bioRxiv Channel: Michigan State University https://biorxiv.org This feed contains articles for bioRxiv Channel "Michigan State University" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ PML and PML-like exonucleases restrict retrotransposons in jawed vertebrates ]]> https://biorxiv.org/content/10.1101/2022.07.29.501749v1?rss=1 Mathavarajah, S. Vergunst, K. L. Williams, S. K. He, R. Maliougina, M. Habib, E. B. Park, M. Salsman, J. Roy, S. Braasch, I. Roger, A. J. Langelaan, D. N. Dellaire, G. 2022-07-30 doi:10.1101/2022.07.29.501749 Cold Spring Harbor Laboratory Press 2022-07-30 <![CDATA[ The impact of primary colonizers on the community composition of river biofilm ]]> https://biorxiv.org/content/10.1101/2022.07.29.501847v1?rss=1 Angoshtari, R. Scribner, K. Marsh, T. L. 2022-07-30 doi:10.1101/2022.07.29.501847 Cold Spring Harbor Laboratory Press 2022-07-30 <![CDATA[ Yield Prediction Through Integration of Genetic, Environment, and Management Data Through Deep Learning ]]> https://biorxiv.org/content/10.1101/2022.07.29.502051v1?rss=1 Kick, D. Wallace, J. Schnable, J. C. Kolkman, J. M. Alaca, B. Beissinger, T. M. Ertl, D. Flint-Garcia, S. Gage, J. L. Hirsch, C. N. Knoll, J. E. de Leon, N. Lima, D. C. Moreta, D. Singh, M. Weldekidan, T. Washburn, J. D. 2022-07-30 doi:10.1101/2022.07.29.502051 Cold Spring Harbor Laboratory Press 2022-07-30 <![CDATA[ A genome wide dosage suppressor network reveals genetic robustness and a novel mechanism for Huntington&#146;s disease ]]> https://biorxiv.org/content/10.1101/000265v1?rss=1 Biranchi Patra Yoshiko Kon Gitanjali Yadav Anthony Sevold Jesse P Frumkin Ravishankar R Vallabhajosyula Arend Hintze Bjørn Østman Jory Schossau Ashish Bhan Bruz Marzolf Jenna K Tamashiro Amardeep Kaur Nitin S Baliga Elizabeth J Grayhack Christoph Adami David J Galas Alpan Raval Eric M Phizicky Animesh Ray 2013-11-12 doi:10.1101/000265 Cold Spring Harbor Laboratory Press 2013-11-12 <![CDATA[ Filling up the tree: considering the self-organization of avian roosting behavior ]]> https://biorxiv.org/content/10.1101/000349v1?rss=1 Bradly J Alicea 2013-11-13 doi:10.1101/000349 Cold Spring Harbor Laboratory Press 2013-11-13 <![CDATA[ The roles of standing genetic variation and evolutionary history in determining the evolvability of anti-predator strategies ]]> https://biorxiv.org/content/10.1101/002493v1?rss=1 Jordan Fish Daniel R O'Donnell Abhijna Parigi Ian Dworkin Aaron P Wagner 2014-02-07 doi:10.1101/002493 Cold Spring Harbor Laboratory Press 2014-02-07 <![CDATA[ Evolutionary rates for multivariate traits: the role of selection and genetic variation ]]> https://biorxiv.org/content/10.1101/002683v1?rss=1 William Pitchers Jason B. Wolf Tom Tregenza John Hunt Ian Dworkin 2014-02-14 doi:10.1101/002683 Cold Spring Harbor Laboratory Press 2014-02-14 <![CDATA[ Adaptation to a novel predator in Drosophila melanogaster: How well are we able to predict evolutionary responses? ]]> https://biorxiv.org/content/10.1101/005322v1?rss=1 Michael DeNieu William Pitchers Ian Dworkin 2014-05-19 doi:10.1101/005322 Cold Spring Harbor Laboratory Press 2014-05-19 <![CDATA[ How the tortoise beats the hare: Slow and steady adaptation in structured populations suggests a rugged fitness landscape in bacteria ]]> https://biorxiv.org/content/10.1101/005793v1?rss=1 Joshua R. Nahum Peter Godfrey-Smith Brittany N. Harding Joseph H. Marcus Jared Carlson-Stevermer Benjamin Kerr 2014-06-03 doi:10.1101/005793 Cold Spring Harbor Laboratory Press 2014-06-03 <![CDATA[ How predator hunting-modes affect prey behaviour: Capture deterrence in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/010330v1?rss=1 Abhijna Parigi Cody Porter Megan Cermak William R. Pitchers Ian Dworkin 2014-10-14 doi:10.1101/010330 Cold Spring Harbor Laboratory Press 2014-10-14 <![CDATA[ Adaptation to larval crowding in Drosophila ananassae and Drosophila nasuta nasuta: increased larval competitive ability without increased larval feeding rate ]]> https://biorxiv.org/content/10.1101/011684v1?rss=1 Archana Nagarajan Sharmila Bharathi Natarajan Mohan Jayaram Ananda Thammanna Sudarshan Chari Joy Bose Shreyas V. Jois Amitabh Joshi 2014-11-20 doi:10.1101/011684 Cold Spring Harbor Laboratory Press 2014-11-20 <![CDATA[ Synthesis of phylogeny and taxonomy into a comprehensive tree of life ]]> https://biorxiv.org/content/10.1101/012260v1?rss=1 Cody Hinchliff Stephen A Smith James F Allman J Gordon Burleigh Ruchi Chaudhary Lyndon M Cognill Keith A Crandall Jiabin Deng Bryan T Drew Romina Gazis Karl Gude David S Hibbett Laura A Katz H Dail Laughinghouse IV Emily Jane McTavish Peter E. Midford Christopher L Owen Richard Ree Jonathan A Rees Doug E Soltis Tiffani Williams Karen Ann Cranston 2014-12-05 doi:10.1101/012260 Cold Spring Harbor Laboratory Press 2014-12-05 <![CDATA[ Modeling and quantifying frequency-dependent fitness in microbial populations with cross-feeding interactions ]]> https://biorxiv.org/content/10.1101/012807v1?rss=1 Noah Ribeck Richard E. Lenski 2014-12-16 doi:10.1101/012807 Cold Spring Harbor Laboratory Press 2014-12-16 <![CDATA[ A Comparison of Methods to Measure Fitness in Escherichia coli ]]> https://biorxiv.org/content/10.1101/016121v1?rss=1 Michael J Wiser Richard E Lenski 2015-03-06 doi:10.1101/016121 Cold Spring Harbor Laboratory Press 2015-03-06 <![CDATA[ Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli ]]> https://biorxiv.org/content/10.1101/017020v1?rss=1 Rohan Maddamsetti Richard E. Lenski Jeffrey E. Barrick 2015-03-25 doi:10.1101/017020 Cold Spring Harbor Laboratory Press 2015-03-25 <![CDATA[ Phenotypic Covariation And Morphological Diversification In The Ruminant Skull ]]> https://biorxiv.org/content/10.1101/017533v1?rss=1 Annat Haber 2015-04-04 doi:10.1101/017533 Cold Spring Harbor Laboratory Press 2015-04-04 <![CDATA[ Selection for Intermediate Genotypes Enables a Key Innovation in Phage Lambda ]]> https://biorxiv.org/content/10.1101/018606v1?rss=1 Alita Burmeister Richard Lenski Justin Meyer 2015-04-27 doi:10.1101/018606 Cold Spring Harbor Laboratory Press 2015-04-27 <![CDATA[ Evolution and coexistence in response to a key innovation in a long-term evolution experiment with Escherichia coli ]]> https://biorxiv.org/content/10.1101/020958v1?rss=1 Caroline B. Turner Zachary D. Blount Daniel H. Mitchell Richard E. Lenski 2015-06-17 doi:10.1101/020958 Cold Spring Harbor Laboratory Press 2015-06-17 <![CDATA[ Evolution of organismal stoichiometry in a 50,000-generation experiment with Escherichia coli ]]> https://biorxiv.org/content/10.1101/021360v1?rss=1 Caroline B. Turner Brian D. Wade Justin R. Meyer Richard E. Lenski 2015-06-29 doi:10.1101/021360 Cold Spring Harbor Laboratory Press 2015-06-29 <![CDATA[ SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis ]]> https://biorxiv.org/content/10.1101/021915v1?rss=1 Benjamin K Johnson Matthew B Scholz Tracy K Teal Robert B Abramovitch 2015-07-05 doi:10.1101/021915 Cold Spring Harbor Laboratory Press 2015-07-05 <![CDATA[ Replaying Evolution to Test the Cause of Extinction of One Ecotype in an Experimentally Evolved Population ]]> https://biorxiv.org/content/10.1101/022798v1?rss=1 Caroline B. Turner Zachary D. Blount Richard E. Lenski 2015-07-19 doi:10.1101/022798 Cold Spring Harbor Laboratory Press 2015-07-19 <![CDATA[ Haplotype-phased synthetic long reads from short-read sequencing ]]> https://biorxiv.org/content/10.1101/022897v1?rss=1 James A Stapleton Jeongwoon Kim John P Hamilton Ming Wu Luiz C Irber Rohan Maddamsetti Bryan Briney Linsey Newton Dennis R Burton C Titus Brown Christina Chan C Robin Buell Timothy A Whitehead 2015-07-21 doi:10.1101/022897 Cold Spring Harbor Laboratory Press 2015-07-21 <![CDATA[ Dis-integrating the fly: A mutational perspective on phenotypic integration and covariation ]]> https://biorxiv.org/content/10.1101/023333v1?rss=1 Annat Haber Ian Dworkin 2015-07-27 doi:10.1101/023333 Cold Spring Harbor Laboratory Press 2015-07-27 <![CDATA[ Population genomic scans reveal novel genes underlie convergent flowering time evolution in the introduced range of Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/023788v1?rss=1 Billie Gould John R Stinchcombe 2015-08-03 doi:10.1101/023788 Cold Spring Harbor Laboratory Press 2015-08-03 <![CDATA[ Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli ]]> https://biorxiv.org/content/10.1101/027391v1?rss=1 Richard E Lenski Michael J Wiser Noah Ribeck Zachary D Blount Joshua R Nahum James Jeffrey Morris Luis Zaman Caroline B Turner Brian D Wade Rohan Maddamsetti Alita R Burmeister Elizabeth J Baird Jay Bundy Nkrumah A Grant Kyle J Card Maia Rowles Kiyana Weatherspoon Spiridon E Papoulis Rachel Sullivan Colleen Clark Joseph S Mulka Neerja Hajela 2015-09-22 doi:10.1101/027391 Cold Spring Harbor Laboratory Press 2015-09-22 <![CDATA[ Genome-wide and single-base resolution DNA methylomes of the Sea Lamprey (Petromyzon marinus) Reveal Gradual Transition of the Genomic Methylation Pattern in Early Vertebrates ]]> https://biorxiv.org/content/10.1101/033233v1?rss=1 Zhao Zhang Gangbiao Liu Yangyun Zhou James P. B. Lloyd David W. McCauley Weiming Li Xun Gu Zhixi Su 2015-11-30 doi:10.1101/033233 Cold Spring Harbor Laboratory Press 2015-11-30 <![CDATA[ Tempo and mode of genome evolution in a 50,000-generation experiment ]]> https://biorxiv.org/content/10.1101/036806v1?rss=1 Olivier Tenaillon Jeffrey E. Barrick Noah Ribeck Daniel E. Deatherage Jeffrey L. Blanchard Aurko Dasgupta Gabriel C. Wu Sebastien Wielgoss Stephane Cruveiller Claudine Medigue Dominique Schneider Richard E. Lenski 2016-01-15 doi:10.1101/036806 Cold Spring Harbor Laboratory Press 2016-01-15 <![CDATA[ The sex-limited effects of mutations in the EGFR and TGF- β signaling pathways on shape and size sexual dimorphism and allometry in the Drosophila wing ]]> https://biorxiv.org/content/10.1101/037630v1?rss=1 Nick Testa Ian Dworkin 2016-01-21 doi:10.1101/037630 Cold Spring Harbor Laboratory Press 2016-01-21 <![CDATA[ Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli ]]> https://biorxiv.org/content/10.1101/042069v1?rss=1 Rohan Maddamsetti Philip J Hatcher Barry L. Williams Richard E. Lenski 2016-03-01 doi:10.1101/042069 Cold Spring Harbor Laboratory Press 2016-03-01 <![CDATA[ Environmental gene regulatory influence networks in rice (Oryza sativa): response to water deficit, high temperature and agricultural environments ]]> https://biorxiv.org/content/10.1101/042317v1?rss=1 Olivia Wilkins Christoph Hafemiester Anne Plessis Meisha-Marika Holloway-Phillips Gina M Pham Addrienne B. Nicotra Glenn B. Gregorio S. V. Krishna Jagadish Endang M. Septiningsih Richard Bonneau Michael Purugganan 2016-03-03 doi:10.1101/042317 Cold Spring Harbor Laboratory Press 2016-03-03 <![CDATA[ The Effects of Evolution and Spatial Structure on Diversity in Biological Reserves ]]> https://biorxiv.org/content/10.1101/043083v1?rss=1 Emily Louise Dolson Michael J Wiser Charles A Ofria 2016-03-10 doi:10.1101/043083 Cold Spring Harbor Laboratory Press 2016-03-10 <![CDATA[ The Higher Plant Plastid Complex I (NDH) is a Reversible Proton Pump that increases ATP production by Cyclic Electron Flow Around Photosystem I ]]> https://biorxiv.org/content/10.1101/049759v1?rss=1 Deserah D Strand Nicholas Fisher David M. Kramer 2016-04-22 doi:10.1101/049759 Cold Spring Harbor Laboratory Press 2016-04-22 <![CDATA[ Different Evolutionary Paths to Complexity for Small and Large Populations of Digital Organisms ]]> https://biorxiv.org/content/10.1101/049767v1?rss=1 Thomas LaBar Christoph Adami 2016-04-22 doi:10.1101/049767 Cold Spring Harbor Laboratory Press 2016-04-22 <![CDATA[ RefSoil: A reference database of soil microbial genomes ]]> https://biorxiv.org/content/10.1101/053397v1?rss=1 Jinlyung Choi Fan Yang Ramunas Stepanauskas Erick Cardenas Aaron Garoutte Ryan Williams Jared Flater James M Tiedje Kirsten S. Hofmockel Brian Gelder Adina Howe 2016-05-14 doi:10.1101/053397 Cold Spring Harbor Laboratory Press 2016-05-14 <![CDATA[ Diagnostic assessments of student thinking about stochastic processes. ]]> https://biorxiv.org/content/10.1101/053991v1?rss=1 Michael W. Klymkowsky Katja Koehler Melanie Cooper 2016-05-20 doi:10.1101/053991 Cold Spring Harbor Laboratory Press 2016-05-20 <![CDATA[ Breaking bud: probing the scalability limits of phylogenetic network inference methods ]]> https://biorxiv.org/content/10.1101/056572v1?rss=1 Hussein A Hejase Kevin J Liu 2016-06-01 doi:10.1101/056572 Cold Spring Harbor Laboratory Press 2016-06-01 <![CDATA[ The PAS domain-containing protein HeuR regulates heme uptake in Campylobacter jejuni ]]> https://biorxiv.org/content/10.1101/057042v1?rss=1 Jeremiah Johnson Jennifer Gaddy Victor DiRita 2016-06-03 doi:10.1101/057042 Cold Spring Harbor Laboratory Press 2016-06-03 <![CDATA[ Tissue Resolved, Gene Structure Refined Equine Transcriptome ]]> https://biorxiv.org/content/10.1101/061952v1?rss=1 Tamer A. Mansour Erica Y Scott Carrie J Finno Rebecca R Bellone Michael J. Mienaltowski M Cecilia Penedo Pablo J Ross Stephanie J. Valberg James D Murray C. Titus Brown 2016-07-03 doi:10.1101/061952 Cold Spring Harbor Laboratory Press 2016-07-03 <![CDATA[ Competition between continuously evolving lineages in asexual populations ]]> https://biorxiv.org/content/10.1101/062976v1?rss=1 Noah Ribeck Joseph S. Mulka Luis Zaman Brian D. Connelly Richard E. Lenski 2016-07-10 doi:10.1101/062976 Cold Spring Harbor Laboratory Press 2016-07-10 <![CDATA[ Understanding How Microbiomes Influence the Systems they Inhabit: Insight from Ecosystem Ecology ]]> https://biorxiv.org/content/10.1101/065128v1?rss=1 Ed Hall Emily Bernhardt Raven Bier Mark Bradford Claudia Boot Jim Cotner Paul del Giorgio Sarah Evans Emily Graham Stuart Jones Jay Lennon Ken Locey Diana Nemergut Brooke Osborne Jenny Rocca Josh Schimel Matt Wallenstein 2016-07-21 doi:10.1101/065128 Cold Spring Harbor Laboratory Press 2016-07-21 <![CDATA[ Direct correlation between motile behavior and protein abundance in single cells ]]> https://biorxiv.org/content/10.1101/067918v1?rss=1 Yann S Dufour Sébastien Gillet Nicholas W Frankel Douglas B Weibel Thierry Emonet 2016-08-04 doi:10.1101/067918 Cold Spring Harbor Laboratory Press 2016-08-04 <![CDATA[ Synthetic Photosynthetic Consortia Define Interactions Leading to Robustness and Photoproduction ]]> https://biorxiv.org/content/10.1101/068130v1?rss=1 Stephanie G. Hays Leo L.W. Yan Pamela A. Silver Daniel C. Ducat 2016-08-05 doi:10.1101/068130 Cold Spring Harbor Laboratory Press 2016-08-05 <![CDATA[ Evolution of Drift Robustness in Small Populations of Digital Organisms ]]> https://biorxiv.org/content/10.1101/071894v1?rss=1 Thomas LaBar Christoph Adami 2016-08-27 doi:10.1101/071894 Cold Spring Harbor Laboratory Press 2016-08-27 <![CDATA[ MathIOmica: An Integrative Platform for Dynamic Omics ]]> https://biorxiv.org/content/10.1101/074260v1?rss=1 George Mias Tahir Yusufaly Raeuf Roushangar Lavida R.K. Brooks Vikas Vikram Singh Christina Christou 2016-09-10 doi:10.1101/074260 Cold Spring Harbor Laboratory Press 2016-09-10 <![CDATA[ Thermally moderated firefly activity is delayed by precipitation extremes ]]> https://biorxiv.org/content/10.1101/074633v1?rss=1 Elizabeth Davidson-Lowe Bahodir Eshchanov Sara Hermann Andrew Myers Logan Rowe Saisi Xue Christie A Bahlai 2016-09-11 doi:10.1101/074633 Cold Spring Harbor Laboratory Press 2016-09-11 <![CDATA[ Evapotranspiration response to land cover and climate change in a Midwest U.S. watershed ]]> https://biorxiv.org/content/10.1101/075598v1?rss=1 Stephen K Hamilton Mir Zaman Hussain Christopher Lowrie Bruno Basso G Philip Robertson 2016-09-16 doi:10.1101/075598 Cold Spring Harbor Laboratory Press 2016-09-16 <![CDATA[ Inhibition of microbial biofuel production in drought stressed switchgrass hydrolysate ]]> https://biorxiv.org/content/10.1101/083758v1?rss=1 Ong, R. G. Higbee, A. Bottoms, S. Dickinson, Q. Xie, D. Smith, S. A. Serate, J. Pohlmann, E. Jones, A. D. Coon, J. J. Sato, T. K. Sanford, G. R. Eilert, D. Oates, L. G. Piotrowski, J. S. Bates, D. M. Cavalier, D. Zhang, Y. 2016-10-26 doi:10.1101/083758 Cold Spring Harbor Laboratory Press 2016-10-26 <![CDATA[ Interpreting deep mutational scanning data resulting from selections on solid media ]]> https://biorxiv.org/content/10.1101/087072v1?rss=1 Klesmith, J. R. Thorwall, S. Whitehead, T. A. 2016-11-10 doi:10.1101/087072 Cold Spring Harbor Laboratory Press 2016-11-10 <![CDATA[ Determining causal genes from GWAS signals using topologically associating domains ]]> https://biorxiv.org/content/10.1101/087718v1?rss=1 Way, G. P. Youngstrom, D. W. Hankenson, K. D. Greene, C. S. Grant, S. F. A. 2016-11-15 doi:10.1101/087718 Cold Spring Harbor Laboratory Press 2016-11-15 <![CDATA[ Genome-Wide Association Study Reveals First Locus for Anorexia Nervosa and Metabolic Correlations ]]> https://biorxiv.org/content/10.1101/088815v1?rss=1 Duncan, L. Yilmaz, Z. Walters, R. Goldstein, J. Antilla, V. Bulik-Sullivan, B. Ripke, S. Adan, R. Alfredsson, L. Ando, T. Andreassen, O. Aschauer, H. Baker, J. Barrett, J. Bencko, V. Bergen, A. Berrettini, W. Birgegard, A. Boni, C. Boraska Perica, V. Brandt, H. Bughardt, R. Carlberg, L. Cassina, M. Cesta, C. Cichon, S. Clementi, M. Cohen-Woods, S. Coleman, J. Cone, R. Courtet, P. Crawford, S. Crow, S. Crowley, J. Danner, U. Davis, O. de Zaan, M. Dedoussis, G. Degortes, D. DeSocio, J. Dick, D. Dikeos, D. Dina, C. Ding, B. Dmitrzak-Weglarz, M. Docampo 2016-11-25 doi:10.1101/088815 Cold Spring Harbor Laboratory Press 2016-11-25 <![CDATA[ Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140 year old naturally established neo-allopolyploid monkeyflower. ]]> https://biorxiv.org/content/10.1101/094797v1?rss=1 Edgar, P. P. Smith, R. D. McKain, M. R. Cooley, A. M. Vallejo-Marin, M. Yuan, Y. Bewick, A. J. Ji, L. Platts, A. E. Bowman, M. J. Childs, K. L. Schmitz, R. J. Smith, G. D. Pires, J. C. Puzey, J. R. 2016-12-16 doi:10.1101/094797 Cold Spring Harbor Laboratory Press 2016-12-16 <![CDATA[ Acidic pH-dependent depletion of Mycobacterium tuberculosis thiol pools potentiates antibiotics and oxidizing agents ]]> https://biorxiv.org/content/10.1101/095448v1?rss=1 Coulson, G. B. Johnson, B. K. Colvin, C. J. Fillinger, R. J. Zheng, H. Haiderer, E. R. Hammer, N. D. Abramovitch, R. B. 2016-12-21 doi:10.1101/095448 Cold Spring Harbor Laboratory Press 2016-12-21 <![CDATA[ Evidence for Transcriptome-wide RNA Editing Among Sus scrofa PRE-1 SINE Elements ]]> https://biorxiv.org/content/10.1101/096321v1?rss=1 Funkhouser, S. A. Steibel, J. P. Bates, R. O. Raney, N. E. Schenk, D. Ernst, C. W. 2017-01-05 doi:10.1101/096321 Cold Spring Harbor Laboratory Press 2017-01-05 <![CDATA[ Brain connectivity dynamics during social interaction reflect social network structure ]]> https://biorxiv.org/content/10.1101/096420v1?rss=1 Schmaelzle, R. Brook O'Donnell, M. Garcia, J. O. Cascio, C. N. C. Bayer, J. Vettel, J. Falk, E. B. 2016-12-23 doi:10.1101/096420 Cold Spring Harbor Laboratory Press 2016-12-23 <![CDATA[ Synthetic OCP Heterodimers are Photoactive and Recapitulate the Fusion of Two Primitive Carotenoproteins in the Evolution of Cyanobacterial Photoprotection ]]> https://biorxiv.org/content/10.1101/102160v1?rss=1 Lechno-Yossef, S. Melnicki, M. R. Bao, H. Montgomery, B. L. Kerfeld, C. A. 2017-01-21 doi:10.1101/102160 Cold Spring Harbor Laboratory Press 2017-01-21 <![CDATA[ The power of a multivariate approach to genome-wide association studies: an example with Drosophila melanogaster wing shape ]]> https://biorxiv.org/content/10.1101/108308v1?rss=1 Pitchers, W. R. Nye, J. Marquez, E. J. Kowalski, A. Dworkin, I. Houle, D. 2017-02-14 doi:10.1101/108308 Cold Spring Harbor Laboratory Press 2017-02-14 <![CDATA[ High variability impairs motor learning regardless of whether it affects task performance ]]> https://biorxiv.org/content/10.1101/111823v1?rss=1 Cardis, M. Casadio, M. Ranganathan, R. 2017-03-04 doi:10.1101/111823 Cold Spring Harbor Laboratory Press 2017-03-04 <![CDATA[ STPGA: Selection of training populations with a genetic algorithm ]]> https://biorxiv.org/content/10.1101/111989v1?rss=1 Akdemir, D. 2017-02-27 doi:10.1101/111989 Cold Spring Harbor Laboratory Press 2017-02-27 <![CDATA[ A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa ]]> https://biorxiv.org/content/10.1101/115345v1?rss=1 Bowman, M. J. Pulman, J. A. Liu, T. L. Childs, K. L. 2017-03-09 doi:10.1101/115345 Cold Spring Harbor Laboratory Press 2017-03-09 <![CDATA[ Asymmetric evolution of the transcription profiles and cis-regulatory sites contributes to the retention of transcription factor duplicates ]]> https://biorxiv.org/content/10.1101/115857v1?rss=1 Panchy, N. L. Azodi, C. B. Winship, E. F. O'Malley, R. C. Shiu, S.-H. 2017-03-10 doi:10.1101/115857 Cold Spring Harbor Laboratory Press 2017-03-10 <![CDATA[ Accuracies Of Univariate And Multivariate Genomic Prediction Models In African Cassava. ]]> https://biorxiv.org/content/10.1101/116301v1?rss=1 Okeke, U. G. Akdemir, D. Rabbi, I. Kulakow, P. Jannink, J.-L. 2017-03-15 doi:10.1101/116301 Cold Spring Harbor Laboratory Press 2017-03-15 <![CDATA[ PHATE: A Dimensionality Reduction Method for Visualizing Trajectory Structures in High-Dimensional Biological Data ]]> https://biorxiv.org/content/10.1101/120378v1?rss=1 Moon, K. R. van Dijk, D. Wang, Z. Chen, W. Hirn, M. J. Coifman, R. R. Ivanova, N. B. Wolf, G. Krishnaswamy, S. 2017-03-24 doi:10.1101/120378 Cold Spring Harbor Laboratory Press 2017-03-24 <![CDATA[ Genome Wide Association Analyses Based On Broadly Different Specifications For Prior Distributions, Genomic Windows, And Estimation Methods ]]> https://biorxiv.org/content/10.1101/120808v1?rss=1 Chen, C. Steibel, J. P. Tempelman, R. J. 2017-03-26 doi:10.1101/120808 Cold Spring Harbor Laboratory Press 2017-03-26 <![CDATA[ Regulatory Divergence In Wound-Responsive Gene Expression In Domesticated And Wild Tomato ]]> https://biorxiv.org/content/10.1101/123992v1?rss=1 Liu, M.-J. Sugimoto, K. Uygun, S. Panchy, N. Campbell, M. S. Yandell, M. Howe, G. A. Shiu, S.-H. 2017-04-04 doi:10.1101/123992 Cold Spring Harbor Laboratory Press 2017-04-04 <![CDATA[ The role of Cdx2 as a lineage specific transcriptional repressor for pluripotent network during trophectoderm and inner cell mass specification ]]> https://biorxiv.org/content/10.1101/124438v1?rss=1 Huang, D. Han, X. Yuan, P. Ralston, A. Sun, L. Huss, M. Mistri, T. Pinello, L. Ng, H. H. Yuan, G. Ji, J. Rossant, J. Robson, P. Guo, G. 2017-04-05 doi:10.1101/124438 Cold Spring Harbor Laboratory Press 2017-04-05 <![CDATA[ Bacterial community composition and dynamics spanning five years in freshwater bog lakes ]]> https://biorxiv.org/content/10.1101/127035v1?rss=1 Linz, A. Crary, B. C. Shade, A. Owens, S. Gilbert, J. Knight, R. McMahon, K. 2017-04-12 doi:10.1101/127035 Cold Spring Harbor Laboratory Press 2017-04-12 <![CDATA[ Defining functional intergenic transcribed regions based on heterogeneous features of phenotype genes and pseudogenes ]]> https://biorxiv.org/content/10.1101/127282v1?rss=1 Lloyd, J. P. Tsai, Z. T. Sowers, R. P. Panchy, N. L. Shiu, S.-H. 2017-04-13 doi:10.1101/127282 Cold Spring Harbor Laboratory Press 2017-04-13 <![CDATA[ Enhancing Multiplex Genome Editing by Natural Transformation (MuGENT) via inactivation of ssDNA exonucleases ]]> https://biorxiv.org/content/10.1101/127308v1?rss=1 2000 bp) surrounding each genome edit, which necessitates laborious in vitro DNA splicing. In Vibrio cholerae, we uncover that this requirement is due to cytoplasmic ssDNA exonucleases, which inhibit natural transformation. In ssDNA exonuclease mutants, one arm of homology can be reduced to as little as 40 bp while still promoting integration of genome edits at rates of ~50% without selection in cis. Consequently, editing constructs are generated in a single PCR reaction where one homology arm is oligonucleotide encoded. To further enhance editing efficiencies, we also developed a strain for transient inactivation of the mismatch repair system. As a proof-of-concept, we used these advances to rapidly mutate 10 high-affinity binding sites for the nucleoid occlusion protein SlmA and generated a duodecuple mutant of 12 diguanylate cyclases in V. cholerae. Whole genome sequencing revealed little to no off-target mutations in these strains. Finally, we show that ssDNA exonucleases inhibit natural transformation in Acinetobacter baylyi. Thus, rational removal of ssDNA exonucleases may be broadly applicable for enhancing the efficacy and ease of MuGENT in diverse naturally transformable species. ]]> Dalia, T. N. Yoon, S. H. Galli, E. Barre, F.-X. Waters, C. M. Dalia, A. B. 2017-04-13 doi:10.1101/127308 Cold Spring Harbor Laboratory Press 2017-04-13 <![CDATA[ Relic DNA contributes minimally to estimates of microbial diversity ]]> https://biorxiv.org/content/10.1101/131284v1?rss=1 Lennon, J. T. Placella, S. A. Muscarella, M. E. 2017-04-26 doi:10.1101/131284 Cold Spring Harbor Laboratory Press 2017-04-26 <![CDATA[ FastNet: Fast and accurate inference of phylogenetic networks using large-scale genomic sequence data ]]> https://biorxiv.org/content/10.1101/132795v1?rss=1 Hejase, H. VandePol, N. Bonito, G. A. Liu, K. J. 2017-05-01 doi:10.1101/132795 Cold Spring Harbor Laboratory Press 2017-05-01 <![CDATA[ Coal-Miner: A Coalescent-Based Method For GWA Studies Of Quantitative Traits With Complex Evolutionary Origins ]]> https://biorxiv.org/content/10.1101/132951v1?rss=1 Hejase, H. A. Vande Pol, N. Bonito, G. M. Edger, P. P. Liu, K. J. 2017-05-02 doi:10.1101/132951 Cold Spring Harbor Laboratory Press 2017-05-02 <![CDATA[ Multi-omic analysis of a hyper-diverse plant metabolic pathway reveals evolutionary routes to biological innovation ]]> https://biorxiv.org/content/10.1101/136937v1?rss=1 Moghe, G. D. Leong, B. J. Hurney, S. Jones, A. D. Last, R. L. 2017-05-11 doi:10.1101/136937 Cold Spring Harbor Laboratory Press 2017-05-11 <![CDATA[ LTR_retriever: A Highly Accurate And Sensitive Program For Identification Of LTR Retrotransposons ]]> https://biorxiv.org/content/10.1101/137141v1?rss=1 Ou, S. Jiang, N. 2017-05-12 doi:10.1101/137141 Cold Spring Harbor Laboratory Press 2017-05-12 <![CDATA[ The Core Transcriptome Of Mammalian Placentas And The Divergence Of Expression With Placental Shape ]]> https://biorxiv.org/content/10.1101/137554v1?rss=1 Armstrong, D. L. McGowen, M. R. Weckle, A. Pantham, P. Caravas, J. Agnew, D. Benirschke, K. Savage-Rumbaugh, S. Nevo, E. Kim, C. J. Wagner, G. P. Romero, R. Wildman, D. E. 2017-05-12 doi:10.1101/137554 Cold Spring Harbor Laboratory Press 2017-05-12 <![CDATA[ Manuscript 101: A Data-Driven Writing Exercise For Beginning Scientists ]]> https://biorxiv.org/content/10.1101/139204v1?rss=1 Halbisen, M. A. Ralston, A. 2017-05-18 doi:10.1101/139204 Cold Spring Harbor Laboratory Press 2017-05-18 <![CDATA[ How Well Do You Know Your Mutation? Complex Effects Of Genetic Background On Expressivity, Complementation, And Ordering Of Allelic Effects ]]> https://biorxiv.org/content/10.1101/139733v1?rss=1 Chandler, C. H. Chari, S. Kowalski, A. Choi, L. Tack, D. DeNieu, M. Pitchers, W. R. Sonnenschein, A. Marvin, L. Hummel, K. Marier, C. Victory, A. Porter, C. Mammel, A. Holms, J. Sivaratnam, G. Dworkin, I. 2017-05-18 doi:10.1101/139733 Cold Spring Harbor Laboratory Press 2017-05-18 <![CDATA[ The Gene Regulatory Landscape of Local Adaptation ]]> https://biorxiv.org/content/10.1101/145805v1?rss=1 Gould, B. A. Chen, Y. Lowry, D. B. 2017-06-03 doi:10.1101/145805 Cold Spring Harbor Laboratory Press 2017-06-03 <![CDATA[ Reciprocal control of motility and biofilm formation by the PdhS2 two-component sensor kinase of Agrobacterium tumefaciens ]]> https://biorxiv.org/content/10.1101/148429v1?rss=1 Heindl, J. E. Crosby, D. Brar, S. Merenich, D. Buechlein, A. M. Bruger, E. L. Waters, C. M. Fuqua, C. 2017-06-09 doi:10.1101/148429 Cold Spring Harbor Laboratory Press 2017-06-09 <![CDATA[ Spatial resource heterogeneity increases diversity and evolutionary potential ]]> https://biorxiv.org/content/10.1101/148973v1?rss=1 Dolson, E. Perez, S. Olson, R. Ofria, C. 2017-06-12 doi:10.1101/148973 Cold Spring Harbor Laboratory Press 2017-06-12 <![CDATA[ Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient ]]> https://biorxiv.org/content/10.1101/149179v1?rss=1 Ryan, S. Fontaine, M. C. Scriber, J. M. Pfrender, M. E. O'Neil, S. T. Hellmann, J. J. 2017-06-12 doi:10.1101/149179 Cold Spring Harbor Laboratory Press 2017-06-12 <![CDATA[ Spatial resource heterogeneity creates local hotspots of evolutionary potential ]]> https://biorxiv.org/content/10.1101/149302v1?rss=1 Dolson, E. Ofria, C. 2017-06-15 doi:10.1101/149302 Cold Spring Harbor Laboratory Press 2017-06-15 <![CDATA[ Evolution of gene expression after whole-genome duplication: new insights from the spotted gar genome ]]> https://biorxiv.org/content/10.1101/151944v1?rss=1 Pasquier, J. Braasch, I. Batzel, P. Cabau, C. Montfort, J. Nguyen, T. Jouanno, E. Berthelot, C. Klopp, C. Journot, L. Postlethwait, J. Guiguen, Y. Bobe, J. 2017-06-19 doi:10.1101/151944 Cold Spring Harbor Laboratory Press 2017-06-19 <![CDATA[ Widespread Negative Frequency-Dependent Selection Maintains Diversity in the Legume-Rhizobia Symbiosis: Balancing nodulation may explain the paradox of rhizobium diversity ]]> https://biorxiv.org/content/10.1101/153866v1?rss=1 Siler, E. Friesen, M. L. 2017-06-27 doi:10.1101/153866 Cold Spring Harbor Laboratory Press 2017-06-27 <![CDATA[ Microevolutionary processes underlying macroevolutionary patterns of electric signal diversity in mormyrid fish ]]> https://biorxiv.org/content/10.1101/154047v1?rss=1 Gallant, J. R. Sperling, J. Cheng, C. Arnegard, M. E. Carlson, B. Hopkins, C. 2017-06-22 doi:10.1101/154047 Cold Spring Harbor Laboratory Press 2017-06-22 <![CDATA[ Mapping Loci that Control Tuber and Foliar Symptoms Caused by PVY in Autotetraploid Potato (Solanum tuberosum L.) ]]> https://biorxiv.org/content/10.1101/156539v1?rss=1 da Silva, W. L. Ingram, J. T. Hackett, C. A. Coombs, J. J. Douches, D. Bryan, G. De Jong, W. Gray, S. 2017-06-27 doi:10.1101/156539 Cold Spring Harbor Laboratory Press 2017-06-27 <![CDATA[ Reliability of fMRI time series:Similarity of neural processing during movie viewing ]]> https://biorxiv.org/content/10.1101/158188v1?rss=1 Schmaelzle, R. Imhof, M. A. Grall, C. Flaisch, T. Schupp, H. T. 2017-07-03 doi:10.1101/158188 Cold Spring Harbor Laboratory Press 2017-07-03 <![CDATA[ Comparative genomic analyses highlight the contribution of pseudogenized protein-coding genes to human lincRNAs ]]> https://biorxiv.org/content/10.1101/163626v1?rss=1 Liu, W.-H. Tsai, Z. T.-Y. Tsai, H.