA[ Barcode identification for single cell genomics ]]> https://biorxiv.org/content/10.1101/136242v1?rss=1 Tambe, A. Pachter, L. 2017-05-09 doi:10.1101/136242 Cold Spring Harbor Laboratory Press 2017-05-09 <![CDATA[ Responses To Mechanically And Visually Cued Water Waves In The Nervous System Of The Medicinal Leech ]]> https://biorxiv.org/content/10.1101/137588v1?rss=1 Lehmkuhl, A. M. Muthusamy, A. Wagenaar, D. A. 2017-05-13 doi:10.1101/137588 Cold Spring Harbor Laboratory Press 2017-05-13 <![CDATA[ Enzyme-Free Nucleic Acid Dynamical Systems ]]> https://biorxiv.org/content/10.1101/138420v1?rss=1 Srinivas, N. Parkin, J. Seelig, G. Winfree, E. Soloveichik, D. 2017-05-16 doi:10.1101/138420 Cold Spring Harbor Laboratory Press 2017-05-16 <![CDATA[ Whole-Ganglion Imaging Of Voltage In The Medicinal Leech Using A Double-Sided Microscope ]]> https://biorxiv.org/content/10.1101/145144v1?rss=1 Tomina, Y. Wagenaar, D. A. 2017-06-02 doi:10.1101/145144 Cold Spring Harbor Laboratory Press 2017-06-02 <![CDATA[ Column subset selection for single-cell RNA-Seq clustering ]]> https://biorxiv.org/content/10.1101/159079v1?rss=1 McCurdy, S. Ntranos, V. Pachter, L. 2017-07-03 doi:10.1101/159079 Cold Spring Harbor Laboratory Press 2017-07-03 <![CDATA[ Cell-free and in vivo characterization of Lux, Las, and Rpa quorum activation systems in E. coli ]]> https://biorxiv.org/content/10.1101/159988v1?rss=1 Halleran, A. Murray, R. M. 2017-07-07 doi:10.1101/159988 Cold Spring Harbor Laboratory Press 2017-07-07 <![CDATA[ Monomerization of Far-Red Fluorescent Proteins ]]> https://biorxiv.org/content/10.1101/162842v1?rss=1 Wannier, T. M. Gillespie, S. Hutchins, N. McIsaac, R. S. Brown, K. S. Mayo, S. L. 2017-07-20 doi:10.1101/162842 Cold Spring Harbor Laboratory Press 2017-07-20 <![CDATA[ Heterogeneous Responses of Hematopoietic Stem Cells to Inflammatory Stimuli are Altered with Age ]]> https://biorxiv.org/content/10.1101/163402v1?rss=1 Mann, M. Mehta, A. de Boer, C. Kowalczyk, M. S. Lee, K. Farouq, D. Regev, A. Baltimore, D. 2017-07-13 doi:10.1101/163402 Cold Spring Harbor Laboratory Press 2017-07-13 <![CDATA[ Fusion detection and quantification by pseudoalignment ]]> https://biorxiv.org/content/10.1101/166322v1?rss=1 Melsted, P. Hateley, S. Joseph, I. C. Pimentel, H. Bray, N. L. Pachter, L. 2017-07-20 doi:10.1101/166322 Cold Spring Harbor Laboratory Press 2017-07-20 <![CDATA[ Systematic mapping of chromatin state landscapes during mouse development ]]> https://biorxiv.org/content/10.1101/166652v1?rss=1 Gorkin, D. Barozzi, I. Zhang, Y. Lee, A. Y. Lee, B. Zhao, Y. Wildberg, A. Ding, B. Zhang, B. Wang, M. Strattan, J. S. Davidson, J. M. Qiu, Y. Afzal, V. Akiyama, J. A. Plajzer-Frick, I. Pickle, C. S. Kato, M. Garvin, T. H. Pham, Q. T. Harrington, A. N. Mannion, B. J. Lee, E. A. Fukuda-Yuzawa, Y. He, Y. Preissl, S. Chee, S. Williams, B. A. Trout, D. Amrhein, H. Yang, H. Cherry, J. M. Shen, Y. Ecker, J. R. Wang, W. Dickel, D. E. Visel, A. Pennacchio, L. A. Ren, B. 2017-07-21 doi:10.1101/166652 Cold Spring Harbor Laboratory Press 2017-07-21 <![CDATA[ Spatiotemporal DNA Methylome Dynamics of the Developing Mammalian Fetus ]]> https://biorxiv.org/content/10.1101/166744v1?rss=1 He, Y. Hariharan, M. Gorkin, D. U. Dickel, D. E. Luo, C. Castanon, R. G. Nery, J. R. Lee, A. Y. Williams, B. A. Trout, D. Amrhein, H. Fang, R. Chen, H. Li, B. Visel, A. Pennacchio, L. Ren, B. Ecker, J. 2017-07-21 doi:10.1101/166744 Cold Spring Harbor Laboratory Press 2017-07-21 <![CDATA[ Tau Internalization is Regulated by 6-O Sulfation on Heparan Sulfate Proteoglycans (HSPGs) ]]> https://biorxiv.org/content/10.1101/167874v1?rss=1 Rauch, J. Chen, J. J. Sorum, A. W. Miller, G. M. Sharf, T. See, S. K. Hsieh-Wilson, L. C. Kampmann, M. Kosik, K. S. 2017-07-24 doi:10.1101/167874 Cold Spring Harbor Laboratory Press 2017-07-24 <![CDATA[ System-level studies of a cell-free transcription-translation platform for metabolic engineering ]]> https://biorxiv.org/content/10.1101/172007v1?rss=1 Wu, Y. Y. Sato, H. Huang, H. Culler, S. J. Khandurina, J. Nagarajan, H. Yang, T. H. Van Dien, S. Murray, R. M. 2017-08-03 doi:10.1101/172007 Cold Spring Harbor Laboratory Press 2017-08-03 <![CDATA[ Modulation of host learning in Aedes aegypti mosquitoes ]]> https://biorxiv.org/content/10.1101/172726v1?rss=1 Vinauger, C. Lahondere, C. Wolff, G. Locke, L. Liaw, J. Parrish, J. Akbari, O. Dickinson, M. Riffell, J. 2017-08-04 doi:10.1101/172726 Cold Spring Harbor Laboratory Press 2017-08-04 <![CDATA[ Accurate typing of class I human leukocyte antigen by Oxford nanopore sequencing ]]> https://biorxiv.org/content/10.1101/178590v1?rss=1 Liu, C. Xiao, F. Hoisington-Lopez, J. Lang, K. Quenzel, P. Duffy, B. Mitra, R. D. 2017-08-20 doi:10.1101/178590 Cold Spring Harbor Laboratory Press 2017-08-20 <![CDATA[ The role of stimulus similarity on the summation effect in human causal learning ]]> https://biorxiv.org/content/10.1101/178954v1?rss=1 Perez, O. D. San Martin, R. Soto, F. A. 2017-08-21 doi:10.1101/178954 Cold Spring Harbor Laboratory Press 2017-08-21 <![CDATA[ What if you are not certain? A common computation underlying action selection, reaction time and confidence judgment ]]> https://biorxiv.org/content/10.1101/180281v1?rss=1 Christopoulos, V. Enachescu, V. Schrater, P. Schaal, S. 2017-08-24 doi:10.1101/180281 Cold Spring Harbor Laboratory Press 2017-08-24 <![CDATA[ Structure of the fission yeast actomyosin ring during constriction ]]> https://biorxiv.org/content/10.1101/194902v1?rss=1 Swulius, M. T. Nguyen, L. T. Ladinsky, M. S. Ortega, D. R. Aich, S. Mishra, M. Jensen, G. J. 2017-10-31 doi:10.1101/194902 Cold Spring Harbor Laboratory Press 2017-10-31 <![CDATA[ Coarse-grained simulations of actomyosin rings point to a nodeless model involving both unipolar and bipolar myosins ]]> https://biorxiv.org/content/10.1101/194910v1?rss=1 Nguyen, L. Swulius, M. T. Aich, S. Mishra, M. Jensen, G. J. 2017-11-18 doi:10.1101/194910 Cold Spring Harbor Laboratory Press 2017-11-18 <![CDATA[ In vivo structures of the Helicobacter pylori cag type IV secretion system ]]> https://biorxiv.org/content/10.1101/195685v1?rss=1 Chang, Y.-W. Shaffer, C. L. Rettberg, L. A. Ghosal, D. Jensen, G. J. 2017-09-28 doi:10.1101/195685 Cold Spring Harbor Laboratory Press 2017-09-28 <![CDATA[ Gene expression dynamics and inter-tissue recognition mechanisms during tissue fusion at the Arabidopsis graft junction ]]> https://biorxiv.org/content/10.1101/198598v1?rss=1 Melnyk, C. W. Gabel, A. Hardcastle, T. J. Robinson, S. Miyashima, S. Grosse, I. Meyerowitz, E. M. 2017-10-05 doi:10.1101/198598 Cold Spring Harbor Laboratory Press 2017-10-05 <![CDATA[ Hox-logic of preadaptations for social insect symbiosis in rove beetles ]]> https://biorxiv.org/content/10.1101/198945v1?rss=1 Parker, J. Eldredge, K. T. Thomas, I. Coleman, R. Davis, S. 2017-10-05 doi:10.1101/198945 Cold Spring Harbor Laboratory Press 2017-10-05 <![CDATA[ Cell Cycle Control by Nuclear Sequestration of CDC20 and CDH1 mRNA in Plant Stem Cells ]]> https://biorxiv.org/content/10.1101/198978v1?rss=1 Yang, W. Wightman, R. Meyerowitz, E. M. 2017-10-05 doi:10.1101/198978 Cold Spring Harbor Laboratory Press 2017-10-05 <![CDATA[ A Deep Recurrent Neural Network Discovers Complex Biological Rules to Decipher RNA Protein-Coding Potential ]]> https://biorxiv.org/content/10.1101/200758v1?rss=1 Hill, S. T. Kuintzle, R. C. Teegarden, A. Merrill, E. Danaee, P. Hendrix, D. A. 2017-10-13 doi:10.1101/200758 Cold Spring Harbor Laboratory Press 2017-10-13 <![CDATA[ Accurate design of translational output by a neural network model of ribosome distribution ]]> https://biorxiv.org/content/10.1101/201517v1?rss=1 Tunney, R. J. McGlincy, N. J. Graham, M. E. Naddaf, N. Pachter, L. Lareau, L. 2017-10-11 doi:10.1101/201517 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ Extracellular DNA promotes efficient extracellular electron transfer by pyocyanin in Pseudomonas aeruginosa biofilms ]]> https://biorxiv.org/content/10.1101/2019.12.12.872085v1?rss=1 Saunders, S. H. Tse, E. C. M. Yates, M. D. Jimenez Otero, F. Trammell, S. A. Stemp, E. D. A. Barton, J. K. Tender, L. M. Newman, D. K. 2019-12-12 doi:10.1101/2019.12.12.872085 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ Contrast-Enhanced, Molecular Imaging of Vascular Inflammation in the Mouse Model by Simultaneous PET/MRI ]]> https://biorxiv.org/content/10.1101/2019.12.16.878652v1?rss=1 Du, S. Ng, T. House, A. Tang, T. Zheng, L. Tu, C. Peake, J. Espiritu, I. Ma, K.-L. Pinkerton, K. Jacobs, R. Louie, A. 2019-12-17 doi:10.1101/2019.12.16.878652 Cold Spring Harbor Laboratory Press 2019-12-17 <![CDATA[ Physiological Adaptability and Parametric Versatility in a Simple Genetic Circuit ]]> https://biorxiv.org/content/10.1101/2019.12.19.878462v1?rss=1 Chure, G. Kaczmarek, Z. A. Phillips, R. 2019-12-19 doi:10.1101/2019.12.19.878462 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ No strong evidence that social network index is associated with gray matter volume from a data-driven investigation ]]> https://biorxiv.org/content/10.1101/2019.12.19.883173v1?rss=1 Lin, C. Keles, U. Tyszka, M. J. Gallo, M. Paul, L. Adolphs, R. 2019-12-27 doi:10.1101/2019.12.19.883173 Cold Spring Harbor Laboratory Press 2019-12-27 <![CDATA[ Dissecting the regulatory activity and key sequence elements of loci with exceptional numbers of transcription factor associations ]]> https://biorxiv.org/content/10.1101/2019.12.21.885830v1?rss=1 Ramaker, R. C. Hardigan, A. A. Goh, S.-T. Partridge, E. C. Wold, B. Cooper, S. J. Myers, R. M. 2019-12-23 doi:10.1101/2019.12.21.885830 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ Plasma membrane damage removal by F-actin-mediated shedding from repurposed filopodia ]]> https://biorxiv.org/content/10.1101/2019.12.23.887638v1?rss=1 Mageswaran, S. K. Yang, W. Y. Chakrabarty, Y. Oikonomou, C. M. Jensen, G. J. 2019-12-24 doi:10.1101/2019.12.23.887638 Cold Spring Harbor Laboratory Press 2019-12-24 <![CDATA[ Sequestration of Methane by Symbiotic Deep-Sea Annelids: Ancient and Future Implications of Redefining the Seep Influence ]]> https://biorxiv.org/content/10.1101/2019.12.23.887653v1?rss=1 Goffredi, S. K. Tilic, E. Mullin, S. W. Dawson, K. S. Keller, A. Lee, R. Wu, F. Levin, L. A. Rouse, G. W. Cordes, E. Orphan, V. J. 2019-12-27 doi:10.1101/2019.12.23.887653 Cold Spring Harbor Laboratory Press 2019-12-27 <![CDATA[ Neuropeptide VF neurons promote sleep via the serotonergic raphe ]]> https://biorxiv.org/content/10.1101/2019.12.27.889402v1?rss=1 Lee, D. A. Oikonomou, G. Cammidge, T. Hong, Y. Prober, D. A. 2019-12-28 doi:10.1101/2019.12.27.889402 Cold Spring Harbor Laboratory Press 2019-12-28 <![CDATA[ Designing signaling environments to steer transcriptional diversity in neural progenitor cell populations ]]> https://biorxiv.org/content/10.1101/2019.12.30.890087v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@e5286corg.highwire.dtl.DTLVardef@c0e69borg.highwire.dtl.DTLVardef@640b20org.highwire.dtl.DTLVardef@16779e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chen, S. Thomson, M. Park, J. H. Tsou, T. Rivaud, P. 2019-12-31 doi:10.1101/2019.12.30.890087 Cold Spring Harbor Laboratory Press 2019-12-31 <![CDATA[ Dual roles of the Sterol Recognition Region in Hedgehog protein modification ]]> https://biorxiv.org/content/10.1101/2019.12.31.892067v1?rss=1 Purohit, R. Peng, D. S. Vielmas, E. Ondrus, A. E. 2020-01-01 doi:10.1101/2019.12.31.892067 Cold Spring Harbor Laboratory Press 2020-01-01 <![CDATA[ Receptor compaction and GTPase movements drive cotranslational protein translocation ]]> https://biorxiv.org/content/10.1101/2020.01.07.897827v1?rss=1 90 [A] movement of the SRP*SR GTPase complex from the vicinity of the ribosome exit, where it initially assembles, to the distal site of SRP. These rearrangements bring translating ribosomes near the membrane, expose conserved Sec61p docking sites on the ribosome and weaken SRPs interaction with the signal sequence on the nascent polypeptide, thus priming the translating ribosome for engaging the translocation machinery. Disruption of these rearrangements severely impairs cotranslational protein translocation and is the cause of failure in an SRP54 mutant linked to severe congenital neutropenia. Our results demonstrate that multiple largescale molecular motions in the SRP*SR complex are required to drive the transition from protein targeting to translocation; these post-targeting rearrangements provide potential new points for biological regulation as well as disease intervention. ]]> Lee, J. H. Chung, S. Hwang Fu, Y.-H. Qian, R. Sun, X. Weiss, S. Shan, S.-o. 2020-01-08 doi:10.1101/2020.01.07.897827 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Construction, characterization, and immunization of nanoparticles that display a diverse array of influenza HA trimers ]]> https://biorxiv.org/content/10.1101/2020.01.18.911388v1?rss=1 Cohen, A. A. Yang, Z. Gnanapragasam, P. Ou, S. Dam, K.-M. Wang, H. Bjorkman, P. J. 2020-01-19 doi:10.1101/2020.01.18.911388 Cold Spring Harbor Laboratory Press 2020-01-19 <![CDATA[ Quantitative microbiome profiling in lumenal and tissue samples with broad coverage and dynamic range via a single-step 16S rRNA gene DNA copy quantification and amplicon barcoding ]]> https://biorxiv.org/content/10.1101/2020.01.22.914705v1?rss=1 Bogatyrev, S. R. Ismagilov, R. F. 2020-01-22 doi:10.1101/2020.01.22.914705 Cold Spring Harbor Laboratory Press 2020-01-22 <![CDATA[ Cancer-associated HIF-2α impacts trunk neural crest stemness ]]> https://biorxiv.org/content/10.1101/2020.01.22.915199v1?rss=1 Mohlin, S. Persson, C. U. Fredlund, E. Monni, E. Lindvall, J. M. Kokaia, Z. Hammarlund, E. Bronner, M. E. 2020-01-23 doi:10.1101/2020.01.22.915199 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Theoretical Design of Paradoxical Signaling-Based Synthetic Population Control Circuit in E. coli ]]> https://biorxiv.org/content/10.1101/2020.01.27.921734v1?rss=1 Mayalu, M. N. Murray, R. M. 2020-01-28 doi:10.1101/2020.01.27.921734 Cold Spring Harbor Laboratory Press 2020-01-28 <![CDATA[ A Prokaryotic Membrane Sculpting BAR Domain Protein ]]> https://biorxiv.org/content/10.1101/2020.01.30.926147v1?rss=1 Phillips, D. A. Zacharoff, L. A. Hampton, C. M. Chong, G. W. Malanoski, A. P. Metskas, L. A. Xu, S. Bird, L. J. Eddie, B. J. Jensen, G. J. Drummy, L. F. El-Naggar, M. Y. Glaven, S. M. 2020-01-31 doi:10.1101/2020.01.30.926147 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ A Combination of Two Human Monoclonal Antibodies Limits Fetal Damage by Zika Virus in Macaques ]]> https://biorxiv.org/content/10.1101/2020.01.31.926899v1?rss=1 Van Rompay, K. K. A. Coffey, L. L. Kapoor, T. Gazumyan, A. Keesler, R. I. Jurado, A. Peace, A. Agudelo, M. Watanabe, J. Usachenko, J. Singapuri, A. Immareddy, R. Ardeshir, A. Stuart, J. B. Bournazos, S. Ravetch, J. V. Balderes, P. J. Lorenz, I. C. Esswein, S. R. Keeffe, J. Bjorkman, P. J. Wang, Q. Rice, C. M. MacDonald, M. R. Nussenzweig, M. C. Robbiani, D. F. 2020-02-02 doi:10.1101/2020.01.31.926899 Cold Spring Harbor Laboratory Press 2020-02-02 <![CDATA[ Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems ]]> https://biorxiv.org/content/10.1101/2020.01.31.928689v1?rss=1 Yu, T. C. Liu, W. L. Brinck, M. S. Davis, J. E. Shek, J. Bower, G. Einav, T. Insigne, K. D. Phillips, R. Kosuri, S. Urtecho, G. 2020-02-02 doi:10.1101/2020.01.31.928689 Cold Spring Harbor Laboratory Press 2020-02-02 <![CDATA[ Instant FLIM enables 4D in vivo lifetime imaging of intact brains ]]> https://biorxiv.org/content/10.1101/2020.02.05.936039v1?rss=1 Zhang, Y. Guldner, I. H. Nichols, E. L. Benirschke, D. Smith, C. J. Zhang, S. Howard, S. S. 2020-02-06 doi:10.1101/2020.02.05.936039 Cold Spring Harbor Laboratory Press 2020-02-06 <![CDATA[ A fast genetically encoded fluorescent sensor for faithful in vivo acetylcholine detection in mice, fish, worms and flies ]]> https://biorxiv.org/content/10.1101/2020.02.07.939504v1?rss=1 Borden, P. M. Zhang, P. Shivange, A. V. Marvin, J. S. Cichon, J. Dan, C. Podgorski, K. Figueiredo, A. Novak, O. Tanimoto, M. Shigetomi, E. Lobas, M. A. Kim, H. Zhu, P. K. Zhang, Y. Zheng, W. S. Fan, C. Wang, G. Xiang, B. Gan, L. Zhang, G.-X. Guo, K. Lin, L. Cai, Y. Yee, A. Aggarwal, A. Ford, C. P. Rees, D. C. Dietrich, D. KHAKH, B. S. Dittman, J. S. Gan, W.-B. Koyama, M. S. Jayaraman, V. Cheer, J. F. Lester, H. A. Zhu, J. J. Looger, L. L. 2020-02-08 doi:10.1101/2020.02.07.939504 Cold Spring Harbor Laboratory Press 2020-02-08 <![CDATA[ Ecotype Simulation 2: An improved algorithm for efficiently demarcating microbial species from large sequence datasets ]]> https://biorxiv.org/content/10.1101/2020.02.10.940734v1?rss=1 Wood, J. M. Becraft, E. M. Cohan, F. Krizanc, D. Ward, D. M. 2020-02-12 doi:10.1101/2020.02.10.940734 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Model Reduction Tools For Phenomenological Modeling of Input-Controlled Biological Circuits ]]> https://biorxiv.org/content/10.1101/2020.02.15.950840v1?rss=1 Pandey, A. Murray, R. M. 2020-02-15 doi:10.1101/2020.02.15.950840 Cold Spring Harbor Laboratory Press 2020-02-15 <![CDATA[ The Structures of Secretory and Dimeric Immunoglobulin A ]]> https://biorxiv.org/content/10.1101/2020.02.16.951780v1?rss=1 Kumar Bharathkar, S. Parker, B. W. Malyutin, A. Haloi, N. Tajkhorshid, E. Stadtmueller, B. 2020-02-17 doi:10.1101/2020.02.16.951780 Cold Spring Harbor Laboratory Press 2020-02-17 <![CDATA[ Distinct representations of finger movement and force in human motor and premotor cortices ]]> https://biorxiv.org/content/10.1101/2020.02.18.952945v1?rss=1 Flint, R. D. Tate, M. C. Li, K. Templer, J. W. Rosenow, J. M. Pandarinath, C. Slutzky, M. W. 2020-02-19 doi:10.1101/2020.02.18.952945 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ A geometric and structural approach to the analysis and design of biological circuit dynamics: a theory tailored for synthetic biology ]]> https://biorxiv.org/content/10.1101/2020.02.18.953620v1?rss=1 Marken, J. P. Xiao, F. Murray, R. M. 2020-02-19 doi:10.1101/2020.02.18.953620 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Imaging cell lineage with a synthetic digital recording system ]]> https://biorxiv.org/content/10.1101/2020.02.21.958678v1?rss=1 Chow, K.-H. K. Budde, M. W. Granados, A. A. Cabrera, M. Yoon, S. Cho, S. Huang, T.-h. Koulena, N. Frieda, K. L. Cai, L. Lois, C. Elowitz, M. B. 2020-02-25 doi:10.1101/2020.02.21.958678 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Metabolic multi-stability and hysteresis in a model aerobe-anaerobe microbiome community ]]> https://biorxiv.org/content/10.1101/2020.02.28.968941v1?rss=1 Khazaei, T. Williams, R. L. Bogatyrev, S. R. Doyle, J. C. Henry, C. S. Ismagilov, R. F. 2020-02-29 doi:10.1101/2020.02.28.968941 Cold Spring Harbor Laboratory Press 2020-02-29 <![CDATA[ Improved reference genome of the arboviral vector Aedes albopictus ]]> https://biorxiv.org/content/10.1101/2020.02.28.969527v1?rss=1 Palatini, U. Masri, R. Cosme, L. V. Koren, S. Thibaud-Nissen, F. Biedler, J. K. Krsticevic, F. Johnston, S. Halbach, R. Crawford, J. E. Antoshechkin, I. Failloux, A.-B. Pischedda, E. Marconcini, M. Ghurye, J. Rhie, A. Sharma, A. Karagodin, D. A. Jentette, J. Gamez, S. Miesen, P. Caccone, A. Sharakhova, M. V. Tu, Z. Papathanos, P. A. van Rij, R. P. Akbari, O. S. Powell, J. Phillippy, A. M. Bonizzoni, M. 2020-02-28 doi:10.1101/2020.02.28.969527 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ A Quantitative Sequencing Framework for Absolute Abundance Measurements of Mucosal and Lumenal Microbial Communities ]]> https://biorxiv.org/content/10.1101/2020.02.28.970087v1?rss=1 Barlow, J. T. Bogatyrev, S. R. Ismagilov, R. F. 2020-02-28 doi:10.1101/2020.02.28.970087 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types ]]> https://biorxiv.org/content/10.1101/2020.02.29.970558v1?rss=1 Yao, Z. Liu, H. Xie, F. Fischer, S. Adkins, R. S. Aldrige, A. I. Ament, S. A. Bartlett, A. Behrens, M. M. Van den Berge, K. Bertagnolli, D. Biancalani, T. Booeshaghi, A. S. Corrada Bravo, H. Casper, T. Colantuoni, C. Crabtree, J. Creasy, H. Crichton, K. Crow, M. Dee, N. Dougherty, E. L. Doyle, W. I. Dudoit, S. Fang, R. Felix, V. Fong, O. Giglio, M. Goldy, J. Hawrylycz, M. Bezieux, H. R. d. Herb, B. R. Hertzano, R. Hou, X. Hu, Q. Huang, Z. J. Kancherla, J. Kroll, M. Lathia, K. Li, Y. E. Lucero, J. D. Luo, C. Mahurkar, A. McMillen, D. Nadaf, N. M. Ner 2020-03-02 doi:10.1101/2020.02.29.970558 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ pAgo-induced DNA interference protects bacteria from invader DNA ]]> https://biorxiv.org/content/10.1101/2020.03.01.971358v1?rss=1 Kuzmenko, A. Oguienko, A. Esyunina, D. Yudin, D. Petrova, M. Kudinova, A. Maslova, O. Ninova, M. Ryazansky, S. Leach, D. Aravin, A. A. Kulbachinskiy, A. 2020-03-03 doi:10.1101/2020.03.01.971358 Cold Spring Harbor Laboratory Press 2020-03-03 <![CDATA[ HCN domain is required for HCN channel expression and couples voltage- and cAMP-dependent gating mechanisms ]]> https://biorxiv.org/content/10.1101/2020.03.02.973560v1?rss=1 Wang, Z.-J. Blanco, I. Hayoz, S. Brelidze, T. I. 2020-03-02 doi:10.1101/2020.03.02.973560 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ CryoEM structure of the Vibrio cholerae Type IV competence pilus secretin PilQ ]]> https://biorxiv.org/content/10.1101/2020.03.03.975896v1?rss=1 Weaver, S. J. Sazinsky, M. H. Dalia, T. N. Dalia, A. B. Jensen, G. J. 2020-03-04 doi:10.1101/2020.03.03.975896 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ Isoform specificity in the mouse primary motor cortex ]]> https://biorxiv.org/content/10.1101/2020.03.05.977991v1?rss=1 Booeshaghi, A. S. Yao, Z. Velthoven, C. v. Smith, K. Tasic, B. Zeng, H. Pachter, L. 2020-03-05 doi:10.1101/2020.03.05.977991 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ An Xist-dependent protein assembly mediates Xist localization and gene silencing ]]> https://biorxiv.org/content/10.1101/2020.03.09.979369v1?rss=1 Plath, K. Black, D. L. Pandya-Jones, A. Markaki, Y. Serizay, J. Chitiashvili, T. Mancia, W. Damianov, A. Chronis, K. Papp, B. Chen, C.-K. McKee, R. Wang, X.-J. Chau, A. Leonhardt, H. Zheng, S. Guttman, M. 2020-03-09 doi:10.1101/2020.03.09.979369 Cold Spring Harbor Laboratory Press 2020-03-09 <![CDATA[ Combined membrane potential imaging and connectome of behavioral circuits in an annelid worm ]]> https://biorxiv.org/content/10.1101/2020.03.09.984013v1?rss=1 Ashaber, M. Tomina, Y. Kassraian-Fard, P. Bushong, E. A. Kristan, W. B. Ellisman, M. H. Wagenaar, D. A. 2020-03-10 doi:10.1101/2020.03.09.984013 Cold Spring Harbor Laboratory Press 2020-03-10 <![CDATA[ Layered Feedback Control Improves Robust Functionality across Heterogeneous Cell Populations ]]> https://biorxiv.org/content/10.1101/2020.03.24.006528v1?rss=1 Ren, X. Murray, R. M. 2020-03-25 doi:10.1101/2020.03.24.006528 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Transient Pupil Constriction Reflects and Affects Facial Attractiveness ]]> https://biorxiv.org/content/10.1101/2020.04.02.021436v1?rss=1 Liao, H.-I. Kashino, M. Shimojo, S. 2020-04-03 doi:10.1101/2020.04.02.021436 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ Decrease in ACE2 mRNA expression in aged mouse lung ]]> https://biorxiv.org/content/10.1101/2020.04.02.021451v1?rss=1 Booeshaghi, A. S. Pachter, L. 2020-04-05 doi:10.1101/2020.04.02.021451 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ Common Fronto-temporal Effective Connectivity in Humans and Monkeys ]]> https://biorxiv.org/content/10.1101/2020.04.03.024042v1?rss=1 Rocchi, F. Oya, H. Balezeau, F. Billig, A. J. Kocsis, Z. Jenison, R. Nourski, K. V. Kovach, C. K. Steinschneider, M. Kikuchi, Y. Rhone, A. E. Dlouhy, B. J. Kawasaki, H. Adolphs, R. Greenlee, J. D. W. Griffiths, T. D. Howard, M. A. Petkov, C. I. 2020-04-05 doi:10.1101/2020.04.03.024042 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ Causally Linking Neural Dominance to Perceptual Dominance in a Multisensory Conflict ]]> https://biorxiv.org/content/10.1101/2020.04.06.027227v1?rss=1 Yun, K. Bhattacharya, J. Sandkuhler, S. Lin, Y.-J. Iwaki, S. Shimojo, S. 2020-04-06 doi:10.1101/2020.04.06.027227 Cold Spring Harbor Laboratory Press 2020-04-06 <![CDATA[ Large hydrogen isotope fractionations distinguish nitrogenase-derived methane from other sources ]]> https://biorxiv.org/content/10.1101/2020.04.10.036657v1?rss=1 Luxem, K. E. Leavitt, W. D. Zhang, X. 2020-04-12 doi:10.1101/2020.04.10.036657 Cold Spring Harbor Laboratory Press 2020-04-12 <![CDATA[ Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy ]]> https://biorxiv.org/content/10.1101/2020.04.12.038331v1?rss=1 Metcalfe, K. S. Murali, R. S. Mullin, S. W. Connon, S. A. Orphan, V. J. 2020-04-13 doi:10.1101/2020.04.12.038331 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ Thermal Control of T-cell Immunotherapy ]]> https://biorxiv.org/content/10.1101/2020.04.16.045146v1?rss=1 Abedi, M. H. Lee, J. Piraner, D. I. Shapiro, M. G. 2020-04-18 doi:10.1101/2020.04.16.045146 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Transcranial Focused Ultrasound Generates Skull-Conducted Shear Waves: Computational Model and Implications for Neuromodulation ]]> https://biorxiv.org/content/10.1101/2020.04.16.045237v1?rss=1 Salahshoor, H. Shapiro, M. G. Ortiz, M. 2020-04-18 doi:10.1101/2020.04.16.045237 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Structure of the bacterial cellulose ribbon and its assembly-guiding cytoskeleton by electron cryotomography ]]> https://biorxiv.org/content/10.1101/2020.04.16.045534v1?rss=1 NICOLAS, W. J. Ghosal, D. Tocheva, E. I. Meyerowitz, E. M. Jensen, G. J. 2020-04-17 doi:10.1101/2020.04.16.045534 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ A shared neural substrate for action verbs and observed actions in human posterior parietal cortex. ]]> https://biorxiv.org/content/10.1101/2020.04.20.039529v1?rss=1 Aflalo, T. Zhang, C. Rosario, E. Pouratian, N. Orban, G. A. Andersen, R. A. 2020-04-20 doi:10.1101/2020.04.20.039529 Cold Spring Harbor Laboratory Press 2020-04-20 <![CDATA[ Neural correlates of cognitive motor signals in primary somatosensory cortex. ]]> https://biorxiv.org/content/10.1101/2020.04.20.041269v1?rss=1 Jaffari, M. Aflalo, T. Chivukula, S. Kellis, S. Armenta Salas, M. Norman, S. Pejsa, K. Liu, C. Andersen, R. A. 2020-04-21 doi:10.1101/2020.04.20.041269 Cold Spring Harbor Laboratory Press 2020-04-21 <![CDATA[ Bacterial defenses against a natural antibiotic promote collateral resilience to clinical antibiotics ]]> https://biorxiv.org/content/10.1101/2020.04.20.049437v1?rss=1 Meirelles, L. A. Perry, E. K. Bergkessel, M. Newman, D. K. 2020-04-20 doi:10.1101/2020.04.20.049437 Cold Spring Harbor Laboratory Press 2020-04-20 <![CDATA[ Term Matrix: A novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns ]]> https://biorxiv.org/content/10.1101/2020.04.21.045195v1?rss=1 Wood, V. Carbon, S. Harris, M. A. Lock, A. Engel, S. R. Hill, D. P. Van Auken, K. Attrill, H. Feuermann, M. Gaudet, P. Lovering, R. C. Poux, S. Rutherford, K. M. Mungall, C. J. 2020-04-23 doi:10.1101/2020.04.21.045195 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ Sensory-evoked extracellular vesicle release and targeting ]]> https://biorxiv.org/content/10.1101/2020.04.21.050690v1?rss=1 Wang, J. Nikonorova, I. A. Gu, A. Sternberg, P. W. Barr, M. M. 2020-04-22 doi:10.1101/2020.04.21.050690 Cold Spring Harbor Laboratory Press 2020-04-22 <![CDATA[ Modulation of the tumour promoting functions of cancer associated fibroblasts by phosphodiesterase type 5 inhibition increases the efficacy of chemotherapy in human preclinical models of esophageal adenocarcinoma. ]]> https://biorxiv.org/content/10.1101/2020.04.21.052647v1?rss=1 Hayden, A. Manousopoulou, A. Cowie, A. Walker, R. Sharpe, B. P. Harrington, J. Izadi, F. Kyle, E. Saunders, J. H. Parsons, S. L. Ritchie, A. A. Clarke, P. A. Collier, P. Garbis, S. D. Rose-Zerilli, M. Grabowska, A. M. Underwood, T. J. 2020-04-23 doi:10.1101/2020.04.21.052647 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ Representation of conscious percept without report in the macaque face patch network ]]> https://biorxiv.org/content/10.1101/2020.04.22.047522v1?rss=1 Hesse, J. K. Tsao, D. Y. 2020-04-24 doi:10.1101/2020.04.22.047522 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Electron tomography visualization of HIV-1 fusion with target cells using fusion inhibitors to trap the pre-hairpin intermediate ]]> https://biorxiv.org/content/10.1101/2020.04.29.068775v1?rss=1 Ladinsky, M. S. Gnanapragasam, P. N. P. Yang, Z. West, A. P. Kay, M. S. Bjorkman, P. J. 2020-04-30 doi:10.1101/2020.04.29.068775 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Catalytic cleavage of HEAT and subsequent covalent binding of the tetralone moiety by the SARS-CoV-2 main protease ]]> https://biorxiv.org/content/10.1101/2020.05.02.043554v1?rss=1 Günther, S. Reinke, P. Y. A. Oberthuer, D. Yefanov, O. Ginn, H. Meier, S. Lane, T. J. Lorenzen, K. Gelisio, L. Brehm, W. Dunkel, I. Domaracky, M. Saouane, S. Lieske, J. Ehrt, C. Koua, F. Tolstikova, A. White, T. A. Groessler, M. Fleckenstein, H. Trost, F. Galchenkova, M. Gevorkov, Y. Li, C. Awel, S. Peck, A. Xavier, P. L. Barthelmess, M. Schlünzen, F. Werner, N. Andaleeb, H. Ullah, N. Falke, S. Franca, B. A. Schwinzer, M. Brognaro, H. Seychell, B. Gieseler, H. Melo, D. Zaitsev-Doyle, J. J. Norton-Baker, B. Knoska, J. Esperanza, G. Mashhour, A. R. G 2020-05-04 doi:10.1101/2020.05.02.043554 Cold Spring Harbor Laboratory Press 2020-05-04 <![CDATA[ Rising through the Ranks: Seasonal and Diel Patterns of Marine Viruses ]]> https://biorxiv.org/content/10.1101/2020.05.07.082883v1?rss=1 Hevroni, G. Flores-Uribe, J. Beja, O. Philosof, A. 2020-05-07 doi:10.1101/2020.05.07.082883 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ MapA, a second large RTX adhesin, contributes to biofilm formation by Pseudomonas fluorescens ]]> https://biorxiv.org/content/10.1101/2020.05.11.089839v1?rss=1 Collins, A. J. Pastora, A. B. Smith, T. J. Dahlstrom, K. M. O'Toole, G. 2020-05-13 doi:10.1101/2020.05.11.089839 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ Single Trial Decoding of Movement Intentions Using Functional Ultrasound Neuroimaging ]]> https://biorxiv.org/content/10.1101/2020.05.12.086132v1?rss=1 Norman, S. L. Maresca, D. Christopoulos, V. N. Griggs, W. S. Demene, C. Tanter, M. Shapiro, M. G. Andersen, R. A. 2020-05-14 doi:10.1101/2020.05.12.086132 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Cell-extracellular matrix interactions in the fluidic phase direct the topology and polarity of self-organized epithelial structures ]]> https://biorxiv.org/content/10.1101/2020.05.12.090068v1?rss=1 Ouyang, M. Yu, J.-Y. Chen, Y. Deng, L. Guo, C.-L. 2020-05-14 doi:10.1101/2020.05.12.090068 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ In situ structure and organisation of the type IX secretion system ]]> https://biorxiv.org/content/10.1101/2020.05.13.094771v1?rss=1 Gorasia, D. G. Chreifi, G. Seers, C. A. Butler, C. A. Heath, J. E. Glew, M. D. McBride, M. J. Subramanian, P. Kjaer, A. Jensen, G. J. Veith, P. D. Reynolds, E. C. 2020-05-14 doi:10.1101/2020.05.13.094771 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Plasma and Fecal Metabolite Profiles in Autism Spectrum Disorder ]]> https://biorxiv.org/content/10.1101/2020.05.17.098806v1?rss=1 Needham, B. D. Adame, M. D. Serena, G. Rose, D. R. Preston, G. M. Conrad, M. C. Campbell, A. S. Donabedian, D. H. Fasano, A. Ashwood, P. Mazmanian, S. D. 2020-05-19 doi:10.1101/2020.05.17.098806 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ log(x+1)* and log(1+x)* ]]> https://biorxiv.org/content/10.1101/2020.05.19.100214v1?rss=1 Booeshaghi, A. S. Pachter, L. 2020-05-19 doi:10.1101/2020.05.19.100214 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ Focused ultrasound excites neurons via mechanosensitive calcium accumulation and ion channel amplification ]]> https://biorxiv.org/content/10.1101/2020.05.19.101196v1?rss=1 Yoo, S. Mittelstein, D. R. Hurt, R. C. Lacroix, J. J. Shapiro, M. G. 2020-05-22 doi:10.1101/2020.05.19.101196 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Rapid Tilt-Series Method for Cryo-Electron Tomography: Characterizing Stage Behavior During FISE Acquisition ]]> https://biorxiv.org/content/10.1101/2020.05.19.104828v1?rss=1 Chreifi, G. Chen, S. Jensen, G. J. 2020-05-21 doi:10.1101/2020.05.19.104828 Cold Spring Harbor Laboratory Press 2020-05-21 <![CDATA[ A workflow for accurate metabarcoding using nanopore MinION sequencing ]]> https://biorxiv.org/content/10.1101/2020.05.21.108852v1?rss=1 45 barcodes). Our pipeline successfully identified all 50 species in the mock community and exhibited comparable sensitivity and accuracy to MiSeq. The use of RCA was integral for increasing consensus accuracy, but it was also the most time-consuming step during the laboratory workflow and most RCA reads were skewed towards a shorter read length range with a median RCA fragment length of up to 1262bp. Our study demonstrates that Nanopore sequencing can be used for metabarcoding but we recommend the exploration of other isothermal amplification procedures to improve consensus length. ]]> Baloglu, B. Chen, Z. Elbrecht, V. Braukmann, T. MacDonald, S. Steinke, D. 2020-05-25 doi:10.1101/2020.05.21.108852 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Proofreading through spatial gradients ]]> https://biorxiv.org/content/10.1101/2020.05.23.112664v1?rss=1 Galstyan, V. Husain, K. Xiao, F. Murugan, A. Phillips, R. 2020-05-24 doi:10.1101/2020.05.23.112664 Cold Spring Harbor Laboratory Press 2020-05-24 <![CDATA[ Engineering multiple levels of specificity in an RNA viral vector ]]> https://biorxiv.org/content/10.1101/2020.05.27.119909v1?rss=1 Gao, X. J. Chong, L. S. Ince, M. H. Kim, M. S. Elowitz, M. B. 2020-05-27 doi:10.1101/2020.05.27.119909 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ Compensatory ion transport buffers daily protein rhythms to regulate osmotic balance and cellular physiology ]]> https://biorxiv.org/content/10.1101/2020.05.28.118398v1?rss=1 Stangherlin, A. Wong, D. C. S. Barbiero, S. Watson, J. L. Zeng, A. Seinkmane, E. Chew, S. P. Beale, A. D. Hayter, E. A. Guna, A. Inglis, A. Bartolami, E. Matile, S. Lequeux, N. Pons, T. Day, J. van Ooijen, G. Voorhees, R. M. Bechtold, D. Derivery, E. Edgar, R. S. Newham, P. O'Neill, J. S. 2020-05-28 doi:10.1101/2020.05.28.118398 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies ]]> https://biorxiv.org/content/10.1101/2020.05.28.121533v1?rss=1 Barnes, C. O. West, A. P. Huey-Tubman, K. Hoffmann, M. A. G. Sharaf, N. G. Hoffman, P. R. Koranda, N. Gristick, H. B. Gaebler, C. Muecksch, F. Cetrulo Lorenzi, J. C. Finkin, S. Hagglof, T. Hurley, A. Millard, K. G. Weisblum, Y. Schmidt, F. Hatziioannou, T. Bieniasz, P. D. Caskey, M. Robbiani, D. Nussenzweig, M. C. Bjorkman, P. J. 2020-05-29 doi:10.1101/2020.05.28.121533 Cold Spring Harbor Laboratory Press 2020-05-29 <![CDATA[ De novo enteric neurogenesis in post-embryonic zebrafish from Schwann cell precursors rather than resident cell types ]]> https://biorxiv.org/content/10.1101/2020.06.01.127712v1?rss=1 Bronner, M. E. El-Nachef, W. N. 2020-06-02 doi:10.1101/2020.06.01.127712 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ Scalable, continuous evolution for the generation of diverse enzyme variants encompassing promiscuous activities ]]> https://biorxiv.org/content/10.1101/2020.06.01.128165v1?rss=1 Rix, G. Watkins-Dulaney, E. J. Almhjell, P. J. Boville, C. E. Arnold, F. H. Liu, C. C. 2020-06-02 doi:10.1101/2020.06.01.128165 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ Global landscape of phenazine biosynthesis and biodegradation reveals species-specific colonization patterns in agricultural soils and crop microbiomes ]]> https://biorxiv.org/content/10.1101/2020.06.05.136879v1?rss=1 800 soil and plant-associated shotgun-metagenomes. We discover novel producer-crop associations and demonstrate that phenazine biosynthesis is prevalent across habitats and preferentially enriched in rhizospheres, whereas biodegrading bacteria are rare. We validate an association between maize and Dyella japonica, a putative producer abundant in crop microbiomes. D. japonica upregulates phenazine biosynthesis during phosphate limitation and robustly colonizes maize seedling roots. This work provides a global picture of phenazines in natural environments and highlights plant-microbe associations of agricultural potential. Our metagenomic approach may be extended to other metabolites and functional traits in diverse ecosystems. ]]> Dar, D. Thomashow, L. S. Weller, D. M. Newman, D. K. 2020-06-05 doi:10.1101/2020.06.05.136879 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ The Role of the Medial Prefrontal Cortex in Spatial Margin of Safety Calculations ]]> https://biorxiv.org/content/10.1101/2020.06.05.137075v1?rss=1 Qi, S. Cross, L. Wise, T. Sui, X. O'Doherty, J. Mobbs, d. 2020-06-08 doi:10.1101/2020.06.05.137075 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ Multiplexed imaging of human tuberculosis granulomas uncovers immunoregulatory features conserved across tissue and blood ]]> https://biorxiv.org/content/10.1101/2020.06.08.140426v1?rss=1 McCaffrey, E. F. Donato, M. Keren, L. Chen, Z. Fitzpatrick, M. Jojic, V. Delmastro, A. Greenwald, N. F. Baranski, A. Graf, W. Bosse, M. Ramdial, P. K. Forgo, E. Van Valen, D. van de Rijn, M. Bendall, S. C. Banaei, N. Steyn, A. J. C. Khatri, P. Angelo, M. 2020-06-09 doi:10.1101/2020.06.08.140426 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ The long-distance flight behavior of Drosophila suggests a general model for wind-assisted dispersal in insects. ]]> https://biorxiv.org/content/10.1101/2020.06.10.145169v1?rss=1 Leitch, K. Ponce, F. V. van Breugel, F. Dickinson, M. H. 2020-06-11 doi:10.1101/2020.06.10.145169 Cold Spring Harbor Laboratory Press 2020-06-11 <![CDATA[ The changing mouse embryo transcriptome at whole tissue and single-cell resolution ]]> https://biorxiv.org/content/10.1101/2020.06.14.150599v1?rss=1 He, P. Williams, B. A. Trout, D. Marinov, G. K. Amrhein, H. Berghella, L. Goh, S.-T. Plajzer-Frick, I. Afzal, V. Pennacchio, L. A. Dickel, D. E. Visel, A. Ren, B. Hardison, R. C. Zhang, Y. Wold, B. J. 2020-06-14 doi:10.1101/2020.06.14.150599 Cold Spring Harbor Laboratory Press 2020-06-14 <![CDATA[ Broad gene expression throughout the mouse and marmoset brain after intravenous delivery of engineered AAV capsids ]]> https://biorxiv.org/content/10.1101/2020.06.16.152975v1?rss=1 Flytzanis, N. C. Goeden, N. Goertsen, D. Cummins, A. Pickel, J. Gradinaru, V. 2020-06-17 doi:10.1101/2020.06.16.152975 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ Team flow is a unique brain state associated with enhanced information integration and neural synchrony ]]> https://biorxiv.org/content/10.1101/2020.06.17.157990v1?rss=1 Shehata, M. Cheng, M. Leung, A. Tsuchiya, N. Wu, D.-A. Tseng, C.-h. Nakauchi, S. Shimojo, S. 2020-06-19 doi:10.1101/2020.06.17.157990 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Cryptosporulation in Kurthia spp. forces a rethinking of asporogenesis in Firmicutes ]]> https://biorxiv.org/content/10.1101/2020.06.18.160689v1?rss=1 Filippidou, S. Fatton, M. Junier, T. Berge, M. Poppleton, D. Blum, T. B. Kaminek, M. Odriozola, A. Blom, J. Johnson, S. L. Abrahams, J. P. Chain, P. S. G. Gribaldo, S. Tocheva, E. I. Zuber, B. Viollier, P. H. Junier, P. 2020-06-20 doi:10.1101/2020.06.18.160689 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ A Biodiversity Composition Map of California Derived from Environmental DNA Metabarcoding and Earth Observation ]]> https://biorxiv.org/content/10.1101/2020.06.19.160374v1?rss=1 Lin, M. Simons, A. L. Curd, E. E. Harrigan, R. J. Schneider, F. D. Ruiz-Ramos, D. V. Gold, Z. Osborne, M. G. Shirazi, S. Schweizer, T. M. Moore, T. N. Fox, E. A. Turba, R. Garcia-Vedrenne, A. E. Helman, S. K. Rutledge, K. Mejia, M. P. Munguia Ramos, M. N. Wetzer, R. Pentcheff, D. McTavish, E. J. Dawson, M. N. Shapiro, B. Wayne, R. K. Meyer, R. S. 2020-06-20 doi:10.1101/2020.06.19.160374 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Discovery of a Cellular Mechanism Regulating Transcriptional Noise ]]> https://biorxiv.org/content/10.1101/2020.06.29.128439v1?rss=1 Desai, R. Hansen, M. M. K. Martin, B. Yu, C. Ding, S. Thomson, M. Weinberger, L. S. 2020-06-30 doi:10.1101/2020.06.29.128439 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ Developmental, cellular, and biochemical basis of transparency in the glasswing butterfly Greta oto ]]> https://biorxiv.org/content/10.1101/2020.07.02.183590v1?rss=1 Pomerantz, A. F. Siddique, R. H. Cash, E. I. Kishi, Y. Pinna, C. Hammar, K. Gomez, D. Elias, M. Patel, N. H. 2020-07-02 doi:10.1101/2020.07.02.183590 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Evolution of DNA Replication Origin Specification and Gene Silencing Mechanisms ]]> https://biorxiv.org/content/10.1101/2020.07.04.187286v1?rss=1 Hu, Y. Tareen, A. Sheu, Y.-J. Ireland, W. T. T. Speck, C. Li, H. Joshua-Tor, L. Kinney, J. B. Stillman, B. 2020-07-04 doi:10.1101/2020.07.04.187286 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq ]]> https://biorxiv.org/content/10.1101/2020.07.06.188003v1?rss=1 Gustafsson, J. Robinson, J. Nielsen, J. Pachter, L. 2020-07-06 doi:10.1101/2020.07.06.188003 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ Repression of interrupted and intact rDNA by the SUMO pathway in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2020.07.14.203158v1?rss=1 Luo, Y. Fefelova, E. Ninova, M. Chen, Y.-C. A. Aravin, A. 2020-07-14 doi:10.1101/2020.07.14.203158 Cold Spring Harbor Laboratory Press 2020-07-14 <![CDATA[ Binding of guide piRNA triggers methylation of the unstructured N-terminal region of Aub leading to assembly of the piRNA amplification complex ]]> https://biorxiv.org/content/10.1101/2020.07.14.203323v1?rss=1 Huang, X. Hu, H. Webster, A. Zou, F. Du, J. Fejes Toth, K. Aravin, A. Li, S. 2020-07-14 doi:10.1101/2020.07.14.203323 Cold Spring Harbor Laboratory Press 2020-07-14 <![CDATA[ Characterizing the diverse cells that associate with the developing commissures of the zebrafish forebrain ]]> https://biorxiv.org/content/10.1101/2020.07.16.205153v1?rss=1 Schnabl, J. Litz, M. P. H. Schneider, C. PenkoffLidbeck, N. Bashiruddin, S. Schwartz, M. S. Alligood, K. Barresi, M. J. F. 2020-07-17 doi:10.1101/2020.07.16.205153 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Generation of ordered protein assemblies using rigid three-body fusion ]]> https://biorxiv.org/content/10.1101/2020.07.18.210294v1?rss=1 Vulovic, I. Yao, Q. Park, Y.-J. Courbet, A. Norris, A. Busch, F. Sahasrabuddhe, A. Merten, H. Sahtoe, D. D. Ueda, G. Fallas, J. A. Hsia, Y. Weaver, S. J. Langan, R. A. Pluckthun, A. Wysocki, V. H. Veesler, D. Jensen, G. J. Baker, D. 2020-07-19 doi:10.1101/2020.07.18.210294 Cold Spring Harbor Laboratory Press 2020-07-19 <![CDATA[ Regulated assembly of the ER membrane protein complex ]]> https://biorxiv.org/content/10.1101/2020.07.20.213066v1?rss=1 Pleiner, T. Januszyk, K. Tomaleri, G. P. Oania, R. S. Hazu, M. Sweredoski, M. J. Moradian, A. Guna, A. Voorhees, R. M. 2020-07-21 doi:10.1101/2020.07.20.213066 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Dynamics and functional roles of splicing factor autoregulation ]]> https://biorxiv.org/content/10.1101/2020.07.22.216887v1?rss=1 Ding, F. Su, C. Chow, K.-H. K. Elowitz, M. 2020-07-24 doi:10.1101/2020.07.22.216887 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Enabling out-of-clinic human immunity studies via single-cell profiling of capillary blood ]]> https://biorxiv.org/content/10.1101/2020.07.25.210468v1?rss=1 Dobreva, T. Brown, D. Park, J. H. Thomson, M. 2020-07-26 doi:10.1101/2020.07.25.210468 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ Predicting the Emergence of SARS-CoV-2 Clades ]]> https://biorxiv.org/content/10.1101/2020.07.26.222117v1?rss=1 Jain, S. Xiao, X. Bogdan, P. Bruck, J. 2020-07-27 doi:10.1101/2020.07.26.222117 Cold Spring Harbor Laboratory Press 2020-07-27 <![CDATA[ The Mouse Action Recognition System (MARS): a software pipeline for automated analysis of social behaviors in mice ]]> https://biorxiv.org/content/10.1101/2020.07.26.222299v1?rss=1 Segalin, C. Williams, J. Karigo, T. Hui, M. Zelikowsky, M. Sun, J. J. Perona, P. Anderson, D. J. Kennedy, A. 2020-07-27 doi:10.1101/2020.07.26.222299 Cold Spring Harbor Laboratory Press 2020-07-27 <![CDATA[ Dorsal raphe dopamine neurons signal motivational salience dependent on internal and external states ]]> https://biorxiv.org/content/10.1101/2020.07.27.222729v1?rss=1 Cho, J. R. Chen, X. Kahan, A. Robinson, E. Wagenaar, D. A. Gradinaru, V. 2020-07-27 doi:10.1101/2020.07.27.222729 Cold Spring Harbor Laboratory Press 2020-07-27 <![CDATA[ NEURAL ENCODING OF FELT AND IMAGINED TOUCH WITHIN HUMAN POSTERIOR PARIETAL CORTEX ]]> https://biorxiv.org/content/10.1101/2020.07.27.223636v1?rss=1 Chivukula, S. Zhang, C. Aflalo, T. Jafari, M. Pejsa, K. Pouratian, N. Andersen, R. A. 2020-07-29 doi:10.1101/2020.07.27.223636 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ P-bodies are sites of rapid RNA decay during the neural crest epithelial-mesenchymal transition ]]> https://biorxiv.org/content/10.1101/2020.07.31.231860v1?rss=1 Hutchins, E. J. Piacentino, M. L. Bronner, M. E. 2020-08-01 doi:10.1101/2020.07.31.231860 Cold Spring Harbor Laboratory Press 2020-08-01 <![CDATA[ BioCRNpyler: Compiling Chemical Reaction Networks from Biomolecular Parts in Diverse Contexts ]]> https://biorxiv.org/content/10.1101/2020.08.02.233478v1?rss=1 Poole, W. Pandey, A. Tuza, Z. Shur, A. Murray, R. M. 2020-08-03 doi:10.1101/2020.08.02.233478 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ A Broadly Neutralizing Macaque Monoclonal Antibody Against the HIV-1 V3-Glycan Patch ]]> https://biorxiv.org/content/10.1101/2020.08.10.244582v1?rss=1 Wang, Z. Barnes, C. O. Gautam, R. Cetrulo Lorenzi, J. C. Mayer, C. T. Oliveira, T. Y. Ramos, V. Cipolla, M. Gordon, K. M. Gristick, H. B. West, A. P. Nishimura, Y. Raina, H. Seaman, M. S. Gazumyan, A. Martin, M. A. Bjorkman, P. J. Escolano, A. Nussenzweig, M. C. 2020-08-10 doi:10.1101/2020.08.10.244582 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ A single-cell method to map higher-order 3D genome organization in thousands of individual cells reveals structural heterogeneity in mouse ES cells ]]> https://biorxiv.org/content/10.1101/2020.08.11.242081v1?rss=1 Arrastia, M. V. Jachowicz, J. W. Ollikainen, N. Curtis, M. S. Lai, C. Quinodoz, S. Selck, D. A. Guttman, M. Ismagilov, R. F. 2020-08-12 doi:10.1101/2020.08.11.242081 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Single position substitution of hairpin pyrrole-imidazole polyamides imparts distinct DNA-binding profiles across the human genome ]]> https://biorxiv.org/content/10.1101/2020.08.13.249730v1?rss=1 Finn, P. B. Bhimsaria, D. Ali, A. Eguchi, A. Ansari, A. Z. Dervan, P. B. 2020-08-14 doi:10.1101/2020.08.13.249730 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Low-cost, bottom-up fabrication of large-scale single-molecule nanoarrays by DNA origami placement ]]> https://biorxiv.org/content/10.1101/2020.08.14.250951v1?rss=1 Shetty, R. M. Brady, S. R. Rothemund, P. W. Hariadi, R. F. Gopinath, A. 2020-08-14 doi:10.1101/2020.08.14.250951 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Coherence Shifts in Attribute Evaluations ]]> https://biorxiv.org/content/10.1101/2020.08.19.258046v1?rss=1 Lee, D. Holyoak, K. 2020-08-20 doi:10.1101/2020.08.19.258046 Cold Spring Harbor Laboratory Press 2020-08-20 <![CDATA[ Modular metabolite assembly in C. elegans lysosome-related organelles ]]> https://biorxiv.org/content/10.1101/2020.08.22.262956v1?rss=1 View larger version (42K): org.highwire.dtl.DTLVardef@6e83cborg.highwire.dtl.DTLVardef@18e9302org.highwire.dtl.DTLVardef@1557670org.highwire.dtl.DTLVardef@1d2ca50_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Le, H. H. Wrobel, C. J. Cohen, S. M. Yu, J. Park, H. Helf, M. J. Curtis, B. J. Rodrigues, P. R. Sternberg, P. W. Schroeder, F. C. 2020-08-24 doi:10.1101/2020.08.22.262956 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ piRNA-mediated gene regulation and adaptation to sex-specific transposon expression in D. melanogaster male germline ]]> https://biorxiv.org/content/10.1101/2020.08.25.266585v1?rss=1 Chen, P. Kotov, A. A. Godneeva, B. K. Bazylev, S. S. Olenina, L. V. Aravin, A. A. 2020-08-25 doi:10.1101/2020.08.25.266585 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ RDC complex executes a dynamic piRNA program during Drosophila spermatogenesis to safeguard male fertility ]]> https://biorxiv.org/content/10.1101/2020.08.25.266643v1?rss=1 Chen, P. Luo, Y. Aravin, A. A. 2020-08-25 doi:10.1101/2020.08.25.266643 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ Distributed Visual Category Processing Across Medial Superior Temporal and Lateral Intraparietal Cortices ]]> https://biorxiv.org/content/10.1101/2020.08.25.266791v1?rss=1 Zhou, Y. Mohan, K. Freedman, D. J. 2020-08-25 doi:10.1101/2020.08.25.266791 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ RNA promotes the formation of spatial compartments in the nucleus ]]> https://biorxiv.org/content/10.1101/2020.08.25.267435v1?rss=1 Quinodoz, S. A. Bhat, P. Ollikainen, N. Jachowicz, J. W. Banerjee, A. K. Chovanec, P. Blanco, M. R. Chow, A. Markaki, Y. Plath, K. Guttman, M. 2020-08-25 doi:10.1101/2020.08.25.267435 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ Structural classification of neutralizing antibodies against the SARS-CoV-2 spike receptor-binding domain suggests vaccine and therapeutic strategies ]]> https://biorxiv.org/content/10.1101/2020.08.30.273920v1?rss=1 Barnes, C. O. Jette, C. A. Abernathy, M. E. Dam, K.-M. A. Esswein, S. R. Gristick, H. B. Malyutin, A. G. Sharaf, N. G. Huey-Tubman, K. E. Lee, Y. E. Robbiani, D. F. Nussenzweig, M. C. West, A. P. Bjorkman, P. J. 2020-08-30 doi:10.1101/2020.08.30.273920 Cold Spring Harbor Laboratory Press 2020-08-30 <![CDATA[ Feature-based encoding of face identity by single neurons in the human medial temporal lobe ]]> https://biorxiv.org/content/10.1101/2020.09.01.278283v1?rss=1 Cao, R. Wang, J. Lin, C. Rutishauser, U. Todorov, A. Li, X. Brandmeir, N. Wang, S. 2020-09-02 doi:10.1101/2020.09.01.278283 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ Synthetic mammalian signaling circuits for robust cell population control ]]> https://biorxiv.org/content/10.1101/2020.09.02.278564v1?rss=1 Ma, Y. Budde, M. W. Mayalu, M. N. Zhu, J. Murray, R. M. Elowitz, M. B. 2020-09-03 doi:10.1101/2020.09.02.278564 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Hmx gene conservation identifies the evolutionary origin of vertebrate cranial ganglia ]]> https://biorxiv.org/content/10.1101/2020.09.07.281501v1?rss=1 Papadogiannis, V. Parker, H. J. Pennati, A. Patthey, C. Bronner, M. E. Shimeld, S. M. 2020-09-07 doi:10.1101/2020.09.07.281501 Cold Spring Harbor Laboratory Press 2020-09-07 <![CDATA[ Targeting Neuroplasticity to Improve Motor Recovery after Stroke ]]> https://biorxiv.org/content/10.1101/2020.09.09.284620v1?rss=1 Norman, S. L. Wolpaw, J. R. Reinkensmeyer, D. J. 2020-09-09 doi:10.1101/2020.09.09.284620 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Neural encoding of socially adjusted value during competitive and hazardous foraging ]]> https://biorxiv.org/content/10.1101/2020.09.11.294058v1?rss=1 Silston, B. Wise, T. Qi, S. Sui, X. Dayan, P. Mobbs, D. 2020-09-12 doi:10.1101/2020.09.11.294058 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ A soluble ACE2 microbody protein fused to a single immunoglobulin Fc domain is a potent inhibitor of SARS-CoV-2 infection in cell culture ]]> https://biorxiv.org/content/10.1101/2020.09.16.300319v1?rss=1 Tada, T. Fan, C. Kaur, R. Stapleford, K. A. Gristick, H. Nimigean, C. Landau, N. R. 2020-09-17 doi:10.1101/2020.09.16.300319 Cold Spring Harbor Laboratory Press 2020-09-17 <![CDATA[ Challenges in solving structures from radiation-damaged tomograms of protein nanocrystals assessed by simulation ]]> https://biorxiv.org/content/10.1101/2020.09.18.298562v1?rss=1 Peck, A. Yao, Q. Brewster, A. S. Zwart, P. H. Heumann, J. M. Sauter, N. K. Jensen, G. J. 2020-09-20 doi:10.1101/2020.09.18.298562 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ The structure of the UDP-Glc/GlcNAc 4-epimerase from the human pathogen Campylobacter jejuni ]]> https://biorxiv.org/content/10.1101/2020.09.22.308395v1?rss=1 Yun, H. G. Jang, K.-S. Tanaka, S. Clemons, W. M. 2020-09-22 doi:10.1101/2020.09.22.308395 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Structural biologists, lets mind our colors ]]> https://biorxiv.org/content/10.1101/2020.09.22.308593v1?rss=1 Saladi, S. M. Maggiolo, A. O. Radford, K. Clemons, W. M. 2020-09-24 doi:10.1101/2020.09.22.308593 Cold Spring Harbor Laboratory Press 2020-09-24 <![CDATA[ Mechanism of cell polarisation and first lineage segregation in the human embryo ]]> https://biorxiv.org/content/10.1101/2020.09.23.310680v1?rss=1 Zhu, M. Shahbazi, M. N. Martin, A. Zhang, C. Sozen, B. Borsos, M. Mandelbaum, R. S. Paulson, R. J. Mole, M. A. Esbert, M. Scott, R. T. Campbell, A. Fishel, S. Gradinaru, V. Zhao, H. Wu, K. Chen, Z. Seli, E. de los Santos, M. J. Zernicka-Goetz, M. 2020-09-23 doi:10.1101/2020.09.23.310680 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Three-Dimensional Impedance Tomographic Mapping of Metabolically Active Endolumen ]]> https://biorxiv.org/content/10.1101/2020.09.24.312025v1?rss=1 Abiri, P. Luo, Y. Huang, Z.-Y. Roustaei, M. Duarte-Vogel, S. Cui, Q. Packard, R. R. S. Ebrahimi, R. Benharash, P. Tai, Y.-C. Hsiai, T. K. 2020-09-25 doi:10.1101/2020.09.24.312025 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Field testing of biohybrid robotic jellyfish to demonstrate enhanced swimming speeds ]]> https://biorxiv.org/content/10.1101/2020.09.24.312322v1?rss=1 Xu, N. W. Townsend, J. P. Costello, J. H. H. Colin, S. Gemmell, B. Dabiri, J. O. 2020-09-25 doi:10.1101/2020.09.24.312322 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Intrinsic and extrinsic noise are distinguishable in a synthesis - export - degradation model of mRNA production ]]> https://biorxiv.org/content/10.1101/2020.09.25.312868v1?rss=1 Gorin, G. Pachter, L. 2020-09-25 doi:10.1101/2020.09.25.312868 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ A multiscale analysis of early flower development in Arabidopsis provides an integrated view of molecular regulation and growth control ]]> https://biorxiv.org/content/10.1101/2020.09.25.313312v1?rss=1 Refahi, Y. Zardilis, A. Michelin, G. Wightman, R. Leggio, B. Legrand, J. Faure, E. Vachez, L. Armezzani, A. Zhao, F. Das, P. Prunet, N. Meyerowitz, E. M. Godin, C. Malandain, G. Jonsson, H. Traas, J. 2020-09-26 doi:10.1101/2020.09.25.313312 Cold Spring Harbor Laboratory Press 2020-09-26 <![CDATA[ Genotypic similarity among algal symbionts corresponds to associations with closely related coral hosts ]]> https://biorxiv.org/content/10.1101/2020.09.26.314773v1?rss=1 Reich, H. G. Kitchen, S. A. Stankiewicz, K. H. Devlin-Durante, M. Fogarty, N. D. Baums, I. B. 2020-09-26 doi:10.1101/2020.09.26.314773 Cold Spring Harbor Laboratory Press 2020-09-26 <![CDATA[ Residue-by-residue analysis of cotranslational membrane protein integration in vivo ]]> https://biorxiv.org/content/10.1101/2020.09.27.315283v1?rss=1 Nicolaus, F. Metola, A. Mermans, D. Liljenstrom, A. Krc, A. Abdullahi, S. M. Zimmer, M. Miller, T. F. Von Heijne, G. 2020-09-28 doi:10.1101/2020.09.27.315283 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ Signal separability in integrated neurophotonics ]]> https://biorxiv.org/content/10.1101/2020.09.27.315556v1?rss=1 Yatsenko, D. Moreaux, L. C. Choi, J. Tolias, A. Shepard, K. L. Roukes, M. L. 2020-09-29 doi:10.1101/2020.09.27.315556 Cold Spring Harbor Laboratory Press 2020-09-29 <![CDATA[ Implantable photonic neural probes for light-sheet fluorescence brain imaging ]]> https://biorxiv.org/content/10.1101/2020.09.30.317214v1?rss=1 Sacher, W. D. Chen, F.-D. Moradi-Chameh, H. Luo, X. Fomenko, A. Shah, P. Lordello, T. Liu, X. Felts Almog, I. Straguzzi, J. N. Fowler, T. M. Jung, Y. Hu, T. Jeong, J. Lozano, A. M. Guo-Qiang Lo, P. Valiante, T. A. Moreaux, L. C. Poon, J. K. S. Roukes, M. L. 2020-09-30 doi:10.1101/2020.09.30.317214 Cold Spring Harbor Laboratory Press 2020-09-30 <![CDATA[ Neurogenetic and genomic approaches reveal roles for Dpr/DIP cell adhesion molecules in Drosophila reproductive behavior ]]> https://biorxiv.org/content/10.1101/2020.10.02.323477v1?rss=1 Arbeitman, M. Brovero, S. G. Fortier, J. C. Hu, H. Lovejoy, P. C. Newell, N. R. Palmateer, C. Tzeng, R.-Y. Lee, P.-T. Zinn, K. 2020-10-04 doi:10.1101/2020.10.02.323477 Cold Spring Harbor Laboratory Press 2020-10-04 <![CDATA[ RNA-binding protein Elavl1/HuR is required for maintenance of cranial neural crest specification ]]> https://biorxiv.org/content/10.1101/2020.10.14.338715v1?rss=1 Hutchins, E. J. Chacon, J. Bronner, M. E. 2020-10-14 doi:10.1101/2020.10.14.338715 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Force transduction creates long-ranged coupling in ribosomes stalled by arrest peptides ]]> https://biorxiv.org/content/10.1101/2020.10.16.342899v1?rss=1 Zimmer, M. H. Niesen, M. J. Miller, T. F. 2020-10-16 doi:10.1101/2020.10.16.342899 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ Fundamental limits on the rate of bacterial growth ]]> https://biorxiv.org/content/10.1101/2020.10.18.344382v1?rss=1 Belliveau, N. M. Chure, G. D. Hueschen, C. L. Garcia, H. G. Kondev, J. Fisher, D. S. Theriot, J. A. Phillips, R. 2020-10-18 doi:10.1101/2020.10.18.344382 Cold Spring Harbor Laboratory Press 2020-10-18 <![CDATA[ Temporal changes in plasma membrane lipid content induce endocytosis to regulate developmental epithelial-to-mesenchymal transition ]]> https://biorxiv.org/content/10.1101/2020.10.18.344523v1?rss=1 Piacentino, M. L. Hutchins, E. J. Andrews, C. J. Bronner, M. E. 2020-10-18 doi:10.1101/2020.10.18.344523 Cold Spring Harbor Laboratory Press 2020-10-18 <![CDATA[ A multimodal cell census and atlas of the mammalian primary motor cortex ]]> https://biorxiv.org/content/10.1101/2020.10.19.343129v1?rss=1 BRAIN Initiative Cell Census Network (BICCN), Adkins, R. S. Aldridge, A. I. Allen, S. Ament, S. A. An, X. Armand, E. Ascoli, G. A. Bakken, T. E. Bandrowski, A. Banerjee, S. Barkas, N. Bartlett, A. Bateup, H. S. Behrens, M. M. Berens, P. Berg, J. Bernabucci, M. Bernaerts, Y. Bertagnolli, D. Biancalani, T. Boggeman, L. Booeshaghi, A. S. Bowman, I. Bravo, H. C. Cadwell, C. R. Callaway, E. M. Carlin, B. O'Connor, C. Carter, R. Casper, T. Castanon, R. G. Castro, J. R. Chance, R. K. Chatterjee, A. Chen, H. Chun, J. Colantuoni, C. Crabtree, J. Creasy, H. Cric 2020-10-21 doi:10.1101/2020.10.19.343129 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ The Brain Knows enough to take into account Light and Shadow ]]> https://biorxiv.org/content/10.1101/2020.10.19.344838v1?rss=1 Yamamoto, M. Shimojo, S. 2020-10-19 doi:10.1101/2020.10.19.344838 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ Juvenile corals inherit mutations acquired during the parents lifespan ]]> https://biorxiv.org/content/10.1101/2020.10.19.345538v1?rss=1 Vasquez-Kuntz, K. L. Kitchen, S. A. Conn, T. L. Vohsen, S. A. Chan, A. N. Vermeij, M. J. Page, C. Marhaver, K. L. Baums, I. B. 2020-10-20 doi:10.1101/2020.10.19.345538 Cold Spring Harbor Laboratory Press 2020-10-20 <![CDATA[ In vivo imaging of retrovirus infection reveals a role for Siglec-1/CD169 in multiple routes of transmission ]]> https://biorxiv.org/content/10.1101/2020.10.20.347427v1?rss=1 Haugh, K. A. Ladinsky, M. S. Ullah, I. Pi, R. Gilardet, A. Kumar, P. Bjorkman, P. Mothes, W. Uchil, P. D. 2020-10-20 doi:10.1101/2020.10.20.347427 Cold Spring Harbor Laboratory Press 2020-10-20 <![CDATA[ Evolution of Antibody Immunity to SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.11.03.367391v1?rss=1 Gaebler, C. Wang, Z. Lorenzi, J. C. C. Muecksch, F. Finkin, S. Tokuyama, M. Ladinsky, M. Cho, A. Jankovic, M. Schaefer-Babajew, D. Oliveira, T. Y. Cipolla, M. Viant, C. Barnes, C. O. Hurley, A. Turroja, M. Gordon, K. Millard, K. G. Ramos, V. Schmidt, F. Weisblum, Y. Jha, D. Tankelevich, M. Yee, J. Shimeliovich, I. Robbiani, D. F. Zhao, Z. Gazumyan, A. Hatziioannou, T. Bjorkman, P. J. Mehandru, S. Bieniasz, P. D. Caskey, M. Nussenzweig, M. C. 2020-11-05 doi:10.1101/2020.11.03.367391 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Sticks and Stones, a conserved cell surface ligand for the Type IIa RPTP Lar, regulates neural circuit wiring in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.11.03.367540v1?rss=1 Bali, N. Lee, H.-K. Zinn, K. 2020-11-05 doi:10.1101/2020.11.03.367540 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Stability and Control of Biomolecular Circuits through Structure ]]> https://biorxiv.org/content/10.1101/2020.11.04.368381v1?rss=1 Xiao, F. Doyle, J. C. Khammash, M. 2020-11-05 doi:10.1101/2020.11.04.368381 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Bistable State Switch Enables Ultrasensitive Feedback Control in Heterogeneous Microbial Populations ]]> https://biorxiv.org/content/10.1101/2020.11.10.377051v1?rss=1 Ren, X. Samaniego, C. C. Murray, R. M. Franco, E. 2020-11-10 doi:10.1101/2020.11.10.377051 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ Engineering Logical Inflammation Sensing Circuit for Modulating Gut Conditions ]]> https://biorxiv.org/content/10.1101/2020.11.10.377085v1?rss=1 Merk, L. N. Shur, A. Pandey, A. Murray, R. M. Green, L. N. 2020-11-10 doi:10.1101/2020.11.10.377085 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ Massive X-ray screening reveals two allosteric drug binding sites of SARS-CoV-2 main protease ]]> https://biorxiv.org/content/10.1101/2020.11.12.378422v1?rss=1 Guenther, S. Reinke, P. Y. A. Fernandez-Garcia, Y. Lieske, J. Lane, T. J. Ginn, H. Koua, F. Ehrt, C. Ewert, W. Oberthuer, D. Yefanov, O. Meier, S. Lorenzen, K. Krichel, B. Kopicki, J. Gelisio, L. Brehm, W. Dunkel, I. Seychell, B. Gieseler, H. Norton-Baker, B. Escudero-Perez, B. Domaracky, M. Saouane, S. Tolstikova, A. White, T. Haenle, A. Groessler, M. Fleckenstein, H. Trost, F. Galchenkova, M. Gevorkov, Y. Li, C. Awel, S. Peck, A. Barthelmess, M. Schluenzen, F. Lourdu, X. P. Werner, N. Andaleeb, H. Ullah, N. Falke, S. Srinivasan, V. Franca, B. Schwi 2020-11-12 doi:10.1101/2020.11.12.378422 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Inhibition of VCP preserves retinal structure and function in autosomal dominant retinal degeneration ]]> https://biorxiv.org/content/10.1101/2020.11.17.384669v1?rss=1 Arango-Gonzalez, B. Sen, M. Guarascio, R. Ziaka, K. del Amo, E. M. Hau, K. Poultney, H. Asfahani, R. Urtti, A. Chou, T.-F. Bolz, S. Deshaies, R. J. Haq, W. Cheetham, M. E. Ueffing, M. 2020-11-19 doi:10.1101/2020.11.17.384669 Cold Spring Harbor Laboratory Press 2020-11-19 <![CDATA[ Mosaic RBD nanoparticles elicit neutralizing antibodies against SARS-CoV-2 and zoonotic coronaviruses ]]> https://biorxiv.org/content/10.1101/2020.11.17.387092v1?rss=1 Bjorkman, P. J. Cohen, A. A. Gnanapragasam, P. N. P. Lee, Y. E. Ou, S. Kakutani, L. M. Keeffe, J. R. Barnes, C. O. Nussenzweig, M. C. 2020-11-17 doi:10.1101/2020.11.17.387092 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ cancerAlign: Stratifying tumors by unsupervised alignment across cancer types ]]> https://biorxiv.org/content/10.1101/2020.11.17.387860v1?rss=1 Gao, B. Luo, Y. Ma, J. Wang, S. 2020-11-20 doi:10.1101/2020.11.17.387860 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ A genetic screen identifies dreammist as a regulator of sleep ]]> https://biorxiv.org/content/10.1101/2020.11.18.388736v1?rss=1 Barlow, I. L. Mackay, E. Wheater, E. Goel, A. Lim, S. Zimmerman, S. Woods, I. Prober, D. A. Rihel, J. 2020-11-18 doi:10.1101/2020.11.18.388736 Cold Spring Harbor Laboratory Press 2020-11-18 <![CDATA[ Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis ]]> https://biorxiv.org/content/10.1101/2020.11.20.391896v1?rss=1 Lohoff, T. Ghazanfar, S. Missarova, A. Koulena, N. Pierson, N. Griffiths, J. A. Bardot, E. S. Eng, C.-H. L. Tyser, R. C. V. Argelaguet, R. Guibentif, C. Srinivas, S. Briscoe, J. Simons, B. D. Hadjantonakis, A.-K. Gottgens, B. Reik, W. Nichols, J. Cai, L. Marioni, J. C. 2020-11-21 doi:10.1101/2020.11.20.391896 Cold Spring Harbor Laboratory Press 2020-11-21 <![CDATA[ A conserved strategy for inducing appendage regeneration ]]> https://biorxiv.org/content/10.1101/2020.11.21.392720v1?rss=1 Abrams, M. J. Tan, F. H. Basinger, T. Heithe, M. L. Li, Y. Raffiee, M. Leahy, P. Dabiri, J. O. Gold, D. A. Goentoro, L. A. 2020-11-22 doi:10.1101/2020.11.21.392720 Cold Spring Harbor Laboratory Press 2020-11-22 <![CDATA[ Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome ]]> https://biorxiv.org/content/10.1101/2020.11.22.393546v1?rss=1 Markaki, Y. Chong, J. G. Luong, C. Tan, S. Y. X. Wang, Y. Jacobson, E. C. Maestrini, D. Dror, I. Mistry, B. A. Schoeneberg, J. Banerjee, A. Guttman, M. Chou, T. Plath, K. 2020-11-23 doi:10.1101/2020.11.22.393546 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ Bidirectional redox cycling of phenazine-1-carboxylic acid by Citrobacter portucalensis MBL drives increased nitrate reduction ]]> https://biorxiv.org/content/10.1101/2020.11.23.395335v1?rss=1 Tsypin, L. M. Newman, D. K. 2020-11-24 doi:10.1101/2020.11.23.395335 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ A two-state ribosome and protein model can robustly capture the chemical reaction dynamics of gene expression ]]> https://biorxiv.org/content/10.1101/2020.11.25.399287v1?rss=1 Pandey, A. Murray, R. M. 2020-11-26 doi:10.1101/2020.11.25.399287 Cold Spring Harbor Laboratory Press 2020-11-26 <![CDATA[ Global architecture of the nucleus in single cells by DNA seqFISH+ and multiplexed immunofluorescence ]]> https://biorxiv.org/content/10.1101/2020.11.29.403055v1?rss=1 Takei, Y. Yun, J. Ollikainen, N. Zheng, S. Pierson, N. White, J. Shah, S. Thomassie, J. Eng, C.-H. L. Guttman, M. Yuan, G.-C. Cai, L. 2020-11-30 doi:10.1101/2020.11.29.403055 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ Stimulus-selective lateral signaling between olfactory afferents enables parallel encoding of distinct CO2 dynamics ]]> https://biorxiv.org/content/10.1101/2020.12.03.410571v1?rss=1 Zocchi, D. Hong, E. J. 2020-12-03 doi:10.1101/2020.12.03.410571 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Machine Learning-Assisted Directed Evolution Navigates a Combinatorial Epistatic Fitness Landscape with Minimal Screening Burden ]]> https://biorxiv.org/content/10.1101/2020.12.04.408955v1?rss=1 Wittmann, B. J. Yue, Y. Arnold, F. H. 2020-12-04 doi:10.1101/2020.12.04.408955 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ Indoxyl sulfate, a gut microbiome-derived uremic toxin, is associated with psychic anxiety and its functional magnetic resonance imaging-based neurologic signature ]]> https://biorxiv.org/content/10.1101/2020.12.08.388942v1?rss=1 Brydges, C. R. Fiehn, O. Mayberg, H. S. Schreiber, H. Mahmoudian Dehkordi, S. Bhattacharyya, S. Cha, J. Choi, K. S. Craighead, W. E. Krishnan, R. R. Rush, A. J. Dunlop, B. W. Kaddurah-Daouk, R. 2020-12-09 doi:10.1101/2020.12.08.388942 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ The context-dependent, combinatorial logic of BMP signaling ]]> https://biorxiv.org/content/10.1101/2020.12.08.416503v1?rss=1 Klumpe, H. E. Langley, M. A. Linton, J. M. Su, C. J. Antebi, Y. E. Elowitz, M. B. 2020-12-08 doi:10.1101/2020.12.08.416503 Cold Spring Harbor Laboratory Press 2020-12-08 <![CDATA[ In vitro characterization of engineered red blood cells as potent viral traps against HIV-1 and SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.12.20.423607v1?rss=1 Hoffmann, M. A. G. Kieffer, C. Bjorkman, P. J. 2020-12-21 doi:10.1101/2020.12.20.423607 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ Liver Electrical Impedance Tomography for Early Identification of Fatty Infiltrate in Obesity ]]> https://biorxiv.org/content/10.1101/2020.12.21.423854v1?rss=1 Chang, C.-C. Huang, Z.-Y. Shih, S.-F. Luo, Y. Ko, A. Cui, Q. Cavallero, S. Das, S. Thames, G. Bui, A. Jacobs, J. P. Pajukanta, P. Wu, H. Tai, Y.-C. Li, Z. Hsiai, T. 2020-12-22 doi:10.1101/2020.12.21.423854 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Neural correlates of orbital telorism ]]> https://biorxiv.org/content/10.1101/2021.01.07.425611v1?rss=1 Pawlak, M. A. Knol, M. J. Vernoiij, M. W. Ikram, M. A. Adams, H. Evans, T. E. 2021-01-08 doi:10.1101/2021.01.07.425611 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ CYK-1/Formin activation in cortical RhoA signaling centers promotes organismal left-right symmetry breaking ]]> https://biorxiv.org/content/10.1101/2021.01.08.425924v1?rss=1 Middelkoop, T. C. Garcia-Baucells, J. Quintero-Cadena, P. Pimpale, L. G. Yazdi, S. Sternberg, P. Gross, P. Grill, S. W. 2021-01-08 doi:10.1101/2021.01.08.425924 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ Super-Resolution Label-free Volumetric Vibrational Imaging ]]> https://biorxiv.org/content/10.1101/2021.01.08.425961v1?rss=1 Qian, C. Miao, K. Lin, L.-E. Chen, X. Du, J. Wei, L. 2021-01-09 doi:10.1101/2021.01.08.425961 Cold Spring Harbor Laboratory Press 2021-01-09 <![CDATA[ High levels of Dorsal transcription factor downregulate, not promote, snail expression by regulating enhancer action ]]> https://biorxiv.org/content/10.1101/2021.01.11.426256v1?rss=1 Irizarry, J. McGehee, J. Stathopoulos, A. 2021-01-11 doi:10.1101/2021.01.11.426256 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants ]]> https://biorxiv.org/content/10.1101/2021.01.15.426911v1?rss=1 Wang, Z. Schmidt, F. Weisblum, Y. Muecksch, F. Barnes, C. O. Finkin, S. Schaefer-Babajew, D. Cipolla, M. Gaebler, C. Lieberman, J. A. Yang, Z. Abernathy, M. E. Huey-Tubman, K. E. Hurley, A. Turroja, M. West, K. A. Gordon, K. Millard, K. G. Ramos, V. Silva, J. D. Xu, J. Colbert, R. A. Patel, R. Dizon, J. P. Unson-O'Brien, C. Shimeliovich, I. Gazumyan, A. Caskey, M. Bjorkman, P. J. Casellas, R. Hatziioannou, T. Bieniasz, P. D. Nussenzweig, M. C. 2021-01-19 doi:10.1101/2021.01.15.426911 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ Intracranial electrical stimulation alters meso-scale network integration as a function of network topology ]]> https://biorxiv.org/content/10.1101/2021.01.16.426941v1?rss=1 Thompson, W. H. Esteban, O. Oya, H. Nair, R. Eberhardt, F. Dubois, J. Poldrack, R. A. Adolphs, R. Shine, J. M. 2021-01-19 doi:10.1101/2021.01.16.426941 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ Evolution of the cytochrome-bd type oxygen reductase superfamily and the function of cydAA in Archaea ]]> https://biorxiv.org/content/10.1101/2021.01.16.426971v1?rss=1 Murali, R. Gennis, R. B. Hemp, J. 2021-01-17 doi:10.1101/2021.01.16.426971 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ Drosophila local search emerges from iterative odometry of consecutive run lengths. ]]> https://biorxiv.org/content/10.1101/2021.01.18.427191v1?rss=1 Behbahani, A. H. Palmer, E. H. Corfas, R. A. Dickinson, M. H. 2021-01-19 doi:10.1101/2021.01.18.427191 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ Direct simulation of a stochastically driven multi-step birth-death process ]]> https://biorxiv.org/content/10.1101/2021.01.20.427480v1?rss=1 Gorin, G. Pachter, L. 2021-01-21 doi:10.1101/2021.01.20.427480 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Bispecific antibody prevents SARS-CoV-2 escape and protects mice from disease ]]> https://biorxiv.org/content/10.1101/2021.01.22.427567v1?rss=1 De Gasparo, R. Pedotti, M. Simonelli, L. Nickl, P. Muecksch, F. Lorenzi, J. C. C. Mazzola, F. Magri, D. Michalcikova, T. Haviernik, J. Honig, V. Cassaniti, I. Percivalle, E. Mrazkova, B. Polakova, N. Fortova, A. Tureckova, J. Iatsiuk, V. Di Girolamo, S. Palus, M. Zudova, D. Bednar, P. Bukova, I. Bianchini, F. Mehn, D. Nencka, R. Strakova, P. Pavlis, O. Rozman, J. Gioria, S. Sammartino, J. C. Giardina, F. Gaiarsa, S. Hammarström, Q. P. Barnes, C. O. Piralla, A. Bjorkman, P. J. Baldanti, F. Calzolai, L. Nussenzweig, M. C. Bieniasz, P. D. Hatziioannou, T. 2021-01-22 doi:10.1101/2021.01.22.427567 Cold Spring Harbor Laboratory Press 2021-01-22 <![CDATA[ Measuring gas vesicle dimensions by electron microscopy ]]> https://biorxiv.org/content/10.1101/2021.01.22.427725v1?rss=1 Dutka, P. Malounda, D. Metskas, L. A. Chen, S. Hurt, R. C. Lu, G. J. Jensen, G. J. Shapiro, M. G. 2021-01-22 doi:10.1101/2021.01.22.427725 Cold Spring Harbor Laboratory Press 2021-01-22 <![CDATA[ Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Plasticity of Clytia Medusa Cell Types ]]> https://biorxiv.org/content/10.1101/2021.01.22.427844v1?rss=1 Chari, T. Weissbourd, B. Gehring, J. Ferraioli, A. Leclere, L. Herl, M. Gao, F. Chevalier, S. Copley, R. R. Houliston, E. Anderson, D. J. Pachter, L. 2021-01-23 doi:10.1101/2021.01.22.427844 Cold Spring Harbor Laboratory Press 2021-01-23 <![CDATA[ From zero to infinity: minimum to maximum diversity of the planet by spatio-parametric Rao's quadratic entropy ]]> https://biorxiv.org/content/10.1101/2021.01.23.427872v1?rss=1 Rocchini, D. Marcantonio, M. Da Re, D. Bacaro, G. Feoli, E. Foody, G. M. Harrigan, R. J. Kleijn, D. Iannacito, M. Lenoir, J. Lin, M. Malavasi, M. Marchetto, E. Meyer, R. S. Moudry, V. Schneider, F. D. Simova, P. Thornhill, A. H. Thouverai, E. Vicario, S. Wayne, R. K. Ricotta, C. 2021-01-25 doi:10.1101/2021.01.23.427872 Cold Spring Harbor Laboratory Press 2021-01-25 <![CDATA[ Benchmarking of lightweight-mapping based single-cell RNA-seq pre-processing ]]> https://biorxiv.org/content/10.1101/2021.01.25.428188v1?rss=1 Booeshaghi, A. S. Pachter, L. 2021-01-26 doi:10.1101/2021.01.25.428188 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Low-cost, scalable, and automated fluid sampling for fluidics applications ]]> https://biorxiv.org/content/10.1101/2021.01.27.428538v1?rss=1 Booeshaghi, A. S. Kil, Y. Min, K. H. Gehring, J. Pachter, L. 2021-01-28 doi:10.1101/2021.01.27.428538 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ The evolution of interdependence in a four-way mealybug symbiosis ]]> https://biorxiv.org/content/10.1101/2021.01.28.428658v1?rss=1 Garber, A. I. Kupper, M. Laetsch, D. R. Weldon, S. R. Ladinsky, M. S. Bjorkman, P. J. McCutcheon, J. P. 2021-01-29 doi:10.1101/2021.01.28.428658 Cold Spring Harbor Laboratory Press 2021-01-29 <![CDATA[ LIFE AND WORK OF RESEARCHERS TRAPPED IN THE COVID-19PANDEMIC VICIOUS CYCLE ]]> https://biorxiv.org/content/10.1101/2021.02.02.429476v1?rss=1 Ghaffarizadeh, S. A. Ghaffarizadeh, S. A. Behbahani, A. H. Mehdizadeh, M. Olechowski, A. 2021-02-03 doi:10.1101/2021.02.02.429476 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ A programmable pAgo nuclease with universal guide and target specificity from the mesophilic bacterium Kurthia massiliensis ]]> https://biorxiv.org/content/10.1101/2021.02.03.429301v1?rss=1 Kropocheva, E. Kuzmenko, A. Aravin, A. Esyunina, D. Kulbachiskiy, A. 2021-02-03 doi:10.1101/2021.02.03.429301 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Synthetic multistability in mammalian cells ]]> https://biorxiv.org/content/10.1101/2021.02.10.430659v1?rss=1 Zhu, R. del Rio-Salgado, J. M. Garcia-Ojalvo, J. Elowitz, M. 2021-02-11 doi:10.1101/2021.02.10.430659 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ The making of cauliflowers: the story of unsuccessful flowers ]]> https://biorxiv.org/content/10.1101/2021.02.12.427428v1?rss=1 Azpeitia, E. Tichtinsky, G. Le Masson, M. Serrano-Mislata, A. Gregis, V. Gimenez, C. Prunet, N. Lucas, J. Farcot, E. Kater, M. Bradley, D. Madueno, F. Godin, C. Parcy, F. 2021-02-12 doi:10.1101/2021.02.12.427428 Cold Spring Harbor Laboratory Press 2021-02-12 <![CDATA[ SARS-CoV-2 lineage B.1.526 emerging in the New York region detected by software utility created to query the spike mutational landscape ]]> https://biorxiv.org/content/10.1101/2021.02.14.431043v1?rss=1 West, A. P. Barnes, C. O. Yang, Z. Bjorkman, P. J. 2021-02-15 doi:10.1101/2021.02.14.431043 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ Affinity Requirements For Control Of Synaptic Targeting And Neuronal Cell Survival By Heterophilic IgSF Cell Adhesion Molecules ]]> https://biorxiv.org/content/10.1101/2021.02.16.431482v1?rss=1 Xu, S. Sergeeva, A. P. Katsamba, P. S. Mannepalli, S. Bahna, F. Bimela, J. Zipursky, L. S. Shapiro, L. Honig, B. Zinn, K. 2021-02-17 doi:10.1101/2021.02.16.431482 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Functional modules within a distributed neural network control feeding in a model medusa ]]> https://biorxiv.org/content/10.1101/2021.02.22.432372v1?rss=1 Weissbourd, B. Momose, T. Nair, A. Kennedy, A. Hunt, B. Anderson, D. J. 2021-02-23 doi:10.1101/2021.02.22.432372 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ The stress-sensing domain of activated IRE1α forms helical filaments in narrow ER membrane tubes ]]> https://biorxiv.org/content/10.1101/2021.02.24.432779v1?rss=1 Carter, S. D. Tran, N.-H. De Maziere, A. Ashkenazi, A. Klumperman, J. Jensen, G. J. Walter, P. 2021-02-24 doi:10.1101/2021.02.24.432779 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ In situ single-cell activities of microbial populations revealed by spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2021.02.24.432792v1?rss=1 Dar, D. Dar, N. Cai, L. Newman, D. K. 2021-02-25 doi:10.1101/2021.02.24.432792 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ A functional logic for neurotransmitter co-release in the cholinergic forebrain pathway ]]> https://biorxiv.org/content/10.1101/2021.02.25.432623v1?rss=1 Nair, A. Graf, M. Teo, Y. Y. Augustine, G. J. 2021-02-25 doi:10.1101/2021.02.25.432623 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Confirmation bias optimizes reward learning ]]> https://biorxiv.org/content/10.1101/2021.02.27.433214v1?rss=1 Tarantola, T. O. Folke, T. Boldt, A. Perez, O. D. De Martino, B. 2021-03-01 doi:10.1101/2021.02.27.433214 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning ]]> https://biorxiv.org/content/10.1101/2021.03.01.431313v1?rss=1 1 million paired whole-cell and nuclear annotations for tissue images from nine organs and six imaging platforms. We created Mesmer, a deep learning-enabled segmentation algorithm trained on TissueNet that performs nuclear and whole-cell segmentation in tissue imaging data. We demonstrated that Mesmer has better speed and accuracy than previous methods, generalizes to the full diversity of tissue types and imaging platforms in TissueNet, and achieves human-level performance for whole-cell segmentation. Mesmer enabled the automated extraction of key cellular features, such as subcellular localization of protein signal, which was challenging with previous approaches. We further showed that Mesmer could be adapted to harness cell lineage information present in highly multiplexed datasets. We used this enhanced version to quantify cell morphology changes during human gestation. All underlying code and models are released with permissive licenses as a community resource. ]]> Greenwald, N. F. Miller, G. Moen, E. Kong, A. Kagel, A. Fullaway, C. C. McIntosh, B. J. Leow, K. Schwartz, M. S. Dougherty, T. Pavelchek, C. Cui, S. Camplisson, I. Bar-Tal, O. Singh, J. Fong, M. Chaudhry, G. Abraham, Z. Moseley, J. Warshawsky, S. Soon, E. Greenbaum, S. Risom, T. Hollmann, T. Keren, L. Graf, W. Angelo, M. Van Valen, D. 2021-03-02 doi:10.1101/2021.03.01.431313 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Placental uptake and metabolism as determinants of pregnancy vitamin D status ]]> https://biorxiv.org/content/10.1101/2021.03.01.431439v1?rss=1 Ashley, B. Simner, C. Manousopoulou, A. Jenkinson, C. Hey, F. Frost, J. M. Rezwan, F. I. White, C. H. Lofthouse, E. M. Hyde, E. Cooke, L. Barton, S. Mahon, P. Curtis, E. M. Moon, R. J. Crozier, S. R. Inskip, H. M. Godfrey, K. M. Holloway, J. W. Cooper, C. Jones, K. S. Lewis, R. M. Hewison, M. Garbis, S. D. Branco, M. R. Harvey, N. C. Cleal, J. K. 2021-03-01 doi:10.1101/2021.03.01.431439 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Modelling the impact of decidual senescence on embryo implantation in human endometrial assembloids ]]> https://biorxiv.org/content/10.1101/2021.03.02.433560v1?rss=1 Rawlings, T. M. Makwana, K. Taylor, D. M. Mole, M. A. Fishwick, K. J. Tryfonos, M. Odendaal, J. Hawkes, A. Zernicka-Goetz, M. Hartshorne, G. Brosens, J. Lucas, E. S. 2021-03-02 doi:10.1101/2021.03.02.433560 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ The Mycobacterium tuberculosis transposon sequencing database (MtbTnDB): a large-scale guide to genetic conditional essentiality ]]> https://biorxiv.org/content/10.1101/2021.03.05.434127v1?rss=1 Jinich, A. Zaveri, A. DeJesus, M. A. Flores-Bautista, E. Smith, C. M. Sassetti, C. M. Rock, J. M. Ehrt, S. Schnappinger, D. Ioerger, T. R. Rhee, K. Y. 2021-03-06 doi:10.1101/2021.03.05.434127 Cold Spring Harbor Laboratory Press 2021-03-06 <![CDATA[ Development of potency, breadth and resilience to viral escape mutations in SARS-CoV-2 neutralizing antibodies ]]> https://biorxiv.org/content/10.1101/2021.03.07.434227v1?rss=1 Muecksch, F. Weisblum, Y. Barnes, C. Schmidt, F. Schaefer-Babajew, D. Lorenzi, J. Flyak, A. DeLaitsch, A. Huey-Tubman, K. Hou, S. Schiffer, C. Gaebler, C. Wang, Z. Da Silva, J. Poston, D. Finkin, S. Cho, A. Cipolla, M. Oliveira, T. Millard, K. Ramos, V. Gazumyan, A. Rutkowska, M. Caskey, M. Nussenzweig, M. Bjorkman, P. Hatziioannou, T. Bieniasz, P. 2021-03-08 doi:10.1101/2021.03.07.434227 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Droplet-based single cell RNA sequencing of bacteria identifies known and previously unseen cellular states ]]> https://biorxiv.org/content/10.1101/2021.03.10.434868v1?rss=1 McNulty, R. A. Sritharan, D. Liu, S. Hormoz, S. Rosenthal, A. Z. 2021-03-10 doi:10.1101/2021.03.10.434868 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Coordination of -1 Programmed Ribosomal Frameshifting by Transcript and Nascent Chain Features Revealed by Deep Mutational Scanning ]]> https://biorxiv.org/content/10.1101/2021.03.11.435011v1?rss=1 Carmody, P. J. Zimmer, M. H. Kuntz, C. P. Harrington, H. R. Duckworth, K. E. Penn, W. D. Mukhopahyay, S. Miller, T. F. Schlebach, J. P. 2021-03-11 doi:10.1101/2021.03.11.435011 Cold Spring Harbor Laboratory Press 2021-03-11 <![CDATA[ Learning accurate path integration in a ring attractor model of the head direction system ]]> https://biorxiv.org/content/10.1101/2021.03.12.435035v1?rss=1 Vafidis, P. Owald, D. D'Albis, T. Kempter, R. 2021-03-12 doi:10.1101/2021.03.12.435035 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Reconstructing human early embryogenesis in vitro with pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2021.03.12.435175v1?rss=1 Zernicka-Goetz, M. Sozen, B. Jorgensen, V. Cui, T. Zhu, M. 2021-03-12 doi:10.1101/2021.03.12.435175 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Nanoparticle Cellular Internalization is Not Required for RNA Delivery to Mature Plant Leaves ]]> https://biorxiv.org/content/10.1101/2021.03.17.435888v1?rss=1 Zhang, H. Goh, N. S. Wang, J. Demirer, G. S. Butrus, S. Park, S.-J. Landry, M. P. 2021-03-19 doi:10.1101/2021.03.17.435888 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Gold nanocluster mediated delivery of siRNA to intact plant cells for efficient gene knockdown ]]> https://biorxiv.org/content/10.1101/2021.03.17.435890v1?rss=1 Zhang, H. Cao, Y. Xu, D. Goh, N. S. Demirer, G. S. Landry, M. P. Yang, P. 2021-03-17 doi:10.1101/2021.03.17.435890 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ A novel approach to comparative RNA-Seq does not support a conserved set of genes underlying animal regeneration ]]> https://biorxiv.org/content/10.1101/2021.03.22.434850v1?rss=1 Sierra, N. Olsman, N. Yi, L. Pachter, L. Goentoro, L. Gold, D. A. 2021-03-23 doi:10.1101/2021.03.22.434850 Cold Spring Harbor Laboratory Press 2021-03-23 <![CDATA[ Live imaging of SARS-CoV-2 infection in mice reveals neutralizing antibodies require Fc function for optimal efficacy ]]> https://biorxiv.org/content/10.1101/2021.03.22.436337v1?rss=1 Ullah, I. Prevost, J. Ladinsky, M. S. Stone, H. Lu, M. Anand, S. P. Beaudoin-Bussieres, G. Benlarbi, M. Ding, S. Gasser, R. Fink, C. Chen, Y. Tauzin, A. Goyette, G. Bourassa, C. Medjahed, H. Mack, M. Chung, K. Wilen, C. B. Dekaban, G. A. Dikeakos, J. D. Bruce, E. A. Kaufmann, D. E. Stamatatos, L. McGuire, A. Richard, J. Pazgier, M. Bjorkman, P. Mothes, W. Finzi, A. Kumar, P. Uchil, P. D. 2021-03-22 doi:10.1101/2021.03.22.436337 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Analytical solutions of the chemical master equation with bursty production and isomerization reactions ]]> https://biorxiv.org/content/10.1101/2021.03.24.436847v1?rss=1 Gorin, G. Pachter, L. 2021-03-24 doi:10.1101/2021.03.24.436847 Cold Spring Harbor Laboratory Press 2021-03-24 <![CDATA[ Acoustic Remote Control of Bacterial Immunotherapy ]]> https://biorxiv.org/content/10.1101/2021.03.25.434639v1?rss=1 Abedi, M. Yao, M. Mittelstein, D. R. Bar-Zion, A. Swift, M. Lee-Gosselin, A. Shapiro, M. G. 2021-03-25 doi:10.1101/2021.03.25.434639 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Tracking the rates and mechanisms of canopy damage and recovery following Hurricane Maria using multitemporal lidar data ]]> https://biorxiv.org/content/10.1101/2021.03.26.436869v1?rss=1 1 m, 2018-2020), whereas 21.6% of forests with initial height losses showed little or no height gain, and 17.8% of forests exhibited no structural changes >|1| m in either period. Canopy layers <10 m accounted for most increases in canopy height and fractional cover between 2018-2020, with gains split evenly between height growth and lateral crown expansion by surviving individuals. These findings benchmark rates of gap formation, crown expansion, and canopy closure following hurricane damage. MANUSCRIPT HIGHLIGHTSO_LIHurricane Maria gave forests a haircut by toppling trees and shearing branches. C_LIO_LIRegrowth after Maria was patchy, with equal areas of height gain and no change. C_LIO_LI3-D measures of forest recovery after hurricanes can improve ecosystem models. C_LI ]]> Leitold, V. Morton, D. C. Martinuzzi, S. Paynter, I. Uriarte, M. Keller, M. Ferraz, A. Cook, B. D. Corp, L. A. Gonzalez, G. 2021-03-28 doi:10.1101/2021.03.26.436869 Cold Spring Harbor Laboratory Press 2021-03-28 <![CDATA[ Paraburkholderia edwinii protects Aspergillus sp. from phenazines by acting as a toxin sponge ]]> https://biorxiv.org/content/10.1101/2021.03.28.437412v1?rss=1 Dahlstrom, K. M. Newman, D. K. 2021-03-28 doi:10.1101/2021.03.28.437412 Cold Spring Harbor Laboratory Press 2021-03-28 <![CDATA[ IQCELL: A platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/2021.04.01.438014v1?rss=1 Heydari, T. Langley, M. A. Fisher, C. Aguilar-Hidalgo, D. Shukla, S. Yachie-Kinoshita, A. Hughes, M. McNagny, K. M. Zandstra, P. W. 2021-04-03 doi:10.1101/2021.04.01.438014 Cold Spring Harbor Laboratory Press 2021-04-03 <![CDATA[ IKKβ signaling mediates metabolic changes in the hypothalamus of a Huntington's disease mouse model ]]> https://biorxiv.org/content/10.1101/2021.04.08.438894v1?rss=1 Soylu Kucharz, R. Khoshnan, A. Petersen, A. 2021-04-09 doi:10.1101/2021.04.08.438894 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ Targeted Neuronal Activation of the Gastrointestinal Tract Shapes the Environment of the Gut in Mice ]]> https://biorxiv.org/content/10.1101/2021.04.12.439539v1?rss=1 Yoo, B. B. Griffiths, J. A. Thuy-Boun, P. Cantu, V. Weldon, K. Challis, C. Sweredoski, M. J. Chan, K. Y. Thron, T. M. Sharon, G. Moradian, A. Humphrey, G. Zhu, Q. Shaffer, J. Wolan, D. W. Dorrestein, P. Knight, R. Gradinaru, V. Mazmanian, S. 2021-04-13 doi:10.1101/2021.04.12.439539 Cold Spring Harbor Laboratory Press 2021-04-13 <![CDATA[ Thiophenesulfonamides are specific inhibitors of quorum sensing in pathogenic Vibrios ]]> https://biorxiv.org/content/10.1101/2021.04.14.439868v1?rss=1 Newman, J. D. Shah, P. Chopra, J. Shi, E. McFadden, M. E. Horness, R. E. Brown, L. C. van Kessel, J. C. 2021-04-14 doi:10.1101/2021.04.14.439868 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Sonicated fibrils of huntingtin exon-1 preferentially seed neurons and produce toxic assemblies ]]> https://biorxiv.org/content/10.1101/2021.04.16.440200v1?rss=1 Chongtham, A. Isas, J. M. Pandey, N. K. Rawat, A. Yoo, J. H. Mastro, T. L. Kennedy, M. Langen, R. Khoshnan, A. 2021-04-18 doi:10.1101/2021.04.16.440200 Cold Spring Harbor Laboratory Press 2021-04-18 <![CDATA[ Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies ]]> https://biorxiv.org/content/10.1101/2021.04.23.441195v1?rss=1 Jette, C. A. Cohen, A. A. Gnanapragasam, P. N. P. Muecksch, F. Lee, Y. E. Huey-Tubman, K. E. Schmidt, F. Hatziioannou, T. Bieniasz, P. D. Nussenzweig, M. C. West, A. P. Keeffe, J. R. Bjorkman, P. Barnes, C. O. 2021-04-26 doi:10.1101/2021.04.23.441195 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Control-theoretic immune tradeoffs explain SARS-CoV-2 virulence and transmission variation ]]> https://biorxiv.org/content/10.1101/2021.04.25.441372v1?rss=1 Sarma, A. A. Sarma, A. Csete, M. Lee, P. P. Doyle, J. C. 2021-04-26 doi:10.1101/2021.04.25.441372 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Genomically Mined Acoustic Reporter Genes Enable On-Demand In Vivo Monitoring of Tumor-Homing Bacteria ]]> https://biorxiv.org/content/10.1101/2021.04.26.441537v1?rss=1 Hurt, R. C. Buss, M. T. Wong, K. Sawyer, D. P. Swift, M. B. Dutka, P. Mittelstein, D. R. Jin, Z. Abedi, M. H. Deshpande, R. Shapiro, M. G. 2021-04-27 doi:10.1101/2021.04.26.441537 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Integrated spatial genomics in tissues reveals invariant and cell type dependent nuclear architecture ]]> https://biorxiv.org/content/10.1101/2021.04.26.441547v1?rss=1 Takei, Y. Zheng, S. Yun, J. Shah, S. Pierson, N. White, J. Schindler, S. Tischbirek, C. Yuan, G.-C. Cai, L. 2021-04-27 doi:10.1101/2021.04.26.441547 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ scvi-tools: a library for deep probabilistic analysis of single-cell omics data ]]> https://biorxiv.org/content/10.1101/2021.04.28.441833v1?rss=1 Gayoso, A. Lopez, R. Xing, G. Boyeau, P. Wu, K. Jayasuriya, M. Mehlman, E. Langevin, M. Liu, Y. Samaran, J. Misrachi, G. Nazaret, A. Clivio, O. Xu, C. Ashuach, T. Lotfollahi, M. Svensson, V. da Veiga Beltrame, E. Talavera-Lopez, C. Pachter, L. Theis, F. J. Streets, A. Jordan, M. I. Regier, J. Yosef, N. 2021-04-29 doi:10.1101/2021.04.28.441833 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Selection of Sites for Field Trials of Genetically Engineered Mosquitoes with Gene Drive. ]]> https://biorxiv.org/content/10.1101/2021.04.28.441877v1?rss=1 Lanzaro, G. C. Campos, M. Crepeau, M. Cornel, A. Estrada, A. Gripkey, H. Haddad, Z. Kormos, A. Palomares, S. Sharpee, W. 2021-04-28 doi:10.1101/2021.04.28.441877 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Virtual partition digital PCR for high precision chromosomal counting applications ]]> https://biorxiv.org/content/10.1101/2021.04.29.441975v1?rss=1 98% single-well sensitivity and specificity. VPdPCR has substantial promise for increasing the utility of dPCR in applications requiring ultra-high-precision quantitation. ]]> Jacky, L. Yurk, D. Alvarado, J. Leatham, B. Schwartz, J. MacDonald, C. Rajagopal, A. 2021-04-29 doi:10.1101/2021.04.29.441975 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Characterization of the ABC methionine transporter from Neisseria meningitidis reveals that MetQ is a lipoprotein ]]> https://biorxiv.org/content/10.1101/2021.05.04.442564v1?rss=1 Sharaf, N. G. Shahgholi, M. Kim, E. Lai, J. Y. VanderVelde, D. G. Lee, A. T. Rees, D. C. 2021-05-04 doi:10.1101/2021.05.04.442564 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Vaccination boosts naturally enhanced neutralizing breadth to SARS-CoV-2 one year after infection ]]> https://biorxiv.org/content/10.1101/2021.05.07.443175v1?rss=1 Wang, Z. Muecksch, F. Schaefer-Babajew, D. Finkin, S. Viant, C. Gaebler, C. Barnes, C. O. Cipolla, M. Ramos, V. Oliveira, T. Y. Cho, A. Schmidt, F. Silva, J. D. Bednarski, E. Daga, M. Turroja, M. Millard, K. G. Jankovic, M. Gazumyan, A. Bieniasz, P. D. Caskey, M. Hatziioannou, T. Nussenzweig, M. C. 2021-05-09 doi:10.1101/2021.05.07.443175 Cold Spring Harbor Laboratory Press 2021-05-09 <![CDATA[ Museum of Spatial Transcriptomics ]]> https://biorxiv.org/content/10.1101/2021.05.11.443152v1?rss=1 Moses, L. Pachter, L. 2021-05-12 doi:10.1101/2021.05.11.443152 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ Evolutionary assembly of cooperating cell types in an animal chemical defense system ]]> https://biorxiv.org/content/10.1101/2021.05.13.444042v1?rss=1 Bruckner, A. Badroos, J. Learsch, R. W. Yousefelahiyeh, M. Kitchen, S. A. Parker, J. 2021-05-15 doi:10.1101/2021.05.13.444042 Cold Spring Harbor Laboratory Press 2021-05-15 <![CDATA[ Thermodynamics drives coenzyme redundancy in metabolism ]]> https://biorxiv.org/content/10.1101/2021.05.17.444566v1?rss=1 Goldford, J. E. George, A. B. Flamholz, A. E. Segre, D. 2021-05-18 doi:10.1101/2021.05.17.444566 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ Ultrafast amplitude modulation for molecular and hemodynamic ultrasound imaging ]]> https://biorxiv.org/content/10.1101/2021.05.18.444561v1?rss=1 Rabut, C. Wu, D. Ling, B. Jin, Z. Malounda, D. Shapiro, M. G. 2021-05-20 doi:10.1101/2021.05.18.444561 Cold Spring Harbor Laboratory Press 2021-05-20 <![CDATA[ Open-Source Thermometer, Temperature Controller, and Light Meter for Use in Animal Facilities and During Experiments ]]> https://biorxiv.org/content/10.1101/2021.05.18.444705v1?rss=1 Andreev, A. Vasnarungruengkul, P. Wagenaar, D. A. Prober, D. A. 2021-05-20 doi:10.1101/2021.05.18.444705 Cold Spring Harbor Laboratory Press 2021-05-20 <![CDATA[ The globular C1q receptor is required for epidermal growth factor receptor signaling during Candida albicans infection ]]> https://biorxiv.org/content/10.1101/2021.05.25.445718v1?rss=1 Phan, Q. T. Lin, J. Solis, N. V. Eng, M. Swidergall, M. Wang, F. LI, S. Gaffen, S. L. Chou, T.-F. Filler, S. G. 2021-05-26 doi:10.1101/2021.05.25.445718 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ Hybridization chain reaction enables a unified approach to multiplexed, quantitative, high-resolution immunohistochemistry and in situ hybridization ]]> https://biorxiv.org/content/10.1101/2021.06.02.446311v1?rss=1 Schwarzkopf, M. Liu, M. C. Schulte, S. J. Ives, R. Husain, N. Choi, H. M. T. Pierce, N. 2021-06-02 doi:10.1101/2021.06.02.446311 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Nitrate reduction stimulates and is stimulated by phenazine-1-carboxylic acid oxidation by Citrobacter portucalensis MBL ]]> https://biorxiv.org/content/10.1101/2021.06.04.447179v1?rss=1 Tsypin, L. M. Newman, D. K. 2021-06-05 doi:10.1101/2021.06.04.447179 Cold Spring Harbor Laboratory Press 2021-06-05 <![CDATA[ Quantitative examination of five stochastic cell-cycle and cell-size control models for Escherichia coli and Bacillus subtilis ]]> https://biorxiv.org/content/10.1101/2021.06.06.447266v1?rss=1 Le Treut, G. Si, F. Li, D. Jun, S. 2021-06-06 doi:10.1101/2021.06.06.447266 Cold Spring Harbor Laboratory Press 2021-06-06 <![CDATA[ Natural variation in the irld gene family affects insulin/IGF signaling and starvation resistance ]]> https://biorxiv.org/content/10.1101/2021.06.07.447366v1?rss=1 Webster, A. K. Chitrakar, R. Powell, M. Chen, J. Fisher, K. Tanny, R. Stevens, L. Evans, K. Antoshechkin, I. Andersen, E. C. Baugh, L. R. 2021-06-07 doi:10.1101/2021.06.07.447366 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Liana optical traits increase tropical forest albedo and reduce ecosystem productivity ]]> https://biorxiv.org/content/10.1101/2021.06.08.447067v1?rss=1 Meunier, F. Visser, M. D. Shiklomanov, A. Dietze, M. C. Guzman, J. A. Sanchez-Azofeifa, A. De Deurwaerder, H. P. T. Krishna Moorty, S. M. Schnitzer, S. A. Marvin, D. C. Longo, M. Chang, L. Broadbent, E. N. Zambrano, A. M. A. Muller-Landau, H. C. Detto, M. Verbeeck, H. 2021-06-09 doi:10.1101/2021.06.08.447067 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ Evolution of the nitric oxide synthase family in vertebrates and novel insights in gill development ]]> https://biorxiv.org/content/10.1101/2021.06.14.448362v1?rss=1 Annona, G. Sato, I. Pascual-Anaya, J. Braasch, I. Voss, R. Stundl, J. Soukup, V. Kuratani, S. Postlethwait, J. D'Aniello, S. 2021-06-14 doi:10.1101/2021.06.14.448362 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ Active feature selection discovers minimal gene-sets for classifying cell-types and disease states in single-cell mRNA-seq data ]]> https://biorxiv.org/content/10.1101/2021.06.15.448478v1?rss=1 Chen, X. Chen, S. Thomson, M. 2021-06-16 doi:10.1101/2021.06.15.448478 Cold Spring Harbor Laboratory Press 2021-06-16 <![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[ Computational neural network provides naturalistic solution for recovery of finger dexterity after stroke ]]> https://biorxiv.org/content/10.1101/2021.06.22.449412v1?rss=1 Kadry, A. Norman, S. Xu, J. Solomonow-Avnon, D. Mawase, F. 2021-06-22 doi:10.1101/2021.06.22.449412 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Deep parallel characterization of AAV tropism and AAV-mediated transcriptional changes via single-cell RNA sequencing ]]> https://biorxiv.org/content/10.1101/2021.06.25.449955v1?rss=1 Brown, D. Altermatt, M. Dobreva, T. Chen, S. Wang, A. Thomson, M. Gradinaru, V. 2021-06-25 doi:10.1101/2021.06.25.449955 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Signaling receptor localization maximizes cellular information acquisition in spatially-structured, natural environments ]]> https://biorxiv.org/content/10.1101/2021.07.01.450787v1?rss=1 Wang, Z. J. Thomson, M. 2021-07-02 doi:10.1101/2021.07.01.450787 Cold Spring Harbor Laboratory Press 2021-07-02 <![CDATA[ Single cell tools for WormBase ]]> https://biorxiv.org/content/10.1101/2021.07.04.451030v1?rss=1 da Veiga Beltrame, E. Arnaboldi, V. Sternberg, P. W. 2021-07-04 doi:10.1101/2021.07.04.451030 Cold Spring Harbor Laboratory Press 2021-07-04 <![CDATA[ UVC inactivation of pathogenic samples suitable for cryoEM analysis ]]> https://biorxiv.org/content/10.1101/2021.07.06.451241v1?rss=1 Depelteau, J. S. Renault, L. Althof, N. Cassidy, C. K. Mendonca, L. M. Jensen, G. J. Resch, G. P. Briegel, A. 2021-07-06 doi:10.1101/2021.07.06.451241 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ FANCD2 directly inhibits DNA2 nuclease at stalled replication forks and acts as a RAD51 mediator in strand exchange ]]> https://biorxiv.org/content/10.1101/2021.07.08.450798v1?rss=1 Liu, W. Roubal, I. Polaczek, P. Meng, Y. Choe, W.-c. Caron, M. C. Sedgeman, C. A. Xi, Y. Liu, C. Wu, Q. Zheng, L. Masson, J. Y. Shen, B. Campbell, J. L. 2021-07-09 doi:10.1101/2021.07.08.450798 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ The geometry of domain-general performance monitoring representations in the human medial frontal cortex ]]> https://biorxiv.org/content/10.1101/2021.07.08.451594v1?rss=1 Fu, Z. Beam, D. Chung, J. M. Reed, C. M. Mamelak, A. N. Adolphs, R. Rutishauser, U. 2021-07-08 doi:10.1101/2021.07.08.451594 Cold Spring Harbor Laboratory Press 2021-07-08 <![CDATA[ Atp13a5 Marker Reveals Pericytes of The Central Nervous System in Mice ]]> https://biorxiv.org/content/10.1101/2021.07.09.451694v1?rss=1 Guo, X. Ge, T. Xia, S. Wu, H. Colt, M. Xie, X. Zhang, B. Zeng, J. Chen, J.-F. Zhu, D. Montagne, A. Gao, F. Zhao, Z. 2021-07-10 doi:10.1101/2021.07.09.451694 Cold Spring Harbor Laboratory Press 2021-07-10 <![CDATA[ In situ imaging of bacterial membrane projections and associated protein complexes using electron cryo-tomography ]]> https://biorxiv.org/content/10.1101/2021.07.13.452161v1?rss=1 Kaplan, M. Chreifi, G. Metskas, L. A. Liedtke, J. Wood, C. R. Oikonomou, C. M. NICOLAS, W. J. Subramanian, P. Zacharoff, L. A. Wang, Y. Chang, Y.-W. Beeby, M. Dobro, M. Mcbride, M. J. Briegel, A. Shaffer, C. Jensen, G. J. 2021-07-13 doi:10.1101/2021.07.13.452161 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ Evolution of a chordate-specific mechanism for myoblast fusion ]]> https://biorxiv.org/content/10.1101/2021.07.24.453587v1?rss=1 Zhang, H. Shang, R. Kim, K. Zheng, W. Johnson, C. J. Sun, L. Niu, X. Liu, L. Uyeno, T. A. Zhou, J. Liu, L. Pei, J. Fissette, S. D. Green, S. A. Samudra, S. P. Wen, J. Zhang, J. Eggenschwiler, J. Menke, D. Bronner, M. E. Grishin, N. V. Li, W. Ye, K. Zhang, Y. Stolfi, A. Bi, P. 2021-07-25 doi:10.1101/2021.07.24.453587 Cold Spring Harbor Laboratory Press 2021-07-25 <![CDATA[ Engineering Viral Vectors for Acoustically Targeted Gene Delivery ]]> https://biorxiv.org/content/10.1101/2021.07.26.453904v1?rss=1 Li, H. Heath, J. E. Trippett, J. S. Shapiro, M. G. Szablowski, J. O. 2021-07-27 doi:10.1101/2021.07.26.453904 Cold Spring Harbor Laboratory Press 2021-07-27 <![CDATA[ The HMCES DNA-protein cross-link functions as a constitutive DNA repair intermediate ]]> https://biorxiv.org/content/10.1101/2021.07.29.454365v1?rss=1 Semlow, D. R. MacKrell, V. A. Walter, J. 2021-07-29 doi:10.1101/2021.07.29.454365 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Length Biases in Single-Cell RNA Sequencing of pre-mRNA ]]> https://biorxiv.org/content/10.1101/2021.07.30.454514v1?rss=1 Gorin, G. Pachter, L. 2021-07-31 doi:10.1101/2021.07.30.454514 Cold Spring Harbor Laboratory Press 2021-07-31 <![CDATA[ Microbial community of recently discovered Auka vent field sheds light on vent biogeography and evolutionary history of thermophily ]]> https://biorxiv.org/content/10.1101/2021.08.02.454472v1?rss=1 Speth, D. R. Yu, F. B. Connon, S. A. Lim, S. Magyar, J. S. Pena, M. E. Quake, S. R. Orphan, V. J. 2021-08-02 doi:10.1101/2021.08.02.454472 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ The kpc-1 (furin) 3'UTR promotes dendritic transport and local translation of mRNAs to regulate dendrite branching and self-avoidance of a nociceptive neuron ]]> https://biorxiv.org/content/10.1101/2021.08.03.453128v1?rss=1 Zou, Y. Shih, M. Chiu, H. Ferreira, T. Suzuki, N. Zou, W. Chuang, C.-F. Chang, C. 2021-08-05 doi:10.1101/2021.08.03.453128 Cold Spring Harbor Laboratory Press 2021-08-05 <![CDATA[ A population of descending neurons that regulate the flight motor of Drosophila ]]> https://biorxiv.org/content/10.1101/2021.08.05.455281v1?rss=1 Namiki, S. Ros, I. G. Morrow, C. Rowell, W. J. Card, G. M. Korff, W. Dickinson, M. H. 2021-08-06 doi:10.1101/2021.08.05.455281 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Recombinant NAGLU-IGF2 prevents physical and neurological disease and improves survival in Sanfilippo B syndrome ]]> https://biorxiv.org/content/10.1101/2021.08.06.455469v1?rss=1 Le, S. Q. Kan, S.-h. Nunez, M. Dearborn, J. Wang, F. LI, S. Snella, L. Jens, J. K. Valentine, B. N. Nelvagal, H. R. Sorensen, A. Cooper, J. D. Chou, T.-F. Ellinwood, N. M. Smith, J. D. Sands, M. S. Dickson, P. 2021-08-08 doi:10.1101/2021.08.06.455469 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ Segregation of neural crest specific lineage trajectories from a heterogeneous neural plate border territory only emerges at neurulation ]]> https://biorxiv.org/content/10.1101/2021.08.08.455573v1?rss=1 Williams, R. Lukoseviciute, M. Sauka-Spengler, T. Bronner, M. E. 2021-08-08 doi:10.1101/2021.08.08.455573 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ Gut bacteria regulate the pathogenesis of Huntington's disease in Drosophila ]]> https://biorxiv.org/content/10.1101/2021.08.12.456124v1?rss=1 Chongtham, A. Yoo, J. H. Chin, T. M. Akingbesote, N. D. Huda, A. Khoshnan, A. 2021-08-13 doi:10.1101/2021.08.12.456124 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Optimal dynamic incentive scheduling for Hawk-Dove evolutionary games ]]> https://biorxiv.org/content/10.1101/2021.08.15.456406v1?rss=1 3, our optimum schedules can drive either population to extinction or fixation. The method described can be used to produce optimal dynamic incentive schedules for many different applications in which the 2 x 2 replicator dynamics is used as a governing model. ]]> Stuckey, K. Dua, R. Ma, Y. Parker, J. Newton, P. K. 2021-08-15 doi:10.1101/2021.08.15.456406 Cold Spring Harbor Laboratory Press 2021-08-15 <![CDATA[ Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription ]]> https://biorxiv.org/content/10.1101/2021.08.16.456551v1?rss=1 Chong, S. Graham, T. G. W. Dugast-Darzacq, C. Dailey, G. M. Darzacq, X. Tjian, R. 2021-08-17 doi:10.1101/2021.08.16.456551 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Distinct neural circuits establish the same chemosensory behavior in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.08.17.456617v1?rss=1 Banerjee, N. Shih, P.-Y. Rojas Palato, E. J. Sternberg, P. W. Hallem, E. 2021-08-17 doi:10.1101/2021.08.17.456617 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Resting Parasympathetic Nervous System Activity is Associated with Greater Antiviral Gene Expression ]]> https://biorxiv.org/content/10.1101/2021.08.21.457209v1?rss=1 Rahal, D. Tashjian, S. M. Karan, M. Eisenberger, N. Galvan, A. Fuligni, A. J. Cole, S. W. 2021-08-23 doi:10.1101/2021.08.21.457209 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ Integrative Genome Modeling Platform reveals essentialityof rare contact events in 3D genome organizations ]]> https://biorxiv.org/content/10.1101/2021.08.22.457288v1?rss=1 Boninsegna, L. Yildirim, A. Polles, G. Quinodoz, S. A. Finn, E. H. Guttman, M. Zhou, X. J. Alber, F. 2021-08-23 doi:10.1101/2021.08.22.457288 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ The Specious Art of Single-Cell Genomics ]]> https://biorxiv.org/content/10.1101/2021.08.25.457696v1?rss=1 Chari, T. Banerjee, J. Pachter, L. 2021-08-26 doi:10.1101/2021.08.25.457696 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ The entomopathogenic nematode Steinernema hermaphroditum is a self-fertilizing hermaphrodite and a genetically tractable system for the study of parasitic and mutualistic symbiosis ]]> https://biorxiv.org/content/10.1101/2021.08.26.457822v1?rss=1 Cao, M. Schwartz, H. T. Tan, C.-H. Sternberg, P. W. 2021-08-27 doi:10.1101/2021.08.26.457822 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ The STAT5-IRF4-BATF pathway drives heightened epigenetic remodeling in naïve CD4+ T cell responses of older adults ]]> https://biorxiv.org/content/10.1101/2021.08.27.457205v1?rss=1 Zhang, H. Jadhav, R. R. Cao, W. Goronzy, I. N. Jin, J. Greenleaf, W. J. Weyand, C. M. Goronzy, J. 2021-08-28 doi:10.1101/2021.08.27.457205 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Hopanoids confer robustness to physicochemical variability in the niche of the plant symbiont Bradyrhizobium diazoefficiens ]]> https://biorxiv.org/content/10.1101/2021.08.31.458470v1?rss=1 Tookmanian, E. M. Junghans, L. Kulkarni, G. Ledermann, R. Saenz, J. P. Newman, D. K. 2021-09-01 doi:10.1101/2021.08.31.458470 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Metabolic modeling of the International Space Station microbiome reveals key microbial interactions ]]> https://biorxiv.org/content/10.1101/2021.09.03.458819v1?rss=1 Kumar, R. K. Singh, N. K. Balakrishnan, S. Parker, C. W. Raman, K. Venkateswaran, K. 2021-09-04 doi:10.1101/2021.09.03.458819 Cold Spring Harbor Laboratory Press 2021-09-04 <![CDATA[ Chronic exposure to odors at naturally occurring concentrations triggers limited plasticity in early stages of Drosophila olfactory processing ]]> https://biorxiv.org/content/10.1101/2021.09.03.458834v1?rss=1 Hong, E. J. Gugel, Z. V. Maurais, E. 2021-09-03 doi:10.1101/2021.09.03.458834 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ A novel widespread bacterial structure related to the flagellar type III secretion system ]]> https://biorxiv.org/content/10.1101/2021.09.03.458937v1?rss=1 Kaplan, M. Oikonomou, C. M. Wood, c. R. Chreifi, G. Ghosal, D. Dobro, M. Yao, Q. McDowall, A. Briegel, A. Beeby, M. Chang, Y.-W. Shaffer, C. Jensen, G. J. 2021-09-04 doi:10.1101/2021.09.03.458937 Cold Spring Harbor Laboratory Press 2021-09-04 <![CDATA[ Single-cell perturbation dissects transcription factor control of progression speed and trajectory choice in early T-cell development ]]> https://biorxiv.org/content/10.1101/2021.09.03.458944v1?rss=1 Zhou, W. Gao, F. Romero-Wolf, M. Jo, S. Rothenberg, E. V. 2021-09-06 doi:10.1101/2021.09.03.458944 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Entry to and exit from diapause arrest in Caenorhabditis elegans are both regulated by a steroid hormone pathway ]]> https://biorxiv.org/content/10.1101/2021.09.04.458989v1?rss=1 Zhang, M. G. Sternberg, P. W. 2021-09-06 doi:10.1101/2021.09.04.458989 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments ]]> https://biorxiv.org/content/10.1101/2021.09.06.459173v1?rss=1 Gorin, G. Vastola, J. J. Fang, M. Pachter, L. 2021-09-06 doi:10.1101/2021.09.06.459173 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Spatio-temporal coordination at the maternal-fetal interface promotes trophoblast invasion and vascular remodeling in the first half of human pregnancy ]]> https://biorxiv.org/content/10.1101/2021.09.08.459490v1?rss=1 Greenbaum, S. Averbukh, I. Soon, E. Rizzuto, G. Baranski, A. Greenwald, N. Bosse, M. Jaswa, E. G. Khair, Z. Kwok, S. Warshawsky, S. Miller, G. Schwartz, M. Graf, W. Van Valen, D. Keren, L. Hollmann, T. van de Rijn, M. Angelo, M. 2021-09-10 doi:10.1101/2021.09.08.459490 Cold Spring Harbor Laboratory Press 2021-09-10 <![CDATA[ Layered Feedback Control Overcomes Performance Trade-off in Synthetic Biomolecular Networks ]]> https://biorxiv.org/content/10.1101/2021.09.12.459953v1?rss=1 View larger version (11K): org.highwire.dtl.DTLVardef@c8312dorg.highwire.dtl.DTLVardef@114c15borg.highwire.dtl.DTLVardef@1a25baaorg.highwire.dtl.DTLVardef@301ebe_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hu, C. Y. Murray, R. M. 2021-09-13 doi:10.1101/2021.09.12.459953 Cold Spring Harbor Laboratory Press 2021-09-13 <![CDATA[ Rapid Identification of Neutralizing Antibodies against SARS-CoV-2 Variants by mRNA Display ]]> https://biorxiv.org/content/10.1101/2021.09.14.460356v1?rss=1 Tanaka, S. Olson, C. A. Barnes, C. O. Higashide, W. Gonzales, M. Taft, J. Richardson, A. Martin-Fernandez, M. Bogunovic, D. Gnanapragasam, P. N. P. Bjorkman, P. Spilman, P. R. Niazi, K. Rabizadeh, S. Soon-Shiong, P. 2021-09-15 doi:10.1101/2021.09.14.460356 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Lysosome-related organelles contain an expansion compartment that mediates delivery of zinc transporters to promote homeostasis ]]> https://biorxiv.org/content/10.1101/2021.09.18.460850v1?rss=1 Mendoza, A. D. Dietrich, N. Tan, C.-H. Herrera, D. E. Kasiah, J. Payne, Z. Schneider, D. L. Kornfeld, K. 2021-09-19 doi:10.1101/2021.09.18.460850 Cold Spring Harbor Laboratory Press 2021-09-19 <![CDATA[ Ratiometric RNA labeling allows dynamic multiplexed analysis of gene circuits in single cells ]]> https://biorxiv.org/content/10.1101/2021.09.23.461487v1?rss=1 Xu, S. Li, K. Ma, L. Zhang, J. Yoon, S. Elowitz, M. B. Lin, Y. 2021-09-23 doi:10.1101/2021.09.23.461487 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ A rise-to-threshold signal for a relative value deliberation ]]> https://biorxiv.org/content/10.1101/2021.09.23.461548v1?rss=1 Vijayan, V. Wang, F. Wang, K. Chakravorty, A. Adachi, A. Akhlaghpour, H. Dickson, B. J. Maimon, G. 2021-09-24 doi:10.1101/2021.09.23.461548 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Mechanics Of Ultrasonic Neuromodulation In A Mouse Subject ]]> https://biorxiv.org/content/10.1101/2021.09.23.461613v1?rss=1 Salahshoor, H. Guo, H. Shapiro, M. G. Ortiz, M. 2021-09-24 doi:10.1101/2021.09.23.461613 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Gene identification and genome annotation in Caenorhabditis briggsae by high throughput 5' RNA end determination ]]> https://biorxiv.org/content/10.1101/2021.09.24.461604v1?rss=1 Jhaveri, N. van den Berg, W. Hwang, B. J. Muller, H.-M. Sternberg, P. W. Gupta, B. P. 2021-09-24 doi:10.1101/2021.09.24.461604 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea ]]> https://biorxiv.org/content/10.1101/2021.09.25.461819v1?rss=1 Chadwick, G. L. Skennerton, C. T. Laso-Perez, R. Leu, A. O. Speth, D. R. Yu, H. Morgan-Lang, C. Hatzenpichler, R. Goudeau, D. Malmstrom, R. Brazelton, W. J. Woyke, T. Hallam, S. J. Tyson, G. W. Wegener, G. Boetius, A. Orphan, V. J. 2021-09-26 doi:10.1101/2021.09.25.461819 Cold Spring Harbor Laboratory Press 2021-09-26 <![CDATA[ Optimization of anastomotic technique and gastric conduit perfusion with hyperspectral imaging in an experimental model for minimally invasive esophagectomy ]]> https://biorxiv.org/content/10.1101/2021.10.03.462901v1?rss=1 Nickel, F. Studier-Fischer, A. Oezdemir, B. Odenthal, J. Mueller, L.-R. Knoedler, S. Kowalewski, K.-F. Camplisson, I. Allers, M. M. Dietrich, M. Schmidt, K. Salg, G. A. Kenngott, H. G. Billeter, A. Gockel, I. Sagiv, C. Etz-Hadar, O. Gildenblat, J. Ayala, L. Seidlitz, S. Maier-Hein, L. Mueller-Stich, B. P. 2021-10-04 doi:10.1101/2021.10.03.462901 Cold Spring Harbor Laboratory Press 2021-10-04 <![CDATA[ Structure of an ant-myrmecophile-microbe community ]]> https://biorxiv.org/content/10.1101/2021.10.04.462948v1?rss=1 Perry, E. K. Siozios, S. Hurst, G. D. D. Parker, J. 2021-10-05 doi:10.1101/2021.10.04.462948 Cold Spring Harbor Laboratory Press 2021-10-05 <![CDATA[ Fluorescence Activation Mechanism and Imaging of Drug Permeation with New Sensors for Smoking-Cessation Ligands ]]> https://biorxiv.org/content/10.1101/2021.10.04.463082v1?rss=1 30 fold. The new nicotinic iDrugSnFRs provide insight into the real-time pharmacokinetic properties of nicotinic agonists and provide a methodology whereby iDrugSnFRs can inform both pharmaceutical neuroscience and addiction neuroscience. ]]> Nichols, A. L. Blumenfeld, Z. Fan, C. Luebbert, L. Blom, A. E. M. Cohen, B. N. Marvin, J. S. Borden, P. M. Kim, C. Muthusamy, A. K. Shivange, A. V. Knox, H. J. Campello, H. R. Wang, J. H. Dougherty, D. A. Looger, L. Gallagher, T. Rees, D. C. Lester, H. A. 2021-10-04 doi:10.1101/2021.10.04.463082 Cold Spring Harbor Laboratory Press 2021-10-04 <![CDATA[ Video-evoked fMRI BOLD responses are highly consistent across different data acquisition sites ]]> https://biorxiv.org/content/10.1101/2021.10.04.463088v1?rss=1 Byrge, L. Kliemann, D. He, Y. Cheng, H. Tyszka, J. M. Adolphs, R. Kennedy, D. P. 2021-10-05 doi:10.1101/2021.10.04.463088 Cold Spring Harbor Laboratory Press 2021-10-05 <![CDATA[ Large-scale comparative genomics unravels great genomic diversity across the Rickettsia and Ca. Megaira genera and identifies Torix group as an evolutionarily distinct clade. ]]> https://biorxiv.org/content/10.1101/2021.10.06.463315v1?rss=1 Davison, H. R. Pilgrim, J. Wybouw, N. Parker, J. Pirro, S. Hunter-Barnett, S. Campbell, P. M. Blow, F. Darby, A. C. Hurst, G. D. D. Siozios, S. 2021-10-06 doi:10.1101/2021.10.06.463315 Cold Spring Harbor Laboratory Press 2021-10-06 <![CDATA[ Preserved motor representations after paralysis ]]> https://biorxiv.org/content/10.1101/2021.10.07.463105v1?rss=1 Guan, C. Aflalo, T. Zhang, C. Rosario, E. R. Pouratian, N. Andersen, R. A. 2021-10-09 doi:10.1101/2021.10.07.463105 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ 3D imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa ]]> https://biorxiv.org/content/10.1101/2021.10.07.463215v1?rss=1 Mondragon-Palomino, O. Poceviciute, R. Lignell, A. Griffiths, J. A. Takko, H. Ismagilov, R. F. 2021-10-08 doi:10.1101/2021.10.07.463215 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ A Systematic Interrogation of MHC Class I Antigen Presentation Identifies Constitutive and Compensatory Protein Degradation Pathways ]]> https://biorxiv.org/content/10.1101/2021.10.07.463289v1?rss=1 Mamrosh, J. L. Li, J. Sherman, D. J. Moradian, A. Sweredoski, M. J. Verma, R. Johnston, J. A. Lipford, J. R. Deshaies, R. J. 2021-10-08 doi:10.1101/2021.10.07.463289 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ Intelligent Resolution: Integrating Cryo-EM with AI-driven Multi-resolution Simulations to Observe the SARS-CoV-2 Replication-Transcription Machinery in Action ]]> https://biorxiv.org/content/10.1101/2021.10.09.463779v1?rss=1 Trifan, A. Gorgun, D. Li, Z. Brace, A. Zvyagin, M. Ma, H. Clyde, A. R. Clark, D. A. Salim, M. Hardy, D. Burnley, T. Huang, L. McCalpin, J. Emani, M. Yoo, H. Yin, J. Tsaris, A. Subbiah, V. Liu, J. Trebesch, N. Wells, G. Mysore, V. Gibbs, T. Phillips, J. Chennubhotla, S. C. Foster, I. Stevens, R. Anandkumar, A. Vishwanath, V. Stone, J. E. Tajkhorshid, E. Harris, S. A. Ramanathan, A. 2021-10-12 doi:10.1101/2021.10.09.463779 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ Novelty and uncertainty interact to regulate the balance between exploration and exploitation in the human brain. ]]> https://biorxiv.org/content/10.1101/2021.10.13.464279v1?rss=1 Cockburn, J. Man, V. Cunningham, W. A. O'Doherty, J. P. 2021-10-14 doi:10.1101/2021.10.13.464279 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ Diversity and evolution of nitric oxide reduction ]]> https://biorxiv.org/content/10.1101/2021.10.15.464467v1?rss=1 Hemp, J. Murali, R. Pace, L. A. Sanford, R. A. Hatzenpichler, R. Ward, L. Lingappa, U. Fischer, W. W. Gennis, R. B. 2021-10-15 doi:10.1101/2021.10.15.464467 Cold Spring Harbor Laboratory Press 2021-10-15 <![CDATA[ Protease-controlled secretion and display of intercellular signals ]]> https://biorxiv.org/content/10.1101/2021.10.18.464444v1?rss=1 Vlahos, A. E. Kang, J. Aldrete, C. A. Zhu, R. Chong, L. S. Elowitz, M. B. Gao, X. J. 2021-10-19 doi:10.1101/2021.10.18.464444 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Commensal bacteria promote type I interferon signaling to maintain immune tolerance ]]> https://biorxiv.org/content/10.1101/2021.10.21.464743v1?rss=1 Vasquez Ayala, A. Matsuo, K. Hsu, C.-Y. Carrillo Terrazas, M. Chu, H. 2021-10-21 doi:10.1101/2021.10.21.464743 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ Architecture of the cytoplasmic face of the nuclear pore ]]> https://biorxiv.org/content/10.1101/2021.10.26.465790v1?rss=1 Bley, C. J. Nie, S. Mobbs, G. Petrovic, S. Gres, A. Liu, X. Mukherjee, S. Harvey, S. Huber, F. M. Lin, D. H. Brown, B. Tang, A. W. Rundlet, E. J. Correia, A. R. Chen, S. Regmi, S. G. Dasso, M. Patke, A. Palazzo, A. F. Kossiakoff, A. A. Hoelz, A. 2021-10-26 doi:10.1101/2021.10.26.465790 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Architecture of the linker-scaffold in the nuclear pore ]]> https://biorxiv.org/content/10.1101/2021.10.26.465796v1?rss=1 Petrovic, S. Samanta, D. Perriches, T. Bley, C. J. Thierbach, K. Brown, B. Nie, S. Mobbs, G. W. Stevens, T. A. Liu, X. Hoelz, A. 2021-10-26 doi:10.1101/2021.10.26.465796 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Transcriptomic profiling of sex-specific olfactory neurons reveals subset-specific receptor expression in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.10.26.465928v1?rss=1 Reilly, D. K. Schwarz, E. M. Muirhead, C. S. Robidoux, A. N. Antoscheckin, I. Narayan, A. Doma, M. Sternberg, P. W. Srinivasan, J. 2021-10-28 doi:10.1101/2021.10.26.465928 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Neurons in human pre-supplementary motor area encode key computations for value-based choice ]]> https://biorxiv.org/content/10.1101/2021.10.27.466000v1?rss=1 Aquino, T. G. Cockburn, J. Mamelak, A. N. Rutishauser, U. O'Doherty, J. P. 2021-10-28 doi:10.1101/2021.10.27.466000 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Xist spatially amplifies SHARP recruitment to balance chromosome-wide silencing and specificity to the X chromosome ]]> https://biorxiv.org/content/10.1101/2021.10.27.466149v1?rss=1 Jachowicz, J. W. Strehle, M. Banerjee, A. K. Blanco, M. R. Thai, J. Guttman, M. 2021-10-28 doi:10.1101/2021.10.27.466149 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ GATA4 regionalizes intestinal metabolism and barrier function to prevent immunopathology ]]> https://biorxiv.org/content/10.1101/2021.10.28.466194v1?rss=1 Earley, Z. M. Lisicka, W. Sifakis, J. J. Gamboa, R. A. Kowalczyk, A. Barlow, J. Shaw, D. G. Discepolo, V. Tan, I. L. Gona, S. Ernest, J. Matzinger, P. Barreiro, L. B. Morgun, A. Bendelac, A. Ismagilov, R. F. Shulzhenko, N. Riesenfeld, S. J. Jabri, B. 2021-10-28 doi:10.1101/2021.10.28.466194 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Elevated Hoxb5b expands vagal neural crest pool and blocks enteric neuronal development in zebrafish ]]> https://biorxiv.org/content/10.1101/2021.10.28.466356v1?rss=1 Howard, A. G. A. Nguyen, A. C. Tworig, J. Ravisankar, P. Singleton, E. W. Li, C. Kotzur, G. Waxman, J. S. Uribe, R. A. 2021-10-29 doi:10.1101/2021.10.28.466356 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ Decoding grasp and speech signals from the cortical grasp circuit in a tetraplegic human ]]> https://biorxiv.org/content/10.1101/2021.10.29.466528v1?rss=1 Wandelt, S. K. Kellis, S. Bjanes, D. Pejsa, K. Lee, B. Liu, C. Andersen, R. A. 2021-11-01 doi:10.1101/2021.10.29.466528 Cold Spring Harbor Laboratory Press 2021-11-01 <![CDATA[ Bacterial growth in multicellular aggregates leads to the emergence of complex lifecycles ]]> https://biorxiv.org/content/10.1101/2021.11.01.466752v1?rss=1 Schwartzman, J. A. Ebrahimi, A. Chadwick, G. Sato, Y. Orphan, V. Cordero, O. X. 2021-11-01 doi:10.1101/2021.11.01.466752 Cold Spring Harbor Laboratory Press 2021-11-01 <![CDATA[ Neutralizing antibodies induced in immunized macaques recognize the CD4-binding site on an occluded-open HIV-1 envelope trimer ]]> https://biorxiv.org/content/10.1101/2021.11.02.466200v1?rss=1 Yang, Z. Dam, K.-M. A. Bridges, M. D. Hoffmann, M. A. G. DeLaitsch, A. T. Gristick, H. B. Escolano, A. Gautam, R. Martin, M. A. Nussenzweig, M. Hubbell, W. Bjorkman, P. J. 2021-11-04 doi:10.1101/2021.11.02.466200 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Montage electron tomography of vitrified specimens ]]> https://biorxiv.org/content/10.1101/2021.11.02.466666v1?rss=1 Peck, A. Carter, S. D. Mai, H. Chen, S. Burt, A. Jensen, G. J. 2021-11-04 doi:10.1101/2021.11.02.466666 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[ FLIP: Benchmark tasks in fitness landscape inference for proteins ]]> https://biorxiv.org/content/10.1101/2021.11.09.467890v1?rss=1 Dallago, C. Mou, J. Johnston, K. E. Wittmann, B. Bhattacharya, N. Goldman, S. L. Madani, A. Yang, K. K. 2021-11-11 doi:10.1101/2021.11.09.467890 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Real-time Image Denoising of Mixed Poisson-Gaussian Noise in Fluorescence Microscopy Images using ImageJ ]]> https://biorxiv.org/content/10.1101/2021.11.10.468102v1?rss=1 8 dB) denoising in less time than other fluorescence microscopy denoising methods. ]]> Mannam, V. Zhang, Y. Zhu, Y. Nichols, E. Wang, Q. Sundaresan, V. Zhang, S. Smith, C. Bohn, P. W. Howard, S. 2021-11-13 doi:10.1101/2021.11.10.468102 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ Resting-state functional connectivity of social brain regions predicts motivated dishonesty ]]> https://biorxiv.org/content/10.1101/2021.11.10.468161v1?rss=1 Pang, L. Li, H. Liu, Q. Luo, Y.-j. Mobbs, D. Wu, H. 2021-11-13 doi:10.1101/2021.11.10.468161 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol ]]> https://biorxiv.org/content/10.1101/2021.11.12.468428v1?rss=1 Dommer, A. Casalino, L. Kearns, F. Rosenfeld, M. Wauer, N. Ahn, S.