-K. 2017-07-17 doi:10.1101/163626 Cold Spring Harbor Laboratory Press 2017-07-17 <![CDATA[ RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response ]]> https://biorxiv.org/content/10.1101/166694v1?rss=1 72% of the genes in the genome). Each module contains a group of genes tightly coexpressed across a large number of environmental conditions and, thus, is likely to be functionally coherent. When a user provides a new differential expression profile, RECoN identifies modules substantially perturbed in their experiment and further suggests deregulated functional and regulatory mechanisms based on the enrichment of current annotations within the predefined modules. We demonstrate the utility of this resource by analyzing new drought transcriptomes of rice in three developmental stages, which revealed large-scale insights into the cellular processes and regulatory mechanisms involved in common and stage-specific drought responses. RECoN enables biologists to functionally explore new data from all abiotic stresses on a genome-scale and to uncover gene candidates, including those that are currently functionally uncharacterized, for engineering stress tolerance. ]]> Krishnan, A. Gupta, C. Ambavaram, M. M. R. Pereira, A. 2017-07-21 doi:10.1101/166694 Cold Spring Harbor Laboratory Press 2017-07-21 <![CDATA[ Temperature selection drives evolution of function-valued traits in a marine diatom ]]> https://biorxiv.org/content/10.1101/167817v1?rss=1 O'Donnell, D. R. Hamman, C. R. Johnson, E. C. Klausmeier, C. A. Litchman, E. 2017-07-24 doi:10.1101/167817 Cold Spring Harbor Laboratory Press 2017-07-24 <![CDATA[ Cell cycle time series gene expression data encoded as cyclic attractors in Hopfield systems ]]> https://biorxiv.org/content/10.1101/170027v1?rss=1 Szedlak, A. Sims, S. Smith, N. Paternostro, G. Piermarocchi, C. 2017-07-31 doi:10.1101/170027 Cold Spring Harbor Laboratory Press 2017-07-31 <![CDATA[ Fog and live fuel moisture in coastal California shrublands ]]> https://biorxiv.org/content/10.1101/171850v1?rss=1 Emery, N. D'Antonio, C. M. Still, C. J. 2017-08-03 doi:10.1101/171850 Cold Spring Harbor Laboratory Press 2017-08-03 <![CDATA[ Genome size and the extinction of small populations ]]> https://biorxiv.org/content/10.1101/173690v1?rss=1 LaBar, T. Adami, C. 2017-08-08 doi:10.1101/173690 Cold Spring Harbor Laboratory Press 2017-08-08 <![CDATA[ Generation and validation of a floxed FosB mouse line ]]> https://biorxiv.org/content/10.1101/179309v1?rss=1 Ohnishi, Y. N. Eagle, A. L. Ohnishi, Y. H. Cahill, M. E. Wirtz, A. J. Robison, A. J. Nestler, E. J. 2017-08-22 doi:10.1101/179309 Cold Spring Harbor Laboratory Press 2017-08-22 <![CDATA[ Identification of Iridoid Synthases from Nepeta species: Iridoid cyclization does not determine nepetalactone stereochemistry ]]> https://biorxiv.org/content/10.1101/179572v1?rss=1 nView larger version (91K):norg.highwire.dtl.DTLVardef@cc600dorg.highwire.dtl.DTLVardef@1b6240dorg.highwire.dtl.DTLVardef@f8e1beorg.highwire.dtl.DTLVardef@1acb9dd_HPS_FORMAT_FIGEXP M_FIG Iridoid synthase from Nepeta cateria (catnip) and Nepeta mussinii, have been cloned and characterized.nnC_FIG AbstractNepetalactones are iridoid monoterpenes with a broad range of biological activities produced by plants in the Nepeta genus. However, none of the genes for nepetalactone biosynthesis have been discovered. Here we report the transcriptomes of two Nepeta species, each with distinctive profiles of nepetalactone stereoisomers. As a starting point for investigation of nepetalactone biosynthesis in Nepeta, these transcriptomes were used to identify candidate genes for iridoid synthase homologs, an enzyme that has been shown to form the core iridoid skeleton in several iridoid producing plant species. Iridoid synthase homologs identified from the transcriptomes were cloned, heterologously expressed, and then assayed with the 8-oxogeranial substrate. These experiments revealed that catalytically active iridoid synthase enzymes are present in Nepeta, though there are unusual mutations in key active site residues. Nevertheless, these enzymes exhibit similar catalytic activity and product profile compared to previously reported iridoid synthases from other plants. Notably, four nepetalactone stereoisomers with differing stereochemistry at the 4 and 7 positions - which are generated during the iridoid synthase reaction - are observed at different ratios in various Nepeta species. This work strongly suggests that the variable stereochemistry at these 4 and 7 positions of nepetalactone diastereomers is established further downstream in the iridoid pathway in Nepeta. Overall, this work provides a gateway into the biosynthesis of nepetalactones in Nepeta.nnHighlightsO_LISpecies within the Nepeta genus (such as catnip) produce nepetalactone iridoidsnC_LIO_LIThe enzymes that produce the iridoid scaffold of nepetalactone were identified from two species of NepetanC_LIO_LIThe iridoid synthase enzymes are not responsible for the stereochemical variation in these iridoidsnC_LI ]]> Sherden, N. H. Lichman, B. Caputi, L. Zhao, D. Kamileen, M. O. Buell, C. R. O'Connor, S. 2017-08-22 doi:10.1101/179572 Cold Spring Harbor Laboratory Press 2017-08-22 <![CDATA[ Pervasive epistasis in cell proliferation pathways modulates neurodevelopmental defects of autism-associated 16p11.2 deletion ]]> https://biorxiv.org/content/10.1101/185355v1?rss=1 Iyer, J. Singh, M. D. Jensen, M. Patel, P. Pizzo, L. Huber, E. Koerselman, H. Weiner, A. T. Lepanto, P. Vadodaria, K. Kubina, A. Wang, Q. Talbert, A. Yennawar, S. Badano, J. Manak, J. R. Rolls, M. M. Krishnan, A. Girirajan, S. 2017-09-20 doi:10.1101/185355 Cold Spring Harbor Laboratory Press 2017-09-20 <![CDATA[ Genetic and metabolic regulation of Mycobacterium tuberculosis acid growth arrest ]]> https://biorxiv.org/content/10.1101/186551v1?rss=1 Baker, J. J. Abramovitch, R. B. 2017-09-09 doi:10.1101/186551 Cold Spring Harbor Laboratory Press 2017-09-09 <![CDATA[ Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection ]]> https://biorxiv.org/content/10.1101/186759v1?rss=1 Maddamsetti, R. Lenski, R. E. 2017-09-10 doi:10.1101/186759 Cold Spring Harbor Laboratory Press 2017-09-10 <![CDATA[ Mitochondrial Dual-coding Genes in Trypanosoma brucei ]]> https://biorxiv.org/content/10.1101/187732v1?rss=1 Kirby, L. E. Koslowsky, D. 2017-09-12 doi:10.1101/187732 Cold Spring Harbor Laboratory Press 2017-09-12 <![CDATA[ Inferring Continuous and Discrete Population Genetic Structure Across Space ]]> https://biorxiv.org/content/10.1101/189688v1?rss=1 Bradburd, G. Coop, G. Ralph, P. 2017-09-15 doi:10.1101/189688 Cold Spring Harbor Laboratory Press 2017-09-15 <![CDATA[ Accurate Genomic Prediction Of Human Height ]]> https://biorxiv.org/content/10.1101/190124v1?rss=1 Lello, L. Avery, S. G. Tellier, L. Vazquez, A. de los Campos, G. Hsu, S. D. H. 2017-09-18 doi:10.1101/190124 Cold Spring Harbor Laboratory Press 2017-09-18 <![CDATA[ A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae) ]]> https://biorxiv.org/content/10.1101/192641v1?rss=1 Schoville, S. D. Chen, Y. H. Andersson, M. N. N. Benoit, J. B. Bhandari, A. Bowsher, J. H. Brevik, K. Cappelle, K. Chen, M.-J. M. Childers, A. K. Childers, C. Christiaens, O. Clements, J. Elpidina, E. N. Engsontia, P. Friedrich, M. Garcia-Robles, I. Goswami, C. Grapputo, A. Gruden, K. Grynberg, M. Henrissat, B. Jennings, E. C. Jones, J. W. Kalsi, M. Khan, S. A. A. Kumar, A. Li, F. Lombard, V. Ma, X. Martynov, A. Miller, N. J. Mitchell, R. F. Munoz-Torres, M. Muszewska, A. Oppert, B. Palli, S. R. Panfilio, K. A. Pauchet, Y. Perkin, L. C. Petek, M. Poelch 2017-09-22 doi:10.1101/192641 Cold Spring Harbor Laboratory Press 2017-09-22 <![CDATA[ Desert Tortoises in the Genomic Age: Population Genetics and the Landscape ]]> https://biorxiv.org/content/10.1101/195743v1?rss=1 nView larger version (147K):norg.highwire.dtl.DTLVardef@b60416org.highwire.dtl.DTLVardef@1c649f2org.highwire.dtl.DTLVardef@120e625org.highwire.dtl.DTLVardef@e59b34_HPS_FORMAT_FIGEXP M_FIG C_FIG PrefaceO_ST_ABSContextC_ST_ABSThe following document is a report that was submitted to the California Department of Fish and Wildlife, describing a series of analyses to help understand the impacts of several alternative spatial configurations of renewable energy development on gene flow of the federally threatened Mojave desert tortoise. These development alternatives were the centerpiece of the Desert Renewable Energy Conservation Plan (DRECP), a landscape-level land use planning initiative undertaken by the Bureau of Land Management (BLM), U.S. Fish and Wildlife Service (USFWS), California Energy Commission (CEC), and the California Department of Fish and Wildlife (CDFW). We were tasked by the California Department of Fish and Wildlife with providing a detailed analysis of these alternative plans on desert tortoise gene flow, and submitted the report for the public comment period for the initial implementation of the DRECP.nnFuture PlansO_ST_ABSCurrent state of landscape-level planning for the Mojave desert tortoiseC_ST_ABSThe five proposed land use configuration alternatives analyzed in the subsequent report include public and private lands spread across several counties in California. Shortly after the end of the DRECPs public comment period, the government agencies that developed the DRECP announced that they would be splitting its implementation into two phases: one that deals with land use decisions on BLM-controlled lands and one that deals with non-BLM areas (Sahagun 2015).nnPhase I of the DRECP was approved by the Bureau of Land Management on September 14, 2016 (U.S. Bureau of Land Management 2016). This phase includes land use planning decisions for BLM-administered lands. Specifically, 388,000 acres of public lands were designated as development focus areas (DFAs). In applications for leasing lands for renewable energy development, DFAs will not require the same degree of environmental evaluation prior to permitting, as theyve already been evaluated in the context of the DRECP. The application process for renewable energy development within DFAs will be streamlined to encourage development in these areas. Phase I also designated a total of 6,527,000 acres for natural resource conservation. This includes California Desert National Conservation Lands, Areas of Critical Environmental Concern, and Wildlife Allocations. A further 2,691,000 acres were designated for recreation under Phase I. Phase II of the DRECP is currently under development in conjunction with county-level governments to extend this landscape-level planning beyond BLM-administered lands.nnAuthor ContributionsThis was a collaborative report. Evan McCartney-Melstad performed the simulations of the low-coverage full genome approach (see Figure 2); conducted all of the laboratory work to generate the genome sequences; performed all of the bioinformatic analyses to bring the raw sequence data to the various stages required for different analyses; wrote the software to quickly estimate pairwise genetic relationships between individuals using read count data in low coverage sequence data (www.github.com/atcg/cPWP); performed some of the population genetic analyses; and wrote and edited several sections of the report.nnO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/195743_fig2.gif" ALT="Figure 2">nView larger version (16K):norg.highwire.dtl.DTLVardef@30a49forg.highwire.dtl.DTLVardef@187c3d8org.highwire.dtl.DTLVardef@4abe98org.highwire.dtl.DTLVardef@126febe_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 2.C_FLOATNO Comparison of two different sequencing approaches in their ability to differentiate very slightly differentiated populations (Fst=0.001)nnC_FIG Peter Ralph (in collaboration with Gideon Bradburd and Erik Lundgren) invented and implemented the random walk-based gene flow model that we used to estimate reductions in gene flow due to development, and also developed the theory behind the read-based pairwise pi and genetic covariance estimation used here, in addition to writing and editing several sections of the report. Gideon Bradburd also performed some of the population genetic analyses and wrote and edited several sections of the report. Jannet Vu collected and curated the spatial environmental data and generated the maps that are included in the report (Figures 10, A10-A13), and also wrote Appendices I and IV. Bridgette Hagerty, Fran Sandmeier, Chava Weitzman, and C. Richard Tracy contributed approximately 1,000 desert tortoise blood samples that they collected (at great effort), in addition to knowledge of tortoise ecology and conservation, as well as the results of previous microsatellite-based genetic analyses and editing of the report. H. Bradley Shaffer wrote and edited several sections of the report, and is listed as the lead author for his role in conceiving of and obtaining funding support for the project.nnO_FIG O_LINKSMALLFIG WIDTH=154 HEIGHT=200 SRC="FIGDIR/small/195743_fig10.gif" ALT="Figure 10">nView larger version (82K):norg.highwire.dtl.DTLVardef@11e99acorg.highwire.dtl.DTLVardef@1faf2f5org.highwire.dtl.DTLVardef@64c440org.highwire.dtl.DTLVardef@1907837_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 10.C_FLOATNO Spatial configuration of the proposed development chunks (see Appendix 4).nnC_FIG ]]> Shaffer, H. B. McCartney-Melstad, E. Ralph, P. L. Bradburd, G. Lundgren, E. Vu, J. Hagerty, B. Sandmeier, F. Weitzman, C. Tracy, C. R. 2017-09-29 doi:10.1101/195743 Cold Spring Harbor Laboratory Press 2017-09-29 <![CDATA[ Improved management facilitates return of an iconic fish species ]]> https://biorxiv.org/content/10.1101/197780v1?rss=1 MacKenzie, B. R. Aarestrup, K. Christoffersen, M. Payne, M. R. Sorensen, C. Lund, H. S. Casini, M. 2017-10-04 doi:10.1101/197780 Cold Spring Harbor Laboratory Press 2017-10-04 <![CDATA[ Compensatory evolution via cryptic genetic variation: Distinct trajectories to phenotypic and fitness recovery ]]> https://biorxiv.org/content/10.1101/200725v1?rss=1 Chari, S. Marier, C. Porter, C. Northrop, E. Belinky, A. Dworkin, I. 2017-10-10 doi:10.1101/200725 Cold Spring Harbor Laboratory Press 2017-10-10 <![CDATA[ Revisiting microbe-metabolite interactions: doing better than random ]]> https://biorxiv.org/content/10.1101/2019.12.10.871905v1?rss=1 Morton, J. McDonald, D. Aksenov, A. Nothias-Scaglia, L.-F. Foulds, J. Quinn, R. A. Badri, M. Swenson, T. Van Goethem, M. Northen, T. Vazquez-Baeza, Y. Wang, M. Bokulich, N. Watters, A. Song, S. J. Bonneau, R. Dorrestein, P. Knight, R. 2019-12-16 doi:10.1101/2019.12.10.871905 Cold Spring Harbor Laboratory Press 2019-12-16 <![CDATA[ Robust Stability of Multicomponent Membranes: theRole of Glycolipids ]]> https://biorxiv.org/content/10.1101/2019.12.19.882092v1?rss=1 Chen, Y. Doelman, A. Promislow, K. Veerman, F. 2019-12-19 doi:10.1101/2019.12.19.882092 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Carbamazepine restores neuronal signaling, protein synthesis and cognitive function in a mouse model of fragile X syndrome ]]> https://biorxiv.org/content/10.1101/2020.01.07.897835v1?rss=1 Ding, Q. Zhang, F. Feng, Y. Wang, H. 2020-01-08 doi:10.1101/2020.01.07.897835 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Sucrose promotes etiolated stem branching through activation of cytokinin accumulation followed by vacuolar invertase activity ]]> https://biorxiv.org/content/10.1101/2020.01.08.897009v1?rss=1 Salam, B. B. Barbier, F. F. Danieli, R. Ziv, C. Spichal, L. Teper-Bamnolker, P. Jiang, J. Ori, N. Beveridge, C. Eshel, D. 2020-01-09 doi:10.1101/2020.01.08.897009 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Within and cross species predictions of plant specialized metabolism genes using transfer learning ]]> https://biorxiv.org/content/10.1101/2020.01.13.112102v1?rss=1 Moore, B. M. Wang, P. Fan, P. Lee, A. Leong, B. Lou, Y.-L. Schenck, C. A. Sugimoto, K. Last, R. Lehti-Shiu, M. D. Barry, C. Shiu, S.-H. 2020-01-14 doi:10.1101/2020.01.13.112102 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS. ]]> https://biorxiv.org/content/10.1101/2020.01.13.905091v1?rss=1 Aksenov, A. Laponogov, I. Zhang, Z. Doran, S. Belluomo, I. Veselkov, D. Bittremieux, W. Nothias, L. F. Nothias-Esposito, M. Maloney, K. N. Misra, B. B. Melnik, A. V. Jones, K. L. Dorrestein, K. Panitchpakdi, M. Ernst, M. van der Hooft, J. J. J. Gonzalez, M. Carazzone, C. Amézquita, A. Callewaert, C. Morton, J. Quinn, R. A. Bouslimani, A. Albarracin Orio, A. Petras, D. Smania, A. M. Couvillion, S. P. Burnet, M. C. Nicora, C. D. Zink, E. Metz, T. O. Artaev, V. Humston-Fulmer, E. Gregor, R. Meijler, M. M. Mizrahi, I. Eyal, S. Anderson, B. Dutton, R. J. 2020-01-14 doi:10.1101/2020.01.13.905091 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Application of Pedimap -- a pedigree visualization tool -- to facilitate the decisioning of rice breeding in Sri Lanka ]]> https://biorxiv.org/content/10.1101/2020.01.20.912477v1?rss=1 Rathnayake, P. Sahibdeen, S. Udawela, U. Weebadde, C. Weerakoon, W. Sooriyapathirana, S. 2020-01-20 doi:10.1101/2020.01.20.912477 Cold Spring Harbor Laboratory Press 2020-01-20 <![CDATA[ Discovery of a spatially and temporally persistent core microbiome of the common bean rhizosphere ]]> https://biorxiv.org/content/10.1101/2020.01.20.913202v1?rss=1 Stopnisek, N. Shade, A. 2020-01-21 doi:10.1101/2020.01.20.913202 Cold Spring Harbor Laboratory Press 2020-01-21 <![CDATA[ Membrane-mediated ligand unbinding of the PK-11195 ligand from the translocator protein (TSPO) ]]> https://biorxiv.org/content/10.1101/2020.01.21.914127v1?rss=1 Dixon, T. Uyar, A. Ferguson-Miller, S. Dickson, A. 2020-01-21 doi:10.1101/2020.01.21.914127 Cold Spring Harbor Laboratory Press 2020-01-21 <![CDATA[ A universal chromosome identification system for maize and wild Zea species ]]> https://biorxiv.org/content/10.1101/2020.01.22.915942v1?rss=1 Tomaz Braz, G. do Vale Martins, L. Zhang, T. S. Albert, P. A. Birchler, J. Jiang, J. 2020-01-23 doi:10.1101/2020.01.22.915942 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment ]]> https://biorxiv.org/content/10.1101/2020.01.22.915975v1?rss=1 Blount, Z. D. Maddamsetti, R. Grant, N. A. Ahmed, S. T. Jagdish, T. Sommerfeld, B. A. Tillman, A. Moore, J. P. Slonczewski, J. L. Barrick, J. E. Lenski, R. E. 2020-01-23 doi:10.1101/2020.01.22.915975 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Neural Circuit Dynamics for Sensory Detection ]]> https://biorxiv.org/content/10.1101/2020.01.28.923839v1?rss=1 Mallik, S. Nizampatnam, S. Nandi, A. Saha, D. Raman, B. Ching, S. 2020-01-29 doi:10.1101/2020.01.28.923839 Cold Spring Harbor Laboratory Press 2020-01-29 <![CDATA[ Improving Heart disease risk through quality-focused diet logging: pre-post study of a diet quality tracking app ]]> https://biorxiv.org/content/10.1101/2020.01.30.926634v1?rss=1 VanDam, C. Kwon, B. C. Chiuve, S. Choi, H.-W. Entler, P. Tan, P.-N. Huh-Yoo, J. 2020-01-30 doi:10.1101/2020.01.30.926634 Cold Spring Harbor Laboratory Press 2020-01-30 <![CDATA[ Machine intelligence design of 2019-nCoV drugs ]]> https://biorxiv.org/content/10.1101/2020.01.30.927889v1?rss=1 Nguyen, D. D. Gao, K. Wang, R. Wei, G. 2020-02-04 doi:10.1101/2020.01.30.927889 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Build a Better Bootstrap and the RAWR Shall Beat a Random Path to Your Door: Phylogenetic Support Estimation Revisited ]]> https://biorxiv.org/content/10.1101/2020.02.02.931063v1?rss=1 Wang, W. Liu, K. J. 2020-02-03 doi:10.1101/2020.02.02.931063 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ Changes in the tumor microenvironment and treatment outcome in glioblastoma: A pilot study ]]> https://biorxiv.org/content/10.1101/2020.02.03.932475v1?rss=1 Ali, S. Borin, T. F. Piranlioglu, R. Ara, R. Lebedyeva, I. Angara, K. Achyut, B. R. Arbab, A. S. Rashid, M. H. 2020-02-04 doi:10.1101/2020.02.03.932475 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Developmental exposure to the organochlorine pesticide dieldrin causes male-specific exacerbation of α-synuclein-preformed fibril-induced toxicity and motor deficits ]]> https://biorxiv.org/content/10.1101/2020.02.03.932681v1?rss=1 Gezer, A. O. Kochmanski, J. VanOeveren, S. E. Cole-Strauss, A. Kemp, C. J. Patterson, J. R. Miller, K. M. Herman, D. E. McIntyre, A. Lipton, J. W. Luk, K. Fleming, S. M. Sortwell, C. E. Bernstein, A. I. 2020-02-04 doi:10.1101/2020.02.03.932681 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Potentially highly potent drugs for 2019-nCoV ]]> https://biorxiv.org/content/10.1101/2020.02.05.936013v1?rss=1 Nguyen, D. Gao, K. Chen, J. Wang, R. Wei, G. 2020-02-13 doi:10.1101/2020.02.05.936013 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Shape matters: cell geometry determines phytoplankton diversity ]]> https://biorxiv.org/content/10.1101/2020.02.06.937219v1?rss=1 Ryabov, A. Kerimoglu, O. Litchman, E. Olenina, I. Roselli, L. Basset, A. Stanca, E. Blasius, B. 2020-02-07 doi:10.1101/2020.02.06.937219 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Modeling How Community Assembly Alters the Functioning of Ecosystems ]]> https://biorxiv.org/content/10.1101/2020.02.10.942656v1?rss=1 Koffel, T. Kremer, C. T. Bannar-Martin, K. Ernest, M. S. K. Eisenhauer, N. Roscher, C. Sarmento Cabral, J. Leibold, M. A. 2020-02-12 doi:10.1101/2020.02.10.942656 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Selective LXR agonist, DMHCA, corrects the retina-bone marrow axis in type 2 diabetes ]]> https://biorxiv.org/content/10.1101/2020.02.11.942292v1?rss=1 Vieira, C. P. Fortmann, S. D. Hossain, M. Longhini, A. L. Hammer, S. S. Asare-Bediako, B. Crossman, D. K. Sielski, M. S. Adu-Agyeiwaah, Y. Dupont, M. Floyd, J. L. Li Calzi, S. Lydic, T. Welner, R. S. Blanchard, G. J. Busik, J. V. Grant, M. B. 2020-02-12 doi:10.1101/2020.02.11.942292 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Genetic Architecture of Complex Traits and Disease Risk Predictors ]]> https://biorxiv.org/content/10.1101/2020.02.12.946608v1?rss=1 Yong, S. Y. Raben, T. G. Lello, L. Hsu, S. D. H. 2020-02-13 doi:10.1101/2020.02.12.946608 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Analysis of variance when both input and output sets are high-dimensional ]]> https://biorxiv.org/content/10.1101/2020.02.15.950949v1?rss=1 de los Campos, G. A. Torsten, P. Gonzalez-Raymundez, A. Simianer, H. Mias, G. Vazquez, A. I. 2020-02-15 doi:10.1101/2020.02.15.950949 Cold Spring Harbor Laboratory Press 2020-02-15 <![CDATA[ Dynamic contrast enhanced MRI with clinical hepatospecific MRI contrast agents in pigs: initial experience ]]> https://biorxiv.org/content/10.1101/2020.02.18.946541v1?rss=1 Hix, J. M. L. Mallett, C. L. Latourette, M. Munoz, K. A. Shapiro, E. M. 2020-02-19 doi:10.1101/2020.02.18.946541 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ SimpylCellCounter: An Automated Solution for Quantifying Cells in Brain Tissue ]]> https://biorxiv.org/content/10.1101/2020.02.22.960948v1?rss=1 Bal, A. Maureira, F. Arguello, A. A. 2020-02-25 doi:10.1101/2020.02.22.960948 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Lower Soil Carbon Loss Due to Persistent Microbial Adaptation to Climate Warming ]]> https://biorxiv.org/content/10.1101/2020.02.23.961300v1?rss=1 Guo, X. Gao, Q. Yuan, M. Wang, G. Zhou, X. Feng, J. Shi, Z. Hale, L. Wu, L. Zhou, A. Tian, R. Liu, F. Wu, B. Chen, L. Gyo Jung, C. Niu, S. Li, D. Xu, X. Jiang, L. Escalas, A. Wu, L. He, Z. Van Nostrand, J. Ning, D. Liu, X. Yang, Y. Schuur, E. Konstantinidis, K. T. Cole, J. R. Penton, C. R. Luo, Y. Tiedje, J. Zhou, J. 2020-02-25 doi:10.1101/2020.02.23.961300 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Kinetics characterization of ASXL1/2-mediated allosteric regulation of BAP1 deubiquitinase ]]> https://biorxiv.org/content/10.1101/2020.02.24.962464v1?rss=1 Peng, H. Cassel, J. McCracken, D. Prokop, J. W. Collop, P. R. Polo, A. Joshi, S. Mandell, J. P. Ayyanathan, K. Hinds, D. Malkowicz, S. B. Harbour, J. W. Bowcock, A. M. Salvino, J. Kennedy, E. J. Testa, J. R. Rauscher, F. J. 2020-02-24 doi:10.1101/2020.02.24.962464 Cold Spring Harbor Laboratory Press 2020-02-24 <![CDATA[ Lanthanide-dependent alcohol dehydrogenases require an essential aspartate residue for metal coordination and function ]]> https://biorxiv.org/content/10.1101/2020.02.25.964783v1?rss=1 Good, N. M. Fellner, M. Demirer, K. Hu, J. Hausinger, R. P. Martinez-Gomez, N. C. C. 2020-02-26 doi:10.1101/2020.02.25.964783 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ The cis-regulatory codes of response to combined heat and drought stress in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2020.02.28.969261v1?rss=1 Azodi, C. B. Lloyd, J. P. Shiu, S.-H. 2020-02-29 doi:10.1101/2020.02.28.969261 Cold Spring Harbor Laboratory Press 2020-02-29 <![CDATA[ Visibility Graph Based Community Detection for Biological Time Series ]]> https://biorxiv.org/content/10.1101/2020.03.02.973263v1?rss=1 Zheng, M. Domanskyi, S. Piermarocchi, C. Mias, G. I. 2020-03-03 doi:10.1101/2020.03.02.973263 Cold Spring Harbor Laboratory Press 2020-03-03 <![CDATA[ Within-Family Validation of Polygenic Risk Scores and Complex Trait Prediction ]]> https://biorxiv.org/content/10.1101/2020.03.04.976654v1?rss=1 Lello, L. Raben, T. Hsu, S. D. H. 2020-03-05 doi:10.1101/2020.03.04.976654 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Solanaceae specialized metabolism in a non-model plant: trichome acylinositol biosynthesis ]]> https://biorxiv.org/content/10.1101/2020.03.04.977181v1?rss=1 Leong, B. Hurney, S. M. Fiesel, P. D. Moghe, G. D. Jones, A. D. Last, R. L. 2020-03-05 doi:10.1101/2020.03.04.977181 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity ]]> https://biorxiv.org/content/10.1101/2020.03.04.977231v1?rss=1 Fan, P. Wang, P. Lou, Y.-R. Leong, B. J. Moore, B. J. Schenck, C. A. Combs, R. Cao, P. Brandizzi, F. Shiu, S.-H. Last, R. L. 2020-03-05 doi:10.1101/2020.03.04.977231 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ ebony affects pigmentation divergence and cuticular hydrocarbons in Drosophila americana and D. novamexicana ]]> https://biorxiv.org/content/10.1101/2020.03.05.977009v1?rss=1 Lamb, A. M. Wang, Z. Simmer, P. Chung, H. Wittkopp, P. J. 2020-03-06 doi:10.1101/2020.03.05.977009 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ Molecular structure of a prevalent amyloid-β fibril polymorph from Alzheimer's disease brain tissue ]]> https://biorxiv.org/content/10.1101/2020.03.06.981381v1?rss=1 Ghosh, U. Thurber, K. R. Yau, W.-M. Tycko, R. 2020-03-07 doi:10.1101/2020.03.06.981381 Cold Spring Harbor Laboratory Press 2020-03-07 <![CDATA[ Machine Learning to Identify Flexibility Signatures of Class A GPCR Inhibition ]]> https://biorxiv.org/content/10.1101/2020.03.10.986612v1?rss=1 Bemister-Buffington, J. Wolf, A. J. Raschka, S. Kuhn, L. 2020-03-12 doi:10.1101/2020.03.10.986612 Cold Spring Harbor Laboratory Press 2020-03-12 <![CDATA[ Early-life microbial intervention reduces colitis risk promoted by antibiotic-induced gut dysbiosis ]]> https://biorxiv.org/content/10.1101/2020.03.11.987412v1?rss=1 Miyoshi, J. Miyoshi, S. Delmont, T. O. Cham, C. Lee, S. T. M. Sakatani, A. Yang, K. Shan, Y. Kiefl, E. Yousef, M. Crosson, S. Sogin, M. Antonopoulos, D. A. Eren, A. M. Leone, V. Chang, E. B. 2020-03-12 doi:10.1101/2020.03.11.987412 Cold Spring Harbor Laboratory Press 2020-03-12 <![CDATA[ TGF-β Family Inhibitors Blunt Adipogenesis Via Non-Canonical Regulation Of SMAD Pathways ]]> https://biorxiv.org/content/10.1101/2020.03.12.988568v1?rss=1 Aykul, S. Maust, J. Floer, M. Martinez-Hackert, E. 2020-03-14 doi:10.1101/2020.03.12.988568 Cold Spring Harbor Laboratory Press 2020-03-14 <![CDATA[ Differential TAM receptor regulation of hepatic physiology and injury ]]> https://biorxiv.org/content/10.1101/2020.03.13.990143v1?rss=1 Lemke, G. E. Zagorska, A. Traves, P. G. Jimenez-Garcia, L. Strickland, J. D. Tapia, F. J. Mayoral Monibas, R. Burrola, P. Copple, B. L. 2020-03-16 doi:10.1101/2020.03.13.990143 Cold Spring Harbor Laboratory Press 2020-03-16 <![CDATA[ The Mitochondrial Permeability Transition Phenomenon Elucidated by Cryo-EM Reveals the Genuine Impact of Calcium Overload on Mitochondrial Structure and Function ]]> https://biorxiv.org/content/10.1101/2020.03.13.991349v1?rss=1 Strubbe, J. O. Schrad, J. R. Pavlov, E. V. Conway, J. F. Parent, K. N. Bazil, J. N. 2020-03-14 doi:10.1101/2020.03.13.991349 Cold Spring Harbor Laboratory Press 2020-03-14 <![CDATA[ CryoGAN: A New Reconstruction Paradigm for Single-particle Cryo-EM Via Deep Adversarial Learning ]]> https://biorxiv.org/content/10.1101/2020.03.20.001016v1?rss=1 Gupta, H. McCann, M. T. Donati, L. Unser, M. 2020-03-22 doi:10.1101/2020.03.20.001016 Cold Spring Harbor Laboratory Press 2020-03-22 <![CDATA[ Ibrutinib blocks YAP1 activation and reverses BRAFi resistance in melanoma cells ]]> https://biorxiv.org/content/10.1101/2020.03.25.006916v1?rss=1 Misek, S. A. Newbury, P. A. Chekalin, E. Paithankar, S. Doseff, A. I. Chen, B. Gallo, K. A. Neubig, R. R. 2020-03-26 doi:10.1101/2020.03.25.006916 Cold Spring Harbor Laboratory Press 2020-03-26 <![CDATA[ Modeling of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Proteins by Machine Learning and Physics-Based Refinement ]]> https://biorxiv.org/content/10.1101/2020.03.25.008904v1?rss=1 Heo, L. Feig, M. 2020-03-28 doi:10.1101/2020.03.25.008904 Cold Spring Harbor Laboratory Press 2020-03-28 <![CDATA[ A second hybrid-binding domain modulates the activity of Drosophila ribonuclease H1 ]]> https://biorxiv.org/content/10.1101/2020.03.26.010645v1?rss=1 Gonzalez de Cozar, J. M. Carretero-Junquera, M. Ciesielski, G. L. Miettinen, S. Varjosalo, M. Kaguni, L. S. Dufour, E. Jacobs, H. T. 2020-03-28 doi:10.1101/2020.03.26.010645 Cold Spring Harbor Laboratory Press 2020-03-28 <![CDATA[ A Flexible, Interpretable, and Accurate Approach for Imputing the Expression of Unmeasured Genes ]]> https://biorxiv.org/content/10.1101/2020.03.30.016675v1?rss=1 2 million publicly-available human microarray gene-expression profiles, these profiles were measured using a variety of platforms that each cover a pre-defined, limited set of genes. Therefore, key to reanalyzing and integrating this massive data collection are methods that can computationally reconstitute the complete transcriptome in partially-measured microarray samples by imputing the expression of unmeasured genes. Current state-of-the-art imputation methods are tailored to samples from a specific platform and rely on gene-gene relationships regardless of the biological context of the target sample. We show that sparse regression models that capture sample-sample relationships (termed SampleLASSO), built on-the-fly for each new target sample to be imputed, outperform models based on fixed gene relationships. Extensive evaluation involving three machine learning algorithms (LASSO, k-nearest-neighbors, and deep-neural-networks), two gene subsets (GPL96-570 and LINCS), and three imputation tasks (within and across microarray/RNA-seq) establishes that SampleLASSO is the most accurate model. Additionally, we demonstrate the biological interpretability of this method by showing that, for imputing a target sample from a certain tissue, SampleLASSO automatically leverages training samples from the same tissue. Thus, SampleLASSO is a simple, yet powerful and flexible approach for harmonizing large-scale gene-expression data. ]]> Mancuso, C. A. Canfield, J. L. Singla, D. Krishnan, A. 2020-03-31 doi:10.1101/2020.03.30.016675 Cold Spring Harbor Laboratory Press 2020-03-31 <![CDATA[ Culture conditions antagonize lineage-promoting signaling in the mouse blastocyst ]]> https://biorxiv.org/content/10.1101/2020.03.31.016717v1?rss=1 Frum, T. Ralston, A. 2020-04-01 doi:10.1101/2020.03.31.016717 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ Overexpression of the chloroplastic 2-oxoglutarate/malate transporter in rice disturbs carbon and nitrogen homeostasis ]]> https://biorxiv.org/content/10.1101/2020.03.31.018226v1?rss=1 Zamani Nour, S. Lin, H.-C. Walker, B. J. Mettler-Altmann, T. Khoshravesh, R. Karki, S. P. Bagunu, E. D. Sage, T. L. Quick, P. Weber, A. P. 2020-03-31 doi:10.1101/2020.03.31.018226 Cold Spring Harbor Laboratory Press 2020-03-31 <![CDATA[ Application of singe nuclei RNA sequencing to assess the hepatic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin ]]> https://biorxiv.org/content/10.1101/2020.04.07.030478v1?rss=1 Nault, R. Fader, K. A. Bhattacharya, S. Zacharewski, T. 2020-04-08 doi:10.1101/2020.04.07.030478 Cold Spring Harbor Laboratory Press 2020-04-08 <![CDATA[ A Single-Objective Light-Sheet Microscope with 200 nm-Scale Resolution. ]]> https://biorxiv.org/content/10.1101/2020.04.07.030569v1?rss=1 Sapoznik, E. Chang, B.-J. Ju, R. J. Welf, E. S. Broadbent, D. Carisey, A. F. Stehbens, S. J. Lee, K.-m. Marin, A. Hanker, A. B. Schmidt, J. C. Arteaga, C. L. Yang, B. Kruithoff, R. Millett-Sikking, A. York, A. G. Dean, K. M. Fiolka, R. P. 2020-04-08 doi:10.1101/2020.04.07.030569 Cold Spring Harbor Laboratory Press 2020-04-08 <![CDATA[ Reversal of Infected Host Gene Expression Identifies Repurposed Drug Candidates for COVID-19 ]]> https://biorxiv.org/content/10.1101/2020.04.07.030734v1?rss=1 Xing, J. Shankar, R. Drelich, A. Paithankar, S. Chekalin, E. Dexheimer, T. Rajasekaran, S. Tseng, C.-T. K. Chen, B. 2020-04-09 doi:10.1101/2020.04.07.030734 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ Triclosan depletes the membrane potential in Pseudomonas aeruginosa biofilms inhibiting aminoglycoside induced adaptive resistance ]]> https://biorxiv.org/content/10.1101/2020.04.09.034033v1?rss=1 Maiden, M. Waters, C. 2020-04-09 doi:10.1101/2020.04.09.034033 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ The regulation of a pigmentation gene in the formation of complex color patterns in Drosophila abdomens ]]> https://biorxiv.org/content/10.1101/2020.04.09.034900v1?rss=1 Raja, K. K. B. Shittu, M. O. Nouhan, P. M. E. Steenwinkel, T. E. Bachman, E. A. Kokate, P. P. McQueeney, A. H. Mundell, E. A. Armentrout, A. A. Peabody, A. M. Werner, T. 2020-04-10 doi:10.1101/2020.04.09.034900 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ Pattern-recognition receptors are required for NLR-mediated plant immunity ]]> https://biorxiv.org/content/10.1101/2020.04.10.031294v1?rss=1 Yuan, M. Jiang, Z. Bi, G. Nomura, K. Liu, M. He, S. Y. Zhou, J.-M. Xin, X.