-H. Russo, J. Oliveira, S. Morris, C. Bogetti, A. Trifan, A. Brace, A. Sztain, T. Clyde, A. Ma, H. Chennubhotla, C. Lee, H. Turilli, M. Khalid, S. Tamayo-Mendoza, T. Welborn, M. Christiansen, A. Smith, D. G. A. Qiao, Z. Sirumalla, S. K. O'Connor, M. Manby, F. Anandkumar, A. Hardy, D. Phillips, J. Stern, A. Romero, J. Clark, D. Dorrell, M. Maiden, T. Huang, L. McCalpin, J. Woods, C. Gray, A. Williams, M. Barker, B. Rajapaksha, H. Pitts, R. Gibbs, T. Stone, J. Zuckerman, D. Muholland, 2021-11-15 doi:10.1101/2021.11.12.468428 Cold Spring Harbor Laboratory Press 2021-11-15 <![CDATA[ Comparative genomics on cultivated and uncultivated, freshwater and marine Candidatus Manganitrophaceae species implies their worldwide reach in manganese chemolithoautotrophy ]]> https://biorxiv.org/content/10.1101/2021.11.15.468770v1?rss=1 Yu, H. Chadwick, G. L. Lingappa, U. F. Leadbetter, J. R. 2021-11-16 doi:10.1101/2021.11.15.468770 Cold Spring Harbor Laboratory Press 2021-11-16 <![CDATA[ Guide-directed DNA cleavage by a prokaryotic Argonaute protein induces chromosome recombination in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2021.11.17.469050v1?rss=1 Huang, S. Wang, K. Mayo, S. L. 2021-11-18 doi:10.1101/2021.11.17.469050 Cold Spring Harbor Laboratory Press 2021-11-18 <![CDATA[ Adaptive ratchets and the evolution of molecular complexity ]]> https://biorxiv.org/content/10.1101/2021.11.18.469165v1?rss=1 Röschinger, T. Moran Tovar, R. Pompei, S. Lässig, M. 2021-11-20 doi:10.1101/2021.11.18.469165 Cold Spring Harbor Laboratory Press 2021-11-20 <![CDATA[ evSeq: Cost-Effective Amplicon Sequencing of Every Variant in a Protein Library ]]> https://biorxiv.org/content/10.1101/2021.11.18.469179v1?rss=1 Wittmann, B. J. Johnston, K. E. Almhjell, P. J. Arnold, F. H. 2021-11-19 doi:10.1101/2021.11.18.469179 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Doppler Slicing for Ultrasound Super-Resolution Without Contrast Agents ]]> https://biorxiv.org/content/10.1101/2021.11.19.469083v1?rss=1 Bar-Zion, A. Solomon, O. Rabut, C. Maresca, D. Eldar, Y. C. Shapiro, M. G. 2021-11-20 doi:10.1101/2021.11.19.469083 Cold Spring Harbor Laboratory Press 2021-11-20 <![CDATA[ Prevalence and correlates of phenazine resistance in culturable bacteria from a dryland wheat field ]]> https://biorxiv.org/content/10.1101/2021.11.23.469799v1?rss=1 Perry, E. Newman, D. K. 2021-11-24 doi:10.1101/2021.11.23.469799 Cold Spring Harbor Laboratory Press 2021-11-24 <![CDATA[ Spectral organ fingerprints for intraoperative tissue classification with hyperspectral imaging ]]> https://biorxiv.org/content/10.1101/2021.11.24.469943v1?rss=1 95 %). We conclude from our study that automatic tissue discrimination based on HSI data is feasible and could thus aid in intraoperative decision making and pave the way for context-aware computer-assisted surgery systems and autonomous robotics. ]]> Studier-Fischer, A. Seidlitz, S. Sellner, J. Wiesenfarth, M. Ayala, L. Oezdemir, B. Odenthal, J. Knoedler, S. Kowalewski, K.-F. Haney, C. M. Camplisson, I. Dietrich, M. Schmidt, K. Salg, G. Kenngott, H. G. Adler, T. J. Schreck, N. Kopp-Schneider, A. Maier-Hein, K. Maier-Hein, L. Mueller-Stich, B. P. Nickel, F. 2021-11-25 doi:10.1101/2021.11.24.469943 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ Redox-active secondary metabolites act as interspecies modulators of antibiotic resilience ]]> https://biorxiv.org/content/10.1101/2021.12.01.470848v1?rss=1 Meirelles, L. A. Newman, D. K. 2021-12-02 doi:10.1101/2021.12.01.470848 Cold Spring Harbor Laboratory Press 2021-12-02 <![CDATA[ Efficient pre-processing of Single-cell ATAC-seq data ]]> https://biorxiv.org/content/10.1101/2021.12.08.471788v1?rss=1 Gao, F. Pachter, L. 2021-12-10 doi:10.1101/2021.12.08.471788 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ The double-edged role of nitric oxide drives predictable microbial community organization according to the microenvironment ]]> https://biorxiv.org/content/10.1101/2021.12.09.472001v1?rss=1 Wilbert, S. A. Newman, D. K. 2021-12-09 doi:10.1101/2021.12.09.472001 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Coral larvae suppress the heat stress response during the onset of symbiosis thereby decreasing their odds of survival ]]> https://biorxiv.org/content/10.1101/2021.12.10.472165v1?rss=1 Kitchen, S. A. Jiang, D. Harii, S. Satoh, N. Weis, V. M. Shinzato, C. 2021-12-12 doi:10.1101/2021.12.10.472165 Cold Spring Harbor Laboratory Press 2021-12-12 <![CDATA[ Glutathione binding to the plant At Atm3 transporter and implications for the conformational coupling of ABC transporters ]]> https://biorxiv.org/content/10.1101/2021.12.13.472443v1?rss=1 Fan, C. Rees, D. C. 2021-12-14 doi:10.1101/2021.12.13.472443 Cold Spring Harbor Laboratory Press 2021-12-14 <![CDATA[ Coupled protein quality control during nonsense mediated mRNA decay ]]> https://biorxiv.org/content/10.1101/2021.12.22.473893v1?rss=1 Inglis, A. J. Guna, A. Merchan, A. G. Pal, A. Esantsi, T. K. Keys, H. R. Frenkel, E. M. Oania, R. Weissman, J. S. Voorhees, R. M. 2021-12-23 doi:10.1101/2021.12.22.473893 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Polyphosphate affects cytoplasmic and chromosomal dynamics in nitrogen-starved Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2021.12.23.473106v1?rss=1 Magkiriadou, S. Habel, A. Stepp, W. L. Newman, D. K. Manley, S. Racki, L. R. 2021-12-23 doi:10.1101/2021.12.23.473106 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Multi-Wavelength Analytical Ultracentrifugation of Biopolymer Mixtures and Interactions ]]> https://biorxiv.org/content/10.1101/2021.12.29.474408v1?rss=1 Henrickson, A. Gorbet, G. E. Savelyev, A. Kim, M. Schultz, S. K. Ding, X. Hargreaves, J. Gradinaru, V. Kothe, U. Demeler, B. 2021-12-30 doi:10.1101/2021.12.29.474408 Cold Spring Harbor Laboratory Press 2021-12-30 <![CDATA[ Intravenous gene transfer throughout the brain of infant Old World primates using AAV ]]> https://biorxiv.org/content/10.1101/2022.01.08.475342v1?rss=1 Chuapoco, M. R. Flytzanis, N. Goeden, N. Octeau, J. C. Roxas, K. M. Chan, K. Y. Scherrer, J. Winchester, J. Blackburn, R. J. Campos, L. J. Arokiaraj, C. M. Miles, T. F. Jang, M. J. Vendemiatti, J. Deverman, B. E. Pickel, J. Fox, A. S. Gradinaru, V. 2022-01-09 doi:10.1101/2022.01.08.475342 Cold Spring Harbor Laboratory Press 2022-01-09 <![CDATA[ Overestimated Polygenic Prediction due to Overlapping Subjects in Genetic Datasets ]]> https://biorxiv.org/content/10.1101/2022.01.19.476997v1?rss=1 Park, D. K. Chen, M. Kim, S. Joo, Y. Y. Loving, R. Kim, H.-S. Cha, J. Yoo, S. Kim, J. H. 2022-01-22 doi:10.1101/2022.01.19.476997 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ Smart sealants for prevention and monitoring of gastrointestinal anastomotic leaks using portable smartphone-controlled ultrasound transducers ]]> https://biorxiv.org/content/10.1101/2022.01.24.477460v1?rss=1 Anthis, A. H. C. Abundo, M. P. Neuer, A. L. Tsolaki, E. Rosendorf, J. Rduch, T. Starsich, F. Liska, V. Schlegel, A. A. Shapiro, M. G. Herrmann, I. K. 2022-01-27 doi:10.1101/2022.01.24.477460 Cold Spring Harbor Laboratory Press 2022-01-27 <![CDATA[ Rubisco forms a lattice inside alpha-carboxysomes ]]> https://biorxiv.org/content/10.1101/2022.01.24.477598v1?rss=1 Metskas, L. A. Ortega, D. R. Oltrogge, L. M. Blikstad, C. Laughlin, T. Savage, D. Jensen, G. J. 2022-01-25 doi:10.1101/2022.01.24.477598 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Bimodally oriented cellulose fibers and reticulated homogalacturonan networks - A direct visualization of Allium cepa primary cell walls ]]> https://biorxiv.org/content/10.1101/2022.01.31.478342v1?rss=1 NICOLAS, W. J. Faessler, F. Schur, F. K. Dutka, P. Meyerowitz, E. M. Jensen, G. J. 2022-02-01 doi:10.1101/2022.01.31.478342 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Machine learning algorithm to characterize antimicrobial resistance associated with the International Space Station surface microbiome ]]> https://biorxiv.org/content/10.1101/2022.02.07.479455v1?rss=1 Madrigal, P. Singh, N. K. Wood, J. M. Gaudioso, E. Hernandez-del-Olmo, F. Mason, C. E. Venkateswaran, K. Beheshti, A. 2022-02-10 doi:10.1101/2022.02.07.479455 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Maternally inherited siRNAs initiate piRNA cluster formation ]]> https://biorxiv.org/content/10.1101/2022.02.08.479612v1?rss=1 Luo, Y. He, P. Kanrar, N. Toth, K. F. Aravin, A. 2022-02-09 doi:10.1101/2022.02.08.479612 Cold Spring Harbor Laboratory Press 2022-02-09 <![CDATA[ RNA velocity unraveled ]]> https://biorxiv.org/content/10.1101/2022.02.12.480214v1?rss=1 Gorin, G. Fang, M. Chari, T. Pachter, L. 2022-02-13 doi:10.1101/2022.02.12.480214 Cold Spring Harbor Laboratory Press 2022-02-13 <![CDATA[ In situ architecture of human kinetochore-microtubule interface visualized by cryo-electron tomography ]]> https://biorxiv.org/content/10.1101/2022.02.17.480955v1?rss=1 Zhao, W. Jensen, G. J. 2022-02-18 doi:10.1101/2022.02.17.480955 Cold Spring Harbor Laboratory Press 2022-02-18 <![CDATA[ Neuromuscular embodiment of feedback control elements in Drosophila flight ]]> https://biorxiv.org/content/10.1101/2022.02.22.481344v1?rss=1 Whitehead, S. C. Leone, S. Lindsay, T. Meiselman, M. R. Cowan, N. Dickinson, M. H. Yapici, N. Stern, D. Shirangi, T. Cohen, I. 2022-02-24 doi:10.1101/2022.02.22.481344 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Three Mutations Convert the Selectivity of a Protein Sensor From Nicotinic Agonists to S-Methadone For Use in Cells, Organelles, and Biofluids ]]> https://biorxiv.org/content/10.1101/2022.02.24.481226v1?rss=1 Muthusamy, A. K. Kim, C. H. Virgil, S. C. Knox, H. J. Marvin, J. S. Nichols, A. L. Cohen, B. N. Dougherty, D. A. Looger, L. L. Lester, H. A. 2022-02-26 doi:10.1101/2022.02.24.481226 Cold Spring Harbor Laboratory Press 2022-02-26 <![CDATA[ Multi-omic analysis along the gut-brain axis points to a functional architecture of autism ]]> https://biorxiv.org/content/10.1101/2022.02.25.482050v1?rss=1 Morton, J. T. Jin, D.-m. Mills, R. Shao, Y. Rahman, G. Harold-Berding, K. Needham, B. D. Zurita, M. F. David, M. Averina, O. Kovtun, A. Noto, A. Mussap, M. Wang, M. Frank, D. Li, E. Zhou, W. Fanos, V. Danilenko, V. Wall, D. P. Cardenas, P. A. Baldeon, M. xavier, r. j. Mazmanian, S. Knight, R. Gilbert, J. Donovan, S. Lawley, T. Carpenter, B. Bonneau, R. Taroncher-Oldenburg, G. 2022-02-26 doi:10.1101/2022.02.25.482050 Cold Spring Harbor Laboratory Press 2022-02-26 <![CDATA[ Enabling spatiotemporal regulation within biomaterials using DNA reaction- diffusion waveguides ]]> https://biorxiv.org/content/10.1101/2022.02.26.482105v1?rss=1 Dorsey, P. J. Scalise, D. Schulman, R. 2022-02-28 doi:10.1101/2022.02.26.482105 Cold Spring Harbor Laboratory Press 2022-02-28 <![CDATA[ Reconstructing the ancestral vertebrate brain using a lamprey neural cell type atlas ]]> https://biorxiv.org/content/10.1101/2022.02.28.482278v1?rss=1 Lamanna, F. Hervas-Sotomayor, F. Oel, A. P. Jandzik, D. Sobrido-Camean, D. Martik, M. L. Green, S. A. Brüning, T. Mössinger, K. Schmidt, J. Schneider, C. Sepp, M. Murat, F. Smith, J. J. Bronner, M. E. Rodicio, M. C. Barreiro-Iglesias, A. Meulemans Medeiros, D. Arendt, D. Kaessmann, H. 2022-03-01 doi:10.1101/2022.02.28.482278 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Structural motifs for subtype-specific pH-sensitive gating of vertebrate otopetrin proton channels ]]> https://biorxiv.org/content/10.1101/2022.03.01.482452v1?rss=1 pH 9.0). Strikingly, we found that we could change pH-sensitive gating of OTOP2 and OTOP3 channels by swapping extracellular linkers that connect transmembrane domains. Swaps of linkers within the N domain changed the relative conductance at alkaline pH, while swaps within the C domain tended to change the rates of OTOP3 current activation. We conclude that members of the OTOP channel family are proton-gated (acid-sensitive) proton channels and that the gating apparatus is distributed across multiple extracellular regions within both the N and C domains of the channels. In addition to the taste system, OTOP channels are found in the vestibular and digestive systems, where pH sensitivity may be tuned to specific functions. ]]> Teng, B. Kaplan, J. Liang, Z. Krieger, Z. Tu, Y.-H. Burendei, B. Ward, A. B. Liman, E. 2022-03-01 doi:10.1101/2022.03.01.482452 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Anthroponumbers.org: A Quantitative Database Of Human Impacts on Planet Earth ]]> https://biorxiv.org/content/10.1101/2022.03.04.483053v1?rss=1 Chure, G. Banks, R. A. Flamholz, A. I. Sarai, N. S. Kamb, M. Lopez-Gomez, I. Bar-On, Y. Milo, R. Phillips, R. 2022-03-07 doi:10.1101/2022.03.04.483053 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Automated reconstruction of dendritic and axonal arbors reveals molecular correlates of neuroanatomy ]]> https://biorxiv.org/content/10.1101/2022.03.07.482900v1?rss=1 Gliko, O. Mallory, M. Dalley, R. Gala, R. Gornet, J. Zeng, H. Sorensen, S. Sumbul, U. 2022-03-08 doi:10.1101/2022.03.07.482900 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Photoacoustic imaging reveals mechanisms of rapid-acting insulin formulations dynamics at the injection site ]]> https://biorxiv.org/content/10.1101/2022.03.10.483309v1?rss=1 Khadria, A. Paavola, C. D. Maslov, K. Valenzuela, F. A. Sperry, A. E. Cox, A. L. Cao, R. Shi, J. Brown-Augsburger, P. L. Lozano, E. Blankenship, R. L. Majumdar, R. Bradley, S. A. Beals, J. M. Oladipupo, S. S. Wang, L. V. 2022-03-13 doi:10.1101/2022.03.10.483309 Cold Spring Harbor Laboratory Press 2022-03-13 <![CDATA[ Visualization of mRNA Expression in Pseudomonas aeruginosa Aggregates Reveals Spatial Patterns of Fermentative and Denitrifying Metabolism ]]> https://biorxiv.org/content/10.1101/2022.03.11.484052v1?rss=1 Livingston, J. Spero, M. A. Lonergan, Z. R. Newman, D. K. 2022-03-12 doi:10.1101/2022.03.11.484052 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ Virgin Birth: A genetic basis for facultative parthenogenesis ]]> https://biorxiv.org/content/10.1101/2022.03.13.484157v1?rss=1 Braun, A. L. Fabian, D. K. Garrison, E. Glover, D. M. 2022-03-14 doi:10.1101/2022.03.13.484157 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ A naturally arising broad and potent CD4-binding site antibody with low somatic mutation ]]> https://biorxiv.org/content/10.1101/2022.03.16.484662v1?rss=1 Barnes, C. O. Schoofs, T. Gnanapragasam, P. N. P. Golijanin, J. Huey-Tubman, K. E. Gruell, H. Schommers, P. Suh-Toma, N. Lee, Y. E. Lorenzi, J. C. C. Piechocka-Trocha, A. Scheid, J. F. West, A. P. Walker, B. D. Seaman, M. S. Klein, F. Nussenzweig, M. C. Bjorkman, P. J. 2022-03-18 doi:10.1101/2022.03.16.484662 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ Stress-tolerant, recyclable, and autonomously renewable biocatalyst platform enabled by engineered bacterial spores ]]> https://biorxiv.org/content/10.1101/2022.03.16.484680v1?rss=1 View larger version (46K): org.highwire.dtl.DTLVardef@6f50d0org.highwire.dtl.DTLVardef@22a9c3org.highwire.dtl.DTLVardef@1b74e9corg.highwire.dtl.DTLVardef@18a11c8_HPS_FORMAT_FIGEXP M_FIG C_FIG Schematic illustration of the T7 RNA polymerase-enabled high-density protein display (TIED) on bacterial spores and its unique features as a biocatalyst platform. ]]> Hui, Y. Cui, Z. Sim, S. 2022-03-17 doi:10.1101/2022.03.16.484680 Cold Spring Harbor Laboratory Press 2022-03-17 <![CDATA[ Periodic spatial patterning with a single morphogen ]]> https://biorxiv.org/content/10.1101/2022.03.21.484932v1?rss=1 Wang, S. Garcia-Ojalvo, J. Elowitz, M. B. 2022-03-22 doi:10.1101/2022.03.21.484932 Cold Spring Harbor Laboratory Press 2022-03-22 <![CDATA[ Mosaic RBD nanoparticles protect against multiple sarbecovirus challenges in animal models ]]> https://biorxiv.org/content/10.1101/2022.03.25.485875v1?rss=1 Cohen, A. A. van Doremalen, N. A. Greaney, A. J. Andersen, H. Sharma, A. Starr, T. N. Keeffe, J. R. Fan, C. Schulz, J. E. Gnanapragasam, P. N. P. Kakutani, L. M. West, A. P. Saturday, G. Lee, Y. E. Gao, H. Jette, C. A. Lewis, M. G. Tan, T. K. Townsend, A. R. Bloom, J. D. Munster, V. J. Bjorkman, P. J. 2022-03-28 doi:10.1101/2022.03.25.485875 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Modeling and mechanical perturbations reveal how spatially regulated anchorage gives rise to spatially distinct mechanics across the mammalian spindle ]]> https://biorxiv.org/content/10.1101/2022.04.08.487649v1?rss=1 Suresh, P. Galstyan, V. Phillips, R. Dumont, S. 2022-04-08 doi:10.1101/2022.04.08.487649 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ From Specification to Implementation: Assume-Guarantee Contracts for Synthetic Biology ]]> https://biorxiv.org/content/10.1101/2022.04.08.487709v1?rss=1 Pandey, A. Incer, I. Sangiovanni-Vincentelli, A. Murray, R. M. 2022-04-11 doi:10.1101/2022.04.08.487709 Cold Spring Harbor Laboratory Press 2022-04-11 <![CDATA[ Specific targeting of plasmids with Argonaute enables genome editing ]]> https://biorxiv.org/content/10.1101/2022.04.14.488398v1?rss=1 Esyunina, D. Okhtienko, A. Olina, A. Prostova, M. Aravin, A. A. Kulbachiskiy, A. 2022-04-14 doi:10.1101/2022.04.14.488398 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ An approximate line attractor in the hypothalamus that encodes an aggressive internal state ]]> https://biorxiv.org/content/10.1101/2022.04.19.488776v1?rss=1 Nair, A. Karigo, T. Yang, B. Linderman, S. W. Anderson, D. J. Kennedy, A. 2022-04-19 doi:10.1101/2022.04.19.488776 Cold Spring Harbor Laboratory Press 2022-04-19 <![CDATA[ Enhanced recovery of single-cell RNA-sequencing reads for missing gene expression data ]]> https://biorxiv.org/content/10.1101/2022.04.26.489449v1?rss=1 Pool, A.-H. Poldsam, H. Chen, S. Thomson, M. Oka, Y. 2022-04-27 doi:10.1101/2022.04.26.489449 Cold Spring Harbor Laboratory Press 2022-04-27 <![CDATA[ A human embryonic limb cell atlas resolved in space and time ]]> https://biorxiv.org/content/10.1101/2022.04.27.489800v1?rss=1 Zhang, B. He, P. Lawrence, J. E. Wang, S. Tuck, E. Williams, B. A. Roberts, K. Kleshchevnikov, V. Mamanova, L. Bolt, L. Polanski, K. Elmentaite, R. Fasouli, E. S. Prete, M. He, X. Yayon, N. Fu, Y. Yang, H. Liang, C. Zhang, H. Fitzpatrick, D. Firth, H. Dean, A. Marioni, J. Barker, R. A. Storer, M. A. Wold, B. Zhang, H. Teichmann, S. 2022-04-28 doi:10.1101/2022.04.27.489800 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Selenocyanate Derived Se-Incorporation into the Nitrogenase Fe Protein Cluster ]]> https://biorxiv.org/content/10.1101/2022.04.29.490034v1?rss=1 Buscagan, T. M. Kaiser, J. T. Rees, D. C. 2022-04-30 doi:10.1101/2022.04.29.490034 Cold Spring Harbor Laboratory Press 2022-04-30 <![CDATA[ Effects of the investigational drug sodium phenylbutyrate-TUDCA (AMX0035) on the transcriptional and metabolic landscape of sporadic ALS fibroblasts ]]> https://biorxiv.org/content/10.1101/2022.05.02.490306v1?rss=1 Fels, J. A. Dash, J. Leslie, K. Manfredi, G. Kawamata, H. 2022-05-02 doi:10.1101/2022.05.02.490306 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ Depth normalization for single-cell genomics count data ]]> https://biorxiv.org/content/10.1101/2022.05.06.490859v1?rss=1 Booeshaghi, A. S. Hallgrimsdottir, I. B. Galvez-Merchan, A. Pachter, L. 2022-05-06 doi:10.1101/2022.05.06.490859 Cold Spring Harbor Laboratory Press 2022-05-06 <![CDATA[ Fixation Can Change the Appearance of Phase Separation in Living Cells ]]> https://biorxiv.org/content/10.1101/2022.05.06.490956v1?rss=1 Irgen-Gioro, S. Walling, V. Chong, S. 2022-05-08 doi:10.1101/2022.05.06.490956 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ Single-cell profiling coupled with lineage analysis reveals distinct sacral neural crest contributions to the developing enteric nervous ]]> https://biorxiv.org/content/10.1101/2022.05.09.491197v1?rss=1 Tang, W. Bronner, M. E. Jacobs-Li, J. Li, C. 2022-05-09 doi:10.1101/2022.05.09.491197 Cold Spring Harbor Laboratory Press 2022-05-09 <![CDATA[ Long-duration and non-invasive photoacoustic imaging of multiple anatomical structures in a live mouse using a single contrast agent ]]> https://biorxiv.org/content/10.1101/2022.05.17.491718v1?rss=1 KHADRIA, A. Paavola, C. D. Zhang, Y. Davis, S. P. X. Grealish, P. Maslov, K. Shi, J. Beals, J. M. Oladipupo, S. S. Wang, L. V. 2022-05-19 doi:10.1101/2022.05.17.491718 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Efficient querying of genomic databases for single-cell RNA-seq with gget ]]> https://biorxiv.org/content/10.1101/2022.05.17.492392v1?rss=1 Luebbert, L. Pachter, L. 2022-05-19 doi:10.1101/2022.05.17.492392 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Precision motor timing via scalar input fluctuations ]]> https://biorxiv.org/content/10.1101/2022.05.18.492498v1?rss=1 Pang, R. Duffy, A. Bell, D. Torok, Z. E. Fairhall, A. L. 2022-05-19 doi:10.1101/2022.05.18.492498 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Metadata retrieval from genomics database with ffq ]]> https://biorxiv.org/content/10.1101/2022.05.18.492548v1?rss=1 Galvez-Merchan, A. Min, K. H. Pachter, L. Booeshaghi, A. S. 2022-05-19 doi:10.1101/2022.05.18.492548 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Magneto-acoustic protein nanostructures for non-invasive imaging of tissue mechanics in vivo ]]> https://biorxiv.org/content/10.1101/2022.05.26.493158v1?rss=1 Kim, W.-S. Min, S. Kim, S. K. Kang, S. Davis, H. Bar-Zion, A. Malounda, D. Kim, Y. H. An, S. Lee, J.-H. Bae, S. H. Lee, J. G. Kwak, M. Cho, S.-W. Shapiro, M. G. Cheon, J. 2022-05-27 doi:10.1101/2022.05.26.493158 Cold Spring Harbor Laboratory Press 2022-05-27 <![CDATA[ A universal system for streamlined genome integrations with CRISPR-associated transposases ]]> https://biorxiv.org/content/10.1101/2022.05.30.494051v1?rss=1 Wang, M. Sanfiorenzo, C. Zhang, R. J. Wang, K. 2022-05-31 doi:10.1101/2022.05.30.494051 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Anaerobic single particle cryoEM of nitrogenase ]]> https://biorxiv.org/content/10.1101/2022.06.04.494841v1?rss=1 Warmack, R. A. Rees, D. C. 2022-06-04 doi:10.1101/2022.06.04.494841 Cold Spring Harbor Laboratory Press 2022-06-04 <![CDATA[ Pseudoalignment facilitates assignment of error-prone Ultima Genomics reads ]]> https://biorxiv.org/content/10.1101/2022.06.04.494845v1?rss=1 Booeshaghi, A. S. Pachter, L. 2022-06-05 doi:10.1101/2022.06.04.494845 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ Improved Version of ChETA Promotes Aggression in the Medial Amygdala ]]> https://biorxiv.org/content/10.1101/2022.06.05.493862v1?rss=1 Hu, R. K. Chen, P. B. Berndt, A. Anderson, D. J. Hong, W. 2022-06-06 doi:10.1101/2022.06.05.493862 Cold Spring Harbor Laboratory Press 2022-06-06 <![CDATA[ Monod: mechanistic analysis of single-cell RNA sequencing count data ]]> https://biorxiv.org/content/10.1101/2022.06.11.495771v1?rss=1 Gorin, G. Pachter, L. 2022-06-12 doi:10.1101/2022.06.11.495771 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Dynamic structural adaptations enable the endobiotic predation of bdellovibrio bacteriovorus ]]> https://biorxiv.org/content/10.1101/2022.06.13.496000v1?rss=1 View larger version (46K): org.highwire.dtl.DTLVardef@35da74org.highwire.dtl.DTLVardef@19923f1org.highwire.dtl.DTLVardef@106a616org.highwire.dtl.DTLVardef@181f2fb_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kaplan, M. Chang, Y.-W. Oikonomou, C. M. Nicolas, W. J. Jewett, A. I. Kreida, S. Dutka, P. Rettberg, L. A. Maggi, S. Jensen, G. J. 2022-06-13 doi:10.1101/2022.06.13.496000 Cold Spring Harbor Laboratory Press 2022-06-13 <![CDATA[ Nemacol is a Small Molecule Inhibitor of C. elegans Vesicular Acetylcholine Transporter with Anthelmintic Potential ]]> https://biorxiv.org/content/10.1101/2022.06.14.496146v1?rss=1 Harrington, S. Pyche, J. Burns, A. R. Spalholz, T. Baker, R. J. Ching, J. Lautens, M. Kulke, D. Deuther-Conrad, W. Brust, P. Roy, P. J. 2022-06-17 doi:10.1101/2022.06.14.496146 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Disrupting cellular memory to overcome drug resistance ]]> https://biorxiv.org/content/10.1101/2022.06.16.496161v1?rss=1 Harmange, G. Reyes Hueros, R. A. Schaff, D. L. Emert, B. L. Saint-Antoine, M. M. Nellore, S. Fane, M. E. Alicea, G. M. Weeraratna, A. T. Singh, A. Shaffer, S. M. 2022-06-17 doi:10.1101/2022.06.16.496161 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Spectral neural approximations for models of transcriptional dynamics ]]> https://biorxiv.org/content/10.1101/2022.06.16.496448v1?rss=1 Gorin, G. Carilli, M. T. Chari, T. Pachter, L. 2022-06-16 doi:10.1101/2022.06.16.496448 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa ]]> https://biorxiv.org/content/10.1101/2022.06.17.496478v1?rss=1 Poceviciute, R. Bogatyrev, S. R. Romano, A. E. Dilmore, A. H. Mondragon-Palomino, O. Takko, H. Ismagilov, R. F. 2022-06-19 doi:10.1101/2022.06.17.496478 Cold Spring Harbor Laboratory Press 2022-06-19 <![CDATA[ Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET ]]> https://biorxiv.org/content/10.1101/2022.06.21.496981v1?rss=1 Dutka, P. Metskas, L. A. Hurt, R. C. Salahshoor, H. Wang, T.-Y. Malounda, D. Lu, G. Chou, T.-F. Shapiro, M. G. Jensen, G. J. 2022-06-21 doi:10.1101/2022.06.21.496981 Cold Spring Harbor Laboratory Press 2022-06-21 <![CDATA[ Trajectories for the evolution of bacterial CO2-concentrating mechanisms ]]> https://biorxiv.org/content/10.1101/2022.06.21.497102v1?rss=1 Flamholz, A. I. Dugan, E. J. Panich, J. Desmarais, J. J. Oltrogge, L. M. Fischer, W. W. Singer, S. W. Savage, D. F. 2022-06-22 doi:10.1101/2022.06.21.497102 Cold Spring Harbor Laboratory Press 2022-06-22 <![CDATA[ Evolution of Carbon Isotope Fractionation in Cyanobacteria ]]> https://biorxiv.org/content/10.1101/2022.06.22.497258v1?rss=1 >1 Ga. This strain, nicknamed ANC, grows in ambient pCO2 and displays larger {varepsilon}p values than WT, despite having a much smaller {varepsilon}Rubisco (17.23 {+/-} 0.61{per thousand} vs. 25.18 {+/-} 0.31{per thousand} respectively). Measuring both enzymatic and biomass fractionation revealed a surprising result--ANC {varepsilon}p exceeded ANC {varepsilon}Rubisco in all conditions tested, contradicting prevailing models of cyanobacterial carbon isotope fractionation. However, these models were corrected by accounting for cyanobacterial physiology, notably the CO2 concentrating mechanism (CCM). Our model suggested that additional fractionating processes like powered inorganic carbon uptake systems contribute to {varepsilon}p, and this effect is exacerbated in ANC. Understanding the evolution of rubisco and the CCM is therefore critical for interpreting the carbon isotope record. Large fluctuations in that record may reflect the evolving efficiency of carbon fixing metabolisms in addition to changes in atmospheric CO2. Significance StatementEarth scientists rely on chemical fossils like the carbon isotope record to derive ancient atmospheric CO2 concentrations, but interpretation of this record is calibrated using modern organisms. We tested this assumption by measuring the carbon isotope fractionation of a reconstructed ancestral rubisco enzyme (>1 billion years old) in vivo and in vitro. Our results contradicted prevailing models of carbon flow in Cyanobacteria, but our data could be rationalized if light-driven uptake of CO2 is taken into account. Our study showed that the carbon isotope record tracks both the evolution of photosynthesis physiology as well as changes in atmospheric CO2, highlighting the value of considering both evolution and physiology for comparative biological approaches to understanding Earths history. ]]> Wang, R. Z. Nichols, R. J. Liu, A. K. Flamholz, A. I. Banda, D. M. Savage, D. F. Eiler, J. M. Shih, P. M. Fischer, W. W. 2022-06-23 doi:10.1101/2022.06.22.497258 Cold Spring Harbor Laboratory Press 2022-06-23 <![CDATA[ Identification of orphan ligand-receptor relationships using a cell-based CRISPRa enrichment screening platform. ]]> https://biorxiv.org/content/10.1101/2022.06.22.497261v1?rss=1 Siepe, D. H. Henneberg, L. T. Wilson, S. C. Hess, G. T. Bassik, M. C. Zinn, K. Garcia, K. C. 2022-06-23 doi:10.1101/2022.06.22.497261 Cold Spring Harbor Laboratory Press 2022-06-23 <![CDATA[ Geometric effects in gas vesicle buckling under ultrasound ]]> https://biorxiv.org/content/10.1101/2022.06.27.497663v1?rss=1 Salahshoor, H. Yao, Y. Dutka, P. Nystrom, N. N. Jin, Z. Min, E. Malounda, D. Jensen, G. J. Shapiro, M. G. 2022-06-29 doi:10.1101/2022.06.27.497663 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice ]]> https://biorxiv.org/content/10.1101/2022.06.27.497828v1?rss=1 Abdel-Haq, R. Schlachetzki, J. C. M. Boktor, J. C. Cantu-Jungles, T. M. Thron, T. Zhang, M. Bostick, J. W. Khazaei, T. Chilakala, S. Morais, L. H. Humphrey, G. Keshavarzian, A. Katz, J. E. Thomson, M. Knight, R. Gradinaru, V. Hamaker, B. R. Glass, C. K. Mazmanian, S. K. 2022-06-30 doi:10.1101/2022.06.27.497828 Cold Spring Harbor Laboratory Press 2022-06-30 <![CDATA[ Neutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes ]]> https://biorxiv.org/content/10.1101/2022.06.28.497989v1?rss=1 Fan, C. Cohen, A. A. Park, M. Hung, A. F.-H. Keeffe, J. R. Gnanapragasam, P. N. Lee, Y. E. Kakutani, L. M. Wu, Z. Malecek, K. E. Williams, J. C. Bjorkman, P. J. 2022-06-28 doi:10.1101/2022.06.28.497989 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease ]]> https://biorxiv.org/content/10.1101/2022.06.29.498132v1?rss=1 Ameen, M. Sundaram, L. Banerjee, A. Shen, M. Kundu, S. Nair, S. Shcherbina, A. Gu, M. Wilson, K. D. Varadarajan, A. Vadgama, N. Balsubramani, A. Wu, J. C. Engreitz, J. Farh, K. Karakikes, I. Wang, K. C. Quertermous, T. Greenleaf, W. Kundaje, A. 2022-06-29 doi:10.1101/2022.06.29.498132 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Competing constraints shape the non-equilibrium limits of cellular decision making ]]> https://biorxiv.org/content/10.1101/2022.07.01.498451v1?rss=1 Lammers, N. C. Flamholz, A. Garcia, H. G. 2022-07-03 doi:10.1101/2022.07.01.498451 Cold Spring Harbor Laboratory Press 2022-07-03 <![CDATA[ Evolutionary Diversification of Methanotrophic Ca. Methanophagales (ANME-1) and Their Expansive Virome ]]> https://biorxiv.org/content/10.1101/2022.07.04.498658v1?rss=1 Laso-Perez, R. Wu, F. Cremiere, A. Speth, D. R. Magyar, J. S. Krupovic, M. Orphan, V. J. 2022-07-04 doi:10.1101/2022.07.04.498658 Cold Spring Harbor Laboratory Press 2022-07-04 <![CDATA[ A synthetic protein-level neural network in mammalian cells ]]> https://biorxiv.org/content/10.1101/2022.07.10.499405v1?rss=1 Chen, Z. Linton, J. M. Zhu, R. Elowitz, M. 2022-07-11 doi:10.1101/2022.07.10.499405 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ Identification of a distinct ductal subpopulation with self-renewal and differentiation potential from the adult murine pancreas ]]> https://biorxiv.org/content/10.1101/2022.07.12.499653v1?rss=1 Tremblay, J. R. Ortiz, J. A. Quijano, J. C. Zook, H. LeBon, J. M. Li, W. Jou, K. Tsark, W. Mann, J. R. Kozlowski, M. Tirrell, D. A. Esni, F. Engle, D. D. Riggs, A. D. Ku, H. T. 2022-07-13 doi:10.1101/2022.07.12.499653 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Fate Bias and Transcriptional Memory of human B cells ]]> https://biorxiv.org/content/10.1101/2022.07.14.499766v1?rss=1 Swift, M. Horns, F. Quake, S. 2022-07-15 doi:10.1101/2022.07.14.499766 Cold Spring Harbor Laboratory Press 2022-07-15 <![CDATA[ Integrated multi-cohort analysis of the Parkinson's disease gut metagenome ]]> https://biorxiv.org/content/10.1101/2022.07.20.500694v1?rss=1 Boktor, J. C. Sharon, G. Verhagen Metman, L. A. Hall, D. A. Engen, P. A. Zreloff, Z. Hakim, D. J. Bostick, J. W. Ousey, J. Lange, D. Humphrey, G. Ackermann, G. Carlin, M. Knight, R. Keshavarzian, A. Mazmanian, S. K. 2022-07-21 doi:10.1101/2022.07.20.500694 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ Single-nucleus resolution mapping of the adult C. elegans and its application to elucidate inter- and trans-generational response to alcohol. ]]> https://biorxiv.org/content/10.1101/2022.07.21.500524v1?rss=1 Truong, L. CHEN, Y.-W. Barrere-Cain, R. Shuck, K. Xiao, W. Levenson, M. T. da Veiga Beltrame, E. Panter, B. Reich, E. Sternberg, P. W. Yang, X. Allard, P. 2022-07-22 doi:10.1101/2022.07.21.500524 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Symbiosis-driven development in an early branching metazoan ]]> https://biorxiv.org/content/10.1101/2022.07.21.500558v1?rss=1 Ohdera, A. H. Darymple, J. Avila-Magana, V. Sharp, V. Watson, K. McCauley, M. Steinworth, B. Diaz-Almeyda, E. M. Kitchen, S. A. Poole, A. Z. Bellantuono, A. J. Haridas, S. Grigoriev, I. V. Goentoro, L. Vallen, E. Baker, D. M. LaJeunesse, T. C. Loesgen, S. martindale, m. q. DeGennaro, M. Fitt, W. K. Medina, M. 2022-07-22 doi:10.1101/2022.07.21.500558 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Modulation of bacterial cell size and growth rate via activation of a cell envelope stress response ]]> https://biorxiv.org/content/10.1101/2022.07.26.501648v1?rss=1 Miguel, A. Zietek, M. Shi, H. Sueki, A. Maier, L. Verheul, J. den Blaauwen, T. Van Valen, D. A. Typas, A. Huang, K. C. 2022-07-27 doi:10.1101/2022.07.26.501648 Cold Spring Harbor Laboratory Press 2022-07-27 <![CDATA[ Antibody recognition of CD4-induced open HIV-1 Env trimers ]]> https://biorxiv.org/content/10.1101/2022.07.27.501785v1?rss=1 Yang, Z. Dam, K.-M. A. Gershoni, J. M. Zolla-Pazner, S. Bjorkman, P. J. 2022-07-28 doi:10.1101/2022.07.27.501785 Cold Spring Harbor Laboratory Press 2022-07-28 <![CDATA[ Mouse-embryo model derived exclusively from embryonic stem cells undergo neurulation and heart development ]]> https://biorxiv.org/content/10.1101/2022.08.01.502371v1?rss=1 Lau, K. Y. C. Rubinstein, H. Gantner, C. W. Amadei, G. Stelzer, Y. Zernicka-Goetz, M. 2022-08-02 doi:10.1101/2022.08.01.502371 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Stem cell-derived mouse embryos develop within an extra-embryonic yolk sac to form anterior brain regions and a beating heart ]]> https://biorxiv.org/content/10.1101/2022.08.01.502375v1?rss=1 Zernicka-Goetz, M. Amadei, G. Handford, C. E. De Jonghe, J. Hollfelder, F. Glover, D. 2022-08-02 doi:10.1101/2022.08.01.502375 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Optical O2 sensors also respond to redox active molecules commonly secreted by bacteria ]]> https://biorxiv.org/content/10.1101/2022.08.08.503264v1?rss=1 Flamholz, A. I. Saccomano, S. Cash, K. J. Newman, D. K. 2022-08-09 doi:10.1101/2022.08.08.503264 Cold Spring Harbor Laboratory Press 2022-08-09 <![CDATA[ Selective Serotonin Reuptake Inhibitors Within Cells: Temporal Resolution in Cytoplasm, Endoplasmic Reticulum, and Membrane ]]> https://biorxiv.org/content/10.1101/2022.08.09.502705v1?rss=1 2.4 h. They inhibit SERT transport-associated currents 6- or 11-fold less potently than the SSRIs (escitalopram or fluoxetine derivative, respectively), providing useful probes for distinguishing compartmentalized SSRI effects. Although our measurements are orders of magnitude faster than the "therapeutic lag" of SSRIs, these data suggest that SSRI-SERT interactions within organelles or membranes may play roles during either the therapeutic effects or the "antidepressant discontinuation syndrome". SIGNIFICANCE STATEMENTSelective serotonin reuptake inhibitors stabilize mood in several disorders. In general, these drugs bind to the serotonin (5-hydroxytryptamine) transporter (SERT), which clears serotonin from CNS and peripheral tissues. SERT ligands are effective and relatively safe; primary care practitioners often prescribe them. However, they have several side effects and require 2 to 6 weeks of continuous administration until they act effectively. How they work remains perplexing, contrasting with earlier assumptions that the therapeutic mechanism involves SERT inhibition followed by increased extracellular serotonin levels. This study establishes that two SERT ligands, fluoxetine and escitalopram, enter neurons within minutes, while simultaneously accumulating in many membranes. Such knowledge will motivate future research, hopefully revealing where and how SERT ligands "engage" their therapeutic target(s). ]]> Nichols, A. L. Blumenfeld, Z. Luebbert, L. Knox, H. J. Muthusamy, A. K. Marvin, J. S. Kim, C. H. Grant, S. N. Walton, D. P. Cohen, B. N. Hammar, R. Looger, L. L. Artursson, P. Dougherty, D. A. Lester, H. A. 2022-08-12 doi:10.1101/2022.08.09.502705 Cold Spring Harbor Laboratory Press 2022-08-12 <![CDATA[ Remote sensing-based forest modeling reveals positive effects of functional diversity on productivity at local spatial scale ]]> https://biorxiv.org/content/10.1101/2022.08.11.503677v1?rss=1 Schneider, F. D. Longo, M. Paul-Limoges, E. Scholl, V. M. Schmid, B. Morsdorf, F. Pavlick, R. P. Schimel, D. S. Schaepman, M. E. Moorcroft, P. R. 2022-08-15 doi:10.1101/2022.08.11.503677 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Pervasive SUMOylation of heterochromatin and piRNA pathway proteins ]]> https://biorxiv.org/content/10.1101/2022.08.15.504007v1?rss=1 Ninova, M. Lomenick, B. Fejes-Toth, K. Aravin, A. A. 2022-08-15 doi:10.1101/2022.08.15.504007 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Combinatorial expression motifs in signaling pathways ]]> https://biorxiv.org/content/10.1101/2022.08.21.504714v1?rss=1 Granados, A. A. Kanrar, N. Elowitz, M. B. 2022-08-22 doi:10.1101/2022.08.21.504714 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ Structural remodeling of Coxiella burnetii during its biphasic developmental cycle revealedby cryo-electron tomography ]]> https://biorxiv.org/content/10.1101/2022.08.23.505044v1?rss=1 Kaplan, M. Shepherd, D. C. Vankadari, N. Kim, K. W. Larson, C. L. Dutka, P. Beare, P. A. Krzymowski, E. Heinzen, R. A. Jensen, G. J. Ghosal, D. 2022-08-24 doi:10.1101/2022.08.23.505044 Cold Spring Harbor Laboratory Press 2022-08-24 <![CDATA[ Timeline of changes in spike conformational dynamics in emergent SARS-CoV-2 variants reveal progressive stabilization of trimer stalk and enhanced NTD dynamics ]]> https://biorxiv.org/content/10.1101/2022.08.26.505369v1?rss=1 Braet, S. M. Buckley, T. S. Venkatakrishnan, V. Dam, K.-M. A. Bjorkman, P. J. Anand, G. S. 2022-08-29 doi:10.1101/2022.08.26.505369 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ S1 represents multisensory contexts and somatotopic locations within and outside the bounds of the cortical homunculus ]]> https://biorxiv.org/content/10.1101/2022.08.29.505313v1?rss=1 Rosenthal, I. A. Bashford, L. Kellis, S. Pejsa, K. Lee, B. Liu, C. Andersen, R. A. 2022-08-31 doi:10.1101/2022.08.29.505313 Cold Spring Harbor Laboratory Press 2022-08-31 <![CDATA[ CRISPR Mediated Transactivation in the Human Disease Vector Aedes aegypti ]]> https://biorxiv.org/content/10.1101/2022.08.31.505972v1?rss=1 Bui, M. Benetta, E. D. Dong, Y. Zhao, Y. Yang, T. Li, M. Antoshechkin, I. A. Buchman, A. Bottino-Rojas, V. James, A. A. Perry, M. W. Dimopoulos, G. Akbari, O. 2022-09-02 doi:10.1101/2022.08.31.505972 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ PEZO-1 and TRP-4 mechanosensors are involved in mating behavior in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2022.08.31.506045v1?rss=1 Brugman, K. I. Susoy, V. Whittaker, A. J. Palma, W. Nava, S. Samuel, A. D. Sternberg, P. W. 2022-09-01 doi:10.1101/2022.08.31.506045 Cold Spring Harbor Laboratory Press 2022-09-01 <![CDATA[ A model-free Data-Driven paradigm for in situ patient-specific prediction of human brain response to ultrasound stimulation ]]> https://biorxiv.org/content/10.1101/2022.09.01.506248v1?rss=1 Salahshoor, H. Ortiz, M. 2022-09-03 doi:10.1101/2022.09.01.506248 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Random and natural non-coding RNA have similar structural motif patterns but can be distinguished by bulge, loop, and bond counts ]]> https://biorxiv.org/content/10.1101/2022.09.01.506257v1?rss=1 Ghaddar, F. Dingle, K. 2022-09-03 doi:10.1101/2022.09.01.506257 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ A cryogenic, coincident fluorescence, electron and ion beam microscope ]]> https://biorxiv.org/content/10.1101/2022.09.02.506334v1?rss=1 Boltje, D. Hoogenboom, J. Jakobi, A. J. Jensen, G. J. Jonker, C. Kaag, M. Koster, A. J. Last, M. de Agrela Pinto, C. Plitzko, J. M. Raunser, S. Tacke, S. Wang, Z. van der Wee, E. Wepf, R. den Hoedt, S. 2022-09-03 doi:10.1101/2022.09.02.506334 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Cognition through internal models: Mirror neurons as one manifestation of a broader mechanism ]]> https://biorxiv.org/content/10.1101/2022.09.06.506071v1?rss=1 Aflalo, T. Chivukula, S. Zhang, C. Rosario, E. R. Pouratian, N. Andersen, R. A. 2022-09-08 doi:10.1101/2022.09.06.506071 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ An extracellular vesicle targeting ligand that binds to Arc proteins and facilitates Arc transport in vivo ]]> https://biorxiv.org/content/10.1101/2022.09.06.506798v1?rss=1 Lee, P. H. Anaya, M. Ladinsky, M. S. Reitsma, J. Zinn, K. 2022-09-08 doi:10.1101/2022.09.06.506798 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Robust control of replication initiation in the absence of DnaA-ATP {leftrightharpoons} DnaA-ADP regulatory elements in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2022.09.08.507175v1?rss=1 Boesen, T. Charbon, G. Fu, H. Jensen, C. Li, D. Jun, S. Lobner-Olesen, A. 2022-09-08 doi:10.1101/2022.09.08.507175 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Bacterial Argonaute nucleases reveal different modes of DNA targeting in vitro and in vivo ]]> https://biorxiv.org/content/10.1101/2022.09.09.507302v1?rss=1 Lisitskaya, L. Kropocheva, E. Agapov, A. Prostova, M. Panteleev, V. Yudin, D. Ryazansky, S. Kuzmenko, A. Aravin, A. Esyunina, D. Kulbachiskiy, A. 2022-09-09 doi:10.1101/2022.09.09.507302 Cold Spring Harbor Laboratory Press 2022-09-09 <![CDATA[ Quantum Biology in Cellular Migration ]]> https://biorxiv.org/content/10.1101/2022.09.09.507322v1?rss=1 Vecheck, A. McNamee, C. Reijo Pera, R. A. Usselman, R. 2022-09-14 doi:10.1101/2022.09.09.507322 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ Drosophila Males Use 5'-to-3' Phased Biogenesis to Make Stellate-silencing piRNAs that Lack Homology to Maternally Deposited piRNA Guides ]]> https://biorxiv.org/content/10.1101/2022.09.12.507655v1?rss=1 Venkei, Z. G. Gainetdinov, I. Starostik, M. Choi, C. Chen, P. Balsara, C. Whitfield, T. Bell, G. W. Feng, S. Jacobsen, S. E. Aravin, A. Kim, J. K. Zamore, P. Yamashita, Y. M. 2022-09-13 doi:10.1101/2022.09.12.507655 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Bacterial Argonaute proteins aid cell division in the presence of topoisomerase inhibitors in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2022.09.13.507849v1?rss=1 Olina, A. Agapov, A. Yudin, D. Kuzmenko, A. Aravin, A. A. Kulbachiskiy, A. 2022-09-13 doi:10.1101/2022.09.13.507849 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ MTCH2 is a mitochondrial outer membrane protein insertase ]]> https://biorxiv.org/content/10.1101/2022.09.15.508165v1?rss=1 Guna, A. Stevens, T. A. Inglis, A. J. Replogle, J. M. Esantsi, T. K. Muthukumar, G. Shaffer, K. C. L. Wang, M. L. Pogson, A. N. Jones, J. J. Lomenick, B. Chou, T.-F. Weissman, J. S. Voorhees, R. M. 2022-09-16 doi:10.1101/2022.09.15.508165 Cold Spring Harbor Laboratory Press 2022-09-16 <![CDATA[ Electrochemical disruption of extracellular electron transfer inhibits Pseudomonas aeruginosa cell survival within biofilms and is synergistic with antibiotic treatment ]]> https://biorxiv.org/content/10.1101/2022.09.15.508205v1?rss=1 Jimenez Otero, F. Newman, D. K. Tender, L. M. 2022-09-19 doi:10.1101/2022.09.15.508205 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ HCR Lateral Flow Assays for Amplified Instrument-Free At-Home SARS-CoV-2 Testing ]]> https://biorxiv.org/content/10.1101/2022.09.18.508442v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@a04874org.highwire.dtl.DTLVardef@f4ba0borg.highwire.dtl.DTLVardef@e2445corg.highwire.dtl.DTLVardef@f63411_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Schulte, S. J. Huang, J. Pierce, N. A. 2022-09-19 doi:10.1101/2022.09.18.508442 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Evaluation of mouse behavioral responses to nutritive versus nonnutritive sugar using a deep learning-based 3D real-time pose estimation system ]]> https://biorxiv.org/content/10.1101/2022.09.19.508605v1?rss=1 Kim, J. Kim, D. Jung, W. Suh, G. S. B. 2022-09-19 doi:10.1101/2022.09.19.508605 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Predicting phenotype transition probabilities via conditional algorithmic probability approximations ]]> https://biorxiv.org/content/10.1101/2022.09.21.508902v1?rss=1 Dingle, K. Novev, J. K. Ahnert, S. E. Louis, A. A. 2022-09-22 doi:10.1101/2022.09.21.508902 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ The Phosphate Deprivation Response is Mediated by an Interaction between Brassinosteroid Signaling and Zinc in Tomato ]]> https://biorxiv.org/content/10.1101/2022.09.21.508943v1?rss=1 Demirer, G. S. Gibson, D. J. Yue, X. Pan, K. Elishav, E. Khandal, H. Horev, G. Tarkowska, D. Canto-Pastor, A. Kong, S. Maloof, J. Savaldi-Goldstein, S. Brady, S. 2022-09-22 doi:10.1101/2022.09.21.508943 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Cryo-EM structure of the Agrobacterium tumefaciens type IV secretion system-associated T-pilus reveals stoichiometric protein-phospholipid assembly ]]> https://biorxiv.org/content/10.1101/2022.09.25.509369v1?rss=1 Kreida, S. Narita, A. Johnson, M. D. Tocheva, E. I. Das, A. Ghosal, D. Jensen, G. J. 2022-09-25 doi:10.1101/2022.09.25.509369 Cold Spring Harbor Laboratory Press 2022-09-25 <![CDATA[ Value-Based Neural Representations Predict Social Decision Preferences ]]> https://biorxiv.org/content/10.1101/2022.09.28.509596v1?rss=1 Guassi Moreira, J. F. Mendez Leal, A. S. Waizman, Y. H. Tashjian, S. M. Galvan, A. Silvers, J. A. 2022-09-30 doi:10.1101/2022.09.28.509596 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Photoacoustic imaging reveals transient decrease of oxygenation in murine blood due to monoclonal IgG4 antibody ]]> https://biorxiv.org/content/10.1101/2022.09.29.509334v1?rss=1 Khadria, A. Paavola, C. D. Maslov, K. Brown-Augsburger, P. L. Grealish, P. F. Lozano, E. Blankenship, R. L. Cao, R. Shi, J. Beals, J. M. Oladipupo, S. S. Wang, L. V. 2022-10-03 doi:10.1101/2022.09.29.509334 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ Digital nanoreactors for control over absolute stoichiometry and spatiotemporal behavior of receptors within lipid bilayers ]]> https://biorxiv.org/content/10.1101/2022.10.04.509789v1?rss=1 Maingi, V. Zhang, Z. Thachuk, C. Sarraf, N. Chapman, E. R. Rothemund, P. W. K. 2022-10-07 doi:10.1101/2022.10.04.509789 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Control of spatio-temporal patterning via cell density in a multicellular synthetic gene circuit ]]> https://biorxiv.org/content/10.1101/2022.10.04.510900v1?rss=1 Santorelli, M. Bhamidipati, P. S. Thomson, M. Morsut, L. 2022-10-05 doi:10.1101/2022.10.04.510900 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Characterization of Integrase and Excisionase Activity in Cell-free Protein Expression System Using a Modeling and Analysis Pipeline ]]> https://biorxiv.org/content/10.1101/2022.10.05.511053v1?rss=1 Pandey, A. Rodriguez, M. L. Poole, W. Murray, R. M. 2022-10-06 doi:10.1101/2022.10.05.511053 Cold Spring Harbor Laboratory Press 2022-10-06 <![CDATA[ Quantifying orthogonal barcodes for sequence census assays ]]> https://biorxiv.org/content/10.1101/2022.10.09.511501v1?rss=1 Booeshaghi, A. S. Min, K. H. Gehring, J. Pachter, L. 2022-10-10 doi:10.1101/2022.10.09.511501 Cold Spring Harbor Laboratory Press 2022-10-10 <![CDATA[ Border-associated macrophages mediate the neuroinflammatory response in an alpha-synuclein model of Parkinson disease ]]> https://biorxiv.org/content/10.1101/2022.10.12.511960v1?rss=1 Schonhoff, A. M. Figge, D. A. Jurkuvenaite, A. J. Gallups, N. J. Childers, G. M. Webster, J. A. Standaert, D. G. Goldman, J. E. Harms, A. S. 2022-10-16 doi:10.1101/2022.10.12.511960 Cold Spring Harbor Laboratory Press 2022-10-16 <![CDATA[ Transient and delay chemical master equations ]]> https://biorxiv.org/content/10.1101/2022.10.17.512599v1?rss=1 Gorin, G. Yoshida, S. R. Pachter, L. 2022-10-19 doi:10.1101/2022.10.17.512599 Cold Spring Harbor Laboratory Press 2022-10-19 <![CDATA[ MicroED structure of a protoglobin reactive carbene intermediate ]]> https://biorxiv.org/content/10.1101/2022.10.18.512604v1?rss=1 Danelius, E. Porter, N. Unge, J. Arnold, F. Gonen, T. 2022-10-18 doi:10.1101/2022.10.18.512604 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Sequencing and chromosome-scale assembly of the giant Pleurodeles waltl genome ]]> https://biorxiv.org/content/10.1101/2022.10.19.512763v1?rss=1 Brown, T. Elewa, A. Iarovenko, S. Subramanian, E. Joven Araus, A. Petzold, A. Suzuki, M. Suzuki, K.-i. Hayashi, T. Toyoda, A. Oliveira, C. Osipova, E. Leigh, N. Simon, A. Yun, M. 2022-10-20 doi:10.1101/2022.10.19.512763 Cold Spring Harbor Laboratory Press 2022-10-20 <![CDATA[ Differential Stability of Task Variable Representations in Retrosplenial Cortex ]]> https://biorxiv.org/content/10.1101/2022.10.19.512933v1?rss=1 Franco, L. M. Goard, M. J. 2022-10-21 doi:10.1101/2022.10.19.512933 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Genetic control of a sex-specific piRNA program ]]> https://biorxiv.org/content/10.1101/2022.10.25.513766v1?rss=1 Chen, P. Aravin, A. A. 2022-10-26 doi:10.1101/2022.10.25.513766 Cold Spring Harbor Laboratory Press 2022-10-26 <![CDATA[ Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions ]]> https://biorxiv.org/content/10.1101/2022.10.28.514297v1?rss=1 Chen, L. Zhang, Z. Han, Q. Rodrigues, L. Zboril, E. Adhikari, R. Li, X. Ko, S.-H. Xue, P. Smith, E. Xu, K. Wang, Q. Huang, T. H.-M. Chong, S. Liu, Z. 2022-10-30 doi:10.1101/2022.10.28.514297 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ Preservation of Conditioned Behavior Based on UV Light Sensitivity in Dissected Tail Halves of Planarians- a Proof by DNN ]]> https://biorxiv.org/content/10.1101/2022.10.30.514395v1?rss=1 Shimojo, K. Shimojo, E. Katsuragi, R. Akashi, T. Shimojo, S. 2022-11-01 doi:10.1101/2022.10.30.514395 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ A microwell platform for high-throughput longitudinal phenotyping and selective retrieval of organoids ]]> https://biorxiv.org/content/10.1101/2022.11.01.514733v1?rss=1 Sockell, A. Wong, W. Longwell, S. Vu, T. Karlsson, K. Mokhtari, D. A. Schaepe, J. Lo, Y.-H. Cornelius, V. Kuo, C. Van Valen, D. A. Curtis, C. Fordyce, P. M. 2022-11-02 doi:10.1101/2022.11.01.514733 Cold Spring Harbor Laboratory Press 2022-11-02 <![CDATA[ Decoding Motor Plans Using a Closed-Loop Ultrasonic Brain-Machine Interface ]]> https://biorxiv.org/content/10.1101/2022.11.10.515371v1?rss=1 Griggs, W. S. Norman, S. L. Deffieux, T. Segura, F. Osmanski, B.-F. Chau, G. Christopoulos, V. N. Liu, C. Tanter, M. Shapiro, M. G. Andersen, R. A. 2022-11-13 doi:10.1101/2022.11.10.515371 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ DNAJB6 Isoform Specific Knockdown: Therapeutic Potential for LGMDD1 ]]> https://biorxiv.org/content/10.1101/2022.11.17.516920v1?rss=1 Findlay, A. R. Paing, M. M. Daw, J. A. Bengoechea, R. Pittman, S. K. Li, S. Wang, F. Miller, T. M. True, H. L. Weihl, C. C. 2022-11-17 doi:10.1101/2022.11.17.516920 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Addressable and adaptable intercellular communication via DNA messaging ]]> https://biorxiv.org/content/10.1101/2022.11.17.516988v1?rss=1 Marken, J. P. Murray, R. M. 2022-11-18 doi:10.1101/2022.11.17.516988 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ Distinct super-enhancer elements differentially control Il2ra gene expression in a cell-type specific fashion ]]> https://biorxiv.org/content/10.1101/2022.11.18.516445v1?rss=1 Spolski, R. Li, P. Chandra, V. Shin, B. Liu, C. Oh, J. Ren, M. Enomoto, Y. West, E. E. Christensen, S. Wan, E. C. K. Ge, M. Lin, J.-X. Vijayanand, P. Rothenberg, E. V. Leonard, W. J. 2022-11-18 doi:10.1101/2022.11.18.516445 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ Runx factors launch T-cell and innate lymphoid programs via direct and gene network-based mechanisms ]]> https://biorxiv.org/content/10.1101/2022.11.18.517146v1?rss=1 Shin, B. Zhou, W. Wang, J. Gao, F. Rothenberg, E. V. 2022-11-19 doi:10.1101/2022.11.18.517146 Cold Spring Harbor Laboratory Press 2022-11-19 <![CDATA[ Physiological adaptation of sulfate reducing bacteria in syntrophic partnership with anaerobic methanotrophic archaea ]]> https://biorxiv.org/content/10.1101/2022.11.23.517749v1?rss=1 Murali, R. Yu, H. Speth, D. Wu, F. Metcalfe, K. S. Cremiere, A. Laso-Perez, R. Malmstrom, R. Goudeau, D. Woyke, T. Hatzenpichler, R. Chadwick, G. Orphan, V. J. 2022-11-23 doi:10.1101/2022.11.23.517749 Cold Spring Harbor Laboratory Press 2022-11-23 <![CDATA[ A selectivity filter in the EMC limits protein mislocalization to the ER ]]> https://biorxiv.org/content/10.1101/2022.11.29.518402v1?rss=1 Pleiner, T. Hazu, M. Tomaleri, G. P. Nguyen, V. N. Januszyk, K. Voorhees, R. M. 2022-12-01 doi:10.1101/2022.11.29.518402 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Annotation-agnostic discovery of associations between novel gene isoforms and phenotypes ]]> https://biorxiv.org/content/10.1101/2022.12.02.518787v1?rss=1 Eldjarn Hjörleifsson, K. Pachter, L. Melsted, P. 2022-12-02 doi:10.1101/2022.12.02.518787 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ Accurate quantification of single-nucleus and single-cell RNA-seq transcripts ]]> https://biorxiv.org/content/10.1101/2022.12.02.518832v1?rss=1 Eldjarn Hjörleifsson, K. Sullivan, D. K. Holley, G. Melsted, P. Pachter, L. 2022-12-02 doi:10.1101/2022.12.02.518832 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ The role of a population of descending neurons in the optomotor response in flying Drosophila ]]> https://biorxiv.org/content/10.1101/2022.12.05.519224v1?rss=1 Palmer, E. H. Omoto, J. J. Dickinson, M. H. 2022-12-06 doi:10.1101/2022.12.05.519224 Cold Spring Harbor Laboratory Press 2022-12-06 <![CDATA[ The Role of 1-O-Acylceramide NP in Structural Organization and Permeability of the Stratum Corneum Lipid Matrix ]]> https://biorxiv.org/content/10.1101/2022.12.06.519381v1?rss=1 Yang, M. Y. Lee, E. O. Park, C. S. Nam, Y. S. 2022-12-10 doi:10.1101/2022.12.06.519381 Cold Spring Harbor Laboratory Press 2022-12-10 <![CDATA[ Characterizing habit learning in the human brain at the individual and group levels: a multi-modal MRI study ]]> https://biorxiv.org/content/10.1101/2022.12.12.520188v1?rss=1 Gera, R. Bar Or, M. Tavor, I. Roll, D. Cockburn, J. Barak, S. Tricomi, E. O'Doherty, J. P. Schonberg, T. 2022-12-13 doi:10.1101/2022.12.12.520188 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Cell-specific occupancy dynamics between the pioneer-like factor Opa/ZIC and Ocelliles/OTX regulate early head development in embryos ]]> https://biorxiv.org/content/10.1101/2022.12.15.519123v1?rss=1 Fenelon, K. Gao, F. Borad, P. Abbasi, S. Pachter, L. Koromila, T. 2022-12-16 doi:10.1101/2022.12.15.519123 Cold Spring Harbor Laboratory Press 2022-12-16 <![CDATA[ Towards Cloud-Native, Machine Learning Based Detection of Crop Disease with Imaging Spectroscopy ]]> https://biorxiv.org/content/10.1101/2022.12.15.520316v1?rss=1 Rubambiza, G. Romero Galvan, F. E. Pavlick, R. P. Weatherspoon, H. Gold, K. 2022-12-19 doi:10.1101/2022.12.15.520316 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Zn2+ potentiation of OTOP proton channels identifies structural elements of the gating apparatus ]]> https://biorxiv.org/content/10.1101/2022.12.15.520539v1?rss=1 Teng, B. Kaplan, J. Liang, Z. Goldschen-Ohm, M. P. Liman, E. 2022-12-18 doi:10.1101/2022.12.15.520539 Cold Spring Harbor Laboratory Press 2022-12-18 <![CDATA[ An auto-release mechanism for HMCES-DNA-protein crosslinks ]]> https://biorxiv.org/content/10.1101/2022.12.18.520715v1?rss=1 Donsbach, M. Dürauer, S. Nguyen, K. T. Grünert, F. Yaneva, D. Semlow, D. Stingele, J. 2022-12-19 doi:10.1101/2022.12.18.520715 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ ESCRT recruitment to mRNA-encoded SARS-CoV-2 spike induces virus-like particles and enhanced antibody responses ]]> https://biorxiv.org/content/10.1101/2022.12.26.521940v1?rss=1 10-fold against Omicron-based variants for three months post-boost. Thus, EABR technology enhances potency and breadth of vaccine-induced responses through antigen presentation on cell surfaces and eVLPs, enabling longer-lasting protection against SARS-CoV-2 and other viruses. ]]> Hoffmann, M. A. Yang, Z. Huey-Tubman, K. E. Cohen, A. A. Gnanapragasam, P. N. Nakatomi, L. M. Storm, K. N. Moon, W. J. Lin, P. J. Bjorkman, P. J. 2022-12-27 doi:10.1101/2022.12.26.521940 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Data-driven model of glycolysis identifies the role of allostery in maintaining ATP homeostasis ]]> https://biorxiv.org/content/10.1101/2022.12.28.522046v1?rss=1 Choe, M. Einav, T. Phillips, R. Titov, D. V. 2022-12-30 doi:10.1101/2022.12.28.522046 Cold Spring Harbor Laboratory Press 2022-12-30 <![CDATA[ 3D genome organization around nuclear speckles drives mRNA splicing efficiency ]]> https://biorxiv.org/content/10.1101/2023.01.04.522632v1?rss=1 Bhat, P. Chow, A. Emert, B. Ettlin, O. Quinodoz, S. A. Takei, Y. Huang, W. Blanco, M. R. Guttman, M. 2023-01-04 doi:10.1101/2023.01.04.522632 Cold Spring Harbor Laboratory Press 2023-01-04 <![CDATA[ Cytokinins regulate spatially-specific ethylene production to control root growth in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2023.01.07.522790v1?rss=1 Yamoune, A. Zdarska, M. Depaepe, T. Korytarova, A. Skalak, J. Berendzen, K. W. Mira-Rodado, V. Tarr, P. Spackova, E. Badurova, L. Parizkova, B. Franczyk, A. Kovacova, I. Pernisova, M. Novak, O. Meyerowitz, E. M. Harter, K. Van Der Straeten, D. Hejatko, J. 2023-01-08 doi:10.1101/2023.01.07.522790 Cold Spring Harbor Laboratory Press 2023-01-08 <![CDATA[ Early life experience with natural odors modifies olfactory behavior through an associative process ]]> https://biorxiv.org/content/10.1101/2023.01.08.523155v1?rss=1 Dylla, K. V. O'Connell, T. F. Hong, E. J. 2023-01-08 doi:10.1101/2023.01.08.523155 Cold Spring Harbor Laboratory Press 2023-01-08 <![CDATA[ APPRAISE: Fast, accurate ranking of engineered proteins by receptor binding propensity using structural modeling ]]> https://biorxiv.org/content/10.1101/2023.01.11.523680v1?rss=1 Ding, X. Chen, X. Sullivan, E. E. Shay, T. F. Gradinaru, V. 2023-01-14 doi:10.1101/2023.01.11.523680 Cold Spring Harbor Laboratory Press 2023-01-14 <![CDATA[ Primate-conserved Carbonic Anhydrase IV and murine-restricted Ly6c1 are new targets for crossing the blood-brain barrier ]]> https://biorxiv.org/content/10.1101/2023.01.12.523632v1?rss=1 Shay, T. F. Sullivan, E. E. Ding, X. Chen, X. Kumar, S. R. Goertsen, D. Brown, D. Vielmetter, J. Borsos, M. Lam, A. W. Gradinaru, V. 2023-01-13 doi:10.1101/2023.01.12.523632 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Functional gene delivery to and across brain vasculature of systemic AAVs with endothelial-specific tropism in rodents and broad tropism in primates ]]> https://biorxiv.org/content/10.1101/2023.01.12.523844v1?rss=1 Chen, X. Wolfe, D. A. Sivadasan Bindu, D. Zhang, M. Taskin, N. Goertsen, D. Shay, T. F. Sullivan, E. Ravindra Kumar, S. Huang, S.-F. Arokiaraj, C. M. Plattner, V. Campos, L. J. Mich, J. K. Monet, D. Ngo, V. Ding, X. Omstead, V. Weed, N. Bishaw, Y. Gore, B. B. Lein, E. S. Akrami, A. Miller, C. Levi, B. P. Keller, A. Ting, J. T. Fox, A. S. Eroglu, C. Gradinaru, V. 2023-01-13 doi:10.1101/2023.01.12.523844 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Dysregulated mammalian estrus cycle rescued by timed activation of VIP neurons in the circadian pacemaker and late afternoon light exposure ]]> https://biorxiv.org/content/10.1101/2023.01.14.524075v1?rss=1 Kahan, A. Coughlin, G. M. Borsos, M. Brunton, B. W. Gradinaru, V. 2023-01-17 doi:10.1101/2023.01.14.524075 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ In situ architecture of Opa1-dependent mitochondrial cristae remodeling ]]> https://biorxiv.org/content/10.1101/2023.01.16.524176v1?rss=1 Fry, M. Y. Navarro, P. P. Qin, X. Inde, Z. Ananda, V. Y. Lugo, C. M. Hakim, P. Luce, B. E. Ge, Y. McDonald, J. L. Ali, I. Ha, L. L. Kleinstiver, B. P. Chan, D. C. Sarosiek, K. Chao, L. H. 2023-01-18 doi:10.1101/2023.01.16.524176 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids ]]> https://biorxiv.org/content/10.1101/2023.01.16.524298v1?rss=1 Haloi, N. Huang, S. Nichols, A. Fine, E. J. Marotta, C. B. Dougherty, D. A. Lindahl, E. Howard, R. J. Mayo, S. L. Lester, H. A. 2023-01-19 doi:10.1101/2023.01.16.524298 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ The telegraph process is not a subordinator ]]> https://biorxiv.org/content/10.1101/2023.01.17.524309v1?rss=1 Gorin, G. Pachter, L. 2023-01-18 doi:10.1101/2023.01.17.524309 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens ]]> https://biorxiv.org/content/10.1101/2023.01.22.525086v1?rss=1 Guna, A. Page, K. R. Replogle, J. R. Esantsi, T. K. Wang, M. L. Weissman, J. S. Voorhees, R. M. 2023-01-22 doi:10.1101/2023.01.22.525086 Cold Spring Harbor Laboratory Press 2023-01-22 <![CDATA[ Network structure influences the strength of learned neural representations ]]> https://biorxiv.org/content/10.1101/2023.01.23.525254v1?rss=1 Kahn, A. E. Szymula, K. Bassett, D. S. Nyema, N. Haggerty, E. B. Aguirre, G. K. 2023-01-24 doi:10.1101/2023.01.23.525254 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ Neural substrates of parallel devaluation-sensitive and devaluation-insensitive Pavlovian learning in humans ]]> https://biorxiv.org/content/10.1101/2023.01.26.525637v1?rss=1 Pool, E. R. Pauli, W. M. Cross, L. O'Doherty, J. P. 2023-01-27 doi:10.1101/2023.01.26.525637 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Staphylococcal secreted cytotoxins are competition sensing signals for Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2023.01.29.526047v1?rss=1 Wang, G. Z. Warren, E. A. Haas, A. L. Pena, A. S. Kiedrowski, M. R. Lomenick, B. Chou, T.-F. Bomberger, J. M. Tirrell, D. A. Limoli, D. H. 2023-01-29 doi:10.1101/2023.01.29.526047 Cold Spring Harbor Laboratory Press 2023-01-29 <![CDATA[ Large-scale brain-wide neural recording in nonhuman primates ]]> https://biorxiv.org/content/10.1101/2023.02.01.526664v1?rss=1 Trautmann, E. M. Hesse, J. K. Stine, G. Xia, R. Shude Zhu, S. O'Shea, D. J. Karsh, B. Colonell, J. Lanfranchi, F. Vyas, S. Zimnik, A. Steinemann, N. A. Wagenaar, D. A. Andrei, A. Mora Lopez, C. OCallaghan, J. M. Putzeys, J. Raducanu, B. C. Welkenhuysen, M. Churchland, M. Moore, T. Shadlen, M. N. Shenoy, K. V. Tsao, D. Dutta, B. Harris, T. 2023-02-03 doi:10.1101/2023.02.01.526664 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Maternal hormones engage a dormant monomorphic aggression circuit, leading to the introduction of an innate behavior in adulthood in females ]]> https://biorxiv.org/content/10.1101/2023.02.02.526862v1?rss=1 Stagkourakis, S. Williams, P. Spigolon, G. Khanal, S. Ziegler, K. Heikkinen, L. Fisone, G. Broberger, C. 2023-02-03 doi:10.1101/2023.02.02.526862 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Mob4 is essential for spermatogenesis in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2023.02.05.527206v1?rss=1 Santos, I. B. Wainman, A. Maraver, J. G. Pires, V. Kovacs, L. Riparbelli, M. G. Callaini, G. Glover, D. M. Tavares, A. A. 2023-02-05 doi:10.1101/2023.02.05.527206 Cold Spring Harbor Laboratory Press 2023-02-05 <![CDATA[ POLCAM: Instant molecular orientation microscopy for the life sciences ]]> https://biorxiv.org/content/10.1101/2023.02.07.527479v1?rss=1 Bruggeman, E. Zhang, O. Needham, L.-M. Koerbel, M. Daly, S. Cheetham, M. Peters, R. Wu, T. Klymchenko, A. S. Davis, S. J. Paluch, E. K. Klenerman, D. Lew, M. D. O'Holleran, K. Lee, S. F. 2023-02-08 doi:10.1101/2023.02.07.527479 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ LINKIN-associated proteins necessary for tissue integrity during collective cell migration ]]> https://biorxiv.org/content/10.1101/2023.02.08.527750v1?rss=1 Tan, C.-H. Cheng, K.-W. Park, H. Chou, T.-F. Sternberg, P. W. 2023-02-09 doi:10.1101/2023.02.08.527750 Cold Spring Harbor Laboratory Press 2023-02-09 <![CDATA[ Restructuring of olfactory representations in the fly brain around odor relationships in natural sources ]]> https://biorxiv.org/content/10.1101/2023.02.15.528627v1?rss=1 Yang, J.-Y. O'Connell, T. F. Hsu, W.-M. M. Bauer, M. S. Dylla, K. V. Sharpee, T. O. Hong, E. J. 2023-02-15 doi:10.1101/2023.02.15.528627 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Pervasive, conserved secondary structure in highly charged protein regions ]]> https://biorxiv.org/content/10.1101/2023.02.15.528637v1?rss=1 40% charged residues), which are routinely presumed to be disordered. Using recent advances in structure prediction and experimental structures, we show that roughly 40% of these regions form well-structured helices. Features often used to predict disorder--high charge density, low hydrophobicity, low sequence complexity, and evolutionarily varying length--are also compatible with solvated, variable-length helices. We show that a simple composition classifier predicts the existence of structure far better than well-established heuristics based on charge and hydropathy. We show that helical structure is more prevalent than previously appreciated in highly charged regions of diverse proteomes and characterize the conservation of highly charged regions. Our results underscore the importance of integrating, rather than choosing between, structure- and disorder-based approaches. ]]> Triandafillou, C. G. Pan, R. W. Dinner, A. R. Drummond, D. A. 2023-02-15 doi:10.1101/2023.02.15.528637 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Dynamical states of self-organized waves in a giant single-celled organism feeding on light ]]> https://biorxiv.org/content/10.1101/2023.02.22.529174v1?rss=1 Afik, E. Liu, T. J. Meyerowitz, E. M. 2023-02-22 doi:10.1101/2023.02.22.529174 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ Multiviral Quartet Nanocages Elicit Broad Anti-Coronavirus Responses for Proactive Vaccinology ]]> https://biorxiv.org/content/10.1101/2023.02.24.529520v1?rss=1 Hills, R. A. Tan, T. K. Cohen, A. A. Keefe, J. R. Keeble, A. H. Gnanapragasam, P. N. Storm, K. N. Hill, M. L. Liu, S. Gilbert-Jaramillo, J. Afzal, M. Napier, A. James, W. S. Bjorkman, P. J. Townsend, A. R. Howarth, M. 2023-02-24 doi:10.1101/2023.02.24.529520 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ Label-free differential imaging of cellular components in mouse brain tissue by wide-band photoacoustic microscopy ]]> https://biorxiv.org/content/10.1101/2023.02.27.530195v1?rss=1 Liu, Y. Wong, T. T. Shi, J. He, Y. Nie, L. V. Wang, L. 2023-02-28 doi:10.1101/2023.02.27.530195 Cold Spring Harbor Laboratory Press 2023-02-28 <![CDATA[ A rapid, multiplex digital PCR assay for EGFR, KRAS, BRAF, ERBB2 variants and ALK, RET, ROS1, NTRK1 gene fusions in non-small cell lung cancer ]]> https://biorxiv.org/content/10.1101/2023.03.09.531949v1?rss=1 Leatham, B. McNall, K. Subramanian, H. K. Jacky, L. Alvarado, J. G. Yurk, D. Wang, M. Green, D. C. Tsongalis, G. J. Rajagopal, A. Schwartz, J. 2023-03-12 doi:10.1101/2023.03.09.531949 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ A nanobody-based strategy for rapid and scalable purification of native human protein complexes ]]> https://biorxiv.org/content/10.1101/2023.03.09.531980v1?rss=1 Stevens, T. A. Tomaleri, G. P. Hazu, M. Wei, S. Nguyen, V. N. DeKalb, C. Voorhees, R. M. Pleiner, T. 2023-03-10 doi:10.1101/2023.03.09.531980 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Connectome-constrained deep mechanistic networks predict neural responses across the fly visual system at single-neuron resolution ]]> https://biorxiv.org/content/10.1101/2023.03.11.532232v1?rss=1 Lappalainen, J. K. Tschopp, F. D. Prakhya, S. McGill, M. Nern, A. Shinomiya, K. Takemura, S.-y. Gruntman, E. Macke, J. H. Turaga, S. C. 2023-03-13 doi:10.1101/2023.03.11.532232 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ Self-regulating living material with temperature-dependent light absorption ]]> https://biorxiv.org/content/10.1101/2023.03.11.532239v1?rss=1 Xiong, L. L. Garrett, M. A. Kornfield, J. A. Shapiro, M. G. 2023-03-12 doi:10.1101/2023.03.11.532239 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Extracellular vesicle-localized miR-203 mediates neural crest-placode communication required for trigeminal ganglia formation ]]> https://biorxiv.org/content/10.1101/2023.03.14.532527v1?rss=1 Bernardi, Y. E. Sanchez-Vasquez, E. Piacentino, M. L. Urrutia, H. Rossi, I. Alcantara Saraiva, K. L. Pereira-Neves, A. Ramirez, M. I. Bronner, M. E. de Miguel, N. Strobl-Mazzulla, P. H. 2023-03-15 doi:10.1101/2023.03.14.532527 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Single-shot 3D photoacoustic tomography using a single-element detector for ultrafast imaging of hemodynamics ]]> https://biorxiv.org/content/10.1101/2023.03.14.532661v1?rss=1 Zhang, Y. Hu, P. Li, L. Cao, R. Khadria, A. Maslov, K. Tong, X. Zeng, Y. Jiang, L. Zhou, Q. Wang, L. 2023-03-15 doi:10.1101/2023.03.14.532661 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ A machine-readable specification for genomics assays ]]> https://biorxiv.org/content/10.1101/2023.03.17.533215v1?rss=1 Booeshaghi, A. S. Chen, X. Pachter, L. 2023-03-21 doi:10.1101/2023.03.17.533215 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Flexible parsing and preprocessing of technical sequences with splitcode ]]> https://biorxiv.org/content/10.1101/2023.03.20.533521v1?rss=1 Sullivan, D. K. Pachter, L. 2023-03-23 doi:10.1101/2023.03.20.533521 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Structure and Function of the Dot/Icm T4SS ]]> https://biorxiv.org/content/10.1101/2023.03.22.533729v1?rss=1 Dutka, P. Liu, Y. Maggi, S. Ghosal, D. Wang, J. Carter, S. D. Zhao, W. Vijayrajratnam, S. Vogel, J. P. Jensen, G. J. 2023-03-22 doi:10.1101/2023.03.22.533729 Cold Spring Harbor Laboratory Press 2023-03-22 <![CDATA[ Probing metabolism in an E. coli-based cell-free system reveals a trade-off between transcription and translation ]]> https://biorxiv.org/content/10.1101/2023.03.22.533877v1?rss=1 View larger version (16K): org.highwire.dtl.DTLVardef@d6ffd7org.highwire.dtl.DTLVardef@1368a05org.highwire.dtl.DTLVardef@19f5b31org.highwire.dtl.DTLVardef@11c14c0_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kapasiawala, M. Murray, R. M. 2023-03-23 doi:10.1101/2023.03.22.533877 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Flux exponent control predicts metabolic dynamics from network structure ]]> https://biorxiv.org/content/10.1101/2023.03.23.533708v1?rss=1 Xiao, F. Li, J. S. Doyle, J. C. 2023-03-25 doi:10.1101/2023.03.23.533708 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Tools and methods for high-throughput single-cell imaging with the mother machine ]]> https://biorxiv.org/content/10.1101/2023.03.27.534286v1?rss=1 Thiermann, R. Sandler, M. Ahir, G. Sauls, J. T. Schroeder, J. W. Brown, S. D. Le Treut, G. Si, F. Li, D. Wang, J. Jun, S. 2023-03-29 doi:10.1101/2023.03.27.534286 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ The structure of the teleost Immunoglobulin M core provides insights on polymeric antibody evolution, assembly, and function ]]> https://biorxiv.org/content/10.1101/2023.03.29.534771v1?rss=1 Lyu, M. Malyutin, A. Stadtmueller, B. 2023-04-01 doi:10.1101/2023.03.29.534771 Cold Spring Harbor Laboratory Press 2023-04-01 <![CDATA[ The ENCODE Uniform Analysis Pipelines ]]> https://biorxiv.org/content/10.1101/2023.04.04.535623v1?rss=1 Hitz, B. C. Lee, J.-W. Jolanki, O. Kagda, M. S. Graham, K. Sud, P. Gabdank, I. Strattan, J. S. Sloan, C. A. Dreszer, T. Rowe, L. D. Podduturi, N. R. Malladi, V. S. Chan, E. T. Davidson, J. M. Ho, M. Miyasato, S. Simison, M. Tanaka, F. Luo, Y. Whaling, I. Lin, K. Jou, J. Hong, E. L. Lee, B. T. Sandstrom, R. Rynes, E. Nelson, J. Nishida, A. Ingersoll, A. Buckley, M. Frerker, M. Kim, D. S. Boley, N. Trout, D. Dobin, A. Rahmanian, S. Wyman, D. Balderrama-Gutierrez, G. Reese, F. Durand, N. C. Dudchenko, O. Weisz, D. Rao, S. S. P. Blackburn, A. Gkountarou 2023-04-06 doi:10.1101/2023.04.04.535623 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Evolution of neuronal cell classes and types in the vertebrate retina ]]> https://biorxiv.org/content/10.1101/2023.04.07.536039v1?rss=1 80% of RGCs in the human retina, subserve high-acuity vision, and were believed to be primate-specific (Berson, 2008); in contrast, the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information. ]]> Hahn, J. Monavarfeshani, A. Qiao, M. Kao, A. Kölsch, Y. Kumar, A. Kunze, V. P. Rasys, A. M. Richardson, R. Baier, H. Lucas, R. J. Li, W. Meister, M. Trachtenberg, J. T. Yan, W. Peng, Y.-R. Sanes, J. Shekhar, K. 2023-04-08 doi:10.1101/2023.04.07.536039 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ Flexibility and sensitivity in gene regulation out of equilibrium ]]> https://biorxiv.org/content/10.1101/2023.04.11.536490v1?rss=1 Mahdavi, S. Salmon, G. L. Daghlian, P. Garcia, H. G. Phillips, R. 2023-04-13 doi:10.1101/2023.04.11.536490 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response ]]> https://biorxiv.org/content/10.1101/2023.04.19.537364v1?rss=1 Jiang, J. Chen, S. Tsou, T. McGinnis, C. S. Khazaei, T. Zhu, Q. Park, J. H. Strazhnik, I.-M. Hanna, J. Chow, E. D. Sivak, D. A. Gartner, Z. J. Thomson, M. 2023-04-21 doi:10.1101/2023.04.19.537364 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ Genomic analysis reveals the presence of emerging pathogenic Klebsiella lineages aboard the International Space Station. ]]> https://biorxiv.org/content/10.1101/2023.05.05.539530v1?rss=1 Miliotis, G. Singh, N. K. McDonagh, F. O'Connor, L. Tuohy, A. Morris, D. Venkateswaran, K. 2023-05-05 doi:10.1101/2023.05.05.539530 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ Direct androgen receptor regulation of sexually dimorphic gene expression in the mammalian kidney ]]> https://biorxiv.org/content/10.1101/2023.05.06.539585v1?rss=1 Xiong, L. Liu, J. Han, S. Y. Koppitch, K. Guo, J.-J. Rommelfanger, M. Gao, F. Hallgrimsdottir, I. B. Pachter, L. Kim, J. MacLean, A. L. McMahon, A. 2023-05-06 doi:10.1101/2023.05.06.539585 Cold Spring Harbor Laboratory Press 2023-05-06 <![CDATA[ High-resolution spatial multi-omics reveals cell-type specific nuclear compartments ]]> https://biorxiv.org/content/10.1101/2023.05.07.539762v1?rss=1 200kb), in a manner distinct from nuclear speckles. Further, our analysis revealed that cell-type specific facultative and constitutive heterochromatin compartments marked by H3K27me3 and H4K20me3 are enriched at specific genes and gene clusters, respectively, and shape radial chromosomal positioning and inter-chromosomal interactions in neurons and glial cells. Together, our results provide a single-cell high-resolution multi-omics view of subnuclear compartments, associated genomic loci, and their impacts on gene regulation, directly within complex tissues. ]]> Takei, Y. Yang, Y. White, J. Yun, J. Prasad, M. Ombelets, L. J. Schindler, S. Cai, L. 2023-05-09 doi:10.1101/2023.05.07.539762 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Jumbo phages are active against extensively-drug-resistant eyedrop-associated Pseudomonas aeruginosa infections. ]]> https://biorxiv.org/content/10.1101/2023.05.08.539869v1?rss=1 200kb in genome size) and non-jumbo phages that were active against these isolates, the former killing more efficiently. Jumbo phages effectively killed the 3 separate XDR P. aeruginosa isolates both on solid and liquid medium. Given the ongoing nature of the XDR P. aeruginosa eyedrop outbreak, the identification of phages active against them provides physicians with several novel potential alternatives for treatment. ]]> Cobian-Guemes, A. G. Ghatbale, P. Blanc, A. N. Morgan, C. J. Garcia, A. Leonard, J. Huang, L. Kovalick, G. Proost, M. Chiu, M. Kuo, P. Oh, J. Karthikeyan, S. Knight, R. Pogliano, J. Schooley, R. Pride, D. 2023-05-08 doi:10.1101/2023.05.08.539869 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Temporally organized representations of reward and risk in the human brain ]]> https://biorxiv.org/content/10.1101/2023.05.09.539916v1?rss=1 Man, V. Cockburn, J. Flouty, O. Gander, P. E. Sawada, M. Kovach, C. K. Kawasaki, H. Oya, H. Howard, M. A. O'Doherty, J. P. 2023-05-09 doi:10.1101/2023.05.09.539916 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ DeCOIL: Optimization of Degenerate Codon Libraries for Machine Learning-Assisted Protein Engineering ]]> https://biorxiv.org/content/10.1101/2023.05.11.540424v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@16ce726org.highwire.dtl.DTLVardef@bb8a2aorg.highwire.dtl.DTLVardef@6be56borg.highwire.dtl.DTLVardef@1a2efb6_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yang, J. Ducharme, J. Johnston, K. E. Li, F.-Z. Yue, Y. Arnold, F. H. 2023-05-11 doi:10.1101/2023.05.11.540424 Cold Spring Harbor Laboratory Press 2023-05-11 <![CDATA[ The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity ]]> https://biorxiv.org/content/10.1101/2023.05.15.540865v1?rss=1 Reese, F. Williams, B. Balderrama-Gutierrez, G. Wyman, D. Celik, M. H. Rebboah, E. Rezaie, N. Trout, D. Razavi-Mohseni, M. Jiang, Y. Borsari, B. Morabito, S. Liang, H. Y. McGill, C. J. Rahmanian, S. Sakr, J. Jiang, S. Zeng, W. Carvalho, K. Weimer, A. K. Dionne, L. A. McShane, A. Bedi, K. Elhajjajy, S. I. Upchurch, S. Jou, J. Youngworth, I. Gabdank, I. Sud, P. Jolanki, O. Strattan, J. S. Kagda, M. S. Snyder, M. P. Hitz, B. C. Moore, J. E. Weng, Z. Bennett, D. Reinholdt, L. Ljungman, M. Beer, M. A. Gerstein, M. B. Pachter, L. Guigo, R. Wold, B. J. Mort 2023-05-16 doi:10.1101/2023.05.15.540865 Cold Spring Harbor Laboratory Press 2023-05-16 <![CDATA[ Practice makes imperfect: stronger implicit interference with practice in individuals at high risk of developing Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2023.05.16.541059v1?rss=1 Hung, S.-M. Adams, S. W. Molloy, C. Wu, D.-A. Shimojo, S. Arakaki, X. 2023-05-17 doi:10.1101/2023.05.16.541059 Cold Spring Harbor Laboratory Press 2023-05-17 <![CDATA[ Recovery of a learned behavior despite partial restoration of neuronal dynamics after chronic inactivation of inhibitory neurons ]]> https://biorxiv.org/content/10.1101/2023.05.17.541057v1?rss=1 Torok, Z. Luebbert, L. Feldman, J. Duffy, A. Nevue, A. Wongso, S. Mello, C. Fairhall, A. Pachter, L. Gonzalez, W. Lois, C. 2023-05-18 doi:10.1101/2023.05.17.541057 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Studying stochastic systems biology of the cell with single-cell genomics data ]]> https://biorxiv.org/content/10.1101/2023.05.17.541250v1?rss=1 Gorin, G. Vastola, J. J. Pachter, L. 2023-05-18 doi:10.1101/2023.05.17.541250 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Neural representations of economic decision variables in human posterior parietal cortex ]]> https://biorxiv.org/content/10.1101/2023.05.18.541297v1?rss=1 Klaes, C. Pilacinski, A. Kellis, S. Aflalo, T. Liu, C. Andersen, R. 2023-05-18 doi:10.1101/2023.05.18.541297 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Periodic hypothalamic attractor-like dynamics during the estrus cycle ]]> https://biorxiv.org/content/10.1101/2023.05.22.541741v1?rss=1 Liu, M. Nair, A. Linderman, S. W. Anderson, D. J. 2023-05-22 doi:10.1101/2023.05.22.541741 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Identification of Biochemical Pathways Responsible for Distinct Phenotypes Using Gene Ontology Causal Activity Models ]]> https://biorxiv.org/content/10.1101/2023.05.22.541760v1?rss=1 Hill, D. Drabkin, H. J. Smith, C. L. Van Auken, K. D'Eustachio, P. 2023-05-24 doi:10.1101/2023.05.22.541760 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Effects of focused ultrasound in a "clean" mouse model of ultrasonic neuromodulation ]]> https://biorxiv.org/content/10.1101/2023.05.22.541780v1?rss=1 Guo, H. Salahshoor, H. Wu, D. Yoo, S. Sato, T. Tsao, D. Shapiro, M. 2023-05-24 doi:10.1101/2023.05.22.541780 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Fgf10 mutant newts can regenerate normal limbs despite severe developmental hindlimb defects ]]> https://biorxiv.org/content/10.1101/2023.05.23.541496v1?rss=1 Suzuki, M. Okumrura, A. Shibata, Y. Endo, T. Teramoto, M. Chihara, A. Agata, K. Bronner, M. E. Suzuki, K.-i. T. 2023-05-24 doi:10.1101/2023.05.23.541496 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Dual-system avoidance: extension of a theory ]]> https://biorxiv.org/content/10.1101/2023.05.24.542134v1?rss=1 Perez, O. D. Dickinson, A. 2023-05-25 doi:10.1101/2023.05.24.542134 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Projectome-defined subtypes and modular intra-hypothalamic subnetworks of peptidergic neurons ]]> https://biorxiv.org/content/10.1101/2023.05.25.542241v1?rss=1 Jiao, Z. Gao, T. Wang, X. Zhang, W. Biglari, N. Boxer, E. E. Steuernagel, L. Ding, X. Yu, Z. Li, M. Hao, M. Zhou, H. Cao, X. Li, S. Jiang, T. Qi, J. Jia, X. Feng, Z. Ren, B. Chen, Y. Shi, X. Wang, D. Wang, X. Han, L. Liang, Y. Wang, C. Li, E. Hu, Y. Tao, Z. Li, H. Xiang, Y. Xu, M. Chang, H.-C. Zhang, Y. Xu, H.-t. Yan, J. Li, A. Luo, Q. Stoop, R. Sternson, S. Bruning, J. C. Poo, M.-m. Anderson, D. J. Gong, H. Sun, Y. Xu, X.-H. 2023-05-25 doi:10.1101/2023.05.25.542241 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Stoichiometric expression of messenger polycistrons by eukaryotic ribosomes (SEMPER) for compact, ratio-tunable multi-gene expression from single mRNAs ]]> https://biorxiv.org/content/10.1101/2023.05.26.541240v1?rss=1 Duan, M. Dev, I. Lu, A. You, M. Y. Shapiro, M. G. 2023-05-26 doi:10.1101/2023.05.26.541240 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ The genomic and cellular basis of biosynthetic innovation in rove beetles ]]> https://biorxiv.org/content/10.1101/2023.05.29.542378v1?rss=1 66,000 described species, rove beetles (Staphylinidae) comprise the largest metazoan family. Their exceptional radiation has been coupled to pervasive biosynthetic innovation whereby numerous lineages bear defensive glands with diverse chemistries. Here, we combine comparative genomic and single-cell transcriptomic data from across the largest rove beetle clade, Aleocharinae. We retrace the functional evolution of two novel secretory cell types that together comprise the tergal gland--a putative catalyst behind Aleocharinaes megadiversity. We identify key genomic contingencies that were critical to the assembly of each cell type and their organ-level partnership in manufacturing the beetles defensive secretion. This process hinged on evolving a mechanism for regulated production of noxious benzoquinones that appears convergent with plant toxin release systems, and synthesis of an effective benzoquinone solvent that weaponized the total secretion. We show that this cooperative biosynthetic system arose at the Jurassic-Cretaceous boundary, and that following its establishment, both cell types underwent [~]150 million years of stasis, their chemistry and core molecular architecture maintained almost clade-wide as Aleocharinae radiated globally into tens of thousands of lineages. Despite this deep conservation, we show that the two cell types have acted as substrates for the emergence of adaptive, biochemical novelties--most dramatically in symbiotic lineages that have infiltrated social insect colonies and produce host behavior-manipulating secretions. Our findings uncover genomic and cell type evolutionary processes underlying the origin, functional conservation and evolvability of a chemical innovation in beetles. ]]> Kitchen, S. A. Naragon, T. H. Bruckner, A. Ladinsky, M. S. Quinodoz, S. A. Badroos, J. M. Viliunas, J. W. Wagner, J. M. Miller, D. R. Yousefelahiyeh, M. Antoshechkin, I. A. Eldredge, K. T. Pirro, S. Guttman, M. Davis, S. R. Aardema, M. L. Parker, J. 2023-05-30 doi:10.1101/2023.05.29.542378 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ Tuning methylation-dependent silencing dynamics by synthetic modulation of CpG density ]]> https://biorxiv.org/content/10.1101/2023.05.30.542205v1?rss=1 Ma, Y. Budde, M. W. Zhu, J. Elowitz, M. 2023-06-01 doi:10.1101/2023.05.30.542205 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Single-cell type analysis of wing premotor circuits in the ventral nerve cord of Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2023.05.31.542897v1?rss=1 Ehrhardt, E. Whitehead, S. C. Namiki, S. Minegishi, R. Siwanowicz, I. Feng, K. Otsuna, H. FlyLight Project Team, Meissner, G. W. Stern, D. Truman, J. Shepherd, D. Dickinson, M. H. Dickson, B. J. Cohen, I. Card, G. M. Korff, W. 2023-06-01 doi:10.1101/2023.05.31.542897 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ The Genetic Architecture of Dietary Iron Overload and Associated Pathology in Mice ]]> https://biorxiv.org/content/10.1101/2023.06.05.543764v1?rss=1 5 fold across the strains, with genetic variation explaining up to 74% of the variation in liver iron. Pathologies included copper deficiency, anemia, and fatty liver, with liver triglycerides varying over 50 fold among the strains. Genetic mapping and network modeling identified significant genetic loci and pathways underlying the response to diet. ]]> Fuqua, B. K. Moses, L. McLachlan, S. Pan, C. Davis, R. C. Hui, S. T. Che, N. Zhou, Z. Ng, C. Charugundla, S. Blencowe, M. Saleem, Z. Miikeda, A. Ozdemir, B. Hui, C. Li, T. Stolin, C. L. Kozuch, M. Zhou, J. Page, K. Irimagawa, H. Ku, N. Taraszka, K. LaPierre, N. Killilea, D. W. Frazer, D. M. Yang, X. Eskin, E. Vulpe, C. D. Lusis, A. J. 2023-06-07 doi:10.1101/2023.06.05.543764 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress ]]> https://biorxiv.org/content/10.1101/2023.06.05.543769v1?rss=1 Wolin, E. Guo, J. K. Blanco, M. R. Perez, A. A. Goronzy, I. N. Abdou, A. A. Gorhe, D. Guttman, M. Jovanovic, M. 2023-06-07 doi:10.1101/2023.06.05.543769 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ Lineage motifs: developmental modules for control of cell type proportions ]]> https://biorxiv.org/content/10.1101/2023.06.06.543925v1?rss=1 Tran, M. Askary, A. Elowitz, M. 2023-06-07 doi:10.1101/2023.06.06.543925 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ Cell type-specific contributions to a persistent aggressive internal state in female Drosophila ]]> https://biorxiv.org/content/10.1101/2023.06.07.543722v1?rss=1 Chiu, H. Robie, A. A. Branson, K. M. Vippa, T. Epstein, S. Rubin, G. M. Anderson, D. J. Schretter, C. E. 2023-06-07 doi:10.1101/2023.06.07.543722 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ Development of cell-free transcription-translation systems in three soil Pseudomonads ]]> https://biorxiv.org/content/10.1101/2023.06.09.544292v1?rss=1 Meyerowitz, J. T. Larsson, E. M. Murray, R. M. 2023-06-09 doi:10.1101/2023.06.09.544292 Cold Spring Harbor Laboratory Press 2023-06-09 <![CDATA[ Functional glycoproteomics by integrated network assembly and partitioning ]]> https://biorxiv.org/content/10.1101/2023.06.13.541482v1?rss=1 Griffin, M. E. Thompson, J. W. Xiao, Y. Sweredoski, M. J. Jensen, E. H. Koldobskaya, Y. Schacht, A. L. Kim, T. D. Choudhry, P. Lomenick, B. Garbis, S. D. Moradian, A. Hsieh-Wilson, L. C. 2023-06-14 doi:10.1101/2023.06.13.541482 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ The representation of colored objects in macaque color patches ]]> https://biorxiv.org/content/10.1101/205104v1?rss=1 Chang, L. Bao, P. Tsao, D. 2017-10-19 doi:10.1101/205104 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ Distinct glycosaminoglycan chain length and sulfation patterns required for cellular uptake of Tau, Aβ, and α-Synuclein ]]> https://biorxiv.org/content/10.1101/207035v1?rss=1 Stopschinski, B. E. Holmes, B. B. Miller, G. M. Vaquer-Alicea, J. Hsieh-Wilson, L. C. Diamond, M. I. 2017-10-21 doi:10.1101/207035 Cold Spring Harbor Laboratory Press 2017-10-21 <![CDATA[ How Cognitive and Reactive Fear Circuits Optimize Escape Decisions in Humans ]]> https://biorxiv.org/content/10.1101/207936v1?rss=1 Qi, S. Sun, J. Guo, F. Daw, N. Hassabis, D. Mobbs, D. 2017-10-23 doi:10.1101/207936 Cold Spring Harbor Laboratory Press 2017-10-23 <![CDATA[ Metabolic Interactions Between Dynamic Bacterial Subpopulations ]]> https://biorxiv.org/content/10.1101/208686v1?rss=1 Rosenthal, A. Z. Qi, Y. Hormoz, S. Park, J. Li, S. H.-J. Elowitz, M. 2017-10-25 doi:10.1101/208686 Cold Spring Harbor Laboratory Press 2017-10-25 <![CDATA[ The self-organization of plant microtubules in three dimensions enables stable cortical localization and sensitivity to external cues ]]> https://biorxiv.org/content/10.1101/210138v1?rss=1 Mirabet, V. Krupinski, P. Hamant, O. Meyerowitz, E. Jonsson, H. Boudaoud, A. 2017-10-27 doi:10.1101/210138 Cold Spring Harbor Laboratory Press 2017-10-27 <![CDATA[ Summarizing Performance for Genome Scale Measurement of miRNA: Reference Samples and Metrics ]]> https://biorxiv.org/content/10.1101/210310v1?rss=1 Pine, P. S. Lund, S. P. Parsons, J. R. Vang, L. K. Mahabal, A. A. Cinquini, L. Kelly, S. C. Kincaid, H. Crichton, D. J. Spira, A. Liu, G. Gower, A. C. Pass, H. I. Goparaju, C. Dubinett, S. M. Krysan, K. Stass, S. A. Kukuruga, D. Van Keuren-Jensen, K. Courtright-Lim, A. Thompson, K. L. Rosenzweig, B. A. Sorbara, L. Srivastava, S. Salit, M. L. 2017-10-27 doi:10.1101/210310 Cold Spring Harbor Laboratory Press 2017-10-27 <![CDATA[ A High-Resolution Probabilistic In Vivo Atlas of Human Subcortical Brain Nuclei ]]> https://biorxiv.org/content/10.1101/211201v1?rss=1 Pauli, W. M. Nili, A. N. Tyszka, J. M. 2017-10-30 doi:10.1101/211201 Cold Spring Harbor Laboratory Press 2017-10-30 <![CDATA[ Causal Mapping of Emotion Networks in the Human Brain: Framework and Preliminary Findings ]]> https://biorxiv.org/content/10.1101/214486v1?rss=1 Dubois, J. Oya, H. Tyszka, J. M. Howard, M. Eberhardt, F. Adolphs, R. 2017-11-05 doi:10.1101/214486 Cold Spring Harbor Laboratory Press 2017-11-05 <![CDATA[ Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos ]]> https://biorxiv.org/content/10.1101/214619v1?rss=1 Trivedi, V. Choi, H. M. T. Fraser, S. E. Pierce, N. A. 2017-11-06 doi:10.1101/214619 Cold Spring Harbor Laboratory Press 2017-11-06 <![CDATA[ Predicting personality traits from resting-state fMRI ]]> https://biorxiv.org/content/10.1101/215129v1?rss=1 Dubois, J. Galdi, P. Han, Y. Paul, L. K. Adolphs, R. 2017-11-07 doi:10.1101/215129 Cold Spring Harbor Laboratory Press 2017-11-07 <![CDATA[ Higher-order inter-chromosomal hubs shape 3-dimensional genome organization in the nucleus ]]> https://biorxiv.org/content/10.1101/219683v1?rss=1 Quinodoz, S. A. Ollikainen, N. Tabak, B. Palla, A. Schmidt, J. M. Detmar, E. Lai, M. Shishkin, A. Bhat, P. Trinh, V. Aznauryan, E. Russell, P. Cheng, C. Jovanovic, M. Chow, A. McDonel, P. Garber, M. Guttman, M. 2017-11-18 doi:10.1101/219683 Cold Spring Harbor Laboratory Press 2017-11-18 <![CDATA[ Length and time scales of cell-cell signaling circuits in agar ]]> https://biorxiv.org/content/10.1101/220244v1?rss=1 Doong, J. Parkin, J. Murray, R. M. 2017-11-18 doi:10.1101/220244 Cold Spring Harbor Laboratory Press 2017-11-18 <![CDATA[ Hard Limits And Performance Tradeoffs In A Class Of Sequestration Feedback Systems ]]> https://biorxiv.org/content/10.1101/222042v1?rss=1 Olsman, N. Baetica, A.-A. Xiao, F. Leong, Y. P. Doyle, J. Murray, R. 2017-11-20 doi:10.1101/222042 Cold Spring Harbor Laboratory Press 2017-11-20 <![CDATA[ Improving the annotation of the Heterorhabditis bacteriophora genome ]]> https://biorxiv.org/content/10.1101/225904v1?rss=1 McLean, F. Berger, D. Laetsch, D. Schwartz, H. Blaxter, M. 2017-11-30 doi:10.1101/225904 Cold Spring Harbor Laboratory Press 2017-11-30 <![CDATA[ An open resource for nonhuman primate imaging ]]> https://biorxiv.org/content/10.1101/227462v1?rss=1 Milham, M. Ai, L. Koo, B. Xu, T. Balezeau, F. Baxter, M. G. Croxson, P. L. Damatac, C. G. Harel, N. Freiwald, W. Griffiths, T. D. Everling, S. Jung, B. Kastner, S. Leopold, D. A. Mars, R. B. Menon, R. S. Messinger, A. Morrison, J. H. Nacef, J. Nagy, J. Rios, M. O. Petkov, C. I. Pinsk, M. Poirier, C. Rajimehr, R. Rushworth, M. F. Russ, B. E. Schmid, M. Schwiedrzik, C. M. Sallet, J. Seidlitz, J. Ungerleider, L. Thiele, A. Tsao, D. Yacoub, E. Ye, F. Zarco, W. Margulies, D. S. Schroeder, C. E. 2017-11-30 doi:10.1101/227462 Cold Spring Harbor Laboratory Press 2017-11-30 <![CDATA[ MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides ]]> https://biorxiv.org/content/10.1101/227504v1?rss=1 Mohimani, H. Gurevich, A. Alexander, K. L. Naman, C. B. Leao, T. Glukhov, E. Moss, N. A. Luzzatto Knaan, T. Vargas, F. Nothias, L.-F. Singh, N. K. Sanders, J. G. Benitez, R. A. S. Thompson, L. R. Hamid, M. N. Morton, J. T. Mikheenko, A. Shlemov, A. Korobeynikov, A. Friedberg, I. Knight, R. Venkateswaran, K. Gerwick, W. Gerwick, L. Dorrestein, P. C. Pevzner, P. A. 2017-12-03 doi:10.1101/227504 Cold Spring Harbor Laboratory Press 2017-12-03 <![CDATA[ Drosophila have distinct activity-gated pathways that mediate attraction and aversion to CO2 ]]> https://biorxiv.org/content/10.1101/227991v1?rss=1 van Breugel, F. Huda, A. Dickinson, M. H. 2017-12-03 doi:10.1101/227991 Cold Spring Harbor Laboratory Press 2017-12-03 <![CDATA[ The functional organization of descending sensory-motor pathways in Drosophila ]]> https://biorxiv.org/content/10.1101/231696v1?rss=1 Namiki, S. Dickinson, M. H. Wong, A. M. Korff, W. Card, G. M. 2017-12-11 doi:10.1101/231696 Cold Spring Harbor Laboratory Press 2017-12-11 <![CDATA[ Ultrasonic Neuromodulation Causes Widespread Cortical Activation via an Indirect Auditory Mechanism ]]> https://biorxiv.org/content/10.1101/234211v1?rss=1 Sato, T. Shapiro, M. Tsao, D. 2017-12-14 doi:10.1101/234211 Cold Spring Harbor Laboratory Press 2017-12-14 <![CDATA[ Theoretical Analysis of Inducer and Operator Binding for Cyclic-AMP Receptor Protein Mutants ]]> https://biorxiv.org/content/10.1101/236455v1?rss=1 Einav, T. Duque, J. Phillips, R. 2017-12-19 doi:10.1101/236455 Cold Spring Harbor Laboratory Press 2017-12-19 <![CDATA[ A systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria ]]> https://biorxiv.org/content/10.1101/239335v1?rss=1 Belliveau, N. M. Barnes, S. L. Ireland, W. T. Jones, D. L. Sweredoski, M. Moradian, A. Hess, S. Kinney, J. B. Phillips, R. 2017-12-23 doi:10.1101/239335 Cold Spring Harbor Laboratory Press 2017-12-23 <![CDATA[ Acoustically Targeted Chemogenetics for Noninvasive Control of Neural Circuits ]]> https://biorxiv.org/content/10.1101/241406v1?rss=1 Szablowski, J. O. Lue, B. Lee-Gosselin, A. Malounda, D. Shapiro, M. G. 2018-01-01 doi:10.1101/241406 Cold Spring Harbor Laboratory Press 2018-01-01 <![CDATA[ Observing the Cell in Its Native State: Imaging Subcellular Dynamics in Multicellular Organisms ]]> https://biorxiv.org/content/10.1101/243352v1?rss=1 Liu, T.-l. Upadhyayula, S. Milkie, D. E. Singh, V. Wang, K. Swinburne, I. A. Mosaliganti, K. R. Collin, Z. M. Hiscock, T. W. Shea, J. Kohrman, A. Q. Medwig, T. N. Dambournet, D. Forster, R. Cunniff, B. Ruan, Y. Yashiro, H. Scholpp, S. Meyerowitz, E. M. Hockemeyer, D. Drubin, D. G. Martin, B. L. Matus, D. Q. Koyama, M. Megason, S. G. Kirchhausen, T. Betzig, E. 2018-01-08 doi:10.1101/243352 Cold Spring Harbor Laboratory Press 2018-01-08 <![CDATA[ FAIRsharing: working with and for the community to describe and link data standards, repositories and policies ]]> https://biorxiv.org/content/10.1101/245183v1?rss=1 Sansone, S.-A. McQuilton, P. Rocca-Serra, P. Gonzalez-Beltran, A. Izzo, M. Lister, A. Thurston, M. FAIRsharing Community, 2018-01-17 doi:10.1101/245183 Cold Spring Harbor Laboratory Press 2018-01-17 <![CDATA[ Direct Imaging of the circular chromosome of a live bacterium ]]> https://biorxiv.org/content/10.1101/246389v1?rss=1 Wu, F. Japaridze, A. Zheng, X. Kerssemakers, J. W. J. Dekker, C. 2018-01-11 doi:10.1101/246389 Cold Spring Harbor Laboratory Press 2018-01-11 <![CDATA[ Widespread and targeted gene expression by systemic AAV vectors: Production, purification, and administration ]]> https://biorxiv.org/content/10.1101/246405v1?rss=1 Challis, R. C. Kumar, S. R. Chan, K. Y. Challis, C. Jang, M. J. Rajendran, P. S. Tompkins, J. D. Shivkumar, K. Deverman, B. E. Gradinaru, V. 2018-01-11 doi:10.1101/246405 Cold Spring Harbor Laboratory Press 2018-01-11 <![CDATA[ Harmonizing semantic annotations for computational models in biology ]]> https://biorxiv.org/content/10.1101/246470v1?rss=1 Neal, M. L. König, M. Nickerson, D. Mısırlı, G. Kalbasi, R. Dräger, A. Atalag, K. Chelliah, V. Cooling, M. Cook, D. L. Crook, S. de Alba, M. Friedman, S. H. Garny, A. Gennari, J. H. Gleeson, P. Golebiewski, M. Hucka, M. Juty, N. Le Novere, N. Myers, C. Olivier, B. G. Sauro, H. M. Scharm, M. Snoep, J. L. Toure, V. Wipat, A. Wolkenhauer, O. Waltemath, D. 2018-01-23 doi:10.1101/246470 Cold Spring Harbor Laboratory Press 2018-01-23 <![CDATA[ Attentional set to safety recruits the medial prefrontal cortex ]]> https://biorxiv.org/content/10.1101/249326v1?rss=1 Yao, S. Qi, S. Kendrick, K. Mobbs, D. 2018-01-17 doi:10.1101/249326 Cold Spring Harbor Laboratory Press 2018-01-17 <![CDATA[ Imaging neural activity in the ventral nerve cord of behaving adult Drosophila ]]> https://biorxiv.org/content/10.1101/250118v1?rss=1 Chen, C.-L. Hermans, L. Viswanathan, M. C. Fortun, D. Unser, M. Cammarato, A. Dickinson, M. H. Ramdya, P. 2018-01-22 doi:10.1101/250118 Cold Spring Harbor Laboratory Press 2018-01-22 <![CDATA[ A distributed brain network predicts general intelligence from resting-state human neuroimaging data ]]> https://biorxiv.org/content/10.1101/257865v1?rss=1 Dubois, J. C. Galdi, P. Paul, L. K. Adolphs, R. 2018-01-31 doi:10.1101/257865 Cold Spring Harbor Laboratory Press 2018-01-31 <![CDATA[ Identification of transcriptional signatures for cell types from single-cell RNA-Seq ]]> https://biorxiv.org/content/10.1101/258566v1?rss=1 Ntranos, V. Yi, L. Melsted, P. Pachter, L. 2018-02-01 doi:10.1101/258566 Cold Spring Harbor Laboratory Press 2018-02-01 <![CDATA[ Development of photoactivatable drugs enables nicotinic optopharmacology ]]> https://biorxiv.org/content/10.1101/260232v1?rss=1 Banala, S. Arvin, M. C. Bannon, N. M. Jin, X.-T. Wang, Y. Zhao, G. Marshall, J. J. Gee, K. R. Wokosin, D. L. Contractor, A. Henry, L. A. Kozorovitskiy, Y. Drenan, R. M. Lavis, L. D. 2018-02-05 doi:10.1101/260232 Cold Spring Harbor Laboratory Press 2018-02-05 <![CDATA[ Single day construction of multi-gene circuits with 3G assembly ]]> https://biorxiv.org/content/10.1101/260851v1?rss=1 Halleran, A. D. Swaminathan, A. Murray, R. M. 2018-02-10 doi:10.1101/260851 Cold Spring Harbor Laboratory Press 2018-02-10 <![CDATA[ A conserved regulatory program drives emergence of the lateral plate mesoderm ]]> https://biorxiv.org/content/10.1101/261115v1?rss=1 Hess, C. Prummel, K. D. Nieuwenhuize, S. Parker, H. Rogers, K. W. Kozmikova, I. Racioppi, C. Burger, S. Brombacher, E. C. Burger, A. Felker, A. Chiavacci, E. Shah, G. Huisken, J. Kozmik, Z. Christiaen, L. Mueller, P. Bronner, M. Krumlauf, R. Mosimann, C. 2018-02-07 doi:10.1101/261115 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ Representation of multiple objects in macaque category-selective areas ]]> https://biorxiv.org/content/10.1101/264465v1?rss=1 Bao, P. Tsao, D. Y. 2018-02-13 doi:10.1101/264465 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ ProtaBank: A repository for protein design and engineering data ]]> https://biorxiv.org/content/10.1101/272211v1?rss=1 Wang, C. Y. Chang, P. M. Ary, M. L. Allen, B. D. Chica, R. A. Mayo, S. L. Olafson, B. D. 2018-02-26 doi:10.1101/272211 Cold Spring Harbor Laboratory Press 2018-02-26 <![CDATA[ Decomposing spatially dependent and cell type specific contributions to cellular heterogeneity ]]> https://biorxiv.org/content/10.1101/275156v1?rss=1 Zhu, Q. Shah, S. Dries, R. Cai, L. Yuan, G.-C. 2018-03-02 doi:10.1101/275156 Cold Spring Harbor Laboratory Press 2018-03-02 <![CDATA[ A genome-wide assessment of the ancestral neural crest gene regulatory network ]]> https://biorxiv.org/content/10.1101/275875v1?rss=1 Hockman, D. Chong-Morrison, V. Gavriouchkina, D. Green, S. Amemiya, C. Smith, J. J. Bronner, M. Sauka-Spengler, T. 2018-03-12 doi:10.1101/275875 Cold Spring Harbor Laboratory Press 2018-03-12 <![CDATA[ Bacterial swarming reduces Proteus mirabilis and Vibrio parahaemolyticus cell stiffness and increases β-lactam susceptibility ]]> https://biorxiv.org/content/10.1101/275941v1?rss=1 10-100 m) and multinucleate during their growth and motility on polymer surfaces. We demonstrate increasing cell length is accompanied by a large increase in flexibility. Using a microfluidic assay to measure single-cell mechanics, we identified large differences in swarmer cell stiffness of (bending rigidity of P. mirabilis, 9.6 x 10-22 N m2; V. parahaemolyticus, 9.7 x 10-23 N m2) compared to vegetative cells (1.4 x 10-20 N m2 and 3.2 x 10-22 N m2, respectively). The reduction in bending rigidity (~3-15 fold) was accompanied by a decrease in the average polysaccharide strand length of the peptidoglycan layer of the cell wall from 28-30 to 19-22 disaccharides. Atomic force microscopy revealed a reduction in P. mirabilis peptidoglycan thickness from 1.5 nm (vegetative) to 1.0 nm (swarmer) and electron cryotomography indicated changes in swarmer cell wall morphology. P. mirabilis and V. parahaemolyticus swarmer cells became increasingly sensitive to osmotic pressure and susceptible to cell wall-modifying antibiotics (compared to vegetative cells)--they were ~30% more likely to die after 3 h of treatment with minimum inhibitory concentrations of the {beta}-lactams cephalexin and penicillin G. The adaptive cost of swarming is offset by the increase in cell susceptibility to physical and chemical changes in their environment, thereby suggesting the development of new chemotherapies for bacteria that leverage swarming for colonization of hosts and survival. ImportanceProteus mirabilis and Vibrio parahaemolyticus are bacteria that infect humans. To adapt to environmental changes, these bacteria alter their cell morphology and move collectively to access new sources of nutrients in a process referred to as swarming. We found that a change in the composition and thickness of the peptidoglycan layer of the cell wall makes swarmer cells of P. mirabilis and V. parahaemolyticus more flexible (i.e., reduced cell stiffness) and increases their sensitivity to osmotic pressure and cell-wall targeting antibiotics (e.g., {beta}-lactams). These results highlight the importance of assessing the extracellular environment in determining antibiotic doses and the use of {beta}-lactams antibiotics for treating infections caused by swarmer cells of P. mirabilis and V. parahaemolyticus. ]]> Auer, G. K. Oliver, P. M. Rajendram, M. Yao, Q. Jensen, G. J. Weibel, D. B. 2018-03-03 doi:10.1101/275941 Cold Spring Harbor Laboratory Press 2018-03-03 <![CDATA[ Bacillus safensis FO-36b and Bacillus pumilus SAFR-032: A Whole Genome Comparison of Two Spacecraft Assembly Facility Isolates ]]> https://biorxiv.org/content/10.1101/283937v1?rss=1 Tirumalai, M. Stepanov, V. G. Wunsche, A. Montazari, S. Gonzalez, R. O. Venkateswaran, K. Fox, G. E. 2018-03-16 doi:10.1101/283937 Cold Spring Harbor Laboratory Press 2018-03-16 <![CDATA[ A re-examination of responding on ratio and regulated-probability interval schedules ]]> https://biorxiv.org/content/10.1101/284216v1?rss=1 Perez, O. D. Milton, A. L. Aitken, M. R. F. Dickinson, A. 2018-03-18 doi:10.1101/284216 Cold Spring Harbor Laboratory Press 2018-03-18 <![CDATA[ Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust ]]> https://biorxiv.org/content/10.1101/285213v1?rss=1 Choi, H. M. T. Schwarzkopf, M. Fornace, M. E. Acharya, A. Artavanis, G. Stegmaier, J. Cunha, A. Pierce, N. A. 2018-03-19 doi:10.1101/285213 Cold Spring Harbor Laboratory Press 2018-03-19 <![CDATA[ Role of communication network topology in controlling microbial population in consortia ]]> https://biorxiv.org/content/10.1101/288142v1?rss=1 Ren, X. Murray, R. M. 2018-03-24 doi:10.1101/288142 Cold Spring Harbor Laboratory Press 2018-03-24 <![CDATA[ Robust Perfect Adaptation in Biomolecular Reaction Networks ]]> https://biorxiv.org/content/10.1101/299057v1?rss=1 Xiao, F. Doyle, J. C. 2018-04-11 doi:10.1101/299057 Cold Spring Harbor Laboratory Press 2018-04-11 <![CDATA[ Forces on nascent polypeptides during membrane insertion and translocation via the Sec translocon ]]> https://biorxiv.org/content/10.1101/310698v1?rss=1 Niesen, M. Muller-Lucks, A. Hedman, R. von Heijne, G. Miller, T. F. 2018-04-29 doi:10.1101/310698 Cold Spring Harbor Laboratory Press 2018-04-29 <![CDATA[ Molecular architecture of the Legionella Dot/Icm type IV secretion system ]]> https://biorxiv.org/content/10.1101/312009v1?rss=1 Ghosal, D. Chang, Y.-W. Jeong, K. C. Vogel, J. P. Jensen, G. 2018-05-01 doi:10.1101/312009 Cold Spring Harbor Laboratory Press 2018-05-01 <![CDATA[ Structural survey of HIV-1-neutralizing antibodies targeting Env trimer delineates epitope categories and suggests vaccine templates ]]> https://biorxiv.org/content/10.1101/312579v1?rss=1 25% of HIV-1 strains have now been identified that recognize all major exposed surfaces of the prefusion-closed Env trimer. Here we analyzed all 206 broadly neutralizing antibody-HIV-1 Env complexes in the PDB with resolution suitable to define their interaction chemistries. These segregated into 20 antibody classes based on ontogeny and recognition, and into 6 epitope categories (V1V2, glycan-V3, CD4-binding site, silent face center, fusion peptide, and subunit interface) based on recognized Env residues. We measured antibody neutralization on a 208-isolate panel and analyzed features of paratope and B cell ontogeny. The number of protruding loops, CDR H3 length, and level of somatic hypermutation for broadly HIV-1 neutralizing antibodies were significantly higher than for a comparison set of non-HIV-1 antibodies. For epitope, the number of independent sequence segments was higher (P < 0.0001), as well as the glycan component surface area (P = 0.0005). Based on B cell ontogeny, paratope, and breadth, the CD4-binding site antibody IOMA appeared to be a promising candidate for lineage-based vaccine design. In terms of epitope-based vaccine design, antibody VRC34.01 had few epitope segments, low epitope-glycan content, and high epitope-conformational variability, which may explain why VRC34.01-based design is yielding promising vaccine results. ]]> Chuang, G.-Y. Zhou, J. Rawi, R. Shen, C.-H. Sheng, Z. West, A. P. Zhang, B. Zhou, T. Bailer, R. T. Doria-Rose, N. A. Louder, M. K. McKee, K. Mascola, J. R. Bjorkman, P. J. Shapiro, L. Kwong, P. D. 2018-05-02 doi:10.1101/312579 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ Cis-activation in the Notch signaling pathway ]]> https://biorxiv.org/content/10.1101/313171v1?rss=1 Elowitz, M. B. Santat, L. A. Nandagopal, N. 2018-05-02 doi:10.1101/313171 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ Sun navigation requires compass neurons in Drosophila ]]> https://biorxiv.org/content/10.1101/315176v1?rss=1 Giraldo, Y. M. Leitch, K. J. Ros, I. K. Warren, T. L. Weir, P. T. Dickinson, M. 2018-05-07 doi:10.1101/315176 Cold Spring Harbor Laboratory Press 2018-05-07 <![CDATA[ Highly Multiplexed Single-Cell RNA-seq for Defining Cell Population and Transcriptional Spaces ]]> https://biorxiv.org/content/10.1101/315333v1?rss=1 Gehring, J. Park, J. H. Chen, S. Thomson, M. Pachter, L. 2018-05-05 doi:10.1101/315333 Cold Spring Harbor Laboratory Press 2018-05-05 <![CDATA[ Polar targeting and assembly of the Legionella Dot/Icm type IV secretion system (T4SS) by T6SS-related components ]]> https://biorxiv.org/content/10.1101/315721v1?rss=1 Jeong, K. C. Gyore, J. Teng, L. Ghosal, D. Jensen, G. J. Vogel, J. P. 2018-05-07 doi:10.1101/315721 Cold Spring Harbor Laboratory Press 2018-05-07 <![CDATA[ The Genetic Insulator RiboJ Increases Expression of Insulated Genes ]]> https://biorxiv.org/content/10.1101/317875v1?rss=1 Clifton, K. P. Jones, E. M. Paudel, S. Marken, J. P. Monette, C. E. Halleran, A. D. Epp, L. Saha, M. S. 2018-05-09 doi:10.1101/317875 Cold Spring Harbor Laboratory Press 2018-05-09 <![CDATA[ A stochastic epigenetic switch controls the dynamics of T-cell lineage commitment ]]> https://biorxiv.org/content/10.1101/318675v1?rss=1 Ng, K. K. N. Yui, M. A. Mehta, A. Siu, S. Irwin, B. Pease, S. Hirose, S. Elowitz, M. B. Rothenberg, E. V. Kueh, H. Y. 2018-05-10 doi:10.1101/318675 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds light on metabolic versatility of the Methanomassiliicoccales ]]> https://biorxiv.org/content/10.1101/328906v1?rss=1 Speth, D. R. Orphan, V. J. 2018-05-23 doi:10.1101/328906 Cold Spring Harbor Laboratory Press 2018-05-23 <![CDATA[ Towards measuring growth rates of pathogens during infections by D2O-labeling lipidomics ]]> https://biorxiv.org/content/10.1101/330464v1?rss=1 0.03 at% D). In the E. coli cultures, labeling dynamics of phospholipids depend largely on their acyl chains and between phospholipids we notice differences that are not obvious from absolute concentrations alone. For example, cyclopropyl-containing lipids reflect the regulation of cyclopropane fatty acid synthase, which is predominantly expressed at the beginning of stationary phase. The deuterium incorporation into a lipid that is specific for S. aureus in CF sputum, indicates an average generation time of the pathogen on the order of one cell doubling per day.nnCONCLUSIONSThis study demonstrates how trace level measurement of stable isotopes in intact lipids can be used to quantify lipid metabolism in pure cultures and provides guidelines that enable growth rate measurements in microbiome samples after incubation with a low percentage of D2O. ]]> Neubauer, C. Sessions, A. L. Booth, I. R. Bowen, B. P. Kopf, S. H. Newman, D. K. Dalleska, N. F. 2018-05-25 doi:10.1101/330464 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Mapping DNA sequence to transcription factor binding energy in vivo ]]> https://biorxiv.org/content/10.1101/331124v1?rss=1 Barnes, S. L. Belliveau, N. M. Ireland, W. T. Kinney, J. B. Phillips, R. 2018-05-25 doi:10.1101/331124 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Pioneering, chromatin remodeling, and epigenetic constraint in early T-cell gene regulation by PU.1 ]]> https://biorxiv.org/content/10.1101/331710v1?rss=1 Ungerback, J. Hosokawa, H. Wang, X. Strid, T. Williams, B. A. Sigvardsson, M. Rothenberg, E. V. 2018-05-25 doi:10.1101/331710 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Human-induced decrease of ectomycorrhizal vegetation led to loss in global soil carbon content ]]> https://biorxiv.org/content/10.1101/331884v1?rss=1 Soudzilovskaia, N. A. van Bodegom, P. M. Terrer Moreno, C. van't Zelfde, M. McCallum, I. Fisher, J. B. McCormack, L. M. Brundrett, M. Tedersoo, L. 2018-05-26 doi:10.1101/331884 Cold Spring Harbor Laboratory Press 2018-05-26 <![CDATA[ Optogenetic manipulation of medullary neurons in the locust optic lobe ]]> https://biorxiv.org/content/10.1101/334003v1?rss=1 Wang, H. Dewell, R. B. Ehrengruber, M. U. Segev, E. Reimer, J. Roukes, M. L. Gabbiani, F. 2018-05-30 doi:10.1101/334003 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ The Metabolic Capability and Phylogenetic Diversity of Mono Lake During a Bloom of the Eukaryotic Phototroph Picocystis strain ML ]]> https://biorxiv.org/content/10.1101/334144v1?rss=1 Stamps, B. W. Nunn, H. S. Petryshyn, V. A. Oremland, R. S. Miller, L. G. Rosen, M. Bauer, K. W. Thompson, K. J. Tookmanian, E. M. Waldeck, A. R. Lloyd, S. J. Johnson, H. A. Stevenson, B. S. Berelson, W. Corsetti, F. A. Spear, J. R. 2018-05-30 doi:10.1101/334144 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ Binary transcriptional control of pattern formation in development ]]> https://biorxiv.org/content/10.1101/335919v1?rss=1 Lammers, N. C. Galstyan, V. Reimer, A. Medin, S. A. Wiggins, C. H. Garcia, H. G. 2018-05-31 doi:10.1101/335919 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ Regulation of neural stem cell fate by the transcriptional repressor Capicua ]]> https://biorxiv.org/content/10.1101/335984v1?rss=1 Ahmad, S. T. Rogers, A. D. Chen, M. J. Dixit, R. Adnani, L. Frankiw, L. Lawn, S. O. Blough, M. D. Alshehri, M. Wu, W. Robbins, S. M. Cairncross, G. Schuurmans, C. Chan, J. 2018-05-31 doi:10.1101/335984 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ Dynamics and spatial genomics of the nascent transcriptome in single mESCs by intron seqFISH ]]> https://biorxiv.org/content/10.1101/339234v1?rss=1 Shah, S. Takei, Y. Zhou, W. Lubeck, E. Yun, J. Koulena, N. Liaw, E. J. Amin, M. Cai, L. 2018-06-05 doi:10.1101/339234 Cold Spring Harbor Laboratory Press 2018-06-05 <![CDATA[ Connecting the dots between mechanosensitive channel abundance, osmotic shock, and survival at single-cell resolution ]]> https://biorxiv.org/content/10.1101/339259v1?rss=1 Chure, G. D. Lee, H. J. Phillips, R. 2018-06-05 doi:10.1101/339259 Cold Spring Harbor Laboratory Press 2018-06-05 <![CDATA[ Refining the application of microbial lipids as tracers of Staphylococcus aureus growth rates in cystic fibrosis sputum ]]> https://biorxiv.org/content/10.1101/348037v1?rss=1 Neubauer, C. Kasi, A. S. Grahl, N. Sessions, A. L. Kopf, S. Kato, R. Hogan, D. A. Newman, D. K. 2018-06-15 doi:10.1101/348037 Cold Spring Harbor Laboratory Press 2018-06-15 <![CDATA[ Cell boundary confinement sets the size and position of the E. coli chromosome ]]> https://biorxiv.org/content/10.1101/348052v1?rss=1 Wu, F. Swain, P. Kuijpers, L. Zheng, X. Felter, K. Guurink, M. Chaudhuri, D. Mulder, B. Dekker, C. 2018-06-15 doi:10.1101/348052 Cold Spring Harbor Laboratory Press 2018-06-15 <![CDATA[ Resource limitation modulates the fate of dissimilated nitrogen in a dual-pathway Actinobacterium ]]> https://biorxiv.org/content/10.1101/364331v1?rss=1 Vuono, D. C. Read, R. W. Hemp, J. Sullivan, B. W. Arnone, J. A. Neveux, I. Blank, B. Staub, C. Loney, E. Miceli, D. Winkler, M. Chakraborty, R. Stahl, D. A. Grzymski, J. J. 2018-07-08 doi:10.1101/364331 Cold Spring Harbor Laboratory Press 2018-07-08 <![CDATA[ Expression reflects population structure ]]> https://biorxiv.org/content/10.1101/364448v1?rss=1 Brown, B. C. Bray, N. L. Pachter, L. 2018-07-08 doi:10.1101/364448 Cold Spring Harbor Laboratory Press 2018-07-08 <![CDATA[ The expanded universe of prokaryotic Argonaute proteins ]]> https://biorxiv.org/content/10.1101/366930v1?rss=1 Ryazansky, S. Kulbachinskiy, A. Aravin, A. 2018-07-10 doi:10.1101/366930 Cold Spring Harbor Laboratory Press 2018-07-10 <![CDATA[ Selective Permeability of Carboxysome Shell Pores to Anionic Molecules ]]> https://biorxiv.org/content/10.1101/367714v1?rss=1 Mahinthichaichan, P. Morris, D. M. Wang, Y. Jensen, G. J. Tajkhorshid, E. 2018-07-11 doi:10.1101/367714 Cold Spring Harbor Laboratory Press 2018-07-11 <![CDATA[ The structural complexity of the Gammaproteobacteria flagellar motor is related to the type of its torque-generating stators ]]> https://biorxiv.org/content/10.1101/369397v1?rss=1 Kaplan, M. Ghosal, D. Subramanian, P. Oikonomou, C. M. Kjaer, A. Pirbadian, S. Ortega, D. R. El-Naggar, M. Y. Jensen, G. J. 2018-07-14 doi:10.1101/369397 Cold Spring Harbor Laboratory Press 2018-07-14 <![CDATA[ Stable sub-complexes observed in situ suggest a modular assembly pathway of the bacterial flagellar motor ]]> https://biorxiv.org/content/10.1101/369405v1?rss=1 Kaplan, M. Subramanian, P. Ghosal, D. Oikonomou, C. M. Pirbadian, S. Starwalt-Lee, R. Gralnick, J. A. El-Naggar, M. Y. Jensen, G. J. 2018-07-14 doi:10.1101/369405 Cold Spring Harbor Laboratory Press 2018-07-14 <![CDATA[ 3D-printable tools for developmental biology: Improving embryo injection and screening techniques through 3D-printing technology ]]> https://biorxiv.org/content/10.1101/376657v1?rss=1 Truchado-Garcia, M. Harland, R. M. Abrams, M. J. 2018-07-25 doi:10.1101/376657 Cold Spring Harbor Laboratory Press 2018-07-25 <![CDATA[ Flexibly-oriented double Cdc45-MCM-GINS intermediates during eukaryotic replicative helicase maturation ]]> https://biorxiv.org/content/10.1101/388470v1?rss=1 Liu, L. Zhang, Y. Zhang, J. Wang, J.-H. Cao, Q. Li, Z. Campbell, J. L. Dong, M. Lou, H. 2018-08-09 doi:10.1101/388470 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ Fluorescence-Based Detection of Fusion State on a Cryo-EM Grid using Correlated Cryo-Fluorescence and Cryo-Electron Microscopy ]]> https://biorxiv.org/content/10.1101/388579v1?rss=1 Metskas, L. A. Briggs, J. A. G. 2018-08-10 doi:10.1101/388579 Cold Spring Harbor Laboratory Press 2018-08-10 <![CDATA[ One read per cell per gene is optimal for single-cell RNA-Seq ]]> https://biorxiv.org/content/10.1101/389296v1?rss=1 Zhang, M. J. Ntranos, V. Tse, D. 2018-08-09 doi:10.1101/389296 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi ]]> https://biorxiv.org/content/10.1101/390617v1?rss=1 Boyd, J. Jungbluth, S. Leu, A. Evans, P. Woodcroft, B. Chadwick, G. Orphan, V. Amend, J. Rappe, M. Tyson, G. 2018-08-13 doi:10.1101/390617 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ An efficient genome editing strategy to generate putative null mutants in Caenorhabditis elegans using CRISPR/Cas9 ]]> https://biorxiv.org/content/10.1101/391243v1?rss=1 Sternberg, P. W. Wang, H. Park, H. Liu, J. 2018-08-13 doi:10.1101/391243 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ Maintaining trunk neural crest cells as crestospheres ]]> https://biorxiv.org/content/10.1101/391599v1?rss=1 Mohlin, S. Kunttas, E. Persson, C. U. Abdel-Haq, R. Castillo, A. Murko, C. Bronner, M. E. Kerosuo, L. 2018-08-14 doi:10.1101/391599 Cold Spring Harbor Laboratory Press 2018-08-14 <![CDATA[ Reading at the speed of speech: the rate of eye movements aligns with auditory language processing ]]> https://biorxiv.org/content/10.1101/391896v1?rss=1 Gagl, B. Golch, J. Hawelka, S. Sassenhagen, J. Poeppel, D. Fiebach, C. J. 2018-08-14 doi:10.1101/391896 Cold Spring Harbor Laboratory Press 2018-08-14 <![CDATA[ Epigenetic inactivation of miR-203 as a key step in neural crest epithelial-to-mesenchymal transition ]]> https://biorxiv.org/content/10.1101/392142v1?rss=1 Sanchez-Vasquez, E. Bronner, M. Strobl-Mazzulla, P. H. 2018-08-14 doi:10.1101/392142 Cold Spring Harbor Laboratory Press 2018-08-14 <![CDATA[ RAD51 AND MITOTIC FUNCTION OF MUS81 ARE ESSENTIAL FOR RECOVERY FROM LOW-DOSE OF CAMPTOTHECIN IN THE ABSENCE OF THE WRN EXONUCLEASE ]]> https://biorxiv.org/content/10.1101/399881v1?rss=1 Pichierri, P. Aiello, F. A. Palma, A. Malacaria, E. Zheng, L. Campbell, J. L. Shen, B. Franchitto, A. 2018-08-25 doi:10.1101/399881 Cold Spring Harbor Laboratory Press 2018-08-25 <![CDATA[ Simulations suggest a constrictive force is required for Gram-negative bacterial cell division ]]> https://biorxiv.org/content/10.1101/406389v1?rss=1 Nguyen, L. T. Oikonomou, C. M. Ding, H. J. Kaplan, M. Yao, Q. Chang, Y.-W. Beeby, M. Jensen, G. J. 2018-09-01 doi:10.1101/406389 Cold Spring Harbor Laboratory Press 2018-09-01 <![CDATA[ Quantifying the Entropic and Energetic Effects of Linker Length and Rigidity within Synthetic HIV-1 Antibodies designed to Bind Bivalently to Env Spikes ]]> https://biorxiv.org/content/10.1101/406454v1?rss=1 Galimidi, R. P. Einav, T. Gnanapragasam, P. N. P. Joshi, D. S. Lynch, A. M. Yazdi, S. West, A. P. Phillips, R. Bjorkman, P. J. 2018-09-03 doi:10.1101/406454 Cold Spring Harbor Laboratory Press 2018-09-03 <![CDATA[ Draxin alters laminin expression during basement membrane reorganization to control cranial neural crest EMT ]]> https://biorxiv.org/content/10.1101/407882v1?rss=1 Hutchins, E. J. Bronner, M. E. 2018-09-03 doi:10.1101/407882 Cold Spring Harbor Laboratory Press 2018-09-03 <![CDATA[ A data-driven approach to the automated study of cross-species homologies ]]> https://biorxiv.org/content/10.1101/412114v1?rss=1 Pauli, W. M. 2018-09-09 doi:10.1101/412114 Cold Spring Harbor Laboratory Press 2018-09-09 <![CDATA[ Extended hopanoid lipids promote bacterial motility, surface attachment, and root nodule development in the Bradyrhizobium diazoefficiens-Aeschynomene afraspera symbiosis ]]> https://biorxiv.org/content/10.1101/423301v1?rss=1 Belin, B. J. Tookmanian, E. T. de Anda, J. Wong, G. Newman, D. K. 2018-09-21 doi:10.1101/423301 Cold Spring Harbor Laboratory Press 2018-09-21 <![CDATA[ The dormancy specific regulator, SutA, is an intrinsically-disordered protein that modulates transcription initiation in Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/423384v1?rss=1 Bergkessel, M. Babin, B. M. VanderVelde, D. Sweredoski, M. Moradian, A. Eggleston-Rangel, R. Hess, S. Tirrell, D. Artsimovitch, I. Newman, D. K. 2018-09-20 doi:10.1101/423384 Cold Spring Harbor Laboratory Press 2018-09-20 <![CDATA[ Transsynaptic interactions between IgSF proteins DIP-α and Dpr10 are required for motor neuron targeting specificity in Drosophila ]]> https://biorxiv.org/content/10.1101/424416v1?rss=1 Ashley, J. Sorrentino, V. Nagarkar-Jaiswal, S. Tan, L. Xu, S. Xiao, Q. Zinn, K. Carrillo, R. A. 2018-09-21 doi:10.1101/424416 Cold Spring Harbor Laboratory Press 2018-09-21 <![CDATA[ Collection of continuous rotation MicroED Data from Ion Beam Milled Crystals of Any Size ]]> https://biorxiv.org/content/10.1101/425611v1?rss=1 Martynowycz, M. Zhao, W. Hattne, J. Jensen, G. Gonen, T. 2018-09-24 doi:10.1101/425611 Cold Spring Harbor Laboratory Press 2018-09-24 <![CDATA[ Architectural Principles for Characterizing the Performance of Sequestration Feedback Networks ]]> https://biorxiv.org/content/10.1101/428300v1?rss=1 Olsman, N. Xiao, F. Doyle, J. C. 2018-09-27 doi:10.1101/428300 Cold Spring Harbor Laboratory Press 2018-09-27 <![CDATA[ Molecular basis of human asparagine synthetase inhibitor specificity ]]> https://biorxiv.org/content/10.1101/428508v1?rss=1 Zhu, W. Radadiya, A. Bisson, C. Nordin, B. Baumann, P. Imasaki, T. Wenzel, S. Sedelnikova, S. Berry, A. Nomanbhoy, T. Kozarich, J. Jin, Y. Takagi, Y. Rice, D. Richards, N. 2018-09-29 doi:10.1101/428508 Cold Spring Harbor Laboratory Press 2018-09-29 <![CDATA[ Thermophilic Lithotrophy and Phototrophy in an Intertidal, Iron-rich, Geothermal Spring ]]> https://biorxiv.org/content/10.1101/428698v1?rss=1 Ward, L. M. Idei, A. Nakagawa, M. Ueno, Y. Fischer, W. W. McGlynn, S. E. 2018-09-27 doi:10.1101/428698 Cold Spring Harbor Laboratory Press 2018-09-27 <![CDATA[ Signal Transduction in Human Cell Lysate via Dynamic RNA Nanotechnology ]]> https://biorxiv.org/content/10.1101/439273v1?rss=1 nView larger version (10K):norg.highwire.dtl.DTLVardef@fb2a0org.highwire.dtl.DTLVardef@98517dorg.highwire.dtl.DTLVardef@e0fe8org.highwire.dtl.DTLVardef@1364f8d_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hochrein, L. M. Ge, T. J. Schwarzkopf, M. Pierce, N. A. 2018-10-11 doi:10.1101/439273 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ Coupled Reaction Networks for Noise Suppression ]]> https://biorxiv.org/content/10.1101/440453v1?rss=1 Xiao, F. Fang, M. Doyle, J. C. 2018-10-11 doi:10.1101/440453 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ A direct comparison of genome alignment and transcriptome pseudoalignment ]]> https://biorxiv.org/content/10.1101/444620v1?rss=1 Yi, L. Liu, L. Melsted, P. Pachter, L. 2018-10-16 doi:10.1101/444620 Cold Spring Harbor Laboratory Press 2018-10-16 <![CDATA[ Connectional architecture of a mouse hypothalamic circuit node controlling social behavior ]]> https://biorxiv.org/content/10.1101/445312v1?rss=1 Lo, L. Kim, D.-W. Yao, S. Cetin, A. Harris, J. Zeng, H. Anderson, D. J. Weissbourd, B. 2018-10-16 doi:10.1101/445312 Cold Spring Harbor Laboratory Press 2018-10-16 <![CDATA[ Transduction of the Geomagnetic Field as Evidenced from Alpha-band Activity in the Human Brain ]]> https://biorxiv.org/content/10.1101/448449v1?rss=1 Wang, C. X. Hilburn, I. A. Wu, D.-A. Mizuhara, Y. Couste, C. P. Abrams, J. N. H. Bernstein, S. E. Matani, A. Shimojo, S. Kirschvink, J. L. 2018-10-20 doi:10.1101/448449 Cold Spring Harbor Laboratory Press 2018-10-20 <![CDATA[ ETDB-Caltech: a blockchain-based distributed public database for electron tomography ]]> https://biorxiv.org/content/10.1101/453662v1?rss=1 Ortega, D. R. Oikonomou, C. M. Ding, H. J. Rees-Lee, P. Alexandria, Jensen, G. J. 2018-10-25 doi:10.1101/453662 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ Visual cue-related activity of cells in the medial entorhinal cortex during navigation in virtual reality ]]> https://biorxiv.org/content/10.1101/453787v1?rss=1 Kinkhabwala, A. Gu, Y. Aronov, D. Tank, D. W. 2018-10-25 doi:10.1101/453787 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ Rapid Tilt-Series Acquisition for Electron Cryotomography ]]> https://biorxiv.org/content/10.1101/454587v1?rss=1 Chreifi, G. Chen, S. Metskas, L. A. Kaplan, M. Jensen, G. J. 2018-10-26 doi:10.1101/454587 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ Fusion of DARPin to aldolase enables visualization of small protein by cryoEM ]]> https://biorxiv.org/content/10.1101/455063v1?rss=1 Yao, Q. Weaver, S. J. Mock, J.-Y. Jensen, G. J. 2018-10-30 doi:10.1101/455063 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ Design Guidelines For Sequestration Feedback Networks ]]> https://biorxiv.org/content/10.1101/455493v1?rss=1 Baetica, A.