-F. 2020-04-10 doi:10.1101/2020.04.10.031294 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ Rank-dependent social inheritance determines social network structure in a wild mammal population ]]> https://biorxiv.org/content/10.1101/2020.04.10.036087v1?rss=1 Ilany, A. Holekamp, K. E. Akcay, E. 2020-04-12 doi:10.1101/2020.04.10.036087 Cold Spring Harbor Laboratory Press 2020-04-12 <![CDATA[ VIBRIO CHOLERAE ADAPTS TO SESSILE AND MOTILE LIFESTYLES BY CYCLIC DI-GMP REGULATION OF CELL SHAPE ]]> https://biorxiv.org/content/10.1101/2020.04.15.043257v1?rss=1 Fernandez, N. L. Nhu, N. T. Hsueh, B. Y. Franklin, J. L. Dufour, Y. S. Waters, C. M. 2020-04-16 doi:10.1101/2020.04.15.043257 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Targeting subtype-specific metabolic preferences in nucleotide biosynthesis inhibits mouse mammary tumor growth ]]> https://biorxiv.org/content/10.1101/2020.04.19.049577v1?rss=1 Ogrodzinski, M. P. Teoh, S. T. Lunt, S. 2020-04-20 doi:10.1101/2020.04.19.049577 Cold Spring Harbor Laboratory Press 2020-04-20 <![CDATA[ Mechanical and signaling mechanisms that guide pre-implantation embryo movement. ]]> https://biorxiv.org/content/10.1101/2020.04.20.051094v1?rss=1 Flores, D. Madhavan, M. Wright, S. Arora, R. 2020-04-21 doi:10.1101/2020.04.20.051094 Cold Spring Harbor Laboratory Press 2020-04-21 <![CDATA[ Redesigned Reporter Gene for Improved Proton Exchange-based Molecular MRI Contrast ]]> https://biorxiv.org/content/10.1101/2020.04.21.053157v1?rss=1 Perlman, O. Ito, H. Gilad, A. A. McMahon, M. T. Chiocca, E. A. Nakashima, H. Farrar, C. T. 2020-04-23 doi:10.1101/2020.04.21.053157 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ RADSex: a computational workflow to study sex determination using Restriction Site-Associated DNA Sequencing data ]]> https://biorxiv.org/content/10.1101/2020.04.22.054866v1?rss=1 Feron, R. Pan, Q. Wen, M. Imarazene, B. Jouanno, E. Anderson, J. Herpin, A. Journot, L. Parrinello, H. Klopp, C. Kottler, V. A. Roco, A. S. Du, K. Kneitz, S. Adolfi, M. Wilson, C. A. McCluskey, B. Amores, A. Desvignes, T. Goetz, F. W. Takanashi, A. Kawaguchi, M. Detrich, H. W. Oliveira, M. Nobrega, R. Sakamoto, T. Nakamoto, M. Wargelius, A. Karlsen, O. Wang, Z. Stöck, M. Waterhouse, R. M. Braasch, I. Postlethwait, J. H. Schartl, M. Guiguen, Y. 2020-04-23 doi:10.1101/2020.04.22.054866 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ Charge-Driven Phase Separation of RNA and Proteins without Disorder ]]> https://biorxiv.org/content/10.1101/2020.04.23.057901v1?rss=1 Dutagaci, B. Nawrocki, G. Goodluck, J. Lapidus, L. J. Feig, M. 2020-04-24 doi:10.1101/2020.04.23.057901 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Artemisia annua and Artemisia afra extracts exhibit strong bactericidal activity against Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2020.04.26.062331v1?rss=1 Martini, M. C. Zhang, T. Williams, J. T. Abramovitch, R. Weathers, P. J. Shell, S. 2020-04-26 doi:10.1101/2020.04.26.062331 Cold Spring Harbor Laboratory Press 2020-04-26 <![CDATA[ Conserved Molecular Function and Regulatory Subfunctionalization of the LORELEI Gene Family in Brassicaceae ]]> https://biorxiv.org/content/10.1101/2020.04.27.062893v1?rss=1 Noble, J. A. Liu, M.-C. J. DeFalco, T. A. Stegmann, M. McNamara, K. Sullivan, B. Dinh, K. K. Khuu, N. Hancock, S. Shiu, S.-H. Zipfel, C. Beilstein, M. A. Cheung, A. Y. Palanivelu, R. 2020-04-29 doi:10.1101/2020.04.27.062893 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ Genomic and immunogenic changes over the history of the Viral Hemorrhagic Septicemia (VHS-IVb) fish virus (=Piscine novirhabdovirus) in the Laurentian Great Lakes ]]> https://biorxiv.org/content/10.1101/2020.04.27.063842v1?rss=1 32 fish species in large 2005 and 2006. Periods of apparent dormancy punctuated smaller outbreaks in 2007, 2008, and 2017. We conducted the first whole genome analysis of IVb, evaluating its evolutionary changes using 46 isolates, in reference to immunogenicity in cell culture, and the genomes of other VHS genogroups (I-IVa) and other Novirhabdoviruses. IVb isolates had 253 genomic nucleotide substitutions (2.3% of the total 11,158 nucleotides), with 85 (16.6%) being non-synonymous. The greatest number of substitutions occurred in the non-coding region (NCDS; 4.3%) followed by the Nv- (3.8%), and M- (2.8%) genes. The M-gene possessed the greatest proportions of amino acid changes (52.9%), followed by the Nv- (50.0%), G- (48.6%), N- (35.7%) and L- (23.1%) genes. Among VHS genogroups, IVa from the northeastern Pacific exhibited the fastest substitution rate (2.01x10-3), followed by Ivb (6.64x10-5), and I/III from Europe (4.09x10-5). A 2016 gizzard shad isolate from Lake Erie was the most divergent IVb isolate (38 NT, 15.0%, 15 AA), yet exhibited reduced virulence with in vitro immunogenicity analyses, as did other 2016 isolates, in comparison to the first IVb isolate (2003). The 2016 isolates exhibited lower impact on innate antiviral responses, suggesting phenotypic effects. Results suggest continued sequence change and lower virulence over the history of IVb, which may facilitate its long-term persistence in fish host populations. ]]> Stepien, C. A. Niner, M. D. Gorgoglione, B. Leaman, D. W. 2020-04-29 doi:10.1101/2020.04.27.063842 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ Remodeling of Chemotaxis is a Cornerstone of Bacterial Swarming ]]> https://biorxiv.org/content/10.1101/2020.04.27.064519v1?rss=1 Partridge, J. D. Nguyen, N. Q. Dufour, Y. S. Harshey, R. M. 2020-04-28 doi:10.1101/2020.04.27.064519 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Infanticide by females is a leading source of juvenile mortality in a large social carnivore ]]> https://biorxiv.org/content/10.1101/2020.05.02.074237v1?rss=1 Brown, A. K. Holekamp, K. Strauss, E. D. 2020-05-02 doi:10.1101/2020.05.02.074237 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ One gene, multiple ecological strategies: a biofilm regulator is a capacitor for sustainable diversity ]]> https://biorxiv.org/content/10.1101/2020.05.02.074534v1?rss=1 20,000 generations with Burkholderia cenocepacia populations grown in a model of the biofilm life cycle and identified parallel mutations in one gene, rpfR, that is a conserved central regulator. Because RpfR has multiple sensor and catalytic domains, different mutations can produce different ecological strategies that can coexist and even increase net growth. This study demonstrates that a single gene may coordinate complex life histories in biofilm-dwelling bacteria and that selection in defined environments can reshape niche breadth by single mutations. ]]> Mhatre, E. R. Snyder, D. J. Sileo, E. Turner, C. B. Buskirk, S. W. Fernandez, N. L. Neiditch, M. B. Waters, C. M. Cooper, V. S. 2020-05-03 doi:10.1101/2020.05.02.074534 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ Hypotheses and models linking epigenetic transgenerational effects to population dynamics: Exploring oscillations and applications to wildlife cycles ]]> https://biorxiv.org/content/10.1101/2020.05.05.079129v1?rss=1 Juckett, D. A. 2020-05-07 doi:10.1101/2020.05.05.079129 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ The shapes of wine and table grape leaves: an ampelometric study inspired by the methods of Pierre Galet ]]> https://biorxiv.org/content/10.1101/2020.05.08.085175v1?rss=1 Chitwood, D. H. 2020-05-10 doi:10.1101/2020.05.08.085175 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Identifying a supramodal language network in human brain with individual fingerprint ]]> https://biorxiv.org/content/10.1101/2020.05.10.085787v1?rss=1 Liu, L. Yan, X. Li, H. Gao, D. Ding, G. 2020-05-12 doi:10.1101/2020.05.10.085787 Cold Spring Harbor Laboratory Press 2020-05-12 <![CDATA[ Metabolomic signatures of coral bleaching history ]]> https://biorxiv.org/content/10.1101/2020.05.10.087072v1?rss=1 Roach, T. N. F. Dilworth, J. Martin H., C. Jones, A. D. Quinn, R. A. Drury, C. 2020-05-11 doi:10.1101/2020.05.10.087072 Cold Spring Harbor Laboratory Press 2020-05-11 <![CDATA[ Homogeneity among glyphosate-resistant Amaranthus palmeri in geographically distant locations ]]> https://biorxiv.org/content/10.1101/2020.05.14.095729v1?rss=1 Molin, W. Patterson, E. L. Saski, C. A. 2020-05-14 doi:10.1101/2020.05.14.095729 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ The effect of vascular health factors on white matter microstructure mediates age-related differences in executive function performance ]]> https://biorxiv.org/content/10.1101/2020.05.14.096677v1?rss=1 Hoagey, D. A. Lazarus, L. T. T. Rodrigue, K. M. Kennedy, K. M. 2020-05-16 doi:10.1101/2020.05.14.096677 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ SARS-CoV2 (COVID-19) Structural/Evolution Dynamicome: Insights into functional evolution and human genomics. ]]> https://biorxiv.org/content/10.1101/2020.05.15.098616v1?rss=1 Gupta, R. Charron, J. Stenger, C. Painter, J. Steward, H. Cook, T. Faber, W. Frisch, A. Lind, E. Bauss, J. Li, X. Sirpilla, O. Soehnlen, X. Underwood, A. Hinds, D. Morris, M. Lamb, N. Carcillo, J. Bupp, C. Uhal, B. Rajasekaran, S. Prokop, J. W. 2020-05-15 doi:10.1101/2020.05.15.098616 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Co-expression signatures of combinatorial gene regulation ]]> https://biorxiv.org/content/10.1101/2020.05.19.104935v1?rss=1 Gomez-Cano, F. Qian, X. Shiu, S.-H. Krishnan, A. Grotewold, E. 2020-05-22 doi:10.1101/2020.05.19.104935 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Vein-to-blade ratio is an allometric indicator of climate-induced changes in grapevine leaf size and shape ]]> https://biorxiv.org/content/10.1101/2020.05.20.106906v1?rss=1 Chitwood, D. H. Mullins, J. Migicovsky, Z. Frank, M. VanBuren, R. Londo, J. P. 2020-05-22 doi:10.1101/2020.05.20.106906 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Rapture-ready darters: sequence capture outperforms whole genome data regardless of reference genome in Etheostoma ]]> https://biorxiv.org/content/10.1101/2020.05.21.108274v1?rss=1 Reid, B. N. Moran, R. L. Kopack, C. J. Fitzpatrick, S. W. 2020-05-21 doi:10.1101/2020.05.21.108274 Cold Spring Harbor Laboratory Press 2020-05-21 <![CDATA[ A Simple Test to Infer Mode of Selection in Metagenomics Time Series of Evolving Asexual Populations ]]> https://biorxiv.org/content/10.1101/2020.05.23.112508v1?rss=1 Maddamsetti, R. Grant, N. A. 2020-05-26 doi:10.1101/2020.05.23.112508 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Using Genome-Wide Association Study to Identify Genes and Pathways associated with Hypersensitivity Pneumonitis ]]> https://biorxiv.org/content/10.1101/2020.05.27.118539v1?rss=1 Wang, L. Millerick, M. M. Rosenman, K. D. Cui, Y. Uhal, B. Wang, J. Gerlach, J. 2020-05-27 doi:10.1101/2020.05.27.118539 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ Dual thermal ecotypes detected within a nearly genetically-identical population of the unicellular marine cyanobacterium Synechococcus ]]> https://biorxiv.org/content/10.1101/2020.05.27.119842v1?rss=1 99.9%, with 98.6-100% of the genome aligning), thermal performance curves revealed selection at warm and cool temperatures had subdivided the initial population into thermotypes with pronounced differences in maximum growth temperatures. Within the fine-scale genetic diversity that did exist within this population, the two divergent thermal ecotypes differed at a locus containing genes for the phycobilisome antenna complex. Our study demonstrates that present-day marine microbial populations can contain microdiversity in the form of cryptic but environmentally-relevant thermotypes that may increase their resilience to future rising temperatures. SignificanceNumerous studies exist comparing the responses of distinct taxonomic groups of marine microbes to a warming ocean (interspecific thermal diversity). For example, Synechococcus, a nearly globally distributed unicellular marine picocyanobacterium that makes significant contributions to oceanic primary productivity, contains numerous taxonomically distinct lineages with well documented temperature relationships. Little is known though about the diversity of functional responses to temperature within a given population where genetic similarity is high (intraspecific thermal diversity). This study suggests that understanding the extent of this functional intraspecific microdiversity is an essential prerequisite to predicting the resilience of biogeochemically essential microbial groups such as marine Synechococcus to a changing climate. ]]> Kling, J. Lee, M. D. Webb, E. A. Coelho, J. T. Wilburn, P. Anderson, S. I. Zhou, Q. Wang, C. Phan, M. D. Kremer, C. T. Litchman, E. Rynearson, T. A. Hutchins, D. A. 2020-05-27 doi:10.1101/2020.05.27.119842 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ Functional Characterization of fer-ts, a ts- FERONIA Mutant Allele That Alters Root Hair Growth ]]> https://biorxiv.org/content/10.1101/2020.05.27.119891v1?rss=1 Kim, D. Gu, F. Park, S. Combs, J. Adams, A. Mayes, H. B. Nielsen, E. 2020-05-30 doi:10.1101/2020.05.27.119891 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ UDP-Glucose 6-Dehydrogenase Knockout Impairs Migration and Decreases in vivo Metastatic Ability of Breast Cancer Cells ]]> https://biorxiv.org/content/10.1101/2020.05.30.125419v1?rss=1 Teoh, S. T. Ogrodzinski, M. P. Lunt, S. 2020-05-31 doi:10.1101/2020.05.30.125419 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Switchgrass metabolomics reveals striking genotypic and developmental differences in saponins ]]> https://biorxiv.org/content/10.1101/2020.06.01.127720v1?rss=1 Last, R. L. Jones, A. D. Li, X. 2020-06-01 doi:10.1101/2020.06.01.127720 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ A human TSC1 mutation screening platform in GABAergic cortical interneurons for Genotype to Phenotype assessments ]]> https://biorxiv.org/content/10.1101/2020.06.01.128611v1?rss=1 Wundrach, D. Martinetti, L. E. Stafford, A. M. Bilinovich, S. M. Angara, K. Crandall, S. R. Vogt, D. 2020-06-02 doi:10.1101/2020.06.01.128611 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ Maintenance of metabolic plasticity despite relaxed selection in a long-term evolution experiment with Escherichia coli ]]> https://biorxiv.org/content/10.1101/2020.06.02.130138v1?rss=1 30 years in the presence of oxygen, with relaxed selection for anaerobic growth and the associated metabolic plasticity. We asked whether evolution led to the loss, improvement, or maintenance of anaerobic growth, and we analyzed gene expression and mutational datasets to understand the outcomes. We identified genomic signatures of both positive and purifying selection on aerobic-specific genes, while anaerobic-specific genes showed clear evidence of relaxed selection. We also found parallel evolution at two interacting loci that regulate anaerobic growth. We competed the ancestor and evolved clones from each population in an anoxic environment, and we found that anaerobic fitness had not decayed, despite relaxed selection. In summary, relaxed section does not necessarily reduce an organisms fitness in other environments. Instead, the genetic architecture of the traits under relaxed selection and their correlations with traits under positive and purifying selection may sometimes determine evolutionary outcomes. ]]> Grant, N. A. Maddamsetti, R. Lenski, R. E. 2020-06-03 doi:10.1101/2020.06.02.130138 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Divergent evolution of mutation rates and biases in the long-term evolution experiment with Escherichia coli ]]> https://biorxiv.org/content/10.1101/2020.06.02.130906v1?rss=1 Maddamsetti, R. Grant, N. 2020-06-03 doi:10.1101/2020.06.02.130906 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Wistar rats and C57BL/6J mice differ in their motivation to seek social interaction versus food in the Social versus Food Preference Test ]]> https://biorxiv.org/content/10.1101/2020.06.04.134437v1?rss=1 View larger version (13K): org.highwire.dtl.DTLVardef@1b23f85org.highwire.dtl.DTLVardef@168732eorg.highwire.dtl.DTLVardef@61e431org.highwire.dtl.DTLVardef@cc848e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Reppucci, C. J. Brown, L. A. Chambers, A. Q. Veenema, A. H. 2020-06-05 doi:10.1101/2020.06.04.134437 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Abiotic treatment contributes to an alteration of the seed microbiome of common bean ]]> https://biorxiv.org/content/10.1101/2020.06.05.134445v1?rss=1 Bintarti, A. F. Kearns, P. J. Sulesky, A. Shade, A. 2020-06-05 doi:10.1101/2020.06.05.134445 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Exometabolite dynamics over stationary phase reveal strain-specific responses to nutrient limitation ]]> https://biorxiv.org/content/10.1101/2020.06.05.137489v1?rss=1 Chodkowski, J. L. Shade, A. 2020-06-06 doi:10.1101/2020.06.05.137489 Cold Spring Harbor Laboratory Press 2020-06-06 <![CDATA[ Multi-model evaluation of phenology prediction for wheat in Australia ]]> https://biorxiv.org/content/10.1101/2020.06.06.133504v1?rss=1 Wallach, D. Palosuo, T. Thorburn, P. Hochman, Z. Andrianasolo, F. Asseng, S. Basso, B. Buis, S. Crout, N. Dumont, B. Ferrise, R. Gaiser, T. Gayler, S. Hiremath, S. Hoek, S. Horan, H. Hoogenboom, G. Huang, M. Jabloun, M. Jansson, P.-E. Jing, Q. Justes, E. Kersebaum, K. C. Launay, M. Lewan, E. Luo, Q. Maestrini, B. Moriondo, M. Padovan, G. Olesen, J. E. Poyda, A. Priesack, E. Pullens, J. W. M. Qian, B. Schütze, N. Shelia, V. Souissi, A. Specka, X. Srivastava, A. K. Stella, T. Streck, T. Trombi, G. Wallor, E. Wang, J. Weber, T. K. D. Weihermüller, L. 2020-06-06 doi:10.1101/2020.06.06.133504 Cold Spring Harbor Laboratory Press 2020-06-06 <![CDATA[ How understudied populations have contributed to our understanding of Alzheimer's disease genetics ]]> https://biorxiv.org/content/10.1101/2020.06.11.146993v1?rss=1 Dehghani, N. Bras, J. Guerreiro, R. 2020-06-12 doi:10.1101/2020.06.11.146993 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ A temporal map of maternal immune activation-induced changes reveals a shift in neurodevelopmental timing and perturbed cortical development in mice. ]]> https://biorxiv.org/content/10.1101/2020.06.13.150359v1?rss=1 Canales, C. P. Estes, M. L. Cichewicz, K. Angara, K. Aboubechara, J. P. Cameron, S. Prendergast, K. Su-Feher, L. P. Zdilar, I. Kreun, E. J. Connolly, E. C. Seo, J. M. Goon, J. B. Farrelly, K. Stradleigh, T. van der List, D. Haapanen, L. Van de Water, J. Vogt, D. McAllister, A. K. Nord, A. S. 2020-06-14 doi:10.1101/2020.06.13.150359 Cold Spring Harbor Laboratory Press 2020-06-14 <![CDATA[ Surprising amount of stasis in repetitive genome content across the Brassicales ]]> https://biorxiv.org/content/10.1101/2020.06.15.153296v1?rss=1 Beric, A. Mabry, M. E. Harkess, A. E. Schranz, M. E. Conant, G. C. Edger, P. P. Meyers, B. C. Pires, J. C. 2020-06-15 doi:10.1101/2020.06.15.153296 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Estrogen withdrawal alters oxytocin signaling in the paraventricular hypothalamus and dorsal raphe nucleus to increase postpartum anxiety ]]> https://biorxiv.org/content/10.1101/2020.06.16.154492v1?rss=1 Hedges, V. L. Heaton, E. C. Amaral, C. Benedetto, L. E. Bodie, C. L. D'Antonio, B. I. Davila Portillo, D. R. Lee, R. H. Levine, M. T. O'Sullivan, E. C. Pisch, N. P. Taveras, S. Wild, H. R. Ross, A. P. Albers, H. E. Been, L. E. 2020-06-17 doi:10.1101/2020.06.16.154492 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ Aerobic metabolism in Vibrio cholerae is required for population expansion during infection ]]> https://biorxiv.org/content/10.1101/2020.06.16.155382v1?rss=1 Van Alst, A. J. DiRita, V. J. 2020-06-17 doi:10.1101/2020.06.16.155382 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ Longitudinal Saliva Omics Responses to Immune Perturbation: A Case Study ]]> https://biorxiv.org/content/10.1101/2020.06.16.156133v1?rss=1 Mias, G. I. Singh, V. V. Rogers, L. R. Xue, S. Zheng, M. Domanskyi, S. Kanada, M. Piermarocchi, C. He, J. 2020-06-18 doi:10.1101/2020.06.16.156133 Cold Spring Harbor Laboratory Press 2020-06-18 <![CDATA[ Environmental and physiological factors affecting high-throughput measurements of bacterial growth ]]> https://biorxiv.org/content/10.1101/2020.06.16.156182v1?rss=1 Atolia, E. Cesar, S. Arjes, H. Rajendram, M. Shi, H. Knapp, B. Khare, S. Aranda-Diaz, A. Lenski, R. Huang, K. C. 2020-06-18 doi:10.1101/2020.06.16.156182 Cold Spring Harbor Laboratory Press 2020-06-18 <![CDATA[ The genomics of trait combinations and their influence on adaptive divergence ]]> https://biorxiv.org/content/10.1101/2020.06.19.161539v1?rss=1 Calvert, M. B. Doellman, M. M. Feder, J. L. Hood, G. R. Meyers, P. Egan, S. P. Powell, T. H. Q. Glover, M. Tait, C. Schuler, H. Berlocher, S. Smith, J. J. Nosil, P. Hahn, D. A. Ragland, G. J. 2020-06-20 doi:10.1101/2020.06.19.161539 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Contribution of different host plants to the adult population of western bean cutworm ]]> https://biorxiv.org/content/10.1101/2020.06.19.162016v1?rss=1 Bunn, D. C. Dias de Oliveira, E. Springborn, F. Gonzalez-Meler, M. A. Miller, N. J. 2020-06-20 doi:10.1101/2020.06.19.162016 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Life history scaling and the division of energy in forests ]]> https://biorxiv.org/content/10.1101/2020.06.22.163659v1?rss=1 114,000 woody plants in a tropical, old growth forest to test and predict patterns of niche partitioning with size and light. Consistent with predictions, the relative abundance, production, light capture, and richness of species in life histories with fast growth follow a power law relationship, increasing 1-2 orders of magnitude along a solar and size gradient. Competitive neutrality between size classes emerges above the sapling layer, where increasing access to light is counterbalanced by stronger self-shading. Convergent power law patterns of resource partitioning across taxa and spatial scale suggest general life history tradeoffs drive the organization of diverse communities. ]]> Grady, J. M. Read, Q. D. Record, S. Ruger, N. Zarnetske, P. L. Dell, A. I. Hubbell, S. P. Michaletz, S. T. Shenkin, A. Enquist, B. J. 2020-06-23 doi:10.1101/2020.06.22.163659 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ Composite modeling of leaf shape across shoots discriminates Vitis species better than individual leaves ]]> https://biorxiv.org/content/10.1101/2020.06.22.163899v1?rss=1 Bryson, A. E. Wilson Brown, M. Mullins, J. Dong, W. Bahmani, K. Bornowski, N. Chiu, C. Engelgau, P. Gettings, B. Gomezcano, F. Gregory, L. M. Haber, A. C. Hoh, D. Jennings, E. E. Ji, Z. Kaur, P. Kenchanmane Raju, S. K. Long, Y. Lotreck, S. G. Mathieu, D. T. Ranaweera, T. Ritter, E. J. Sadohara, R. Shrote, R. Z. Smith, K. E. Teresi, S. J. Venegas, J. Wang, H. Wilson, M. L. Tarrant, A. R. Frank, M. H. Migicovsky, Z. Kumar, J. VanBuren, R. Londo, J. P. Chitwood, D. H. 2020-06-23 doi:10.1101/2020.06.22.163899 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ Response of Regulatory Genetic Variation in Gene Expression to Environmental Change in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2020.06.23.163501v1?rss=1 Huang, W. Carbone, M. A. Lyman, R. F. Anholt, R. H. Mackay, T. F. 2020-06-23 doi:10.1101/2020.06.23.163501 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ Proto-sex locus in large yellow croaker provides insights into early evolution of the sex chromosome ]]> https://biorxiv.org/content/10.1101/2020.06.23.166249v1?rss=1 Wang, Z. Xiao, S. Cai, M. Han, Z. Li, W. Xie, Y. Xu, G. Lin, A. Zhang, Y. Ye, K. Luo, H. Liao, M. Han, F. Liu, X. Zhang, D. Wang, Q. Wang, B. Li, W. Li, J.-T. 2020-06-24 doi:10.1101/2020.06.23.166249 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Genetic and Genomic Resources to Study Natural Variation in Brassica rapa ]]> https://biorxiv.org/content/10.1101/2020.06.23.167270v1?rss=1 Lou, P. Woody, S. Greenham, K. vanBuren, R. Colle, M. Edger, P. P. Sartor, R. Zheng, Y. Levendoski, N. Lim, J. So, C. Stoveken, B. J. Woody, T. Zhao, J. Shen, S. Amasino, R. M. McClung, C. R. 2020-06-24 doi:10.1101/2020.06.23.167270 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ GENERATION OF HEART ORGANOIDS MODELING EARLY HUMAN CARDIAC DEVELOPMENT UNDER DEFINED CONDITIONS ]]> https://biorxiv.org/content/10.1101/2020.06.25.171611v1?rss=1 Israeli, Y. Gabalski, M. Ball, K. Wasserman, A. Zou, J. Ni, G. Zhou, C. Aguirre, A. 2020-06-26 doi:10.1101/2020.06.25.171611 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ The Evolution of Insect Metallothioneins ]]> https://biorxiv.org/content/10.1101/2020.06.25.172213v1?rss=1 Luo, M. Finet, C. Cong, H. Wei, H.-y. Chung, H. 2020-06-27 doi:10.1101/2020.06.25.172213 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ Pseudomonas aeruginosa uses c-di-GMP phosphodiesterases RmcA and MorA to regulate biofilm maintenance ]]> https://biorxiv.org/content/10.1101/2020.06.26.174680v1?rss=1 Katharios-Lanwermeyer, S. Whitfield, G. B. Howell, P. L. O'Toole, G. 2020-06-27 doi:10.1101/2020.06.26.174680 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ Unique Proteomes Implicate Functional Specialization across Heterocysts, Akinetes, and Vegetative Cells in Anabaena cylindrica ]]> https://biorxiv.org/content/10.1101/2020.06.29.176149v1?rss=1 Qiu, Y. Gu, L. Brozel, V. S. Whitten, D. Hildreth, M. Zhou, R. 2020-06-29 doi:10.1101/2020.06.29.176149 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Quorum sensing provides a molecular mechanism for evolution to tune and maintain investment in cooperation ]]> https://biorxiv.org/content/10.1101/2020.06.29.178467v1?rss=1 Bruger, E. L. Synder, D. J. Cooper, V. S. Waters, C. M. 2020-06-30 doi:10.1101/2020.06.29.178467 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ Leaf trichome distribution pattern in Arabidopsis reveals gene expression variation associated with environmental adaptation ]]> https://biorxiv.org/content/10.1101/2020.07.01.180794v1?rss=1 Morohashi, K. Okamoto, S. Negishi, K. Toyama, Y. Ushijima, T. 2020-07-02 doi:10.1101/2020.07.01.180794 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ MetaFunPrimer: primer design for targeting genes observed in metagenomes ]]> https://biorxiv.org/content/10.1101/2020.07.01.183509v1?rss=1 Liu, J. Villanueva, P. Choi, J. Gunturu, S. Ouyang, Y. Tiemann, L. Cole, J. R. Lee, J. Howe, A. 2020-07-02 doi:10.1101/2020.07.01.183509 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ An algorithm for quantifying and characterizing misleading trajectories in ecological processes ]]> https://biorxiv.org/content/10.1101/2020.07.07.192211v1?rss=1 Christie A. Bahlai Easton R. White Julia D. Perrone Sarah Cusser Kaitlin Stack Whitney 2020-07-08 doi:10.1101/2020.07.07.192211 Cold Spring Harbor Laboratory Press 2020-07-08 <![CDATA[ Reference data based insights expand understanding of human metabolomes ]]> https://biorxiv.org/content/10.1101/2020.07.08.194159v1?rss=1 Julia M Gauglitz Wout Bittremieux Candace L Williams Kelly C Weldon Morgan W Panitchpakdi Francesca Di Ottavio Christine M Aceves Elizabeth Brown Nicole C Sikora Alan K. Jarmusch Cameron Martino Anupriya Tripathi Erfan Sayyari Justin Shaffer Roxana Coras Fernando Vargas Lindsay DeRight Goldasich Tara Schwartz MacKenzie Bryant Gregory Humphrey Abigail J. Johnson Katharina Spengler Pedro Belda-Ferre Edgar Diaz Daniel McDonald Qiyun Zhu Dominic S. Nguyen Emmanuel O. Elijah Mingxun Wang Clarisse Marotz Kate E. Sprecher Daniela Vargas-Robles Dana Withrow Gail Ackerm 2020-07-11 doi:10.1101/2020.07.08.194159 Cold Spring Harbor Laboratory Press 2020-07-11 <![CDATA[ Activity throughout the lichen phylogeny indicates a focus on regulation of specialized metabolites ]]> https://biorxiv.org/content/10.1101/2020.07.09.195743v1?rss=1 Ludmila V. Roze Maris Laivenieks Kristi Gdanetz John E. Linz Alan M. Fryday Frances Trail 2020-07-09 doi:10.1101/2020.07.09.195743 Cold Spring Harbor Laboratory Press 2020-07-09 <![CDATA[ The phytobiomes of a three-crop rotation: Influence of land management, host, and plant organ on microbial diversity ]]> https://biorxiv.org/content/10.1101/2020.07.10.178426v1?rss=1 Kristi Gdanetz Zachary A Noel Frances Trail 2020-07-10 doi:10.1101/2020.07.10.178426 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Development of Magnetic Particle Imaging (MPI) for Cell Tracking and Detection ]]> https://biorxiv.org/content/10.1101/2020.07.12.197780v1?rss=1 Melo, K. P. Makela, A. V. Hamilton, A. M. Foster, P. J. 2020-07-13 doi:10.1101/2020.07.12.197780 Cold Spring Harbor Laboratory Press 2020-07-13 <![CDATA[ Eleven biosynthetic genes explain the majority of natural variation for carotenoid levels in maize grain ]]> https://biorxiv.org/content/10.1101/2020.07.15.203448v1?rss=1 Diepenbrock, C. H. Ilut, D. C. Magallanes-Lundback, M. Kandianis, C. B. Lipka, A. E. Bradbury, P. J. Holland, J. B. Hamilton, J. P. Wooldridge, E. Vaillancourt, B. Gongora-Castillo, E. Wallace, J. G. Cepela, J. Mateos-Hernandez, M. Owens, B. F. Tiede, T. Buckler, E. S. Rocheford, T. Buell, C. R. Gore, M. A. DellaPenna, D. 2020-07-15 doi:10.1101/2020.07.15.203448 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ Optimizing the use of gene expression data to predict metabolic pathway memberships with unsupervised and supervised machine learning ]]> https://biorxiv.org/content/10.1101/2020.07.15.204222v1?rss=1 600 expression values and similarity data combinations from tomato, three strategies for predicting membership in 85 pathways were explored: naive prediction (identifying pathways with the most similarly expressed genes), unsupervised and supervised learning. Optimal predictions for different pathways require distinct data combinations that, in some cases, are indicative of biological processes relevant to pathway functions. Naive prediction produced higher error rates compared with machine learning methods. In 52 pathways, unsupervised learning performed better than a supervised approach, which may be due to the limited availability of training data. Furthermore, using gene-to-pathway expression similarities led to prediction models that outperformed those based simply on gene expression levels. Our study highlights the need to extensively explore expression-based features and prediction strategies to maximize the accuracy of metabolic pathway membership assignment. We anticipate that the prediction framework outlined here can be applied to other species and also be used to improve plant pathway annotation. ]]> Wang, P. Moore, B. M. Uygun, S. Lehti-Shiu, M. D. Barry, C. Shiu, S.-H. 2020-07-16 doi:10.1101/2020.07.15.204222 Cold Spring Harbor Laboratory Press 2020-07-16 <![CDATA[ Modeling gene regulation in response to wounding: temporal variations, hormonal variations, and specialized metabolism pathways induced by wounding ]]> https://biorxiv.org/content/10.1101/2020.07.15.204313v1?rss=1 Moore, B. M. Lee, Y. S. Grotewold, E. Shiu, S.-H. 2020-07-16 doi:10.1101/2020.07.15.204313 Cold Spring Harbor Laboratory Press 2020-07-16 <![CDATA[ Digital Cell Sorter (DCS): a cell type identification, anomaly detection, and Hopfield landscapes toolkit for single-cell transcriptomics ]]> https://biorxiv.org/content/10.1101/2020.07.17.208710v1?rss=1 Domanskyi, S. Hakansson, A. Bertus, T. Paternostro, G. Piermarocchi, C. 2020-07-17 doi:10.1101/2020.07.17.208710 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Lactate promotes cardiomyocyte dedifferentiation through metabolic reprogramming ]]> https://biorxiv.org/content/10.1101/2020.07.21.213736v1?rss=1 Ordono, J. Perez-Amodio, S. Ball, K. Aguirre, A. Engel, E. 2020-07-21 doi:10.1101/2020.07.21.213736 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Flagellar perturbations activate adhesion through two distinct pathways in Caulobacter crescentus ]]> https://biorxiv.org/content/10.1101/2020.07.21.215269v1?rss=1 Hershey, D. M. Fiebig, A. Crosson, S. 2020-07-22 doi:10.1101/2020.07.21.215269 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ PecanPy: a fast, efficient, and parallelized Python implementation of node2vec ]]> https://biorxiv.org/content/10.1101/2020.07.23.218487v1?rss=1 Liu, R. Krishnan, A. 2020-07-24 doi:10.1101/2020.07.23.218487 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Mycobacterium tuberculosis evasion of Guanylate Binding Protein-mediated host defense in mice requires the ESX1 secretion system. ]]> https://biorxiv.org/content/10.1101/2020.07.27.223362v1?rss=1 Olive, A. J. Smith, C. M. Baer, C. E. Coers, J. Sassetti, C. M. 2020-07-27 doi:10.1101/2020.07.27.223362 Cold Spring Harbor Laboratory Press 2020-07-27 <![CDATA[ The genetic architecture and evolution of life history divergence among perennials in the Mimulus guttatus species complex ]]> https://biorxiv.org/content/10.1101/2020.07.28.225896v1?rss=1 Coughlan, J. M. Wilson Brown, M. Willis, J. H. 2020-07-29 doi:10.1101/2020.07.28.225896 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Polygenic Risk Score for Smoking is associated with Externalizing Psychopathology and Disinhibited Personality Traits but not Internalizing Psychopathology in Adolescence ]]> https://biorxiv.org/content/10.1101/2020.07.29.227405v1?rss=1 Hicks, B. M. Clark, D. A. Deak, J. D. Liu, M. Durbin, C. E. Schafer, J. D. Wilson, S. Iacono, W. G. McGue, M. Vrieze, S. 2020-07-30 doi:10.1101/2020.07.29.227405 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ Polygenic Risk Scores Predict the Development of Alcohol and Nicotine Use Problems from Adolescence through Young Adulthood ]]> https://biorxiv.org/content/10.1101/2020.07.29.227439v1?rss=1 Deak, J. D. Clark, D. A. Liu, M. Durbin, C. E. Iacono, W. G. McGue, M. Vrieze, S. I. Hicks, B. M. 2020-07-30 doi:10.1101/2020.07.29.227439 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ Local adaptation contributes to gene expression divergence in maize ]]> https://biorxiv.org/content/10.1101/2020.08.01.231217v1?rss=1 Blanc, J. Kremling, K. A. G. Buckler, E. S. Josephs, E. B. 2020-08-03 doi:10.1101/2020.08.01.231217 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ Vorinostat corrects cognitive and non-cognitive symptoms in a mouse model of fragile X syndrome ]]> https://biorxiv.org/content/10.1101/2020.08.05.238568v1?rss=1 Ding, Q. Wu, X. Li, X. Wang, H. 2020-08-06 doi:10.1101/2020.08.05.238568 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ Change in social rank and brain dopamine levels: findings from a novel pig model ]]> https://biorxiv.org/content/10.1101/2020.08.06.239780v1?rss=1 Cheng, H. Mohammed, A. M. Pease, A. P. Gehrke, J. Bohart, G. Burnett, R. Nader, M. A. Anthony, J. C. 2020-08-06 doi:10.1101/2020.08.06.239780 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ The Contributions of the Allopolyploid Parents of the Mesopolyploid Brassiceae are Evolutionarily Distinct but Functionally Compatible ]]> https://biorxiv.org/content/10.1101/2020.08.10.245258v1?rss=1 Hao, Y. Mabry, M. E. Edger, P. Freeling, M. Zheng, C. Jin, L. VanBuren, R. Colle, M. An, H. Abrahams, R. S. Qi, X. Barry, K. Daum, C. Shu, S. Schmutz, J. Sankoff, D. Barker, M. S. Lyons, E. Pires, J. C. Conant, G. C. 2020-08-12 doi:10.1101/2020.08.10.245258 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ A genome-wide screen in macrophages identifies new regulators of IFNγ-inducible MHCII that contribute to T cell activation ]]> https://biorxiv.org/content/10.1101/2020.08.12.248252v1?rss=1 Kiritsy, M. C. Ankley, L. M. Trombley, J. D. Huizinga, G. P. Lord, A. E. Orning, P. Elling, R. Fitzgerald, K. A. Olive, A. 2020-08-12 doi:10.1101/2020.08.12.248252 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Temporal instability of lake charr phenotypes: synchronicity of growth rates and morphology linked to environmental variables? ]]> https://biorxiv.org/content/10.1101/2020.08.13.249557v1?rss=1 Chavarie, L. Voelker, S. Hansen, M. Bronte, C. Muir, A. Zimmerman, M. Krueger, c. 2020-08-14 doi:10.1101/2020.08.13.249557 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues ]]> https://biorxiv.org/content/10.1101/2020.08.13.249870v1?rss=1 Halstead, M. M. Kern, C. Saelao, P. Wang, Y. Chanthavixay, G. Medrano, J. F. Van Eenennaam, A. L. Korf, I. Tuggle, C. K. Ernst, C. W. Zhou, H. ROSS, P. J. 2020-08-14 doi:10.1101/2020.08.13.249870 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Swimming direction of the Glass Catfish, Kryptopterus bicirrhis, is responsive to magnetic stimulation ]]> https://biorxiv.org/content/10.1101/2020.08.13.250035v1?rss=1 Hunt, R. D. Ashbaugh, R. C. Reimers, M. Udpa, L. Saldana De Jimenez, G. Moore, M. Gilad, A. A. Pelled, G. 2020-08-14 doi:10.1101/2020.08.13.250035 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Genome-wide predictions of genetic redundancy in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2020.08.13.250225v1?rss=1 Cusack, S. A. Wang, P. Moore, B. M. Meng, F. Conner, J. K. Krysan, P. J. Lehti-Shiu, M. D. Shiu, S.-H. 2020-08-14 doi:10.1101/2020.08.13.250225 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Changes in Cell Size and Shape During 50,000 Generations of Experimental Evolution with Escherichia coli ]]> https://biorxiv.org/content/10.1101/2020.08.13.250415v1?rss=1 Grant, N. A. Abdel Magid, A. Franklin, J. Dufour, Y. S. Lenski, R. 2020-08-14 doi:10.1101/2020.08.13.250415 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Developmentally regulated activation of defense allows for rapid inhibition of infectionin age-related resistance to Phytophthora capsici in cucumber fruit ]]> https://biorxiv.org/content/10.1101/2020.08.14.251603v1?rss=1 Mansfeld, B. N. Colle, M. Zhang, C. Lin, Y.-C. Grumet, R. 2020-08-14 doi:10.1101/2020.08.14.251603 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Structural defects caused by Acrodermatitis Enteropathica mutations in the extracellular domain account for mistrafficking and malfunction of ZIP4 ]]> https://biorxiv.org/content/10.1101/2020.08.16.253294v1?rss=1 Kuliyev, E. Zhang, C. Sui, D. Hu, J. 2020-08-18 doi:10.1101/2020.08.16.253294 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Transcriptional Profiling of Identified Neurons in Leech ]]> https://biorxiv.org/content/10.1101/2020.08.17.254631v1?rss=1 Heath-Heckman, E. Yoo, S. Winchell, C. Pellegrino, M. Angstadt, J. Lammardo, V. Bautista, D. M. de Miguel, F. F. Weisblat, D. A. 2020-08-19 doi:10.1101/2020.08.17.254631 Cold Spring Harbor Laboratory Press 2020-08-19 <![CDATA[ Associations of early social experience with offspring DNA methylation and later life stress phenotype ]]> https://biorxiv.org/content/10.1101/2020.08.17.254805v1?rss=1 Laubach, Z. M. Greenberg, J. R. Turner, J. W. Montgomery, T. Pioon, M. O. Smale, L. Cavalcante, R. Padmanabhan, K. R. Lalancette, C. vonHoldt, B. Faulk, C. D. Dolinoy, D. C. Holekamp, K. E. Perng, W. 2020-08-18 doi:10.1101/2020.08.17.254805 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Distinct roles of two RDL GABA-receptors in fipronil action in the diamondback moth (Plutella xylostella) ]]> https://biorxiv.org/content/10.1101/2020.08.17.255026v1?rss=1 Li, B. Wang, K. Chen, D. Yan, Y. Cai, X. Chen, H. Dong, K. Lin, F. Xu, H. 2020-08-19 doi:10.1101/2020.08.17.255026 Cold Spring Harbor Laboratory Press 2020-08-19 <![CDATA[ Genomic evolution of antibiotic resistance is contingent on genetic background following a long-term experiment with Escherichia coli ]]> https://biorxiv.org/content/10.1101/2020.08.19.258384v1?rss=1 Card, K. J. Thomas, M. D. Graves, J. L. Barrick, J. E. Lenski, R. E. 2020-08-20 doi:10.1101/2020.08.19.258384 Cold Spring Harbor Laboratory Press 2020-08-20 <![CDATA[ Host immunity increases Mycobacterium tuberculosis reliance on cytochrome bd oxidase ]]> https://biorxiv.org/content/10.1101/2020.08.21.260737v1?rss=1 Cai, Y. Jaecklein, E. Mackenzie, J. Papavinasasundaram, K. Olive, A. J. Chen, X. Steyn, A. J. C. Sassetti, C. M. 2020-08-21 doi:10.1101/2020.08.21.260737 Cold Spring Harbor Laboratory Press 2020-08-21 <![CDATA[ Enhancing c-MYC degradation via 20S proteasome activation induces in vivo anti-tumor efficacy ]]> https://biorxiv.org/content/10.1101/2020.08.24.265470v1?rss=1 Njomen, E. Lansdell, T. Vanecek, A. Benham, V. Bernard, M. Yang, Y.-T. Schall, P. Isaac, D. Alkharabsheh, O. Al-Janadi, A. Giletto, m. Elsworth, E. Taylor, C. Yang, T. Bailie, m. Bernard, J. Yuzbasiyan-Gurkan, V. Tepe, J. 2020-08-24 doi:10.1101/2020.08.24.265470 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ A unique view of SARS-CoV-2 through the lens of ORF8 protein ]]> https://biorxiv.org/content/10.1101/2020.08.25.267328v1?rss=1 Hassan, S. S. Ghosh, S. Attrish, D. Choudhury, P. P. Seyran, M. Pizzol, D. Adadi, P. Abd El Aziz, T. M. Soares, A. Kandimalla, R. Lundstrom, K. Tambuwala, M. Aljabali, A. A. Lal, A. Azad, G. K. Uversky, V. N. Sherchan, S. P. Baetas-da-Cruz, W. Uhal, B. Rezaei, N. Brufsky, A. 2020-08-26 doi:10.1101/2020.08.25.267328 Cold Spring Harbor Laboratory Press 2020-08-26 <![CDATA[ Toxoplasma gondii infections are associated with boldness towards lions in wild hyena hosts ]]> https://biorxiv.org/content/10.1101/2020.08.26.268805v1?rss=1 Gering, E. Laubach, Z. M. Weber, P. Hussey, G. S. Lehmann, K. D. S. Montgomery, T. M. Turner, J. W. Perng, W. Pioon, M. O. Holekamp, K. E. Getty, T. 2020-08-27 doi:10.1101/2020.08.26.268805 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ Efficient generation of endogenous protein reporters for mouse preimplantation embryos ]]> https://biorxiv.org/content/10.1101/2020.08.27.266627v1?rss=1 O'Hagan, D. Ralston, A. 2020-08-27 doi:10.1101/2020.08.27.266627 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ DNA methylation signatures of duplicate gene evolution in angiosperms ]]> https://biorxiv.org/content/10.1101/2020.08.31.275362v1?rss=1 Kenchanmane Raju, S. K. Ledford, S. M. Niederhuth, C. E. 2020-08-31 doi:10.1101/2020.08.31.275362 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Notable sequence homology of the ORF10 protein introspects the architecture of SARS-COV-2 ]]> https://biorxiv.org/content/10.1101/2020.09.06.284976v1?rss=1 Hassan, S. S. Attrish, D. Ghosh, S. Pal Choudhury, P. Uversky, V. N. Uhal, B. Lundstrom, K. Rezaei, N. Aljabali, A. A. A. Seyran, M. Pizzol, D. Adadi, P. Abd El-Aziz, T. M. Soares, A. Kandimalla, R. Tambuwala, M. Lal, A. Azad, G. K. P. Sherchan, S. Baetas-da-Cruz, W. Palu, G. Brufsky, A. 2020-09-06 doi:10.1101/2020.09.06.284976 Cold Spring Harbor Laboratory Press 2020-09-06 <![CDATA[ Hybrid Chemomechanical Promotion of PEDOT Adhesion onto Flexible Microelectrode Arrays for Chronic Neural Stimulation ]]> https://biorxiv.org/content/10.1101/2020.09.09.289405v1?rss=1 70x enhancement to the interfacial capacitive impedance. ]]> Mazaheri Kouhani, M. H. Istomin, A. Datta, P. Talbot, N. 2020-09-10 doi:10.1101/2020.09.09.289405 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Migration through a major Andean ecogeographic disruption as a driver of genotypic and phenotypic diversity in a wild tomato species ]]> https://biorxiv.org/content/10.1101/2020.09.09.289744v1?rss=1 Landis, J. B. Miller, C. M. Broz, A. K. Bennett, A. A. Carrasquilla-Garcia, N. Cook, D. R. Last, R. L. Bedinger, P. A. Moghe, G. D. 2020-09-10 doi:10.1101/2020.09.09.289744 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Idiosyncratic variation in the fitness costs of tetracycline-resistance mutations in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2020.09.12.294355v1?rss=1 Card, K. J. Jordan, J. A. Lenski, R. E. 2020-09-12 doi:10.1101/2020.09.12.294355 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ The chaos in calibrating crop models ]]> https://biorxiv.org/content/10.1101/2020.09.12.294744v1?rss=1 Wallach, D. Palosuo, T. Thorburn, P. Hochman, Z. Gourdain, E. Andrianasolo, F. Asseng, S. Basso, B. Buis, S. Crout, N. Dibari, C. Dumont, B. Ferrise, R. Gaiser, T. Garcia, C. Gayler, S. Ghahramani, A. Hiremath, S. Hoek, S. Horan, H. Hoogenboom, G. Huang, M. Jabloun, M. Jansson, P.-E. Jing, Q. Justes, E. Kersebaum, K. C. Klosterhalfen, A. Launay, M. Lewan, E. Luo, Q. Maestrini, B. Mielenz, H. Moriondo, M. Nariman Zadeh, H. Padovan, G. Olesen, J. E. Poyda, A. Priesack, E. Pullens, J. W. M. Qian, B. Schuetze, N. Shelia, V. Souissi, A. Specka, X. Srivas 2020-09-14 doi:10.1101/2020.09.12.294744 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ Functional assessment of the "two-hit" model for neurodevelopmental defects in Drosophila and X. laevis ]]> https://biorxiv.org/content/10.1101/2020.09.14.295923v1?rss=1 Lucilla, P. Lasser, M. Yusuff, T. Jensen, M. Ingraham, P. Huber, E. Singh, M. D. Monahan, C. Iyer, J. Desai, I. Karthikeyan, S. Gould, D. J. Yennawar, S. Weiner, A. T. Krishnan, A. Rolls, M. Lowery, L. A. Girirajan, S. 2020-09-14 doi:10.1101/2020.09.14.295923 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.) ]]> https://biorxiv.org/content/10.1101/2020.09.15.298315v1?rss=1 McGrath, J. M. Funk, A. Galewski, P. Ou, S. Townsend, B. J. Davenport, K. Daligault, H. Johnson, S. Lee, J. Hastie, A. R. Darracq, A. Willems, G. Barnes, S. Liachko, I. Sullivan, S. Koren, S. Phillippy, A. Wang, J. Liu, T. Pulman, J. A. Childs, K. Yocum, A. Fermin, D. Mutasa-Gottgens, E. Stevanato, P. Taguchi, K. Dorn, K. 2020-09-16 doi:10.1101/2020.09.15.298315 Cold Spring Harbor Laboratory Press 2020-09-16 <![CDATA[ A Constrained Mixture Theory Model to Study Autoregulation in the Coronary Circulation ]]> https://biorxiv.org/content/10.1101/2020.09.21.304030v1?rss=1 Gharahi, H. Beard, D. A. Figueroa, C. A. Baek, S. 2020-09-22 doi:10.1101/2020.09.21.304030 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Environmental influences and individual characteristics that affect learner-centered teaching practices ]]> https://biorxiv.org/content/10.1101/2020.09.21.306407v1?rss=1 Emery, N. Maher, J. M. Ebert-May, D. 2020-09-22 doi:10.1101/2020.09.21.306407 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Robust normalization and transformation techniques for constructing gene coexpression networks from RNA-seq data ]]> https://biorxiv.org/content/10.1101/2020.09.22.308577v1?rss=1 Johnson, K. A. Krishnan, A. 2020-09-23 doi:10.1101/2020.09.22.308577 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ INTEGRINS MEDIATE PLACENTAL EXTRACELLULAR VESICLE TRAFFICKING TO LUNG AND LIVER IN VIVO ]]> https://biorxiv.org/content/10.1101/2020.09.22.309047v1?rss=1 Nguyen, S. L. Ahn, S. H. Greenberg, J. Collaer, B. Agnew, D. Arora, R. Petroff, M. 2020-09-23 doi:10.1101/2020.09.22.309047 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scales ]]> https://biorxiv.org/content/10.1101/2020.09.23.299727v1?rss=1 Rojas, C. A. Ramirez-Barahona, S. Holekamp, K. E. Theis, K. R. 2020-09-24 doi:10.1101/2020.09.23.299727 Cold Spring Harbor Laboratory Press 2020-09-24 <![CDATA[ Endometrial epithelial ARID1A is critical for uterine gland function in early pregnancy establishment ]]> https://biorxiv.org/content/10.1101/2020.09.23.308528v1?rss=1 Marquardt, R. Kim, T.-H. Yoo, J.-Y. Teasley, H. E. Fazleabas, A. T. Young, S. L. Lessey, B. A. Arora, R. Jeong, J.-W. 2020-09-24 doi:10.1101/2020.09.23.308528 Cold Spring Harbor Laboratory Press 2020-09-24 <![CDATA[ Phage-shock-protein (Psp) Envelope Stress Response: Evolutionary History and Discovery of Novel Players ]]> https://biorxiv.org/content/10.1101/2020.09.24.301986v1?rss=1 Ravi, J. Anantharaman, V. Chen, S. Z. Datta, P. Aravind, L. Gennaro, M. L. 2020-09-25 doi:10.1101/2020.09.24.301986 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Oxicam-type nonsteroidal anti-inflammatory drugs inhibit NPR1-mediated salicylic acid pathway ]]> https://biorxiv.org/content/10.1101/2020.09.25.311100v1?rss=1 Ishihama, N. Choi, S.-w. Noutoshi, Y. Saska, I. Asai, S. Takizawa, K. He, S.-Y. Osada, H. Shirasu, K. 2020-09-25 doi:10.1101/2020.09.25.311100 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Adaptive and maladaptive expression plasticity underlying herbicide resistance in an agricultural weed. ]]> https://biorxiv.org/content/10.1101/2020.09.25.313650v1?rss=1 Josephs, E. Van Etten, M. Harkess, A. Platts, A. Baucom, R. 2020-09-25 doi:10.1101/2020.09.25.313650 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Gut microbiome dysbiosis is associated with elevated toxic bile acids in Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2020.09.26.279851v1?rss=1 Li, P. Killinger, B. A. Beddows, I. Ensink, E. Yilmaz, A. Lubben, N. Lamp, J. Schilthuis, M. Vega, I. E. Britschgi, M. Pospisilik, A. J. Brundin, P. Brundin, L. Graham, S. Labrie, V. 2020-09-28 doi:10.1101/2020.09.26.279851 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ Gut metabolites are more predictive of disease- and cohoused- states than gut bacterial features in a mouse model of polycystic ovary syndrome ]]> https://biorxiv.org/content/10.1101/2020.10.01.322701v1?rss=1 Ho, B. Ryback, D. Benson, B. Torres, P. J. Quinn, R. A. Thackray, V. G. Kelley, S. T. 2020-10-01 doi:10.1101/2020.10.01.322701 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Opportunities and limits of combining microbiome and genome data for complex trait prediction ]]> https://biorxiv.org/content/10.1101/2020.10.05.325977v1?rss=1 Perez-Enciso, M. Zingaretti, L. M. Ramayo-Caldas, Y. de los Campos, G. 2020-10-05 doi:10.1101/2020.10.05.325977 Cold Spring Harbor Laboratory Press 2020-10-05 <![CDATA[ Functional Characterization of an Electromagnetic Perceptive Protein ]]> https://biorxiv.org/content/10.1101/2020.10.07.329946v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@1ce4aborg.highwire.dtl.DTLVardef@e8bb89org.highwire.dtl.DTLVardef@1705113org.highwire.dtl.DTLVardef@dadf23_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Mitra, S. Barnaba, C. Schmidt, J. C. Pelled, G. Gilad, A. A. 2020-10-07 doi:10.1101/2020.10.07.329946 Cold Spring Harbor Laboratory Press 2020-10-07 <![CDATA[ Possible transmission flow of SARS-CoV-2 based on ACE2 features ]]> https://biorxiv.org/content/10.1101/2020.10.08.332452v1?rss=1 Hassan, S. S. Ghosh, S. Attrish, D. Pal Choudhury, P. Uversky, V. N. Uhal, B. Lundstrom, K. Rezaei, N. Aljabali, A. A. A. Seyran, M. Pizzol, D. Adadi, P. Soares, A. Abd El-Aziz, T. M. Kandimalla, R. Tambuwala, M. Azad, G. K. Sherchan, S. P. Baetas-da-Cruz, W. Takayama, K. Serrano-Aroca, A. Chauhan, G. Palu, G. Brufsky, A. 2020-10-09 doi:10.1101/2020.10.08.332452 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Practice modifies the response to errors during a novel motor sequence learning task ]]> https://biorxiv.org/content/10.1101/2020.10.09.334169v1?rss=1 Rachaveti, D. Ranganathan, R. SKM, V. 2020-10-10 doi:10.1101/2020.10.09.334169 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation ]]> https://biorxiv.org/content/10.1101/2020.10.14.339960v1?rss=1 Arthurs, C. J. Khlebnikov, R. Melville, A. Mar?an, M. Gomez, A. Dillon-Murphy, D. Cuomo, F. Silva Vieira, M. Schollenberger, J. Lynch, S. R. Tossas-Betancourt, C. Iyer, K. Hopper, S. Livingston, E. Youssefi, P. Noorani, A. Ben Ahmed, S. Nauta, F. J. H. van Bakel, T. M. J. Ahmed, Y. van Bakel, P. A. J. Mynard, J. Di Achille, P. Gharahi, H. Lau, K. D. Filonova, V. Aguirre, M. Nama, N. Xiao, N. Baek, S. Garikipati, K. Sahni, O. Nordsletten, D. Figueroa, C. A. 2020-10-15 doi:10.1101/2020.10.14.339960 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Signature of selection in composite Vrindavani cattle of India ]]> https://biorxiv.org/content/10.1101/2020.10.19.344747v1?rss=1 Singh, A. Mehrotra, A. Gondro, C. Romero, A. R. Pandey, A. K. A, K. Bashir, A. Mishra, B. P. Dutt, T. KUMAR, A. 2020-10-21 doi:10.1101/2020.10.19.344747 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Motor variability prior to learning is a poor predictor of the ability to adopt new movement solutions ]]> https://biorxiv.org/content/10.1101/2020.10.23.350819v1?rss=1 Ranganathan, R. Lin, M. Carey, S. Lokesh, R. Lee, M.-H. Krishnan, C. 2020-10-23 doi:10.1101/2020.10.23.350819 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ Responses of Neurons in the Medullary Lateral Tegmental Field and Nucleus Tractus Solitarius to Vestibular Stimuli in Conscious Felines ]]> https://biorxiv.org/content/10.1101/2020.10.23.352542v1?rss=1 Bielanin, J. P. Douglas, N. O. Shulgach, J. A. McCall, A. A. Miller, D. M. Amin, P. R. Murphey, C. P. Barman, S. M. Yates, B. J. 2020-10-25 doi:10.1101/2020.10.23.352542 Cold Spring Harbor Laboratory Press 2020-10-25 <![CDATA[ Alignment-free methods for polyploid genomes: quick and reliable genetic distance estimation ]]> https://biorxiv.org/content/10.1101/2020.10.23.352963v1?rss=1 VanWallendael, A. Alvarez, M. 2020-10-25 doi:10.1101/2020.10.23.352963 Cold Spring Harbor Laboratory Press 2020-10-25 <![CDATA[ Loss of a plant receptor kinase recruits beneficial rhizosphere-associated Pseudomonas ]]> https://biorxiv.org/content/10.1101/2020.11.02.364109v1?rss=1 Song, Y. Wilson, A. J. Zhang, X.-C. Thoms, D. Sohrabi, R. Song, S. Geissmann, Q. Liu, Y. Walgren, L. He, S. Y. Haney, C. H. 2020-11-02 doi:10.1101/2020.11.02.364109 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ Variability of Accessory Proteins Rules the SARS-CoV-2 Pathogenicity ]]> https://biorxiv.org/content/10.1101/2020.11.06.372227v1?rss=1 ORF8>ORF7a>ORF6>ORF10>ORF7b. The highest and lowest unique variations of ORF3a were observed in South America and Oceania, respectively. This finding suggests that the wide variations of accessory proteins seem to govern the pathogenicity of SARS-CoV-2, and consequently, certain propositions and recommendations can be made in the public interest. ]]> Hassan, S. S. Pal Choudhury, P. Uversky, V. N. Dayhoff, G. W. Aljabali, A. A. A. Uhal, B. Lundstrom, K. Rezaei, N. Seyran, M. Pizzol, D. Adadi, P. Lal, A. Soares, A. Abd El-Aziz, T. M. Kandimalla, R. Tambuwala, M. Azad, G. K. Sherchan, S. P. Baetas-da-Cruz, W. Takayama, K. Serrano Aroca, A. Chauhan, G. Palu, G. Brufsky, A. 2020-11-08 doi:10.1101/2020.11.06.372227 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ Multi-session delivery of synchronous rTMS and sensory stimulation induces long-term plasticity ]]> https://biorxiv.org/content/10.1101/2020.11.08.373241v1?rss=1 Zhong, M. Cywiak, C. Metto, A. C. Liu, X. Qian, C. Pelled, G. 2020-11-09 doi:10.1101/2020.11.08.373241 Cold Spring Harbor Laboratory Press 2020-11-09 <![CDATA[ Neuromesodermal Progenitors Advance Network Formation of Spinal Neurons and Support Cells in Neural Ribbons In Vitro and Unprotected Survival in a Rat Subacute Contusion Model ]]> https://biorxiv.org/content/10.1101/2020.11.10.374876v1?rss=1 Olmsted, Z. T. Stigliano, C. Scimemi, A. Marzullo, B. Wolfe, T. Cibelli, J. Horner, P. J. Paluh, J. L. 2020-11-11 doi:10.1101/2020.11.10.374876 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ Root system influence on high dimensional leaf phenotypes over the grapevine growing season ]]> https://biorxiv.org/content/10.1101/2020.11.10.376947v1?rss=1 Harris, Z. N. Klein, L. L. Awale, M. Swift, J. F. Migicovsky, Z. Bhakta, N. Frawley, E. Chitwood, D. H. Fennell, A. Kovacs, L. G. Kwasniewski, M. Londo, J. P. Ma, Q. Miller, A. J. 2020-11-11 doi:10.1101/2020.11.10.376947 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ CV-α: designing validations sets to increase the precision and enable multiple comparison tests in genomic prediction ]]> https://biorxiv.org/content/10.1101/2020.11.11.376343v1?rss=1 Yassue, R. M. Sabadin, J. F. G. Galli, G. Alves, F. C. Fritsche-Neto, R. F. 2020-11-12 doi:10.1101/2020.11.11.376343 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Repression precedes the stepwise evolution of a highly specific gene expression pattern ]]> https://biorxiv.org/content/10.1101/2020.11.11.378737v1?rss=1 Pu, J. Wang, Z. Cong, H. Chin, J. S. R. Justen, J. Yew, J. Y. Chung, H. 2020-11-12 doi:10.1101/2020.11.11.378737 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Extended spectrum β-lactamase and carbapenemase genes are substantially and sequentially reduced during conveyance and treatment of urban sewage ]]> https://biorxiv.org/content/10.1101/2020.11.12.379032v1?rss=1 Li, L. Nesme, J. Quintela-Baluja, M. Balboa, S. Hashsham, S. Williams, M. R. Yu, Z. Sorensen, S. J. Graham, D. W. Romalde, J. L. Dechesne, A. Smets, B. F. 2020-11-12 doi:10.1101/2020.11.12.379032 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Quantification of Brucella abortus population structure in a natural host ]]> https://biorxiv.org/content/10.1101/2020.11.12.380766v1?rss=1 Fiebig, A. Vrentas, C. E. Le, T. M. Huebner, M. Boggiatto, P. M. Olsen, S. C. Crosson, S. 2020-11-13 doi:10.1101/2020.11.12.380766 Cold Spring Harbor Laboratory Press 2020-11-13 <![CDATA[ Directional phyllotactic bias in calatheas (Goeppertia, Marantaceae): a citizen science approach ]]> https://biorxiv.org/content/10.1101/2020.11.13.382317v1?rss=1 Durrington, B. Chong, F. Chitwood, D. H. Twitter Calathea Poll Participants, 2020-11-15 doi:10.1101/2020.11.13.382317 Cold Spring Harbor Laboratory Press 2020-11-15 <![CDATA[ Gene Expression Meta-Analysis Identifies Molecular Changes Associated with SARS-CoV Infection in Lungs ]]> https://biorxiv.org/content/10.1101/2020.11.14.382697v1?rss=1 Park, A. Harris, L. 2020-11-16 doi:10.1101/2020.11.14.382697 Cold Spring Harbor Laboratory Press 2020-11-16 <![CDATA[ Domestication has altered within-plant trait variability in a crop plant ]]> https://biorxiv.org/content/10.1101/2020.11.14.382788v1?rss=1 Robinson, M. L. Wetzel, W. C. Schilmiller, A. L. 2020-11-16 doi:10.1101/2020.11.14.382788 Cold Spring Harbor Laboratory Press 2020-11-16 <![CDATA[ Loss of ASH1L in developing brains causes autistic-like behaviors in a mouse model ]]> https://biorxiv.org/content/10.1101/2020.11.16.377259v1?rss=1 Gao, Y. Duque-Wilckens, N. Aljazi, M. B. Wu, Y. Moeser, A. J. Mias, G. I. Robison, A. J. He, J. 2020-11-16 doi:10.1101/2020.11.16.377259 Cold Spring Harbor Laboratory Press 2020-11-16 <![CDATA[ Cellular and molecular mechanisms of frontal bone development in spotted gar (Lepisosteus oculatus) ]]> https://biorxiv.org/content/10.1101/2020.11.16.383802v1?rss=1 Enny, A. Thompson, A. W. Racicot, B. Braasch, I. Nakamura, T. 2020-11-17 doi:10.1101/2020.11.16.383802 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ Inactivation of mitochondrial Complex I stimulates chloroplast ATPase in Physcomitrella (Physcomitrium patens). ]]> https://biorxiv.org/content/10.1101/2020.11.20.390153v1?rss=1 Mellon, M. Storti, M. Vera Vives, A. M. Kramer, D. M. Alboresi, A. Morosinotto, T. 2020-11-20 doi:10.1101/2020.11.20.390153 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Mitochondrial respiration contributes to the interferon gamma response in antigen presenting cells ]]> https://biorxiv.org/content/10.1101/2020.11.22.393538v1?rss=1 Kiritsy, M. Mott, D. Behar, S. M. Sassetti, C. M. Olive, A. J. 2020-11-23 doi:10.1101/2020.11.22.393538 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ Peptide Ancestry Informative Markers in Uterine Neoplasms from Women of European, African and Asian Ancestry ]]> https://biorxiv.org/content/10.1101/2020.11.23.380337v1?rss=1 260K SNPs (R2=0.9905). Multiplexed proteomic analysis of >100 human endometrial cancer cell lines and uterine leiomyoma tissues resulted in the quantitation of 62 pAIMs that correlate with self-described race and genotype-confirmed patient ancestry. Candidates include a D451E substitution in GC vitamin D-binding protein previously associated with altered vitamin D levels in African and European populations. These efforts describe a generalized set of markers for proteoancestry assessment that will further support studies investigating the impact of ancestry on the human proteome and how this relates to the pathogenesis of uterine neoplasms. ]]> Bateman, N. W. Tarney, C. Abulez, T. Hood, B. L. Conrads, K. Zhou, M. Soltis, A. R. Teng, P.-i. Jackson, A. Tian, C. Dalgard, C. Wilkerson, M. Kessler, M. Shriver, C. D. Hu, H. Cote, M. Parker, G. J. Segars, J. Al-Hendy, A. Risinger, J. Darcy, K. Casablanca, Y. George, M. L. Conrads, T. P. O'Connor, T. D. 2020-11-23 doi:10.1101/2020.11.23.380337 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ RpoS Contributes to Successful Opportunistic Colonization by Human Enteric Pathogens during Plant Disease ]]> https://biorxiv.org/content/10.1101/2020.11.24.397208v1?rss=1 Lovelace, A. H. Lee, S. Downs, D. M. Soufi, Z. Bota, P. Preston, G. M. Kvitko, B. H. 2020-11-25 doi:10.1101/2020.11.24.397208 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ The molecular basis of Kale domestication: Transcription profiling of leaves and meristems provides new insights into the evolution of a Brassica oleracea vegetative morphotype ]]> https://biorxiv.org/content/10.1101/2020.11.25.398347v1?rss=1 Arias, T. Niederhuth, C. McSteen, P. Pires, C. 2020-11-25 doi:10.1101/2020.11.25.398347 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ Heuristic hyperparameter optimization of deep learning models for genomic prediction ]]> https://biorxiv.org/content/10.1101/2020.11.25.398800v1?rss=1 Han, J. Gondro, C. Reid, K. Steibel, J. P. 2020-11-25 doi:10.1101/2020.11.25.398800 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ Host-pathogen genetic interactions underlie tuberculosis susceptibility in genetically diverse mice ]]> https://biorxiv.org/content/10.1101/2020.12.01.405514v1?rss=1 Smith, C. M. Baker, R. E. Proulx, M. K. Mishra, B. B. Long, J. E. Park, S. W. Lee, H.-N. Kiritsy, M. C. Bellerose, M. M. Olive, A. J. Murphy, K. C. Papavinasasundaram, K. Boehm, F. J. Reames, C. J. Meade, R. K. Hampton, B. K. Linnertz, C. Ehrt, S. Schnappinger, D. Pardo-Manuel de Villena, F. Ferris, M. T. Ioerger, T. R. Sassetti, C. M. 2020-12-01 doi:10.1101/2020.12.01.405514 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ A Complex Containing HNRNPA2B1 and N6-methyladenosine Modified Transcripts Mediates Actions of Toxic Tau Oligomers ]]> https://biorxiv.org/content/10.1101/2020.12.03.409334v1?rss=1 Jiang, L. Lin, W. Zhang, C. Verma, M. Kwan, J. Vliet, E. v. Ash, P. E. A. Cruz, A. L. Boudeau, S. Maziuk, B. F. Lei, S. Song, J. Alvarez, V. E. Kayed, R. Kanaan, N. Murray, M. E. Crary, J. F. Petrucelli, L. Li, H. E. Emili, A. Wolozin, B. 2020-12-03 doi:10.1101/2020.12.03.409334 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Proteasomal degradation of human SERINC4: a potent host anti-HIV-1 factor that is antagonized by Nef ]]> https://biorxiv.org/content/10.1101/2020.12.07.414888v1?rss=1 Qiu, X. Eke, I. E. Johnson, S. F. Ding, C. Zheng, Y.-H. 2020-12-07 doi:10.1101/2020.12.07.414888 Cold Spring Harbor Laboratory Press 2020-12-07 <![CDATA[ Heartbeats entrain breathing via baroreceptor-mediated modulation of expiratory activity ]]> https://biorxiv.org/content/10.1101/2020.12.09.416776v1?rss=1 Barnett, W. H. Baekey, D. M. Paton, J. F. R. Dick, T. E. Wehrwein, E. A. Molkov, Y. I. 2020-12-11 doi:10.1101/2020.12.09.416776 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Disruptions in effort-based decision-making following acute optogenetic stimulation of ventral tegmental area dopamine cells ]]> https://biorxiv.org/content/10.1101/2020.12.09.417832v1?rss=1 Fry, B. Pence, N. McLocklin, A. Johnson, A. 2020-12-09 doi:10.1101/2020.12.09.417832 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Transcriptomic divergence predicts morphological and ecological variation underlying an adaptive radiation ]]> https://biorxiv.org/content/10.1101/2020.12.15.422975v1?rss=1 Bernal, M. A. Yule, D. L. Stott, W. Evrard, L. Dowling, T. E. Krabbenhoft, T. J. 2020-12-16 doi:10.1101/2020.12.15.422975 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ Automation of Leaf Counting in Maize and Sorghum Using Deep Learning ]]> https://biorxiv.org/content/10.1101/2020.12.19.423626v1?rss=1 Miao, C. Guo, A. Yang, J. Ge, Y. Schnable, J. C. 2020-12-21 doi:10.1101/2020.12.19.423626 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ Response of benthic macroinvertebrates to dam removal in the restoration of the Boardman River, Michigan, USA ]]> https://biorxiv.org/content/10.1101/2020.12.22.423935v1?rss=1 Van Dyke, F. Mahan, D. C. Betts, J. T. Nord, E. Outcalt, J. 2020-12-22 doi:10.1101/2020.12.22.423935 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Cysteine biosynthesis is a determinant of Brucella ovis stress survival and fitness in the intracellular niche ]]> https://biorxiv.org/content/10.1101/2020.12.22.424080v1?rss=1 Varesio, L. Fiebig, A. Crosson, S. 2020-12-23 doi:10.1101/2020.12.22.424080 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ Multi-Modal Biomarkers of Cerebral Edema in Low Resolution MRI ]]> https://biorxiv.org/content/10.1101/2020.12.23.424020v1?rss=1 Tu, D. Goyal, M. S. Dworkin, J. D. Kampondeni, S. Vidal, L. Biondo-Savin, E. Juvvadi, S. Raghavan, P. Nicholas, J. Chetcuti, K. Clark, K. Satterthwaite, T. D. Yushkevich, P. Davatzikos, C. Erus, G. Postels, D. G. Taylor, T. E. Small, D. S. Shinohara, R. T. 2020-12-25 doi:10.1101/2020.12.23.424020 Cold Spring Harbor Laboratory Press 2020-12-25 <![CDATA[ Land-use and forest floor explain prokaryotic metacommunity structuring and spatial turnover in Amazonian forest-to-pasture conversion areas ]]> https://biorxiv.org/content/10.1101/2020.12.30.424814v1?rss=1 Rocha, F. I. Ribeiro, T. G. Fontes, M. A. Shwab, S. Coelho, M. R. R. Lumbreras, J. F. da Motta, P. E. F. Teixeira, W. G. Cole, J. R. Borsanelli, A. C. Dutra, I. d. S. Howe, A. de Oliveira, A. P. Jesus, E. d. C. 2020-12-30 doi:10.1101/2020.12.30.424814 Cold Spring Harbor Laboratory Press 2020-12-30 <![CDATA[ An increase in atypical petal numbers during a shift to autogamy in a coastal sand verbena and potential evolutionary mechanisms ]]> https://biorxiv.org/content/10.1101/2021.01.03.425117v1?rss=1 LoPresti, E. Mickley, J. Edwards, C. Weber, M. G. 2021-01-04 doi:10.1101/2021.01.03.425117 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ Comberons from single cell transcriptomics in endothelial cells ]]> https://biorxiv.org/content/10.1101/2021.01.04.425317v1?rss=1 Domanskyi, S. Hakansson, A. Meng, M. Graff Zivin, J. S. Piermarocchi, C. Paternostro, G. Ferrara, N. 2021-01-05 doi:10.1101/2021.01.04.425317 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Environmental enrichment delays the development of stereotypic behavior and reduces variability in behavioral experiments using California mice (Peromyscus californicus). ]]> https://biorxiv.org/content/10.1101/2021.01.05.425454v1?rss=1 Minie, V. Ramos-Maciel, S. Wright, E. C. Petric, R. Trainor, B. C. Duque-Wilckens, N. 2021-01-06 doi:10.1101/2021.01.05.425454 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ Skin-resident immune cells actively coordinate their distribution with epidermal cells during homeostasis ]]> https://biorxiv.org/content/10.1101/2021.01.08.425932v1?rss=1 Park, S. Matte-Martone, C. Gonzalez, D. G. Lathrop, E. A. May, D. P. Pineda, C. M. Moore, J. L. Boucher, J. D. Marsh, E. D. Schmitter, A. Cockburn, K. Bellaiche, Y. Greco, V. 2021-01-09 doi:10.1101/2021.01.08.425932 Cold Spring Harbor Laboratory Press 2021-01-09 <![CDATA[ Quantitative dissection of color patterning in the foliar ornamental Coleus reveals underlying features driving aesthetic value ]]> https://biorxiv.org/content/10.1101/2021.01.11.426252v1?rss=1 Li, M. Coneva, V. Clark, D. Chitwood, D. H. Frank, M. 2021-01-11 doi:10.1101/2021.01.11.426252 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Parallel functional testing identifies enhancers active in early postnatal mouse brain ]]> https://biorxiv.org/content/10.1101/2021.01.15.426772v1?rss=1 Lambert, J. T. Su-Feher, L. Cichewicz, K. Warren, T. L. Zdilar, I. Wang, Y. Lim, K. J. Haigh, J. Morse, S. J. Stradleigh, T. W. Castillo, E. Haghani, V. Moss, S. D. Parolini, H. Quintero, D. Shrestha, D. Vogt, D. Byrne, L. Nord, A. S. 2021-01-15 doi:10.1101/2021.01.15.426772 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ Applying cis-regulatory codes to predict conserved and variable heat and cold stress response in maize ]]> https://biorxiv.org/content/10.1101/2021.01.15.426829v1?rss=1 Zhou, P. Enders, T. A. Myers, Z. A. Magnusson, E. Crisp, P. A. Noshay, J. Cano, F. A. G. Liang, Z. Grotewold, E. Greenham, K. Springer, N. M. 2021-01-17 doi:10.1101/2021.01.15.426829 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ Thioesterase induction by 2,3,7,8-tetrachlorodibenzo-p-dioxin results in a futile cycle that inhibits hepatic β-oxidation ]]> https://biorxiv.org/content/10.1101/2021.01.21.427582v1?rss=1 Cholico, G. N. Fling, R. R. Zacharewski, N. A. Fader, K. A. Nault, R. Zacharewski, T. R. 2021-01-21 doi:10.1101/2021.01.21.427582 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Category-specific item encoding in the medial temporal lobe and beyond: The role of reward. ]]> https://biorxiv.org/content/10.1101/2021.01.22.427769v1?rss=1 Schultz, H. Yoo, J. Meshi, D. Heekeren, H. R. 2021-01-23 doi:10.1101/2021.01.22.427769 Cold Spring Harbor Laboratory Press 2021-01-23 <![CDATA[ Separable pupillary signatures of perception and action during perceptual multistability ]]> https://biorxiv.org/content/10.1101/2021.01.22.427816v1?rss=1 Brascamp, J. De Hollander, G. Wertheimer, M. D. DePew, A. N. Knapen, T. 2021-01-24 doi:10.1101/2021.01.22.427816 Cold Spring Harbor Laboratory Press 2021-01-24 <![CDATA[ Heterogeneity in PHGDH protein expression potentiates cancer cell dissemination and metastasis ]]> https://biorxiv.org/content/10.1101/2021.01.24.427949v1?rss=1 Rossi, M. Doglioni, G. Bornes, L. Broekart, D. Planque, M. Fernandez-Garcia, J. Rinaldi, G. Van Elsen, J. Nittner, D. Jauset, C. Rizzollo, F. Riera Domingo, C. Orth, M. Dobrolecki, L. E. Van Brussel, T. Teoh, S. T. Aurora, A. Eelen, G. Karras, P. Sotlar, K. Bartsch, H. Marine, J.