-A. Leong, Y. P. Olsman, N. Murray, R. M. 2018-10-30 doi:10.1101/455493 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ Identification of peripheral neural circuits that regulate heart rate using optogenetic and viral vector strategies ]]> https://biorxiv.org/content/10.1101/456483v1?rss=1 Rajendran, P. S. Challis, R. C. Fowlkes, C. C. Hanna, P. Tompkins, J. D. Jordan, M. C. Hiyari, S. Gabris-Weber, B. A. Greenbaum, A. Chan, K. Y. Deverman, B. E. Munzberg, H. Ardell, J. L. Salama, G. Gradinaru, V. Shivkumar, K. 2018-10-29 doi:10.1101/456483 Cold Spring Harbor Laboratory Press 2018-10-29 <![CDATA[ A new family of neural wiring receptors across bilaterians defined by phylogenetic, biochemical and structural evidence ]]> https://biorxiv.org/content/10.1101/462036v1?rss=1 Cheng, S. Park, Y. Kurleto, J. D. Jeon, M. Zinn, K. Thornton, J. W. Özkan, E. 2018-11-05 doi:10.1101/462036 Cold Spring Harbor Laboratory Press 2018-11-05 <![CDATA[ Occupancy patterns of 208 DNA-associated proteins in a single human cell type ]]> https://biorxiv.org/content/10.1101/464800v1?rss=1 1,600 transcription factors (TFs) encoded in the human genome has been assayed. Here we present data and analyses of ChIP-seq experiments for 208 DNA-associated proteins (DAPs) in the HepG2 hepatocellular carcinoma line, spanning nearly a quarter of its expressed TFs, transcriptional co-factors, and chromatin regulator proteins. The DAP binding profiles classify into major groups associated predominantly with promoters or enhancers, or with both. We confirm and expand the current catalog of DNA sequence motifs; 77 factors showed similar motifs to those previously described using in vivo and/or in vitro methods, and 17 yielded novel motifs. We also describe motifs corresponding to other TFs that co-enrich with the primary ChIP target. FOX family motifs are, for example, significantly enriched in ChIP-seq peaks of 37 other DAPs. We show that promoters and enhancers can be discriminated based on motif content and occupancy patterns. This large catalog reveals High Occupancy Target (HOT) regions at which many DAPs associate, although each contains motifs for only a minority of the numerous associated DAPs. These analyses provide a deeper and more complete overview of the gene regulatory networks that define this cell type. ]]> Partridge, E. C. Chhetri, S. B. Prokop, J. W. Ramaker, R. C. Jansen, C. S. Goh, S.-T. Mackiewicz, M. Newberry, K. M. Brandsmeier, L. A. Meadows, S. K. Messer, C. L. Hardigan, A. A. Dean, E. C. Jiang, S. Savic, D. Mortazavi, A. Wold, B. J. Myers, R. M. Mendenhall, E. M. 2018-11-07 doi:10.1101/464800 Cold Spring Harbor Laboratory Press 2018-11-07 <![CDATA[ Oxytocin effects on the resting-state mentalizing brain network ]]> https://biorxiv.org/content/10.1101/465658v1?rss=1 Wu, H. Feng, C. Lu, X. Liu, X. Liu, Q. 2018-11-08 doi:10.1101/465658 Cold Spring Harbor Laboratory Press 2018-11-08 <![CDATA[ Mouse Academy: high-throughput automated training and trial-by-trial behavioral analysis during learning ]]> https://biorxiv.org/content/10.1101/467878v1?rss=1 Qiao, M. Zhang, T. Segalin, C. Sam, S. Perona, P. Meister, M. 2018-11-16 doi:10.1101/467878 Cold Spring Harbor Laboratory Press 2018-11-16 <![CDATA[ The Barcode, UMI, Set format and BUStools ]]> https://biorxiv.org/content/10.1101/472571v1?rss=1 Melsted, P. Ntranos, V. Pachter, L. 2018-11-18 doi:10.1101/472571 Cold Spring Harbor Laboratory Press 2018-11-18 <![CDATA[ Cooperation Enhances Robustness of Coexistence in Spatially Structured Consortia ]]> https://biorxiv.org/content/10.1101/472811v1?rss=1 Ren, X. Murray, R. M. 2018-11-19 doi:10.1101/472811 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Refinement of metabolite detection in cystic fibrosis sputum reveals heme negatively correlates with lung function ]]> https://biorxiv.org/content/10.1101/475525v1?rss=1 Glasser, N. R. Hunter, R. C. Liou, T. G. Newman, D. K. K. Mountain West CF Consortium Investigators, 2018-11-23 doi:10.1101/475525 Cold Spring Harbor Laboratory Press 2018-11-23 <![CDATA[ Modular, part-based control of gene expression response time using protein degradation tags ]]> https://biorxiv.org/content/10.1101/482331v1?rss=1 Jones, E. M. Monette, C. E. Marken, J. P. Dhawan, S. Gibney, T. Li, C. Liu, W. Luz-Ricca, A. Ren, X. Zheng, X. Saha, M. 2018-11-29 doi:10.1101/482331 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ High-molecular-weight polymers from dietary fiber drive aggregation of particulates in the murine small intestine ]]> https://biorxiv.org/content/10.1101/490920v1?rss=1 Preska Steinberg, A. Datta, S. S. Naragon, T. Rolando, J. C. Bogatyrev, S. R. Ismagilov, R. F. 2018-12-10 doi:10.1101/490920 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ Dynamics of microRNA expression during mouse prenatal development ]]> https://biorxiv.org/content/10.1101/492918v1?rss=1 Murad, R. Rahmanian, S. Breschi, A. Zeng, W. Williams, B. A. Mackiewicz, M. Roberts, B. Meadows, S. Moore, D. Davis, C. Trout, D. Zaleski, C. Dobin, A. Sei, L.-H. Drenkow, J. Scavelli, A. Gingeras, T. R. Wold, B. Myers, R. M. Guigo, R. Mortazavi, A. 2018-12-10 doi:10.1101/492918 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ Combinatorial Control through Allostery ]]> https://biorxiv.org/content/10.1101/508226v1?rss=1 Galstyan, V. Funk, L. Einav, T. Phillips, R. 2018-12-31 doi:10.1101/508226 Cold Spring Harbor Laboratory Press 2018-12-31 <![CDATA[ Visual-olfactory integration in the human disease vector mosquito, Aedes aegypti ]]> https://biorxiv.org/content/10.1101/512996v1?rss=1 Vinauger, C. Van Breugel, F. Locke, L. Tobin, K. Dickinson, M. Fairhall, A. Akbari, O. Riffell, J. 2019-01-07 doi:10.1101/512996 Cold Spring Harbor Laboratory Press 2019-01-07 <![CDATA[ The client-binding domain of the cochaperone SGTA/Sgt2 has a helical-hand structure that binds a short hydrophobic helix ]]> https://biorxiv.org/content/10.1101/517573v1?rss=1 Lin, K.-F. Fry, M. Y. Saladi, S. Clemons, W. M. 2019-01-10 doi:10.1101/517573 Cold Spring Harbor Laboratory Press 2019-01-10 <![CDATA[ Cancer Classification from Healthy DNA using Machine Learning ]]> https://biorxiv.org/content/10.1101/517839v1?rss=1 Jain, S. Mazaheri, B. Raviv, N. Bruck, J. 2019-01-11 doi:10.1101/517839 Cold Spring Harbor Laboratory Press 2019-01-11 <![CDATA[ Short Tandem Repeats Information in TCGA is Statistically Biased by Amplification ]]> https://biorxiv.org/content/10.1101/518878v1?rss=1 Jain, S. Mazaheri, B. Raviv, N. Bruck, J. 2019-01-11 doi:10.1101/518878 Cold Spring Harbor Laboratory Press 2019-01-11 <![CDATA[ Design principles for open source bioinstrumentation: the poseidon syringe pump system as an example ]]> https://biorxiv.org/content/10.1101/521096v1?rss=1 Booeshaghi, A. S. da Veiga Beltrame, E. Bannon, D. Gehring, J. Pachter, L. 2019-01-17 doi:10.1101/521096 Cold Spring Harbor Laboratory Press 2019-01-17 <![CDATA[ In vivo structure of the Legionella type II secretion system by electron cryotomography ]]> https://biorxiv.org/content/10.1101/525063v1?rss=1 Ghosal, D. Kim, K. W. Zheng, H. Kaplan, M. Vogel, J. P. Cianciotto, N. P. Jensen, G. J. 2019-01-19 doi:10.1101/525063 Cold Spring Harbor Laboratory Press 2019-01-19 <![CDATA[ Conditional Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function in Bacteria via Dynamic RNA Nanotechnology ]]> https://biorxiv.org/content/10.1101/525857v1?rss=1 Hanewich-Hollatz, M. H. Chen, Z. Huang, J. Hochrein, L. M. Pierce, N. A. 2019-01-21 doi:10.1101/525857 Cold Spring Harbor Laboratory Press 2019-01-21 <![CDATA[ Multi-Cell ECM compaction is predictable via superposition of nonlinear cell dynamics linearized in augmented state space ]]> https://biorxiv.org/content/10.1101/526426v1?rss=1 Mayalu, M. N. Kim, M. Asada, H. H. 2019-01-21 doi:10.1101/526426 Cold Spring Harbor Laboratory Press 2019-01-21 <![CDATA[ Phototrophic Methane Oxidation in a Member of the Chloroflexi Phylum ]]> https://biorxiv.org/content/10.1101/531582v1?rss=1 Ward, L. Shih, P. M. Hemp, J. Kakegawa, T. Fischer, W. W. McGlynn, S. E. 2019-01-26 doi:10.1101/531582 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ The SUMO ligase Su(var)2-10 links piRNA-guided target recognition to chromatin silencing ]]> https://biorxiv.org/content/10.1101/533091v1?rss=1 Ninova, M. Chen, Y.-C. A. Godneeva, B. Rogers, A. K. Luo, Y. Aravin, A. A. Fejes Toth, K. 2019-01-29 doi:10.1101/533091 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ The SUMO ligase Su(var)2-10 controls eu- and heterochromatic gene expression via establishment of H3K9 trimethylation and negative feedback regulation ]]> https://biorxiv.org/content/10.1101/533232v1?rss=1 Ninova, M. Godneeva, B. Chen, Y.-C. A. Luo, Y. Prakash, S. J. Jankovics, F. Erdelyi, M. Fejes Toth, K. Aravin, A. A. 2019-01-29 doi:10.1101/533232 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ A novel mesocosm set-up reveals strong methane emission reduction in submerged peat moss Sphagnum cuspidatum by tightly associated methanotrophs. ]]> https://biorxiv.org/content/10.1101/536268v1?rss=1 Kox, M. A. R. Smolders, A. J. P. Speth, D. R. Lamers, L. P. M. Op den Camp, H. J. M. Jetten, M. S. M. Van Kessel, M. A. H. J. 2019-01-31 doi:10.1101/536268 Cold Spring Harbor Laboratory Press 2019-01-31 <![CDATA[ 96 Eyes: Parallel Fourier Ptychographic Microscopy for high throughput screening ]]> https://biorxiv.org/content/10.1101/547265v1?rss=1 Chan, A. C. S. Kim, J. Pan, A. Xu, H. Nojima, D. Hale, C. Wang, S. Yang, C. 2019-02-13 doi:10.1101/547265 Cold Spring Harbor Laboratory Press 2019-02-13 <![CDATA[ Electrophysiology and transcriptomics reveal two photoreceptor classes and complex visual integration in Hirudo verbana ]]> https://biorxiv.org/content/10.1101/552018v1?rss=1 Stowasser, A. Stahl, A. Benoit, J. B. Wagenaar, D. A. 2019-02-15 doi:10.1101/552018 Cold Spring Harbor Laboratory Press 2019-02-15 <![CDATA[ RecV recombinase system for spatiotemporally controlled light-inducible genomic modifications. ]]> https://biorxiv.org/content/10.1101/553271v1?rss=1 Cetin, A. H. Yao, S. Ouellette, B. Balaram, P. Zhou, T. Mortrud, M. Chatterjee, S. Wang, Y. Daigle, T. L. Tasic, B. Kuang, X. Gong, H. Luo, Q. Zeng, S. Kahan, A. Gradinaru, V. Zeng, H. 2019-02-18 doi:10.1101/553271 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ Programmable DNA cleavage by Ago nucleases from mesophilic bacteria Clostridium butyricum and Limnothrix rosea ]]> https://biorxiv.org/content/10.1101/558684v1?rss=1 Kuzmenko, A. Yudin, D. Ryazansky, S. Kulbachinskiy, A. Aravin, A. 2019-02-22 doi:10.1101/558684 Cold Spring Harbor Laboratory Press 2019-02-22 <![CDATA[ Persistence of neuronal representations through time and damage in the hippocampus. ]]> https://biorxiv.org/content/10.1101/559104v1?rss=1 Gonzalez, W. G. Zhang, H. Harutyunyan, A. Lois, C. 2019-02-24 doi:10.1101/559104 Cold Spring Harbor Laboratory Press 2019-02-24 <![CDATA[ Compositional Data Analysis is necessary for simulating and analyzing RNA-Seq data ]]> https://biorxiv.org/content/10.1101/564955v1?rss=1 McGee, W. A. Pimentel, H. Pachter, L. Wu, J. Y. 2019-03-02 doi:10.1101/564955 Cold Spring Harbor Laboratory Press 2019-03-02 <![CDATA[ An atlas of anterior hox gene expression in the embryonic sea lamprey head: hox-code evolution in vertebrates ]]> https://biorxiv.org/content/10.1101/571448v1?rss=1 Parker, H. J. Bronner, M. E. Krumlauf, R. 2019-03-09 doi:10.1101/571448 Cold Spring Harbor Laboratory Press 2019-03-09 <![CDATA[ T Cell Receptor Immunotherapy Drives Human Immunodeficiency Virus Evolution in Humanized Mice ]]> https://biorxiv.org/content/10.1101/574608v1?rss=1 Joglekar, A. V. Swift, M. Leonard, M. T. Jeppson, J. D. Sandoval, S. Baltimore, D. 2019-03-12 doi:10.1101/574608 Cold Spring Harbor Laboratory Press 2019-03-12 <![CDATA[ A multi-state model of the CaMKII dodecamer suggests a role for calmodulin in maintenance of autophosphorylation ]]> https://biorxiv.org/content/10.1101/575712v1?rss=1 Pharris, M. C. Bartol, T. M. Sejnowski, T. J. Kennedy, M. B. Stefan, M. I. Kinzer-Ursem, T. L. 2019-03-12 doi:10.1101/575712 Cold Spring Harbor Laboratory Press 2019-03-12 <![CDATA[ Ultrasound Imaging of Gene Expression in Mammalian Cells ]]> https://biorxiv.org/content/10.1101/580647v1?rss=1 Farhadi, A. Ho, G. H. Sawyer, D. P. Bourdeau, R. W. Shapiro, M. G. 2019-03-18 doi:10.1101/580647 Cold Spring Harbor Laboratory Press 2019-03-18 <![CDATA[ Identification of histological features to predict MUC2 expression in colon cancer tissues ]]> https://biorxiv.org/content/10.1101/584292v1?rss=1 Periyakoil, P. K. Clarke, M. Sahoo, D. 2019-03-21 doi:10.1101/584292 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Lineage does not regulate the connectivity of projection neurons in the mouse olfactory bulb ]]> https://biorxiv.org/content/10.1101/584805v1?rss=1 Lois, C. Sanchez-Guardado, L. 2019-03-21 doi:10.1101/584805 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Hippocampal-midbrain circuit enhances the pleasure of anticipation in the prefrontal cortex ]]> https://biorxiv.org/content/10.1101/588699v1?rss=1 Iigaya, K. Hauser, T. U. Kurth-Nelson, Z. O'Doherty, J. P. Dayan, P. Dolan, R. J. 2019-03-26 doi:10.1101/588699 Cold Spring Harbor Laboratory Press 2019-03-26 <![CDATA[ Addressable, \"Packet-Based\" Intercellular Communication through Plasmid Conjugation ]]> https://biorxiv.org/content/10.1101/591552v1?rss=1 Marken, J. P. Murray, R. M. 2019-03-27 doi:10.1101/591552 Cold Spring Harbor Laboratory Press 2019-03-27 <![CDATA[ Changepoint detection versus reinforcement learning: Separable neural substrates approximate different forms of Bayesian inference ]]> https://biorxiv.org/content/10.1101/591818v1?rss=1 Pauli, W. M. Jones, M. 2019-03-28 doi:10.1101/591818 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ FIND: Identifying Functionally and Structurally Important Features in Protein Sequences with Deep Neural Networks ]]> https://biorxiv.org/content/10.1101/592808v1?rss=1 Murali, R. Hemp, J. Orphan, V. Bisk, Y. 2019-03-30 doi:10.1101/592808 Cold Spring Harbor Laboratory Press 2019-03-30 <![CDATA[ First-principles prediction of the information processing capacity of a simple genetic circuit ]]> https://biorxiv.org/content/10.1101/594325v1?rss=1 Razo-Mejia, M. Phillips, R. 2019-03-31 doi:10.1101/594325 Cold Spring Harbor Laboratory Press 2019-03-31 <![CDATA[ Quantitative characterization of random partitioning in the evolution of plasmid-encoded traits ]]> https://biorxiv.org/content/10.1101/594879v1?rss=1 Halleran, A. D. Flores-Bautista, E. Murray, R. M. 2019-03-31 doi:10.1101/594879 Cold Spring Harbor Laboratory Press 2019-03-31 <![CDATA[ Biomolecular Contrast Agents for Optical Coherence Tomography ]]> https://biorxiv.org/content/10.1101/595157v1?rss=1 Lu, G. J. Chou, L.-d. Malounda, D. Patel, A. K. Welsbie, D. S. Chao, D. L. Ramalingam, T. Shapiro, M. G. 2019-03-31 doi:10.1101/595157 Cold Spring Harbor Laboratory Press 2019-03-31 <![CDATA[ A Method for Cost-Effective and Rapid Characterization of Engineered T7-based Transcription Factors by Cell-Free Protein Synthesis Reveals Insights into the Regulation of T7 RNA Polymerase-Driven Expression ]]> https://biorxiv.org/content/10.1101/614545v1?rss=1 McManus, J. Murray, R. Emanuel, P. Lux, M. 2019-04-20 doi:10.1101/614545 Cold Spring Harbor Laboratory Press 2019-04-20 <![CDATA[ The Contribution of Parietal Cortex to Visual Salience ]]> https://biorxiv.org/content/10.1101/619643v1?rss=1 Chen, X. Zirnsak, M. Vega, G. M. Govil, E. Lomber, S. Moore, T. 2019-04-28 doi:10.1101/619643 Cold Spring Harbor Laboratory Press 2019-04-28 <![CDATA[ Acoustically Detonated Biomolecules for Genetically Encodable Inertial Cavitation ]]> https://biorxiv.org/content/10.1101/620567v1?rss=1 Bar-Zion, A. Nourmahnad, A. Mittelstein, D. Yoo, S. Malounda, D. Abedi, M. Lee-Gosselin, A. Maresca, D. Shapiro, M. G. 2019-04-29 doi:10.1101/620567 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ Aggregation of nontuberculous mycobacteria is regulated by carbon:nitrogen balance ]]> https://biorxiv.org/content/10.1101/631283v1?rss=1 DePas, W. H. Bergkessel, M. Newman, D. K. 2019-05-08 doi:10.1101/631283 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ Quantitative visualization of gene expression in Pseudomonas aeruginosa aggregates reveals peak expression of alginate in the hypoxic zone ]]> https://biorxiv.org/content/10.1101/632893v1?rss=1 Jorth, P. Spero, M. Newman, D. K. 2019-05-09 doi:10.1101/632893 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ The Energetics of Molecular Adaptation in Transcriptional Regulation ]]> https://biorxiv.org/content/10.1101/638270v1?rss=1 Chure, G. Razo-Mejia, M. Belliveau, N. M. Einav, T. Kaczmarek, Z. A. Barnes, S. L. Lewis, M. Phillips, R. 2019-05-15 doi:10.1101/638270 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ An automated model reduction tool to guide the design and analysis of synthetic biological circuits ]]> https://biorxiv.org/content/10.1101/640276v1?rss=1 Pandey, A. Murray, R. M. 2019-05-17 doi:10.1101/640276 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ MCH4 is a multicopy suppressor of glycine toxicity in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/653444v1?rss=1 Melnykov, A. V. Elson, E. L. 2019-05-29 doi:10.1101/653444 Cold Spring Harbor Laboratory Press 2019-05-29 <![CDATA[ Repurposing a macromolecular machine: Architecture and evolution of the F7 chemosensory system ]]> https://biorxiv.org/content/10.1101/653600v1?rss=1 Ortega, D. R. Subramanian, P. Mann, P. Kjaer, A. Chen, S. Watts, K. J. Pirbadian, S. Collins, D. A. Kooger, R. Kalyuzhnaya, M. G. Ringgaard, S. Briegel, A. Jensen, G. J. 2019-05-30 doi:10.1101/653600 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids ]]> https://biorxiv.org/content/10.1101/654756v1?rss=1 Quinn, R. A. Vrbanac, A. Melnik, A. V. Patras, K. A. Christy, M. Nelson, A. T. Aksenov, A. A. Tripathi, A. Humphrey, G. da Silva, R. Bussell, R. Thron, T. Wang, M. Vargas, F. Gauglitz, J. Meehan, M. J. Poulsen, O. Boland, B. S. Chang, J. T. Sandborn, W. J. Lim, M. Garg, N. Lumeng, J. Kazmierczak, B. I. Jain, R. Egan, M. Rhee, K. E. Haddad, G. G. Siegel, D. Mazmanian, S. Nizet, V. Knight, R. Dorrestein, P. C. 2019-06-03 doi:10.1101/654756 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ RNA velocity and protein acceleration from single-cell multiomics experiments ]]> https://biorxiv.org/content/10.1101/658401v1?rss=1 Gorin, G. Svensson, V. Pachter, L. 2019-06-06 doi:10.1101/658401 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ Bacterial Controller Aided Wound Healing: A Case Study in Dynamical Population Controller Design ]]> https://biorxiv.org/content/10.1101/659714v1?rss=1 Green, L. N. Hu, C. Y. Ren, X. Y. Murray, R. M. 2019-06-04 doi:10.1101/659714 Cold Spring Harbor Laboratory Press 2019-06-04 <![CDATA[ Defining the Energetic Costs of Cellular Structures ]]> https://biorxiv.org/content/10.1101/666040v1?rss=1 Mahmoudabadi, G. Phillips, R. Lynch, M. Milo, R. 2019-06-10 doi:10.1101/666040 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Multi-scale dynamical modelling of T-cell development from an early thymic progenitor state to lineage commitment ]]> https://biorxiv.org/content/10.1101/667709v1?rss=1 Olariu, V. Yui, M. Krupinski, P. Zhou, W. Deichmann, J. Rothenberg, E. V. Peterson, C. 2019-06-11 doi:10.1101/667709 Cold Spring Harbor Laboratory Press 2019-06-11 <![CDATA[ A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification ]]> https://biorxiv.org/content/10.1101/672931v1?rss=1 Wyman, D. Balderrama-Gutierrez, G. Reese, F. Jiang, S. Rahmanian, S. Zeng, W. Williams, B. A. Trout, D. England, W. Chu, S. Spitale, R. C. Tenner, A. J. Wold, B. Mortazavi, A. 2019-06-18 doi:10.1101/672931 Cold Spring Harbor Laboratory Press 2019-06-18 <![CDATA[ Modular and efficient pre-processing of single-cell RNA-seq ]]> https://biorxiv.org/content/10.1101/673285v1?rss=1 Melsted, P. Booeshaghi, A. S. Gao, F. da Veiga Beltrame, E. Lu, L. Hjorleifsson, K. E. Gehring, J. Pachter, L. 2019-06-17 doi:10.1101/673285 Cold Spring Harbor Laboratory Press 2019-06-17 <![CDATA[ Transcriptome Dynamics Reveals Progressive Transition from Effector to Memory in CD4+ T cells. ]]> https://biorxiv.org/content/10.1101/675967v1?rss=1 Soon, M. S. F. Lee, H. J. Engel, J. A. Straube, J. Thomas, B. S. Clarke, L. S. Laohamonthonkul, P. Pernold, C. P. S. Haldar, R. N. Williams, C. G. Lansink, L. I. M. Koufariotis, R. Lakis, V. Wood, S. Chen, X. James, K. R. Lönnberg, T. Lane, S. W. Davenport, M. P. Khoury, D. S. Svensson, V. Teichmann, S. A. Haque, A. 2019-06-19 doi:10.1101/675967 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ Interactions with presynaptic photoreceptors mediated by the Dpr11 and DIP-γ cell surface proteins control selection and survival of Drosophila amacrine neurons ]]> https://biorxiv.org/content/10.1101/679704v1?rss=1 Menon, K. Kulkarni, V. Takemura, S.-y. Anaya, M. Zinn, K. 2019-06-22 doi:10.1101/679704 Cold Spring Harbor Laboratory Press 2019-06-22 <![CDATA[ Ciliary photoreceptors in sea urchin larvae indicate pan-deuterostome cell type conservation ]]> https://biorxiv.org/content/10.1101/683318v1?rss=1 Valencia, J. E. Feuda, R. Mellott, D. O. Burke, R. Peter, I. S. 2019-06-27 doi:10.1101/683318 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Restructuring of amygdala subregion apportion across adolescence ]]> https://biorxiv.org/content/10.1101/690875v1?rss=1 Campbell, C. E. Mezher, A. F. Eckel, S. P. Tyszka, J. M. Pauli, W. M. Nagel, B. J. Herting, M. M. 2019-07-09 doi:10.1101/690875 Cold Spring Harbor Laboratory Press 2019-07-09 <![CDATA[ Genetically encoded nanostructures enable acoustic manipulation of engineered cells ]]> https://biorxiv.org/content/10.1101/691105v1?rss=1 Wu, D. Baresch, D. Cook, C. Malounda, D. Maresca, D. Abundo, M. P. Mittelstein, D. R. Shapiro, M. G. 2019-07-06 doi:10.1101/691105 Cold Spring Harbor Laboratory Press 2019-07-06 <![CDATA[ Modular Thermal Control of Protein Dimerization ]]> https://biorxiv.org/content/10.1101/694448v1?rss=1 Piraner, D. I. Wu, Y. Shapiro, M. G. 2019-07-13 doi:10.1101/694448 Cold Spring Harbor Laboratory Press 2019-07-13 <![CDATA[ Giotto, a pipeline for integrative analysis and visualization of single-cell spatial transcriptomic data ]]> https://biorxiv.org/content/10.1101/701680v1?rss=1 Dries, R. Zhu, Q. Eng, C.-H. L. Sarkar, A. Bao, F. George, R. E. Pierson, N. Cai, L. Yuan, G.-C. 2019-07-13 doi:10.1101/701680 Cold Spring Harbor Laboratory Press 2019-07-13 <![CDATA[ MATE-Seq: Microfluidic Antigen-TCR Engagement Sequencing ]]> https://biorxiv.org/content/10.1101/706606v1?rss=1 Ng, A. H. Peng, S. Xu, A. M. Noh, W. J. Guo, K. Bethune, M. T. Chour, W. Choi, J. Yang, S. Baltimore, D. Heath, J. R. 2019-07-18 doi:10.1101/706606 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ Deep Multi-State Dynamic Recurrent Neural Networks Operating on Wavelet Based Neural Features for Robust Brain Machine Interfaces ]]> https://biorxiv.org/content/10.1101/710327v1?rss=1 Haghi, B. Kellis, S. Shah, S. Ashok, M. Bashford, L. Kramer, D. Lee, B. Liu, C. Andersen, R. A. Emami, A. 2019-07-22 doi:10.1101/710327 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ Visual search mimics configural processing in human causal learning ]]> https://biorxiv.org/content/10.1101/713420v1?rss=1 Perez, O. D. Narasiwodeyar, S. Soto, F. A. 2019-07-24 doi:10.1101/713420 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ Modeling predicts that CRISPR-based activators, unlike CRISPR-based repressors, scale well with increasing gRNA competition and dCas9 bottlenecking ]]> https://biorxiv.org/content/10.1101/719278v1?rss=1 10-fold activation. ]]> Clamons, S. Murray, R. 2019-07-30 doi:10.1101/719278 Cold Spring Harbor Laboratory Press 2019-07-30 <![CDATA[ Myogenesis modelled by human pluripotent stem cells uncovers Duchenne muscular dystrophy phenotypes prior to skeletal muscle commitment ]]> https://biorxiv.org/content/10.1101/720920v1?rss=1 Mournetas, V. Massourides, E. Dupont, J.-B. Kornobis, E. Polveche, H. Jarrige, M. Gosselin, M. Garbis, S. D. Gorecki, D. C. Pinset, C. 2019-08-04 doi:10.1101/720920 Cold Spring Harbor Laboratory Press 2019-08-04 <![CDATA[ Kinetic Inference Resolves Epigenetic Mechanism of Drug Resistance in Melanoma ]]> https://biorxiv.org/content/10.1101/724740v1?rss=1 Su, Y. Lu, X. Li, G. Liu, C. Kong, Y. Lee, J. Ng, R. Wong, S. Robert, L. Warden, C. Liu, V. Chen, J. Wang, Z. Yapeng, Y. Cheng, H. Ng, A. Qin, G. Peng, S. Xue, M. Johnson, D. Xu, Y. Wang, J. Wu, X. Shmulevich, I. Shi, Q. Levine, R. Ribas, A. Baltimore, D. Guo, J. Heath, J. R. Wei, W. 2019-08-05 doi:10.1101/724740 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ Acoustic biomolecules enhance hemodynamic functional ultrasound imaging of neural activity ]]> https://biorxiv.org/content/10.1101/734939v1?rss=1 Maresca, D. Payen, T. Lee-Gosselin, A. Ling, B. Malounda, D. Demene, C. Tanter, M. Shapiro, M. G. 2019-08-15 doi:10.1101/734939 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ NEURONS THAT FUNCTION WITHIN AN INTEGRATOR TO PROMOTE A PERSISTENT BEHAVIORAL STATE IN DROSOPHILA ]]> https://biorxiv.org/content/10.1101/735985v1?rss=1 Jung, Y. Kennedy, A. Chiu, H. Mohammad, F. Claridge-Chang, A. Anderson, D. J. 2019-08-15 doi:10.1101/735985 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Simulations of proposed mechanisms of FtsZ-driven cell constriction ]]> https://biorxiv.org/content/10.1101/737189v1?rss=1 Nguyen, L. T. Oikonomou, C. M. Jensen, G. J. 2019-08-15 doi:10.1101/737189 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Interpretable factor models of single-cell RNA-seq via variational autoencoders ]]> https://biorxiv.org/content/10.1101/737601v1?rss=1 Svensson, V. Pachter, L. 2019-08-16 doi:10.1101/737601 Cold Spring Harbor Laboratory Press 2019-08-16 <![CDATA[ SVFX: a machine-learning framework to quantify the pathogenicity of structural variants ]]> https://biorxiv.org/content/10.1101/739474v1?rss=1 kumar, s. Harmanci, A. Vytheeswaran, J. Gerstein, M. 2019-08-19 doi:10.1101/739474 Cold Spring Harbor Laboratory Press 2019-08-19 <![CDATA[ A curated database reveals trends in single cell transcriptomics ]]> https://biorxiv.org/content/10.1101/742304v1?rss=1 Svensson, V. da Veiga Beltrame, E. 2019-08-21 doi:10.1101/742304 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Interdimer zipping in the chemoreceptor signaling domain revealed by molecular dynamics simulations ]]> https://biorxiv.org/content/10.1101/745117v1?rss=1 Petukh, M. G. Ortega, D. R. Baudry, J. Zhulin, I. B. 2019-08-22 doi:10.1101/745117 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq ]]> https://biorxiv.org/content/10.1101/762773v1?rss=1 Svensson, V. da Veiga Beltrame, E. Pachter, L. 2019-09-09 doi:10.1101/762773 Cold Spring Harbor Laboratory Press 2019-09-09 <![CDATA[ Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals ]]> https://biorxiv.org/content/10.1101/767061v1?rss=1 Wolff, A. M. Young, I. D. Sierra, R. G. Brewster, A. S. Martynowycz, M. W. Nango, E. Sugahara, M. Nakane, T. Ito, K. Aquila, A. Bhowmick, A. Biel, J. T. Carbajo, S. Cohen, A. E. Cortez, S. Gonzalez, A. Hino, T. Im, D. Koralek, J. D. Kubo, M. Lazarou, T. S. Nomura, T. Owada, S. Samelson, A. Tanaka, R. Tanaka, T. Thompson, E. M. van den Bedem, H. Woldeyes, R. A. Yumoto, F. Zhao, W. Tono, K. Boutet, S. Iwata, S. Gonen, T. Sauter, N. K. Fraser, J. S. Thompson, M. C. 2019-09-12 doi:10.1101/767061 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ TRAF6 controls excitatory spinogenesis and excitation-inhibition balance thought binding neuroplastin ]]> https://biorxiv.org/content/10.1101/768341v1?rss=1 Kumar Vemula, S. Malci, A. Junge, L. Lehmann, A.-C. Rama, R. Hradsky, J. Matute, R. A. Naumann, M. Kreutz, M. R. Seidenbecher, C. I. Gundelfinger, E. D. Herrera-Molina, R. 2019-09-14 doi:10.1101/768341 Cold Spring Harbor Laboratory Press 2019-09-14 <![CDATA[ Selective Ablation of Cancer Cells with Low Intensity Pulsed Ultrasound ]]> https://biorxiv.org/content/10.1101/779124v1?rss=1 Mittelstein, D. R. Ye, J. Schibber, E. F. Roychoudhury, A. Troyas, S. L. Fekrazad, M. H. Ortiz, M. Lee, P. P. Shapiro, M. G. Gharib, M. 2019-10-01 doi:10.1101/779124 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ Learning with naturalistic odor representations in a dynamic model of the Drosophila olfactory system ]]> https://biorxiv.org/content/10.1101/783191v1?rss=1 Kennedy, A. 2019-09-26 doi:10.1101/783191 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Cytoskeletal organization in isolated plant cells under geometry control. ]]> https://biorxiv.org/content/10.1101/784595v1?rss=1 Durand-Smet, P. Spelman, T. Meyerowitz, E. M. Jonsson, H. 2019-09-26 doi:10.1101/784595 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Bacterial flagellar motor PL-ring disassembly sub-complexes are widespread and ancient ]]> https://biorxiv.org/content/10.1101/786715v1?rss=1 Kaplan, M. Sweredoski, M. J. Rodrigues, J. Tocheva, E. I. Chang, Y.-W. Ortega, D. R. Beeby, M. Jensen, G. J. 2019-09-30 doi:10.1101/786715 Cold Spring Harbor Laboratory Press 2019-09-30 <![CDATA[ Cotranslational Folding Stimulates Programmed Ribosomal Frameshifting in the Alphavirus Structural Polyprotein ]]> https://biorxiv.org/content/10.1101/790444v1?rss=1 Harrington, H. R. Zimmer, M. H. Chamness, L. M. Nash, V. Penn, W. D. Miller, T. F. Mukhopadhyay, S. Schlebach, J. P. 2019-10-02 doi:10.1101/790444 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Micro-scale fluid behavior during cryo-EM sample blotting ]]> https://biorxiv.org/content/10.1101/791285v1?rss=1 Armstrong, M. Han, B.-G. Gomez, S. Turner, J. Fletcher, D. A. Glaeser, R. M. 2019-10-02 doi:10.1101/791285 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Sequence-Dependent Dynamics of Synthetic and Endogenous RSSs in V(D)J Recombination ]]> https://biorxiv.org/content/10.1101/791954v1?rss=1 Hirokawa, S. Chure, G. Belliveau, N. M. Lovely, G. A. Anaya, M. Schatz, D. G. Baltimore, D. Phillips, R. 2019-10-04 doi:10.1101/791954 Cold Spring Harbor Laboratory Press 2019-10-04 <![CDATA[ ASM-Clust: classifying functionally diverse protein families using alignment score matrices ]]> https://biorxiv.org/content/10.1101/792739v1?rss=1 Speth, D. R. Orphan, V. J. 2019-10-03 doi:10.1101/792739 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ Live imaging-assisted domain-specific CRISPR genome editing at single cell resolution in plants ]]> https://biorxiv.org/content/10.1101/793240v1?rss=1 Li, T. Yan, A. Meyerowitz, E. M. 2019-10-04 doi:10.1101/793240 Cold Spring Harbor Laboratory Press 2019-10-04 <![CDATA[ Listener’s vmPFC simulates speaker choices when reading between the lines ]]> https://biorxiv.org/content/10.1101/800359v1?rss=1 Mi, Q. Wang, C. Camerer, C. F. Zhu, L. 2019-10-10 doi:10.1101/800359 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ A sex difference in the composition of the rodent postsynaptic density ]]> https://biorxiv.org/content/10.1101/802538v1?rss=1 Mastro, T. L. Preza, A. Basu, S. Chattarji, S. Till, S. M. Kind, P. C. Kennedy, M. B. 2019-10-12 doi:10.1101/802538 Cold Spring Harbor Laboratory Press 2019-10-12 <![CDATA[ Accurate cell tracking and lineage construction in live-cell imaging experiments with deep learning ]]> https://biorxiv.org/content/10.1101/803205v1?rss=1 Moen, E. Borba, E. Miller, G. Schwartz, M. Bannon, D. Koe, N. Camplisson, I. Kyme, D. Pavelchek, C. Price, T. Kudo, T. Pao, E. Graf, W. Van Valen, D. A. 2019-10-13 doi:10.1101/803205 Cold Spring Harbor Laboratory Press 2019-10-13 <![CDATA[ Robust Estimation of Bacterial Cell Count from Optical Density ]]> https://biorxiv.org/content/10.1101/803239v1?rss=1 Beal, J. Farny, N. G. Haddock-Angelli, T. Selvarajah, V. Baldwin, G. S. Buckley-Taylor, R. Gershater, M. Kiga, D. Marken, J. P. Sanchania, V. Sison, A. Workman, C. iGEM Interlab Study Contributors, 2019-10-13 doi:10.1101/803239 Cold Spring Harbor Laboratory Press 2019-10-13 <![CDATA[ Stimulus-specific neural encoding of a persistent, internal defensive state in the hypothalamus ]]> https://biorxiv.org/content/10.1101/805317v1?rss=1 Kennedy, A. Kunwar, P. S. Li, L. Wagenaar, D. A. Anderson, D. J. 2019-10-16 doi:10.1101/805317 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ A theory of actions and habits in free-operant behavior: The interaction of rate correlation and contiguity systems. ]]> https://biorxiv.org/content/10.1101/807800v1?rss=1 Perez, O. D. Dickinson, A. 2019-10-17 doi:10.1101/807800 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Interactions between calmodulin and neurogranin govern the dynamics of CaMKII as a leaky integrator ]]> https://biorxiv.org/content/10.1101/809905v1?rss=1 Ordyan, M. Bartol, T. M. Kennedy, M. B. Rangamani, P. Sejnowski, T. J. 2019-10-18 doi:10.1101/809905 Cold Spring Harbor Laboratory Press 2019-10-18 <![CDATA[ Caenorhabditis elegans AF4/FMR2 family homolog affl-2 is required for heat shock induced gene expression ]]> https://biorxiv.org/content/10.1101/817833v1?rss=1 Walton, S. J. Wang, H. Quintero-Cadena, P. Bateman, A. Sternberg, P. W. 2019-10-25 doi:10.1101/817833 Cold Spring Harbor Laboratory Press 2019-10-25 <![CDATA[ RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting ]]> https://biorxiv.org/content/10.1101/825299v1?rss=1 Quintero-Cadena, P. Lenstra, T. L. Sternberg, P. W. 2019-10-31 doi:10.1101/825299 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ Functional architecture of motion direction in the mouse superior colliculus ]]> https://biorxiv.org/content/10.1101/825711v1?rss=1 Li, Y. Turan, Z. Meister, M. 2019-10-31 doi:10.1101/825711 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ Stochastic simulation platform for visualization and estimation of transcriptional kinetics ]]> https://biorxiv.org/content/10.1101/825869v1?rss=1 Gorin, G. Wang, M. Golding, I. Xu, H. 2019-11-02 doi:10.1101/825869 Cold Spring Harbor Laboratory Press 2019-11-02 <![CDATA[ Differential modes of orphan subunit recognition for the WRB/CAML complex ]]> https://biorxiv.org/content/10.1101/828228v1?rss=1 Inglis, A. J. Page, K. R. Guna, A. Voorhees, R. M. 2019-11-01 doi:10.1101/828228 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ Neuro-computational account of arbitration between imitation and emulation during human observational learning ]]> https://biorxiv.org/content/10.1101/828723v1?rss=1 Charpentier, C. J. Iigaya, K. O'Doherty, J. P. 2019-11-04 doi:10.1101/828723 Cold Spring Harbor Laboratory Press 2019-11-04 <![CDATA[ Genetically encoded phase contrast agents for digital holographic microscopy ]]> https://biorxiv.org/content/10.1101/833830v1?rss=1 Farhadi, A. Bedrossian, M. Lee, J. Ho, G. H. Shapiro, M. G. Nadeau, J. 2019-11-12 doi:10.1101/833830 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ Correlated cryogenic fluorescence microscopy and electron cryotomography shows that exogenous TRIM5α can form hexagonal lattices or autophagy aggregates in vivo ]]> https://biorxiv.org/content/10.1101/835322v1?rss=1 Carter, S. D. Mamede, J. I. Hope, T. J. Jensen, G. J. 2019-11-07 doi:10.1101/835322 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ Crosslinking of nucleotide binding domains improves the coupling efficiency of an ABC transporter ]]> https://biorxiv.org/content/10.1101/836676v1?rss=1 Fan, C. Kaiser, J. T. Rees, D. C. 2019-11-09 doi:10.1101/836676 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ The Degree Distribution of Human Brain Functional Connectivity is Generalized Pareto: A Multi-Scale Analysis ]]> https://biorxiv.org/content/10.1101/840066v1?rss=1 Zucca, R. Arsiwalla, X. D. Le, H. Rubinov, M. Gurgui, A. Verschure, P. 2019-11-13 doi:10.1101/840066 Cold Spring Harbor Laboratory Press 2019-11-13 <![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[ A hydrogel beads based platform for single-cell phenotypic analysis and digital molecular detection ]]> https://biorxiv.org/content/10.1101/848168v1?rss=1 Zhu, Y. Li, J. Lin, X. Huang, X. Hoffmann, M. R. 2019-11-23 doi:10.1101/848168 Cold Spring Harbor Laboratory Press 2019-11-23 <![CDATA[ An improved whole life cycle culture protocol for the hydrozoan genetic model Clytia hemisphaerica. ]]> https://biorxiv.org/content/10.1101/852632v1?rss=1 Lechable, M. Jan, A. Weissbourd, B. C. Uveira, J. Gissat, L. Collet, S. Gilletta, L. Chevalier, S. Leclere, L. Peron, S. Barreau, C. Lasbleiz, R. Houliston, E. Momose, T. 2019-11-25 doi:10.1101/852632 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ Odd-paired is a late-acting pioneer factor coordinating with Zelda to broadly regulate gene expression in early embryos ]]> https://biorxiv.org/content/10.1101/853028v1?rss=1 Koromila, T. Gao, F. Iwasaki, Y. He, P. Pachter, L. S. Gergen, J. P. Stathopoulos, A. 2019-11-23 doi:10.1101/853028 Cold Spring Harbor Laboratory Press 2019-11-23 <![CDATA[ Viscoelastic properties of ECM-rich embryonic microenvironments ]]> https://biorxiv.org/content/10.1101/853044v1?rss=1 Akos, Z. Isai, D. G. Rajasingh, S. Kosa, E. Ghazvini, S. Dhar, P. Czirok, A. 2019-11-23 doi:10.1101/853044 Cold Spring Harbor Laboratory Press 2019-11-23 <![CDATA[ Construction of an inducible amyloid expression circuit in Bacillus megaterium: A case study with CsgA and TasA ]]> https://biorxiv.org/content/10.1101/858266v1?rss=1 Larsson, E. M. McManus, J. B. Murray, R. M. 2019-11-29 doi:10.1101/858266 Cold Spring Harbor Laboratory Press 2019-11-29 <![CDATA[ Theoretical investigation of a genetic switch for metabolic adaptation ]]> https://biorxiv.org/content/10.1101/858993v1?rss=1 Laxhuber, K. S. Morrison, M. Phillips, R. 2019-11-28 doi:10.1101/858993 Cold Spring Harbor Laboratory Press 2019-11-28 <![CDATA[ A Scalable Formulation for Engineering Combination Therapies for Evolutionary Dynamics of Disease ]]> https://biorxiv.org/content/10.1101/000075v1?rss=1 Vanessa Jonsson Anders Rantzer Richard M Murray 2013-11-07 doi:10.1101/000075 Cold Spring Harbor Laboratory Press 2013-11-07 <![CDATA[ Negative autoregulation matches production and demand in synthetic transcriptional networks ]]> https://biorxiv.org/content/10.1101/000430v1?rss=1 Elisa Franco Giulia Giordano Per-Ola Forsberg Richard M Murray 2013-11-14 doi:10.1101/000430 Cold Spring Harbor Laboratory Press 2013-11-14 <![CDATA[ Negative Feedback Facilitates Temperature Robustness in Biomolecular Circuit Dynamics ]]> https://biorxiv.org/content/10.1101/007385v1?rss=1 Shaunak Sen Richard M Murray 2014-07-22 doi:10.1101/007385 Cold Spring Harbor Laboratory Press 2014-07-22 <![CDATA[ Synthesizing Combination Therapies for Evolutionary Dynamics of Disease for Nonlinear Pharmacodynamics ]]> https://biorxiv.org/content/10.1101/009480v1?rss=1 Vanessa Jonsson Nikolai Matni Richard M. Murray 2014-09-21 doi:10.1101/009480 Cold Spring Harbor Laboratory Press 2014-09-21 <![CDATA[ Design of a Toolbox of RNA Thermometers ]]> https://biorxiv.org/content/10.1101/017269v1?rss=1 Shaunak Sen Divyansh Apurva Rohit Satija Dan Siegal Richard M Murray 2015-03-30 doi:10.1101/017269 Cold Spring Harbor Laboratory Press 2015-03-30 <![CDATA[ A cell-free framework for biological systems engineering ]]> https://biorxiv.org/content/10.1101/018317v1?rss=1 Henrike Niederholtmeyer Zachary Sun Yutaka Hori Enoch Yeung Amanda Verpoorte Richard M Murray Sebastian J Maerkl 2015-04-21 doi:10.1101/018317 Cold Spring Harbor Laboratory Press 2015-04-21 <![CDATA[ The effects of time-varying temperature on delays in genetic networks ]]> https://biorxiv.org/content/10.1101/019687v1?rss=1 Marcella M Gomez Richard M Murray Matthew R Bennett 2015-05-22 doi:10.1101/019687 Cold Spring Harbor Laboratory Press 2015-05-22 <![CDATA[ Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs ]]> https://biorxiv.org/content/10.1101/031385v1?rss=1 Jenny Chen Alexander A. Shishkin Xiaopeng Zhu Sabah Kadri Itay Maza Jacob H Hanna Aviv Regev Manuel Garber 2015-11-11 doi:10.1101/031385 Cold Spring Harbor Laboratory Press 2015-11-11 <![CDATA[ Structural and kinetic analysis of the COP9-Signalosome activation and the cullin-RING ubiquitin ligase deneddylation cycle ]]> https://biorxiv.org/content/10.1101/046367v1?rss=1 Ruzbeh Mosadeghi Kurt M Reichermeier Martin Winkler Anne Schreiber Justin M Reitsma Yaru Zhang Florian Stengel Junyue Cao Minsoo Kim Michael J Sweredoski Sonja Hess Alexander Leitner Ruedi Aebersold Matthias Peter Raymond J Deshaies Radolsav I Enchev 2016-03-30 doi:10.1101/046367 Cold Spring Harbor Laboratory Press 2016-03-30 <![CDATA[ Development of prokaryotic cell-free systems for synthetic biology ]]> https://biorxiv.org/content/10.1101/048710v1?rss=1 Abel C Chiao Richard M Murray Zachary Z Sun 2016-04-15 doi:10.1101/048710 Cold Spring Harbor Laboratory Press 2016-04-15 <![CDATA[ Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways ]]> https://biorxiv.org/content/10.1101/072439v1?rss=1 Lynn Yi Harold Pimentel Lior Pachter 2016-08-30 doi:10.1101/072439 Cold Spring Harbor Laboratory Press 2016-08-30 <![CDATA[ Transcriptomic Description of an Endogenous Female State in C. elegans ]]> https://biorxiv.org/content/10.1101/083113v1?rss=1 Angeles-Albores, D. Leighton, D. H. W. Tsou, T. Khaw, T. H. Antoshechkin, I. Sternberg, P. 2016-10-27 doi:10.1101/083113 Cold Spring Harbor Laboratory Press 2016-10-27 <![CDATA[ Resolving the Functional Significance of BRCA1 RING Domain Missense Substitutions ]]> https://biorxiv.org/content/10.1101/092619v1?rss=1 Paquette, A. Tao, K. Stark, A. W. Rosenthal, J. Bell, R. Thompson, B. A. Milash, B. A. Gertz, J. Varley, K. E. Thomas, A. Boucher, K. Foulkes, W. D. Goldgar, D. E. Tavtigian, S. V. 2016-12-08 doi:10.1101/092619 Cold Spring Harbor Laboratory Press 2016-12-08 <![CDATA[ Phenotype and gene ontology enrichment as guides for disease modeling in C. elegans ]]> https://biorxiv.org/content/10.1101/106369v1?rss=1 Angeles-Albores, D. Lee, R. Y. Chan, J. Sternberg, P. W. 2017-02-07 doi:10.1101/106369 Cold Spring Harbor Laboratory Press 2017-02-07 <![CDATA[ An allosteric theory of transcription factor induction ]]> https://biorxiv.org/content/10.1101/111013v1?rss=1 Razo-Mejia, M. Barnes, S. L. Belliveau, N. M. Chure, G. Einav, T. Phillips, R. 2017-02-22 doi:10.1101/111013 Cold Spring Harbor Laboratory Press 2017-02-22 <![CDATA[ Genetic Analysis of a Metazoan Pathway using Transcriptomic Phenotypes ]]> https://biorxiv.org/content/10.1101/112920v1?rss=1 Angeles Albores, D. Puckett Robinson, C. Williams, B. A. Sternberg, P. W. 2017-03-02 doi:10.1101/112920 Cold Spring Harbor Laboratory Press 2017-03-02 <![CDATA[ The Human Cell Atlas ]]> https://biorxiv.org/content/10.1101/121202v1?rss=1 Regev, A. Teichmann, S. Lander, E. S. Amit, I. Benoist, C. Birney, E. Bodenmiller, B. Campbell, P. Carninci, P. Clatworthy, M. Clevers, H. Deplancke, B. Dunham, I. Eberwine, J. Eils, R. Enard, W. Farmer, A. Fugger, L. Gottgens, B. Hacohen, N. Haniffa, M. Hemberg, M. Kim, S. K. Klenerman, P. Kriegstein, A. Lein, E. Linnarsson, S. Lundeberg, J. Majumder, P. Marioni, J. Merad, M. Mhlanga, M. Nawijn, M. Netea, M. Nolan, G. Pe'er, D. Philipakis, A. Ponting, C. P. Quake, S. R. Reik, W. Rozenblatt-Rosen, O. Sanes, J. R. Satija, R. Shumacher, T. Shalek, A. K 2017-05-08 doi:10.1101/121202 Cold Spring Harbor Laboratory Press 2017-05-08 <![CDATA[ A general method to fine-tune fluorophores for live-cell and in vivo imaging ]]> https://biorxiv.org/content/10.1101/127613v1?rss=1 Grimm, J. B. Muthusamy, A. K. Liang, Y. Brown, T. A. Lemon, W. C. Patel, R. Lu, R. Macklin, J. J. Keller, P. J. Ji, N. Lavis, L. D. 2017-04-14 doi:10.1101/127613 Cold Spring Harbor Laboratory Press 2017-04-14 <![CDATA[ Transcranial alternating current stimulation (tACS) mechanisms and protocols ]]> https://biorxiv.org/content/10.1101/138834v1?rss=1 Tavakoli, A. V. Yun, K. 2017-05-17 doi:10.1101/138834 Cold Spring Harbor Laboratory Press 2017-05-17 <![CDATA[ The structural basis for regulation of the nucleo-cytoplasmic distribution of Bag6 by TRC35 ]]> https://biorxiv.org/content/10.1101/154351v1?rss=1 Mock, J.-Y. Xu, Y. Ye, Y. Clemons, W. 2017-06-23 doi:10.1101/154351 Cold Spring Harbor Laboratory Press 2017-06-23 <![CDATA[ Diffusion as a ruler: modeling kinesin diffusion as a length sensor for intraflagellar transport ]]> https://biorxiv.org/content/10.1101/156760v1?rss=1 Hendel, N. L. Thomson, M. Marshall, W. F. 2017-06-27 doi:10.1101/156760 Cold Spring Harbor Laboratory Press 2017-06-27 <![CDATA[ Gene-level differential analysis at transcript-level resolution ]]> https://biorxiv.org/content/10.1101/190199v1?rss=1 Yi, L. Pimentel, H. Bray, N. L. Pachter, L. 2017-09-18 doi:10.1101/190199 Cold Spring Harbor Laboratory Press 2017-09-18 <![CDATA[ Gene drive and resilience through renewal with next generation Cleave and Rescue selfish genetic elements ]]> https://biorxiv.org/content/10.1101/2019.12.13.876169v1?rss=1 Oberhofer, G. Ivy, T. Hay, B. A. 2019-12-15 doi:10.1101/2019.12.13.876169 Cold Spring Harbor Laboratory Press 2019-12-15 <![CDATA[ Deciphering the regulatory genome of Escherichiacoli, one hundred promoters at a time ]]> https://biorxiv.org/content/10.1101/2020.01.18.910323v1?rss=1 Ireland, W. T. T. Beeler, S. M. Flores-Bautista, E. Belliveau, N. M. Sweredoski, M. J. Moradian, A. Kinney, J. B. Phillips, R. 2020-01-18 doi:10.1101/2020.01.18.910323 Cold Spring Harbor Laboratory Press 2020-01-18 <![CDATA[ New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements ]]> https://biorxiv.org/content/10.1101/2020.01.24.918748v1?rss=1 Mageeney, C. M. Lau, B. Y. Wagner, J. M. Hudson, C. M. Schoeniger, J. S. Krishnakumar, R. Williams, K. P. 2020-01-25 doi:10.1101/2020.01.24.918748 Cold Spring Harbor Laboratory Press 2020-01-25 <![CDATA[ Lateral gene transfer drives metabolic flexibility in the anaerobic methane oxidising archaeal family Methanoperedenaceae ]]> https://biorxiv.org/content/10.1101/2020.02.06.936641v1?rss=1 McIlroy, S. J. Leu, A. O. Ye, J. Parks, D. H. Orphan, V. Tyson, G. W. 2020-02-06 doi:10.1101/2020.02.06.936641 Cold Spring Harbor Laboratory Press 2020-02-06 <![CDATA[ Aesthetic preference for art emerges from a weighted integration over hierarchically structured visual features in the brain ]]> https://biorxiv.org/content/10.1101/2020.02.09.940353v1?rss=1 Iigaya, K. Yi, S. Wahle, I. A. Tanwisuth, K. O'Doherty, J. P. 2020-02-10 doi:10.1101/2020.02.09.940353 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ Dynamic changes in tRNA modifications and abundance during T-cell activation ]]> https://biorxiv.org/content/10.1101/2020.03.14.991901v1?rss=1 Rak, R. Polonsky, M. Eizenberg, I. Dahan, O. Friedman, N. Pilpel, Y. T. 2020-03-15 doi:10.1101/2020.03.14.991901 Cold Spring Harbor Laboratory Press 2020-03-15 <![CDATA[ Convergent Antibody Responses to SARS-CoV-2 Infection in Convalescent Individuals ]]> https://biorxiv.org/content/10.1101/2020.05.13.092619v1?rss=1 1:5000. Antibody cloning revealed expanded clones of RBD-specific memory B cells expressing closely related antibodies in different individuals. Despite low plasma titers, antibodies to three distinct epitopes on RBD neutralized at half-maximal inhibitory concentrations (IC50s) as low as single digit ng/mL. Thus, most convalescent plasmas obtained from individuals who recover from COVID-19 do not contain high levels of neutralizing activity. Nevertheless, rare but recurring RBD-specific antibodies with potent antiviral activity were found in all individuals tested, suggesting that a vaccine designed to elicit such antibodies could be broadly effective. ]]> Robbiani, D. F. Gaebler, C. Muecksch, F. Cetrulo Lorenzi, J. Wang, Z. Cho, A. Agudelo, M. Barnes, C. Finkin, S. Hagglof, T. Oliveira, T. Viant, C. Hurley, A. Millard, K. Kost, R. Cipolla, M. Gazumyan, A. Gordon, K. Bianchini, F. Chen, S. Ramos, V. Patel, R. Dizon, J. Shimeliovich, I. Mendoza, P. Hartweger, H. Nogueira, L. Pack, M. Horowitz, J. Schmidt, F. Weisblum, Y. Hoffmann, H.-H. Michailidis, E. Ashbrook, A. Waltari, E. F. Pak, J. Huey-Tubman, K. Koranda, N. Hoffman, P. West, A. Rice, C. Hatziioannou, T. Bjorkman, P. Bieniasz, P. Caskey, M. Nuss 2020-05-15 doi:10.1101/2020.05.13.092619 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Human es-fMRI Resource: Concurrent deep-brain stimulation and whole-brain functional MRI ]]> https://biorxiv.org/content/10.1101/2020.05.18.102657v1?rss=1 Thompson, W. H. Nair, R. Oya, H. Esteban, O. Shine, J. M. Petkov, C. Poldrack, R. A. Howard, M. Adolphs, R. 2020-05-20 doi:10.1101/2020.05.18.102657 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Heuristic Spike Sorting Tuner (HSST), a framework to determine optimal parameter selection for a generic spike sorting algorithm ]]> https://biorxiv.org/content/10.1101/2020.05.21.108902v1?rss=1 Bjanes, D. Fisher, L. E. Gaunt, R. Weber, D. 2020-05-25 doi:10.1101/2020.05.21.108902 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ What computational model provides the best explanation of face representations in the primate brain? ]]> https://biorxiv.org/content/10.1101/2020.06.07.111930v1?rss=1 Chang, L. Egger, B. Vetter, T. Tsao, D. 2020-06-08 doi:10.1101/2020.06.07.111930 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ Reconciling Kinetic and Equilibrium Models of Bacterial Transcription ]]> https://biorxiv.org/content/10.1101/2020.06.13.150292v1?rss=1 Morrison, M. J. Razo-Mejia, M. Phillips, R. 2020-06-14 doi:10.1101/2020.06.13.150292 Cold Spring Harbor Laboratory Press 2020-06-14 <![CDATA[ Secondary single-cell transcriptomic analysis reveals common molecular signatures of cerebrovascular injury between traumatic brain injury and aging ]]> https://biorxiv.org/content/10.1101/2020.06.29.178855v1?rss=1 Guo, X. Zhang, B. Gomez-Pinilla, F. Gao, F. Zhao, Z. 2020-06-30 doi:10.1101/2020.06.29.178855 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ 2-Locus ​ Cleave and Rescue ​ selfish elements harness a recombination rate-dependent generational clock for self limiting gene drive ]]> https://biorxiv.org/content/10.1101/2020.07.09.196253v1?rss=1 Georg Oberhofer Tobin Ivy Bruce Hay 2020-07-09 doi:10.1101/2020.07.09.196253 Cold Spring Harbor Laboratory Press 2020-07-09 <![CDATA[ Experience-dependent plasticity in an innate social behavior is mediated by hypothalamic LTP ]]> https://biorxiv.org/content/10.1101/2020.07.21.214619v1?rss=1 Stagkourakis, S. Spigolon, G. Liu, G. Anderson, D. J. 2020-07-22 doi:10.1101/2020.07.21.214619 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ Non-canonical, potassium-driven cerebrospinal fluid clearance ]]> https://biorxiv.org/content/10.1101/2020.08.03.234260v1?rss=1 Xu, H. Fame, R. M. Sadegh, C. Sutin, J. Naranjo, C. Syau, D. Cui, J. Shipley, F. B. Vernon, A. Gao, F. Zhang, Y. Holtzman, M. J. Heiman, M. Warf, B. C. Lin, P.-Y. Lehtinen, M. K. 2020-08-04 doi:10.1101/2020.08.03.234260 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ A MATLAB Toolbox for Modeling Genetic Circuits in Cell-Free Systems ]]> https://biorxiv.org/content/10.1101/2020.08.05.237990v1?rss=1 Singhal, V. Tuza, Z. A. Sun, Z. Murray, R. M. 2020-08-05 doi:10.1101/2020.08.05.237990 Cold Spring Harbor Laboratory Press 2020-08-05 <![CDATA[ Cryo-EM Structures of HIV-1 trimer bound to CD4-mimetics M48U1 and BNM-III-170 adopt a CD4-bound open conformation ]]> https://biorxiv.org/content/10.1101/2020.08.21.261974v1?rss=1 Jette, C. A. Barnes, C. O. Kirk, S. M. Melillo, B. Smith, A. B. Bjorkman, P. J. 2020-08-22 doi:10.1101/2020.08.21.261974 Cold Spring Harbor Laboratory Press 2020-08-22 <![CDATA[ Wild flies hedge their thermal preference bets in response to seasonal fluctuations ]]> https://biorxiv.org/content/10.1101/2020.09.16.300731v1?rss=1 Akhund-Zade, J. Yoon, D. Bangerter, A. Polizos, N. Campbell, M. K. Soloshenko, A. Zhang, T. Wice, E. Albright, A. Narayanan, A. Schmidt, P. Saltz, J. Ayroles, J. Klein, M. Bergland, A. de Bivort, B. 2020-09-20 doi:10.1101/2020.09.16.300731 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ Benchmarking ensemble docking methods as a scientific outreach project ]]> https://biorxiv.org/content/10.1101/2020.10.02.324343v1?rss=1 Gan, J. L. Kumar, D. Chen, C. Taylor, B. C. Jagger, B. R. Amaro, R. E. Lee, C. T. 2020-10-04 doi:10.1101/2020.10.02.324343 Cold Spring Harbor Laboratory Press 2020-10-04 <![CDATA[ Robotic Multi-Probe-Single-Actuator Inchworm Neural Microdrive ]]> https://biorxiv.org/content/10.1101/2020.10.13.338137v1?rss=1 Smith, R. D. Kolb, I. Tanaka, S. Lee, A. K. Harris, T. D. Barbic, M. 2020-10-16 doi:10.1101/2020.10.13.338137 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ Convergence of a common solution to broad ebolavirus neutralization by glycan cap directed human antibodies ]]> https://biorxiv.org/content/10.1101/2020.10.14.340026v1?rss=1 Murin, C. D. Gilchuk, P. Ilinykh, P. Huang, K. Kuzmina, N. Shen, X. Brunh, J. F. Brunh, A. L. Davidson, E. Doranz, B. Williamson, L. E. Copps, J. Alkutkar, T. Flyak, A. I. Bukreyev, A. Crowe, J. E. Ward, A. B. 2020-10-14 doi:10.1101/2020.10.14.340026 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ The embryonic node functions as an instructive stem cell niche ]]> https://biorxiv.org/content/10.1101/2020.11.10.376913v1?rss=1 Solovieva, T. Lu, H.-C. Moverley, A. Plachta, N. Stern, C. D. 2020-11-11 doi:10.1101/2020.11.10.376913 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ osr1 couples intermediate mesoderm cell fate with temporal dynamics of vessel progenitor cell differentiation ]]> https://biorxiv.org/content/10.1101/2020.11.14.383141v1?rss=1 Perens, E. Diaz, J. Quesnel, A. Askary, A. Crump, G. Yelon, D. 2020-11-15 doi:10.1101/2020.11.14.383141 Cold Spring Harbor Laboratory Press 2020-11-15 <![CDATA[ Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus ]]> https://biorxiv.org/content/10.1101/2020.12.10.420141v1?rss=1 Brueckner, A. Barnett, A. A. Antoshechkin, I. A. Kitchen, S. A. 2020-12-11 doi:10.1101/2020.12.10.420141 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Benzoquinones in the defensive secretion of a bug (Pamillia behrensii): a common chemical trait retrieved in the Heteroptera ]]> https://biorxiv.org/content/10.1101/2020.12.11.421891v1?rss=1 Wagner, J. M. Naragon, T. H. Brueckner, A. 2020-12-12 doi:10.1101/2020.12.11.421891 Cold Spring Harbor Laboratory Press 2020-12-12 <![CDATA[ Analysis of Circuits for Dosage Control in Microbial Populations ]]> https://biorxiv.org/content/10.1101/2020.12.18.423556v1?rss=1 Walton, S. J. Clamons, S. E. Murray, R. M. 2020-12-20 doi:10.1101/2020.12.18.423556 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ Mice in a labyrinth: Rapid learning, sudden insight, and efficient exploration ]]> https://biorxiv.org/content/10.1101/2021.01.14.426746v1?rss=1 Rosenberg, M. Zhang, T. Perona, P. Meister, M. 2021-01-15 doi:10.1101/2021.01.14.426746 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ The coral symbiont Candidatus Aquarickettsia is variably abundant in threatened Caribbean acroporids and transmitted horizontally. ]]> https://biorxiv.org/content/10.1101/2021.01.28.428674v1?rss=1 Baker, L. J. Reich, H. G. Kitchen, S. A. Klinges, J. G. Koch, H. R. Baums, I. B. Muller, E. Vega Thurber, R. 2021-01-29 doi:10.1101/2021.01.28.428674 Cold Spring Harbor Laboratory Press 2021-01-29 <![CDATA[ Discovery of Dynamical Network Models for Genetic Circuits from Time-Series Data with Incomplete Measurements ]]> https://biorxiv.org/content/10.1101/2021.03.10.434835v1?rss=1 Yeung, E. Kim, J. Yuan, Y. Goncalves, J. Murray, R. M. 2021-03-10 doi:10.1101/2021.03.10.434835 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ kinesin recruitment by adapter SKIP on melanosomes is dynamically controlled by LC3B phosphorylation ]]> https://biorxiv.org/content/10.1101/2021.03.11.434917v1?rss=1 Subramaniam, Y. J. Murthy, D. Raja, A. D. Ramkumar, A. Sivasubbu, S. McEwan, D. G. Gokhale, R. S. Natarajan, V. 2021-03-12 doi:10.1101/2021.03.11.434917 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ The geometry of face memory ]]> https://biorxiv.org/content/10.1101/2021.03.12.435023v1?rss=1 She, L. Benna, M. K. Shi, Y. Fusi, S. Tsao, D. Y. 2021-03-12 doi:10.1101/2021.03.12.435023 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Antibody elicited by HIV-1 immunogen vaccination in macaques displaces Env fusion peptide and destroys a neutralizing epitope ]]> https://biorxiv.org/content/10.1101/2021.03.17.435265v1?rss=1 Abernathy, M. E. Gristick, H. B. Vielmetter, J. Keeffe, J. R. Gnanapragasam, P. N. Lee, Y. E. Escolano, A. Gautam, R. Seaman, M. S. Martin, M. A. Nussenzweig, M. C. Bjorkman, P. J. 2021-03-17 doi:10.1101/2021.03.17.435265 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Acetylated α-tubulin residue K394 regulates microtubule stability to shape the growth of axon terminals ]]> https://biorxiv.org/content/10.1101/2021.04.01.438108v1?rss=1 Saunders, H. A. J. Johnson-Schlitz, D. M. Jenkins, B. V. Volkert, P. J. Yang, S. Z. Wildonger, J. 2021-04-02 doi:10.1101/2021.04.01.438108 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ Inhibition is the hallmark of CA3 intracellular dynamics around awake ripples ]]> https://biorxiv.org/content/10.1101/2021.04.20.440699v1?rss=1 Kajikawa, K. Hulse, B. K. Siapas, A. G. Lubenov, E. V. 2021-04-22 doi:10.1101/2021.04.20.440699 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Homologous locus pairing is a transient, diffusion-mediated process in meiotic prophase ]]> https://biorxiv.org/content/10.1101/2021.04.23.440859v1?rss=1 Newman, T. A. Beltran, B. McGehee, J. M. Elnatan, D. Cahoon, C. K. Paddy, M. Chu, D. B. Spakowitz, A. J. Burgess, S. M. 2021-04-24 doi:10.1101/2021.04.23.440859 Cold Spring Harbor Laboratory Press 2021-04-24 <![CDATA[ Mechanical vibration patterns elicit behavioral transitions and habituation in crawling Drosophila larvae ]]> https://biorxiv.org/content/10.1101/2021.04.26.441415v1?rss=1 Berne, A. Zhang, T. Shomar, J. Ferrer, A. J. Valdes, A. Ohyama, T. Klein, M. 2021-04-27 doi:10.1101/2021.04.26.441415 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq ]]> https://biorxiv.org/content/10.1101/2021.04.26.441522v1?rss=1 Rebboah, E. Reese, F. Williams, K. Balderrama-Gutierrez, G. McGill, C. Trout, D. Rodriguez, I. M. Liang, H. Wold, B. J. Mortazavi, A. 2021-04-27 doi:10.1101/2021.04.26.441522 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Vivarium: an interface and engine for integrative multiscale modeling in computational biology ]]> https://biorxiv.org/content/10.1101/2021.04.27.441657v1?rss=1 Agmon, E. Spangler, R. K. Skalnik, C. J. Poole, W. Peirce, S. M. Morrison, J. H. Covert, M. W. 2021-04-28 doi:10.1101/2021.04.27.441657 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ A Method for Cost-Effective and Rapid Characterization of Genetic Parts ]]> https://biorxiv.org/content/10.1101/2021.04.30.440836v1?rss=1 McManus, J. B. Bernhards, C. B. Sharpes, C. E. Garcia, D. C. Murray, R. M. Cole, S. D. Emanuel, P. A. Lux, M. W. 2021-05-01 doi:10.1101/2021.04.30.440836 Cold Spring Harbor Laboratory Press 2021-05-01 <![CDATA[ A somatic piRNA pathway regulates epithelial-to-mesenchymal transition of chick neural crest cells ]]> https://biorxiv.org/content/10.1101/2021.04.30.442165v1?rss=1 Galton, R. Fejes-Toth, K. Bronner, M. E. 2021-04-30 doi:10.1101/2021.04.30.442165 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Dissection of multiple sclerosis genetics identifies B and CD4 T cells as driver cell subsets ]]> https://biorxiv.org/content/10.1101/2021.05.24.445445v1?rss=1 Guo, M. Sama, P. LaBarre, B. Lokhande, H. Balibalos, J. Chu, C. Du, X. Kheradpour, P. Kim, C. Oniskey, T. Snyder, T. Soghoian, D. Weiner, H. Chitnis, T. Patsopoulos, N. 2021-05-25 doi:10.1101/2021.05.24.445445 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Timing of meristem initiation and maintenance determines the morphology of fern gametophytes ]]> https://biorxiv.org/content/10.1101/2021.06.14.448200v1?rss=1 Wu, X. Yan, A. McAdam, S. Banks, J. A. Zhang, S. Zhou, Y. 2021-06-14 doi:10.1101/2021.06.14.448200 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ Atypical gaze patterns in autism are heterogeneous across subjects but reliable within individuals ]]> https://biorxiv.org/content/10.1101/2021.07.01.450793v1?rss=1 Keles, U. Kliemann, D. Byrge, L. Saarimaki, H. Paul, L. K. Kennedy, D. P. Adolphs, R. 2021-07-02 doi:10.1101/2021.07.01.450793 Cold Spring Harbor Laboratory Press 2021-07-02 <![CDATA[ Gene drive that results in addiction to a temperature sensitive version of an essential gene triggers population collapse in Drosophila ]]> https://biorxiv.org/content/10.1101/2021.07.03.451005v1?rss=1 Oberhofer, G. Hay, B. Ivy, T. 2021-07-04 doi:10.1101/2021.07.03.451005 Cold Spring Harbor Laboratory Press 2021-07-04 <![CDATA[ Mice and primates use distinct strategies for visual segmentation ]]> https://biorxiv.org/content/10.1101/2021.07.04.451059v1?rss=1 Luongo, F. J. Liu, L. Ho, C. L. A. Hesse, J. K. Wekselblatt, J. B. Lanfranchi, F. Huber, D. K. Tsao, D. Y. 2021-07-05 doi:10.1101/2021.07.04.451059 Cold Spring Harbor Laboratory Press 2021-07-05 <![CDATA[ Differences in the dynamics of the tandem-SH2 modules of the Syk and ZAP-70 tyrosine kinases ]]> https://biorxiv.org/content/10.1101/2021.07.20.453126v1?rss=1 Hobbs, H. T. Shah, N. H. Badroos, J. M. Gee, C. L. Marqusee, S. Kuriyan, J. 2021-07-20 doi:10.1101/2021.07.20.453126 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ The human neuronal receptor NgR1 bridges reovirus capsid proteins to initiate infection ]]> https://biorxiv.org/content/10.1101/2021.07.23.453469v1?rss=1 Sutherland, D. M. Strebl, M. Koehler, M. Welsh, O. L. Yu, X. Hu, L. dos Santos Natividade, R. Knowlton, J. J. Taylor, G. M. Moreno, R. Woerz, P. Lonergan, Z. L. Aravamudhan, P. Guzman-Cardozo, C. Alsteens, D. Wang, Z. Prasad, B. Stehle, T. Dermody, T. S. 2021-07-24 doi:10.1101/2021.07.23.453469 Cold Spring Harbor Laboratory Press 2021-07-24 <![CDATA[ Mechanics of live cell elimination ]]> https://biorxiv.org/content/10.1101/2021.08.17.456649v1?rss=1 Monfared, S. Ravichandran, G. Andrade, J. E. Doostmohammadi, A. 2021-08-18 doi:10.1101/2021.08.17.456649 Cold Spring Harbor Laboratory Press 2021-08-18 <![CDATA[ Critical Role for Isoprenoids in Apicoplast Biogenesis by Malaria Parasites ]]> https://biorxiv.org/content/10.1101/2021.08.19.456988v1?rss=1 Okada, M. Rajaram, K. Swift, R. P. Mixon, A. Maschek, J. A. Prigge, S. T. Sigala, P. A. 2021-08-19 doi:10.1101/2021.08.19.456988 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Biomechanical interactions of Schistosoma mansoni eggs with vascular endothelial cells facilitate egg extravasation ]]> https://biorxiv.org/content/10.1101/2021.09.16.459846v1?rss=1 Yeh, Y.