-C. Carmeliet, P. Morrison, S. J. Lewis, M. T. Hannon, G. Mazzone, M. Lambrechts, D. van Rheenen, J. Gruenewald, T. G. P. Lunt, S. Y. Fendt, S.-M. 2021-01-26 doi:10.1101/2021.01.24.427949 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ A Catalog of the Diversity and Ubiquity of Metabolic Organelles in Bacteria ]]> https://biorxiv.org/content/10.1101/2021.01.25.427685v1?rss=1 Sutter, M. Melnicki, M. R. Schulz, F. Woyke, T. Kerfeld, C. A. 2021-01-25 doi:10.1101/2021.01.25.427685 Cold Spring Harbor Laboratory Press 2021-01-25 <![CDATA[ Training Data: How can we best prepare instructors to teach data science in undergraduate biology and environmental science courses? ]]> https://biorxiv.org/content/10.1101/2021.01.25.428169v1?rss=1 Emery, N. C. Crispo, E. Supp, S. R. Kerkhoff, A. J. Farrell, K. J. Bledsoe, E. K. O'Donnell, K. L. McCall, A. C. Aeillo-Lammens, M. 2021-01-27 doi:10.1101/2021.01.25.428169 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Aureochromes are necessary for maintaining polyunsaturated fatty acid content in Nannochloropsis oceanica ]]> https://biorxiv.org/content/10.1101/2021.01.27.428447v1?rss=1 Farre, E. M. Poliner, E. Busch, A. W. Newton, L. Kim, Y. U. Clark, R. Gonzalez-Martinez, S. C. Jeong, B.-r. Montgomery, B. L. 2021-01-27 doi:10.1101/2021.01.27.428447 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Structural and functional sex differences in the ventral pallidal vasopressin system are associated with the sex-specific regulation of juvenile social play behavior in rats ]]> https://biorxiv.org/content/10.1101/2021.01.31.429043v1?rss=1 Lee, J. D. A. Reppucci, C. J. Bowden, S. M. Huez, E. D. M. Bredewold, R. Veenema, A. H. 2021-02-01 doi:10.1101/2021.01.31.429043 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ The cyclic di-GMP network is a global regulator of phase-transition and attachment-dependent host colonization in Erwinia amylovora ]]> https://biorxiv.org/content/10.1101/2021.02.01.429191v1?rss=1 Kharadi, R. R. Selbmann, K. Sundin, G. W. 2021-02-02 doi:10.1101/2021.02.01.429191 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Functional classes of SNPs related to psychiatric disorders and behavioral traits contrast with those related to neurological disorders ]]> https://biorxiv.org/content/10.1101/2021.02.04.429714v1?rss=1 Reimers, M. Kendler, K. S. 2021-02-04 doi:10.1101/2021.02.04.429714 Cold Spring Harbor Laboratory Press 2021-02-04 <![CDATA[ Architecture of cell-cell junctions in situ reveals a mechanism for bacterial biofilm inhibition ]]> https://biorxiv.org/content/10.1101/2021.02.08.430230v1?rss=1 Melia, C. Bolla, J. R. Katharios-Lanwermeyer, S. Mihaylov, D. Hoffmann, P. Huo, J. Wozny, M. Elfari, L. Boehning, J. Owens, R. Robinson, C. V. O'Toole, G. Bharat, T. 2021-02-08 doi:10.1101/2021.02.08.430230 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ Integrated analysis of the methylome and transcriptome of twin almonds (Prunus dulcis D.A.Webb) reveals genomic features associated with non-infectious bud failure ]]> https://biorxiv.org/content/10.1101/2021.02.08.430330v1?rss=1 D'Amico-Willman, K. M. Niederhuth, C. Willman, M. R. Gradziel, T. M. Ouma, W. Z. Meulia, T. Fresnedo Ramirez, J. 2021-02-08 doi:10.1101/2021.02.08.430330 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ Interdependent Iron and Phosphorus Availability Controls Photosynthesis Through Retrograde Signaling ]]> https://biorxiv.org/content/10.1101/2021.02.11.430802v1?rss=1 Nam, H.-I. Shahzad, Z. Dorone, Y. Clowez, S. Zhao, K. Bouain, N. Cho, H. Rhee, S. Y. Rouached, H. 2021-02-12 doi:10.1101/2021.02.11.430802 Cold Spring Harbor Laboratory Press 2021-02-12 <![CDATA[ CONSTAX2: Improved taxonomic classification of environmental DNA markers ]]> https://biorxiv.org/content/10.1101/2021.02.15.430803v1?rss=1 Liber, J. A. Bonito, G. Benucci, G. M. N. 2021-02-17 doi:10.1101/2021.02.15.430803 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Organic electron donors and terminal electron acceptors structure anaerobic microbial communities and interactions in a permanently stratified sulfidic lake ]]> https://biorxiv.org/content/10.1101/2021.02.16.431432v1?rss=1 Rojas, C. A. De Santiago-Torio, A. Park, S. Bosak, T. Klepac-Ceraj, V. 2021-02-16 doi:10.1101/2021.02.16.431432 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Bioengineering of genetically encoded gene promoter repressed by flavonoids for constructing intracellular sensor for molecular events ]]> https://biorxiv.org/content/10.1101/2021.02.17.431641v1?rss=1 Desmet, N. M. Dhusia, K. Qi, W. Doseff, A. I. Bhattacharya, S. Gilad, A. 2021-02-18 doi:10.1101/2021.02.17.431641 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Genome-wide association study reveals an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels ]]> https://biorxiv.org/content/10.1101/2021.02.19.432009v1?rss=1 Baseggio, M. Murray, M. Wu, D. Ziegler, G. Kaczmar, N. Chamness, J. Hamilton, J. P. Buell, C. R. Vatamaniuk, O. K. Buckler, E. S. Smith, M. E. Baxter, I. Tracy, W. F. Gore, M. A. 2021-02-20 doi:10.1101/2021.02.19.432009 Cold Spring Harbor Laboratory Press 2021-02-20 <![CDATA[ Genetic Basis of Variation in Cocaine and Methamphetamine Consumption in Outbred Populations of Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2021.03.01.433403v1?rss=1 Baker, B. Carbone, M. A. Huang, W. Anholt, R. R. H. Mackay, T. 2021-03-02 doi:10.1101/2021.03.01.433403 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Perturbation of ACE2 structural ensembles by SARS-CoV-2 spike protein binding ]]> https://biorxiv.org/content/10.1101/2021.03.02.433608v1?rss=1 Uyar, A. Dickson, A. 2021-03-02 doi:10.1101/2021.03.02.433608 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Laminar-specific functional connectivity mapping with multi-slice line-scanning fMRI ]]> https://biorxiv.org/content/10.1101/2021.03.03.433376v1?rss=1 Choi, S. Zeng, H. Chen, Y. Sobczak, F. Qian, C. Yu, X. 2021-03-03 doi:10.1101/2021.03.03.433376 Cold Spring Harbor Laboratory Press 2021-03-03 <![CDATA[ Published Anti-SARS-CoV-2 In Vitro Hits Share Common Mechanisms of Action that Synergize with Antivirals ]]> https://biorxiv.org/content/10.1101/2021.03.04.433931v1?rss=1 Xing, J. Paithankar, S. Liu, K. Uhl, K. Li, X. Ko, M. Kim, S. Haskins, J. Chen, B. 2021-03-04 doi:10.1101/2021.03.04.433931 Cold Spring Harbor Laboratory Press 2021-03-04 <![CDATA[ An in-frame deletion mutation in the degron tail of auxin co-receptor IAA2 confers resistance to the herbicide 2,4-D in Sisymbrium orientale ]]> https://biorxiv.org/content/10.1101/2021.03.04.433944v1?rss=1 Figueiredo, M. R. A. Kuepper, A. Malone, J. M. Petrovic, T. Figueiredo, A. B. T. B. Campagnola, G. Peersen, O. B. Prasad, K. V. S. K. Patterson, E. L. Reddy, A. S. N. Kubes, M. F. Napier, R. Preston, C. Gaines, T. A. 2021-03-05 doi:10.1101/2021.03.04.433944 Cold Spring Harbor Laboratory Press 2021-03-05 <![CDATA[ Combinatorial patterns of gene expression changes contribute to variable expressivity of the developmental delay-associated 16p12.1 deletion ]]> https://biorxiv.org/content/10.1101/2021.03.06.434203v1?rss=1 90% of cases from a mildly-affected parent. While children with the deletion are more likely to carry additional "second-hit" variants than their parents, the mechanisms for how these variants contribute to phenotypic variability are unknown. MethodsWe performed detailed clinical assessments, whole-genome sequencing, and RNA sequencing of lymphoblastoid cell lines for 32 individuals in five large families with multiple members carrying the 16p12.1 deletion. We identified contributions of the 16p12.1 deletion and "second-hit" variants towards a range of expression changes in deletion carriers and their family members, including differential expression, outlier expression, alternative splicing, allele-specific expression, and expression-quantitative trait loci analyses. ResultsWe found that the deletion dysregulates multiple autism and brain development genes such as FOXP1, ANK3, and MEF2. Carrier children also showed an average of 5,323 gene expression changes compared with one or both parents, which matched with 33/39 observed developmental phenotypes. We identified significant enrichments for 13/25 classes of "second-hit" variants in genes with expression changes, where 4/25 variant classes were only enriched when inherited from the non-carrier parent, including loss-of-function SNVs and large duplications. In 11 instances, including for ZEB2 and SYNJ1, gene expression was synergistically altered by both the deletion and inherited "second-hits" in carrier children. Finally, brain-specific interaction network analysis showed strong connectivity between genes carrying "second-hits" and genes with transcriptome alterations in deletion carriers. ConclusionsOur results suggest a potential mechanism for how "second-hit" variants modulate expressivity of complex disorders such as the 16p12.1 deletion through transcriptomic perturbation of gene networks important for early development. Our work further shows that family-based assessments of transcriptome data are highly relevant towards understanding the genetic mechanisms associated with complex disorders. ]]> Jensen, M. Tyryskhina, A. Pizzo, L. Smolen, C. Das, M. Huber, E. Krishnan, A. Girirajan, S. 2021-03-08 doi:10.1101/2021.03.06.434203 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Diversification, Spread, and Admixture of Octoploid Strawberry in the Western Hemisphere ]]> https://biorxiv.org/content/10.1101/2021.03.08.434492v1?rss=1 Bird, K. A. Hardigan, M. A. Ragsdale, A. P. Knapp, S. J. VanBuren, R. Edger, P. P. A. 2021-03-09 doi:10.1101/2021.03.08.434492 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ The Induction of Pyrenoid Synthesis by Hyperoxia and its Implications for the Natural Diversity of Photosynthetic Responses in Chlamydomonas ]]> https://biorxiv.org/content/10.1101/2021.03.10.434646v1?rss=1 Neofotis, P. Temple, J. Tessmer, O. Bibik, J. Norris, N. Poliner, E. Lucker, B. Wijetilleke, S. Withrow, A. Sears, B. Mogos, G. Frame, M. Hall, D. Weissman, J. Kramer, D. M. 2021-03-11 doi:10.1101/2021.03.10.434646 Cold Spring Harbor Laboratory Press 2021-03-11 <![CDATA[ Population structure of Drosophila suzukii and signals of multiple invasions into the continental United States ]]> https://biorxiv.org/content/10.1101/2021.03.14.435345v1?rss=1 Lewald, K. M. Abrieux, A. Wilson, D. A. Lee, Y. Conner, W. R. Andreazza, F. Beers, E. H. Burrack, H. J. Daane, K. M. Diepenbrock, L. Drummond, F. A. Fanning, P. D. Gaffney, M. T. Hesler, S. P. Ioriatti, C. Isaacs, R. Little, B. A. Loeb, G. M. Miller, B. Nava, D. E. Rendo, D. Sial, A. A. da Silva, C. B. Stockton, D. G. Van Timmeren, S. Wallingford, A. Walton, V. M. Wang, X. Zhao, B. Zalom, F. G. Chiu, J. C. 2021-03-16 doi:10.1101/2021.03.14.435345 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Visuomotor information drives interference between the hands more than dynamic motor information during bimanual reaching ]]> https://biorxiv.org/content/10.1101/2021.03.15.435502v1?rss=1 Desrochers, P. C. Brunfeldt, A. T. Kagerer, F. A. 2021-03-16 doi:10.1101/2021.03.15.435502 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ AC2P20 selectively kills M. tuberculosis at acidic pH by depleting free thiols ]]> https://biorxiv.org/content/10.1101/2021.03.16.435645v1?rss=1 Dechow, S. J. Coulson, G. B. Wilson, M. W. Larsen, S. D. Abramovitch, R. B. 2021-03-16 doi:10.1101/2021.03.16.435645 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Topography-dependent gene expression and function of common cell archetypes in large and small porcine airways ]]> https://biorxiv.org/content/10.1101/2021.03.16.435690v1?rss=1 Pezzulo, A. A. Thurman, A. L. Li, X. Villacreses, R. Yu, W. Mather, S. E. Romano-Ibarra, G. S. Meyerholz, D. K. Stoltz, D. A. Welsh, M. J. Thornell, I. M. Zabner, J. 2021-03-17 doi:10.1101/2021.03.16.435690 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Multimodal characterization of Yucatan minipig behavior and physiology through maturation ]]> https://biorxiv.org/content/10.1101/2021.03.18.436053v1?rss=1 Netzley, A. H. Hunt, R. D. Franco-Arellano, J. Arnold, N. Munoz, K. A. Colbath, A. C. Bush, T. R. Pelled, G. 2021-03-20 doi:10.1101/2021.03.18.436053 Cold Spring Harbor Laboratory Press 2021-03-20 <![CDATA[ Machine learning approaches to identify core and dispensable genes in pangenomes ]]> https://biorxiv.org/content/10.1101/2021.03.22.436446v1?rss=1 Yocca, A. E. Edger, P. P. 2021-03-22 doi:10.1101/2021.03.22.436446 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ DrosoPhyla: genomic resources for drosophilid phylogeny and systematics ]]> https://biorxiv.org/content/10.1101/2021.03.23.436709v1?rss=1 Finet, C. Kassner, V. A. Carvalho, A. B. Chung, H. Day, J. P. Delaney, E. K. De Re, F. C. Dufour, H. D. Dupim, E. Izumitani, H. F. Gauterio, T. B. Justen, J. Katoh, T. Kopp, A. Koshikawa, S. Longdon, B. Loreto, E. L. Nunes, M. D. Raja, K. K. Rebeiz, M. Ritchie, M. G. Saakyan, G. Sneddon, T. Teramoto, M. Tyukmaeva, V. Vanderlinde, T. Wey, E. E. Werner, T. Williams, T. M. Robe, L. J. Toda, M. J. Marletaz, F. 2021-03-24 doi:10.1101/2021.03.23.436709 Cold Spring Harbor Laboratory Press 2021-03-24 <![CDATA[ 2,3,7,8-Tetrachlorodibenzo-p-dioxin elicited decreases in cobalamin inhibits methylmalonyl-CoA mutase activity redirecting propionyl-CoA metabolism to the β-oxidation-like pathway resulting in hepatic accumulation of the toxic intermediate acrylyl-CoA ]]> https://biorxiv.org/content/10.1101/2021.03.24.436837v1?rss=1 Orlowska, K. Fling, R. R. Nault, R. Zacharewski, T. 2021-03-25 doi:10.1101/2021.03.24.436837 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Too little, too late: transcription during imbibition of lethally aged soybean seeds is weak and delayed, but not aberrant ]]> https://biorxiv.org/content/10.1101/2021.03.25.437023v1?rss=1 Fleming, M. B. Patterson, E. L. Walters, C. 2021-03-25 doi:10.1101/2021.03.25.437023 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Massively parallel, computationally-guided design of a pro-enzyme ]]> https://biorxiv.org/content/10.1101/2021.03.25.437042v1?rss=1 Yachnin, B. J. Azouz, L. R. White, R. E. Minetti, C. A. S. A. Remeta, D. P. Tan, V. M. Drake, J. M. Khare, S. D. 2021-03-26 doi:10.1101/2021.03.25.437042 Cold Spring Harbor Laboratory Press 2021-03-26 <![CDATA[ Host genetic control of succession in the switchgrass leaf fungal microbiome ]]> https://biorxiv.org/content/10.1101/2021.03.26.437207v1?rss=1 VanWallendael, A. Benucci, G. M. N. da Costa, P. B. Fraser, L. Bonito, G. Fritschi, F. B. Juenger, T. E. Lovell, J. T. Sreedasyam, A. Lowry, D. 2021-03-28 doi:10.1101/2021.03.26.437207 Cold Spring Harbor Laboratory Press 2021-03-28 <![CDATA[ Every cog and wheel: Unraveling biocomplexity at the genomic and phenotypic level in a population complex of Chinook salmon. ]]> https://biorxiv.org/content/10.1101/2021.03.26.437213v1?rss=1 O'Leary, S. J. Thompson, T. Q. Meek, M. H. 2021-03-28 doi:10.1101/2021.03.26.437213 Cold Spring Harbor Laboratory Press 2021-03-28 <![CDATA[ Measuring hidden phenotype: Quantifying the shape of barley seeds using the Euler Characteristic Transform ]]> https://biorxiv.org/content/10.1101/2021.03.27.437348v1?rss=1 Amezquita, E. J. Quigley, M. Y. Ophelders, T. Landis, J. B. Koenig, D. Munch, E. Chitwood, D. H. 2021-03-28 doi:10.1101/2021.03.27.437348 Cold Spring Harbor Laboratory Press 2021-03-28 <![CDATA[ Fine-tuning of SUMOylation modulates drought tolerance ]]> https://biorxiv.org/content/10.1101/2021.03.29.437542v1?rss=1 Guan, Q. Li, X. Zhou, S.-X. Lu, L. Dang, H. Liu, Z. Li, H. Chu, B. Chen, P. Ma, Z. Zhao, S. Van Nocker, S. Ma, F. 2021-03-31 doi:10.1101/2021.03.29.437542 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Depleting Hypothalamic Somatostatinergic Neurons Recapitulates Diabetic Phenotypes in Brain, Bone Marrow, Adipose, and Retina ]]> https://biorxiv.org/content/10.1101/2021.03.30.437706v1?rss=1 Huang, C. Rosencrans, R. F. Bugescu, R. Vieira, C. P. Hu, P. Adu-Agyeiwaah, Y. Gamble, K. Longhini, A. L. F. Fuller, P. M. Leinninger, G. M. Grant, M. 2021-03-31 doi:10.1101/2021.03.30.437706 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ A Broadly Conserved Deoxycytidine Deaminase Protects Bacteria from Phage Infection ]]> https://biorxiv.org/content/10.1101/2021.03.31.437871v1?rss=1 Severin, G. B. Hsueh, B. Y. Elg, C. A. Dover, J. A. Rhoades, C. R. Wessel, A. J. Ridenhour, B. J. Top, E. M. Ravi, J. Parent, K. N. Waters, C. M. 2021-03-31 doi:10.1101/2021.03.31.437871 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Focal fMRI signal enhancement with implantable inductively coupled detectors ]]> https://biorxiv.org/content/10.1101/2021.04.02.438254v1?rss=1 Chen, Y. Wang, Q. Choi, S. Zeng, H. Takahashi, K. Qian, C. Yu, X. 2021-04-04 doi:10.1101/2021.04.02.438254 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ Brassica rapa domestication: untangling wild and feral forms and convergence of crop morphotypes ]]> https://biorxiv.org/content/10.1101/2021.04.05.438488v1?rss=1 McAlvay, A. C. Ragsdale, A. P. Mabry, M. E. Qi, X. Bird, K. Velasco, P. An, H. Pires, C. Emshwiller, E. 2021-04-06 doi:10.1101/2021.04.05.438488 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ The meta-gut: Hippo inputs lead to community coalescence of animal and environmental microbiomes. ]]> https://biorxiv.org/content/10.1101/2021.04.06.438626v1?rss=1 Dutton, C. L. Subalusky, A. L. Sanchez, A. S. Estrela, S. L. Lu, N. Hamilton, S. Njoroge, L. Rosi, E. J. Post, D. M. 2021-04-08 doi:10.1101/2021.04.06.438626 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ The Evolutionary History of Wild, Domesticated, and Feral Brassica oleracea (Brassicaceae) ]]> https://biorxiv.org/content/10.1101/2021.04.06.438638v1?rss=1 Mabry, M. E. Turner, S. D. Gallagher, E. Y. McAlvay, A. C. An, H. Edger, P. P. Moore, J. D. Pink, D. A. C. Teakle, G. R. Stevens, C. J. Barker, G. Labate, J. Fuller, D. Q. Allaby, R. G. Beissinger, T. M. Decker, J. E. Gore, M. A. Pires, C. 2021-04-06 doi:10.1101/2021.04.06.438638 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ The dual nature of metacommunity variability ]]> https://biorxiv.org/content/10.1101/2021.04.09.439168v1?rss=1 Lamy, T. Wisnoski, N. I. Andrade, R. M. Castorani, M. C. Compagnoni, A. Lany, N. K. Marazzi, L. Record, S. Swan, C. Tonkin, J. D. Wang, S. Voelker, N. Zarnetske, P. L. Sokol, E. R. 2021-04-11 doi:10.1101/2021.04.09.439168 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Measuring salivary cortisol in wild carnivores ]]> https://biorxiv.org/content/10.1101/2021.04.11.438354v1?rss=1 Montgomery, T. M. Greenberg, J. R. Gunson, J. L. John, K. Laubach, Z. M. Nonnamaker, E. Person, E. S. Rogers, H. Ronis, E. Smale, L. Steinfield, K. Strong, R. Holekamp, K. E. Beehner, J. C. 2021-04-12 doi:10.1101/2021.04.11.438354 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Revealing the threat of emerging SARS-CoV-2 mutations to antibody therapies ]]> https://biorxiv.org/content/10.1101/2021.04.12.439473v1?rss=1 Chen, J. Gao, K. Wang, R. Wei, G.-W. 2021-04-12 doi:10.1101/2021.04.12.439473 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ BRAF inhibitor resistance confers increased sensitivity to mitotic inhibitors ]]> https://biorxiv.org/content/10.1101/2021.04.15.439990v1?rss=1 Misek, S. Dexheimer, T. Akram, M. Conrad, S. E. Schmidt, J. C. Neubig, R. R. Gallo, K. A. 2021-04-15 doi:10.1101/2021.04.15.439990 Cold Spring Harbor Laboratory Press 2021-04-15 <![CDATA[ The ChvG-ChvI and NtrY-NtrX two-component systems coordinately regulate growth of Caulobacter crescentus ]]> https://biorxiv.org/content/10.1101/2021.04.17.440287v1?rss=1 Stein, B. J. Fiebig, A. Crosson, S. 2021-04-17 doi:10.1101/2021.04.17.440287 Cold Spring Harbor Laboratory Press 2021-04-17 <![CDATA[ A biosensor to gauge protein homeostasis resilience differences in the nucleus compared to cytosol of mammalian cells ]]> https://biorxiv.org/content/10.1101/2021.04.19.440383v1?rss=1 Raeburn, C. B. Ormsby, A. R. Moily, N. S. Cox, D. Ebbinghaus, S. Dickson, A. McColl, G. Hatters, D. M. 2021-04-19 doi:10.1101/2021.04.19.440383 Cold Spring Harbor Laboratory Press 2021-04-19 <![CDATA[ Genome-centric analyses of seasonal phyllosphere microbiome activities in perennial crops ]]> https://biorxiv.org/content/10.1101/2021.04.20.440608v1?rss=1 50% complete. Classes represented by these MAGs (Actinomycetia, Alpha- and Gamma-Proteobacteria, and Bacteroidota) were active and had seasonal dynamics in key functions, including enrichments in transcripts for of short chain dehydrogenase, molybdopterin oxioreductase, and polyketide cyclase in the late season. The majority of MAGs had activated stress-associated pathways, including trehalose metabolism, indole acetic acid degradation, betaine biosynthesis, and reactive oxygen species degradation, suggesting direct engagement with the host environment. We also detected seasonally activated biosynthetic pathways for terpenes (carotenoid and isoprenoids), and for various non-ribosomal peptide pathways that were poorly annotated. Overall, this study overcame laboratory and bioinformatic challenges associated with field-based leaf metatranscriptome analysis to inform potential key activities of these phyllosphere populations. These activities collectively support that leaf-associated bacterial populations are seasonally dynamic, responsive to host cues and interactively engage in feedbacks with the plant. ]]> Howe, A. C. Stopnisek, N. Dooley, S. K. Yang, F. M. Grady, K. L. Shade, A. 2021-04-20 doi:10.1101/2021.04.20.440608 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Multiple morphogens and rapid elongation promote segmental patterning during development ]]> https://biorxiv.org/content/10.1101/2021.04.22.440966v1?rss=1 Qiu, Y. Fung, L. Schilling, T. F. Nie, Q. 2021-04-22 doi:10.1101/2021.04.22.440966 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Independent Promoter Recognition by TcpP Precedes Cooperative Promoter Activation by TcpP and ToxR ]]> https://biorxiv.org/content/10.1101/2021.04.25.441279v1?rss=1 Calkins, A. L. Demey, L. M. Karslake, J. D. Donarski, E. D. Biteen, J. S. DiRita, V. J. 2021-04-26 doi:10.1101/2021.04.25.441279 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Endophytic microbiome variation at the level of a single plant seed ]]> https://biorxiv.org/content/10.1101/2021.04.27.441449v1?rss=1 Bintarti, A. F. Sulesky-Grieb, A. Stopnisek, N. Shade, A. 2021-04-27 doi:10.1101/2021.04.27.441449 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Sustained coevolution of phage Lambda and Escherichia coli involves inner as well as outer membrane defenses and counter-defenses ]]> https://biorxiv.org/content/10.1101/2021.04.27.441663v1?rss=1 Burmeister, A. R. Sullivan, R. M. Gallie, J. Lenski, R. E. 2021-04-28 doi:10.1101/2021.04.27.441663 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Capturing site-to-site variability through Hierarchical Bayesian calibration of a process-based dynamic vegetation model ]]> https://biorxiv.org/content/10.1101/2021.04.28.441243v1?rss=1 Fer, I. Shiklomanov, A. N. Novick, K. A. Gough, C. M. Arain, M. A. Chen, J. Murphy, B. Desai, A. R. Dietze, M. C. 2021-04-29 doi:10.1101/2021.04.28.441243 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ How the footprint of history shapes the evolution of digital organisms ]]> https://biorxiv.org/content/10.1101/2021.04.29.442046v1?rss=1 Bundy, J. Ofria, C. Lenski, R. E. 2021-04-29 doi:10.1101/2021.04.29.442046 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Crowdsourcing biocuration: the Community Assessment of Community Annotation with Ontologies (CACAO) ]]> https://biorxiv.org/content/10.1101/2021.04.30.440339v1?rss=1 Ramsey, J. McIntosh, B. Renfro, D. Aleksander, S. A. LaBonte, S. Ross, C. Zweifel, A. E. Liles, N. Farrar, S. Gill, J. J. Erill, I. Ades, S. Berardini, T. Z. Bennett, J. A. Brady, S. M. Britton, R. Carbon, S. Caruso, S. M. Clements, D. Dalia, R. Defelice, M. Doyle, E. L. Friedberg, I. Gurney, S. M. Hughes, L. Johnson, A. Kowalski, J. M. Li, D. Lovering, R. C. Mans, T. L. McCarthy, F. Moore, S. D. Murphy, R. Paustian, T. D. Perdue, S. Peterson, C. N. Pruess, B. M. Saha, M. S. Sheehy, R. R. Tansey, J. T. Temple, L. Thorman, A. W. Trevino, S. Vollmer, A. 2021-05-01 doi:10.1101/2021.04.30.440339 Cold Spring Harbor Laboratory Press 2021-05-01 <![CDATA[ Hypermethylation is associated with increased age in almond (Prunus dulcis D.A. Webb) accessions ]]> https://biorxiv.org/content/10.1101/2021.05.02.442365v1?rss=1 D'Amico-Willman, K. M. Niederhuth, C. Anderson, E. S. Gradziel, T. M. Fresnedo Ramirez, J. 2021-05-03 doi:10.1101/2021.05.02.442365 Cold Spring Harbor Laboratory Press 2021-05-03 <![CDATA[ yEvo: Experimental evolution in high school classrooms selects for novel mutations and epistatic interactions that impact clotrimazole resistance in S. cerevisiae. ]]> https://biorxiv.org/content/10.1101/2021.05.02.442375v1?rss=1 Taylor, M. B. Skophammer, R. Warwick, A. R. Boyer, J. M. Students, y. Walson, M. Large, C. R. L. Hickey, A. S.-M. Rowley, P. A. Dunham, M. J. 2021-05-03 doi:10.1101/2021.05.02.442375 Cold Spring Harbor Laboratory Press 2021-05-03 <![CDATA[ Short-interval fires and vegetation change in southern California ]]> https://biorxiv.org/content/10.1101/2021.05.08.443193v1?rss=1 Lucero, S. M. Emery, N. D'Antonio, C. M. 2021-05-10 doi:10.1101/2021.05.08.443193 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ Systematic tissue annotations of -omics samples by modeling unstructured metadata ]]> https://biorxiv.org/content/10.1101/2021.05.10.443525v1?rss=1 1.3 million human -omics samples that are publicly available. This valuable resource remains acutely underused because discovering particular samples from this ever-growing data collection remains a significant challenge. The major impediment is that sample attributes are routinely described using varied terminologies written in unstructured natural language. We propose a natural-language-processing-based machine learning approach (NLP-ML) to infer tissue and cell-type annotations for -omics samples based only on their free-text metadata. NLP-ML works by creating numerical representations of sample descriptions and using these representations as features in a supervised learning classifier that predicts tissue/cell-type terms. Our approach significantly outperforms an advanced graph-based reasoning annotation method (MetaSRA) and a baseline exact string matching method (TAGGER). Model similarities between related tissues demonstrate that NLP-ML models capture biologically-meaningful signals in text. Additionally, these models correctly classify tissue-associated biological processes and diseases based on their text descriptions alone. NLP-ML models are nearly as accurate as models based on gene-expression profiles in predicting sample tissue annotations but have the distinct capability to classify samples irrespective of the -omics experiment type based on their text metadata. Python NLP-ML prediction code and trained tissue models are available at https://github.com/krishnanlab/txt2onto. ]]> Hawkins, N. T. Maldaver, M. Yannakopoulos, A. Guare, L. A. Krishnan, A. 2021-05-11 doi:10.1101/2021.05.10.443525 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ Implicit Laplacian of Enhanced Edge (ILEE): An unguided quantitative cytoskeletal imaging algorithm ]]> https://biorxiv.org/content/10.1101/2021.05.11.442512v1?rss=1 Li, P. Zhang, Z. Day, B. Tong, Y. 2021-05-12 doi:10.1101/2021.05.11.442512 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ Lipid Bilayer Induces Contraction of the Denatured State Ensemble of a Helical-Bundle Membrane Protein ]]> https://biorxiv.org/content/10.1101/2021.05.17.444377v1?rss=1 Gaffney, K. Guo, R. Bridges, M. D. Chen, D. Muhammednazaar, S. Kim, M. yang, Z. Schilmiller, A. L. Faruk, N. F. Peng, X. Jones, A. D. Sun, L. Hubbell, W. L. Sosnick, T. Hong, H. 2021-05-17 doi:10.1101/2021.05.17.444377 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Biochar alters soil properties, microbial community diversity, and enzyme activities, while decreasing conifer performance ]]> https://biorxiv.org/content/10.1101/2021.05.17.444392v1?rss=1 Nash, J. Miesel, J. Bonito, G. Sakalidis, M. Ren, H. Warnock, D. Tiemann, L. 2021-05-17 doi:10.1101/2021.05.17.444392 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Implications Derived from S-Protein Variants of SARS-CoV-2 from Six Continents ]]> https://biorxiv.org/content/10.1101/2021.05.18.444675v1?rss=1 Hassan, S. S. Lundstrom, K. Pal Choudhury, P. Palu, G. Uhal, B. Kandimalla, R. Seyran, M. Lal, A. Sherchan, S. P. Azad, G. K. Aljabali, A. A. A. Brufsky, A. Serrano-Aroca, A. Adadi, P. Abd El-Aziz, T. M. Redwan, E. M. Takayama, K. Barh, D. Rezaei, N. Tambuwala, M. Uversky, V. N. 2021-05-18 doi:10.1101/2021.05.18.444675 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ Hybridization and range expansion in tamarisk beetles (Diorhabda spp.) introduced to North America for classical biological control ]]> https://biorxiv.org/content/10.1101/2021.05.18.444725v1?rss=1 Stahlke, A. R. Bitume, E. V. Ozsoy, A. Z. Bean, D. W. Veillet, A. Clark, M. I. Clark, E. I. Moran, P. Hufbauer, R. A. Hohenlohe, P. A. 2021-05-18 doi:10.1101/2021.05.18.444725 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ ppe51 variants promote non-replicating Mycobacterium tuberculosis to grow at acidic pH by selectively promoting glycerol uptake ]]> https://biorxiv.org/content/10.1101/2021.05.19.444820v1?rss=1 Dechow, S. J. Baker, J. J. Murto, M. R. Abramovitch, R. B. 2021-05-19 doi:10.1101/2021.05.19.444820 Cold Spring Harbor Laboratory Press 2021-05-19 <![CDATA[ Genetic isolation by distance underlies color pattern divergence in red-eyed treefrogs (Agalychnis callidryas) ]]> https://biorxiv.org/content/10.1101/2021.05.21.445051v1?rss=1 Clark, M. I. Bradburd, G. S. Akopyan, M. Vega, A. Rosenblum, E. B. Robertson, J. M. 2021-05-23 doi:10.1101/2021.05.21.445051 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ Intrapopulation adaptive variance supports selective breeding in a reef-building coral ]]> https://biorxiv.org/content/10.1101/2021.05.21.445206v1?rss=1 Drury, C. Bean, N. Harris, C. Hancock, J. Huckeba, J. H, C. M. Roach, T. Quinn, R. Gates, R. D. 2021-05-23 doi:10.1101/2021.05.21.445206 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ HIV-1 Nef and CycK:CDK13 antagonize SERINC5 for optimal viral infectivity ]]> https://biorxiv.org/content/10.1101/2021.05.24.445478v1?rss=1 Chai, Q. Li, S. Collins, M. K. Li, R. Ahmad, I. Johnson, S. F. Frabutt, D. A. Yang, Z. Shen, X. Sun, L. Hu, J. Hultquist, J. F. Peterlin, B. M. Zheng, Y.-H. 2021-05-24 doi:10.1101/2021.05.24.445478 Cold Spring Harbor Laboratory Press 2021-05-24 <![CDATA[ Adaptive phenotypic plasticity stabilizes evolution in fluctuating environments ]]> https://biorxiv.org/content/10.1101/2021.05.25.445672v1?rss=1 Lalejini, A. M. Ferguson, A. J. Grant, N. A. Ofria, C. 2021-05-26 doi:10.1101/2021.05.25.445672 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ TCAB1 is necessary for telomerase assembly ]]> https://biorxiv.org/content/10.1101/2021.05.27.445986v1?rss=1 Al-Masraf, B. S. Perez, G. I. Adams-Boone, K. Cohen, S. B. Han, L. Yu, K. Schmidt, J. C. 2021-05-27 doi:10.1101/2021.05.27.445986 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Lessons from 20 years of plant genome sequencing: an unprecedented resource in need of more diverse representation ]]> https://biorxiv.org/content/10.1101/2021.05.31.446451v1?rss=1 Marks, R. A. Hotaling, S. Frandsen, P. B. VanBuren, R. 2021-05-31 doi:10.1101/2021.05.31.446451 Cold Spring Harbor Laboratory Press 2021-05-31 <![CDATA[ Augmentation of task-relevant variability enhances consolidation of motor learning ]]> https://biorxiv.org/content/10.1101/2021.06.03.446469v1?rss=1 Pagano, M. Stochino, G. Casadio, M. Ranganathan, R. 2021-06-03 doi:10.1101/2021.06.03.446469 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ Computer-Assisted Mitotic Count Using a Deep Learning-based Algorithm Improves Inter-Observer Reproducibility and Accuracy in canine cutaneous mast cell tumors ]]> https://biorxiv.org/content/10.1101/2021.06.04.446287v1?rss=1 Bertram, C. A. Aubreville, M. Donovan, T. A. Bartel, A. Wilm, F. Marzahl, C. Assenmacher, C.-A. Becker, K. Bennett, M. Corner, S. Cossic, B. Denk, D. Dettwiler, M. Gonzalez, B. G. Gurtner, C. Haverkamp, A.-K. Heier, A. Lehmbecker, A. Merz, S. Noland, E. L. Plog, S. Schmidt, A. Sebastian, F. Sledge, D. G. Smedley, R. C. Tecilla, M. Thaiwong, T. Fuchs-Baumgartinger, A. Meuten, D. J. Breininger, K. Kiupel, M. Maier, A. Klopfleisch, R. 2021-06-05 doi:10.1101/2021.06.04.446287 Cold Spring Harbor Laboratory Press 2021-06-05 <![CDATA[ Multi-omics profiling of Earth's biomes reveals that microbial and metabolite composition are shaped by the environment ]]> https://biorxiv.org/content/10.1101/2021.06.04.446988v1?rss=1 Shaffer, J. P. Nothias, L.-F. Thompson, L. R. Jon, S. G. Salido, R. A. Couvillion, S. P. Brejnrod, A. D. Huang, S. Lejzerowicz, F. Lutz, H. L. Zhu, Q. Martino, C. Morton, J. T. Karthikeyan, S. Nothias-Esposito, M. Dührkop, K. Böcker, S. Kim, H. Aksenov, A. A. Bittremieux, W. Minich, J. J. Marotz, C. Bryant, M. M. Sanders, K. Schwartz, T. Humphrey, G. Vasquez-Baeza, Y. Tripathi, A. Parida, L. Carrieri, A. P. Haiminen, N. Beck, K. L. Das, P. Gonzalez, A. McDonald, D. Karst, S. M. Albertsen, M. Ackermann, G. DeReus, J. Thomas, T. Petras, D. Shade, A. St 2021-06-06 doi:10.1101/2021.06.04.446988 Cold Spring Harbor Laboratory Press 2021-06-06 <![CDATA[ BSCL2/Seipin Deficiency in Heart Causes Energy Deficit and Heart Failure via Inducing Excessive Lipid Catabolism ]]> https://biorxiv.org/content/10.1101/2021.06.07.447355v1?rss=1 Zhou, H. Li, J. Su, H. Li, J. Lydic, T. A. Young, M. E. Chen, W. 2021-06-07 doi:10.1101/2021.06.07.447355 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Bioelectromagnetic platform for stimulation ]]> https://biorxiv.org/content/10.1101/2021.06.07.447412v1?rss=1 Ashbaugh, R. C. Udpa, L. Israeli, R. R. Gilad, A. A. Pelled, G. 2021-06-07 doi:10.1101/2021.06.07.447412 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ It happened again: convergent evolution of acylglucose specialized metabolism in black nightshade and wild tomato ]]> https://biorxiv.org/content/10.1101/2021.06.08.447545v1?rss=1 Lou, Y.-R. Anthony, T. M. Fiesel, P. D. Arking, R. E. Christensen, E. M. Jones, A. D. Last, R. L. 2021-06-09 doi:10.1101/2021.06.08.447545 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ NDR1 and the Arabidopsis Plasma Membrane ATPase AHA5 are Required for Processes that Converge on Drought Tolerance and Immunity ]]> https://biorxiv.org/content/10.1101/2021.06.10.445978v1?rss=1 Lu, Y.-J. Chen, H. Corrion, A. Li, P. Buyuk, I. Samaradivakara, S. Wai, C.-M. Sakamoto, H. Santos, P. F. VanBuren, R. Kim, Y. Day, B. 2021-06-11 doi:10.1101/2021.06.10.445978 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Development of the Wheat Practical Haplotype Graph Database as a Resource for Genotyping Data Storage and Genotype Imputation ]]> https://biorxiv.org/content/10.1101/2021.06.10.447944v1?rss=1 Jordan, K. Bradbury, P. Miller, Z. R. Nyine, M. He, F. Fraser, M. Anderson, J. Mason, E. Katz, A. Pearce, S. Carter, A. H. Prather, S. Pumphrey, M. Chen, J. Cook, J. Liu, S. Rudd, J. Wang, Z. Chu, C. Ibrahim, A. M. H. Turkus, J. Olson, E. Nagarajan, R. Carver, B. Yan, L. Taagen, E. Sorrells, M. E. Ward, B. Ren, J. Akhunova, A. Bai, G. Bowden, R. Fiedler, J. Faris, J. Dubcovsky, J. Guttieri, M. Brown-Guedira, G. Buckler, E. S. Jannink, J.-L. Akhunov, E. 2021-06-11 doi:10.1101/2021.06.10.447944 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Holosteans contextualize the role of the teleost genome duplication in promoting the rise of evolutionary novelties in the ray-finned fish innate immune system ]]> https://biorxiv.org/content/10.1101/2021.06.11.448072v1?rss=1 Dornburg, A. Wcisel, D. J. Zapfe, K. Ferraro, E. Roupe-Abrams, L. Thompson, A. W. Braasch, I. Ota, T. Yoder, J. A. 2021-06-11 doi:10.1101/2021.06.11.448072 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Harnessing methylotrophs as a bacterial platform to reduce adverse effects of the use of the heavy lanthanide gadolinium in magnetic resonance imaging ]]> https://biorxiv.org/content/10.1101/2021.06.12.448192v1?rss=1 Good, N. M. Lee, H. Hawker, E. R. Gilad, A. Martinez-Gomez, N. C. 2021-06-12 doi:10.1101/2021.06.12.448192 Cold Spring Harbor Laboratory Press 2021-06-12 <![CDATA[ Longitudinal developmental trajectories do not follow cross-sectional age associations in hippocampal subfield and memory development ]]> https://biorxiv.org/content/10.1101/2021.06.14.448300v1?rss=1 Keresztes, A. Raffington, L. Bender, A. R. Bögl, K. Heim, C. Shing, Y. L. 2021-06-15 doi:10.1101/2021.06.14.448300 Cold Spring Harbor Laboratory Press 2021-06-15 <![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[ Bioluminescent Genetically Encoded Glutamate Indicator for Molecular Imaging of Neuronal Activity ]]> https://biorxiv.org/content/10.1101/2021.06.16.448690v1?rss=1 Petersen, E. D. Crespo, E. C. Lambert, G. G. Zanca, A. T. Orcutt, R. Hochgeschwender, U. Nathan, S. C. Gilad, A. 2021-06-17 doi:10.1101/2021.06.16.448690 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Supervised Capacity Preserving Mapping: A Clustering Guided Visualization Method for scRNAseq data ]]> https://biorxiv.org/content/10.1101/2021.06.18.448900v1?rss=1 Zhai, Z. Lei, Y. L. Wang, R. Xie, Y. 2021-06-19 doi:10.1101/2021.06.18.448900 Cold Spring Harbor Laboratory Press 2021-06-19 <![CDATA[ Genome-wide ChIPseq analysis of AhR, COUP-TF, and HNF4 enrichment in TCDD-treated mouse liver ]]> https://biorxiv.org/content/10.1101/2021.06.18.448955v1?rss=1 Cholico, G. N. Nault, R. Zacharewski, T. R. 2021-06-18 doi:10.1101/2021.06.18.448955 Cold Spring Harbor Laboratory Press 2021-06-18 <![CDATA[ LD-CNV: rapid and simple discovery of chromosomal translocations using linkage disequilibrium between copy number variable loci ]]> https://biorxiv.org/content/10.1101/2021.06.18.449059v1?rss=1 Comai, L. Amundson, K. R. Ordonez, B. Zhao, X. Tomaz Braz, G. Jiang, J. Henry, I. M. 2021-06-18 doi:10.1101/2021.06.18.449059 Cold Spring Harbor Laboratory Press 2021-06-18 <![CDATA[ A selective adenylyl cyclase 1 inhibitor relieves pain without causing tolerance ]]> https://biorxiv.org/content/10.1101/2021.06.23.448127v1?rss=1 Giacoletti, G. Price, T. Hoelz, L. V. B. Shremo Msdi, A. Vazquez-Falto, K. Amorim Fernandes, T. V. Santos de Pontes, V. Wang, H. Boechat, N. Nornoo, A. Brust, T. 2021-06-23 doi:10.1101/2021.06.23.448127 Cold Spring Harbor Laboratory Press 2021-06-23 <![CDATA[ Short-term dynamics of long-range corticocortical synapses revealed by selective optical stimulation ]]> https://biorxiv.org/content/10.1101/2021.06.24.449770v1?rss=1 Martinetti, L. E. Bonekamp, K. E. Autio, D. M. Crandall, S. R. 2021-06-25 doi:10.1101/2021.06.24.449770 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Intramolecular 13C/12C signals inform about carbon allocation in plant leaves ]]> https://biorxiv.org/content/10.1101/2021.06.25.449710v1?rss=1 Wieloch, T. Sharkey, T. D. Werner, R. A. Schleucher, J. 2021-06-25 doi:10.1101/2021.06.25.449710 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Carbohydrate sulfation as a mechanism for fine-tuning Siglec ligands ]]> https://biorxiv.org/content/10.1101/2021.06.27.450109v1?rss=1 Jung, J. Enterina, J. R. Bui, D. T. Mozaneh, F. Lin, P.-H. Nitin, H. Kuo, C.-W. Rodrigues, E. Bhattacherjee, A. Raeisimakiani, P. Daskhan, G. C. St. Laurent, C. D. Khoo, K.-H. Mahal, L. K. Zandberg, W. F. Huang, X. Klassen, J. S. Macauley, M. S. 2021-06-28 doi:10.1101/2021.06.27.450109 Cold Spring Harbor Laboratory Press 2021-06-28 <![CDATA[ Systems Genetics of Single Nucleotide Polymorphisms at the Drosophila Obp56h Locus ]]> https://biorxiv.org/content/10.1101/2021.06.28.450219v1?rss=1 Mokashi, S. S. Shankar, V. Johnstun, J. A. Huang, W. Mackay, T. F. C. Anholt, R. R. H. 2021-06-29 doi:10.1101/2021.06.28.450219 Cold Spring Harbor Laboratory Press 2021-06-29 <![CDATA[ High throughput measurement of Arabidopsis thaliana fitness traits using transfer learning ]]> https://biorxiv.org/content/10.1101/2021.07.01.450758v1?rss=1 Wang, P. Meng, F. Donaldson, P. Horan, S. Panchy, N. L. Vischulis, E. Winship, E. Conner, J. K. Lehti-Shiu, M. D. Shiu, S.-H. 2021-07-01 doi:10.1101/2021.07.01.450758 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ Identifying Site-specific Superoxide and Hydrogen Peroxide Production Rates from the Mitochondrial Electron Transport System Using a Computational Strategy ]]> https://biorxiv.org/content/10.1101/2021.07.01.450791v1?rss=1 Duong, Q. V. Levitsky, Y. Dessinger, M. J. Bazil, J. N. 2021-07-02 doi:10.1101/2021.07.01.450791 Cold Spring Harbor Laboratory Press 2021-07-02 <![CDATA[ FishExp: a comprehensive database and analysis platform for gene expression and alternative splicing of fish species ]]> https://biorxiv.org/content/10.1101/2021.07.01.450804v1?rss=1 Tan, S. Wang, W. Jie, W. Liu, J. 2021-07-02 doi:10.1101/2021.07.01.450804 Cold Spring Harbor Laboratory Press 2021-07-02 <![CDATA[ The crucial role of genome-wide genetic variation in conservation ]]> https://biorxiv.org/content/10.1101/2021.07.05.451163v1?rss=1 Kardos, M. Armstrong, E. Fitzpatrick, S. W. Hauser, S. Hedrick, P. Miller, J. Tallmon, D. Funk, W. C. 2021-07-06 doi:10.1101/2021.07.05.451163 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Selection-Enriched Genomic Loci (SEGL) Reveals Genetic Loci for Environmental Adaptation and Photosynthetic Productivity in Chlamydomonas reinhardtii. ]]> https://biorxiv.org/content/10.1101/2021.07.06.451237v1?rss=1 Lucker, B. F. Panchy, N. Temple, J. Benning, U. Bibik, J. Neofotis, P. Weissman, J. Baxter, I. Shu, S.-H. Kramer, D. 2021-07-06 doi:10.1101/2021.07.06.451237 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Pseudomonas syringae effector AvrE associates with plant membrane nanodomains and binds phosphatidylinositides in vitro ]]> https://biorxiv.org/content/10.1101/2021.07.08.451616v1?rss=1 Xin, X. Kinch, L. Cai, B. Paasch, B. C. Kvitko, B. Grishin, N. V. He, S. Y. 2021-07-08 doi:10.1101/2021.07.08.451616 Cold Spring Harbor Laboratory Press 2021-07-08 <![CDATA[ scSGL: Signed Graph Learning for Single-Cell Gene Regulatory Network Inference ]]> https://biorxiv.org/content/10.1101/2021.07.08.451697v1?rss=1 Karaaslanli, A. Saha, S. Aviyente, S. Maiti, T. 2021-07-11 doi:10.1101/2021.07.08.451697 Cold Spring Harbor Laboratory Press 2021-07-11 <![CDATA[ Inhibitory Proteins Block Substrate Access to the Active Site of Bacillus subtilis Intramembrane Metalloprotease SpoIVFB ]]> https://biorxiv.org/content/10.1101/2021.07.09.451828v1?rss=1 Olenic, S. Heo, L. Feig, M. Kroos, L. 2021-07-10 doi:10.1101/2021.07.09.451828 Cold Spring Harbor Laboratory Press 2021-07-10 <![CDATA[ Evolution with private resources reverses some changes from long-term evolution with public resources ]]> https://biorxiv.org/content/10.1101/2021.07.11.451942v1?rss=1 van Raay, K. Stolyar, S. Sevigny, J. Draghi, J. Lenski, R. E. Marx, C. J. Kerr, B. Zaman, L. 2021-07-12 doi:10.1101/2021.07.11.451942 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ A rapid F0 CRISPR screen in zebrafish to identify regulators of neuronal development in the enteric nervous system ]]> https://biorxiv.org/content/10.1101/2021.07.17.452230v1?rss=1 Davidson, A. E. Straquadine, N. R. Cook, S. A. Liu, C. G. Ganz, J. 2021-07-18 doi:10.1101/2021.07.17.452230 Cold Spring Harbor Laboratory Press 2021-07-18 <![CDATA[ Cytolytic memory CD4+ T cell clonotypes are expanded during Plasmodium falciparum infection ]]> https://biorxiv.org/content/10.1101/2021.07.21.453277v1?rss=1 Furtado, R. Delahaye, F. Zhang, J. Sung, J. Karell, P. Kim, R. S. Caillat-Zucman, S. Liang, L. Felgner, P. Bauleni, A. Gama, S. Buchwald, A. Taylor, T. Seydel, K. Laufer, M. Daily, J. Lauvau, G. 2021-07-23 doi:10.1101/2021.07.21.453277 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ In vitro and in vivo analysis of microvesicle-mediated metastasis using a bright, red-shifted bioluminescent reporter protein of extracellular vesicles ]]> https://biorxiv.org/content/10.1101/2021.07.23.453512v1?rss=1 Zarea, A. A. Perez, G. I. Broadbent, D. Dolgikh, B. Bernard, M. P. Withrow, A. McGill, A. Toomajian, V. Thampy, L. K. Harkema, J. Walker, J. R. Kirkland, T. A. Bachmann, M. H. Schmidt, J. Kanada, M. 2021-07-25 doi:10.1101/2021.07.23.453512 Cold Spring Harbor Laboratory Press 2021-07-25 <![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[ Average stride length and stride rate of Thoroughbreds and Quarter Horses during 'Sprint and 'Classic races ]]> https://biorxiv.org/content/10.1101/2021.07.27.453998v1?rss=1 Vergara-Hernandez, F. B. Nielsen, B. D. Robison, C. I. Fabus, T. A. Kompare, J. L. LeCompte Lazic, R. A. Colbath, A. C. 2021-07-27 doi:10.1101/2021.07.27.453998 Cold Spring Harbor Laboratory Press 2021-07-27 <![CDATA[ A non-functional copy of the salmonid sex determining gene (sdY) is responsible for the "apparent" XY females in Chinook salmon, Oncorhynchus tshawytscha. ]]> https://biorxiv.org/content/10.1101/2021.07.28.454148v1?rss=1 Bertho, S. Herpin, A. Jouanno, E. Yano, A. Bobe, J. Parrinello, H. Journot, L. Guyomard, R. Thomas, M. Swanson, P. McKinney, G. J. Kevin, W. Mariah, M. Schartl, M. Guiguen, Y. 2021-07-28 doi:10.1101/2021.07.28.454148 Cold Spring Harbor Laboratory Press 2021-07-28 <![CDATA[ Competitive advantage of oral streptococci for colonization of the middle ear mucosa ]]> https://biorxiv.org/content/10.1101/2021.07.28.454259v1?rss=1 Jacob, K. M. Reguera, G. 2021-07-29 doi:10.1101/2021.07.28.454259 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Neural temporal context reinstatement of event structure during memory recall ]]> https://biorxiv.org/content/10.1101/2021.07.30.454370v1?rss=1 Lohnas, L. J. Healey, K. Davachi, L. 2021-08-01 doi:10.1101/2021.07.30.454370 Cold Spring Harbor Laboratory Press 2021-08-01 <![CDATA[ Catalase protects against non-enzymatic decarboxylations during photorespiration ]]> https://biorxiv.org/content/10.1101/2021.08.04.455084v1?rss=1 Bao, H. Morency, M. Rianti, W. Saeheng, S. Roje, S. Weber, A. P. M. Walker, B. J. 2021-08-05 doi:10.1101/2021.08.04.455084 Cold Spring Harbor Laboratory Press 2021-08-05 <![CDATA[ Histone H3K36me2-specific methyltransferase ASH1L is required for the MLL-AF9-induced leukemogenesis ]]> https://biorxiv.org/content/10.1101/2021.08.05.455280v1?rss=1 Aljazi, M. B. Gao, Y. Wu, Y. Mias, G. I. He, J. 2021-08-06 doi:10.1101/2021.08.05.455280 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Charting Brain Growth and Aging at High Spatial Precision ]]> https://biorxiv.org/content/10.1101/2021.08.08.455487v1?rss=1 Rutherford, S. Fraza, C. Dinga, R. Kia, S. M. Wolfers, T. Zabihi, M. Berthet, P. Worker, A. Verdi, S. Andrews, D. Han, L. Bayer, J. Dazzan, P. McGuire, P. Mocking, R. T. Schene, A. Sripada, C. Tso, I. F. Duval, E. R. Chang, S.-E. Pennix, B. W. Heitzeg, M. M. Burt, S. A. Hyde, L. Amaral, D. Nordahl, C. W. Andreasssen, O. A. Westlye, L. T. Zahn, R. Ruhe, H. G. Beckmann, C. Marquand, A. F. 2021-08-08 doi:10.1101/2021.08.08.455487 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ Deterministic shifts in molecular evolution correlate with convergence to annualism in killifishes ]]> https://biorxiv.org/content/10.1101/2021.08.09.455723v1?rss=1 Thompson, A. W. Black, A. C. Huang, Y. Shi, Q. Furness, A. I. Braasch, I. Hoffmann, F. G. Orti, G. 2021-08-10 doi:10.1101/2021.08.09.455723 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Live imaging YAP signaling in vivo with fusion reporter mice ]]> https://biorxiv.org/content/10.1101/2021.08.11.456026v1?rss=1 Gu, B. Bradshaw, B. Zhu, M. Sun, Y. Hopyan, S. Rossant, J. 2021-08-12 doi:10.1101/2021.08.11.456026 Cold Spring Harbor Laboratory Press 2021-08-12 <![CDATA[ ColabFold - Making protein folding accessible to all ]]> https://biorxiv.org/content/10.1101/2021.08.15.456425v1?rss=1 Mirdita, M. Ovchinnikov, S. Steinegger, M. 2021-08-15 doi:10.1101/2021.08.15.456425 Cold Spring Harbor Laboratory Press 2021-08-15 <![CDATA[ The SEEL Motif and Members of the MYB-related REVEILLE Transcription Factor Family are Important for the Expression of LORELEI in the Synergid Cells of the Arabidopsis Female Gametophyte ]]> https://biorxiv.org/content/10.1101/2021.08.17.456723v1?rss=1 Noble, J. A. Seddon, A. Uygun, S. Smith, S. E. Shiu, S.-H. Palanivelu, R. 2021-08-19 doi:10.1101/2021.08.17.456723 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Mapping of genotype-by-environment interactions in phenology identifies two cues for flowering in switchgrass (Panicum virgatum) ]]> https://biorxiv.org/content/10.1101/2021.08.19.456975v1?rss=1 MacQueen, A. H. Zhang, L. Bonette, J. Boe, A. R. Fay, P. A. Fritschi, F. B. Lowry, D. B. Mitchell, R. B. Rouquette, F. M. Wu, Y. Juenger, T. E. 2021-08-19 doi:10.1101/2021.08.19.456975 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Disruption of Brachypodium Lichenase Alters Metabolism of Mixed-linkage Glucan and Starch ]]> https://biorxiv.org/content/10.1101/2021.08.20.457123v1?rss=1 Fan, M. Jensen, J. K. Zemelis-Durfee, S. Kim, S.-J. Chan, J.-Y. Beaudry, C. M. Brandizzi, F. Wilkerson, C. G. 2021-08-21 doi:10.1101/2021.08.20.457123 Cold Spring Harbor Laboratory Press 2021-08-21 <![CDATA[ Frequency-dependent hybridization contributes to habitat segregation in monkeyflowers ]]> https://biorxiv.org/content/10.1101/2021.08.21.457231v1?rss=1 Toll, K. Lowry, D. 2021-08-23 doi:10.1101/2021.08.21.457231 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ Differential gene expression reveals host factors for viral shedding variation in mallards (Anas platyrhynchos) infected with low-pathogenic avian influenza virus ]]> https://biorxiv.org/content/10.1101/2021.08.23.457327v1?rss=1 Dolinski, A. C. Homola, J. J. Jankowski, M. D. Robinson, J. D. Owen, J. C. 2021-08-23 doi:10.1101/2021.08.23.457327 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ Production and composition of group B streptococcal membrane vesicles varies across diverse lineages ]]> https://biorxiv.org/content/10.1101/2021.08.24.457602v1?rss=1 McCutcheon, C. R. Gaddy, J. Aronoff, D. M. Petroff, M. Manning, S. D. 2021-08-25 doi:10.1101/2021.08.24.457602 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ Light Potentials of Photosynthetic Energy Storage in the Field: What limits the ability to use or dissipate rapidly increased light energy? ]]> https://biorxiv.org/content/10.1101/2021.08.26.457798v1?rss=1 Kanazawa, A. Chattopadhyay, A. Kuhlgert, S. Tuitupou, H. Maiti, T. Kramer, D. M. 2021-08-28 doi:10.1101/2021.08.26.457798 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Predation risk differentially affects aphid morphotypes: impacts on prey behavior, fecundity and transgenerational dispersal morphology ]]> https://biorxiv.org/content/10.1101/2021.08.30.458248v1?rss=1 Hermann, S. L. Bird, S. Ellis, D. Landis, D. 2021-09-01 doi:10.1101/2021.08.30.458248 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Complex genetic patterns and distribution limits mediated by native congeners of the worldwide invasive red-eared slider turtle ]]> https://biorxiv.org/content/10.1101/2021.09.02.458785v1?rss=1 Espindola, S. Vazquez-Dominguez, E. Nakamura, M. Osorio-Olvera, L. Martinez-Meyer, E. Myers, E. A. Overcast, I. Reid, B. N. Burbrink, F. 2021-09-04 doi:10.1101/2021.09.02.458785 Cold Spring Harbor Laboratory Press 2021-09-04 <![CDATA[ Bioactive exometabolites drive maintenance competition in simple bacterial communities ]]> https://biorxiv.org/content/10.1101/2021.09.05.459016v1?rss=1 Chodkowski, J. L. Shade, A. 2021-09-05 doi:10.1101/2021.09.05.459016 Cold Spring Harbor Laboratory Press 2021-09-05 <![CDATA[ Parkinson's Disease-Associated, Sex-specific Changes in DNA Methylation at PARK7 (DJ-1), ATXN1, SLC17A6, NR4A2, and PTPRN2 in Cortical Neurons ]]> https://biorxiv.org/content/10.1101/2021.09.08.459434v1?rss=1 Kochmanski, J. Kuhn, N. C. Bernstein, A. I. 2021-09-09 doi:10.1101/2021.09.08.459434 Cold Spring Harbor Laboratory Press 2021-09-09 <![CDATA[ Benchmarking of a Bayesian single cell RNAseq differential gene expression test for dose-response study designs. ]]> https://biorxiv.org/content/10.1101/2021.09.08.459475v1?rss=1 Nault, R. Saha, S. Bhattacharya, S. Dodson, J. P. Sinha, S. Maiti, T. Zacharewski, T. R. 2021-09-10 doi:10.1101/2021.09.08.459475 Cold Spring Harbor Laboratory Press 2021-09-10 <![CDATA[ Prevention of Drug-Induced Lung Fibrosis via Inhibition of the MRTF/SRF Transcription Pathway ]]> https://biorxiv.org/content/10.1101/2021.09.09.459118v1?rss=1 Pawelec, K. Varnum, M. Harkema, J. R. Auerbach, B. Larsen, S. D. Neubig, R. R. 2021-09-10 doi:10.1101/2021.09.09.459118 Cold Spring Harbor Laboratory Press 2021-09-10 <![CDATA[ Fine-tuning functional syndromes for stressful environments: lessons on survival from the South African resurrection plant Myrothamnus flabellifolia ]]> https://biorxiv.org/content/10.1101/2021.09.12.459909v1?rss=1 Marks, R. A. Mbobe, M. Greyling, M. Pretorius, J. McLetchie, D. N. VanBuren, R. Farrant, J. 2021-09-15 doi:10.1101/2021.09.12.459909 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Impaired KDM2B-mediated PRC1 recruitment to chromatin causes neural stem cell senescence and ASD/ID-like behavioral deficits ]]> https://biorxiv.org/content/10.1101/2021.09.13.459918v1?rss=1 Gao, Y. Duque-Wilckens, N. Aljazi, M. B. Moeser, A. J. Mias, G. I. Robison, A. J. Zhang, Y. He, J. 2021-09-15 doi:10.1101/2021.09.13.459918 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Elevated phosphorylation of EGFR in NSCLC due to mutations in PTPRH ]]> https://biorxiv.org/content/10.1101/2021.09.14.460311v1?rss=1 Swiatnicki, M. R. Rennhack, J. P. Hollern, D. Perry, A. V. Kubiak, R. Riveria Riveria, S. M. O'Reilly, S. Andrechek, E. R. 2021-09-14 doi:10.1101/2021.09.14.460311 Cold Spring Harbor Laboratory Press 2021-09-14 <![CDATA[ Actively translated uORFs reduce translation and mRNA stability independent of NMD in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2021.09.16.460672v1?rss=1 Wu, H.-Y. L. Hsu, P. Y. 2021-09-16 doi:10.1101/2021.09.16.460672 Cold Spring Harbor Laboratory Press 2021-09-16 <![CDATA[ Effects of early life adversity on meningeal mast cells and proinflammatory gene expression in male and female Mus musculus ]]> https://biorxiv.org/content/10.1101/2021.09.17.460793v1?rss=1 Duque-Wilckens, N. Sarno, E. Teis, R. Stoelting, F. Khalid, S. Dairi, Z. Douma, A. Maradiaga, N. Thelen, K. Robison, A. J. Moeser, A. 2021-09-17 doi:10.1101/2021.09.17.460793 Cold Spring Harbor Laboratory Press 2021-09-17 <![CDATA[ Darwin's finches - an adaptive radiation constructed from ancestral genetic modules ]]> https://biorxiv.org/content/10.1101/2021.09.17.460815v1?rss=1 Rubin, C.-J. Enbody, E. D. Dobreva, M. P. Abzhanov, A. Davis, B. W. Lamichhaney, S. Pettersson, M. E. Sprehn, C. G. Valle, C. A. Vasco, K. Wallerman, O. Grant, B. R. Grant, P. Andersson, L. 2021-09-18 doi:10.1101/2021.09.17.460815 Cold Spring Harbor Laboratory Press 2021-09-18 <![CDATA[ Identification and Functional Annotation of Long Intergenic Non-coding RNAs in the Brassicaceae ]]> https://biorxiv.org/content/10.1101/2021.09.17.460835v1?rss=1 24 Tbp of RNA-seq data from >16,000 experiments to identify ~130,000 lincRNAs in four Brassicaceae: Arabidopsis thaliana, Camelina sativa, Brassica rapa, and Eutrema salsugineum. We used Nanopore RNA-seq, transcriptome-wide structural information, peptide data, and epigenomic data to characterize these lincRNAs and identify functional motifs. We then used comparative genomic and transcriptomic approaches to highlight lincRNAs in our dataset with sequence or transcriptional evolutionary conservation, including lincRNAs transcribed adjacent to orthologous genes that display little sequence similarity and likely function as transcriptional regulators. Finally, we used guilt-by-association techniques to further classify these lincRNAs according to putative function. LincRNAs with Brassicaceae-conserved putative miRNA binding motifs, short ORFs, and whose expression is modulated by abiotic stress are a few of the annotations that will prioritize and guide future functional analyses. ]]> Palos, K. R. Nelson Dittrich, A. C. Yu, L. Brock, J. R. Wu, L. Sokolowska, E. Skirycz, A. Hsu, P. Y. Lyons, E. Beilstein, M. Nelson, A. D. L. 2021-09-20 doi:10.1101/2021.09.17.460835 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ Non-target impacts of fungicide disturbance on phyllosphere yeasts in different crop species and management systems ]]> https://biorxiv.org/content/10.1101/2021.09.20.461135v1?rss=1 Noel, Z. A. Longley, R. Benucci, G. M. Trail, F. Chilvers, M. I. Bonito, G. M. 2021-09-21 doi:10.1101/2021.09.20.461135 Cold Spring Harbor Laboratory Press 2021-09-21 <![CDATA[ Differential Network Analysis of Longitudinal Gene Expression in Response to Perturbations. ]]> https://biorxiv.org/content/10.1101/2021.09.21.461277v1?rss=1 Xue, S. Rogers, L. R. Zheng, M. He, J. Piermarocchi, C. Mias, G. I. 2021-09-24 doi:10.1101/2021.09.21.461277 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Mice With Monoallelic GNAO1 Loss Exhibit Reduced Inhibitory Synaptic Input To Cerebellar Purkinje Cells ]]> https://biorxiv.org/content/10.1101/2021.09.23.461583v1?rss=1 Feng, H. Yuan, Y. Williams, M. R. Roy, A. Leipprandt, J. Neubig, R. R. 2021-09-24 doi:10.1101/2021.09.23.461583 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Insight into mammary gland development and tumor prevention in a newly developed metastatic mouse model of breast cancer ]]> https://biorxiv.org/content/10.1101/2021.09.24.461727v1?rss=1 To, B. Broeker, C. Jhan, J.-R. Rempel, R. Rennhack, J. P. Hollern, D. Jackson, L. Judah, D. Swiatnicki, M. Bylett, E. Kubiak, R. Honeysett, J. Reaz, S. Nevins, J. R. Andrechek, E. R. 2021-09-25 doi:10.1101/2021.09.24.461727 Cold Spring Harbor Laboratory Press 2021-09-25 <![CDATA[ Transcriptome-wide association and prediction for carotenoids and tocochromanols in fresh sweet corn kernels ]]> https://biorxiv.org/content/10.1101/2021.09.24.461734v1?rss=1 Hershberger, J. Tanaka, R. Wood, J. C. Kaczmar, N. Wu, D. Hamilton, J. P. DellaPenna, D. Buell, C. R. Gore, M. A. 2021-09-25 doi:10.1101/2021.09.24.461734 Cold Spring Harbor Laboratory Press 2021-09-25 <![CDATA[ Attachment strength of seed mucilage prevents seed dislodgement in high surface flow: a mechanistic investigation ]]> https://biorxiv.org/content/10.1101/2021.09.25.461784v1?rss=1 Pan, V. S. Girvin, C. LoPresti, E. F. 2021-09-25 doi:10.1101/2021.09.25.461784 Cold Spring Harbor Laboratory Press 2021-09-25 <![CDATA[ Atomic-Resolution Prediction of Degrader-mediated Ternary Complex Structures by Combining Molecular Simulations with Hydrogen Deuterium Exchange ]]> https://biorxiv.org/content/10.1101/2021.09.26.461830v1?rss=1 Dixon, T. MacPherson, D. Mostofian, B. Dauzhenka, T. Lotz, S. McGee, D. Shechter, S. Shrestha, U. Wiewiora, R. McDargh, Z. A. Pei, F. Pal, R. Ribeiro, J. V. Wilkerson, T. Sachdeva, V. Gao, N. Jain, S. Sparks, S. Li, Y. Vinitsky, A. Razavi, A. M. Kolossvary, I. Imbriglio, J. Evdokimov, A. Bergeron, L. Dickson, A. Xu, H. Sherman, W. Izaguirre, J. A. 2021-09-26 doi:10.1101/2021.09.26.461830 Cold Spring Harbor Laboratory Press 2021-09-26 <![CDATA[ Long-term experimental evolution decouples size and production costs in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2021.09.28.462250v1?rss=1 Marshall, D. Malerba, M. Lines, T. Sezmis, A. Hasan, C. Lenski, R. McDonald, M. 2021-09-28 doi:10.1101/2021.09.28.462250 Cold Spring Harbor Laboratory Press 2021-09-28 <![CDATA[ Daily ranging and den usage patterns structure fission-fusion dynamics and social associations in spotted hyenas ]]> https://biorxiv.org/content/10.1101/2021.10.01.462772v1?rss=1 Strauss, E. D. Jensen, F. H. Gersick, A. S. Thomas, M. Holekamp, K. E. Strandburg-Peshkin, A. 2021-10-01 doi:10.1101/2021.10.01.462772 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ A general theoretical framework for trait-based eco-evolutionary dynamics: population structure, intraspecific variation, and community assembly ]]> https://biorxiv.org/content/10.1101/2021.10.01.462789v1?rss=1 Wickman, J. Koffel, T. Klausmeier, C. A. 2021-10-02 doi:10.1101/2021.10.01.462789 Cold Spring Harbor Laboratory Press 2021-10-02 <![CDATA[ OXPHOS Promotes Apoptotic Resistance and Persistence in TH17 cells ]]> https://biorxiv.org/content/10.1101/2021.10.01.462812v1?rss=1 Hong, H. Mbah, N. Shan, M. Loesel, K. Lin, L. Sajjakulnukit, P. Andren, A. Hayashi, A. Magnuson, B. Li, Z. Xie, Y. Zhang, L. Lei, Y. L. Opipari, A. Arguello, R. J. Kryczek, I. Kamada, N. Zou, W. Franchi, L. Lyssiotis, C. A. 2021-10-01 doi:10.1101/2021.10.01.462812 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Engineered endosymbionts capable of directing mammalian cell gene expression ]]> https://biorxiv.org/content/10.1101/2021.10.05.463266v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@2b5935org.highwire.dtl.DTLVardef@1edd8edorg.highwire.dtl.DTLVardef@3cb5b9org.highwire.dtl.DTLVardef@1be9b5f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Madsen, C. S. Makela, A. V. Greeson, E. M. Hardy, J. W. Contag, C. H. 2021-10-06 doi:10.1101/2021.10.05.463266 Cold Spring Harbor Laboratory Press 2021-10-06 <![CDATA[ Tracking the fates of iron-labeled tumor cells in vivo using Magnetic Particle Imaging ]]> https://biorxiv.org/content/10.1101/2021.10.06.463387v1?rss=1 Makela, A. V. Schott, M. A. Sehl, O. C. Gevaert, J. J. Foster, P. J. Contag, C. H. 2021-10-07 doi:10.1101/2021.10.06.463387 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ Convergent evolution of polyploid genomes from across the eukaryotic tree of life ]]> https://biorxiv.org/content/10.1101/2021.10.08.463691v1?rss=1 Hao, Y. Fleming, J. Petterson, J. Lyons, E. Edger, P. P. Pires, C. Thorne, J. L. Conant, G. C. 2021-10-10 doi:10.1101/2021.10.08.463691 Cold Spring Harbor Laboratory Press 2021-10-10 <![CDATA[ Investigating the growth of an engineered strain of Cyanobacteria with an Agent-Based Model and a Recurrent Neural Network ]]> https://biorxiv.org/content/10.1101/2021.10.11.463942v1?rss=1 Sakkos, J. Weaver, J. Robertson, C. Li, B. Taniguchi, D. Maheshwari, K. Ducat, D. Zuliani, P. McGough, A. S. Curtis, T. P. Fuentes-Cabrera, M. 2021-10-12 doi:10.1101/2021.10.11.463942 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ Multi-layer Regulation of Rubisco in Response to Altered Carbon Status in Synechococcus elongatus PCC 7942 ]]> https://biorxiv.org/content/10.1101/2021.10.11.463961v1?rss=1 Singh, A. K. Santos-Merino, M. Sakkos, J. K. Walker, B. J. Ducat, D. C. 2021-10-12 doi:10.1101/2021.10.11.463961 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ The edible seaweed Laminaria japonica contains cholesterol analogues that inhibit Lipid Peroxidation and Cyclooxygenase Enzymes ]]> https://biorxiv.org/content/10.1101/2021.10.11.463984v1?rss=1 50% than the other compounds. In addition, the results of molecular docking revealed that the 5 sterols were located in different pocket of COX-1 and -2 and fucosterol with tetracyclic skeletons and olefin methine achieved the highest binding energy (-7.85 and -9.02 kcal/mol) through hydrophobic interactions and hydrogen bond. Our results confirm the presence of 5 sterols in L. japonica and its significant anti-inflammatory and antioxidant activity. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/463984v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@16c3f43org.highwire.dtl.DTLVardef@1ad7385org.highwire.dtl.DTLVardef@7b3c4borg.highwire.dtl.DTLVardef@b3675a_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LISterols 29-hydroperoxy-stigmasta-5,24(28)-dien-3{beta}-ol and 24-hydroperoxy-24-vinyl-cholesterol are identified for the first time in L. japonica. C_LIO_LISaringosterol, 24-methylenecholesterol and fucosterol showed strong LPO inhibitory activity. C_LIO_LIFucosterol showed highest binding affinity for COX-1 and -2 enzymes through hydrophobic interactions. C_LI ]]> Lu, X. Dissanayake, A. Xiao, C. Gao, J. Zhao, M. Nair, M. G. 2021-10-11 doi:10.1101/2021.10.11.463984 Cold Spring Harbor Laboratory Press 2021-10-11 <![CDATA[ Uncovering the Genetic Architecture of Broad Antisocial Behavior through a Genome-Wide Association Study Meta-analysis. ]]> https://biorxiv.org/content/10.1101/2021.10.19.462578v1?rss=1 Tielbeek, J. J. Uffelmann, E. Williams, B. S. Colodro-Conde, L. Gagnon, E. Mallard, T. T. Levitt, B. E. Jansen, P. R. Johansson, A. Sallis, H. M. Pistis, G. Saunders, G. R. Allegrini, A. G. Rimfeld, K. Konte, B. Klein, M. Hartmann, A. M. Salvatore, J. E. Nolte, I. M. Demontis, D. Malmberg, A. Burt, S. A. Savage, J. E. Sugden, K. Poulton, R. Harris, K. M. Vrieze, S. McGue, M. Iacono, W. G. Mota, N. R. Mill, J. Viana, J. F. Mitchell, B. L. Morosoli, J. J. Andlauer, T. F. M. Ouellet-Morin, I. Tremblay, R. E. Cote, S. M. Gouin, J.-P. Brendgen, M. R. Dionne, 2021-10-20 doi:10.1101/2021.10.19.462578 Cold Spring Harbor Laboratory Press 2021-10-20 <![CDATA[ The glutathione import system satisfies the Staphylococcus aureus nutrient sulfur requirement and promotes interspecies competition. ]]> https://biorxiv.org/content/10.1101/2021.10.26.465763v1?rss=1 Lensmire, J. M. Wischer, M. R. Sosinski, L. M. Ensink, E. Dodson, J. P. Shook, J. C. Delekta, P. C. Cooper, C. C. Havlichek, D. Mulks, M. H. Lunt, S. Y. Ravi, J. Hammer, N. D. 2021-10-26 doi:10.1101/2021.10.26.465763 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Qualitative and quantitative top-down proteomics of human colorectal cancer cell lines identified 23000 proteoforms and revealed drastic proteoform-level differences between metastatic and non-metastatic cancer cells ]]> https://biorxiv.org/content/10.1101/2021.10.27.466093v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@3ee5faorg.highwire.dtl.DTLVardef@16cae5forg.highwire.dtl.DTLVardef@2c0bd0org.highwire.dtl.DTLVardef@1bb9530_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> McCool, E. N. Xu, T. Chen, W. Beller, N. C. Nolan, S. M. Hummon, A. B. Liu, X. Sun, L. 2021-10-28 doi:10.1101/2021.10.27.466093 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ The plastoglobule-localized AtABC1K6 is a Mn2+-dependent protein kinase necessary for timely transition to reproductive growth ]]> https://biorxiv.org/content/10.1101/2021.10.28.466314v1?rss=1 Espinoza-Corral, R. Lundquist, P. K. 2021-10-28 doi:10.1101/2021.10.28.466314 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Evaluation of machine learning models for proteoform retention and migration time prediction in top-down mass spectrometry ]]> https://biorxiv.org/content/10.1101/2021.10.31.466700v1?rss=1 0.91) for proteoform retention time prediction and that the Prosit model and a fully connected neural network model obtained a high accuracy (R2 > 0.94) for proteoform migration time prediction. ]]> Chen, W. McCool, E. N. Sun, L. Zang, Y. Xia, N. Liu, X. 2021-11-03 doi:10.1101/2021.10.31.466700 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Oxytocin promotes epicardial cell activation and heart regeneration after cardiac injury ]]> https://biorxiv.org/content/10.1101/2021.11.01.466355v1?rss=1 Wasserman, A. H. Lewis-Israeli, Y. R. Huang, A. R. Dooley, M. D. Mitchell, A. L. Venkatesan, M. Aguirre, A. 2021-11-03 doi:10.1101/2021.11.01.466355 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Partial characterization and the evaluation of antimicrobial activities of silver nanoparticles biosynthesized from Cymbopogon citratus leaf extract ]]> https://biorxiv.org/content/10.1101/2021.11.01.466798v1?rss=1 Rakib-Uz-Zaman, S. M. Nimeree Muntasir, M. Hoque Apu, E. Mowna, S. A. Khanom, M. G. Jahan, S. S. Akter, N. R. Khan, M. A. Shuborna, N. S. Shams, S. M. Khan, K. 2021-11-03 doi:10.1101/2021.11.01.466798 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Aryl hydrocarbon receptor (AhR) activation by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) dose-dependently shifts the gut microbiome consistent with the progression of steatosis to steatohepatitis with fibrosis ]]> https://biorxiv.org/content/10.1101/2021.11.02.466980v1?rss=1 Fling, R. R. Zacharewski, T. 2021-11-02 doi:10.1101/2021.11.02.466980 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Blueprint for Phasing and Assembling the Genomes of Heterozygous Polyploids: Application to the Octoploid Genome of Strawberry ]]> https://biorxiv.org/content/10.1101/2021.11.03.467115v1?rss=1 Hardigan, M. A. Feldmann, M. J. Pincot, D. D. Famula, R. A. Vachev, M. V. Madera, M. A. Zerbe, P. J. Mars, K. Peluso, P. Rank, D. Ou, S. Saski, C. A. Acharya, C. B. Cole, G. S. Yocca, A. E. Platts, A. E. Edger, P. P. Knapp, S. J. 2021-11-04 doi:10.1101/2021.11.03.467115 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Evaluation of plasma N-terminal pro-B-type natriuretic peptide levels in healthy North American Salukis with normal echocardiographic measurements. ]]> https://biorxiv.org/content/10.1101/2021.11.03.467139v1?rss=1 Gunasekaran, T. Brennan, C. Sanders, R. 2021-11-03 doi:10.1101/2021.11.03.467139 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ A New Bioink For Improved 3D Bioprinting Of Bone-Like Constructs ]]> https://biorxiv.org/content/10.1101/2021.11.04.467312v1?rss=1 Marsh, A. Apu, E. H. Bunn, M. Contag, C. H. Ashammakhi, N. Chatzistavrou, X. 2021-11-05 doi:10.1101/2021.11.04.467312 Cold Spring Harbor Laboratory Press 2021-11-05 <![CDATA[ Functional characterization of mutants deficient in N-terminal phosphorylation of the CF1 subunit beta ]]> https://biorxiv.org/content/10.1101/2021.11.04.467332v1?rss=1 Bock, R. Strand, D. D. Karcher, D. Ruf, S. Schadach, A. Schöttler, M. A. Sandoval-Ibanez, O. 2021-11-06 doi:10.1101/2021.11.04.467332 Cold Spring Harbor Laboratory Press 2021-11-06 <![CDATA[ Multiview Graph Learning for single-cell RNA sequencing data ]]> https://biorxiv.org/content/10.1101/2021.11.05.467476v1?rss=1 Karaaslanli, A. SAHA, S. Aviyente, S. Maiti, T. 2021-11-08 doi:10.1101/2021.11.05.467476 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ State-dependent modulation of activity in distinct layer 6 corticothalamic neurons in barrel cortex of awake mice ]]> https://biorxiv.org/content/10.1101/2021.11.08.467762v1?rss=1 Dash, S. Autio, D. M. Crandall, S. R. 2021-11-10 doi:10.1101/2021.11.08.467762 Cold Spring Harbor Laboratory Press 2021-11-10 <![CDATA[ Zymomonas mobilis ZM4 utilizes an acetaldehyde dehydrogenase to produce acetate ]]> https://biorxiv.org/content/10.1101/2021.11.09.468001v1?rss=1 Felczak, M. M. TerAvest, M. A. 2021-11-10 doi:10.1101/2021.11.09.468001 Cold Spring Harbor Laboratory Press 2021-11-10 <![CDATA[ Oxidative respiration through the bd-I and cbb3 oxidases is required for Vibrio cholerae pathogenicity and proliferation in vivo. ]]> https://biorxiv.org/content/10.1101/2021.11.11.468188v1?rss=1 Van Alst, A. J. Demey, L. M. DiRita, V. 2021-11-12 doi:10.1101/2021.11.11.468188 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ Investigating Carboxysome Morphology Dynamics with a Rotationally Invariant Variational Autoencoder ]]> https://biorxiv.org/content/10.1101/2021.11.15.468661v1?rss=1 Fuentes-Cabrera, M. Sakkos, J. K. Ducat, D. C. Ziatdinov, M. 2021-11-15 doi:10.1101/2021.11.15.468661 Cold Spring Harbor Laboratory Press 2021-11-15 <![CDATA[ Interleukin-6 Drives Key Pathologic Outcomes in Experimental Acetaminophen-induced Liver Failure ]]> https://biorxiv.org/content/10.1101/2021.11.15.468664v1?rss=1 Roth, K. Strickland, J. Gonzalez-Pons, R. Pant, A. Yen, T.-C. Freeborn, R. Kennedy, R. Bhushan, B. Boss, A. Rockwell, C. E. Dorrance, A. M. Apte, U. Luyendyk, J. P. Copple, B. L. 2021-11-16 doi:10.1101/2021.11.15.468664 Cold Spring Harbor Laboratory Press 2021-11-16 <![CDATA[ A genome in flux: homoeologous exchanges, subgenome dominance, and gene dosage balance constraints in resynthesized allopolyploid Brassica napus ]]> https://biorxiv.org/content/10.1101/2021.11.16.468838v1?rss=1 Bird, K. A. Pires, J. C. VanBuren, R. Xiong, Z. Edger, P. P. 2021-11-19 doi:10.1101/2021.11.16.468838 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Pre-implantation mouse embryo movement under hormonally altered conditions ]]> https://biorxiv.org/content/10.1101/2021.11.19.469319v1?rss=1 Lufkin, H. Flores, D. Raider, Z. Madhavan, M. Dawson, M. Coronel, A. Sharma, D. Arora, R. 2021-11-19 doi:10.1101/2021.11.19.469319 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Genome of the bi-annual Rio Pearlfish (Nematolebias whitei), a killifish model species for Eco-Evo-Devo ]]> https://biorxiv.org/content/10.1101/2021.11.24.469934v1?rss=1 Thompson, A. W. Wojtas, H. Davoll, M. Braasch, I. 2021-11-25 doi:10.1101/2021.11.24.469934 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ Multi-state Modeling of G-protein Coupled Receptors at Experimental Accuracy ]]> https://biorxiv.org/content/10.1101/2021.11.26.470086v1?rss=1 Heo, L. Feig, M. 2021-11-27 doi:10.1101/2021.11.26.470086 Cold Spring Harbor Laboratory Press 2021-11-27 <![CDATA[ Overexpression of NDR1 Leads to Pathogen Resistance at Elevated Temperatures ]]> https://biorxiv.org/content/10.1101/2021.12.01.470751v1?rss=1 Samaradivakara, S. Chen, H. Lu, Y.-J. Li, P. Kim, Y. S. Tsuda, K. Mine, A. Day, B. 2021-12-01 doi:10.1101/2021.12.01.470751 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Magnetic particle imaging of magnetotactic bacteria as living contrast agents is improved by altering magnetosome structures ]]> https://biorxiv.org/content/10.1101/2021.12.03.471101v1?rss=1 Makela, A. V. Schott, M. A. Madsen, C. S. Greeson, E. M. Contag, C. H. 2021-12-04 doi:10.1101/2021.12.03.471101 Cold Spring Harbor Laboratory Press 2021-12-04 <![CDATA[ A Spatial Transcriptomics Study of the Brain-Electrode Interface in Rat Motor Cortex ]]> https://biorxiv.org/content/10.1101/2021.12.03.471147v1?rss=1 Whitsitt, Q. A. Patel, B. Hunt, B. Purcell, E. K. 2021-12-04 doi:10.1101/2021.12.03.471147 Cold Spring Harbor Laboratory Press 2021-12-04 <![CDATA[ Does extracellular DNA mask microbial responses to a pulse disturbance? ]]> https://biorxiv.org/content/10.1101/2021.12.04.471228v1?rss=1 Kittredge, H. Dougherty, K. Glanville, K. Evans, S. E. 2021-12-04 doi:10.1101/2021.12.04.471228 Cold Spring Harbor Laboratory Press 2021-12-04 <![CDATA[ Horizontal gene transfer facilitates the spread of extracellular antibiotic resistance genes in soil ]]> https://biorxiv.org/content/10.1101/2021.12.05.471230v1?rss=1 30%). While eARGs transformed into live cells at a low frequency, exposure to a low dose of antibiotic allowed a small number of transformants to reach high abundances in laboratory populations, suggesting even rare transformation events pose a risk to human health. Overall, this work demonstrates that dead bacteria and their eARGs are an overlooked path to antibiotic resistance, and that disinfection alone is insufficient to stop the spread of antibiotic resistance. More generally, the spread of eARGs in antibiotic-free soil suggests that transformation allows genetic variants to establish at low frequencies in the absence of antibiotic selection. ImportanceOver the last decade, antibiotics in the environment have gained increasing attention because they can select for drug-resistant phenotypes that would have otherwise gone extinct. To counter this effect, bacterial populations exposed to antibiotics often undergo disinfection. However, the release of extracellular antibiotic resistance genes (eARGs) into the environment following disinfection can promote the transfer of eARGs through natural transformation. This phenomenon is well-documented in wastewater and drinking water, but yet to be investigated in soil. Our results directly demonstrate that eARGs from dead bacteria are an important, but often overlooked source of antibiotic resistance in soil. We conclude that disinfection alone is insufficient to prevent the spread of ARGs. Special caution should be taken in releasing antibiotics into the environment, even if there are no live antibiotic resistant bacteria in the community, as transformation allows DNA to maintain its biological activity past microbial death. ]]> Kittredge, H. A. Dougherty, K. M. Evans, S. E. 2021-12-05 doi:10.1101/2021.12.05.471230 Cold Spring Harbor Laboratory Press 2021-12-05 <![CDATA[ Changes in natural transformation after salt adaptation ]]> https://biorxiv.org/content/10.1101/2021.12.05.471276v1?rss=1 Kittredge, H. A. Evans, S. E. 2021-12-07 doi:10.1101/2021.12.05.471276 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ Scalable Adaptive Protein Ensemble Refinement Integrating Flexible Fitting ]]> https://biorxiv.org/content/10.1101/2021.12.07.471672v1?rss=1 Sarkar, D. Lee, H. Vant, J. W. Turilli, M. Jha, S. Singharoy, A. 2021-12-09 doi:10.1101/2021.12.07.471672 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Temporal response characterization across individual multiomics profiles of prediabetic and diabetic subjects ]]> https://biorxiv.org/content/10.1101/2021.12.08.471816v1?rss=1 Zheng, M. Piermarocchi, C. Mias, G. I. 2021-12-10 doi:10.1101/2021.12.08.471816 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes ]]> https://biorxiv.org/content/10.1101/2021.12.08.471837v1?rss=1 Toh, H. Yang, C. Formenti, G. Raja, K. Yan, L. Tracey, A. Chow, W. Howe, K. Bergeron, L. A. Zhang, G. Haase, B. Mountcastle, J. Fedrigo, O. Fogg, J. Kirilenko, B. Munegowda, C. Hiller, M. Jain, A. Kihara, D. Rhie, A. Phillippy, A. M. Swanson, S. A. Jiang, P. Clegg, D. O. Jarvis, E. D. Thomson, J. A. Stewart, R. Chaisson, M. J. P. Bukhman, Y. V. 2021-12-10 doi:10.1101/2021.12.08.471837 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ FLAMs: A self-replicating ex vivo model of alveolar macrophages for functional genetic studies ]]> https://biorxiv.org/content/10.1101/2021.12.12.472259v1?rss=1 Thomas, S. Wierenga, K. Pestka, J. Olive, A. 2021-12-13 doi:10.1101/2021.12.12.472259 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ A Dual-reporter Platform for Screening Tumor-targeted Extracellular Vesicles ]]> https://biorxiv.org/content/10.1101/2021.12.12.472298v1?rss=1 Kanada, M. Linenfelser, L. Cox, E. Gilad, A. 2021-12-12 doi:10.1101/2021.12.12.472298 Cold Spring Harbor Laboratory Press 2021-12-12 <![CDATA[ Clustering and visualization of single-cell RNA-seq data using path metrics ]]> https://biorxiv.org/content/10.1101/2021.12.14.472627v1?rss=1 Manousidaki, A. Little, A. Xie, Y. 2021-12-16 doi:10.1101/2021.12.14.472627 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Linnemannia elongata (Mortierellaceae) stimulates Arabidopsis thaliana aerial growth and responses to auxin, ethylene, and reactive oxygen species ]]> https://biorxiv.org/content/10.1101/2021.12.14.472664v1?rss=1 Vandepol, N. Liber, J. Yocca, A. Matlock, J. Edger, P. Bonito, G. 2021-12-14 doi:10.1101/2021.12.14.472664 Cold Spring Harbor Laboratory Press 2021-12-14 <![CDATA[ Effects of periodic bottlenecks on the dynamics of adaptive evolution in microbial populations ]]> https://biorxiv.org/content/10.1101/2021.12.29.474457v1?rss=1 Izutsu, M. Lake, D. M. Matson, Z. W. D. Dodson, J. P. Lenski, R. E. 2021-12-30 doi:10.1101/2021.12.29.474457 Cold Spring Harbor Laboratory Press 2021-12-30 <![CDATA[ Northward Expansion of Amblyomma americanum (Acari: Ixodidae) into Southern Michigan ]]> https://biorxiv.org/content/10.1101/2021.12.31.474651v1?rss=1 Fowler, P. D. Nguyentran, S. Quantroche, L. M. Porter, M. Kobbekaduwa, V. Tippin, S. Miller, G. Dinh, E. Foster, E. Tsao, J. 2022-01-02 doi:10.1101/2021.12.31.474651 Cold Spring Harbor Laboratory Press 2022-01-02 <![CDATA[ Development, Structure, and Mechanism of Synthetic Antibodies that Target Claudin and Clostridium perfringens Enterotoxin Complexes ]]> https://biorxiv.org/content/10.1101/2022.01.01.474715v1?rss=1 Orlando, B. J. Dominik, P. K. Roy, S. Ogbu, C. Erramilli, S. K. Kossiakoff, A. A. Vecchio, A. J. 2022-01-02 doi:10.1101/2022.01.01.474715 Cold Spring Harbor Laboratory Press 2022-01-02 <![CDATA[ The last missing piece of the Triangle of U: the evolution of the tetraploid Brassica carinata genome ]]> https://biorxiv.org/content/10.1101/2022.01.03.474831v1?rss=1 Yim, W. C. Swain, M. L. Ma, D. An, H. Bird, K. A. Curdie, D. D. Wang, S. Ham, H. D. Luzuriaga-Neira, A. Kirkwood, J. S. Hur, M. Solomon, J. K. Q. Harper, J. F. Kosma, D. K. Alvarez-Ponce, D. Cushman, J. C. Edger, P. P. Mason, A. S. Pires, J. C. Tang, H. Zhang, X. 2022-01-04 doi:10.1101/2022.01.03.474831 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ The generation of a Nutm1 knock-in reporter mouse line for imaging post-meiotic spermatogenesis ]]> https://biorxiv.org/content/10.1101/2022.01.04.474959v1?rss=1 Hakun, M. C. Rossant, J. Gu, B. 2022-01-04 doi:10.1101/2022.01.04.474959 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ Sex-specific evolution of a Drosophila sensory system via interacting cis- and trans-regulatory changes ]]> https://biorxiv.org/content/10.1101/2022.01.12.475924v1?rss=1 View larger version (65K): org.highwire.dtl.DTLVardef@1b5b5borg.highwire.dtl.DTLVardef@ac2ceorg.highwire.dtl.DTLVardef@7b6db0org.highwire.dtl.DTLVardef@15e4c6b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Luecke, D. M. Rice, G. R. Kopp, A. 2022-01-12 doi:10.1101/2022.01.12.475924 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Rapid and specific degradation of endogenous proteins in mouse models using auxin-inducible degrons ]]> https://biorxiv.org/content/10.1101/2022.01.13.476100v1?rss=1 Macdonald, L. A. Taylor, G. C. A. Brisbane, J. M. Christodoulou, E. Scott, L. Von Kriegsheim, A. Rossant, J. J. Gu, B. Wood, A. J. 2022-01-13 doi:10.1101/2022.01.13.476100 Cold Spring Harbor Laboratory Press 2022-01-13 <![CDATA[ Coupled abiotic-biotic cycling of nitrous oxide in tropical peatlands ]]> https://biorxiv.org/content/10.1101/2022.01.14.475290v1?rss=1 Buessecker, S. Sarno, A. F. Reynolds, M. C. Chavan, R. Park, J. Fontanez Ortiz, M. Perez-Castillo, A. G. Panduro Pisco, G. Urquiza-Munoz, J. D. Reis, L. P. Ferreira-Ferreira, J. Furtunato Maia, J. M. Holbert, K. E. Penton, C. R. Hall, S. J. Ghandi, H. Boechat, I. G. Guecker, B. Ostrom, N. E. Cadillo-Quiroz, H. 2022-01-15 doi:10.1101/2022.01.14.475290 Cold Spring Harbor Laboratory Press 2022-01-15 <![CDATA[ Neural hyperactivity is a core pathophysiological change induced by deletion of an autism risk gene Ash1l in the mouse brain ]]> https://biorxiv.org/content/10.1101/2022.01.19.476965v1?rss=1 Gao, Y. Aljazi, M. B. He, J. 2022-01-20 doi:10.1101/2022.01.19.476965 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Longitudinal Morphological and Functional Characterization of Human Heart Organoids Using Optical Coherence Tomography ]]> https://biorxiv.org/content/10.1101/2022.01.19.476972v1?rss=1 Ming, Y. Hao, S. Xu, Z. Goestenkors, A. Lewis-Israeli, Y. R. Volmert, B. D. Aguirre, A. Zhou, C. 2022-01-21 doi:10.1101/2022.01.19.476972 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Novel Internalin P homologs in Listeria ]]> https://biorxiv.org/content/10.1101/2022.01.19.476994v1?rss=1 Conner, K. N. Burke, J. T. Hardy, J. W. Ravi, J. 2022-01-20 doi:10.1101/2022.01.19.476994 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Additive genetic effects in interacting species jointly determine the outcome of caterpillar herbivory ]]> https://biorxiv.org/content/10.1101/2022.01.20.476992v1?rss=1 Gompert, Z. Saley, T. Philbin, C. Yoon, S. Perry, E. Sneck, M. E. Harrison, J. G. Buerkle, A. C. Fordyce, J. A. Nice, C. C. Dodson, C. Lebeis, S. L. Lucas, L. K. Forister, M. L. 2022-01-22 doi:10.1101/2022.01.20.476992 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ Alternative Assembly of Qβ Virus Like Particles ]]> https://biorxiv.org/content/10.1101/2022.01.23.477406v1?rss=1 Jin, X. Shaw, V. Sungsuwan, S. McFall-Boegeman, H. Huang, X. 2022-01-24 doi:10.1101/2022.01.23.477406 Cold Spring Harbor Laboratory Press 2022-01-24 <![CDATA[ A murine Wac model exhibits phenotypes relevant to DeSanto-Shinawi Syndrome ]]> https://biorxiv.org/content/10.1101/2022.01.24.477600v1?rss=1 Stafford, A. M. Pacheco-Vergara, M. Uhl, K. L. Jager, T. E. Li, X. Jeong, J. Vogt, D. 2022-01-27 doi:10.1101/2022.01.24.477600 Cold Spring Harbor Laboratory Press 2022-01-27 <![CDATA[ DciA helicase operators exhibit diversity across bacterial phyla ]]> https://biorxiv.org/content/10.1101/2022.01.24.477630v1?rss=1 Blaine, H. C. Burke, J. T. Ravi, J. Stallings, C. L. 2022-01-25 doi:10.1101/2022.01.24.477630 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Metabolic strategies shared by basement residents of the Lost City hydrothermal field ]]> https://biorxiv.org/content/10.1101/2022.01.25.477282v1?rss=1 Brazelton, W. J. McGonigle, J. M. Motamedi, S. Pendleton, H. L. Twing, K. I. Miller, B. C. Lowe, W. J. Hoffman, A. M. Prator, C. A. Chadwick, G. L. Anderson, R. E. Thomas, E. Butterfield, D. A. Aquino, K. A. Früh-Green, G. L. Schrenk, M. O. Lang, S. Q. 2022-01-25 doi:10.1101/2022.01.25.477282 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Compartment-specific energy requirements of photosynthetic carbon metabolism in Camelina sativa leaves ]]> https://biorxiv.org/content/10.1101/2022.01.28.478172v1?rss=1 Wieloch, T. Sharkey, T. D. 2022-01-28 doi:10.1101/2022.01.28.478172 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Feedback in the β-catenin destruction complex imparts bistability and cellular memory ]]> https://biorxiv.org/content/10.1101/2022.01.28.478206v1?rss=1 Cantoria, M. J. Alizadeh, E. Ravi, J. Bunnag, N. Kettenbach, A. N. Ahmed, Y. Paek, A. L. Tyson, J. J. Doubrovinski, K. Lee, E. Thorne, C. A. 2022-01-29 doi:10.1101/2022.01.28.478206 Cold Spring Harbor Laboratory Press 2022-01-29 <![CDATA[ The grapevine leaves that are (or were) not: constraints on leaf development and choosing to see what seemingly is not ]]> https://biorxiv.org/content/10.1101/2022.01.29.478336v1?rss=1 Chitwood, D. H. Mullins, J. 2022-01-30 doi:10.1101/2022.01.29.478336 Cold Spring Harbor Laboratory Press 2022-01-30 <![CDATA[ Coexistence between similar invaders: The case of two cosmopolitan exotic insects ]]> https://biorxiv.org/content/10.1101/2022.02.03.479030v1?rss=1 Arnold, M. B. Back, M. Crowell, M. D. Farooq, N. Ghimire, P. Obarein, O. A. Smart, K. E. Taucher, T. VanderJeugdt, E. Perry, K. I. Landis, D. A. Bahlai, C. 2022-02-05 doi:10.1101/2022.02.03.479030 Cold Spring Harbor Laboratory Press 2022-02-05 <![CDATA[ CRSP: Comparative RNA-seq pipeline for species lacking both of sequenced genomes and reference transcripts ]]> https://biorxiv.org/content/10.1101/2022.02.04.479193v1?rss=1 Bagheri, A. Dewey, C. Stewart, R. Jiang, P. 2022-02-08 doi:10.1101/2022.02.04.479193 Cold Spring Harbor Laboratory Press 2022-02-08 <![CDATA[ Idiosyncratic fitness costs of ampicillin-resistant mutants derived from a long-term experiment with Escherichia coli ]]> https://biorxiv.org/content/10.1101/2022.02.06.479266v1?rss=1 Jordan, J. A. Lenski, R. E. Card, K. J. 2022-02-06 doi:10.1101/2022.02.06.479266 Cold Spring Harbor Laboratory Press 2022-02-06 <![CDATA[ The dynamics of non-photochemical quenching and cyclic electron transport in A.thaliana exposed to harmonically oscillating light ]]> https://biorxiv.org/content/10.1101/2022.02.09.479783v1?rss=1 Niu, Y. Lazar, D. Holzwarth, A. R. Kramer, D. M. Matsubara, S. Schrey, S. D. Nedbal, L. 2022-02-10 doi:10.1101/2022.02.09.479783 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ A network-based drug repurposing approach identifies new treatment opportunities for the systemic chronic inflammation underlying multiple complex diseases ]]> https://biorxiv.org/content/10.1101/2022.02.10.479987v1?rss=1 Hickey, S. L. McKim, A. Mancuso, C. A. Krishnan, A. 2022-02-11 doi:10.1101/2022.02.10.479987 Cold Spring Harbor Laboratory Press 2022-02-11 <![CDATA[ Endometriotic Organoids as an In Vitro Model of Endometriotic Lesion Development. ]]> https://biorxiv.org/content/10.1101/2022.02.15.480583v1?rss=1 Song, Y. Burns, G. W. Joshi, N. R. Arora, R. Kim, J. J. Fazleabas, A. T. 2022-02-16 doi:10.1101/2022.02.15.480583 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ Regulatory dynamics distinguishing desiccation tolerance strategies within resurrection grasses ]]> https://biorxiv.org/content/10.1101/2022.02.16.480747v1?rss=1 St. Aubin, B. Wai, C. M. Raju, S. K. K. Niederhuth, C. E. VanBuren, R. 2022-02-19 doi:10.1101/2022.02.16.480747 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ MolEvolvR: a web-app for characterizing proteins using molecular evolution and phylogeny ]]> https://biorxiv.org/content/10.1101/2022.02.18.461833v1?rss=1 Burke, J. T. Chen, S. Z. Sosinski, L. M. Johnston, J. B. Ravi, J. 2022-02-22 doi:10.1101/2022.02.18.461833 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ Dynamic genetic adaptation of Bacteroides thetaiotaomicron murine gut colonization ]]> https://biorxiv.org/content/10.1101/2022.02.23.481734v1?rss=1 Zhang, M. Kennedy, M. DeLeon, O. Bissell, J. Trigodet, F. Lolans, K. Temelkova, S. Carroll, K. T. Fiebig, A. Deutschbauer, A. M. Sidebottom, A. M. Henry, C. S. Rice, P. A. Bergelson, J. Chang, E. 2022-02-24 doi:10.1101/2022.02.23.481734 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Association Mapping Across a Multitude of Traits Collected in Diverse Environments Identifies Pleiotropic Loci in Maize. ]]> https://biorxiv.org/content/10.1101/2022.02.25.480753v1?rss=1 Mural, R. V. Sun, G. Grzybowski, M. Tross, M. C. Jin, H. Smith, C. Newton, L. Andorf, C. M. Woodhouse, M. R. Thompson, A. M. Sigmon, B. V. Schnable, J. C. 2022-02-25 doi:10.1101/2022.02.25.480753 Cold Spring Harbor Laboratory Press 2022-02-25 <![CDATA[ Natural Variation Meets Synthetic Biology: Promiscuous Trichome Expressed Acyltransferases from Nicotiana acuminata ]]> https://biorxiv.org/content/10.1101/2022.02.25.482030v1?rss=1 25 acylsugar variants could be produced in a single enzyme assay with four acylsugar acyltransferases (NacASAT1-4) together with structurally diverse acyl-CoAs and sucrose. Liquid chromatography coupled with mass spectrometry screening of in vitro products revealed the ability of these enzymes to make acylsugars not present in Nicotiana plant extracts. In vitro acylsugar production also provided insights into acyltransferase acyl donor promiscuity and acyl acceptor specificity as well as regiospecificity of some ASATs. This study suggests that promiscuous Nicotiana acyltransferases can be used as synthetic biology tools to produce novel and potentially useful metabolites. ONE SENTENCE SUMMARYAnalysis of Nicotiana glandular trichome metabolites and BAHD acyltransferases revealed diverse sucrose and glucose based acylesters. ]]> Schenck, C. Anthony, T. M. Jacobs, M. L. Jones, A. D. Last, R. L. 2022-02-26 doi:10.1101/2022.02.25.482030 Cold Spring Harbor Laboratory Press 2022-02-26 <![CDATA[ ARID1A maintains transcriptionally repressive H3.3 associated with CHD4-ZMYND8 chromatin interactions ]]> https://biorxiv.org/content/10.1101/2022.02.27.482165v1?rss=1 Reske, J. J. Wilson, M. R. Armistead, B. Perez, C. Hrit, J. Adams, M. Rothbart, S. B. Missmer, S. A. Fazleabas, A. T. Chandler, R. L. 2022-02-28 doi:10.1101/2022.02.27.482165 Cold Spring Harbor Laboratory Press 2022-02-28 <![CDATA[ Introduction of a condensed, reverse tricarboxylic acid cycle for additional CO2 fixation in plants ]]> https://biorxiv.org/content/10.1101/2022.03.04.483018v1?rss=1 Wilson, N. J. Smith-Moore, C. M. Xu, Y. Edwards, B. La Hovary, C. Barampuram, S. Lin, X. Li, K. Aslett, D. Ji, M. Vintila, S. Kleiner, M. Xie, D. Shachar-Hill, Y. Grunden, A. Sederoff, H. 2022-03-05 doi:10.1101/2022.03.04.483018 Cold Spring Harbor Laboratory Press 2022-03-05 <![CDATA[ Protein Optimization Evolving Tool (POET) based on Genetic Programming ]]> https://biorxiv.org/content/10.1101/2022.03.05.483103v1?rss=1 Bricco, A. R. Miralavy, I. Bo, S. Perlman, O. Farrar, C. T. McMahon,, M. T. Banzhaf, W. Gilad, A. 2022-03-06 doi:10.1101/2022.03.05.483103 Cold Spring Harbor Laboratory Press 2022-03-06 <![CDATA[ Increases in vein length compensate for leaf area lost to lobing in grapevine ]]> https://biorxiv.org/content/10.1101/2022.03.15.484490v1?rss=1 Migicovsky, Z. Swift, J. F. Helget, Z. Klein, L. L. Ly, A. Maimaitiyiming, M. Woodhouse, K. Fennell, A. Kwasniewski, M. Miller, A. J. Cousins, P. Chitwood, D. H. 2022-03-16 doi:10.1101/2022.03.15.484490 Cold Spring Harbor Laboratory Press 2022-03-16 <![CDATA[ A coevolution experiment reveals parallel mutations in the AcrA-AcrB-TolC efflux pump that contributes to bacterial antibiotic resistance ]]> https://biorxiv.org/content/10.1101/2022.03.16.484489v1?rss=1 Chodkowski, J. L. Shade, A. 2022-03-16 doi:10.1101/2022.03.16.484489 Cold Spring Harbor Laboratory Press 2022-03-16 <![CDATA[ Distilling complex evolutionary histories with shiftPlot ]]> https://biorxiv.org/content/10.1101/2022.03.16.484646v1?rss=1 Miller, E. T. Martin, B. S. 2022-03-18 doi:10.1101/2022.03.16.484646 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ Towards understanding diversity, endemicity and global change vulnerability of soil fungi ]]> https://biorxiv.org/content/10.1101/2022.03.17.484796v1?rss=1 Tedersoo, L. Mikryukov, V. Zizka, A. Bahram, M. Hagh-Doust, N. Anslan, S. Prylutskyi, O. Delgado-Baquerizo, M. Maestre, F. T. Parn, J. opik, M. Moora, M. Zobel, M. Espenberg, M. Mander, u. Khalid, A. N. Corrales, A. Agan, A. Vasco-Palacios, A.-M. Saitta, A. Rinaldi, A. C. Verbeken, A. Sulistyo, B. P. Tamgnoue, B. Furneaux, B. Ritter, C. D. Nyamukondiwa, C. Sharp, C. Marin, C. Gohar, D. Klavina, D. Sharmah, D. Dai, D. Nouhra, E. Biersma, E. M. Rahn, E. Cameron, E. K. De Crop, E. Otsing, E. Davydov, E. A. Albornoz, F. E. Brearley, F. Q. Buegger, F. Zahn 2022-03-19 doi:10.1101/2022.03.17.484796 Cold Spring Harbor Laboratory Press 2022-03-19 <![CDATA[ Alpha-mannosidase-2 modulates arbovirus infection in a pathogen- and Wolbachia-specific manner in Aedes aegypti mosquitoes ]]> https://biorxiv.org/content/10.1101/2022.03.18.484928v1?rss=1 Urakova, N. Joseph, R. E. Huntsinger, A. Macias, V. M. Jones, M. J. Sigle, L. T. Li, M. Akbari, O. S. Xi, Z. Lymperopoulos, K. Sayre, R. T. McGraw, E. A. Rasgon, J. L. 2022-03-19 doi:10.1101/2022.03.18.484928 Cold Spring Harbor Laboratory Press 2022-03-19 <![CDATA[ Modeling the Evolution of Rates of Continuous Trait Evolution ]]> https://biorxiv.org/content/10.1101/2022.03.18.484930v1?rss=1 Martin, B. S. Bradburd, G. S. Harmon, L. J. Weber, M. G. 2022-03-19 doi:10.1101/2022.03.18.484930 Cold Spring Harbor Laboratory Press 2022-03-19 <![CDATA[ Identification of BAHD acyltransferases associated with acylinositol biosynthesis in Solanum quitoense (naranjilla) ]]> https://biorxiv.org/content/10.1101/2022.03.21.485185v1?rss=1 Leong, B. J. Hurney, S. M. Fiesel, P. D. Anthony, T. M. Moghe, G. D. Jones, A. D. Last, R. L. 2022-03-21 doi:10.1101/2022.03.21.485185 Cold Spring Harbor Laboratory Press 2022-03-21 <![CDATA[ Wolbachia wAlbB inhibit dengue and Zika infection in the mosquito Aedes aegypti with an Australian background ]]> https://biorxiv.org/content/10.1101/2022.03.22.485408v1?rss=1 98% Australian ancestry, confirming the successful introduction of the wAlbB2 infection into the Australian genomic background through backcrossing. Genotypic and phenotypic analyses showed the wAlbB2-F4 strain retains the insecticide susceptibility phenotype and genotype of the Australian mosquitoes. We demonstrate that the Wolbachia wAlbB2-F4, in addition to being suitable for suppression programs, can be effective in population replacement programs given its high inhibition of virus infection in mosquitoes. The ease at which a target mosquito population can be transfected with wAlbB2, while retaining genotypes and phenotypes of the target population, shows the robustness of this strain as a biocontrol agent against the Ae. aegypti mosquito itself as well as the pathogens it transmits. IMPORTANCEEpidemics of arthopod-borne virus (arbovirus) diseases affect millions of people and are becoming more frequent and widespread. A successful strategy to control these diseases is by infecting mosquito populations with benign, insect-specific Wolbachia bacteria that render mosquitoes refractory to infection with pathogenic arboviruses. Here we show that a strain of the major mosquito vector Ae. aegypti that was infected with Wolbachia following a simple back-cross mating procedure is refractory to infection with dengue and Zika viruses. Importantly, the genetic background of the strain is equivalent to the target population, which is important for persistence of the strain and regulatory approval. ]]> Hugo, L. E. Rasic, G. Maynard, A. J. Ambrose, L. Liddington, C. Nath, N. S. Graham, M. Winterford, C. Wimalasiri-Yapa, B. M. C. R. Xi, Z. Beebe, N. W. Devine, G. J. E. 2022-03-23 doi:10.1101/2022.03.22.485408 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ Unearthing the global impact of mining construction minerals on biodiversity ]]> https://biorxiv.org/content/10.1101/2022.03.23.485272v1?rss=1 Torres, A. zu Ermgassen, S. O. S. E. Ferri-Yanez, F. Navarro, L. M. Rosa, I. M. D. Teixeira, F. Z. Wittkopp, C. Liu, J. 2022-03-26 doi:10.1101/2022.03.23.485272 Cold Spring Harbor Laboratory Press 2022-03-26 <![CDATA[ Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain ]]> https://biorxiv.org/content/10.1101/2022.04.01.486706v1?rss=1 Wu, D. Li, X. Tanaka, R. Wood, J. C. Tibbs-Cortes, L. E. Magallanes-Lundback, M. Bornowski, N. Hamilton, J. P. Vaillancourt, B. Diepenbrock, C. H. Li, X. Deason, N. T. Schoenbaum, G. R. Yu, J. Buell, C. R. DellaPenna, D. Gore, M. A. 2022-04-03 doi:10.1101/2022.04.01.486706 Cold Spring Harbor Laboratory Press 2022-04-03 <![CDATA[ Artificial selection methods from evolutionary computing show promise for directed evolution of microbes ]]> https://biorxiv.org/content/10.1101/2022.04.01.486727v1?rss=1 Lalejini, A. Dolson, E. Vostinar, A. E. Zaman, L. 2022-04-02 doi:10.1101/2022.04.01.486727 Cold Spring Harbor Laboratory Press 2022-04-02 <![CDATA[ Asynchrony rescues statistically-optimal group decisions from information cascades through emergent leaders ]]> https://biorxiv.org/content/10.1101/2022.04.05.487127v1?rss=1 Reina, A. Bose, T. Srivastava, V. Marshall, J. A. R. 2022-04-07 doi:10.1101/2022.04.05.487127 Cold Spring Harbor Laboratory Press 2022-04-07 <![CDATA[ Host range expansion of Shigella phage Sf6 evolves through the dual roles of its tailspike ]]> https://biorxiv.org/content/10.1101/2022.04.06.487239v1?rss=1 Subramanian, S. Dover, J. A. Parent, K. N. Doore, S. M. 2022-04-06 doi:10.1101/2022.04.06.487239 Cold Spring Harbor Laboratory Press 2022-04-06 <![CDATA[ Genome structures resolve the early diversification of teleost fishes ]]> https://biorxiv.org/content/10.1101/2022.04.07.487469v1?rss=1 Parey, E. Louis, A. Montfort, J. Bouchez, O. Roques, C. Iampietro, C. Lluch, J. Castinel, A. Donnadieu, C. Desvignes, T. Bucao, C. F. Jouanno, E. Wen, M. Mejri, S. Dirks, R. P. Jansen, H. J. Henkel, C. V. Chen, W.