-T. Skinner, D. E. Criado-Hidalgo, E. Chen, N. S. Garcia-De Herreros, A. El-Sakary, N. Liu, L. Zhang, S. Chien, S. Lasheras, J. C. del Alamo, J. C. Caffrey, C. R. 2021-09-17 doi:10.1101/2021.09.16.459846 Cold Spring Harbor Laboratory Press 2021-09-17 <![CDATA[ Endotaxis: A Universal Algorithm for Mapping, Goal-Learning, and Navigation ]]> https://biorxiv.org/content/10.1101/2021.09.24.461751v1?rss=1 Zhang, T. Rosenberg, M. Perona, P. Meister, M. 2021-09-25 doi:10.1101/2021.09.24.461751 Cold Spring Harbor Laboratory Press 2021-09-25 <![CDATA[ How to model DNA replication in stochastic models of synthetic genetic circuits (and why) ]]> https://biorxiv.org/content/10.1101/2021.09.26.461880v1?rss=1 Clamons, S. Murray, R. M. 2021-09-27 doi:10.1101/2021.09.26.461880 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ Control of protein activity by photoinduced spin polarized charge reorganization ]]> https://biorxiv.org/content/10.1101/2021.10.12.464058v1?rss=1 Ghosh, S. Ghosh, K. B. Levy, D. Scheerer, D. Riven, I. Shin, J. Gray, H. Naaman, R. Haran, G. 2021-10-13 doi:10.1101/2021.10.12.464058 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Single-Shot Optical Projection tomography for high-speed volumetric imaging ]]> https://biorxiv.org/content/10.1101/2021.10.15.464407v1?rss=1 Darling, C. J. Davis, S. P. X. Kumar, S. French, P. M. W. McGinty, J. A. 2021-10-16 doi:10.1101/2021.10.15.464407 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ Motor processivity and speed determine structure and dynamics of microtubule-motor assemblies ]]> https://biorxiv.org/content/10.1101/2021.10.22.465381v1?rss=1 Banks, R. A. Galstyan, V. Lee, H. J. Hirokawa, S. Ierokomos, A. Ross, T. D. Bryant, Z. Thomson, M. Phillips, R. 2021-10-23 doi:10.1101/2021.10.22.465381 Cold Spring Harbor Laboratory Press 2021-10-23 <![CDATA[ Hypothermia Suppresses Uncoupling of Oxidative-Phosphorylation after Neonatal Cerebral Hypoxia-Ischemia ]]> https://biorxiv.org/content/10.1101/2021.11.29.470404v1?rss=1 Sun, N. Sun, Y.-Y. Cao, R. Chen, H.-R. Wang, Y. Fugate, E. Smucker, M. R. Kuo, Y.-M. Grant, P. E. Lindquist, D. M. Kuan, C.-Y. Hu, S. 2021-11-30 doi:10.1101/2021.11.29.470404 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ Precise quantification of behavioral individuality from 80 million decisions across 183,000 flies ]]> https://biorxiv.org/content/10.1101/2021.12.15.472856v1?rss=1 de Bivort, B. L. Buchanan, S. M. Skutt-Kakaria, K. J. Gajda, E. O'Leary, C. J. Reimers, P. Akhund-Zade, J. Senft, R. Maloney, R. Ho, S. Werkhoven, Z. Smith, M. A.-Y. 2021-12-17 doi:10.1101/2021.12.15.472856 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ Cell Chromatography: Biocompatible chromatographic separation and interrogation of microbial cells ]]> https://biorxiv.org/content/10.1101/2022.03.07.482710v1?rss=1 Hazu, M. Ahmed, A. Curry, E. A. Hornby, D. P. Gjerde, D. T. 2022-03-07 doi:10.1101/2022.03.07.482710 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ HIV-1 CD4-binding site germline antibody-Env structures inform vaccine design ]]> https://biorxiv.org/content/10.1101/2022.03.25.485873v1?rss=1 Dam, K.-M. A. Barnes, C. O. Gristick, H. B. Schoofs, T. Nussenzweig, M. C. Bjorkman, P. J. 2022-03-26 doi:10.1101/2022.03.25.485873 Cold Spring Harbor Laboratory Press 2022-03-26 <![CDATA[ Functional Cell Types in the Mouse Superior Colliculus ]]> https://biorxiv.org/content/10.1101/2022.04.01.486789v1?rss=1 Li, Y. Meister, M. 2022-04-05 doi:10.1101/2022.04.01.486789 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Isometric Spiracular Scaling in Scarab Beetles: Implications for Diffusive and Advective Oxygen Transport ]]> https://biorxiv.org/content/10.1101/2022.04.06.487277v1?rss=1 Wagner, J. M. Klok, C. J. Duell, M. E. Socha, J. Cao, G. Gong, H. Harrison, J. F. 2022-04-08 doi:10.1101/2022.04.06.487277 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ Restricting α-Synuclein Transport into Mitochondria by Inhibition of α-Synuclein-VDAC Complexation as a Potential Therapeutic Target for Parkinson's Disease Treatment ]]> https://biorxiv.org/content/10.1101/2022.04.07.487541v1?rss=1 Rajendran, M. Queralt-Martin, M. Gurnev, P. A. Rosencrans, W. M. Rovini, A. Jacobs, D. Abrantes, K. Hoogerheide, D. P. Bezrukov, S. M. Rostovtseva, T. K. 2022-04-08 doi:10.1101/2022.04.07.487541 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ BANKSY: A Spatial Omics Algorithm that Unifies Cell Type Clustering and Tissue Domain Segmentation ]]> https://biorxiv.org/content/10.1101/2022.04.14.488259v1?rss=1 Singhal, V. Chou, N. Lee, J. Liu, J. Chock, W. K. Lin, L. Chang, Y.-C. Teo, E. Lee, H. K. Chen, K. H. Prabhakar, S. 2022-04-15 doi:10.1101/2022.04.14.488259 Cold Spring Harbor Laboratory Press 2022-04-15 <![CDATA[ Honey bee functional genomics using symbiont-mediated RNAi ]]> https://biorxiv.org/content/10.1101/2022.04.22.489157v1?rss=1 Lariviere, P. J. Leonard, S. P. Horak, R. D. Powell, J. E. Barrick, J. E. 2022-04-25 doi:10.1101/2022.04.22.489157 Cold Spring Harbor Laboratory Press 2022-04-25 <![CDATA[ ST6GAL1 sialyltransferase promotes acinar to ductal metaplasia and pancreatic cancer progression ]]> https://biorxiv.org/content/10.1101/2022.04.28.489561v1?rss=1 Chakraborty, A. Bhalerao, N. Marciel, M. P. Hwang, J. Britain, C. Eltoum, E. E. Jones, R. B. Alexander, K. L. Smythies, L. E. Smith, P. D. Crossman, D. K. Crowley, M. R. Shin, B. Harrington, L. E. Yan, Z. Bethea, M. M. Hunter, C. S. Klug, C. A. Buchsbaum, D. J. Bellis, S. L. 2022-04-28 doi:10.1101/2022.04.28.489561 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Emergent Actin Flows Explain Diverse Parasite Gliding Modes ]]> https://biorxiv.org/content/10.1101/2022.06.08.495399v1?rss=1 Hueschen, C. L. Segev Zarko, L.-a. Chen, J.-H. LeGros, M. A. Larabell, C. A. Boothroyd, J. C. Phillips, R. Dunn, A. R. 2022-06-09 doi:10.1101/2022.06.08.495399 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Strengthening of enterococcal biofilms by Esp ]]> https://biorxiv.org/content/10.1101/2022.06.09.495547v1?rss=1 Spiegelman, L. Bahn-Suh, A. Montano, E. Zhang, L. Hura, G. Patras, K. Kumar, A. Tezcan, A. Nizet, V. Tsutakawa, S. Ghosh, P. 2022-06-09 doi:10.1101/2022.06.09.495547 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Wildebeest Herds on Rolling Hills: Flocking on Arbitrary Curved Surfaces ]]> https://biorxiv.org/content/10.1101/2022.06.22.497052v1?rss=1 Hueschen, C. L. Dunn, A. R. Phillips, R. 2022-06-25 doi:10.1101/2022.06.22.497052 Cold Spring Harbor Laboratory Press 2022-06-25 <![CDATA[ Comparative genomic insights into bacterial induction of larval settlement and metamorphosis in the upside-down jellyfish Cassiopea ]]> https://biorxiv.org/content/10.1101/2022.06.24.497576v1?rss=1 Ohdera, A. Medina, M. Fitt, W. Hofmann, D. K. Attarwala, K. Henry, R. Wu, V. Laird, H. 2022-06-25 doi:10.1101/2022.06.24.497576 Cold Spring Harbor Laboratory Press 2022-06-25 <![CDATA[ Genotyping, sequencing and analysis of 140,000 adults from the Mexico City Prospective Study ]]> https://biorxiv.org/content/10.1101/2022.06.26.495014v1?rss=1 Ziyatdinov, A. Torres, J. Alegre-Diaz, J. Backman, J. Mbatchou, J. Turner, M. Gaynor, S. M. Joseph, T. Zou, Y. Liu, D. Wade, R. Staples, J. Panea, R. Popov, A. Maxwell, E. Jones, M. Garcia-Ortiz, H. Ramirez-Reyes, R. Santacruz-Benitez, R. Nag, A. Smith, K. R. Regeneron Genetics Center, Reppell, M. Zollner, S. Jorgenson, E. Salerno, W. Petrovski, S. Overton, J. Reid, J. Thornton, T. Abecasis, G. Berumen, J. Orozco-Orozco, L. Collins, R. Baras, A. Hill, M. R. Emberson, J. R. Marchini, J. Kuri-Morales, P. Tapia-Conyer, R. 2022-06-29 doi:10.1101/2022.06.26.495014 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Isoform- and ligand-specific modulation of the adhesion GPCR ADGRL3/Latrophilin3 by a synthetic binder ]]> https://biorxiv.org/content/10.1101/2022.07.20.500857v1?rss=1 Kordon, S. P. Dutka, P. Adamska, J. M. Bandekar, S. J. Leon, K. Adams, B. Li, J. Kossiakoff, A. A. Arac, D. 2022-07-21 doi:10.1101/2022.07.20.500857 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ Functional Ultrasound Imaging of the Human Spinal Cord ]]> https://biorxiv.org/content/10.1101/2022.08.06.503044v1?rss=1 Agyeman, K. Lee, D. J. Russin, J. Kreydin, E. I. Choi, W. Abedi, A. Edgerton, V. R. Liu, C. Christopoulos, V. 2022-08-06 doi:10.1101/2022.08.06.503044 Cold Spring Harbor Laboratory Press 2022-08-06 <![CDATA[ A discrete mode of endosomal GPCR signaling that does not require β-arrestin ]]> https://biorxiv.org/content/10.1101/2022.09.07.506997v1?rss=1 Blythe, E. E. Von Zastrow, M. 2022-09-08 doi:10.1101/2022.09.07.506997 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ CD4-binding site immunogens elicit heterologous anti-HIV-1 neutralizing antibodies in transgenic and wildtype animals ]]> https://biorxiv.org/content/10.1101/2022.09.08.507086v1?rss=1 Gristick, H. B. Hartweger, H. Loewe, M. van Schooten, J. Ramos, V. Oliviera, T. Y. Nishimura, Y. Koranda, N. S. Wall, A. Yao, K.-H. Poston, D. Gazumyan, A. Wiatr, M. Horning, M. Keeffe, J. R. Hoffmann, M. A. Yang, Z. Abernathy, M. E. Dam, K.-M. A. Gao, H. Gnanapragasam, P. N. Kakutani, L. M. Pavlovitch-Bedzyk, A. J. Seaman, M. S. Howarth, M. McGuire, A. T. Stamatatos, L. Martin, M. A. West, A. P. Nussenzweig, M. C. Bjorkman, P. J. 2022-09-12 doi:10.1101/2022.09.08.507086 Cold Spring Harbor Laboratory Press 2022-09-12 <![CDATA[ Unsupervised Restoration of a Complex Learned Behavior After Large-Scale Neuronal Perturbation ]]> https://biorxiv.org/content/10.1101/2022.09.09.507372v1?rss=1 Wang, B. Torok, Z. Duffy, A. Bell, D. Wongso, S. Velho, T. Fairhall, A. Lois, C. 2022-09-10 doi:10.1101/2022.09.09.507372 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Cells in the Polyaneuploid Cancer Cell (PACC) state have increased metastatic potential ]]> https://biorxiv.org/content/10.1101/2022.09.16.508155v1?rss=1 Mallin, M. M. Kim, N. Choudhury, M. I. Lee, S. J. An, S. S. Sun, S. X. Konstantopoulos, K. Pienta, K. J. Amend, S. R. 2022-09-19 doi:10.1101/2022.09.16.508155 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes ]]> https://biorxiv.org/content/10.1101/2022.09.26.509520v1?rss=1 Voelker, W. G. Krishnan, K. Chougule, K. Alexander, L. C. Lu, Z. Olson, A. Ware, D. Songsomboon, K. Ponce, C. M. Brenton, Z. Boatwright, J. L. Cooper, E. A. 2022-09-27 doi:10.1101/2022.09.26.509520 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Drosophila epidermal cells are intrinsically mechanosensitive and drive nociceptive behavioral outputs ]]> https://biorxiv.org/content/10.1101/2022.10.07.511265v1?rss=1 Yoshino, J. Mali, S. Williams, C. Morita, T. Emerson, C. Arp, C. Sophie, M. Yin, C. The, L. Chikaya, H. Motoyoshi, M. Ishii, K. Emoto, K. Bautista, D. M. Parrish, J. Z. 2022-10-10 doi:10.1101/2022.10.07.511265 Cold Spring Harbor Laboratory Press 2022-10-10 <![CDATA[ The Plasmodium falciparum apicoplast cysteine desulfurase provides sulfur for both iron sulfur cluster assembly and tRNA modification ]]> https://biorxiv.org/content/10.1101/2022.10.31.514511v1?rss=1 Prigge, S. T. Swift, R. P. Elahi, R. Rajaram, K. Liu, H. B. 2022-11-01 doi:10.1101/2022.10.31.514511 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Root Walker: an automated pipeline for large scale quantification of early root growth responses at high spatial and temporal resolution ]]> https://biorxiv.org/content/10.1101/2022.11.16.516796v1?rss=1 Platre, M. P. Halvorson, Z. Mehta, P. Brent, L. Matias, G. F. Faizi, K. Busch, W. 2022-11-17 doi:10.1101/2022.11.16.516796 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Tools for comprehensive reconstruction and analysis of Drosophila motor circuits ]]> https://biorxiv.org/content/10.1101/2022.12.15.520299v1?rss=1 Azevedo, A. W. Lesser, E. Mark, B. Phelps, J. S. Elabbady, L. Kuroda, S. Sustar, A. E. Moussa, A. J. Kandelwal, A. Dallmann, C. J. Agrawal, S. Lee, S.-Y. J. Pratt, B. G. Cook, A. Skutt-Kakari, K. Gerhard, S. Lu, R. Kemnitz, N. Lee, K. Halageri, A. Castro, M. Ih, D. Gager, J. Tammam, M. Dorkenwald, S. Collman, F. C. Schneider-Mizell, C. M. Brittain, D. Jordan, C. S. Dickinson, M. H. Pacureanu, A. Seung, H. S. Macrina, T. Lee, W.-C. A. Tuthill, J. C. 2022-12-15 doi:10.1101/2022.12.15.520299 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content ]]> https://biorxiv.org/content/10.1101/2023.01.12.523500v1?rss=1 de Jonghe, J. Kaminski, T. S. Morse, D. Tabaka, M. Ellermann, A. L. Kohler, T. N. Amadei, G. Handford, C. Findlay, G. Zernicka-Goetz, M. Teichmann, S. Hollfelder, F. 2023-01-13 doi:10.1101/2023.01.12.523500 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Structural characterization of HIV-1 Env heterotrimers bound to one or two CD4 receptors reveals intermediate Env conformations ]]> https://biorxiv.org/content/10.1101/2023.01.27.525985v1?rss=1 Dam, K.-M. A. Fan, C. Yang, Z. Bjorkman, P. J. 2023-01-28 doi:10.1101/2023.01.27.525985 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ Evolution of connectivity architecture in the Drosophila mushroom body ]]> https://biorxiv.org/content/10.1101/2023.02.10.528036v1?rss=1 Caron, S. J. C. Ellis, K. E. Smihula, H. Ganguli, I. Vigato, E. Bervoets, S. Auer, T. O. Benton, R. Litwin Kumar, A. 2023-02-12 doi:10.1101/2023.02.10.528036 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ Encoding of predictive associations in human prefrontal and medial temporal neurons during Pavlovian conditioning ]]> https://biorxiv.org/content/10.1101/2023.02.10.528055v1?rss=1 Aquino, T. G. Courellis, H. S. Mamelak, A. Rutishauser, U. O'Doherty, J. 2023-02-12 doi:10.1101/2023.02.10.528055 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ Discovery and characterization of a chemical probe targeting the zinc-finger ubiquitin-binding domain of HDAC6 ]]> https://biorxiv.org/content/10.1101/2023.02.21.525740v1?rss=1 Harding, R. J. Franzoni, I. Mann, M. K. Szewczyk, M. Mirabi, B. Owens, D. D. Ackloo, S. Scheremetjew, A. Juarez-Ornelas, K. A. Sanichar, R. Baker, R. J. Dank, C. Brown, P. J. Barsyte-Lovejoy, D. Santhakumar, V. Schapira, M. Lautens, M. Arrowsmith, C. H. 2023-02-22 doi:10.1101/2023.02.21.525740 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ Migration and establishment of progenitor pool of melanocytes is governed by SEMA3E-PLXND1 signaling ]]> https://biorxiv.org/content/10.1101/2023.02.28.530560v1?rss=1 Natarajan, V. T. Subramaniam, Y. Sharma, B. Aggarwal, A. Raja, D. A. Gupta, I. Ghazi, M. Sivasubbu, S. 2023-03-02 doi:10.1101/2023.02.28.530560 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Bacterial Form I' rubisco has smaller carbon isotope fractionation than its Form I counterpart ]]> https://biorxiv.org/content/10.1101/2023.03.01.530675v1?rss=1 Wang, R. Z. Liu, A. K. Banda, D. M. Fischer, W. W. Shih, P. M. 2023-03-02 doi:10.1101/2023.03.01.530675 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Hyperconnectivity of two separate long-range cholinergic systems contributes to the reorganization of the brain functional connectivity during nicotine withdrawal in male mice ]]> https://biorxiv.org/content/10.1101/2023.03.29.534836v1?rss=1 Carrette, L. L. G. Kimbrough, A. Davoudian, P. A. Kwan, A. C. Collazo, A. George, O. 2023-03-31 doi:10.1101/2023.03.29.534836 Cold Spring Harbor Laboratory Press 2023-03-31 <![CDATA[ Tunable photoinitiated hydrogel microspheres for direct quantification of cell-generated forces in complex three-dimensional environments ]]> https://biorxiv.org/content/10.1101/2023.03.31.535168v1?rss=1 Garcia-Herreros, A. Yeh, Y.-T. Tu, Y. Kandasamy, A. del Alamo, J. C. Criado Hidalgo, E. 2023-04-03 doi:10.1101/2023.03.31.535168 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ SUMOylation of Bonus, the Drosophila homolog of Transcription Intermediary Factor 1, safeguards germline identity by recruiting repressive chromatin complexes to silence tissue-specific genes ]]> https://biorxiv.org/content/10.1101/2023.04.14.536936v1?rss=1 Godneeva, B. Ninova, M. Fejes Toth, K. Aravin, A. 2023-04-15 doi:10.1101/2023.04.14.536936 Cold Spring Harbor Laboratory Press 2023-04-15 <![CDATA[ Integrative mapping of spatial transcriptomic and amyloid pathology in Alzheimer's disease at single-cell resolution ]]> https://biorxiv.org/content/10.1101/2023.05.07.539389v1?rss=1 Zhang, G.-W. Xia, S. Zhang, N. K. Gao, F. Zlokovic, B. V. Zhang, L. I. Zhao, Z. Tao, H. 2023-05-07 doi:10.1101/2023.05.07.539389 Cold Spring Harbor Laboratory Press 2023-05-07 <![CDATA[ Frequency- and circuit- specific effects of septohippocampal deep brain stimulation in mice as measured by functional ultrasound imaging. ]]> https://biorxiv.org/content/10.1101/2023.05.21.541598v1?rss=1 Crown, L. M. Agyeman, K. Choi, W. Zepeda, N. Siegel, S. Liu, C. Christopoulos, V. Lee, D. 2023-05-22 doi:10.1101/2023.05.21.541598 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Synaptic architecture of leg and wing motor control networks in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.05.30.542725v1?rss=1 Lesser, E. Azevedo, A. W. Phelps, J. S. Elabbady, L. Cook, A. P. Mark, B. Kuroda, S. Sustar, A. Moussa, A. J. Dallmann, C. J. Agrawal, S. Lee, S.-Y. J. Pratt, B. G. Skutt-Kakari, K. Gerhard, S. Lu, R. Kemnitz, N. Lee, K. Halageri, A. Castro, M. Ih, D. Gager, J. Tammam, M. Dorkenwald, S. Collman, F. C. Schneider-Mizell, C. M. Brittain, D. Jordan, C. S. Seung, H. S. Macrina, T. Dickinson, M. H. Lee, W.-C. A. Tuthill, J. C. 2023-05-31 doi:10.1101/2023.05.30.542725 Cold Spring Harbor Laboratory Press 2023-05-31 <![CDATA[ Closed ecosystems extract energy through self-organized nutrient cycles ]]> https://biorxiv.org/content/10.1101/2023.05.30.542875v1?rss=1 Goyal, A. Flamholz, A. I. Petroff, A. P. Murugan, A. 2023-06-01 doi:10.1101/2023.05.30.542875 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Cellular reprogramming of human monocytes is regulated by time-dependent IL4 signalling and NCOR2 ]]> https://biorxiv.org/content/10.1101/204180v1?rss=1 Sander, J. Schmidt, S. V. Cirovic, B. McGovern, N. Papantonopoulou, O. Hardt, A.-L. Aschenbrenner, A. Kreer, C. Quast, T. Xu, A. M. Schmidtleithner, L. M. Theis, H. Do, T. H. L. Bin Sumatoh, H. R. Lauterbach, M. A. R. Schulte-Schrepping, J. Guenther, P. Xue, J. Bassler, K. Ulas, T. Klee, K. Herresthal, S. Krebs, W. Martin, B. Latz, E. Haendler, K. Kraut, M. Kolanus, W. Beyer, M. Falk, C. S. Wiegmann, B. Burgdorf, S. Melosh, N. A. Newell, E. W. Ginhoux, F. Schlitzer, A. Schultze, J. L. 2017-10-16 doi:10.1101/204180 Cold Spring Harbor Laboratory Press 2017-10-16 <![CDATA[ A study of allelic series using transcriptomic phenotypes in a metazoan ]]> https://biorxiv.org/content/10.1101/210724v1?rss=1 Angeles-Albores, D. Sternberg, P. 2017-10-29 doi:10.1101/210724 Cold Spring Harbor Laboratory Press 2017-10-29 <![CDATA[ Control of bacterial population density with population feedback and molecular sequestration ]]> https://biorxiv.org/content/10.1101/225045v1?rss=1 McCardell, R. D. Huang, S. Green, L. N. Murray, R. M. 2017-11-25 doi:10.1101/225045 Cold Spring Harbor Laboratory Press 2017-11-25 <![CDATA[ Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control ]]> https://biorxiv.org/content/10.1101/240747v1?rss=1 Matthews, B. J. Dudchenko, O. Kingan, S. Koren, S. Antoshechkin, I. Crawford, J. E. Glassford, W. J. Herre, M. Redmond, S. N. Rose, N. H. Weedall, G. D. Wu, Y. Batra, S. S. Brito-Sierra, C. A. Buckingham, S. D. Campbell, C. L. Chan, S. Cox, E. Evans, B. R. Fansiri, T. Filipovic, I. Fontaine, A. Gloria-Soria, A. Hall, R. Joardar, V. S. Jones, A. K. Kay, R. G. G. Kodali, V. Lee, J. Lycett, G. J. Mitchell, S. N. Muehling, J. Murphy, M. R. Omer, A. Partridge, F. A. Peluso, P. Aiden, A. P. Ramasamy, V. Rasic, G. Roy, S. Saavedra-Rodriguez, K. Sharan, S. Sha 2017-12-29 doi:10.1101/240747 Cold Spring Harbor Laboratory Press 2017-12-29 <![CDATA[ VideoTagger: User-Friendly Software for Annotating Video Experiments of Any Duration ]]> https://biorxiv.org/content/10.1101/272468v1?rss=1 Rennert, P. Mac Aodha, O. Piper, M. Brostow, G. 2018-02-27 doi:10.1101/272468 Cold Spring Harbor Laboratory Press 2018-02-27 <![CDATA[ Evolutionary analysis implicates RNA polymerase II pausing and chromatin structure in nematode piRNA biogenesis ]]> https://biorxiv.org/content/10.1101/281360v1?rss=1 Beltran, T. Barruso, C. Birkle, T. Stevens, L. Schwartz, H. T. Sternberg, P. Fradin, H. Gunsalus, K. Piano, F. Martinez-Perez, E. Blaxter, M. Sarkies, P. 2018-03-13 doi:10.1101/281360 Cold Spring Harbor Laboratory Press 2018-03-13 <![CDATA[ Behavior of homing endonuclease gene drives targeting genes required for viability or female fertility with multiplexed guide RNAs ]]> https://biorxiv.org/content/10.1101/289546v1?rss=1 Oberhofer, G. Ivy, T. Hay, B. A. 2018-03-27 doi:10.1101/289546 Cold Spring Harbor Laboratory Press 2018-03-27 <![CDATA[ Augmented Reality Powers a Cognitive Prosthesis for the Blind ]]> https://biorxiv.org/content/10.1101/321265v1?rss=1 Liu, Y. Stiles, N. R. B. Meister, M. 2018-05-22 doi:10.1101/321265 Cold Spring Harbor Laboratory Press 2018-05-22 <![CDATA[ Long-distance communication in synthetic bacterial consortia through active signal propagation ]]> https://biorxiv.org/content/10.1101/321307v1?rss=1 Parkin, J. M. Murray, R. M. 2018-05-14 doi:10.1101/321307 Cold Spring Harbor Laboratory Press 2018-05-14 <![CDATA[ Genetic, biochemical, and molecular characterization of Methanosarcina barkeri mutants lacking three distinct classes of hydrogenase ]]> https://biorxiv.org/content/10.1101/334656v1?rss=1 Kulkarni, G. Mand, T. D. Metcalf, W. W. 2018-05-30 doi:10.1101/334656 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ Energy conservation via hydrogen cycling in the methanogenic archaeon Methanosarcina barkeri ]]> https://biorxiv.org/content/10.1101/335794v1?rss=1 Kulkarni, G. Mand, T. D. Metcalf, W. W. 2018-05-31 doi:10.1101/335794 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ Single-cell transcriptomics identifies CD44 as a new marker and regulator of haematopoietic stem cells development ]]> https://biorxiv.org/content/10.1101/338178v1?rss=1 Oatley, M. Vargel Bolukbasi, O. Svensson, V. Shvartsman, M. Ganter, K. Zirngibl, K. Pavlovich, P. V. Milchevskaya, V. Foteva, V. Natarajan, K. N. Baying, B. Benes, V. Patil, K. R. Teichmann, S. A. Lancrin, C. 2018-06-06 doi:10.1101/338178 Cold Spring Harbor Laboratory Press 2018-06-06 <![CDATA[ A command-like descending neuron that coordinately activates backward and inhibits forward locomotion ]]> https://biorxiv.org/content/10.1101/339556v1?rss=1 Doe, C. Q. Zarin, A. A. Carreira-Rosario, A. Clark, M. Q. Manning, L. Cardona, A. Fetter, R. D. 2018-06-05 doi:10.1101/339556 Cold Spring Harbor Laboratory Press 2018-06-05 <![CDATA[ Multiple sclerosis-associated changes in the composition and immune functions of spore-forming bacteria ]]> https://biorxiv.org/content/10.1101/343558v1?rss=1 Cekanaviciute, E. Probstel, A.-K. Thomann, A. Runia, T. Casaccia, P. Katz Sand, I. Crabtree, E. Singh, S. Morrissey, J. Barba, P. Gomez, R. Knight, R. Mazmanian, S. Graves, J. Cree, B. C. A. Zamvil, S. S. Baranzini, S. 2018-06-11 doi:10.1101/343558 Cold Spring Harbor Laboratory Press 2018-06-11 <![CDATA[ Context Dependence of Biological Circuits ]]> https://biorxiv.org/content/10.1101/360040v1?rss=1 Catanach, T. McCardell, R. D. Baetica, A.-A. Murray, R. 2018-07-03 doi:10.1101/360040 Cold Spring Harbor Laboratory Press 2018-07-03 <![CDATA[ Precision measurement of cis-regulatory energetics in living cells ]]> https://biorxiv.org/content/10.1101/380972v1?rss=1 Forcier, T. Ayaz, A. Gill, M. S. Jones, D. Phillips, R. Kinney, J. B. 2018-07-31 doi:10.1101/380972 Cold Spring Harbor Laboratory Press 2018-07-31 <![CDATA[ Multiple C2 domains and Transmembrane region Proteins (MCTPs) tether membranes at plasmodesmata ]]> https://biorxiv.org/content/10.1101/423905v1?rss=1 Brault, M. L. Petit, J. D. Immel, F. Nicolas, W. J. Brocard, L. Gaston, A. Fouche, M. Hawkins, T. J. Crowet, J.-M. Grison, M. S. Kraner, M. Alva, V. Claverol, S. Deleu, M. Lins, L. Tilsner, J. Bayer, E. E. 2018-09-23 doi:10.1101/423905 Cold Spring Harbor Laboratory Press 2018-09-23 <![CDATA[ Diverse food-sensing neurons trigger idiothetic local search in Drosophila ]]> https://biorxiv.org/content/10.1101/433771v1?rss=1 Corfas, R. A. Dickinson, M. H. 2018-10-03 doi:10.1101/433771 Cold Spring Harbor Laboratory Press 2018-10-03 <![CDATA[ Programmed Delayed Splicing: A Mechanism for Timed Inflammatory Gene Expression ]]> https://biorxiv.org/content/10.1101/443796v1?rss=1 Majumdar, D. Frankiw, L. Burns, C. H. Garcia-Flores, Y. Baltimore, D. 2018-10-15 doi:10.1101/443796 Cold Spring Harbor Laboratory Press 2018-10-15 <![CDATA[ Bud13 Promotes a Type I Interferon Response By Countering Intron Retention in Irf7 ]]> https://biorxiv.org/content/10.1101/443820v1?rss=1 Frankiw, L. S. Majumdar, D. Burns, C. Vlach, L. Moradian, A. Sweredoski, M. Baltimore, D. 2018-10-15 doi:10.1101/443820 Cold Spring Harbor Laboratory Press 2018-10-15 <![CDATA[ Quantitative single-cell splicing analysis reveals an ‘economy of scale’ filter for gene expression ]]> https://biorxiv.org/content/10.1101/457432v1?rss=1 Ding, F. Elowitz, M. 2018-10-30 doi:10.1101/457432 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ Controlling Organization and Forces in Active Matter Through Optically-Defined Boundaries ]]> https://biorxiv.org/content/10.1101/504456v1?rss=1 Ross, T. Lee, H. J. Qu, Z. Banks, R. A. Phillips, R. Thomson, M. 2018-12-21 doi:10.1101/504456 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ Does testosterone impair men’s cognitive empathy? Evidence from two large-scale randomized controlled trials ]]> https://biorxiv.org/content/10.1101/516344v1?rss=1 Nadler, A. Zava, D. Ortiz, T. Watson, N. Carre, J. Camerer, C. Nave, G. 2019-01-13 doi:10.1101/516344 Cold Spring Harbor Laboratory Press 2019-01-13 <![CDATA[ Human Phageprints: A high-resolution exploration of oral phages reveals globally-distributed phage families with individual-specific and temporally-stable community compositions ]]> https://biorxiv.org/content/10.1101/516864v1?rss=1 Mahmoudabadi, G. Homyk, K. Catching, A. Foley, H. Tadmor, A. Mahmoudabadi, A. Cheung, A. Phillips, R. 2019-01-10 doi:10.1101/516864 Cold Spring Harbor Laboratory Press 2019-01-10 <![CDATA[ Prospective, brain-wide labeling of neuronal subclasses with enhancer-driven AAVs ]]> https://biorxiv.org/content/10.1101/525014v1?rss=1 Graybuck, L. T. Sedeno-Cortes, A. Nguyen, T. N. Walker, M. Szelenyi, E. Lenz, G. Sieverts, L. Kim, T. K. Garren, E. Kalmbach, B. Yao, S. Mortrud, M. Mich, J. Goldy, J. Smith, K. A. Dee, N. Yao, Z. Cetin, A. Levi, B. P. Lein, E. Ting, J. Zeng, H. Daigle, T. Tasic, B. 2019-01-20 doi:10.1101/525014 Cold Spring Harbor Laboratory Press 2019-01-20 <![CDATA[ The fitness cost of a congenital heart defect shapes its genetic architecture ]]> https://biorxiv.org/content/10.1101/531988v1?rss=1 Akhirome, E. O. Regmi, S. D. Magnan, R. Ugwu, N. Qin, Y. Schulkey, C. E. Cheverud, J. M. Jay, P. Y. 2019-01-27 doi:10.1101/531988 Cold Spring Harbor Laboratory Press 2019-01-27 <![CDATA[ Repressive gene regulation synchronizes development with cellular metabolism ]]> https://biorxiv.org/content/10.1101/548032v1?rss=1 Cassidy, J. J. Bernasek, S. Bakker, R. Giri, R. Pelaez, N. Eder, B. Bobrowska, A. Bagheri, N. Amaral, L. A. Carthew, R. W. 2019-02-12 doi:10.1101/548032 Cold Spring Harbor Laboratory Press 2019-02-12 <![CDATA[ Machine learning-guided channelrhodopsin engineering enables minimally-invasive optogenetics ]]> https://biorxiv.org/content/10.1101/565606v1?rss=1 Bedbrook, C. N. Yang, K. K. Robinson, J. E. Gradinaru, V. Arnold, F. H. 2019-03-03 doi:10.1101/565606 Cold Spring Harbor Laboratory Press 2019-03-03 <![CDATA[ A response to Zhang et al. (2018), \"Can Mouse-tracking Reveal Attribute Processing Speeds in Dietary Self-control? Commentary on Sullivan et al. (2015) and Lim et al. (2018)\" ]]> https://biorxiv.org/content/10.1101/572974v1?rss=1 Sullivan, N. J. Hutcherson, C. Harris, A. M. Rangel, A. 2019-03-11 doi:10.1101/572974 Cold Spring Harbor Laboratory Press 2019-03-11 <![CDATA[ How the Avidity of Polymerase Binding to the -35/-10 Promoter Sites Affects Gene Expression ]]> https://biorxiv.org/content/10.1101/597989v1?rss=1 Einav, T. Phillips, R. 2019-04-04 doi:10.1101/597989 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ Tunable integrase-mediated differentiation facilitates improved output of burdensome functions in E. coli ]]> https://biorxiv.org/content/10.1101/614529v1?rss=1 Williams, R. L. Murray, R. M. 2019-04-20 doi:10.1101/614529 Cold Spring Harbor Laboratory Press 2019-04-20 <![CDATA[ Control of density and composition in an engineered two-member bacterial community ]]> https://biorxiv.org/content/10.1101/632174v1?rss=1 McCardell, R. D. Pandey, A. Murray, R. M. 2019-05-09 doi:10.1101/632174 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Design of a genetic layered feedback controller in synthetic biological circuitry ]]> https://biorxiv.org/content/10.1101/647057v1?rss=1 Hu, C. Y. Murray, R. M. 2019-05-24 doi:10.1101/647057 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Regular Architecture (RegArch): A standard expression language for describing protein architectures ]]> https://biorxiv.org/content/10.1101/679910v1?rss=1 Ortega, D. R. Jensen, G. J. 2019-06-22 doi:10.1101/679910 Cold Spring Harbor Laboratory Press 2019-06-22 <![CDATA[ Coordination of tissue cell polarity by auxin transport and signaling ]]> https://biorxiv.org/content/10.1101/680090v1?rss=1 Verna, C. Ravichandran, S. J. Sawchuk, M. G. Linh, N. M. Scarpella, E. 2019-07-11 doi:10.1101/680090 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ Estimating the heritability of psychological measures in the Human Connectome Project dataset ]]> https://biorxiv.org/content/10.1101/704023v1?rss=1 Han, Y. Adolphs, R. 2019-07-16 doi:10.1101/704023 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ Characterization of the brain functional architecture of psychostimulant withdrawal using single-cell whole brain imaging ]]> https://biorxiv.org/content/10.1101/743799v1?rss=1 Kimbrough, A. Smith, L. C. Kallupi, M. Simpson, S. Collazo, A. George, O. 2019-08-22 doi:10.1101/743799 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ A metabolic pathway for bile acid dehydroxylation by the gut microbiome ]]> https://biorxiv.org/content/10.1101/758557v1?rss=1 Funabashi, M. Grove, T. Pascal, V. Varma, Y. McFadden, M. Brown, L. Guo, C. Medema, M. H. Almo, S. Fischbach, M. A. 2019-09-05 doi:10.1101/758557 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Assessment of Robustness to Temperature in a Negative Feedback Loop and a Feedforward Loop ]]> https://biorxiv.org/content/10.1101/774042v1?rss=1 Patel, A. Murray, R. M. Sen, S. 2019-09-18 doi:10.1101/774042 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila ]]> https://biorxiv.org/content/10.1101/775783v1?rss=1 Bernasek, S. M. Pelaez, N. Carthew, R. Bagheri, N. Amaral, L. 2019-09-19 doi:10.1101/775783 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ The structure of behavioral variation within a genotype ]]> https://biorxiv.org/content/10.1101/779363v1?rss=1 Werkhoven, Z. Bravin, A. Skutt-Kakaria, K. Reimers, P. Pallares, L. F. Ayroles, J. de Bivort, B. L. 2019-09-23 doi:10.1101/779363 Cold Spring Harbor Laboratory Press 2019-09-23 <![CDATA[ A dynamic pattern of local auxin sources is required for root regeneration ]]> https://biorxiv.org/content/10.1101/783480v1?rss=1 Matosevich, R. Cohen, I. Gil-Yarom, N. Modrego, A. Verna, C. Scarpella, E. Efroni, I. 2019-09-26 doi:10.1101/783480 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ A neural circuit basis for context-modulation of individual locomotor behavior ]]> https://biorxiv.org/content/10.1101/797126v1?rss=1 Skutt-Kakaria, K. Reimers, P. Currier, T. A. Werkhoven, Z. de Bivort, B. L. 2019-10-08 doi:10.1101/797126 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Flexible recruitment of memory-based choice representations by human medial-frontal cortex ]]> https://biorxiv.org/content/10.1101/809673v1?rss=1 Minxha, J. Adolphs, R. Fusi, S. Mamelak, A. Rutishauser, U. 2019-10-18 doi:10.1101/809673 Cold Spring Harbor Laboratory Press 2019-10-18 <![CDATA[ Live-Cell Imaging and Quantification of PolyQ Aggregates by Stimulated Raman Scattering of Selective Deuterium Labeling ]]> https://biorxiv.org/content/10.1101/820217v1?rss=1 Miao, K. Wei, L. 2019-10-28 doi:10.1101/820217 Cold Spring Harbor Laboratory Press 2019-10-28 <![CDATA[ Variability in the analysis of a single neuroimaging dataset by many teams ]]> https://biorxiv.org/content/10.1101/843193v1?rss=1 Botvinik-Nezer, R. Holzmeister, F. Camerer, C. Dreber, A. Huber, J. Johannesson, M. Kirchler, M. Nichols, T. E. Poldrack, R. A. Schonberg, T. 2019-11-15 doi:10.1101/843193 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ Organogenesis and Distribution of the Ocular Lymphatic Vessels in the Anterior Eye: Implication to Glaucoma Surgery Site Selection ]]> https://biorxiv.org/content/10.1101/847970v1?rss=1 Wu, Y. Seong, Y. J. Kin, L. Choi, D. Park, E. Daghlian, G. Jung, E. Bui, K. Luping, Z. Madhavan, S. Saren, D. Patill, D. Chin, D. Cho, I.-T. Wong, A. Heur, M. Zhang-Nunes, S. Tan, J. Ema, M. Huang, A. S. Hong, Y.-K. 2019-12-03 doi:10.1101/847970 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ Electrode pooling: How to boost the yield of switchable silicon probes for neuronal recordings ]]> https://biorxiv.org/content/10.1101/851691v1?rss=1 Lee, K. H. Ni, Y.-L. Meister, M. 2019-11-26 doi:10.1101/851691 Cold Spring Harbor Laboratory Press 2019-11-26 <![CDATA[ Value-related neuronal responses in the human amygdala during observational learning ]]> https://biorxiv.org/content/10.1101/865568v1?rss=1 Aquino, T. G. Minxha, J. Dunne, S. Ross, I. B. Mamelak, A. N. Rutishauser, U. O'Doherty, J. P. 2019-12-06 doi:10.1101/865568 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ Vein Patterning by Tissue-Specific Auxin Transport ]]> https://biorxiv.org/content/10.1101/866632v1?rss=1 Govindaraju, P. Verna, C. Zhu, T. Scarpella, E. 2019-12-06 doi:10.1101/866632 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ A window to the brain: ultrasound imaging of human neural activity through a permanent acoustic window ]]> https://biorxiv.org/content/10.1101/2023.06.14.544094v1?rss=1 Rabut, C. Norman, S. L. Griggs, W. S. Russin, J. J. Jann, K. Christopoulos, V. Liu, C. Andersen, R. A. Shapiro, M. G. 2023-06-15 doi:10.1101/2023.06.14.544094 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities ]]> https://biorxiv.org/content/10.1101/2023.06.18.545353v1?rss=1 Knecht, A. Sirias, D. Utter, D. R. Gibbs, K. A. 2023-06-18 doi:10.1101/2023.06.18.545353 Cold Spring Harbor Laboratory Press 2023-06-18 <![CDATA[ Patterning and folding of intestinal villi by active mesenchymal dewetting ]]> https://biorxiv.org/content/10.1101/2023.06.25.546328v1?rss=1 Huycke, T. R. Miyazaki, H. Häkkinen, T. Srivastava, V. Barruet, E. McGinnis, C. S. Kalantari, A. Cornwall-Scoones, J. Vaka, D. Zhu, Q. Jo, H. DeGrado, W. F. Thomson, M. Garikipati, K. Boffelli, D. Klein, O. D. Gartner, Z. J. 2023-06-26 doi:10.1101/2023.06.25.546328 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ 50-nm gas-filled protein nanostructures to enable the access of lymphatic cells by ultrasound technologies ]]> https://biorxiv.org/content/10.1101/2023.06.27.546433v1?rss=1 Shen, Q. Li, Z. Meyer, M. D. De Guzman, M. T. Lim, J. C. Bouchard, R. R. Lu, G. J. 2023-06-28 doi:10.1101/2023.06.27.546433 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ Truly tiny acoustic biomolecules for ultrasound imaging and therapy ]]> https://biorxiv.org/content/10.1101/2023.06.27.546773v1?rss=1 Ling, B. Gungoren, B. Yao, Y. Dutka, P. Smith, C. A. B. Lee, J. Swift, M. B. Shapiro, M. G. 2023-06-28 doi:10.1101/2023.06.27.546773 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ Processive movement of Staphylococcus aureus essential septal peptidoglycan synthases is independent of FtsZ treadmilling and drives cell constriction ]]> https://biorxiv.org/content/10.1101/2023.06.29.547026v1?rss=1 Schaeper, S. Brito, A. D. Saraiva, B. M. Squyres, G. R. Holmes, M. J. Garner, E. C. Hensel, Z. Henriques, R. Pinho, M. G. 2023-06-29 doi:10.1101/2023.06.29.547026 Cold Spring Harbor Laboratory Press 2023-06-29 <![CDATA[ Quantitative assessment of single-cell RNA-seq clustering with CONCORDEX ]]> https://biorxiv.org/content/10.1101/2023.06.28.546949v1?rss=1 Jackson, K. C. Booeshaghi, A. S. Galvez-Merchan, A. Moses, L. Chari, T. Pachter, L. 2023-06-30 doi:10.1101/2023.06.28.546949 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Machine learning reveals the control mechanics of the insect wing hinge ]]> https://biorxiv.org/content/10.1101/2023.06.29.547116v1?rss=1 Melis, J. M. Dickinson, M. H. 2023-06-30 doi:10.1101/2023.06.29.547116 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Configurational entropy is an intrinsic driver of tissue structural heterogeneity ]]> https://biorxiv.org/content/10.1101/2023.07.01.546933v1?rss=1 Srivastava, V. Hu, J. L. Garbe, J. C. Veytsman, B. Shalabi, S. F. Yllanes, D. Thomson, M. LaBarge, M. A. Huber, G. Gartner, Z. J. 2023-07-02 doi:10.1101/2023.07.01.546933 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Activity-Induced MeCP2 Phosphorylation Regulates Retinogeniculate Synapse Refinement ]]> https://biorxiv.org/content/10.1101/2023.07.03.547549v1?rss=1 Tzeng, C. P. Whitwam, T. Boxer, L. D. Li, E. Silberfeld, A. Trowbridge, S. Mei, K. Lin, C. Shamah, R. Griffith, E. C. Renthal, W. Chen, C. Greenberg, M. E. 2023-07-03 doi:10.1101/2023.07.03.547549 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Modeling the Correlation between Z and B in an X-ray Crystal Structure Refinement ]]> https://biorxiv.org/content/10.1101/2023.07.04.547724v1?rss=1 Buscagan, T. M. Rees, D. C. 2023-07-04 doi:10.1101/2023.07.04.547724 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ Neural subspaces of imagined movements in parietal cortex remain stable over several years in humans. ]]> https://biorxiv.org/content/10.1101/2023.07.05.547767v1?rss=1 Bashford, L. Rosenthal, I. A. Kellis, S. Bjanes, D. Pejsa, K. Brunton, B. W. Andersen, R. 2023-07-07 doi:10.1101/2023.07.05.547767 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ Sea lamprey enlightens the origin of the coupling of retinoic acid signaling to vertebrate hindbrain segmentation ]]> https://biorxiv.org/content/10.1101/2023.07.07.548143v1?rss=1 Bedois, A. Parker, H. J. Bronner, M. E. Krumlauf, R. 2023-07-07 doi:10.1101/2023.07.07.548143 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ Conservation and divergence of regulatory architecture in nitrate-responsive plant gene circuits ]]> https://biorxiv.org/content/10.1101/2023.07.17.549299v1?rss=1 Bian, C. Demirer, G. S. Oz, M. T. Cai, Y. Witham, S. Mason, G. A. Shen, R. Ahn, J. Gaudinier, A. Brady, S. Patron, N. 2023-07-17 doi:10.1101/2023.07.17.549299 Cold Spring Harbor Laboratory Press 2023-07-17 <![CDATA[ Voyager: exploratory single-cell genomics data analysis with geospatial statistics ]]> https://biorxiv.org/content/10.1101/2023.07.20.549945v1?rss=1 Moses, L. Einarsson, P. H. Jackson, K. C. Luebbert, L. Booeshaghi, A. S. Antonsson, S. E. Melsted, P. Pachter, L. 2023-07-22 doi:10.1101/2023.07.20.549945 Cold Spring Harbor Laboratory Press 2023-07-22 <![CDATA[ Multiplex, quantitative, high-resolution imaging of protein:protein complexes via hybridization chain reaction ]]> https://biorxiv.org/content/10.1101/2023.07.22.550181v1?rss=1 View larger version (21K): org.highwire.dtl.DTLVardef@dee6f4org.highwire.dtl.DTLVardef@cc6a6org.highwire.dtl.DTLVardef@c5ea79org.highwire.dtl.DTLVardef@1a4edee_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Schulte, S. J. Shin, B. Rothenberg, E. V. Pierce, N. A. 2023-07-23 doi:10.1101/2023.07.22.550181 Cold Spring Harbor Laboratory Press 2023-07-23 <![CDATA[ Computational and neural mechanisms underlying the influence of action affordances on value-based choice ]]> https://biorxiv.org/content/10.1101/2023.07.21.550102v1?rss=1 Yi, S. O'Doherty, J. P. 2023-07-25 doi:10.1101/2023.07.21.550102 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Gas vesicle-blood interactions enhance ultrasound imaging contrast ]]> https://biorxiv.org/content/10.1101/2023.07.24.550434v1?rss=1 Ling, B. Ko, J. H. Stordy, B. Zhang, Y. Didden, T. F. Malounda, D. Swift, M. B. Chan, W. C. W. Shapiro, M. G. 2023-07-25 doi:10.1101/2023.07.24.550434 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Pseudomonas aeruginosa AlgF is a protein-protein interaction mediator required for acetylation of the alginate exopolysaccharide ]]> https://biorxiv.org/content/10.1101/2023.07.25.550544v1?rss=1 Low, K. Gheorghita, A. A. Tammam, S. Whitfield, G. B. Li, Y. E. Riley, L. M. Weadge, J. Caldwell, S. Chong, P. A. Walvoort, M. Kitova, E. Klassen, J. Howell, P. L. 2023-07-25 doi:10.1101/2023.07.25.550544 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Systematic assessment of long-read RNA-seq methods for transcript identification and quantification ]]> https://biorxiv.org/content/10.1101/2023.07.25.550582v1?rss=1 Pardo-Palacios, F. J. Wang, D. Reese, F. Diekhans, M. Carbonell-Sala, S. Williams, B. Loveland, J. E. De Maria, M. Adams, M. S. Balderrama-Gutierrez, G. Behera, A. K. Gonzalez, J. M. Hunt, T. Lagarde, J. Liang, C. E. Li, H. Meade, M. J. Amador, D. A. M. Prjibelski, A. D. Birol, I. Bostan, H. Brooks, A. M. Celik, M. H. Chen, Y. Du, M. R. M. Felton, C. Goke, J. Hafezqorani, S. Herwig, R. Kawaji, H. Lee, J. Li, J.-L. Lienhard, M. Mikheenko, A. Mulligan, D. Nip, K. M. Pertea, M. Ritchie, M. E. Sim, A. D. Tang, A. D. Wan, Y. K. Wang, C. Wong, B. Y. Yang, C 2023-07-27 doi:10.1101/2023.07.25.550582 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Unraveling cell differentiation mechanisms through topological exploration of single-cell developmental trajectories ]]> https://biorxiv.org/content/10.1101/2023.07.28.551057v1?rss=1 Flores-Bautista, E. Thomson, M. 2023-07-30 doi:10.1101/2023.07.28.551057 Cold Spring Harbor Laboratory Press 2023-07-30 <![CDATA[ A feedback control mechanism governs the synthesis of lipid-linked precursors of the bacterial cell wall ]]> https://biorxiv.org/content/10.1101/2023.08.01.551478v1?rss=1 Marmont, L. S. Orta, A. K. Corey, R. A. Sychantha, D. Fernandez-Galliano, A. Li, Y. E. Baileeves, B. W. Greene, N. G. Stansfeld, P. J. Clemons, W. M. Bernhardt, T. G. 2023-08-01 doi:10.1101/2023.08.01.551478 Cold Spring Harbor Laboratory Press 2023-08-01 <![CDATA[ Functional potential and evolutionary response to long-term heat selection of bacterial associates of coral photosymbionts ]]> https://biorxiv.org/content/10.1101/2023.08.04.552070v1?rss=1 Maire, J. Philip, G. K. Livingston, J. Judd, L. M. Blackall, L. van Oppen, M. 2023-08-04 doi:10.1101/2023.08.04.552070 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ EasyFlow: An open source, user friendly cytometry analyzer with graphic user interface (GUI) ]]> https://biorxiv.org/content/10.1101/2023.08.07.552387v1?rss=1 Ma, Y. Antebi, Y. 2023-08-09 doi:10.1101/2023.08.07.552387 Cold Spring Harbor Laboratory Press 2023-08-09 <![CDATA[ An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event ]]> https://biorxiv.org/content/10.1101/2023.08.08.552427v1?rss=1 Davin, A. A. Woodcroft, B. J. Soo, R. M. Murali, R. Schrempf, D. Clark, J. Boussau, B. Moody, E. R. R. 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Razavi, P. Wang, B. Callejas-Marin, A. Lois, C. 2023-08-15 doi:10.1101/2023.08.14.553299 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ Changes in an Enzyme Ensemble During Catalysis Observed by High Resolution XFEL Crystallography ]]> https://biorxiv.org/content/10.1101/2023.08.15.553460v1?rss=1 Smith, N. Dasgupta, M. Wych, D. C. Dolamore, C. Sierra, R. G. Lisova, S. Marchany-Rivera, D. Cohen, A. E. Boutet, S. Hunter, M. S. Kupitz, C. Poitevin, F. Moss, F. R. Brewster, A. S. Sauter, N. K. Young, I. D. Wolff, A. M. Tiwari, V. K. Kumar, N. Berkowitz, D. B. Hadt, R. G. Thompson, M. C. Follmer, A. H. Wall, M. E. Wilson, M. A. 2023-08-16 doi:10.1101/2023.08.15.553460 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ Triaging of -helical proteins to the mitochondrial outer membrane by distinct chaperone machinery based on substrate topology ]]> https://biorxiv.org/content/10.1101/2023.08.16.553624v1?rss=1 Muthukumar, G. Stevens, T. A. Inglis, A. J. Esantsi, T. K. Saunders, R. A. Schulte, F. Voorhees, R. M. Guna, A. Weissman, J. S. 2023-08-17 doi:10.1101/2023.08.16.553624 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Intracellular Pseudomonas aeruginosa within the airway epithelium of Cystic Fibrosis lung tissues ]]> https://biorxiv.org/content/10.1101/2023.08.17.552973v1?rss=1 Malet, J. K. Faure, E. Adam, D. Donner, J. Liu, L. Pilon, S.-J. Fraser, R. Jorth, P. Newman, D. K. Brochiero, E. Rousseau, S. Nguyen, D. 2023-08-17 doi:10.1101/2023.08.17.552973 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Designed Endocytosis-Triggering Proteins mediate Targeted Degradation and amplify signaling ]]> https://biorxiv.org/content/10.1101/2023.08.19.553321v1?rss=1 Huang, B. Abedi, M. Ahn, G. Coventry, B. Sappington, I. Wang, R. Schlichthaerle, T. Zhang, J. Z. Wang, Y. Goreshnik, I. Chiu, C. W. Chazin-Gray, A. Chan, S. Gerben, S. Murray, A. Wang, S. O'Neill, J. Yeh, R. Misquith, A. Wolf, A. Tomasovic, L. M. Piraner, D. I. Gonzalez, M. J. D. Bennett, N. R. Venkatesh, P. Ahlrichs, M. Dobbins, C. Yang, W. Wang, X. Vafeados, D. Mout, R. Shivaei, S. Cao, L. Carter, L. Stewart, L. Spangler, J. B. Bernardes, G. J. L. Roybal, K. T. Greisen, P. J. Li, X. Bertozzi, C. Baker, D. 2023-08-21 doi:10.1101/2023.08.19.553321 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Diversity in Notch ligand-receptor signaling interactions ]]> https://biorxiv.org/content/10.1101/2023.08.24.554677v1?rss=1 Kuintzle, R. Santat, L. A. Elowitz, M. B. 2023-08-25 doi:10.1101/2023.08.24.554677 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ Using a multiscale lidar approach to determine variation in canopy structure from African forest elephant trails. ]]> https://biorxiv.org/content/10.1101/2023.08.25.554381v1?rss=1 Keany, J. M. Burns, P. Abraham, A. Jantz, P. Makaga, L. Saatchi, S. Maisels, F. Abernethy, K. Doughty, C. 2023-08-27 doi:10.1101/2023.08.25.554381 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ HCR spectral imaging: 10-plex, quantitative, high-resolution RNA and protein imaging in highly autofluorescent samples ]]> https://biorxiv.org/content/10.1101/2023.08.30.555626v1?rss=1 Schulte, S. J. Fornace, M. E. Hall, J. K. Pierce, N. A. 2023-08-30 doi:10.1101/2023.08.30.555626 Cold Spring Harbor Laboratory Press 2023-08-30 <![CDATA[ Metabolic evolution of pyranopterin-dependent biochemistry ]]> https://biorxiv.org/content/10.1101/2023.09.01.555371v1?rss=1 Goldford, J. E. Murali, R. Valentine, J. S. Fischer, W. W. 2023-09-05 doi:10.1101/2023.09.01.555371 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning ]]> https://biorxiv.org/content/10.1101/2023.09.03.556122v1?rss=1 Laubscher, E. Wang, X. Razin, N. Dougherty, T. Xu, R. Ombelets, L. Pao, E. Moffitt, J. Yue, Y. Van Valen, D. A. 2023-09-05 doi:10.1101/2023.09.03.556122 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ HIF1A contributes to the survival of aneuploid and mosaic pre-implantation embryos ]]> https://biorxiv.org/content/10.1101/2023.09.04.556218v1?rss=1 Sanchez-Vasquez, E. Zernicka-Goetz, M. Bronner, M. 2023-09-05 doi:10.1101/2023.09.04.556218 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Descending control and regulation of spontaneous flight turns in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.09.06.555791v1?rss=1 Ros, I. G. Omoto, J. J. Dickinson, M. H. 2023-09-06 doi:10.1101/2023.09.06.555791 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Conformational flexibility of HIV-1 envelope glycoproteins modulates transmitted / founder sensitivity to broadly neutralizing antibodies ]]> https://biorxiv.org/content/10.1101/2023.09.13.557082v1?rss=1 Ratnapriya, S. Pothula, K. R. Dam, K.-M. A. Parthasarathy, D. Benet, H. C. Parsons, R. Huang, X. Sammour, S. Janowska, K. Harris, M. Ahmed, S. Sacco, S. Sodroski, J. Bridges, M. Hubbell, W. Acharya, P. Herschhorn, A. 2023-09-13 doi:10.1101/2023.09.13.557082 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Resolving the nanoscale structure of β-sheet assemblies using single-molecule orientation-localization microscopy ]]> https://biorxiv.org/content/10.1101/2023.09.13.557571v1?rss=1 Zhou, W. O'Neill, C. L. Ding, T. Zhang, O. Rudra, J. S. Lew, M. D. 2023-09-14 doi:10.1101/2023.09.13.557571 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ Universal preprocessing of single-cell genomics data ]]> https://biorxiv.org/content/10.1101/2023.09.14.543267v1?rss=1 Booeshaghi, A. S. Sullivan, D. K. Pachter, L. 2023-09-15 doi:10.1101/2023.09.14.543267 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Comparison of image registration techniques in functional ultrasound imaging ]]> https://biorxiv.org/content/10.1101/2023.09.15.557999v1?rss=1 Zhong, S. Agyeman, K. Syed, S. Tobing, R. L. Choi, W. Liu, C. Lee, D. J. Christopoulos, V. 2023-09-16 doi:10.1101/2023.09.15.557999 Cold Spring Harbor Laboratory Press 2023-09-16 <![CDATA[ Biophysically Interpretable Inference of Cell Types from Multimodal Sequencing Data ]]> https://biorxiv.org/content/10.1101/2023.09.17.558131v1?rss=1 Chari, T. Gorin, G. Pachter, L. 2023-09-17 doi:10.1101/2023.09.17.558131 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Automated construction of cognitive maps with predictive coding ]]> https://biorxiv.org/content/10.1101/2023.09.18.558369v1?rss=1 Gornet, J. A. Thomson, M. 2023-09-19 doi:10.1101/2023.09.18.558369 Cold Spring Harbor Laboratory Press 2023-09-19 <![CDATA[ Serotonin predictively encodes value ]]> https://biorxiv.org/content/10.1101/2023.09.19.558526v1?rss=1 Harkin, E. F. Grossman, C. D. Cohen, J. Y. Beïque, J.-C. Naud, R. 2023-09-21 doi:10.1101/2023.09.19.558526 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ AgRP neuron activity promotes associations between sensory and nutritive signals to guide flavor preference ]]> https://biorxiv.org/content/10.1101/2023.09.19.558483v1?rss=1 Nyema, N. T. McKnight, A. D. Vargas-Elvira, A. G. Schneps, H. M. Gold, E. G. Myers, K. P. Alhadeff, A. L. 2023-09-22 doi:10.1101/2023.09.19.558483 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Redox Active Plant Phenolic, Acetosyringone, for Electrogenetic Signaling ]]> https://biorxiv.org/content/10.1101/2023.09.20.558642v1?rss=1 Zakaria, F. R. Chen, C.-Y. Li, J. Wang, S. P. Payne, G. F. Bentley, W. E. 2023-09-22 doi:10.1101/2023.09.20.558642 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Engineering antigen-specific tolerance to an artificial protein hydrogel ]]> https://biorxiv.org/content/10.1101/2023.09.23.559120v1?rss=1 Rapp, P. B. Baccile, J. A. Galimidi, R. P. Vielmetter, J. 2023-09-23 doi:10.1101/2023.09.23.559120 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ HI-FISH: WHOLE BRAIN IN SITU MAPPING OF NEURONAL ACTIVATION IN DROSOPHILA DURING SOCIAL BEHAVIORS AND OPTOGENETIC STIMULATION ]]> https://biorxiv.org/content/10.1101/2023.09.28.560045v1?rss=1 Anderson, D. J. Chiu, H. V. Watanabe, K. 2023-09-29 doi:10.1101/2023.09.28.560045 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Adaptation to space conditions of novel bacterial species isolated from the International Space Station revealed by functional gene annotations and comparative genome analysis ]]> https://biorxiv.org/content/10.1101/2023.09.28.559980v1?rss=1 SZYDLOWSKI, L. M. Bulbul, A. Simpson, A. C. Kaya, D. E. Singh, N. K. Sezerman, U. O. Labaj, P. P. Kosciolek, T. Venkateswaran, K. 2023-09-30 doi:10.1101/2023.09.28.559980 Cold Spring Harbor Laboratory Press 2023-09-30 <![CDATA[ Antagonists of the stress and opioid systems restore the functional connectivity of the prefrontal cortex during alcohol withdrawal through divergent mechanisms. ]]> https://biorxiv.org/content/10.1101/2023.09.30.560339v1?rss=1 Carrette, L. L. G. Santos, A. Brennan, M. Othman, D. Collazo, A. George, O. 2023-10-02 doi:10.1101/2023.09.30.560339 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Method for Spatially Confined Stimulation by Retinal Scanning Displays: Are Blind Spots Really Blind? ]]> https://biorxiv.org/content/10.1101/2023.10.03.560249v1?rss=1 Tavakoli, A.-V. Omata, T. Imamura, T. Ogawa, R. Iwasaki, M. del Rio Salgado, J. Rossi, I. Hung, S.-M. Wu, D.-A. Shimojo, S. 2023-10-05 doi:10.1101/2023.10.03.560249 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Co-transcriptional production of programmable RNA condensates and synthetic organelles ]]> https://biorxiv.org/content/10.1101/2023.10.06.561174v1?rss=1 Fabrini, G. Nuccio, S. P. Stewart, J. M. Lin, S. Tang, A. Rothemund, P. W. K. Franco, E. Di Antonio, M. Di Michele, L. 2023-10-06 doi:10.1101/2023.10.06.561174 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Histone H3 E50K mutation confers oncogenic activity and supports an EMT phenotype ]]> https://biorxiv.org/content/10.1101/2023.10.11.561775v1?rss=1 Sad, K. Jones, C. Y. Lustenberger, S. Lee, R. S. Elayavalli, S. R. Farhi, J. Lemon, L. D. Fasken, M. B. Corbett, A. H. Spangle, J. M. 2023-10-12 doi:10.1101/2023.10.11.561775 Cold Spring Harbor Laboratory Press 2023-10-12 <![CDATA[ Widespread detoxifying NO reductases impart a distinct isotopic fingerprint on N2O under anoxia ]]> https://biorxiv.org/content/10.1101/2023.10.13.562248v1?rss=1 Wang, R. Lonergan, Z. Wilbert, S. Eiler, J. Newman, D. K. 2023-10-14 doi:10.1101/2023.10.13.562248 Cold Spring Harbor Laboratory Press 2023-10-14 <![CDATA[ The fatty liver disease-causing protein PNPLA3-I148M alters lipid droplet-Golgi dynamics ]]> https://biorxiv.org/content/10.1101/2023.10.13.562302v1?rss=1 Sherman, D. J. Liu, L. Mamrosh, J. L. Xie, J. Ferbas, J. Lomenick, B. Ladinsky, M. S. Verma, R. Rulifson, I. C. Deshaies, R. J. 2023-10-14 doi:10.1101/2023.10.13.562302 Cold Spring Harbor Laboratory Press 2023-10-14 <![CDATA[ Cleave and Rescue gamete killers create conditions for gene drive in plants ]]> https://biorxiv.org/content/10.1101/2023.10.13.562303v1?rss=1 Oberhofer, G. Johnson, M. Ivy, T. Hay, B. 2023-10-14 doi:10.1101/2023.10.13.562303 Cold Spring Harbor Laboratory Press 2023-10-14 <![CDATA[ Generating counterfactual explanations of tumor spatial proteomes to discover effective strategies for enhancing immune infiltration ]]> https://biorxiv.org/content/10.1101/2023.10.12.562107v1?rss=1 Wang, Z. J. Xu, A. M. Bhargava, A. Thomson, M. 2023-10-16 doi:10.1101/2023.10.12.562107 Cold Spring Harbor Laboratory Press 2023-10-16 <![CDATA[ The Interferon-inducible NAMPT acts as a protein phosphoribosylase to restrict viral infection ]]> https://biorxiv.org/content/10.1101/2023.10.12.562112v1?rss=1 Feng, S. Xie, N. Liu, Y. Qin, C. Savas, A. C. Wang, T.-y. Li, S. Rao, Y. Shambayate, A. Chou, T.-f. Brenner, C. Huang, C. Feng, P. 2023-10-16 doi:10.1101/2023.10.12.562112 Cold Spring Harbor Laboratory Press 2023-10-16 <![CDATA[ Fluorescence dynamics of lysosomal-related organelle flashing in the intestinal cells of Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2023.10.16.562538v1?rss=1 Tan, C.-H. Ding, K. Zhang, M. G. Sternberg, P. W. 2023-10-18 doi:10.1101/2023.10.16.562538 Cold Spring Harbor Laboratory Press 2023-10-18 <![CDATA[ Distinct function of Chlamydomonas CTRA-CTR transporters in Cu assimilation and intracellular mobilization ]]> https://biorxiv.org/content/10.1101/2023.10.19.563170v1?rss=1 Strenkert, D. Schmollinger, S. Paruthiyil, S. Brown, B. C. Green, S. Shafer, C. M. Salome, P. A. Nelson, H. Blaby-Haas, C. E. Moseley, J. L. Merchant, S. S. 2023-10-19 doi:10.1101/2023.10.19.563170 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ T-cell commitment inheritance - an agent-based multi-scale model ]]> https://biorxiv.org/content/10.1101/2023.10.18.562905v1?rss=1 Andersson, E. Rothenberg, E. V. Peterson, C. Olariu, V. 2023-10-20 doi:10.1101/2023.10.18.562905 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Engineering the soil bacterium Pseudomonas synxantha 2-79 into a ratiometric bioreporter for phosphorus limitation ]]> https://biorxiv.org/content/10.1101/2023.10.20.563366v1?rss=1 Larsson, E. M. Murray, R. M. Newman, D. K. 2023-10-21 doi:10.1101/2023.10.20.563366 Cold Spring Harbor Laboratory Press 2023-10-21 <![CDATA[ Growth couples temporal and spatial fluctuations of tissue properties during morphogenesis ]]> https://biorxiv.org/content/10.1101/2023.10.23.563640v1?rss=1 Fruleux, A. Hong, L. Roeder, A. H. K. Li, C.-B. Boudaoud, A. 2023-10-25 doi:10.1101/2023.10.23.563640 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ TRILL: Orchestrating Modular Deep-Learning Workflows for Democratized, Scalable Protein Analysis and Engineering ]]> https://biorxiv.org/content/10.1101/2023.10.24.563881v1?rss=1 Martinez, Z. A. Murray, R. M. Thomson, M. W. 2023-10-27 doi:10.1101/2023.10.24.563881 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Metabolic similarity and the predictability of microbial community assembly ]]> https://biorxiv.org/content/10.1101/2023.10.25.564019v1?rss=1 Vila, J. C. C. Goldford, J. Estrela, S. Bajic, D. Sanchez-Gorostiaga, A. Damian-Serrano, A. Lu, N. Marsland, R. Rebolleda-Gomez, M. Mehta, P. Sanchez, A. 2023-10-28 doi:10.1101/2023.10.25.564019 Cold Spring Harbor Laboratory Press 2023-10-28 <![CDATA[ Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen deficient zones with diverse metabolic potential ]]> https://biorxiv.org/content/10.1101/2023.10.30.564641v1?rss=1 Zhang, I. H. Borer, B. Zhao, R. Wilbert, S. Newman, D. K. Babbin, A. R. 2023-10-30 doi:10.1101/2023.10.30.564641 Cold Spring Harbor Laboratory Press 2023-10-30 <![CDATA[ Principles of Computation by Competitive Protein Dimerization Networks ]]> https://biorxiv.org/content/10.1101/2023.10.30.564854v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@1917f39org.highwire.dtl.DTLVardef@13795bcorg.highwire.dtl.DTLVardef@47913eorg.highwire.dtl.DTLVardef@90bd30_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Parres-Gold, J. Levine, M. Emert, B. Stuart, A. Elowitz, M. 2023-11-02 doi:10.1101/2023.10.30.564854 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Neuropeptide Signaling Is Required To Implement A Line Attractor Encoding A Persistent Internal Behavioral State ]]> https://biorxiv.org/content/10.1101/2023.11.01.565073v1?rss=1 Mountoufaris, G. Nair, A. Yang, B. Kim, D.-W. Anderson, D. J. 2023-11-02 doi:10.1101/2023.11.01.565073 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Catalytic and non-catalytic functions of DNA polymerase kappa in translesion DNA synthesis ]]> https://biorxiv.org/content/10.1101/2023.11.06.565773v1?rss=1 Selles-Baiget, S. Ambjorn, S. M. Carli, A. Hendriks, I. A. Gallina, I. Davey, N. E. Benedict, B. Meeusen, B. Hertz, E. P. T. Slappendel, L. Semlow, D. Gadi, S. A. Sturla, S. Nielsen, M. L. Nilsson, J. Miller, T. C. R. Duxin, J. P. 2023-11-06 doi:10.1101/2023.11.06.565773 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Molecular identification of a peroxidase gene controlling body size in the entomopathogenic nematode Steinernema hermaphroditum ]]> https://biorxiv.org/content/10.1101/2023.11.07.566113v1?rss=1 Schwartz, H. T. T. Tan, C.-H. Peraza, J. Raymundo, K. L. T. Sternberg, P. W. 2023-11-10 doi:10.1101/2023.11.07.566113 Cold Spring Harbor Laboratory Press 2023-11-10 <![CDATA[ Abstract representations emerge in human hippocampal neurons during inference behavior ]]> https://biorxiv.org/content/10.1101/2023.11.10.566490v1?rss=1 Courellis, H. S. Minxha, J. Ramirez Cardenas, A. Kimmel, D. L. Reed, C. M. Valiante, T. A. Salzman, C. D. Mamelak, A. N. Adolphs, R. Fusi, S. Rutishauser, U. 2023-11-11 doi:10.1101/2023.11.10.566490 Cold Spring Harbor Laboratory Press 2023-11-11 <![CDATA[ Ultrasonic reporters of calcium for deep tissue imaging of cellular signals ]]> https://biorxiv.org/content/10.1101/2023.11.09.566364v1?rss=1 Jin, Z. Lakshmanan, A. Zhang, R. Tran, T. A. Rabut, C. Dutka, P. Duan, M. Hurt, R. C. Malounda, D. Yao, Y. Shapiro, M. G. 2023-11-12 doi:10.1101/2023.11.09.566364 Cold Spring Harbor Laboratory Press 2023-11-12 <![CDATA[ Genetically dissecting the electron transport chain of a soil bacterium reveals a generalizable mechanism for biological phenazine-1-carboxylic acid oxidation ]]> https://biorxiv.org/content/10.1101/2023.11.14.567096v1?rss=1 Tsypin, L. M. Z. Saunders, S. H. Chen, A. W. Newman, D. K. 2023-11-14 doi:10.1101/2023.11.14.567096 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ Simultaneous single-cell calcium imaging of neuronal population activity and brain-wide BOLD fMRI ]]> https://biorxiv.org/content/10.1101/2023.11.14.566368v1?rss=1 Ubaghs, R. L. E. M. Boehringer, R. Marks, M. Hesse, H. K. Yanik, M. F. Zerbi, V. Grewe, B. F. 2023-11-16 doi:10.1101/2023.11.14.566368 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Fast and scalable querying of eukaryotic linear motifs with gget elm ]]> https://biorxiv.org/content/10.1101/2023.11.15.567056v1?rss=1 Luebbert, L. Hoang, C. Kumar, M. Pachter, L. 2023-11-17 doi:10.1101/2023.11.15.567056 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ A Foundation Model for Cell Segmentation ]]> https://biorxiv.org/content/10.1101/2023.11.17.567630v1?rss=1 Israel, U. Marks, M. Dilip, R. Li, Q. Schwartz, M. S. Pradhan, E. Pao, E. Li, S. Pearson-Goulart, A. Perona, P. Gkioxari, G. Barnowski, R. Yue, Y. Van Valen, D. A. 2023-11-20 doi:10.1101/2023.11.17.567630 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ Updates to the Alliance of Genome Resources Central Infrastructure ]]> https://biorxiv.org/content/10.1101/2023.11.20.567935v1?rss=1 Sternberg, P. W. Alliance of Genome Resources Consortium, 2023-11-22 doi:10.1101/2023.11.20.567935 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq ]]> https://biorxiv.org/content/10.1101/2023.11.21.568164v1?rss=1 Sullivan, D. K. Min, K. H. Hjörleifsson, K. E. Luebbert, L. Holley, G. Moses, L. Gustafsson, J. Bray, N. L. Pimentel, H. Booeshaghi, A. S. Melsted, P. Pachter, L. 2023-11-22 doi:10.1101/2023.11.21.568164 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Spatial transcriptomics defines injury-specific microenvironments in the adult mouse kidney and novel cellular interactions in regeneration and disease ]]> https://biorxiv.org/content/10.1101/2023.11.22.568217v1?rss=1 Polonsky, M. Gerhardt, L. M. S. Yun, J. Koppitch, K. Colon, K. Amrhein, H. Zheng, S. Yuan, G.-C. Thomson, M. Cai, L. McMahon, A. P. 2023-11-22 doi:10.1101/2023.11.22.568217 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Role of a holo-insertase complex in the biogenesis of biophysically diverse ER membrane proteins ]]> https://biorxiv.org/content/10.1101/2023.11.28.569054v1?rss=1 Page, K. R. Nguyen, V. N. Pleiner, T. Tomaleri, G. P. Wang, M. L. Guna, A. Wang, T.-Y. Chou, T.-F. Voorhees, R. M. 2023-11-29 doi:10.1101/2023.11.28.569054 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Multi-ContrastiveVAE disentangles perturbation effects in single cell images from optical pooled screens ]]> https://biorxiv.org/content/10.1101/2023.11.28.569094v1?rss=1 Wang, Z. J. Lopez, R. Huetter, J.-C. Kudo, T. Yao, H. Hanslovsky, P. Hoeckendorf, B. Regev, A. 2023-11-29 doi:10.1101/2023.11.28.569094 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ FAIR Header Reference genome: A TRUSTworthy standard ]]> https://biorxiv.org/content/10.1101/2023.11.29.569306v1?rss=1 Wright, A. Wilkinson, M. D. Mungall, C. Cain, S. Richards, S. Sternberg, P. Provin, E. Jacobs, J. L. Geib, S. Raciti, D. Yook, K. Stein, L. Molik, D. C. 2023-12-01 doi:10.1101/2023.11.29.569306 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Bioorthogonal labeling enables in situ fluorescence imaging of expressed gas vesicle nanostructures ]]> https://biorxiv.org/content/10.1101/2023.11.30.569486v1?rss=1 Schrunk, E. Dutka, P. Hurt, R. C. Wu, D. Shapiro, M. G. 2023-12-01 doi:10.1101/2023.11.30.569486 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Rapid, concerted switching of the neural code in inferotemporal cortex ]]> https://biorxiv.org/content/10.1101/2023.12.06.570341v1?rss=1 Shi, Y. Bi, D. Hesse, J. K. Lanfranchi, F. F. Chen, S. Tsao, D. Y. 2023-12-06 doi:10.1101/2023.12.06.570341 Cold Spring Harbor Laboratory Press 2023-12-06 <![CDATA[ Machine-learning-based Structural Analysis of Interactions between Antibodies and Antigens ]]> https://biorxiv.org/content/10.1101/2023.12.06.570397v1?rss=1 Zhang, G. Su, Z. Zhang, T. Wu, Y. 2023-12-08 doi:10.1101/2023.12.06.570397 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Single tissue proteomics in Caenorhabditis elegans reveals proteins resident in intestinal lysosome-related organelles ]]> https://biorxiv.org/content/10.1101/2023.12.29.573592v1?rss=1 Tan, C.-H. Wang, T.-Y. Park, H. Lomenick, B. Chou, T.-F. Sternberg, P. W. 2023-12-29 doi:10.1101/2023.12.29.573592 Cold Spring Harbor Laboratory Press 2023-12-29 <![CDATA[ A Supervised Contrastive Framework for Learning Disentangled Representations of Cell Perturbation Data ]]> https://biorxiv.org/content/10.1101/2024.01.05.574421v1?rss=1 Tu, X. Hutter, J.-C. Wang, Z. J. Kudo, T. Regev, A. Lopez, R. 2024-01-08 doi:10.1101/2024.01.05.574421 Cold Spring Harbor Laboratory Press 2024-01-08 <![CDATA[ Data-driven system matrix manipulation enabling fast functional imaging and intra-image nonrigid motion correction in tomography ]]> https://biorxiv.org/content/10.1101/2024.01.07.574504v1?rss=1 Hu, P. Tong, X. Lin, L. Wang, L. 2024-01-08 doi:10.1101/2024.01.07.574504 Cold Spring Harbor Laboratory Press 2024-01-08 <![CDATA[ Integrative genomic analysis identifies unique immune environments associated with immunotherapy response in diffuse large B cell lymphoma ]]> https://biorxiv.org/content/10.1101/2024.01.17.576100v1?rss=1 Tumuluru, S. Godfrey, J. K. Cooper, A. Yu, J. Chen, X. MacNabb, B. W. Venkataraman, G. Zha, Y. Pelzer, B. Song, J. Duns, G. Bolen, C. Penuel, E. Postovalova, E. Kotlov, N. Bagaev, A. Fowler, N. Smith, S. M. Steidl, C. Kline, J. 2024-01-22 doi:10.1101/2024.01.17.576100 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Age-related memory CD8 T cells induce and track Alzheimers-like neurodegeneration ]]> https://biorxiv.org/content/10.1101/2024.01.22.576704v1?rss=1 Panwar, A. Rentsendorj, A. Jhun, M. Cohen, R. M. Cordner, R. Gull, N. Pechnick, R. N. Duvall, G. Mardiros, A. Golchian, D. Schubloom, H. Jin, L.-W. Van Dam, D. Vermeiren, Y. De Reu, H. De Deyn, P. P. Raskatov, J. A. Black, K. L. Irvin, D. K. Williams, B. A. Wheeler, C. J. 2024-01-22 doi:10.1101/2024.01.22.576704 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Adeno-Associated Viral Tools to Trace Neural Development and Connectivity Across Amphibians ]]> https://biorxiv.org/content/10.1101/2024.02.15.580289v1?rss=1 Jaeger, E. C. B. Vijatovic, D. Deryckere, A. Zorin, N. Nguyen, A. L. Ivanian, G. Woych, J. Arnold, R. C. Ortega Gurrola, A. Shvartsman, A. Barbieri, F. Toma, F. A. Gorbsky, G. J. Horb, M. E. Cline, H. T. Shay, T. F. Kelley, D. B. Yamaguchi, A. Shein-Idelson, M. Tosches, M. A. Sweeney, L. B. 2024-02-16 doi:10.1101/2024.02.15.580289 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ Unethical amnesia brain: Memory and metacognitive distortion induced by dishonesty ]]> https://biorxiv.org/content/10.1101/2024.03.03.583239v1?rss=1 Xu, X. J. Mobbs, D. Wu, H. 2024-03-06 doi:10.1101/2024.03.03.583239 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Variant mutation in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation ]]> https://biorxiv.org/content/10.1101/2024.03.08.584120v1?rss=1 Kubinski, H. C. Despres, H. W. Johnson, B. A. Schmidt, M. M. Jaffrani, S. A. Mills, M. G. Lokugamage, K. Dumas, C. M. Shirley, D. J. Estes, L. K. Pekosz, A. Crothers, J. W. Roychoudhury, P. Greninger, A. L. Jerome, K. R. Martorelli Di Genova, B. Walker, D. H. Ballif, B. A. Ladinsky, M. S. Bjorkman, P. J. Menachery, V. D. Bruce, E. A. 2024-03-11 doi:10.1101/2024.03.08.584120 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Non-invasive laser speckle imaging of extra-embryonic blood vessels in intact few-days-old avian eggs ]]> https://biorxiv.org/content/10.1101/2024.03.11.584528v1?rss=1 Dong, Z. Mahler, S. Readhead, C. Chen, X. Dickson, M. Bronner, M. E. Yang, C. 2024-03-14 doi:10.1101/2024.03.11.584528 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ miRNA circuit modules for precise, tunable control of gene expression ]]> https://biorxiv.org/content/10.1101/2024.03.12.583048v1?rss=1 Du, R. Flynn, M. J. Honsa, M. Jungmann, R. Elowitz, M. B. 2024-03-12 doi:10.1101/2024.03.12.583048 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Synthetic dosage-compensating miRNA circuits for quantitative gene therapy ]]> https://biorxiv.org/content/10.1101/2024.03.13.584179v1?rss=1 Flynn, M. J. Mayfield, A. M. Du, R. Gradinaru, V. Elowitz, M. B. 2024-03-14 doi:10.1101/2024.03.13.584179 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Amyloid Beta Oligomers Accelerate ATP-Dependent Phase Separation of Ago2 to RNA Processing Bodies ]]> https://biorxiv.org/content/10.1101/2024.03.14.584939v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@1fe06eeorg.highwire.dtl.DTLVardef@7904b1org.highwire.dtl.DTLVardef@1231746org.highwire.dtl.DTLVardef@cd1405_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LImiRNA bound Ago2 gets phase separated in vitro to RNA processing bodies (PBs) in detergent permeabilized mammalian cells. C_LIO_LIPhase separation of Ago2 to PBs is controlled by presence of ATP and RNA. C_LIO_LIAmyloid beta oligomers retard dynamics of Ago2 bodies to inhibit miRNA function and enhance PB targeting of Ago2 miRNPs. C_LIO_LImicroRNA binding protein HuR can rescue Ago2 miRNP from PBs and inverse the effect of amyloid beta oligomers. C_LI ]]> Ray, S. Roychowdhury, S. Chakraborty, Y. Banerjee, S. Chattopadhyay, K. Mukherjee, K. Bhattacharyya, S. N. 2024-03-14 doi:10.1101/2024.03.14.584939 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Thoracic epidural blockade after myocardial infarction benefits from anti-arrhythmic pathways mediated in part by parasympathetic modulation ]]> https://biorxiv.org/content/10.1101/2024.03.14.585127v1?rss=1 View larger version (44K): org.highwire.dtl.DTLVardef@1150b29org.highwire.dtl.DTLVardef@8fd741org.highwire.dtl.DTLVardef@17d16bforg.highwire.dtl.DTLVardef@1608799_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hoang, J. D. Van Weperen, V. Y. Kang, K.-W. Jani, N. Swid, M. A. Chan, C. A. Lokhandwala, Z. A. Lux, R. L. Vaseghi, M. 2024-03-16 doi:10.1101/2024.03.14.585127 Cold Spring Harbor Laboratory Press 2024-03-16 <![CDATA[ Correspondence of fentanyl brain pharmacokinetics and behavior measured via engineering opioids biosensors and computational ethology ]]> https://biorxiv.org/content/10.1101/2024.03.15.584894v1?rss=1 Muthusamy, A. K. Rosenberg, M. Kim, C. H. Wang, A. Z. Ebisu, H. Chin, T. M. Koranne, A. Marvin, J. S. Cohen, B. N. Looger, L. L. Oka, Y. Meister, M. Lester, H. A. 2024-03-16 doi:10.1101/2024.03.15.584894 Cold Spring Harbor Laboratory Press 2024-03-16 <![CDATA[ Impact of Chemical Dynamics of Commercial PURE Systems on Malachite Green Aptamer Fluorescence ]]> https://biorxiv.org/content/10.1101/2024.03.15.585317v1?rss=1 Jurado, Z. Murray, R. M. 2024-03-16 doi:10.1101/2024.03.15.585317 Cold Spring Harbor Laboratory Press 2024-03-16 <![CDATA[ Allele Sails: launching traits and fates into wild populations with DNA sequence modifiers ]]> https://biorxiv.org/content/10.1101/2024.03.18.585647v1?rss=1 Johnson, M. L. Hay, B. Maselko, M. 2024-03-19 doi:10.1101/2024.03.18.585647 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[ A human commons cell atlas reveals cell type specificity for OAS1 isoforms ]]> https://biorxiv.org/content/10.1101/2024.03.23.586412v1?rss=1 Galvez-Merchan, A. Booeshaghi, A. S. Pachter, L. 2024-03-24 doi:10.1101/2024.03.23.586412 Cold Spring Harbor Laboratory Press 2024-03-24 <![CDATA[ Algorithms for a Commons Cell Atlas ]]> https://biorxiv.org/content/10.1101/2024.03.23.586413v1?rss=1 Booeshaghi, A. S. Galvez-Merchan, A. Pachter, L. 2024-03-26 doi:10.1101/2024.03.23.586413 Cold Spring Harbor Laboratory Press 2024-03-26 <![CDATA[ Kilohertz volumetric imaging of in-vivo dynamics using squeezed light field microscopy ]]> https://biorxiv.org/content/10.1101/2024.03.23.586416v1?rss=1 Wang, Z. Zhao, R. Wagenaar, D. A. Kang, W. Lee, C. Schmidt, W. Pammar, A. Zhu, E. Wong, G. C. L. Liang, R. Hsiai, T. Gao, L. 2024-03-27 doi:10.1101/2024.03.23.586416 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Nonadjacent Dependencies and Syntactic Structure of Chimpanzee Action During a Natural Tool-Use Task ]]> https://biorxiv.org/content/10.1101/2024.03.25.586385v1?rss=1 Howard-Spink, E. Hayashi, M. Matsuzawa, T. Schofield, D. Gruber, T. Biro, D. 2024-03-29 doi:10.1101/2024.03.25.586385 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Directed Evolution of Acoustic Reporter Genes Using High-Throughput Acoustic Screening ]]> https://biorxiv.org/content/10.1101/2024.03.30.587094v1?rss=1 Hurt, R. C. Jin, Z. Soufi, M. Wong, K. K. Sawyer, D. P. Shen, H. K. Dutka, P. Deshpande, R. Zhang, R. Mittelstein, D. R. Shapiro, M. G. 2024-04-01 doi:10.1101/2024.03.30.587094 Cold Spring Harbor Laboratory Press 2024-04-01 <![CDATA[ The impact of package selection and versioning on single-cell RNA-seq analysis ]]> https://biorxiv.org/content/10.1101/2024.04.04.588111v1?rss=1 Rich, J. M. Moses, L. Einarsson, P. H. Jackson, K. Luebbert, L. Booeshaghi, A. S. Antonsson, S. Sullivan, D. K. Bray, N. Melsted, P. Pachter, L. 2024-04-05 doi:10.1101/2024.04.04.588111 Cold Spring Harbor Laboratory Press 2024-04-05 <![CDATA[ Generation of a zebrafish neurofibromatosis model via inducible knockout of nf2 ]]> https://biorxiv.org/content/10.1101/2024.04.23.590787v1?rss=1 Desingu Rajan, A. R. Huang, Y. Stundl, J. Irodi, A. Yang, Z. Applegate, B. E. Bronner, M. 2024-04-27 doi:10.1101/2024.04.23.590787 Cold Spring Harbor Laboratory Press 2024-04-27 <![CDATA[ Emergence of metabolic coupling to the heterotroph Alteromonas promotes dark survival in Prochlorococcus ]]> https://biorxiv.org/content/10.1101/2024.05.01.591941v1?rss=1 Coe, A. Braakman, R. Biller, S. J. Arellano, A. Bliem, C. Vo, N. N. von Emster, K. Thomas, E. DeMers, M. Steglich, C. Huisman, J. Chisholm, S. W. 2024-05-01 doi:10.1101/2024.05.01.591941 Cold Spring Harbor Laboratory Press 2024-05-01 <![CDATA[ HisCl1 regulates gustatory habituation in sweet taste neurons and mediates sugar ingestion in Drosophila ]]> https://biorxiv.org/content/10.1101/2024.05.06.592591v1?rss=1 Kim, H. Zhong, Z. Cui, X. Sung, H. Agrawal, N. Jiang, T. Dus, M. Yapici, N. 2024-05-08 doi:10.1101/2024.05.06.592591 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ Machine learning models can identify individuals based on a resident oral bacteriophage family ]]> https://biorxiv.org/content/10.1101/2024.05.06.592821v1?rss=1 Mahmoudabadi, G. Homyk, K. Catching, A. Mahmoudabadi, A. Foley, H. B. Tadmor, A. D. Phillips, R. 2024-05-08 doi:10.1101/2024.05.06.592821 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ The microbiome shapes immunity in a sex-specific manner in mouse models of Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2024.05.07.593011v1?rss=1 Bostick, J. W. Connerly, T. J. Thron, T. Needham, B. D. de Castro Fonseca, M. Kaddurah-Daouk, R. Knight, R. Mazmanian, S. K. 2024-05-08 doi:10.1101/2024.05.07.593011 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ Ultrasound-actuated drug delivery with acoustic percolation switches ]]> https://biorxiv.org/content/10.1101/2024.05.10.593654v1?rss=1 Abundo, M. P. Tifrea, A. T. Buss, M. T. Barturen-Larrea, P. Jin, Z. Malounda, D. Shapiro, M. G. 2024-05-14 doi:10.1101/2024.05.10.593654 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Visual context affects the perceived timing of tactile sensations elicited through intra-cortical microstimulation ]]> https://biorxiv.org/content/10.1101/2024.05.13.593529v1?rss=1 Rosenthal, I. A. Bashford, L. Bjanes, D. Pejsa, K. Lee, B. Liu, C. Andersen, R. A. 2024-05-14 doi:10.1101/2024.05.13.593529 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Flavin-containing siderophore-interacting protein of Shewanella putrefaciens DSM 9451 reveals substrate specificity in ferric-siderophore reduction ]]> https://biorxiv.org/content/10.1101/2024.05.13.594011v1?rss=1 Trindade, I. B. Fonseca, B. M. Catarino, T. Matias, P. M. Moe, E. Louro, R. O. 2024-05-13 doi:10.1101/2024.05.13.594011 Cold Spring Harbor Laboratory Press 2024-05-13 <![CDATA[ Mapping Endothelial-Macrophage Interactions in Diabetic Vasculature: Role of TREM2 in Vascular Inflammation and Ischemic Response ]]> https://biorxiv.org/content/10.1101/2024.05.14.594235v1?rss=1 Malhi, N. K. Luo, Y. Tang, X. Chadha, R. S. Tapia, A. Liu, X. Chen, M. Yuan, D. Qi, M. Wei, L. Cooke, J. P. Natarajan, R. Southerland, K. W. Chen, Z. B. 2024-05-17 doi:10.1101/2024.05.14.594235 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ Stable, chronic in-vivo recordings from a fully wireless subdural-contained 65,536-electrode brain-computer interface device ]]> https://biorxiv.org/content/10.1101/2024.05.17.594333v1?rss=1 Jung, T. Zeng, N. Fabbri, J. D. Eichler, G. Li, Z. Willeke, K. Wingel, K. E. Dubey, A. Huq, R. Sharma, M. Hu, Y. Ramakrishnan, G. Tien, K. Mantovani, P. Parihar, A. Yin, H. Oswalt, D. Misdorp, A. Uguz, I. Shinn, T. Rodriguez, G. J. Nealley, C. Gonzales, I. Roukes, M. Knecht, J. Yoshor, D. Canoll, P. Spinazzi, E. Carloni, L. P. Pesaran, B. Patel, S. Youngerman, B. Cotton, R. J. Tolias, A. Shepard, K. L. 2024-05-17 doi:10.1101/2024.05.17.594333 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ Long-term imaging of three-dimensional hyphal development using the ePetri dish ]]> https://biorxiv.org/content/10.1101/2024.05.18.594613v1?rss=1 Zhang, O. Dahlquist, N. Leete, Z. Xu, M. Schneider, D. Yang, C. 2024-05-19 doi:10.1101/2024.05.18.594613 Cold Spring Harbor Laboratory Press 2024-05-19 <![CDATA[ Target gene responses differ when transcription factor levels are acutely decreased by nuclear export versus degradation ]]> https://biorxiv.org/content/10.1101/2024.05.20.595009v1?rss=1 McGehee, J. Stathopoulos, A. 2024-05-20 doi:10.1101/2024.05.20.595009 Cold Spring Harbor Laboratory Press 2024-05-20 <![CDATA[ Intrinsic dynamics and neural implementation of a hypothalamic line attractor encoding an internal behavioral state ]]> https://biorxiv.org/content/10.1101/2024.05.21.595051v1?rss=1 Vinograd, A. Nair, A. Linderman, S. W. Anderson, D. J. 2024-05-22 doi:10.1101/2024.05.21.595051 Cold Spring Harbor Laboratory Press 2024-05-22 <![CDATA[ Norepinephrine changes behavioral state via astroglial purinergic signaling ]]> https://biorxiv.org/content/10.1101/2024.05.23.595576v1?rss=1 Chen, A. B. Duque, M. Wang, V. M. Dhanasekar, M. Mi, X. Rymbek, A. Tocquer, L. Narayan, S. Prober, D. A. Yu, G. Wyart, C. Engert, F. Ahrens, M. B. 2024-05-23 doi:10.1101/2024.05.23.595576 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ Automated classification of cellular expression in multiplexed imaging data with Nimbus ]]> https://biorxiv.org/content/10.1101/2024.06.02.597062v1?rss=1 Rumberger, L. Greenwald, N. F. Ranek, J. Boonrat, P. Walker, C. Franzen, J. Varra, S. Kong, A. Sowers, C. Liu, C. C. Averbukh, I. Piyadasa, H. Vanguri, R. Nederlof, I. Wang, X. J. Van Valen, D. A. Kok, M. Hollmann, T. J. Kainmueller, D. Angelo, M. 2024-06-03 doi:10.1101/2024.06.02.597062 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ α-Synuclein Overexpression and the Microbiome Shape the Gut and Brain Metabolome in Mice ]]> https://biorxiv.org/content/10.1101/2024.06.07.597975v1?rss=1 Morais, L. H. Boktor, J. C. MahmoudianDehkordi, S. Kaddurah-Daouk, R. Mazmanian, S. K. 2024-06-10 doi:10.1101/2024.06.07.597975 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Congenital heart defects differ following left versus right avian cardiac neural crest ablation ]]> https://biorxiv.org/content/10.1101/2024.06.10.598133v1?rss=1 Solovieva, T. Bronner, M. E. 2024-06-10 doi:10.1101/2024.06.10.598133 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ The ENCODE mouse postnatal developmental time course identifies regulatory programs of cell types and cell states ]]> https://biorxiv.org/content/10.1101/2024.06.12.598567v1?rss=1 Rebboah, E. Rezaie, N. Williams, B. A. Weimer, A. K. Shi, M. Yang, X. Liang, H. Y. Dionne, L. Reese, F. Trout, D. Jou, J. Youngworth, I. Reinholdt, L. G. Morabito, S. Snyder, M. Wold, B. Mortazavi, A. 2024-06-14 doi:10.1101/2024.06.12.598567 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ Escalation of genome defense capacity enables control of an expanding meiotic driver ]]> https://biorxiv.org/content/10.1101/2024.06.12.598716v1?rss=1 Chen, P. Pan, K. C. Park, E. H. Luo, Y. Lee, G. Y. C. Aravin, A. A. 2024-06-14 doi:10.1101/2024.06.12.598716 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ Low-dimensional olfactory signatures of fruit ripening and fermentation ]]> https://biorxiv.org/content/10.1101/2024.06.16.599229v1?rss=1 Zhou, Y. O'Connell, T. F. Ghaninia, M. Smith, B. Hong, E. J. Sharpee, T. O. 2024-06-17 doi:10.1101/2024.06.16.599229 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ A combinatorially complete epistatic fitness landscape in an enzyme active site ]]> https://biorxiv.org/content/10.1101/2024.06.23.600144v1?rss=1 Johnston, K. E. Almhjell, P. J. Watkins-Dulaney, E. J. Liu, G. Porter, N. J. Yang, J. Arnold, F. H. 2024-06-26 doi:10.1101/2024.06.23.600144 Cold Spring Harbor Laboratory Press 2024-06-26 <![CDATA[ Functional ultrasound neuroimaging reveals mesoscopic organization of saccades in the lateral intraparietal area of posterior parietal cortex ]]> https://biorxiv.org/content/10.1101/2024.06.28.600796v1?rss=1 Griggs, W. S. Norman, S. L. Tanter, M. Liu, C. Christopoulos, V. Shapiro, M. G. Andersen, R. A. 2024-07-02 doi:10.1101/2024.06.28.600796 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Time-resolved functional connectivity during visuomotor graph learning ]]> https://biorxiv.org/content/10.1101/2024.07.04.602005v1?rss=1 Loman, S. Caciagli, L. Kahn, A. E. Szymula, K. P. Nyema, N. Bassett, D. S. 2024-07-08 doi:10.1101/2024.07.04.602005 Cold Spring Harbor Laboratory Press 2024-07-08 <![CDATA[ Wide-field bond-selective fluorescence imaging: from single-molecule to cellular imaging beyond video-rate ]]> https://biorxiv.org/content/10.1101/2024.07.05.601986v1?rss=1 Lee, D. Wang, H. Kocheril, P. A. Bi, X. Naji, N. Wei, L. 2024-07-10 doi:10.1101/2024.07.05.601986 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Rapid evolution of gene expression patterns in flowering plants ]]> https://biorxiv.org/content/10.1101/2024.07.08.602577v1?rss=1 Schuster, C. Gabel, A. Drost, H.-G. Grosse, I. Leyser, O. Meyerowitz, E. M. 2024-07-10 doi:10.1101/2024.07.08.602577 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Estimating cis and trans contributions todifferences in gene regulation ]]> https://biorxiv.org/content/10.1101/2024.07.13.603403v1?rss=1 Hallgrimsdottir, I. B. Carilli, M. Pachter, L. 2024-07-16 doi:10.1101/2024.07.13.603403 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Spatial evidence of cryptic methane cycling and methylotrophic metabolisms along a land-ocean transect in a California coastal wetland ]]> https://biorxiv.org/content/10.1101/2024.07.16.603764v1?rss=1 Krause, S. J. E. Wipfler, R. L. Liu, J. Yousavich, D. J. Robinson, D. Hoyt, D. W. Orphan, V. J. Treude, T. 2024-07-16 doi:10.1101/2024.07.16.603764 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Neural dynamics underlying minute-timescale persistent behavior in the human brain ]]> https://biorxiv.org/content/10.1101/2024.07.16.603717v1?rss=1 Courellis, H. Valiante, T. A. Mamelak, A. N. Adolphs, R. Rutishauser, U. 2024-07-19 doi:10.1101/2024.07.16.603717 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ Adaptive Safety Coding in the Prefrontal Cortex ]]> https://biorxiv.org/content/10.1101/2024.07.19.604228v1?rss=1 Tashjian, S. M. Cussen, J. Deng, W. Zhang, B. Mobbs, D. 2024-07-23 doi:10.1101/2024.07.19.604228 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Long-lived adult-born hippocampal neurons promote successful cognitive aging ]]> https://biorxiv.org/content/10.1101/2024.07.19.604332v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@524afforg.highwire.dtl.DTLVardef@b9b2b1org.highwire.dtl.DTLVardef@182a19corg.highwire.dtl.DTLVardef@1402b64_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Blin, N. Charrier, V. Farrugia, F. Cartier, E. Pacary, E. Koehl, M. Lois, C. Lie, D. C. Masachs, N. Abrous, N. 2024-07-23 doi:10.1101/2024.07.19.604332 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Asynchronous mouse embryo polarization leads to heterogeneity in cell fate specification ]]> https://biorxiv.org/content/10.1101/2024.07.26.605266v1?rss=1 Lamba, A. Zhu, M. Meglicki, M. Czukiewska, S. Balasubramaniam, L. Hadas, R. Weishaupt, N. Patel, E. Kavanagh, Y. H. Wang, R. Jing, N. Zernicka-Goetz, M. 2024-07-26 doi:10.1101/2024.07.26.605266 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ Active Learning-Assisted Directed Evolution ]]> https://biorxiv.org/content/10.1101/2024.07.27.605457v1?rss=1 Yang, J. Lal, R. G. Bowden, J. C. Astudillo, R. Hameedi, M. A. Kaur, S. Hill, M. Yue, Y. Arnold, F. H. 2024-07-28 doi:10.1101/2024.07.27.605457 Cold Spring Harbor Laboratory Press 2024-07-28 <![CDATA[ Nonlinear sound-sheet microscopy: imaging opaque organs at the capillary and cellular scale ]]> https://biorxiv.org/content/10.1101/2024.07.31.605825v1?rss=1 Heiles, B. Nelissen, F. Terwiel, D. Park, B. M. Munoz Ibarra, E. Matalliotakis, A. Waasdorp, R. Ara, T. Barturen-Larrea, P. Duan, M. Shapiro, M. G. Gazzola, V. Maresca, D. 2024-07-31 doi:10.1101/2024.07.31.605825 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ Neutralizing antibodies elicited in sequentially immunized macaques recognize V3 residues on altered conformations of HIV-1 Env trimer ]]> https://biorxiv.org/content/10.1101/2024.07.31.605918v1?rss=1 View larger version (46K): org.highwire.dtl.DTLVardef@6210b1org.highwire.dtl.DTLVardef@35f683org.highwire.dtl.DTLVardef@cb2d3corg.highwire.dtl.DTLVardef@106e066_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> DeLaitsch, A. T. Keeffe, J. R. Gristick, H. B. Lee, J. A. Ding, W. Liu, W. Skelly, A. N. Shaw, G. M. Hahn, B. H. Bjorkman, P. J. 2024-08-01 doi:10.1101/2024.07.31.605918 Cold Spring Harbor Laboratory Press 2024-08-01 <![CDATA[ Root traits and tree functional groups determine variability in root exudation and N uptake rates in mature temperate trees ]]> https://biorxiv.org/content/10.1101/2024.08.01.606171v1?rss=1 Oh, Y. E. Midgley, M. G. McCormack, M. L. Beidler, K. V. McCall, M. Henderson, S. Braghiere, R. K. Phillips, R. P. 2024-08-04 doi:10.1101/2024.08.01.606171 Cold Spring Harbor Laboratory Press 2024-08-04 <![CDATA[ Electron tomography visualization of HIV-1 virions trapped by fusion inhibitors to host cells in infected tissues ]]> https://biorxiv.org/content/10.1101/2024.08.19.608557v1?rss=1 Bjorkman, P. J. Ladinsky, M. S. Zhu, L. Ullah, I. Uchil, P. D. Kumar, P. Kay, M. S. 2024-08-19 doi:10.1101/2024.08.19.608557 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Motor-driven microtubule diffusion in a photobleached dynamical coordinate system ]]> https://biorxiv.org/content/10.1101/2024.08.20.608861v1?rss=1 Hirokawa, S. Lee, H. J. Banks, R. A. Duarte, A. I. Najma, B. Thomson, M. Phillips, R. 2024-08-20 doi:10.1101/2024.08.20.608861 Cold Spring Harbor Laboratory Press 2024-08-20 <![CDATA[ Quantifying microbial fitness in high-throughput experiments ]]> https://biorxiv.org/content/10.1101/2024.08.20.608874v1?rss=1 Fink, J. W. Manhart, M. 2024-08-20 doi:10.1101/2024.08.20.608874 Cold Spring Harbor Laboratory Press 2024-08-20 <![CDATA[ Cellular and molecular networks of intercellular signaling in bone marrow hematopoiesis ]]> https://biorxiv.org/content/10.1101/2024.08.25.609544v1?rss=1 Thomas, Z. Wang, B. Boohar, W. Vergel, M. Eerdeng, J. Shon, D. Elowitz, M. B. Lu, R. 2024-08-26 doi:10.1101/2024.08.25.609544 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Brain Charts for the Rhesus Macaque Lifespan ]]> https://biorxiv.org/content/10.1101/2024.08.28.610193v1?rss=1 Alldritt, S. Ramirez, J. S. B. Vos de Wael, R. Bethlehem, R. Seidlitz, J. Wang, Z. Nenning, K.-H. Esper, N. B. Smallwood, J. Franco, A. R. Byeon, K. Alexander-Bloch, A. Messinger, A. Chen, A. Thiele, A. Weiss, A. R. Shmuel, A. Fox, A. Tusche, A. Brambrink, A. M. Falchier, A. Hiba, B. Jarraya, B. Jung, B. Butler, B. Russ, B. E. Howell, B. R. Drzewiecki, C. M. Guedj, C. Schwiedrzik, C. M. Amiez, C. Wilson, C. R. E. Klink, C. Kroenke, C. Constantinidis, C. Garin, C. M. Poirier, C. Gale, D. J. Leopold, D. A. Rudko, D. A. Amaral, D. G. Tsao, D. Cook, D. J. 2024-08-30 doi:10.1101/2024.08.28.610193 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Benchmarking Protein Language Models for Protein Crystallization ]]> https://biorxiv.org/content/10.1101/2024.09.02.610758v1?rss=1 Mall, R. Kaushik, R. Martinez, Z. A. Thomson, M. Castiglione, F. 2024-09-03 doi:10.1101/2024.09.02.610758 Cold Spring Harbor Laboratory Press 2024-09-03 <![CDATA[ LevSeq: Rapid Generation of Sequence-Function Data for Directed Evolution and Machine Learning ]]> https://biorxiv.org/content/10.1101/2024.09.04.611255v1?rss=1 Long, Y. Mora, A. Guersoy, E. Johnston, K. E. Li, F.-Z. Arnold, F. H. 2024-09-04 doi:10.1101/2024.09.04.611255 Cold Spring Harbor Laboratory Press 2024-09-04 <![CDATA[ Human NLRP3 inflammasome activation leads to formation of condensate at the microtubule organizing center ]]> https://biorxiv.org/content/10.1101/2024.09.12.612739v1?rss=1 Wang, J. Wu, M. Magupalli, V. Dahlberg, P. Wu, H. Jensen, G. 2024-09-15 doi:10.1101/2024.09.12.612739 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ An integrated view of the structure and function of the human 4D nucleome ]]> https://biorxiv.org/content/10.1101/2024.09.17.613111v1?rss=1 The 4D Nucleome Consortium, Dekker, J. Oksuz, B. A. Zhang, Y. Wang, Y. Minsk, M. K. Kuang, S. Yang, L. Gibcus, J. H. Krietenstein, N. Rando, O. Xu, J. Janssens, D. H. Henikoff, S. Kukalev, A. Willemin, A. Winick-Ng, W. Kempfer, R. Pombo, A. Yu, M. Kumar, P. Zhang, L. Belmont, A. S. Sasaki, T. van Schaik, T. Brueckner, L. Peric-Hupkes, D. van Steensel, B. Wang, P. Chai, H. Kim, M. Ruan, Y. Zhang, R. Quinodoz, S. A. Bhat, P. Guttman, M. Zhao, W. Chien, S. Liu, Y. Venev, S. V. Plewczynski, D. Irastorza Azcarate, I. Szabo, D. Thieme, C. J. Szczepinska, 2024-09-19 doi:10.1101/2024.09.17.613111 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Organ-specific Sympathetic Innervation Defines Visceral Functions ]]> https://biorxiv.org/content/10.1101/2024.09.19.613934v1?rss=1 Wang, T. Teng, B. Yao, D. R. Gao, W. Oka, Y. 2024-09-20 doi:10.1101/2024.09.19.613934 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics ]]> https://biorxiv.org/content/10.1101/2024.09.18.613276v1?rss=1 Matentzoglu, N. Bello, S. M. Stefancsik, R. Alghamdi, S. M. Anagnostopoulos, A. V. Balhoff, J. P. Balk, M. A. Bradford, Y. M. Bridges, Y. Callahan, T. J. Caufield, H. Cuzick, A. Carmody, L. C. Caron, A. R. de Souza, V. Engel, S. R. Fey, P. Fisher, M. Gehrke, S. Grove, C. Hansen, P. Harris, N. L. Harris, M. A. Harris, L. Ibrahim, A. Jacobsen, J. O. B. Köhler, S. McMurry, J. A. Munoz-Fuentes, V. Munoz-Torres, M. C. Parkinson, H. Pendlington, Z. M. Pilgrim, C. Robb, S. M. C. Robinson, P. N. Seager, J. Segerdell, E. Smedley, D. Sollis, E. Toro, S. Vasilevsk 2024-09-22 doi:10.1101/2024.09.18.613276 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Achieving Single Cell Acoustic Localisation with Deactivation Super Resolution ]]> https://biorxiv.org/content/10.1101/2024.09.20.614052v1?rss=1 Smith, C. A. B. Duan, M. Yan, J. Taylor, L. Shapiro, M. G. Tang, M.-X. 2024-09-24 doi:10.1101/2024.09.20.614052 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Probiotic acoustic biosensors for noninvasive imaging of gut inflammation ]]> https://biorxiv.org/content/10.1101/2024.09.23.614598v1?rss=1 Buss, M. T. Zhu, L. Kwon, J. H. Tabor, J. J. Shapiro, M. G. 2024-09-25 doi:10.1101/2024.09.23.614598 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ Application of hsp60 amplicon sequencing to characterize microbial communities associated with juvenile and adult Euprymna scolopes squid ]]> https://biorxiv.org/content/10.1101/2024.09.23.614625v1?rss=1 Smith, S. Bongrand, C. Lawhorn, S. Ruby, E. G. Septer, A. 2024-09-25 doi:10.1101/2024.09.23.614625 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ Characterisation of Gas Vesicles as Cavitation Nuclei for Ultrasound Therapy using Passive Acoustic Mapping ]]> https://biorxiv.org/content/10.1101/2024.09.24.614126v1?rss=1 Smith, C. A. B. Bar-Zion, A. Wu, Q. Malounda, D. Bau, L. Stride, E. Shapiro, M. G. Coussios, C. C. 2024-09-26 doi:10.1101/2024.09.24.614126 Cold Spring Harbor Laboratory Press 2024-09-26 <![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[ PPARγ downregulation in colonic CD8+ T cells results in epithelial barrier disruption in people with HIV on antiretroviral therapy ]]> https://biorxiv.org/content/10.1101/2024.10.02.616363v1?rss=1 Das Adhikari, U. Froehle, L. M. Pipkin, A. N. Baharlou, H. Linder, A. H. Shah, P. Hussey, A. Zhang, Q. Nyquist, S. Khwaled, S. Chi, F. Goswami, S. Dieffenbach, T. J. Read, B. J. Kim, B. Irvine, D. J. Asowata, O. Ladinsky, M. S. Bjorkman, P. Madela, F. Khader, S. Shalek, A. K. Ghebremichael, M. Kloverpris, H. Ringel, A. Yilmaz, O. H. Kwon, D. S. 2024-10-03 doi:10.1101/2024.10.02.616363 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ A shared code for perceiving and imagining objects in human ventral temporal cortex ]]> https://biorxiv.org/content/10.1101/2024.10.05.616828v1?rss=1 Wadia, V. S. Reed, C. M. Chung, J. M. Bateman, L. M. Mamelak, A. N. Rutishauser, U. Tsao, D. Y. 2024-10-06 doi:10.1101/2024.10.05.616828 Cold Spring Harbor Laboratory Press 2024-10-06 <![CDATA[ Amygdala Subregion Volumes and Apportionment in Preadolescents -- Associations with Age, Sex, and Body Mass Index ]]> https://biorxiv.org/content/10.1101/2024.10.07.617048v1?rss=1 Overholtzer, L. N. Torgerson, C. Morrel, J. Ahmadi, H. Tyszka, J. M. Herting, M. 2024-10-11 doi:10.1101/2024.10.07.617048 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Nonlinear Singular Value Decomposition Beamforming for Ultrasound Imaging of Gas Vesicles ]]> https://biorxiv.org/content/10.1101/2024.10.14.618186v1?rss=1 Zhang, G. Vert, M. Nouhoum, M. Rivera, E. Haidour, N. Jimenez, A. Deffieux, T. Barral, S. Hersen, P. Rabut, C. Shapiro, M. Tanter, M. 2024-10-16 doi:10.1101/2024.10.14.618186 Cold Spring Harbor Laboratory Press 2024-10-16 <![CDATA[ Outdoor Air Pollution Relates to Amygdala Subregion Volume and Apportionment in Early Adolescents ]]> https://biorxiv.org/content/10.1101/2024.10.14.617429v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@e9f2ecorg.highwire.dtl.DTLVardef@14b677forg.highwire.dtl.DTLVardef@177f8daorg.highwire.dtl.DTLVardef@172dc0c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Morrel, J. Overholtzer, L. N. Sukumaran, K. Cotter, D. L. Cardenas-Iniguez, C. Tyszka, J. M. Schwartz, J. Hackman, D. A. Chen, J.-C. Herting, M. 2024-10-17 doi:10.1101/2024.10.14.617429 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Inducible, but not constitutive, pancreatic REG/Reg isoforms are regulated by intestinal microbiota and pancreatic diseases ]]> https://biorxiv.org/content/10.1101/2024.10.18.619139v1?rss=1 Zhou, Y. Komnick, M. R. Sepulveda, F. Liu, G. Nieves-Ortiz, E. Meador, K. Ndatabaye, O. Fatkhullina, A. Wu-Woods, N. Naydenkov, P. M. Kent, J. Christiansen, N. Madariaga, M. L. Witkowski, P. Ismagilov, R. F. Esterhazy, D. 2024-10-22 doi:10.1101/2024.10.18.619139 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ CABO-16S : A Combined Archaea, Bacteria, Organelle 16S database for amplicon analysis of prokaryotes and eukaryotes in environmental samples ]]> https://biorxiv.org/content/10.1101/2024.10.23.619938v1?rss=1 Eitel, E. M. Utter, D. Connon, S. Orphan, V. J. Murali, R. 2024-10-23 doi:10.1101/2024.10.23.619938 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ Optical control of sphingolipid biosynthesis using photoswitchable sphingosines ]]> https://biorxiv.org/content/10.1101/2024.10.24.619506v1?rss=1 Kol, M. Novak, A. J. E. Morstein, J. Schroer, C. Sokoya, T. Mensing, S. Korneev, S. M. Trauner, D. Holthuis, J. C. M. 2024-10-24 doi:10.1101/2024.10.24.619506 Cold Spring Harbor Laboratory Press 2024-10-24 <![CDATA[ Bystander base editing interferes with visual function restoration in Leber congenital amaurosis ]]> https://biorxiv.org/content/10.1101/2024.10.23.619839v1?rss=1 Lee, S.-H. Wu, J. Im, D. Hwang, G.-H. Jeong, Y. K. Jiang, H. Lee, S. J. Jo, D. H. Goddard, W. A. Kim, J. H. Bae, S. 2024-10-27 doi:10.1101/2024.10.23.619839 Cold Spring Harbor Laboratory Press 2024-10-27 <![CDATA[ Synaptic composition, activity, mRNA translation and dynamics in combined single-synapse profiling using multimodal imaging ]]> https://biorxiv.org/content/10.1101/2024.10.28.620504v1?rss=1 Falkovich, R. Aryal, S. Wang, J. Sheng, M. Bathe, M. 2024-10-28 doi:10.1101/2024.10.28.620504 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Phosphorylation of HP1/Swi6 relieves competition with Suv39/Clr4 on nucleosomes and enables H3K9 trimethyl spreading. ]]> https://biorxiv.org/content/10.1101/2024.10.25.620326v1?rss=1 Kennedy, D. R. Lemiere, J. Tan, C. Simental, E. Braxton, J. Maxwell, R. A. Amine, A. A. Al-Sady, B. 2024-10-29 doi:10.1101/2024.10.25.620326 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Design of Novel Dehalogenases using Protein Large Language Models ]]> https://biorxiv.org/content/10.1101/2024.10.28.620469v1?rss=1 Garcia, L. N. Nauber, W. Dahlgren, C. Reyes, T. Santos, J. Chung, R. Kapur, M. Barsever, M. Thomson, M. Lourenco, A. 2024-10-31 doi:10.1101/2024.10.28.620469 Cold Spring Harbor Laboratory Press 2024-10-31 <![CDATA[ Interactions of N- and C-terminal parts of Ana1 permitting centriole duplication but not elongation ]]> https://biorxiv.org/content/10.1101/2024.10.28.620588v1?rss=1 Nagy, A. Kovacs, L. Rangone, H. Fu, J. Ladinsky, M. S. Glover, D. M. 2024-10-31 doi:10.1101/2024.10.28.620588 Cold Spring Harbor Laboratory Press 2024-10-31 <![CDATA[ Spatial Transcriptomics Reveals the Temporal Architecture of the Seminiferous Epithelial Cycle and Precise Sertoli-Germ Synchronization ]]> https://biorxiv.org/content/10.1101/2024.10.28.620681v1?rss=1 View larger version (54K): org.highwire.dtl.DTLVardef@10a78c7org.highwire.dtl.DTLVardef@7f5a95org.highwire.dtl.DTLVardef@113f6b6org.highwire.dtl.DTLVardef@1aa41f3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chakravorty, A. Simons, B. D. Yoshida, S. Cai, L. 2024-10-31 doi:10.1101/2024.10.28.620681 Cold Spring Harbor Laboratory Press 2024-10-31 <![CDATA[ Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles ]]> https://biorxiv.org/content/10.1101/2024.10.31.621310v1?rss=1 Song, Y. J. Shinn, M. K. Bangru, S. Wang, Y. Sun, Q. Hao, Q. Chaturvedi, P. Freier, S. M. Perez-Pinera, P. Nelson, E. R. Belmont, A. S. Guttman, M. Prasantth, S. G. Kalsotra, A. Pappu, R. V. Kannanganattu, P. V. 2024-10-31 doi:10.1101/2024.10.31.621310 Cold Spring Harbor Laboratory Press 2024-10-31 <![CDATA[ Phenotypic plasticity in bacterial elongation among closely related species ]]> https://biorxiv.org/content/10.1101/2024.11.07.622495v1?rss=1 Delaby, M. Yang, L. Jacq, M. Gallagher, K. A. Kysela, D. T. Hughes, V. Pulido, F. Veyrier, F. J. VanNieuwenhze, M. S. Brun, Y. V. 2024-11-07 doi:10.1101/2024.11.07.622495 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ Conformational plasticity of mitochondrial VDAC2 controls the kinetics of its interaction with cytosolic proteins ]]> https://biorxiv.org/content/10.1101/2024.11.08.622687v1?rss=1 Rosencrans, W. M. Khuntia, H. Larimi, M. G. Mahalakshmi, R. Yu, T.-Y. D. Bezrukov, S. M. Rostovtseva, T. K. 2024-11-11 doi:10.1101/2024.11.08.622687 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Discovery of lydiamycin A biosynthetic gene cluster in the plant pathogen Rhodococcus fascians guides structural revision and identification of molecular target ]]> https://biorxiv.org/content/10.1101/2024.11.13.623425v1?rss=1 Ford, J. J. Santos-Aberturas, J. Hems, E. S. Sallmen, J. W. Bögeholz, L. A. K. Polturak, G. Osbourn, A. Wright, J. A. Rodnina, M. V. Vereecke, D. Francis, I. M. Truman, A. W. 2024-11-13 doi:10.1101/2024.11.13.623425 Cold Spring Harbor Laboratory Press 2024-11-13 <![CDATA[ Real-time volumetric imaging of cells and molecules in deep tissues with Takoyaki ultrasound ]]> https://biorxiv.org/content/10.1101/2024.11.14.623368v1?rss=1 Lee, S. Wu, D. Malounda, D. Rabut, C. Shapiro, M. G. 2024-11-15 doi:10.1101/2024.11.14.623368 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Filling-in of the Blindspot is Multisensory ]]> https://biorxiv.org/content/10.1101/2024.11.15.623713v1?rss=1 Chan, A. Stiles, N. R. B. Levitan, C. A. Tanguay, A. R. Shimojo, S. 2024-11-15 doi:10.1101/2024.11.15.623713 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Cellular behavior analysis from live-cell imaging of TCR T cell-cancer cell interactions ]]> https://biorxiv.org/content/10.1101/2024.11.19.624390v1?rss=1 Verma, A. Yu, C. Bachl, S. Lopez, I. Schwartz, M. S. Moen, E. Kale, N. Ching, C. Miller, G. Dougherty, T. Pao, E. Graf, W. Ward, C. Jena, S. G. Marson, A. Carnevale, J. Van Valen, D. A. Engelhardt, B. E. 2024-11-21 doi:10.1101/2024.11.19.624390 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Switchable client specificity in a dual functional chaperone coordinates light harvesting complex biogenesis ]]> https://biorxiv.org/content/10.1101/2024.11.21.624570v1?rss=1 Siegel, A. R. Kroon, G. Wright, P. E. Shan, S.-o. 2024-11-21 doi:10.1101/2024.11.21.624570 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Efficient pheromone navigation via antagonistic detectors ]]> https://biorxiv.org/content/10.1101/2024.11.22.624901v1?rss=1 Wan, X. Zhou, T. Susoy, V. Park, C. F. Groaz, A. Brady, J. F. Samuel, A. D. T. Sternberg, P. W. 2024-11-22 doi:10.1101/2024.11.22.624901 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ Cells transit through a quiescent-like state to convert to neurons at high rates ]]> https://biorxiv.org/content/10.1101/2024.11.22.624928v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@ee2127org.highwire.dtl.DTLVardef@1c2a39dorg.highwire.dtl.DTLVardef@183bf46org.highwire.dtl.DTLVardef@82b98d_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Beitz, A. M. Teves, J. Oakes, C. G. Johnstone, C. P. Wang, N. B. Brickman, J. M. Galloway, K. E. 2024-11-25 doi:10.1101/2024.11.22.624928 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Optogenetic manipulation of nuclear Dorsal reveals temporal requirements and consequences for transcription ]]> https://biorxiv.org/content/10.1101/2024.11.28.623729v1?rss=1 Pimmett, V. L. McGehee, J. Trullo, A. Douaihy, M. Radulescu, O. Stathopoulos, A. Lagha, M. 2024-11-28 doi:10.1101/2024.11.28.623729 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Mapping essential somatic hypermutations in a CD4-binding site bNAb informs HIV-1 vaccine design ]]> https://biorxiv.org/content/10.1101/2024.11.26.625503v1?rss=1 Dam, K.-M. A. Gristick, H. B. Li, Y. E. Yang, Z. Gnanapragasam, P. N. P. West, A. P. Seaman, M. S. Bjorkman, P. J. 2024-11-29 doi:10.1101/2024.11.26.625503 Cold Spring Harbor Laboratory Press 2024-11-29 <![CDATA[ Hydrogel encapsulation of a designed fluorescent protein biosensor for continuous measurements of sub-100 nanomolar nicotine ]]> https://biorxiv.org/content/10.1101/2024.12.02.625538v1?rss=1 Nichols, A. L. Marotta, C. B. Wagenaar, D. A. Mayo, S. L. Dougherty, D. A. Lester, H. A. 2024-12-02 doi:10.1101/2024.12.02.625538 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ A CRISPRi Library Screen in Group B Streptococcus Identifies Surface Immunogenic Protein (Sip) as a Mediator of Multiple Host Interactions ]]> https://biorxiv.org/content/10.1101/2024.12.06.627252v1?rss=1 Firestone, K. Gopalakrishna, K. P. Rogers, L. M. Peters, A. Gaddy, J. Nichols, C. Hall, M. H. Varela, H. N. Carlin, S. M. Hillebrand, G. H. Giacobe, E. J. Aronoff, D. M. Hooven, T. A. 2024-12-07 doi:10.1101/2024.12.06.627252 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ Deep homology of a brachyury regulatory syntax and origin of the notochord ]]> https://biorxiv.org/content/10.1101/2024.12.12.628285v1?rss=1 Fan, T.-P. Lee, J.-R. Lin, C.-Y. Chen, Y.-C. Cutting, A. E. Cameron, R. A. Yu, J.-K. Su, Y.-H. 2024-12-13 doi:10.1101/2024.12.12.628285 Cold Spring Harbor Laboratory Press 2024-12-13 <![CDATA[ Predictive Modeling of Gene Expression and Localization of DNA Binding Site Using Deep Convolutional Neural Networks ]]> https://biorxiv.org/content/10.1101/2024.12.17.629042v1?rss=1 Karshenas, A. Roschinger, T. Garcia, H. 2024-12-20 doi:10.1101/2024.12.17.629042 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ The clumped isotope signatures of multiple methanogenesis metabolisms ]]> https://biorxiv.org/content/10.1101/2024.12.18.629299v1?rss=1 Li, J. Ash, J. L. Cobban, A. Kubik, B. C. Rizzo, G. Thompson, M. Guibourdenche, L. Berger, S. Morra, K. Lin, Y. Mueller, E. P. Masterson, A. L. Stein, R. Fogel, M. Torres, M. A. Feng, X. Holden, J. F. Martini, A. Welte, C. Jetten, M. S. M. Young, E. D. Leavitt, W. D. 2024-12-20 doi:10.1101/2024.12.18.629299 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ The gut microbiome promotes mitochondrial respiration in the brain of a Parkinson's disease mouse model ]]> https://biorxiv.org/content/10.1101/2024.12.18.629251v1?rss=1 Morais, L. H. Stiles, L. Freeman, M. Oguienko, A. D. Hoang, J. D. Jones, J. Quan, B. Devine, J. Bois, J. S. Chou, T.-F. Trinh, J. Picard, M. Gradinaru, V. Mazmanian, S. K. 2024-12-21 doi:10.1101/2024.12.18.629251 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ Protein CREATE enables closed-loop design of de novo synthetic protein binders ]]> https://biorxiv.org/content/10.1101/2024.12.20.629847v1?rss=1 Lourenco, A. L. Subramanian, A. M. Spencer, R. K. Miao, J. Anaya, M. Fu, W. Chow, E. D. Thomson, M. 2024-12-22 doi:10.1101/2024.12.20.629847 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Acoustic tumor paint for real-time imaging, surgical guidance and recurrence monitoring of brain tumors with ultrasound ]]> https://biorxiv.org/content/10.1101/2024.12.22.629782v1?rss=1 Rabut, C. Daghlian, G. H. Barturen-Larrea, P. Li, H. R. Vorder Bruegge, R. Jones, R. M. Malounda, D. Pinton, G. F. Shapiro, M. G. 2024-12-22 doi:10.1101/2024.12.22.629782 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Reducing Cofilin dosage makes embryos resilient to heat stress ]]> https://biorxiv.org/content/10.1101/2025.01.02.631102v1?rss=1 Biel, N. Rashid, F. Natua, S. Wang, T.-Y. Chou, T.-F. Nguyen, T. V. P. Golding, I. Kalsotra, A. Sokac, A. M. 2025-01-03 doi:10.1101/2025.01.02.631102 Cold Spring Harbor Laboratory Press 2025-01-03 <![CDATA[ Cross-reactive sarbecovirus antibodies induced by mosaic RBD-nanoparticles ]]> https://biorxiv.org/content/10.1101/2025.01.02.631145v1?rss=1 Fan, C. Keeffe, J. R. Malecek, K. E. Cohen, A. A. West, A. P. Baharani, V. A. Rorick, A. V. Gao, H. Gnanapragasam, P. N. P. Rho, S. Alvarez, J. Segovia, L. N. Hatziioannou, T. Bieniasz, P. D. Bjorkman, P. J. 2025-01-03 doi:10.1101/2025.01.02.631145 Cold Spring Harbor Laboratory Press 2025-01-03 <![CDATA[ Optimizing the Efficacy of Vaccine-Induced Immunotherapy in Melanomas ]]> https://biorxiv.org/content/10.1101/2025.01.06.631283v1?rss=1 Chamseddine, I. Kambara, M. Bhatt, P. Pilon-Thomas, S. Rejniak, K. A. 2025-01-08 doi:10.1101/2025.01.06.631283 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ Characterization and automated classification of sentences in the biomedical literature: a case study for biocuration of gene expression and protein kinase activity ]]> https://biorxiv.org/content/10.1101/2025.01.06.631539v1?rss=1 Raciti, D. Van Auken, K. Arnaboldi, V. Tabone, C. J. Muller, H.-M. Sternberg, P. W. 2025-01-08 doi:10.1101/2025.01.06.631539 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ Design and characterization of HIV-1 vaccine candidates to elicit antibodies targeting multiple epitopes ]]> https://biorxiv.org/content/10.1101/2025.01.08.632013v1?rss=1 Gristick, H. B. Hartweger, H. Nishimura, Y. Gavor, E. Nagashima, K. Koranda, N. S. Gnanapragasam, P. N. P. Kakutani, L. M. Segovia, L. Donau, O. Keeffe, J. R. West, A. P. Martin, M. A. Nussenzweig, M. C. Bjorkman, P. J. 2025-01-09 doi:10.1101/2025.01.08.632013 Cold Spring Harbor Laboratory Press 2025-01-09 <![CDATA[ Genomes of the entomopathogenic nematode Steinernema hermaphroditum and its associated bacteria ]]> https://biorxiv.org/content/10.1101/2025.01.09.632278v1?rss=1 Schwarz, E. M. Baniya, A. Heppert, J. K. Schwartz, H. T. Tan, C.-H. Antoshechkin, I. Sternberg, P. W. Goodrich-Blair, H. Dillman, A. R. 2025-01-12 doi:10.1101/2025.01.09.632278 Cold Spring Harbor Laboratory Press 2025-01-12 <![CDATA[ Systematic characterization of zinc in a series of breast cancer cell lines reveals significant changes in zinc homeostasis ]]> https://biorxiv.org/content/10.1101/2025.01.11.632547v1?rss=1 Woyciehowsky, M. Larson, P. Stephan, A. R. Dandridge, S. L. Idonije, D. Berg, K. A. Lanthier, A. Araiza Acuna, S. Stites, S. W. Gebhardt, W. J. Holtzen, S. E. Rakshit, A. Palmer, A. E. 2025-01-13 doi:10.1101/2025.01.11.632547 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Two stages of substrate discrimination dictate selectivity in the E. coli MetNI-Q ABC transporter system ]]> https://biorxiv.org/content/10.1101/2025.01.20.633972v1?rss=1 Yang, J. G. Chen, H. Y. Guardado, J. H. Gardner, M. Foronda, M. S. 2025-01-21 doi:10.1101/2025.01.20.633972 Cold Spring Harbor Laboratory Press 2025-01-21 <![CDATA[ Recruiting ESCRT to single-chain heterotrimer peptide-MHCI releases antigen-presenting vesicles that stimulate T cells selectively ]]> https://biorxiv.org/content/10.1101/2025.01.17.633600v1?rss=1 Olson, B. A. Huey-Tubman, K. E. Mao, Z. Hoffmann, M. A. G. Murray, R. M. Mayo, S. L. 2025-01-22 doi:10.1101/2025.01.17.633600 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Unveiling Hidden Microbial Diversity in Mars2020 Mission Assembly Cleanrooms withMolecular Insights into the Persistent andPerseverance of Novel Species DefyingMetagenome Sequencing ]]> https://biorxiv.org/content/10.1101/2025.01.21.633868v1?rss=1 Muthamilselvi Sivabalan, S. K. Vijayakumar, V. Sengupta, P. Palmal, S. Krishnamurthi, S. Kumar Singh, N. Kyrpides, N. C. Raman, K. Venkateswaran, K. 2025-01-24 doi:10.1101/2025.01.21.633868 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Auto-methylation of the histone methyltransferase SetDB1 at its histone-mimic motifs ensures the spreading and maintenance of heterochromatin ]]> https://biorxiv.org/content/10.1101/2025.01.21.634156v1?rss=1 Tang, Q. Zhang, A. Sullivan, M. Fejes Toth, K. Aravin, A. A. 2025-01-24 doi:10.1101/2025.01.21.634156 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Building Foundation Models to Characterize Cellular Interactions via Geometric Self-Supervised Learning on Spatial Genomics ]]> https://biorxiv.org/content/10.1101/2025.01.25.634867v1?rss=1 You, Y. Wang, Z. Fleisher, K. Liu, R. Thomson, M. 2025-01-27 doi:10.1101/2025.01.25.634867 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ Designing biochemical circuits with tree search ]]> https://biorxiv.org/content/10.1101/2025.01.27.635147v1?rss=1 Bhamidipati, P. S. Thomson, M. 2025-01-29 doi:10.1101/2025.01.27.635147 Cold Spring Harbor Laboratory Press 2025-01-29 <![CDATA[ Plasticity and invariance of Arabidopsis inflorescence and floral shoot apical meristems in response to mineral nutrients ]]> https://biorxiv.org/content/10.1101/2025.01.31.635844v1?rss=1 Landrein, B. Abley, K. Formosa-Jordan, P. Meyerowitz, E. M. Jonsson, H. Locke, J. C. W. 2025-01-31 doi:10.1101/2025.01.31.635844 Cold Spring Harbor Laboratory Press 2025-01-31 <![CDATA[ FETCH enables fluorescent labeling of membrane proteins in vivo with spatiotemporal control in Drosophila ]]> https://biorxiv.org/content/10.1101/2025.01.31.635819v1?rss=1 Rostam, K. D. Morano, N. C. Menon, K. P. Lopez, D. H. Shapiro, L. Zinn, K. Feng, S. Mann, R. S. 2025-02-01 doi:10.1101/2025.01.31.635819 Cold Spring Harbor Laboratory Press 2025-02-01 <![CDATA[ Hookworm genes encoding intestinal excreted-secreted proteins are transcriptionally upregulated in response to the host's immune system ]]> https://biorxiv.org/content/10.1101/2025.02.01.636063v1?rss=1 Schwarz, E. M. Noon, J. B. Chicca, J. D. Garceau, C. Li, H. Antoshechkin, I. Ilik, V. Pafco, B. Weeks, A. M. Homan, E. J. Ostroff, G. R. Aroian, R. V. 2025-02-03 doi:10.1101/2025.02.01.636063 Cold Spring Harbor Laboratory Press 2025-02-03 <![CDATA[ CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes from Azotobacter vinelandii ]]> https://biorxiv.org/content/10.1101/2025.02.04.636493v1?rss=1 View larger version (64K): org.highwire.dtl.DTLVardef@59bd1eorg.highwire.dtl.DTLVardef@18f0f36org.highwire.dtl.DTLVardef@12fe3a7org.highwire.dtl.DTLVardef@10aeda7_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Warmack, R. A. Maggiolo, A. O. Shen, Y. Zhang, T. 2025-02-04 doi:10.1101/2025.02.04.636493 Cold Spring Harbor Laboratory Press 2025-02-04 <![CDATA[ Distinct Microbial Communities Within and On Seep Carbonates Support Long-term Anaerobic Oxidation of Methane and Novel pMMO Diversity ]]> https://biorxiv.org/content/10.1101/2025.02.04.636526v1?rss=1 Mayr, M. J. Parra, S. A. Connon, S. A. Narayanan, A. K. Murali, R. Cremiere, A. Orphan, V. J. 2025-02-08 doi:10.1101/2025.02.04.636526 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Molecularly-guided spatial proteomics captures single-cell identity and heterogeneity of the nervous system ]]> https://biorxiv.org/content/10.1101/2025.02.10.637505v1?rss=1 Dutta, S. Pang, M. Coughlin, G. M. Gudavalli, S. Roukes, M. L. Chou, T.-F. Gradinaru, V. 2025-02-11 doi:10.1101/2025.02.10.637505 Cold Spring Harbor Laboratory Press 2025-02-11 <![CDATA[ Perception and neural representation of intermittent odor stimuli in mice ]]> https://biorxiv.org/content/10.1101/2025.02.12.637969v1?rss=1 Boero, L. E. Wu, H. Zak, J. D. Masset, P. Pashakhanloo, F. Jayakumar, S. Tolooshams, B. Ba, D. Murthy, V. N. 2025-02-13 doi:10.1101/2025.02.12.637969 Cold Spring Harbor Laboratory Press 2025-02-13 <![CDATA[ Transcriptome analysis of the winter tick (Dermacentor albipictus) reveals sex-specific expression patterns ]]> https://biorxiv.org/content/10.1101/2025.02.17.638687v1?rss=1 Edwards, R. T. M. Antoshechkin, I. Hill, E. Perry, M. W. Olafson, P. U. Saelao, P. Lohmeyer, K. H. Akbari, O. S. 2025-02-21 doi:10.1101/2025.02.17.638687 Cold Spring Harbor Laboratory Press 2025-02-21 <![CDATA[ The forkhead transcription factor FKH-7/FOXP acts in chemosensory neurons to regulate developmental decision-making ]]> https://biorxiv.org/content/10.1101/2025.02.17.638733v1?rss=1 Chai, C. M. Taylor, S. R. Tischbirek, C. H. Wong, W.-R. Cai, L. Miller, D. M. Sternberg, P. W. 2025-02-21 doi:10.1101/2025.02.17.638733 Cold Spring Harbor Laboratory Press 2025-02-21 <![CDATA[ Combining MicroED and native mass spectrometry for structural discovery of enzyme-biosynthetic inhibitor complexes ]]> https://biorxiv.org/content/10.1101/2025.02.20.638743v1?rss=1 Vlahakis, N. W. Flowers, C. W. Liu, M. Agdanowski, M. Johnson, S. Summers, J. A. Keyser, C. Russell, P. Rose, S. Orlans, J. Adhami, N. Chen, Y. Sawaya, M. R. Basu, S. De Sanctis, D. Wakatsuki, S. Nelson, H. M. Loo, J. Tang, Y. Rodriguez, J. A. 2025-02-26 doi:10.1101/2025.02.20.638743 Cold Spring Harbor Laboratory Press 2025-02-26 <![CDATA[ Diversity and single-cell activity of endolithic microbes in sediment-hosted carbonate nodules within and below the sulfate-methane transition zone ]]> https://biorxiv.org/content/10.1101/2025.02.26.640391v1?rss=1 Parra, S. A. Mayr, M. Mullahoo, J. Quinn, L. K. Wipfler, R. L. Orphan, V. J. 2025-02-26 doi:10.1101/2025.02.26.640391 Cold Spring Harbor Laboratory Press 2025-02-26 <![CDATA[ Machine-Guided Dual-Objective Protein Engineering for Deimmunization and Therapeutic Functions ]]> https://biorxiv.org/content/10.1101/2025.02.24.639918v1?rss=1 Wolfsberg, E. Paul, J.-S. Tycko, J. Chen, B. Bassik, M. C. Bintu, L. Alizadeh, A. A. Gao, X. J. 2025-02-28 doi:10.1101/2025.02.24.639918 Cold Spring Harbor Laboratory Press 2025-02-28 <![CDATA[ The Neural Basis of Habit Formation Measured in Goal-Directed Response Switching ]]> https://biorxiv.org/content/10.1101/2025.03.13.643040v1?rss=1 Michiels, M. Man, V. Luque, D. Obeso, I. 2025-03-13 doi:10.1101/2025.03.13.643040 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ A nutrient bottleneck limits antibiotic efficacy in structured bacterial populations ]]> https://biorxiv.org/content/10.1101/2025.03.12.642894v1?rss=1 Hancock, A. M. Dill-Macky, A. S. Moore, J. A. Day, C. Donia, M. S. Datta, S. S. 2025-03-14 doi:10.1101/2025.03.12.642894 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Vacuum and sonication treatment enables efficient transient gene expression in various monocot and eudicot plant seedlings ]]> https://biorxiv.org/content/10.1101/2025.03.13.642903v1?rss=1 Li, E. Geng, Y. Khristoforova, T. R. Wang, Y. Jones, J. W. Demirer, G. S. 2025-03-14 doi:10.1101/2025.03.13.642903 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Revealing a coherent cell state landscape across single cell datasets with CONCORD ]]> https://biorxiv.org/content/10.1101/2025.03.13.643146v1?rss=1 Zhu, Q. Jiang, Z. Thomson, M. Gartner, Z. J. 2025-03-15 doi:10.1101/2025.03.13.643146 Cold Spring Harbor Laboratory Press 2025-03-15 <![CDATA[ Nucleotide and metalloid-driven conformational changes in the arsenite efflux ATPase ArsA ]]> https://biorxiv.org/content/10.1101/2025.03.21.644500v1?rss=1 Mahajan, S. Pall, A. E. Li, Y. E. Stemmler, T. L. Rees, D. C. Clemons, W. M. 2025-03-21 doi:10.1101/2025.03.21.644500 Cold Spring Harbor Laboratory Press 2025-03-21 <![CDATA[ The representation and valuation of subgoals in the human brain during model-based hierarchical behavior ]]> https://biorxiv.org/content/10.1101/2025.03.24.645084v1?rss=1 Grossman, C. D. Man, V. O'Doherty, J. P. 2025-03-25 doi:10.1101/2025.03.24.645084 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ Pulsatory response of the BcLOV4 photoreceptor through intramolecular feed-forward regulation ]]> https://biorxiv.org/content/10.1101/2025.04.08.647774v1?rss=1 300 million years ago, and the characteristic temperature of pulsatory responses had adapted to match the ecological niche of the hosts, ranging from Antarctica to thermal ponds. These findings uncover a class of dynamic proteins, determine molecular principles of time-varying protein activation, and suggest functional importance for light- and temperature-conditioned protein activity pulses. One-Sentence SummaryIndividual proteins can dynamically encode information through interactions between their component domains, revealing principles for complex signal processing in natural and engineered proteins. ]]> Huang, Z. Forson, M. Benman, W. Gardner, K. H. Bugaj, L. J. 2025-04-14 doi:10.1101/2025.04.08.647774 Cold Spring Harbor Laboratory Press 2025-04-14 <![CDATA[ Engineered protein circuits for cancer therapy ]]> https://biorxiv.org/content/10.1101/2025.04.16.647665v1?rss=1 Lu, A. C. Moeller, L. Moore, S. Xia, S. Ho, K. Zhang, E. Budde, M. W. Larson, H. Ahmed Diaz, A. Gu, B. Linton, J. M. Klock, L. Flynn, M. J. Gao, X. J. Siegwart, D. J. Zhu, H. Elowitz, M. B. 2025-04-16 doi:10.1101/2025.04.16.647665 Cold Spring Harbor Laboratory Press 2025-04-16 <![CDATA[ KDM5B expression is suppressed by MYC in a negative feedback loop to promote cell survival. ]]> https://biorxiv.org/content/10.1101/2025.04.12.648490v1?rss=1 Chatterjee, T. Beffert, E. Dewson, G. S. Sullivan, D. K. Anchang, B. Sears, R. C. Liefwalker, D. 2025-04-18 doi:10.1101/2025.04.12.648490 Cold Spring Harbor Laboratory Press 2025-04-18 <![CDATA[ AAVs Targeting Human Carbonic Anhydrase IV Enhance Gene Delivery to the Brain ]]> https://biorxiv.org/content/10.1101/2025.04.21.649868v1?rss=1 Lin, C. Chen, X. Hoang, J. D. Ristic, F. Fan, Y. Jang, S. Chung, J. H. A. Sullivan, E. E. Gawda, T. Kavvathas, B. Tran, I. Li, Y. Steele, A. D. Shay, T. F. Gradinaru, V. 2025-04-22 doi:10.1101/2025.04.21.649868 Cold Spring Harbor Laboratory Press 2025-04-22 <![CDATA[ VARS-fUSI: Variable Sampling for Fast and Efficient Functional Ultrasound Imaging using Neural Operators ]]> https://biorxiv.org/content/10.1101/2025.04.16.649237v1?rss=1 Tolooshams, B. Lin, L. Callier, T. Wang, J. Pal, S. Chandrashekar, A. Rabut, C. Li, Z. Blagden, C. Norman, S. L. Azizzadenesheli, K. Liu, C. Shapiro, M. G. Andersen, R. A. Anandkumar, A. 2025-04-23 doi:10.1101/2025.04.16.649237 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ Exploring non-invasive sexing of early chick embryos in intact eggs using Laser Speckle Contrast Imaging (LSCI) and Deep Neural Network (DNN) ]]> https://biorxiv.org/content/10.1101/2025.04.17.649355v1?rss=1 Mahler, S. Arora, A. Readhead, C. Yin, S. Hari, S. N. Wang, E. Moxley, C. I. Adeboye, A. A. Dong, Z. Zhou, H. Chen, X. Bronner, M. Yang, C. 2025-04-23 doi:10.1101/2025.04.17.649355 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ Whole-Proteome Screening and Multi-Modal Profiling of Antigen-Specific CD4+ T Cells at Single-Cell Resolution ]]> https://biorxiv.org/content/10.1101/2025.04.21.649828v1?rss=1 Zhang, R. Qi, J. McKasson, M. Choi, J. Gutierrez, V. Brennan, C. Hong, S. Chour, W. Ng, R. H. Xie, J. Yuan, D. Webster, A. Sidhu, S. K. Anderson, A. Chen, D. Edmark, R. Murray, K. M. Li, S. McDonald, C. Rowen, L. Wang, S. Rasheed, Y. Su, Y. Wagner, J. R. Chen, J. Narwaly, K. Fu, J. Duven, A. Forman, S. J. Song, M. Priceman, S. Brown, C. E. Ribas, A. Wong, D. Paulson, K. G. Drescher, C. W. Puig-Saus, C. Goldman, J. D. Trimble, C. L. Heath, J. R. 2025-04-23 doi:10.1101/2025.04.21.649828 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ SynGAP forms biocondensates at sub-micromolar concentrations and recruits PSD95 and receptor oligomers, functioning as a key initiator of PSD formation ]]> https://biorxiv.org/content/10.1101/2025.04.22.649955v1?rss=1 Acharya, S. Tsunoyama, T. A. Hoffmann, C. Aguilar, P. G. Meshcheryakova, I. Nakamura-Norimoto, A. Mastro, T. Walkup, W. G. Fujiwara, T. K. Kennedy, M. B. Milovanovic, D. Kusumi, A. 2025-04-23 doi:10.1101/2025.04.22.649955 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ Systematic cell-type resolved transcriptomes of 8 tissues in 8 lab and wild-derived mouse strains captures global and local expression variation ]]> https://biorxiv.org/content/10.1101/2025.04.21.649844v1?rss=1 Rebboah, E. Weber, R. Abdollahzadeh, E. Swarna, N. P. Sullivan, D. K. Trout, D. Reese, F. Liang, H. Y. Filimban, G. Mahdipour, P. Duffield, M. Mojaverzargar, R. Taghizadeh, E. Fattahi, N. Mojgani, N. Zhang, H. Loving, R. K. Carilli, M. Booeshaghi, A. S. Kawauchi, S. Hallgrimsdottir, I. B. Williams, B. A. MacGregor, G. Pachter, L. Wold, B. Mortazavi, A. 2025-04-24 doi:10.1101/2025.04.21.649844 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Subcellular proteomics of Paramecium tetraurelia reveals mosaic localization of glycolysis and gluconeogenesis ]]> https://biorxiv.org/content/10.1101/2025.04.24.650466v1?rss=1 Jirsova, D. Licknack, T. Poh, Y.-P. Qiu, Y. Quan, N. Karr, T. Chou, T.-F. Lynch, M. Wideman, J. G. 2025-04-25 doi:10.1101/2025.04.24.650466 Cold Spring Harbor Laboratory Press 2025-04-25 <![CDATA[ LOSS OF ROR2 TYROSINE KINASE RECEPTOR IS ASSOCIATED WITH ENDOTHELIAL DYSFUNCTION IN PAH VIA INAPPROPRIATE INTEGRIN BETA 1 ACTIVATION ]]> https://biorxiv.org/content/10.1101/2025.04.28.651135v1?rss=1 Mitra, A. Chakraborty, A. Zhong, B. Heo, L. Agarwal, S. Pacheco, A. Auer, N. Dunn, A. Chelladurai, P. Jain, A. Matos, J. Bankar, A. Guardado, E. YI, D. Zhao, H. Wai Dede Man, K. Nair, R. V. Guenat, O. T. Dai, Z. de Jesus Perez, V. A. 2025-04-29 doi:10.1101/2025.04.28.651135 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Is the whole the sum of its parts? Neural computation of consumer bundle valuation in humans ]]> https://biorxiv.org/content/10.1101/2025.04.28.650827v1?rss=1 Cross, L. M. Webb, R. O'Doherty, J. P. 2025-05-01 doi:10.1101/2025.04.28.650827 Cold Spring Harbor Laboratory Press 2025-05-01 <![CDATA[ A SUMO-interacting motif in the guanine nucleotide exchange factor EPAC1 is required for subcellular targeting and function ]]> https://biorxiv.org/content/10.1101/2025.05.02.651912v1?rss=1 Yang, W. Mei, F. Lin, W. Lee, J. E. Nie, S. Bley, C. J. Hoelz, A. J. Cheng, X. 2025-05-03 doi:10.1101/2025.05.02.651912 Cold Spring Harbor Laboratory Press 2025-05-03 <![CDATA[ Endothelial AGO1 Drives Vascular Inflammation and Atherosclerosis via a Non-Canonical Nuclear Mechanism ]]> https://biorxiv.org/content/10.1101/2025.05.01.651783v1?rss=1 Liu, X. Yuan, D. Luo, Y. Tang, X. Tapia, A. Malhi, N. K. Chadha, R. S. Tiwari, S. Swiderski, P. Wang, K.-C. Kortylewski, M. Pardi, N. Wei, L. Huang, W. Chen, Z. B. 2025-05-07 doi:10.1101/2025.05.01.651783 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ CellTune: An integrative software for accurate cell classification in spatial proteomics ]]> https://biorxiv.org/content/10.1101/2025.05.05.652215v1?rss=1 Bussi, Y. Shainshein, D. Ovits, E. Posner, S. Azulay, N. Maimon, N. Keidar Haran, T. Ben-uri, R. Brown, C. Schuldiner, N. Yaniv, E. Van Valen, D. A. Milo, I. Elhanani, O. Schiemann, R. Keren, L. 2025-05-09 doi:10.1101/2025.05.05.652215 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ Spindle-localized F-actin regulates polar MTOC organization and the fidelity of meiotic spindle formation ]]> https://biorxiv.org/content/10.1101/2025.05.07.652730v1?rss=1 Soto-Moreno, E. J. Ali, N. N. Kuller, F. Nasufovic, V. Frolikova, M. Tepla, O. Masata, J. Trauner, D. Patterson, A. A. Arndt, H.-D. Komrskova, K. Zernicka-Goetz, M. Glover, D. M. Balboula, A. Z. 2025-05-11 doi:10.1101/2025.05.07.652730 Cold Spring Harbor Laboratory Press 2025-05-11 <![CDATA[ Pseudoassembly of k-mers ]]> https://biorxiv.org/content/10.1101/2025.05.11.653354v1?rss=1 Sullivan, D. K. Boffelli, M. Pachter, L. 2025-05-13 doi:10.1101/2025.05.11.653354 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Single-Cell Metabolic Imaging Reveals Glycogen Driven-Adaptations in Endothelial Cells ]]> https://biorxiv.org/content/10.1101/2025.05.11.653328v1?rss=1 Chadha, R. S. Yang, B. Yuan, D. Kocheril, P. A. Mahajan, S. Colazo, A. Malhi, N. K. Ambarian, J. A. Liu, X. Chen, Z. B. Wei, L. 2025-05-14 doi:10.1101/2025.05.11.653328 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ The Dynamics of Inducible Genetic Circuits ]]> https://biorxiv.org/content/10.1101/2025.05.11.653320v1?rss=1 Yang, Z. Rousseau, R. J. Mahdavi, S. D. Garcia, H. G. Phillips, R. 2025-05-15 doi:10.1101/2025.05.11.653320 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ GFP-Free Live-Neuron Quantitative Imaging Reveals Compartmentalization and Growth Dynamics of PolyQ Aggregates ]]> https://biorxiv.org/content/10.1101/2025.05.12.653542v1?rss=1 Bi, X. Lin, L.-E. Miao, K. Wei, L. 2025-05-15 doi:10.1101/2025.05.12.653542 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Selective GSK3α Inhibition Promotes Self-Renewal Across Different Stem Cell States ]]> https://biorxiv.org/content/10.1101/2025.05.16.653860v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@4e371eorg.highwire.dtl.DTLVardef@104b287org.highwire.dtl.DTLVardef@164bd96org.highwire.dtl.DTLVardef@daf1ba_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIGSK3 inhibition by BRD0705 promotes self-renewal of ESCs, EpiSCs, and NSCs C_LIO_LIBRD0705/IWR1 enables long-term co-culture of ESCs and EpiSCs C_LIO_LICo-cultured ESCs and EpiSCs retain distinct naive or primed identities C_LIO_LIBRD0705 preserves stem cell states independently of {beta}-catenin signaling C_LI ]]> Wang, D. Wang, X. Wang, S. Shi, K.-X. Malki, S. Chan, Y. Feng, J. Tang, J. Chen, X. McKim, D. Zhang, C. Hu, G. Ying, Q.-L. 2025-05-17 doi:10.1101/2025.05.16.653860 Cold Spring Harbor Laboratory Press 2025-05-17 <![CDATA[ Structural basis of liver de-targeting and neuronal tropism of CNS-targeted AAV capsids ]]> https://biorxiv.org/content/10.1101/2025.06.02.655683v1?rss=1 Brittain, T. J. Jang, S. Coughlin, G. M. Barcelona, B. H. Giriat, I. Ristic, F. Appling, N. Chossis, C. P. Shay, T. F. Gradinaru, V. 2025-06-03 doi:10.1101/2025.06.02.655683 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Implantable CMOS Deep-Brain Fluorescence Imager with Single-Neuron Resolution ]]> https://biorxiv.org/content/10.1101/2025.06.03.657675v1?rss=1 Yilmaz, S. Choi, J. Uguz, I. Kim, J. Akrouh, A. Taal, A. J. Andino-Pavlovsky, V. Yin, H. Fabbri, J. D. Moreaux, L. Roukes, M. L. Shepard, K. L. 2025-06-06 doi:10.1101/2025.06.03.657675 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Metabolic controls on the carbon isotope fractionations of bacterial fermentation ]]> https://biorxiv.org/content/10.1101/2025.06.06.655161v1?rss=1 Mueller, E. Heuer, V. B. Leadbetter, J. R. Hinrichs, K.-U. Sessions, A. L. 2025-06-06 doi:10.1101/2025.06.06.655161 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Rational Design of Immunogenic Nanoparticles as a Platform for Enhanced Ovarian Cancer Immunotherapy in Mice ]]> https://biorxiv.org/content/10.1101/2025.06.05.657862v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@1434599org.highwire.dtl.DTLVardef@18e79e6org.highwire.dtl.DTLVardef@e5285corg.highwire.dtl.DTLVardef@bcc604_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Tang, L. Marwedel, B. Dang, C. Olewine, M. Jun, M. Naydenkov, P. Medina, L. Y. Gayoso, V. Doan, N. OLeary, S. L. Schiavone, C. Cave, J. Howard, T. Watt, J. D. Dogra, P. Serda, R. E. Noureddine, A. 2025-06-09 doi:10.1101/2025.06.05.657862 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Biological Processes as Exploratory Dynamics ]]> https://biorxiv.org/content/10.1101/2025.06.06.657857v1?rss=1 Kondev, J. Kirschner, M. W. Garcia, H. G. Salmon, G. Phillips, R. 2025-06-09 doi:10.1101/2025.06.06.657857 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ A DNA part library for reliable engineering of the emerging model nematode symbiotic bacterium Xenorhabdus griffiniae HGB2511 ]]> https://biorxiv.org/content/10.1101/2025.06.09.658710v1?rss=1 Larsson, E. M. Wang, O. Y. Murray, R. M. 2025-06-09 doi:10.1101/2025.06.09.658710 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ SpoIIE drives asymmetric cell division in B. subtilis by sequential modulation of the cytokinesis machinery ]]> https://biorxiv.org/content/10.1101/2025.06.09.658746v1?rss=1 Ryan, A. Squyres, G. R. Holmes, M. J. Bisson, A. Garner, E. C. Bradshaw, N. 2025-06-10 doi:10.1101/2025.06.09.658746 Cold Spring Harbor Laboratory Press 2025-06-10 <![CDATA[ Thermally controlled state switches for macrophage immunotherapy ]]> https://biorxiv.org/content/10.1101/2025.06.09.658763v1?rss=1 Liu, A. Farooq, A. S. Abedi, M. H. Smith, C. A. B. Wu, D. Shapiro, M. G. 2025-06-13 doi:10.1101/2025.06.09.658763 Cold Spring Harbor Laboratory Press 2025-06-13 <![CDATA[ Untangling overlapping barcodes in spatial genomics data ]]> https://biorxiv.org/content/10.1101/2025.06.10.658913v1?rss=1 White, J. A. Lu, C. Ombelets, L. Cai, L. 2025-06-16 doi:10.1101/2025.06.10.658913 Cold Spring Harbor Laboratory Press 2025-06-16 <![CDATA[ The nematode symbiotic bacterium Xenorhabdus griffiniae can sense and respond to the presence of its host Steinernema hermaphroditum ]]> https://biorxiv.org/content/10.1101/2025.06.16.660008v1?rss=1 Larsson, E. M. Myers, C. Newman, D. K. Cao, M. 2025-06-16 doi:10.1101/2025.06.16.660008 Cold Spring Harbor Laboratory Press 2025-06-16 <![CDATA[ Sono-uncaging for Spatiotemporal Control of Chemical Reactivity ]]> https://biorxiv.org/content/10.1101/2025.06.11.659141v1?rss=1 Schrunk, E. Lee, S. Dutka, P. Wu, D. Shapiro, M. G. 2025-06-17 doi:10.1101/2025.06.11.659141 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Surface-Tethering Enhances Precision in Measuring Diffusion Within 3D Protein Condensates ]]> https://biorxiv.org/content/10.1101/2025.06.11.659185v1?rss=1 View larger version (48K): org.highwire.dtl.DTLVardef@1f0ae11org.highwire.dtl.DTLVardef@341574org.highwire.dtl.DTLVardef@16c75daorg.highwire.dtl.DTLVardef@1ad5ed1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sumrall, E. R. Gao, G. Stakenas, S. Walter, N. G. 2025-06-17 doi:10.1101/2025.06.11.659185 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Pulsed-laser lensing for phase modulation in electron microscopy ]]> https://biorxiv.org/content/10.1101/2025.06.12.659428v1?rss=1 Du, D. X. Bartnik, A. C. Duncan, C. J. R. Choudhry, U. Tabachnik, T. Sallah, C. Ogawa, Y. Najafi, E. Yang, D.-S. Maxson, J. M. Fitzpatrick, A. W. P. 2025-06-17 doi:10.1101/2025.06.12.659428 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ ER tethering and active transport govern condensate diffusion during hyperosmotic stress ]]> https://biorxiv.org/content/10.1101/2025.06.13.659610v1?rss=1 Halder, B. Gao, G. Ahnoud, A. Stakenas, S. Sumrall, E. R. Walter, N. G. 2025-06-17 doi:10.1101/2025.06.13.659610 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Squidly: Enzyme Catalytic Residue Prediction Harnessing a Biology-Informed Contrastive Learning Framework ]]> https://biorxiv.org/content/10.1101/2025.06.13.659624v1?rss=1 Rieger, W. J. Boden, M. Arnold, F. H. Mora, A. 2025-06-20 doi:10.1101/2025.06.13.659624 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ Tau-seed interactome analysis reveals distinct functional signatures in Alzheimer's disease across model systems. ]]> https://biorxiv.org/content/10.1101/2025.06.17.660179v1?rss=1 Martinez, P. Patel, H. You, Y. Lopes, D. Amaro, A. Jury-Garfe, N. Min, Y. Redding-Ochoa, J. Dutta, S. Rochet, C. Ertekin-Taner, N. Troncoso, J. Lasagna-Reeves, C. A. 2025-06-20 doi:10.1101/2025.06.17.660179 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ Expansion of chromosome F heterochromatin in parthenogenetic Drosophila mercatorum ]]> https://biorxiv.org/content/10.1101/2025.06.22.660940v1?rss=1 Sperling, A. L. Fabian, D. K. Glover, D. M. 2025-06-27 doi:10.1101/2025.06.22.660940 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Functionalizing hydrogel nanovials with vesicles mimicking antigen-presenting vesicles and cancer exosomes improves T cell capture and activation ]]> https://biorxiv.org/content/10.1101/2025.06.24.661128v1?rss=1 Olson, B. A. Mellody, M. P. Soemardy, C. Mao, Z. Mei, A. Lippert, K. Hoffmann, M. A. G. Di Carlo, D. Mayo, S. L. 2025-06-27 doi:10.1101/2025.06.24.661128 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Core microRNAs regulate neural crest delamination and condensation in the developing trigeminal ganglion ]]> https://biorxiv.org/content/10.1101/2025.06.27.661967v1?rss=1 Marquez, R. B. Sanchez Vazquez, E. Alonso, A. M. Bernardi, Y. E. Santillan, E. M. Lwigale, P. Cochella, L. Bronner, M. Strobl-Mazzulla, P. H. 2025-06-28 doi:10.1101/2025.06.27.661967 Cold Spring Harbor Laboratory Press 2025-06-28 <![CDATA[ Representation Learning Methods for Single-Cell Microscopy are Confounded by Background Cells ]]> https://biorxiv.org/content/10.1101/2025.06.26.661577v1?rss=1 Gupta, A. Moses, A. Lu, A. X. 2025-06-30 doi:10.1101/2025.06.26.661577 Cold Spring Harbor Laboratory Press 2025-06-30 <![CDATA[ Deep sea anaerobic microbial community couples the degradation of insoluble chitin to extracellular electron transfer ]]> https://biorxiv.org/content/10.1101/2025.06.30.662270v1?rss=1 Jangir, Y. Guo, Y. Connon, S. Pontrelli, S. Wu, F. Schwartzman, J. Lim, S. Sauer, U. Cordero, O. X. Orphan, V. J. 2025-06-30 doi:10.1101/2025.06.30.662270 Cold Spring Harbor Laboratory Press 2025-06-30 <![CDATA[ Two parallel lineage-committed progenitors contribute to the developing brain ]]> https://biorxiv.org/content/10.1101/2025.07.02.662771v1?rss=1 Dundes, C. E. Jokhai, R. T. Ahsan, H. Kang, R. S. Salomon-Shulman, R. E. A. Rajan, A. Kim, Y. S. Stanton, L. J. Xu, C. Do, S. McDonald, B. D. Lopez, J. M. A. Urrutia, H. A. Greenfeld, H. Wong, A. Qu, Y. Petkovic, A. S. Miao, Y. Garcia, K. C. Monje, M. Wagner, D. E. Bronner, M. E. Lowe, C. J. Loh, K. M. 2025-07-03 doi:10.1101/2025.07.02.662771 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Symbiotic entrenchment through ecological Catch-22 ]]> https://biorxiv.org/content/10.1101/2025.07.02.662832v1?rss=1 Naragon, T. H. Viliunas, J. W. Yousefelahiyeh, M. Bruckner, A. Wagner, J. M. Ryon, H. M. Collinson, D. Kitchen, S. A. Wijker, R. S. Sessions, A. L. Parker, J. 2025-07-03 doi:10.1101/2025.07.02.662832 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Models and Algorithms for Equilibrium Analysis of Mixed-Material Nucleic Acid Systems ]]> https://biorxiv.org/content/10.1101/2025.06.30.662484v1?rss=1 View larger version (19K): org.highwire.dtl.DTLVardef@1363811org.highwire.dtl.DTLVardef@9af312org.highwire.dtl.DTLVardef@cc4d1corg.highwire.dtl.DTLVardef@da876c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Nanjundiah, A. Fornace, M. E. Schulte, S. J. Pierce, N. A. 2025-07-04 doi:10.1101/2025.06.30.662484 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Association of E. coli Nissle with insect-parasitic nematode Steinernema hermaphroditum ]]> https://biorxiv.org/content/10.1101/2025.07.03.663106v1?rss=1 Chen, V. Marken, J. P. Murray, R. M. Cao, M. 2025-07-04 doi:10.1101/2025.07.03.663106 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Ultrasound imaging of in situ transcriptional activity in opaque tissue ]]> https://biorxiv.org/content/10.1101/2025.07.06.663365v1?rss=1 Shivaei, S. Cheung, K. Y. M. Yadav, A. Hurvitz, I. U. Lee, S. Revilla, J. Rabut, C. Criado-Hidalgo, E. Zhang, R. J. Shapiro, M. G. 2025-07-07 doi:10.1101/2025.07.06.663365 Cold Spring Harbor Laboratory Press 2025-07-07 <![CDATA[ An Automated End-to-End Workflow for Production of Secreted Proteins in Transfected Mammalian Cells ]]> https://biorxiv.org/content/10.1101/2025.07.13.664612v1?rss=1 Vasnarungruengkul, P. Anaya, M. A. Lam, A. W. Gonzalez, E. Zhang, A. Wang, M. L. Wojtowicz, W. Zinn, K. Vielmetter, J. 2025-07-13 doi:10.1101/2025.07.13.664612 Cold Spring Harbor Laboratory Press 2025-07-13 <![CDATA[ A multiplex extracellular interactome screening method employing high-avidity nanoparticles ]]> https://biorxiv.org/content/10.1101/2025.07.09.663943v1?rss=1 Anaya, M. Wang, M. L. Gonzalez, E. Lam, A. W. Vasnarungruengkul, P. Vielmetter, J. Wojtowicz, W. M. Zinn, K. 2025-07-14 doi:10.1101/2025.07.09.663943 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ Transcriptomic responses to endurance exercise training in rats ]]> https://biorxiv.org/content/10.1101/2025.07.11.664421v1?rss=1 Oakes, C. G. Pachter, L. 2025-07-17 doi:10.1101/2025.07.11.664421 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Genetically encoded assembly recorder temporally resolves cellular histories in cellulo and in vivo ]]> https://biorxiv.org/content/10.1101/2025.07.16.664392v1?rss=1 Yan, Y. Lu, J. Li, Z. Zhao, Z.-H. Shay, T. F. Wang, S. Lei, Y. Wang, Y. Chen, W. Parker, P. Yang, H. Qi, A. Sun, Y. Bergles, D. Baker, D. Lin, D. 2025-07-18 doi:10.1101/2025.07.16.664392 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Mapping the Exit Route of Hydrogen Peroxide From the Manganese Superoxide Dismutase (MnSOD) Active Site. ]]> https://biorxiv.org/content/10.1101/2025.07.17.665311v1?rss=1 Borgstahl, G. E. DASGUPTA, M. Slobodnik, K. Cone, E. Kroll, T. Azadmanesh, J. 2025-07-19 doi:10.1101/2025.07.17.665311 Cold Spring Harbor Laboratory Press 2025-07-19 <![CDATA[ The History of Enzyme Evolution Embedded in Metabolism ]]> https://biorxiv.org/content/10.1101/2025.07.16.665256v1?rss=1 Corlett, T. Smith, H. B. Smith, E. Goldford, J. Longo, L. M. 2025-07-21 doi:10.1101/2025.07.16.665256 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Viral communities from long-term anaerobic alkane-oxidizing enrichments may promote cell surface adhesion ]]> https://biorxiv.org/content/10.1101/2025.07.20.664993v1?rss=1 Narayanan, A. K. Philosof, A. Murali, R. Connon, S. A. Wegener, G. Orphan, V. J. 2025-07-21 doi:10.1101/2025.07.20.664993 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Food-activated Microneedle Sensor for Real-time, Colorimetric Spoilage Monitoring of Pre-packaged Food ]]> https://biorxiv.org/content/10.1101/2025.07.18.665560v1?rss=1 Khan, S. Prasad, A. Javed, M. Maclachlan, R. Filipe, C. D. M. Didar, T. 2025-07-22 doi:10.1101/2025.07.18.665560 Cold Spring Harbor Laboratory Press 2025-07-22 <![CDATA[ Harmonic Amplitude-Modulated Singular Value Decomposition for Ultrafast Ultrasound Imaging of Gas Vesicles ]]> https://biorxiv.org/content/10.1101/2025.07.21.665910v1?rss=1 Zhang, G. Leroy, H. Haidour, N. Rivera, E. Zucker, N. Nouhoum, M. Jimenez, A. Deffieux, T. Malounda, D. Nayak, R. Pezet, S. Shapiro, M. Pernot, M. Tanter, M. 2025-07-24 doi:10.1101/2025.07.21.665910 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ Growth Cost and Transport Efficiency Tradeoffs Define Root System Optimization Across Varying Developmental Stages and Environments in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2025.07.25.666579v1?rss=1 Faizi, K. Mehta, P. Maida, A. Humphreys, T. Berrigan, E. McKee-Reid, L. McCorkell, R. Tagade, A. Rumbelow, J. Showalter, J. Brent, L. Coroenne, C. Rigaud, A. Chandrasekhar, A. Navlakha, S. Martin, A. Pradal, C. Lee, S. Busch, W. Platre, M. P. 2025-07-26 doi:10.1101/2025.07.25.666579 Cold Spring Harbor Laboratory Press 2025-07-26 <![CDATA[ Dynamic Reworking of Marine Diatom Endometabolomes ]]> https://biorxiv.org/content/10.1101/2025.07.25.666871v1?rss=1 Olofsson, M. Uchimiya, M. Ferrer-Gonzalez, F. X. Schreier, J. E. Powers, M. A. Smith, C. B. Edison, A. S. Moran, M. A. 2025-07-31 doi:10.1101/2025.07.25.666871 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ A molecular switch in NAC prevents mitochondrial protein mistargeting by SRP ]]> https://biorxiv.org/content/10.1101/2025.07.29.667405v1?rss=1 Maldosevic, E. Gora, R. Lin, L. L. Zhou, L. E. Li, Z. J. Peskova, Y. Qi, L. Shan, S.-o. Jomaa, A. 2025-08-01 doi:10.1101/2025.07.29.667405 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ NAC promotes co-translational folding at the ribosomal tunnel exit ]]> https://biorxiv.org/content/10.1101/2025.08.02.668148v1?rss=1 Santos, J. Gunnigmann, M. Gora, R. J. Iljina, M. Predin, M. Kotan, I. E. De, P. Choudhary, D. Jang, J. Tippmann, F. Ban, N. Tans, S. J. Shan, S.-o. Kramer, G. Bukau, B. 2025-08-02 doi:10.1101/2025.08.02.668148 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Illuminating the active virosphere with BONCAT and single virus genomic sequencing technologies ]]> https://biorxiv.org/content/10.1101/2025.08.05.666878v1?rss=1 Alvarez-Sanchez, M. Martinez-Hernandez, F. Llorenc-Vicedo, A. Vila-Nistal, M. Philosof, A. Narayanan, A. K. Tijerina, J. C. Martinez-Garcia, M. Orphan, V. J. 2025-08-05 doi:10.1101/2025.08.05.666878 Cold Spring Harbor Laboratory Press 2025-08-05 <![CDATA[ A modular method for rapidly prototyping targeted gas vesicle protein nanoparticles ]]> https://biorxiv.org/content/10.1101/2025.08.06.668980v1?rss=1 Vassallo, R. Ling, B. Criado-Hidalgo, E. Robinson, N. Schrunk, E. Liu, A. Daghlian, G. Li, H. R. Swift, M. B. Mannar, D. Malounda, D. Goldenberg, S. L. Salcudean, S. E. Shapiro, M. G. Black, P. C. Cox, M. E. 2025-08-07 doi:10.1101/2025.08.06.668980 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ O-Acyltransferase Genes Involved in the Production of Volatile Sex Pheromones in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2025.08.10.669515v1?rss=1 Wan, X. Cohen, S. M. Yu, Y. Le, H. H. Park, H. Groaz, A. Moreno, R. Tan, M. Gronquist, M. R. Shinya, R. Schroeder, F. C. Sternberg, P. W. 2025-08-12 doi:10.1101/2025.08.10.669515 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Covalent Drug binding in Live Cells Monitored by Mid-IR Quantum Cascade Laser Spectroscopy: Photoactive Yellow Protein as a Model System ]]> https://biorxiv.org/content/10.1101/2025.08.15.670201v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@13bd30forg.highwire.dtl.DTLVardef@9db2bcorg.highwire.dtl.DTLVardef@141590forg.highwire.dtl.DTLVardef@13dfcf2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Mukherjee, S. Fried, S. D. E. Hong, N. Y. Bagheri, N. Kozuch, J. Mathews, I. I. Kirsh, J. M. Boxer, S. G. 2025-08-19 doi:10.1101/2025.08.15.670201 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ Bivalent mRNA booster encoding virus-like particles elicits potent polyclass RBD antibodies in pre-vaccinated mice ]]> https://biorxiv.org/content/10.1101/2025.08.18.670983v1?rss=1 Fan, C. Cohen, A. A. Dam, K.-M. A. Rorick, A. V. Priso Fils, A.-C. I. Yang, Z. Gnanapragasam, P. N. Segovia, L. N. Huey-Tubman, K. E. Moon, W. J. Lin, P. J. Bjorkman, P. J. Hoffmann, M. A. 2025-08-19 doi:10.1101/2025.08.18.670983 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ Optimized R2 Retroelement Complexes Enable Precise and Efficient DNA Insertion into Plant Genomes ]]> https://biorxiv.org/content/10.1101/2025.08.22.671877v1?rss=1 Muchenje, K. T. Wang, Y. Oz, T. M. Li, E. Saffron, A. Demirer, G. S. 2025-08-24 doi:10.1101/2025.08.22.671877 Cold Spring Harbor Laboratory Press 2025-08-24 <![CDATA[ GeneSys: Generative Modeling of Developmental System ]]> https://biorxiv.org/content/10.1101/2025.08.20.671385v1?rss=1 Hsu, C.-W. Chen, C.-Y. Nolan, T. M. Benfey, P. N. Ohler, U. 2025-08-25 doi:10.1101/2025.08.20.671385 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ Extracellular contractile injection systems for high efficiency protein delivery to plants ]]> https://biorxiv.org/content/10.1101/2025.08.22.671880v1?rss=1 Legendre, M. G. Heredia, C. A. Colee, C. M. Demirer, G. S. 2025-08-28 doi:10.1101/2025.08.22.671880 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ A global map of wood density ]]> https://biorxiv.org/content/10.1101/2025.08.25.671920v1?rss=1 Fischer, F. J. Chave, J. Zanne, A. Jucker, T. Fajardo, A. Fayolle, A. de Lima, R. A. F. Vieilledent, G. Beeckman, H. Hubau, W. De Mil, T. Wallenus, D. Aldana, A. M. Alvarez-Davila, E. Alves, L. F. Apgaua, D. M. G. Arcanjo, F. Bastin, J.-F. Bilous, A. Birnbaum, P. Blyshchyk, V. Borah, J. Boukili, V. Camarero, J. J. Casas, L. Cazzolla Gatti, R. Chambers, J. Q. Chimbioputo Fabiano, E. Choat, B. Cifuentes, E. Conti, G. Coomes, D. Cornwell, W. Dar, J. A. Das, A. K. Dobler, M. Dougabka, D. Edwards, D. P. Eggli, U. Evans, R. Falster, D. Fearnside, P. Flores, 2025-08-28 doi:10.1101/2025.08.25.671920 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ Light on its feet: Acclimation to high and low diurnal light is flexible in Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.1101/2025.08.28.672467v1?rss=1 Dupuis, S. Chastain, J. L. Han, G. Zhong, V. Gallaher, S. D. Nicora, C. D. Purvine, S. O. Lipton, M. S. Niyogi, K. K. Iwai, M. Merchant, S. S. 2025-09-02 doi:10.1101/2025.08.28.672467 Cold Spring Harbor Laboratory Press 2025-09-02 <![CDATA[ Zebrafish sleep displays distinct sub-states ]]> https://biorxiv.org/content/10.1101/2025.08.28.672887v1?rss=1 Tripathi, R. Oikonomou, G. Prober, D. A. Goodhill, G. 2025-09-02 doi:10.1101/2025.08.28.672887 Cold Spring Harbor Laboratory Press 2025-09-02 <![CDATA[ The Global Canopy Atlas: analysis-ready maps of 3D structure for the world's woody ecosystems ]]> https://biorxiv.org/content/10.1101/2025.08.31.673375v1?rss=1 Fischer, F. J. Morgan, B. Jackson, T. Chave, J. Coomes, D. Cushman, K. Dalagnol, R. Dalponte, M. Duncanson, L. Saatchi, S. Seidl, R. Sterenczak, K. Laurin, G. V. Adu-Bredu, S. Aguirre-Gutierrez, J. Antonielli, B. Armston, J. D. de Assis, M. L. Barbier, N. Burt, A. Cesar, R. G. Cervenka, J. Coops, N. Cullen, L. Dalling, J. W. Davies, A. Demol, M. Ebenbeck, J. Fassnacht, F. Fatoyinbo, L. Garcia, M. Gasparri, N. I. Gobakken, T. Goodbody, T. R. H. Görgens, E. B. Gorum, T. Gosper, C. Guan, H. Heiskanen, J. Heurich, M. Hobi, M. Höfle, B. Hooijer, A. Huth, 2025-09-04 doi:10.1101/2025.08.31.673375 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Reference-based variant detection with varseek ]]> https://biorxiv.org/content/10.1101/2025.09.03.674039v1?rss=1 Rich, J. M. Luebbert, L. Sullivan, D. K. Rosa, R. Pachter, L. 2025-09-05 doi:10.1101/2025.09.03.674039 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ Identification of a broad and potent V3 glycan site bNAb targeting anN332gp120 glycan-independent epitope ]]> https://biorxiv.org/content/10.1101/2025.09.05.674437v1?rss=1 Gieselmann, L. DeLaitsch, A. T. Rohde, M. Radford, C. Worczinski, J. Momot, A. Ahmadov, E. Burger, J. A. Havenar-Daughton, C. Deshpande, S. Giovannoni, F. Corti, D. Kreer, C. Ercanoglu, M. S. Schommers, P. Georgiev, I. West, A. P. Knuefer, J. Stumpf, R. Kroidl, A. Geldmacher, C. Maganga, L. William, W. Ntinginya, N. E. Hoelscher, M. Yang, Z. Wei, Q. Renfrow, M. Green, T. J. Novak, J. van Gils, M. Gristick, H. B. Gruell, H. Bloom, J. D. Seaman, M. S. Bjorkman, P. Klein, F. 2025-09-10 doi:10.1101/2025.09.05.674437 Cold Spring Harbor Laboratory Press 2025-09-10 <![CDATA[ stk32a links sleep homeostasis to suppression of sensory and motor systems ]]> https://biorxiv.org/content/10.1101/2025.09.09.675098v1?rss=1 Tran, S. Emtage, J. Zhang, C. Liu, X. Lecoeuche, M. Andreev, A. Oikonomou, G. Narayan, S. Garcia, B. Cammidge, T. Gonzales, C. Hurley, H. Yap, M. Li, S. Wang, F. Wang, T.-Y. Ahrens, M. B. Chou, T.-F. Xu, M. Liu, Q. Prober, D. A. 2025-09-11 doi:10.1101/2025.09.09.675098 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Next-generation hybridization chain reaction tools with enhanced sensitivities to detect challenging targets ]]> https://biorxiv.org/content/10.1101/2025.09.09.675218v1?rss=1 Singh, C. Bali, N. Coughlin, G. M. Xu, J. Polansky, J. Y. Herget, U. Gilbert, M. S. Cammidge, T. Spigolon, G. Smirnova, Y. Gradinaru, V. Zinn, K. Prober, D. A. 2025-09-11 doi:10.1101/2025.09.09.675218 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Pth4 neurons define a novel hypothalamic circuit that promotes sleep via brainstem monoaminergic neurons ]]> https://biorxiv.org/content/10.1101/2025.09.09.675233v1?rss=1 Herget, U. Tran, S. Singh, C. Oikonomou, G. Ryu, S. Rotllant, J. Prober, D. A. 2025-09-11 doi:10.1101/2025.09.09.675233 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Proliferation to suppress neoplasia: a general model and a first test in the moon jelly ]]> https://biorxiv.org/content/10.1101/2025.09.07.674745v1?rss=1 Sarma, A. A. Goentoro, L. Doyle, J. C. 2025-09-12 doi:10.1101/2025.09.07.674745 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ Soil texture regulates bacterial motility and chemotactic recruitment to plant roots ]]> https://biorxiv.org/content/10.1101/2025.09.08.674882v1?rss=1 Al Harraq, A. Choi, G. Datta, S. S. Shaevitz, J. W. 2025-09-12 doi:10.1101/2025.09.08.674882 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ Leveraging bioorthogonal conjugation for alpha synuclein fibril surveillance ]]> https://biorxiv.org/content/10.1101/2025.09.12.675751v1?rss=1 Jenkins, R. A. Wu, S. Fujimura, G. Heredia, A. Flowers, C. Sun, C. Sawaya, M. Loo, J. Rodriguez, J. A. 2025-09-17 doi:10.1101/2025.09.12.675751 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ A male-derived volatile sex pheromone in <Caenorhabditis> nematodes identified through its mimicry by a predator ]]> https://biorxiv.org/content/10.1101/2025.09.12.675966v1?rss=1 Gronquist, M. R. Wan, X. Leighton, D. Togawa, Y. Sagawa, M. Sternberg, P. W. Schroeder, F. C. Shinya, R. 2025-09-17 doi:10.1101/2025.09.12.675966 nematodes identified through its mimicry by a predator]]> Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Influence of heterotrophs on phage infection of marine picocyanobacteria ]]> https://biorxiv.org/content/10.1101/2025.09.17.676900v1?rss=1 Coe, A. Parker, S. M. Vo, N. N. Kearney, S. M. Pollak, S. von Emster, K. Mullet, J. I. Castro, K. G. Chisholm, S. W. 2025-09-18 doi:10.1101/2025.09.17.676900 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Phage-mediated lysis increases growth rate of surviving bacterial cells ]]> https://biorxiv.org/content/10.1101/2025.09.18.677064v1?rss=1 Fara, E. Raach, B. Cavallaro, A. Fink, J. W. Ramesh, D. Guo, Y. Orphan, V. J. Hall, A. R. Micali, G. Ackermann, M. Schubert, O. T. 2025-09-18 doi:10.1101/2025.09.18.677064 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Extracellular matrix chemistry tunes bacterial biofilm metabolism and optimizes fitness ]]> https://biorxiv.org/content/10.1101/2025.09.18.677115v1?rss=1 Li, J. Squyres, G. R. Duong, K. Reichhardt, C. Newman, D. K. Parsek, M. R. 2025-09-18 doi:10.1101/2025.09.18.677115 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Model-based and model-free valuation signals in the human brain vary markedly in their relationship to individual differences in behavioral control ]]> https://biorxiv.org/content/10.1101/2025.09.17.676398v1?rss=1 Ding, W. Cockburn, J. Simon, J. P. Johri, A. Cho, S. J. Oh, S. Feusner, J. D. Tadayonnejad, R. O'Doherty, J. P. 2025-09-19 doi:10.1101/2025.09.17.676398 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Faecalibacterium prausnitzii, depleted in the Parkinson's disease microbiome, improves motor deficits in α-synuclein overexpressing mice ]]> https://biorxiv.org/content/10.1101/2025.09.18.677192v1?rss=1 Moiseyenko, A. Antonello, G. Schonhoff, A. M. Boktor, J. C. Long, K. Dirks, B. Oguienko, A. D. Winnett, A. V. Simpson, P. Daeizadeh, D. Ismagilov, R. F. Krajmalnik-Brown, R. Segata, N. Waldron, L. D. Mazmanian, S. K. 2025-09-21 doi:10.1101/2025.09.18.677192 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Cyclohexyl acetate functions like a volatile sex pheromone mimic in Caenorhabditis nematodes ]]> https://biorxiv.org/content/10.1101/2025.09.19.677433v1?rss=1 Wan, X. Togawa, Y. Gronquist, M. R. Sagawa, M. Leighton, D. Chan, C. M. Schroeder, F. C. Chow, K. L. Sternberg, P. W. Shinya, R. 2025-09-21 doi:10.1101/2025.09.19.677433 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Designing signaling environments to modulate neural progenitor cell differentiation with regulatory network models ]]> https://biorxiv.org/content/10.1101/2025.09.20.677552v1?rss=1 Jiang, J. Chen, S. Park, J. H. Tsou, T. Yang, V. Rivaud, P. Thomson, M. 2025-09-21 doi:10.1101/2025.09.20.677552 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Carbon monoxide oxidation expands the known metabolic capacity in anaerobic methanotrophic consortia ]]> https://biorxiv.org/content/10.1101/2025.09.21.677609v1?rss=1 Guo, Y. Utter, D. R. Murali, R. Orphan, V. J. 2025-09-21 doi:10.1101/2025.09.21.677609 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Lzp Ablation Ameliorates Dyslipidemia and Suppresses Atherosclerosis by Reducing Circulating Apolipoprotein B-Containing Lipoproteins ]]> https://biorxiv.org/content/10.1101/2025.09.24.678175v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@118ead8org.highwire.dtl.DTLVardef@e215baorg.highwire.dtl.DTLVardef@1007212org.highwire.dtl.DTLVardef@412757_HPS_FORMAT_FIGEXP M_FIG C_FIG HightlightsO_LILzp deficiency attenuates atherosclerosis and improves plasma lipid profiles in ApoE-/- mice fed chow or Western diets. C_LIO_LILzp deficiency reduces hepatic and circulating apolipoprotein B levels in hyperlipidemic ApoE-/- mice without exacerbating hepatic steatosis or injury. C_LIO_LILzp represents a candidate therapeutic target, warranting further mechanistic and translational studies for atherosclerosis. C_LI ]]> He, K. Ku, X. Chen, Z. Wu, C. Liao, C. Li, L. Qu, H. Hong, P. Bai, S. Cui, X. Su, X. Han, Z.-G. K. 2025-09-26 doi:10.1101/2025.09.24.678175 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ De novo design of phospho-tyrosine peptide binders ]]> https://biorxiv.org/content/10.1101/2025.09.29.678898v1?rss=1 Bauer, M. S. Zhang, J. Z. Wu, K. Lee, G. R. Coventry, B. Klupt, K. A. Shi, J. Brent, R. I. Li, X. Moller, C. Roullier, N. Vafeados, D. K. Kalvet, I. Skotheim, R. K. Zhu, S. Motmaen, A. Herrmann, L. C. Sturmfels, P. Tischer, D. Altae-Tran, H. R. Juergens, D. Krishna, R. Ahern, W. Yim, J. Bera, A. K. Kang, A. Joyce, E. Lu, A. Stewart, L. DiMaio, F. Baker, D. 2025-09-30 doi:10.1101/2025.09.29.678898 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ Flow Autoencoders are Effective Protein Tokenizers ]]> https://biorxiv.org/content/10.1101/2025.10.01.679645v1?rss=1 Dilip, R. Varshney, A. Zhang, E. Van Valen, D. A. 2025-10-03 doi:10.1101/2025.10.01.679645 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Pretrained protein language models choose between sequence novelty and structural completeness ]]> https://biorxiv.org/content/10.1101/2025.10.01.679905v1?rss=1 Subramanian, A. M. Martinez, Z. A. Thomson, M. 2025-10-03 doi:10.1101/2025.10.01.679905 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Mapping function in the tree shrew visual system using functional ultrasound imaging. ]]> https://biorxiv.org/content/10.1101/2025.10.03.680247v1?rss=1 Wekselblatt, J. B. Nayak, R. lanfranchi, F. Luongo, F. Wagenaar, D. A. Tsao, D. Y. Shapiro, M. 2025-10-03 doi:10.1101/2025.10.03.680247 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Consistent Induction of Broadly Neutralizing HIV Antibodies by a Novel Two-Step Mechanism Informs Immunogen Design ]]> https://biorxiv.org/content/10.1101/2025.10.06.680687v1?rss=1 Skelly, A. N. Gristick, H. B. Li, H. Gavor, E. Connell, A. J. Kreider, E. F. Marchitto, L. Hogarty, M. P. Newby, M. L. Allen, J. D. Liu, W. West, A. P. Ayyanathan, K. Campion, M. S. Winters, K. Gordon, C. G. Osbaldeston, R. A. Akeley, M. J. Li, Y. Singh, A. Cruickshank, K. Park, Y. Zhao, C. Li, X. Amereh, K. Van Itallie, E. Carey, J. W. Albertus, A. DeLaitsch, A. T. Keeffe, J. R. Lituchy, M. G. Walsh, A. A. Morris, D. J. Habib, R. Bibollet-Ruche, F. Mishra, N. Avillion, G. Koranda, N. S. Plante, S. J. Martella, C. L. Lora, J. Wang, E. J. D. Lewis, M. G 2025-10-06 doi:10.1101/2025.10.06.680687 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ ATM promotes reversed fork processing during DNA interstrand cross-link repair ]]> https://biorxiv.org/content/10.1101/2025.10.08.680157v1?rss=1 Altshuller, M. MacKrell, V. A. Tzeng, J. Nigam, R. Wang, T.-Y. Chou, T.-F. Semlow, D. R. 2025-10-09 doi:10.1101/2025.10.08.680157 Cold Spring Harbor Laboratory Press 2025-10-09 <![CDATA[ Plasmidome, resistome, and virulence-associated genes characterization of Acinetobacter johnsonii in NASA cleanrooms and a clinical setting. ]]> https://biorxiv.org/content/10.1101/2025.10.09.681420v1?rss=1 10 years post initial isolation. ImportanceAcinetobacter johnsonii is increasingly recognized as an emerging human pathogen, with growing evidence of its ability to persist in controlled, high-stakes environments, posing risks as both persisting environmental contaminant and antimicrobial resistance (AMR) reservoir. Yet, gaps remain in our understanding of its AMR profile and the mechanisms that enable its enhanced environmental adaptability. This knowledge is necessary in contexts where biological cleanliness is a priority such as clinical settings and spacecraft assembly facilities cleanrooms, where contamination of hardware with terrestrial microorganisms is concerning. In this study, we aim to address some of key knowledge gaps by providing genomic insights into a rare multi-drug resistant clinical isolate and 22 NASA cleanroom isolates that persisted for over a decade in extremely clean conditions. Our findings will help evaluate the contamination risk of A. johnsonii in high-stakes environments and ultimately strengthen our ability to manage this microbial contaminant across terrestrial and extraterrestrial settings. HighlightsO_LICleanrooms-derived A. johnsonii genomes show favorable traits for increased adaptability C_LIO_LIGenomic signatures of A. johnsonii persisted in the cleanrooms for >10 years C_LIO_LIblaOXA is ubiquitously found in the genome of all A. johnsonii C_LIO_LIE154408A is the first patient colonization by carbapenem-resistant A. johnsonii in Europe C_LI ]]> Tumeo, A. Miliotis, G. O'Connor, A. Vijayakumar, V. Sengupta, P. McDonagh, F. Kovarova, A. Clarke, C. Hooban, B. Singh, N. K. Rosado, A. S. Raman, K. Venkateswaran, K. 2025-10-10 doi:10.1101/2025.10.09.681420 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ The neural computations underlying context dependent attribute-based valuation of complex stimuli. ]]> https://biorxiv.org/content/10.1101/2025.10.10.681681v1?rss=1 Fransen, A. Man, V. Iigaya, K. O`Doherty, J. P. 2025-10-12 doi:10.1101/2025.10.10.681681 Cold Spring Harbor Laboratory Press 2025-10-12 <![CDATA[ Electrical synapses mediate visual approach behavior ]]> https://biorxiv.org/content/10.1101/2025.10.14.682373v1?rss=1 Frighetto, G. Dombrovski, M. Castillo, L. M. P. Meera, P. Mirshahidi, P. S. Sanfilippo, P. Vaccari, A. Kandimalla, P. Hartenstein, V. Kurmangaliyev, Y. Z. Zipursky, S. L. Frye, M. A. 2025-10-15 doi:10.1101/2025.10.14.682373 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Natural evolution of intermale sexual behavior by multiple pheromone switches among Drosophila species ]]> https://biorxiv.org/content/10.1101/2025.10.14.682417v1?rss=1 Ouadah, Y. Naragon, T. H. Smihula, H. Behrman, E. L. Khallaf, M. A. Ding, Y. Stern, D. L. Parker, J. Anderson, D. J. 2025-10-15 doi:10.1101/2025.10.14.682417 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ CRISPR-Cas9 based Mutagenesis in the Entomopathogenic Nematode Steinernema hermaphroditum and the Maintenance of Mutant Lines ]]> https://biorxiv.org/content/10.1101/2025.10.14.682448v1?rss=1 Ireri, S. W. Cao, M. 2025-10-15 doi:10.1101/2025.10.14.682448 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Survival of NASA-cleanroom microbial isolates under simulated space and Martian conditions ]]> https://biorxiv.org/content/10.1101/2025.10.15.682532v1?rss=1 Chander, A. M. Burr, D. J. Wipf, S. Nitsche, R. Fujimura, G. Schubert, W. W. Kumar Singh, N. Bell, J. Brandl, A. Weil, M. M. Elsaesser, A. Venkateswaran, K. 2025-10-15 doi:10.1101/2025.10.15.682532 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Shifts in ruminant fermentation during inhibition of methanogenesis are reflected in the isotope compositions of volatile fatty acids. ]]> https://biorxiv.org/content/10.1101/2025.10.16.682381v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@1368f20org.highwire.dtl.DTLVardef@ee87baorg.highwire.dtl.DTLVardef@10f714org.highwire.dtl.DTLVardef@1cd4f6a_HPS_FORMAT_FIGEXP M_FIG C_FIG Of particular importance is microbial fermentation, which generates easily digested volatile fatty acids (VFAs) from hard-to-breakdown plant matter. To better understand how fermentation responds to methane mitigation strategies, we measured the isotope composition of VFAs in cow rumen. Our results indicate that fermentation changes pathways when methane production is inhibited to those that generate less energy for the cell. As methane mitigation strategies are developed in the coming decade, isotopic analysis of VFAs may be a useful and accessible contribution to our understanding of rumen microbiology. ]]> Mueller, E. Duong, R. Sessions, A. Eiler, J. Hess, M. 2025-10-16 doi:10.1101/2025.10.16.682381 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ A line attractor maintains aggressiveness during feeding in hangry mice ]]> https://biorxiv.org/content/10.1101/2025.10.16.682711v1?rss=1 Kim, J. J. Nair, A. Coria, N. Huynh, S. Vinograd, A. Xu, J. Liu, M. Anderson, D. J. 2025-10-17 doi:10.1101/2025.10.16.682711 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ mRNA delivery of genetically encoded mosaic-8 pan-sarbecovirus RBD vaccines ]]> https://biorxiv.org/content/10.1101/2025.10.21.683747v1?rss=1 Cohen, A. A. Keeffe, J. R. Manasyan, L. Madireddy, I. Fils, A.-C. I. P. Dam, K.-M. A. Stober, H. E. Hills, R. A. Moon, W. J. Lin, P. J. C. Howarth, M. R. Hoffmann, M. A. G. Bjorkman, P. J. 2025-10-22 doi:10.1101/2025.10.21.683747 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ MillionFull enables massive, full-length enzyme sequence-fitness data collection at low cost for machine learning-guided enzyme engineering ]]> https://biorxiv.org/content/10.1101/2025.10.24.684421v1?rss=1 Li, J. Erichsen, B. Krarup, S. R. Yuan, S. Jijakli, K. Karst, S. Yang, L. Nielsen, A. T. 2025-10-25 doi:10.1101/2025.10.24.684421 Cold Spring Harbor Laboratory Press 2025-10-25 <![CDATA[ Neural control of coordinated wing and leg movements during a terrestrial threat display ]]> https://biorxiv.org/content/10.1101/2025.10.25.684556v1?rss=1 Cao, S. Anderson, D. J. 2025-10-26 doi:10.1101/2025.10.25.684556 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Determining Multivalent Interactomes of Intrinsically Disordered Proteins in Phase-Separated Condensates in Live Cells ]]> https://biorxiv.org/content/10.1101/2025.10.27.684971v1?rss=1 Han, Q. Zhong, Y. Quan, B. Wang, T.-Y. Chou, T.-F. Chong, S. 2025-10-28 doi:10.1101/2025.10.27.684971 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ Spatiotemporal Microbial Ecoevolutionary Dynamics on the International Space Station ]]> https://biorxiv.org/content/10.1101/2025.10.28.685245v1?rss=1 Hill, M. S. Simpson, A. C. Minnis, V. Salas Garcia, M. C. Mahnert, A. Lax, S. Rushton, E. Chung, R. Bone, D. Parker, C. W. Allard, S. M. Matty, M. Venkateswaran, K. Gilbert, J. A. 2025-10-29 doi:10.1101/2025.10.28.685245 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ Trimodal brain-wide ultrasound imaging of brain-tumor interaction ]]> https://biorxiv.org/content/10.1101/2025.10.29.685462v1?rss=1 Rabut, C. Shivaei, S. Heiles, B. Shapiro, M. G. 2025-10-31 doi:10.1101/2025.10.29.685462 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Fine-tuned Protein Language Model Identifies Antigen-specific B Cell Receptors from Immune Repertoires ]]> https://biorxiv.org/content/10.1101/2025.10.30.685465v1?rss=1 Paco, K. Mendivil, M. P. Zhang, Z. Zebardast, S. Davila, C. Mooney, R. M. Olatoyinbo, P. Yang, T. Bassi, S. Gonzales, V. Chen, E. Ashraf, F. B. Roman, I. C. Felix, J. R. Alam, R. M. Lay, J. A. Johal, M. S. Le Roch, K. G. Tolstorukov, I. Hernandez, J. B. da Silva, F. L. B. Lonardi, S. Sazinsky, M. H. Ray, A. 2025-10-31 doi:10.1101/2025.10.30.685465 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ How tp1, an indirect wing steering muscle, stabilizes Drosophila's flight ]]> https://biorxiv.org/content/10.1101/2025.11.02.686144v1?rss=1 Teoh, H. K. Biswas, D. Leung, A. Ludlow, B. K. Whitehead, S. C. Ehrhard, E. Dickinson, M. H. Beatus, T. Cowan, N. Cohen, I. 2025-11-04 doi:10.1101/2025.11.02.686144 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Nitric oxide tunes secreted metabolite bioactivity ]]> https://biorxiv.org/content/10.1101/2025.11.05.686753v1?rss=1 Lonergan, Z. R. Weisflog, S. L. Scurria, M. Li, J. Thalhammer, K. Gutierrez, O. Conway, S. J. Newman, D. K. 2025-11-05 doi:10.1101/2025.11.05.686753 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Electron Cryo-Tomography Reveals the Caulobacter vibrioidesTight Adherence Pilus Architecture ]]> https://biorxiv.org/content/10.1101/2025.11.06.686991v1?rss=1 Maggi, S. Rosenzweig, R. Panis, G. Viollier, P. H. Jensen, G. J. 2025-11-07 doi:10.1101/2025.11.06.686991 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ Uncovering the molecular basis of kinase activity and substrate recognition with phospho-PCA ]]> https://biorxiv.org/content/10.1101/2025.11.07.687244v1?rss=1 Yu, C. Pao, E. Van Valen, D. A. 2025-11-07 doi:10.1101/2025.11.07.687244 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ Parkinsons disease modeling in regenerative spiny mice (Acomys dimidiatus) captures key disease-relevant behavioral, histological, and molecular signatures ]]> https://biorxiv.org/content/10.1101/2025.11.06.687049v1?rss=1 Dutta, S. Pang, M. Donahue, R. R. Chou, T.-F. Seifert, A. W. Gradinaru, V. 2025-11-08 doi:10.1101/2025.11.06.687049 Cold Spring Harbor Laboratory Press 2025-11-08 <![CDATA[ Hierarchical and Context-Dependent Encoding of Actions in Human Posterior Parietal and Motor Cortex ]]> https://biorxiv.org/content/10.1101/2025.11.10.687245v1?rss=1 Bougou, V. Gamez, J. Rosario, E. R. Liu, C. Pejsa, K. Bari, A. Andersen, R. A. 2025-11-11 doi:10.1101/2025.11.10.687245 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ Phosphorus stress and spatial confinement lower the threshold for quorum-sensing activation of redox-active metabolite production in Pseudomonas synxantha ]]> https://biorxiv.org/content/10.1101/2025.11.11.687776v1?rss=1 Alcade, R. E. Jeckel, H. Zhang, O. Avila, R. L. Dalleska, N. Mavrodi, D. Yang, C. Newman, D. K. 2025-11-11 doi:10.1101/2025.11.11.687776 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ SHORT DISORDERED PEPTIDES ARE SUFFICIENT TO CONVERT PROTEINS INTO MECHANOSENSORS THAT RESPOND TO PHYSIOLOGICAL CELLULAR FORCES ]]> https://biorxiv.org/content/10.1101/2025.11.11.685779v1?rss=1 Callejas Marin, A. Gonzalez, W. Pleiner, T. De la Cruz, A. Pandey, A. Sanchez Guardado, L. Jafar-Nejad, H. Voorhees, R. Lois, C. 2025-11-12 doi:10.1101/2025.11.11.685779 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Elucidating Neurodevelopmental Trajectories in Cancer with Topic Modeling: Revealing Persistent External Granule Layer Lineages in Medulloblastoma ]]> https://biorxiv.org/content/10.1101/2025.11.12.687706v1?rss=1 Rajendran, A. Haldipur, P. Arora, S. Grama, K. Subramanian, S. S. Galan, L. M. Johnson, D. Aldinger, K. A. Shendure, J. Millen, K. J. Gennari, J. H. Pattwell, S. S. 2025-11-13 doi:10.1101/2025.11.12.687706 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Proteome-wide identification of metamorphic protein candidates using mass spectrometry ]]> https://biorxiv.org/content/10.1101/2025.11.12.688092v1?rss=1 750 proteolytic sites across >250 abundant proteins (>10% of the identified proteome) whose local susceptibility shifts as temperature decreases from 35 {degrees}C to 5 {degrees}C, including five Sa1V90T peptides recapitulating purified-protein behavior. A site-level scoring model yields 338 destabilized peptides (177 proteins) and 426 stabilized peptides (138 proteins). Cold stabilization prominently marks translation machinery (>15 ribosomal proteins), while cooling also exposes regions in chaperones and cell-division factors. Sequence analysis links temperature sensitivity to charge-enriched composition, consistent with thermodynamic expectations. These data provide a proteome-wide view of cold-sensitive folding, implicate translation and cytokinetic systems in low-temperature remodeling, and illuminate a new strategy for identifying metamorphic proteins on an unprecedented scale. ]]> Quan, B. Qiu, Y. Carillo, K. Liwang, A. Orban, J. Chou, T.-F. 2025-11-13 doi:10.1101/2025.11.12.688092 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Joint Biophysical Modeling of Paired Single-Cell RNA and Protein Measurements ]]> https://biorxiv.org/content/10.1101/2025.11.14.688548v1?rss=1 Felce, C. Fang, M. Pachter, L. 2025-11-15 doi:10.1101/2025.11.14.688548 Cold Spring Harbor Laboratory Press 2025-11-15 <![CDATA[ Quantitative profiling of whole-brain connectomes at single-axon resolution using deep learning and high-resolution light sheet microscopy ]]> https://biorxiv.org/content/10.1101/2025.11.14.688340v1?rss=1 Attarpour, A. Raffiee, M. Xu, T. Osmann, J. Patel, S. Yu, F. Au, B. Clappison, A. Biparva, M. Zhu, R. Crow, A. Eshaghi Gharagoz, B. Rozak, M. W. Aubert, I. McLaurin, J. Deisseroth, K. Stefanovic, B. Goubran, M. 2025-11-16 doi:10.1101/2025.11.14.688340 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ Deep Learning-Augmented Stimulated Raman Imaging for Cell-Type-Specific Metabolic Profiling in Live Neuronal Co-Cultures ]]> https://biorxiv.org/content/10.1101/2025.11.18.689078v1?rss=1 Lin, L.-E. Bi, X. Colazo, A. Wang, H. Wei, L. 2025-11-18 doi:10.1101/2025.11.18.689078 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ The LAST mile: Evaluating genetic biocontrol as a supplemental tool for eradicating invasive rodents on islands ]]> https://biorxiv.org/content/10.1101/2025.11.20.688920v1?rss=1 Birand, A. Hay, B. Combs, M. Gierus, L. Horak, K. E. Oh, K. P. Robertson, L. J. Thomas, P. Velasquez-Escobar, A. M. Will, D. J. Maselko, M. Piaggio, A. J. 2025-11-21 doi:10.1101/2025.11.20.688920 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Determining gene specificity from multivariate single-cell RNA sequencing data ]]> https://biorxiv.org/content/10.1101/2025.11.21.689845v1?rss=1 Swarna, N. P. Booeshaghi, A. S. Rebboah, E. Gordon, M. G. Kathail, P. Li, T. Alvarez, M. Ye, C. J. Wold, B. J. Mortazavi, A. Pachter, L. 2025-11-24 doi:10.1101/2025.11.21.689845 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Biophysical constraints on mRNA decay rates shape macroevolutionary divergence in steady-state abundances ]]> https://biorxiv.org/content/10.1101/2025.11.24.690267v1?rss=1 Felce, C. Cope, A. L. Schraiber, J. G. Krishnaswamy, M. Pachter, L. Pennell, M. 2025-11-24 doi:10.1101/2025.11.24.690267 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ RAPMS 2.0 Improves Specificity and Throughput for Proteomic Identification of RNA Binding Proteins ]]> https://biorxiv.org/content/10.1101/2025.11.23.690051v1?rss=1 Honson, D. Deng, W. Blanco, M. Sha, J. Plath, K. Wohlschlegl, J. A. Guttman, M. Majumdar, D. 2025-11-25 doi:10.1101/2025.11.23.690051 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ k-spaces: Mixtures of Gaussian latent variable models ]]> https://biorxiv.org/content/10.1101/2025.11.24.690254v1?rss=1 Markarian, N. Engelhardt, B. E. Pierce, N. A. Sternberg, P. W. Pachter, L. 2025-11-28 doi:10.1101/2025.11.24.690254 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ Distributed activity in the human posterior putamen distinguishes goal-directed from habitual control in humans ]]> https://biorxiv.org/content/10.1101/2025.11.26.690863v1?rss=1 Johri, A. Kluen, L. M. Gera, R. Man, V. Perez, O. D. Simon, J. P. Ding, W. Fransen, A. Cho, S. Oh, S. Cockburn, J. Feusner, J. Tadayon-Nejad, R. O'Doherty, J. 2025-11-28 doi:10.1101/2025.11.26.690863 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ Nanoscale imaging of native symbiotic animal tissue using amultimodal large volume imaging pipeline for cryo-electrontomography ]]> https://biorxiv.org/content/10.1101/2025.11.30.691379v1?rss=1 Gundlach, K. A. Schiotz, O. H. Ladinsky, M. S. Raimann, C. Rheinberger, M. Beck, F. Guenduez, B. Langelaan, R. Ruecklin, M. Limpens, R. W. A. L. Ruby, E. G. McFall-Ngai, M. Plitzko, J. M. Briegel, A. 2025-11-30 doi:10.1101/2025.11.30.691379 Cold Spring Harbor Laboratory Press 2025-11-30 <![CDATA[ Development of a Recombinant Single-Cycle Influenza Viral Vector as an Intranasal Vaccine against SARS-CoV-2 and SARS-like Betacoronaviruses ]]> https://biorxiv.org/content/10.1101/2025.11.28.691177v1?rss=1 Munro, J. Melnyk, D. Schimanski, L. Afzal, M. Cohen, A. A. Keeffe, J. Bjorkman, P. J. James, W. S. Townsend, A. R. Tan, T. K. 2025-12-01 doi:10.1101/2025.11.28.691177 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Naegleria amoebae seek confinement and crawl persistently through narrow spaces ]]> https://biorxiv.org/content/10.1101/2025.11.30.691445v1?rss=1 50 m/min) and unidirectionally over long distances (>1 mm) using only bleb-based motility. We also introduced Naegleria to granular hydrogel matrices that mimic pond sediments and found that cells readily enter and migrate through these three-dimensional matrices using both blebs and lamellar protrusions. Although cells in matrices showed lower persistence at short timescales, longer time scales correlate with increased persistence, suggesting Naegleria cells may retain memory of past orientation. We propose that pond life may select for three behaviors that prime Naegleria for pathogenesis: memory-guided motility that would facilitate exploration of sinus cavities, confinement-seeking ("claustrophilia") that would promote entry into narrow passages along olfactory axons, and fast bleb-based migration that would allow rapid transit along axons to the brain. SIGNIFICANCE STATEMENTThe "brain-eating amoeba" Naegleria fowleri causes a devastating brain infection with a [~]95% fatality rate, yet how these normally harmless pond-dwellers invade the human brain remains mysterious. Using the model species N. gruberi, we show that Naegleria amoebae exhibit three key behaviors: they retain directional memory during exploration, actively enter confined spaces, and crawl rapidly and persistently through narrow channels for millimeter-scale distances. We propose these behaviors are adaptations for hunting bacteria in pond sediments that inadvertently enable pathogenesis--directional memory facilitates sinus exploration, confinement-seeking draws amoebae into spaces between olfactory axons, and persistent channel migration enables rapid transit to the brain. ]]> Velle, K. Ramaswamy, M. Hokmabad, B. V. Martin-Perez, T. Carrasco, T. T. Callahan, W. S. Kim, H. S. Datta, S. S. Edwards, M. Fritz-Laylin, L. 2025-12-01 doi:10.1101/2025.11.30.691445 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Ultrasonic Reporter of Kinase Activity ]]> https://biorxiv.org/content/10.64898/2025.11.30.691048v1?rss=1 Yang, J. W. Jin, Z. Wang, T. Y. Shapiro, M. G. 2025-12-02 doi:10.64898/2025.11.30.691048 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Cycling of sulfur redox intermediates drives microbial activity in the sulfate-methane transition zone of cold methane seeps ]]> https://biorxiv.org/content/10.64898/2025.11.30.691342v1?rss=1 Eitel, E. M. Murali, R. Utter, D. R. Wu, F. Lim, S. Connon, S. A. Sessions, A. Orphan, V. J. 2025-12-02 doi:10.64898/2025.11.30.691342 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Uniform pre-processing of bacterial single-cell RNA-seq ]]> https://biorxiv.org/content/10.64898/2025.12.04.692398v1?rss=1 Oakes, C. G. Beilinson, V. McFall-Ngai, M. J. Pachter, L. G. 2025-12-06 doi:10.64898/2025.12.04.692398 Cold Spring Harbor Laboratory Press 2025-12-06 <![CDATA[ Structures of bacterial and human phosphoglycosyltransferases bound to a common inhibitor inform selective therapeutics ]]> https://biorxiv.org/content/10.64898/2025.12.16.694696v1?rss=1 Kirsh, J. Mitachi, K. Ochoa, J. Soroush-Pejrimovsky, M.-T. Li, Y. E. Nguyen, V. N. Kurosu, M. Clemons, W. 2025-12-16 doi:10.64898/2025.12.16.694696 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Computational array reconstruction for spatial transcriptomics ]]> https://biorxiv.org/content/10.64898/2025.12.19.695576v1?rss=1 Oakes, C. G. Pachter, L. 2025-12-23 doi:10.64898/2025.12.19.695576 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Did you see the sound? A Bayesian Perspective on Crossmodal Perception in Low Vision ]]> https://biorxiv.org/content/10.64898/2025.12.24.696433v1?rss=1 Chan, A. Y. C. Stiles, N. R. B. Levitan, C. A. Tanguay, A. R. Shimojo, S. 2025-12-26 doi:10.64898/2025.12.24.696433 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Trainable computation in molecular networks ]]> https://biorxiv.org/content/10.64898/2025.12.28.696421v1?rss=1 Trifonova, K. Falk, M. J. Rouches, M. Vaikuntanathan, S. Elowitz, M. B. Murugan, A. 2025-12-30 doi:10.64898/2025.12.28.696421 Cold Spring Harbor Laboratory Press 2025-12-30 <![CDATA[ A view of bird's eyes -- Pigeons lock their eyes in place during flight ]]> https://biorxiv.org/content/10.64898/2026.01.07.698303v1?rss=1 Ros, I. G. Bhagavatula, P. S. Biewener, A. A. 2026-01-08 doi:10.64898/2026.01.07.698303 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Starvation enhances bacterial survival through drying and rewetting at the single cell level ]]> https://biorxiv.org/content/10.64898/2026.01.12.697931v1?rss=1 Kwiecinski, J. V. Squyres, G. R. Or, D. Newman, D. K. 2026-01-12 doi:10.64898/2026.01.12.697931 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ How the olfactory bulb maintains stable odor manifolds amid adaptation and representational drift ]]> https://biorxiv.org/content/10.64898/2026.01.23.701335v1?rss=1 Zheng, C. X. Yu, B. Navlakha, S. Koulakov, A. 2026-01-25 doi:10.64898/2026.01.23.701335 Cold Spring Harbor Laboratory Press 2026-01-25 <![CDATA[ Dynamic regulation of endogenous transcription factor hubs at single-molecule resolution ]]> https://biorxiv.org/content/10.64898/2026.01.25.701606v1?rss=1 Yoshida, S. R. Zhong, Y. Kumagai, A. Dunphy, W. G. Chong, S. 2026-01-27 doi:10.64898/2026.01.25.701606 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ BiomarkerKB: FAIR and Integrated Biomarker Knowledge Connecting Biomolecular and Clinical Data Types ]]> https://biorxiv.org/content/10.64898/2026.01.26.701395v1?rss=1 Masood, D. Kim, M. Vora, J. Kahsay, R. McNeeley, P. Kim, S. Kulkarni, S. V. Natale, D. A. Maurya, M. Ramachandran, S. Gupta, S. Bologa, C. G. DeNapoli, T. S. Metzger, V. T. Kumar, P. Ahmed, N. Evangelista, J. E. Kelly, S. C. Sepulveda, J. Ma'ayan, A. Silverstein, J. Taylor, D. M. Crichton, D. J. Mahabal, A. Yang, J. J. Lambert, C. G. Subramaniam, S. Tiemeyer, M. Ranzinger, R. Mazumder, R. 2026-01-27 doi:10.64898/2026.01.26.701395 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Death & Chemotaxis: Bacterial chemotaxis enables collective escape from phage predation ]]> https://biorxiv.org/content/10.64898/2026.01.28.702367v1?rss=1 Muir, V. G. Martinez-Calvo, A. Wingreen, N. S. Datta, S. S. 2026-01-28 doi:10.64898/2026.01.28.702367 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ Principles of in situ protein sequencing: expansion microscopy-adapted Edman degradation and amino acid recognition ]]> https://biorxiv.org/content/10.64898/2026.01.29.702630v1?rss=1 Mitchell, C. M. Tavana, S. Z. Peng, J. Wang, H. Shi, J. Zhang, C. Evgeniou, L. Domecillo, M. Wang, S. Estandian, D. M. Choueiri, A. G. Wong, E. Dohadwala, S. Polizzi, N. Kiessling, L. L. Boyden, E. S. 2026-01-30 doi:10.64898/2026.01.29.702630 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Science should be machine-readable ]]> https://biorxiv.org/content/10.64898/2026.01.30.702911v1?rss=1 Booeshaghi, A. S. Luebbert, L. Pachter, L. 2026-02-02 doi:10.64898/2026.01.30.702911 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Quantitative measurement of synthetic repression curves reveals design challenges for genetic circuit engineering under growth arrest ]]> https://biorxiv.org/content/10.64898/2026.02.01.703179v1?rss=1 100-fold reduction in unrepressed expression levels. Growth arrest caused gene expression noise to increase moderately and had only minimal impacts on the sensitivity and sharpness of the repression curves. Our work shows both that conventional genetic circuit design paradigms are currently insufficient to develop circuits that can function properly under growth arrest, but also that addressing the reduction in just a single performance parameter would be sufficient to resolve this problem. This work expands our understanding of bacterial gene regulation under growth arrest and lays the groundwork for new design paradigms that will be essential in ensuring the safe and reliable performance of synthetic biology systems in real-world environments. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/703179v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@104ecd2org.highwire.dtl.DTLVardef@57f992org.highwire.dtl.DTLVardef@1c215c2org.highwire.dtl.DTLVardef@122a8c5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Marken, J. P. Prator, M. L. Hay, B. A. Murray, R. M. 2026-02-02 doi:10.64898/2026.02.01.703179 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ A unified pipeline for discovering previously unknown enzyme activities ]]> https://biorxiv.org/content/10.64898/2026.02.02.703255v1?rss=1 Mora, A. Reisenbauer, J. C. Schmid, H. Miyazaki, I. Long, Y. Yang, J. OMeara, R. Arnold, F. H. 2026-02-02 doi:10.64898/2026.02.02.703255 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Stem cell control and cancer initiation by an autocrine, injury-activated Igf complex ]]> https://biorxiv.org/content/10.64898/2026.02.02.703150v1?rss=1 Zhang, Y. Ouadah, Y. Liu, Y. Kumar, M. Morck, M. Krasnow, M. A. 2026-02-04 doi:10.64898/2026.02.02.703150 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ Regenerative base editing enables deep lineage recording ]]> https://biorxiv.org/content/10.64898/2026.02.06.703857v1?rss=1 Chadly, D. M. Hadas, R. Klock, L. Yue, J. Horns, F. Askary, A. Granados, A. A. Bouckaert, R. Lois, C. Cai, L. Elowitz, M. B. 2026-02-07 doi:10.64898/2026.02.06.703857 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ Differential analysis of genomics count data with edge ]]> https://biorxiv.org/content/10.64898/2026.02.16.706223v1?rss=1 Pachter, L. 2026-02-18 doi:10.64898/2026.02.16.706223 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Structural evolution of the MTCH family of mitochondrial insertases ]]> https://biorxiv.org/content/10.64898/2026.02.17.705849v1?rss=1 Stevens, T. A. Luo, Z. Lee, C. Hazu, M. Galatis, E. G. Inglis, A. J. Guna, A. Voorhees, R. M. 2026-02-18 doi:10.64898/2026.02.17.705849 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Structural basis of metalloid transport by the arsenite efflux pump ArsB ]]> https://biorxiv.org/content/10.64898/2026.02.19.706881v1?rss=1 Mahajan, S. Demirer, K. Clemons, W. M. Rees, D. C. 2026-02-20 doi:10.64898/2026.02.19.706881 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Nucleotide-level chemical reaction network modeling enables quantitative prediction of reconstituted cell-free expression system ]]> https://biorxiv.org/content/10.64898/2026.02.22.707325v1?rss=1 Jurado, Z. Pandey, A. Murray, R. M. 2026-02-23 doi:10.64898/2026.02.22.707325 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ The orbitofrontal cortex constructs allocentric schemas by integrating dynamic mobile agents with static environmental anchors ]]> https://biorxiv.org/content/10.64898/2026.03.01.708836v1?rss=1 Zhu, Z. Zhang, B. Zhang, X. Naya, Y. 2026-03-03 doi:10.64898/2026.03.01.708836 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Single-Cell Genomics Decontamination with CellSweep ]]> https://biorxiv.org/content/10.64898/2026.03.04.709349v1?rss=1 Caskey, M. Rich, J. Weber, R. Mortazavi, A. Pachter, L. Hallgrimsdottir, I. B. 2026-03-06 doi:10.64898/2026.03.04.709349 Cold Spring Harbor Laboratory Press 2026-03-06 <![CDATA[ Multitasking boosts muscular endurance task performance due to elevated arousal level unattainable by the endurance task alone ]]> https://biorxiv.org/content/10.64898/2026.03.06.710139v1?rss=1 Nagisa, S. Oblak, E. Shimojo, S. Shibata, K. 2026-03-10 doi:10.64898/2026.03.06.710139 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ Statistical BURST imaging for high-fidelity biomolecular ultrasound ]]> https://biorxiv.org/content/10.64898/2026.03.13.711726v1?rss=1 Lee, S. Shivaei, S. Shapiro, M. G. 2026-03-17 doi:10.64898/2026.03.13.711726 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Sentinel plants enable quantitative monitoring of bioavailable nitrate in soils and microbial environments ]]> https://biorxiv.org/content/10.64898/2026.03.18.712767v1?rss=1 Li, E. Berruto, C. Oz, T. Grillo, E. Griffin, C. Wang, Y. Jones, J. Demirer, G. 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