-J. Zahm, M. Cabau, C. Klopp, C. Thompson, A. W. Robinson-Rechavi, M. Braasch, I. Lecointre, G. Bobe, J. Postlethwait, J. H. Berthelot, C. Roest Crollius, H. Guiguen, Y. 2022-04-10 doi:10.1101/2022.04.07.487469 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ TwinEQTL: Ultra Fast and Powerful Association Analysis for eQTL and GWAS in Twin Studies ]]> https://biorxiv.org/content/10.1101/2022.04.08.487703v1?rss=1 Xia, K. Zou, F. Shabalin, A. A. Knickmeyer, R. C. Gilmore, J. H. Chung, W. Styner, M. Sullivan, P. F. Wright, F. A. Yin, Z. 2022-04-10 doi:10.1101/2022.04.08.487703 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ Bile acid-CoA:amino acid N-acyltransferase gene knockout alters early life development, the gut microbiome and reveals unusual bile acid conjugates in mice ]]> https://biorxiv.org/content/10.1101/2022.04.10.487642v1?rss=1 Neugebauer, K. A. Guzior, D. V. Feiner, J. Rzepka, M. Schillmiller, A. O'Reilly, S. Jones, A. D. Watson, V. E. Luyendyk, J. P. McCabe, L. Quinn, R. A. 2022-04-10 doi:10.1101/2022.04.10.487642 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ MPI region of interest (ROI) analysis and quantification of iron in different volumes ]]> https://biorxiv.org/content/10.1101/2022.04.10.487778v1?rss=1 Sehl, O. C. Tiret, B. Berih, M. A. Makela, A. V. Goodwill, P. Foster, P. J. 2022-04-10 doi:10.1101/2022.04.10.487778 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ Carbon dioxide regulates Mycobacterium tuberculosis PhoPR signaling and virulence ]]> https://biorxiv.org/content/10.1101/2022.04.12.488064v1?rss=1 Dechow, S. J. Goyal, R. Johnson, B. K. Abramovitch, R. B. 2022-04-13 doi:10.1101/2022.04.12.488064 Cold Spring Harbor Laboratory Press 2022-04-13 <![CDATA[ Infection with Listeria monocytogenes alters the placental transcriptome and eicosanome ]]> https://biorxiv.org/content/10.1101/2022.04.14.488381v1?rss=1 Conner, K. N. Holman, D. Lydic, T. Hardy, J. W. 2022-04-14 doi:10.1101/2022.04.14.488381 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ The shape of aroma: measuring and modeling citrus oil gland distribution ]]> https://biorxiv.org/content/10.1101/2022.04.14.488418v1?rss=1 Amezquita, E. J. Quigley, M. Y. Ophelders, T. Seymour, D. Munch, E. Chitwood, D. H. 2022-04-15 doi:10.1101/2022.04.14.488418 Cold Spring Harbor Laboratory Press 2022-04-15 <![CDATA[ A general framework for species-abundance distributions: linking traits and dispersal to explain commonness and rarity ]]> https://biorxiv.org/content/10.1101/2022.04.15.488506v1?rss=1 Koffel, T. Umemura, K. Litchman, E. Klausmeier, C. A. 2022-04-16 doi:10.1101/2022.04.15.488506 Cold Spring Harbor Laboratory Press 2022-04-16 <![CDATA[ Listeria monocytogenes Infection Alters Extracellular Vesicles Produced by Trophoblast Stem Cells to Confer a Pro-Inflammatory State ]]> https://biorxiv.org/content/10.1101/2022.04.19.488859v1?rss=1 Kaletka, J. Lee, K. H. Kanada, M. Hardy, J. 2022-04-20 doi:10.1101/2022.04.19.488859 Cold Spring Harbor Laboratory Press 2022-04-20 <![CDATA[ Comparative transcriptomics and metabolomics reveal specialized metabolite drought stress responses in switchgrass (Panicum virgatum L.) ]]> https://biorxiv.org/content/10.1101/2022.04.20.488672v1?rss=1 Tiedge, K. J. Li, X. Merrill, A. T. Davisson, D. L. Chen, Y. Yu, P. Tantillo, D. J. Last, R. Zerbe, P. 2022-04-21 doi:10.1101/2022.04.20.488672 Cold Spring Harbor Laboratory Press 2022-04-21 <![CDATA[ An essential host dietary fatty acid promotes TcpH inhibition of TcpP proteolysis enabling virulence gene expression in Vibrio cholerae ]]> https://biorxiv.org/content/10.1101/2022.04.28.489952v1?rss=1 Demey, L. M. Sinha, R. DiRita, V. J. 2022-04-28 doi:10.1101/2022.04.28.489952 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Genetic architecture of spatially complex color patterning in hybrid Mimulus ]]> https://biorxiv.org/content/10.1101/2022.04.29.490035v1?rss=1 Cooley, A. M. Schlutius, C. Matthews, M. Zheng, X. Thomas, D. Edger, P. Platts, A. George, L. Williams, A. LaFountain, A. Hundley, D. Yuan, Y.-w. Twyford, A. D. Puzey, J. D. 2022-05-01 doi:10.1101/2022.04.29.490035 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Bacterial Infection of the Placenta Induces Sex-Specific Responses in the Fetal Brain ]]> https://biorxiv.org/content/10.1101/2022.05.03.490463v1?rss=1 Lee, K. H. Kiupel, M. Woods, T. Pingle, P. Hardy, J. 2022-05-03 doi:10.1101/2022.05.03.490463 Cold Spring Harbor Laboratory Press 2022-05-03 <![CDATA[ Vertical gradients in physiological function and resource allocation of white spruce diverge at the northern- and southern-most range extremes ]]> https://biorxiv.org/content/10.1101/2022.05.06.490824v1?rss=1 Schmiege, S. C. Griffin, K. L. Boelman, N. T. Vierling, L. A. Bruner, S. G. Min, E. Maguire, A. J. Jensen, J. Eitel, J. U. H. 2022-05-06 doi:10.1101/2022.05.06.490824 Cold Spring Harbor Laboratory Press 2022-05-06 <![CDATA[ Complexities of recapitulating polygenic effects in natural populations: replication of genetic effects on wing shape in artificially selected and wild caught populations of Drosophila melanogaster. ]]> https://biorxiv.org/content/10.1101/2022.05.12.491649v1?rss=1 Pelletier, K. Pitchers, W. R. Mammel, A. Northrop-Albrecht, E. J. Marquez, E. J. Moscarella, R. A. Houle, D. Dworkin, I. 2022-05-12 doi:10.1101/2022.05.12.491649 Cold Spring Harbor Laboratory Press 2022-05-12 <![CDATA[ Predictive Models of Genome-wide Aryl Hydrocarbon Receptor DNA Binding Reveal Tissue Specific Binding Determinants ]]> https://biorxiv.org/content/10.1101/2022.05.13.491754v1?rss=1 Filipovic, D. Qi, W. Kana, O. Z. Marri, D. LeCluyse, E. L. Andersen, M. E. Cuddapah, S. Bhattacharya, S. 2022-05-13 doi:10.1101/2022.05.13.491754 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Parallel changes in gene essentiality over 50,000 generations of evolution ]]> https://biorxiv.org/content/10.1101/2022.05.17.492023v1?rss=1 Limdi, A. Owen, S. V. Herren, C. Lenski, R. E. Baym, M. 2022-05-17 doi:10.1101/2022.05.17.492023 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ The evolution of fitness effects during long-term adaptation in bacteria ]]> https://biorxiv.org/content/10.1101/2022.05.17.492360v1?rss=1 Couce, A. Magnan, M. Lenski, R. E. Tenaillon, O. 2022-05-17 doi:10.1101/2022.05.17.492360 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ X-ray imaging of 30 year old wine grape wood reveals cumulative impacts of rootstocks on scion secondary growth and harvest index ]]> https://biorxiv.org/content/10.1101/2022.05.17.492371v1?rss=1 Migicovsky, Z. Quigley, M. Y. Mullins, J. Ali, T. Swift, J. F. Agasaveeran, A. R. Dougherty, J. D. Grant, B. M. Korkmaz, I. Malpeddi, M. R. McNichol, E. L. Sharp, A. W. Harris, J. L. Hopkins, D. R. Jordan, L. M. Kwasniewski, M. T. Striegler, R. K. Dowtin, A. L. Stotts, S. Cousins, P. Chitwood, D. H. 2022-05-17 doi:10.1101/2022.05.17.492371 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ Profiles of secoiridoids and alkaloids in tissue of susceptible and resistant green ash progeny reveal patterns of induced responses to emerald ash borer in Fraxinus pennsylvanica ]]> https://biorxiv.org/content/10.1101/2022.05.18.492370v1?rss=1 99%) in green ash infested by the invasive emerald ash borer (EAB). However, high standing genetic variation may produce a few individuals capable of an effective defense, as seen in the rare surviving green ash. In an investigation of this plant-insect interaction, we annotated metabolites associated with generalized but ineffective responses to EAB, and others associated with successful defensive responses. Untargeted metabolomics combined with intensive phenotyping of structured populations provides a framework for understanding resistance to invasive species in naive host populations. ]]> Stanley, R. K. Carey, D. W. Mason, M. E. Poland, T. M. Koch, J. L. Jones, A. D. Romero-Severson, J. 2022-05-19 doi:10.1101/2022.05.18.492370 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Nucleotide resolution genetic mapping in pigs by publicly accessible whole genome imputation ]]> https://biorxiv.org/content/10.1101/2022.05.18.492518v1?rss=1 Ding, R. Savegnago, R. Liu, J. Long, N. Tan, C. Cai, G. Zhuang, Z. Wu, J. Yang, M. Qiu, Y. Ruan, D. Quan, J. Zheng, E. Hong, L. Li, Z. Tan, S. Bedhane, M. Schnabel, R. Steibel, J. Gondro, C. Yang, J. Huang, W. Wu, Z. 2022-05-20 doi:10.1101/2022.05.18.492518 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ TransCell: In silico characterization of genomic landscape and cellular responses from gene expressions through a two-step deep transfer learning ]]> https://biorxiv.org/content/10.1101/2022.05.19.492662v1?rss=1 Yeh, S.-J. Paithankar, S. Chen, R. Xing, J. Sun, M. Liu, K. Zhou, J. Chen, B. 2022-05-20 doi:10.1101/2022.05.19.492662 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ A cryptic transcription factor regulates Caulobacter adhesin development ]]> https://biorxiv.org/content/10.1101/2022.05.23.493133v1?rss=1 McLaughlin, M. Hershey, D. Reyes-Ruiz, L. Fiebig, A. Crosson, S. 2022-05-23 doi:10.1101/2022.05.23.493133 Cold Spring Harbor Laboratory Press 2022-05-23 <![CDATA[ Harnessing insect olfactory neural circuits for noninvasive detection of human cancer ]]> https://biorxiv.org/content/10.1101/2022.05.24.493311v1?rss=1 Farnum, A. Parnas, M. Apu, E. H. Cox, E. Lefevre, N. Contag, C. H. Saha, D. 2022-05-25 doi:10.1101/2022.05.24.493311 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ yEvo: a modular eukaryotic genetics and evolution research experience for high school students ]]> https://biorxiv.org/content/10.1101/2022.05.26.493490v1?rss=1 Taylor, B. Warwick, A. R. Skophammer, R. Boyer, J. M. Geck, R. C. Gunkelman, K. Walson, M. Rowley, P. A. Dunham, M. J. 2022-05-28 doi:10.1101/2022.05.26.493490 Cold Spring Harbor Laboratory Press 2022-05-28 <![CDATA[ FcRγ- NK cell induction by specific CMV and expansion by subclinical viral infections in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2022.05.26.493509v1?rss=1 Lee, J. Chang, W. Scott, J. M. Hong, S. Lee, T. Deere, J. D. Park, P. Sparger, E. E. Dandekar, S. Hartigan-O'Connor, D. Barry, P. A. Kim, S. 2022-05-27 doi:10.1101/2022.05.26.493509 Cold Spring Harbor Laboratory Press 2022-05-27 <![CDATA[ Determinants of hyena participation in risky collective action ]]> https://biorxiv.org/content/10.1101/2022.05.30.494003v1?rss=1 Montgomery, T. M. Lehmann, K. D. S. Gregg, S. Keyser, K. McTigue, L. E. Beehner, J. C. Holekamp, K. E. 2022-05-31 doi:10.1101/2022.05.30.494003 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ GDNF-RET signaling and EGR1 form a positive feedback loop that promotes tamoxifen resistance via cyclin D1 ]]> https://biorxiv.org/content/10.1101/2022.05.31.492660v1?rss=1 Marks, B. A. Coonrod, S. A. Rice, E. J. Danko, C. G. Mukai, C. Pipia, I. M. Horibata, S. 2022-05-31 doi:10.1101/2022.05.31.492660 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ A Chloroplast Protein Atlas Reveals Novel Structures and Spatial Organization of Biosynthetic Pathways ]]> https://biorxiv.org/content/10.1101/2022.05.31.493820v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@19c871eorg.highwire.dtl.DTLVardef@16ac46corg.highwire.dtl.DTLVardef@859b7dorg.highwire.dtl.DTLVardef@1a3446e_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LI1,032 candidate chloroplast proteins localized by fluorescent tagging. C_LIO_LIThis protein atlas reveals novel chloroplast structures, functional regions, and components. C_LIO_LIPrevalent dual-organelle localization suggests extensive cross-compartment coordination. C_LIO_LIAtlas-trained machine learning predicts localizations of all C. reinhardtii proteins. C_LI ]]> Wang, L. Patena, W. Van Baalen, K. A. Xie, Y. Singer, E. R. Gavrilenko, S. Warren-Williams, M. Han, L. Harrigan, H. R. Chen, V. Ton, V. T. N. P. Kyin, S. Shwe, H. H. Cahn, M. H. Wilson, A. T. Hu, J. Schnell, D. J. McWhite, C. D. Jonikas, M. 2022-05-31 doi:10.1101/2022.05.31.493820 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ The complex octoploid Craterostigma genome and tissue-specific mechanisms underlying desiccation tolerance ]]> https://biorxiv.org/content/10.1101/2022.05.31.494158v1?rss=1 VanBuren, R. Wai, C. M. Giarola, V. Zupunski, M. Pardo, J. Kalinowski, M. Grossmann, G. Bartels, D. 2022-05-31 doi:10.1101/2022.05.31.494158 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Experimental Test of the Contributions of Initial Variation and New Mutations to Adaptive Evolution in a Novel Environment ]]> https://biorxiv.org/content/10.1101/2022.05.31.494207v1?rss=1 Izutsu, M. Lenski, R. E. 2022-06-01 doi:10.1101/2022.05.31.494207 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ Community assessment of methods to deconvolve cellular composition from bulk gene expression ]]> https://biorxiv.org/content/10.1101/2022.06.03.494221v1?rss=1 White, B. S. de Reynies, A. Newman, A. M. Waterfall, J. J. Lamb, A. Petitprez, F. Yu, T. Guo, X. Valdeolivas, A. Lin, Y. Li, H. Xiao, X. Wang, S. Zheng, F. Yang, W. Yu, R. Guerrero-Gimenez, M. E. Catania, C. A. Lang, B. J. Domanskyi, S. Bertus, T. J. Piermarocchi, C. Monaco, G. Caruso, F. P. Ceccarelli, M. Coller, J. Maecker, H. Duault, C. Sokoohi, V. Patel, S. Liliental, J. E. Simon, S. Tumor Deconvolution DREAM Challenge consortium, Saez-Rodriguez, J. Heiser, L. M. Guinney, J. Gentles, A. J. 2022-06-05 doi:10.1101/2022.06.03.494221 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ A model of coevolution and local adaptation between hosts and parasites in continuous space ]]> https://biorxiv.org/content/10.1101/2022.06.08.494937v1?rss=1 Week, B. Bradburd, G. 2022-06-10 doi:10.1101/2022.06.08.494937 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Targeting ATP12A, a non-gastric proton pump alpha subunit, for idiopathic pulmonary fibrosis treatment ]]> https://biorxiv.org/content/10.1101/2022.06.08.495330v1?rss=1 Abdelgied, M. Uhl, K. Chen, O. G. Schultz, C. Tripp, K. Peraino, A. M. Paithankar, S. Chen, B. Kakazu, M. T. Bahena, A. C. Jager, T. E. Lawson, C. Chesla, D. W. Pestov, N. Modyanov, N. N. Prokop, J. Neubig, R. R. Uhal, B. D. Girgis, R. E. Li, X. 2022-06-08 doi:10.1101/2022.06.08.495330 Cold Spring Harbor Laboratory Press 2022-06-08 <![CDATA[ Heritability and host genomic determinants of switchgrass root-associated microbiota in field sites spanning its natural range. ]]> https://biorxiv.org/content/10.1101/2022.06.09.495345v1?rss=1 2000 samples, suggest field location is the primary determinant of microbiome composition; however, substantial heritable variation is widespread across bacterial taxa, especially those in the Sphingomonadaceae family. Despite diverse compositions, we find that relatively few highly prevalent bacterial taxa make up the majority of the switchgrass root microbiota, a large fraction of which is shared across sites. Local genotypes preferentially recruit / filter for local microbes, supporting the idea of affinity between local plants and their microbiota. Using genome-wide association, we identified loci impacting the abundance of >400 microbial strains and found an enrichment of genes involved in immune responses, signaling pathways, and secondary metabolism. We found loci associated with over half of the core microbiota (i.e. microbes in >80% of samples) regardless of field location. Finally, we show a genetic relationship between a basal plant immunity pathway and relative abundances of root microbiota. This study brings us closer to harnessing and manipulating beneficial microbial associations via host genetics. ]]> Edwards, J. Saran, U. B. Bonnette, J. MacQueen, A. Yin, J. Nguyen, T. u. Schmutz, J. Grimwood, J. Pennacchio, L. A. Daum, C. del Rio, T. G. Fritschi, F. B. Lowry, D. B. Juenger, T. E. 2022-06-09 doi:10.1101/2022.06.09.495345 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Systematic analysis of the molecular and biophysical properties of key DNA damage response factors ]]> https://biorxiv.org/content/10.1101/2022.06.09.495359v1?rss=1 Heyza, J. R. Mikhova, M. Bahl, A. Broadbent, D. Schmidt, J. C. 2022-06-09 doi:10.1101/2022.06.09.495359 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Orphan genes are clustered with allorecognition loci and may be involved in incompatibility and speciation in Neurospora ]]> https://biorxiv.org/content/10.1101/2022.06.10.495464v1?rss=1 Wang, Z. Wang, Y. Kasuga, T. Lopez-Giraldez, F. Zhang, Y. Zhang, Z. Diaz, R. Dong, C. Sil, A. Trail, F. Yarden, O. Townsend, J. P. 2022-06-12 doi:10.1101/2022.06.10.495464 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Fitness seascapes facilitate the prediction of therapy resistance under time-varying selection ]]> https://biorxiv.org/content/10.1101/2022.06.10.495696v1?rss=1 King, E. S. Pelesko, J. Maltas, J. A. Owen, S. J. Dolson, E. Scott, J. G. 2022-06-12 doi:10.1101/2022.06.10.495696 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Gla-domain mediated targeting of externalized phosphatidylserine for intracellular delivery ]]> https://biorxiv.org/content/10.1101/2022.06.13.495901v1?rss=1 Hermiston, T. Hardy, J. Bauzon, M. Blankenberg, F. G. Kanada, M. Makela, A. Chan, C. K. F. Contag, C. H. 2022-06-14 doi:10.1101/2022.06.13.495901 Cold Spring Harbor Laboratory Press 2022-06-14 <![CDATA[ Dose-dependent disruption of hepatic zonation by 2,3,7,8-tetrachlorodibenzo-p-dioxin in mice: integration of single-nuclei RNA sequencing and spatial transcriptomics. ]]> https://biorxiv.org/content/10.1101/2022.06.15.496321v1?rss=1 Nault, R. SAHA, S. Bhattacharya, S. Sinha, S. Maiti, T. Zacharewski, T. 2022-06-17 doi:10.1101/2022.06.15.496321 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Direct Generation of Protein Conformational Ensembles via Machine Learning ]]> https://biorxiv.org/content/10.1101/2022.06.18.496675v1?rss=1 Janson, G. Valdes-Garcia, G. Heo, L. Feig, M. 2022-06-19 doi:10.1101/2022.06.18.496675 Cold Spring Harbor Laboratory Press 2022-06-19 <![CDATA[ Magnetothermal control of temperature-sensitive repressors in superparamagnetic iron nanoparticle-coated Bacillus subtilis ]]> https://biorxiv.org/content/10.1101/2022.06.18.496685v1?rss=1 Greeson, E. M. Madsen, C. S. Makela, A. V. Contag, C. H. 2022-06-19 doi:10.1101/2022.06.18.496685 Cold Spring Harbor Laboratory Press 2022-06-19 <![CDATA[ Bacterial profiles of the human placenta from term and preterm deliveries ]]> https://biorxiv.org/content/10.1101/2022.06.21.497119v1?rss=1 Theis, K. R. Winters, A. D. Romero, R. Alhousseini, A. Greenberg, J. M. Panzer, J. Galaz, J. Pacora, P. Shaffer, Z. D. Jung, E. Gomez-Lopez, N. 2022-06-22 doi:10.1101/2022.06.21.497119 Cold Spring Harbor Laboratory Press 2022-06-22 <![CDATA[ Postsynaptic burst reactivation of hippocampal neurons enables associative plasticity of temporally discontiguous inputs ]]> https://biorxiv.org/content/10.1101/2022.06.23.497305v1?rss=1 Fuchsberger, T. Clopath, C. Jarzebowski, P. Brzosko, Z. Wang, H. Paulsen, O. 2022-06-26 doi:10.1101/2022.06.23.497305 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ DESIGN OF A CHIMERIC ACE-2/Fc-SILENT FUSION PROTEIN WITH ULTRAHIGH AFFINITY AND NEUTRALIZING CAPACITY FOR SARS-CoV-2 VARIANTS ]]> https://biorxiv.org/content/10.1101/2022.06.23.497326v1?rss=1 Uhal, B. Bodie, N. M. Connolly, D. Chu, J. 2022-06-24 doi:10.1101/2022.06.23.497326 Cold Spring Harbor Laboratory Press 2022-06-24 <![CDATA[ The cynosure of CtBP: evolution of a bilaterian transcriptional corepressor ]]> https://biorxiv.org/content/10.1101/2022.06.23.497424v1?rss=1 Raicu, A.-M. Kadiyala, D. Niblock, M. Jain, A. Yang, Y. Bird, K. M. Bertholf, K. Seenivasan, A. Arnosti, D. N. 2022-06-26 doi:10.1101/2022.06.23.497424 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Desiccation resistance differences in Drosophila species can be largely explained by variations in cuticular hydrocarbons ]]> https://biorxiv.org/content/10.1101/2022.06.24.497513v1?rss=1 Wang, Z. Receveur, J. P. Pu, J. Cong, H. Richards, C. Liang, M. Chung, H. 2022-06-28 doi:10.1101/2022.06.24.497513 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ Prediction of mammalian tissue-specific CLOCK-BMAL1 binding to E-box motifs ]]> https://biorxiv.org/content/10.1101/2022.06.27.497767v1?rss=1 Marri, D. K. Filipovic, D. Kana, O. Tischkau, S. Bhattacharya, S. 2022-06-30 doi:10.1101/2022.06.27.497767 Cold Spring Harbor Laboratory Press 2022-06-30 <![CDATA[ Mice lacking dopamine production in neurotensin receptor 1 neurons voluntarily undergo time-restricted feeding of high fat diet and resist obesity ]]> https://biorxiv.org/content/10.1101/2022.06.27.497778v1?rss=1 Farahmand, F. Sidikpramana, M. Yousef, B. Sharif, S. Shao, K. Tang, Q. Leinninger, G. Guler, A. Steele, A. 2022-06-30 doi:10.1101/2022.06.27.497778 Cold Spring Harbor Laboratory Press 2022-06-30 <![CDATA[ PyGenePlexus: A Python package for gene discovery using network-based machine learning ]]> https://biorxiv.org/content/10.1101/2022.07.02.498552v1?rss=1 Mancuso, C. A. Liu, R. Krishnan, A. 2022-07-04 doi:10.1101/2022.07.02.498552 Cold Spring Harbor Laboratory Press 2022-07-04 <![CDATA[ Sublethal and transgenerational effects of lambda-cyhalothrin and abamectin on the development and reproduction of Cydia pomonella ]]> https://biorxiv.org/content/10.1101/2022.07.05.498911v1?rss=1 Ju, D. Liu, Y.-X. Liu, X. Dewer, Y. Mota-Sanchez, D. Yang, X.-Q. 2022-07-06 doi:10.1101/2022.07.05.498911 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ Nascent transcription and the associated cis-regulatory landscape in rice ]]> https://biorxiv.org/content/10.1101/2022.07.06.498888v1?rss=1 Choi, J. Y. Platts, A. E. Johary, A. Purugganan, M. Joly-Lopez, Z. 2022-07-07 doi:10.1101/2022.07.06.498888 Cold Spring Harbor Laboratory Press 2022-07-07 <![CDATA[ Grapevine leaf size influences vine canopy temperature ]]> https://biorxiv.org/content/10.1101/2022.07.07.499216v1?rss=1 Migicovsky, Z. Swift, J. F. Helget, Z. Klein, L. L. Ly, A. Maimaitiyiming, M. Woodhouse, K. Fennell, A. Kwasniewski, M. Miller, A. Chitwood, D. H. Cousins, P. 2022-07-10 doi:10.1101/2022.07.07.499216 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ Machine learning reveals conserved chromatin patterns determining meiotic recombination sites in plants ]]> https://biorxiv.org/content/10.1101/2022.07.11.499557v1?rss=1 Wang, M. Shilo, S. Zhou, A. Zelkowski, M. Olson, M. A. Azuri, I. Shoshani-Hechel, N. Melamed-Bessudo, C. Marand, A. P. Jiang, J. Schnable, J. C. Underwood, C. J. Henderson, I. R. Sun, Q. Pillardy, J. Kianian, P. M. A. Kianian, S. F. Chen, C. Levy, A. A. Pawlowski, W. P. 2022-07-13 doi:10.1101/2022.07.11.499557 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Molecular evolution of the ependymin-related gene epdl2 in African weakly electric fish ]]> https://biorxiv.org/content/10.1101/2022.07.13.499928v1?rss=1 Losilla, M. Gallant, J. R. 2022-07-14 doi:10.1101/2022.07.13.499928 Cold Spring Harbor Laboratory Press 2022-07-14 <![CDATA[ A custom library construction method for super-resolution ribosome profiling in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2022.07.14.499987v1?rss=1 Wu, H.-Y. L. Hsu, P. Y. 2022-07-15 doi:10.1101/2022.07.14.499987 Cold Spring Harbor Laboratory Press 2022-07-15 <![CDATA[ Single-cell transcriptomics of the Arabidopsis floral abscission zone ]]> https://biorxiv.org/content/10.1101/2022.07.14.500021v1?rss=1 Taylor, I. W. Patharkar, O. R. Hsu, C.-W. Baer, J. Niederhuth, C. E. Ohler, U. Benfey, P. N. Walker, J. C. 2022-07-16 doi:10.1101/2022.07.14.500021 Cold Spring Harbor Laboratory Press 2022-07-16 <![CDATA[ Validity Assessment of Michigan's Proposed qPCR Threshold Value for Rapid Water-Quality Monitoring of E. coli Contamination ]]> https://biorxiv.org/content/10.1101/2022.07.16.500300v1?rss=1 McNair, J. N. Lane, M. J. Hart, J. J. Porter, A. Briggs, S. Southwell, B. Sivy, T. Szlag, D. C. Scull, B. T. Pike, S. Dreelin, E. Vernier, C. Carter, B. Sharp, J. Nowlin, P. Rediske, R. R. 2022-07-17 doi:10.1101/2022.07.16.500300 Cold Spring Harbor Laboratory Press 2022-07-17 <![CDATA[ Changes in biomarkers of metabolic stress during late gestation of dairy cows associated with colostrum volume and immunoglobulins content ]]> https://biorxiv.org/content/10.1101/2022.07.18.500308v1?rss=1 Rossi, R. M. Cullens, F. Bacigalupo Sanguesa, P. Sordillo, L. Abuelo, A. 2022-07-19 doi:10.1101/2022.07.18.500308 Cold Spring Harbor Laboratory Press 2022-07-19 <![CDATA[ Phyllosphere exudates select for distinct microbiome members in sorghum epicuticular wax and aerial root mucilage ]]> https://biorxiv.org/content/10.1101/2022.07.18.500406v1?rss=1 Mechan Llontop, M. Mullet, J. Shade, A. 2022-07-18 doi:10.1101/2022.07.18.500406 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ Phase Heterogeneity in Cholesterol-containing Ternary Phospholipid Lamellar Phases ]]> https://biorxiv.org/content/10.1101/2022.07.18.500534v1?rss=1 Gater, D. L. Hughes, K. I. Stojanoff, V. Isakovic, A. F. 2022-07-20 doi:10.1101/2022.07.18.500534 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Mechanism of strand displacement DNA synthesis by the coordinated activities of human mitochondrial DNA polymerase and SSB ]]> https://biorxiv.org/content/10.1101/2022.07.19.500644v1?rss=1 Plaza-G.A., I. Lemishko, K. M. Crespo, R. Truong, T. Q. Kaguni, L. S. Cao-Garcia, F. J. Ciesielski, G. L. Ibarra, B. 2022-07-20 doi:10.1101/2022.07.19.500644 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Developing cyanobacterial quorum sensing toolkits: towards interspecies coordination in mixed autotroph/heterotroph communities ]]> https://biorxiv.org/content/10.1101/2022.07.20.500858v1?rss=1 Kokarakis, E. J. Rillema, R. Ducat, D. C. Sakkos, J. K. 2022-07-21 doi:10.1101/2022.07.20.500858 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ Physiological responses to drought stress and recovery reflect differences in leaf function and anatomy among grass lineages ]]> https://biorxiv.org/content/10.1101/2022.07.30.502130v1?rss=1 Bachle, S. Zaricor, M. Griffith, D. Qui, F. Still, C. Ungerer, M. Nippert, J. 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Weinreich, M. 2017-10-21 doi:10.1101/207266 Cold Spring Harbor Laboratory Press 2017-10-21 <![CDATA[ Stimulation of the final cell cycle in the stomatal lineage by the cyclin CYCD7;1 under regulation of the MYB transcription factor FOUR-LIPS ]]> https://biorxiv.org/content/10.1101/207845v1?rss=1 Patell-Socha, F. Newman, D. Lee, E. Xie, Z. Collins, C. Grotewold, E. Murray, J. Dewitte, W. 2017-10-23 doi:10.1101/207845 Cold Spring Harbor Laboratory Press 2017-10-23 <![CDATA[ QTLseqr: An R package for bulk segregant analysis with next-generation sequencing ]]> https://biorxiv.org/content/10.1101/208140v1?rss=1 Mansfeld, B. Grumet, R. 2017-10-24 doi:10.1101/208140 Cold Spring Harbor Laboratory Press 2017-10-24 <![CDATA[ Neural Coding of Noisy and Reverberant Speech in Human Auditory Cortex ]]> https://biorxiv.org/content/10.1101/229153v1?rss=1 Puvvada, K. C. Villafane-Delgado, M. Brodbeck, C. Simon, J. Z. 2017-12-04 doi:10.1101/229153 Cold Spring Harbor Laboratory Press 2017-12-04 <![CDATA[ Exploring the Genetics of Lesion and Nodal Resistance in Pea (Pisum sativum L.) to Sclerotinia sclerotiorum Using Genome-wide Association Studies and RNA-Seq ]]> https://biorxiv.org/content/10.1101/233288v1?rss=1 Chang, H.-X. Sang, H. Wang, J. McPhee, K. E. Zhuang, X. Porter, L. D. Chilvers, M. 2017-12-13 doi:10.1101/233288 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ Genomic heritability estimates in sweet cherry reveal non-additive genetic variance is relevant for industry-prioritized traits ]]> https://biorxiv.org/content/10.1101/233296v1?rss=1 Piaskowski, J. Hardner, C. Cai, L. Zhao, Y. Iezzoni, A. Peace, C. 2017-12-13 doi:10.1101/233296 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ ClassificaIO: machine learning for classification graphical user interface ]]> https://biorxiv.org/content/10.1101/240184v1?rss=1 Roushangar, R. Mias, G. I. 2017-12-28 doi:10.1101/240184 Cold Spring Harbor Laboratory Press 2017-12-28 <![CDATA[ Resistance gene discovery and cloning by sequence capture and association genetics ]]> https://biorxiv.org/content/10.1101/248146v1?rss=1 Arora, S. Steuernagel, B. Chandramohan, S. Long, Y. Matny, O. Johnson, R. Enk, J. Periyannan, S. Hatta, M. A. M. Athiyannan, N. Cheema, J. Yu, G. Kangara, N. Ghosh, S. Szabo, L. J. Poland, J. Bariana, H. Jones, J. D. G. Bentley, A. R. Ayliffe, M. Olson, E. Xu, S. S. Steffenson, B. J. Lagudah, E. Wulff, B. B. H. 2018-01-15 doi:10.1101/248146 Cold Spring Harbor Laboratory Press 2018-01-15 <![CDATA[ Enabling the hypothesis-driven prioritization of ligand candidates in big databases: Screenlamp and its application to GPCR inhibitor discovery for invasive species control ]]> https://biorxiv.org/content/10.1101/249151v1?rss=1 Raschka, S. Scott, A. M. Liu, N. Gunturu, S. Huertas, M. Li, W. Kuhn, L. A. 2018-01-17 doi:10.1101/249151 Cold Spring Harbor Laboratory Press 2018-01-17 <![CDATA[ FlowPot axenic plant growth system for microbiota research ]]> https://biorxiv.org/content/10.1101/254953v1?rss=1 Kremer, J. M. Paasch, B. C. Rhodes, D. Thireault, C. Froehlich, J. E. Schulze-Lefert, P. Tiedje, J. M. He, S. Y. 2018-01-30 doi:10.1101/254953 Cold Spring Harbor Laboratory Press 2018-01-30 <![CDATA[ De novo haplotype reconstruction in viral quasispecies using paired-end read guided path finding ]]> https://biorxiv.org/content/10.1101/254987v1?rss=1 Chen, J. Zhao, Y. Sun, Y. 2018-01-28 doi:10.1101/254987 Cold Spring Harbor Laboratory Press 2018-01-28 <![CDATA[ Rare variants in the genetic background modulate the expressivity of neurodevelopmental disorders ]]> https://biorxiv.org/content/10.1101/257758v1?rss=1 Pizzo, L. Jensen, M. Polyak, A. Rosenfeld, J. A. Mannik, K. Krishnan, A. McCready, E. Pichon, O. Le Caignec, C. Van Dijck, A. Pope, K. Voorhoeve, E. Yoon, J. Stankiewicz, P. Cheung, S. W. Pazuchanics, D. Huber, E. Kumar, V. Kember, R. Mari, F. Curro, A. Castiglia, L. Galesi, O. Avola, E. Mattina, T. Fichera, M. Mandara, L. Vincent, M. Nizon, M. Mercier, S. Beneteau, C. Blesson, S. Martin-Coignard, D. Mosca-Boidron, A.-L. Caberg, J. H. Bucan, M. Zeesman, S. Nowaczyk, M. J. M. Lefebvre, M. Faivre, L. Callier, P. Skinner, C. Keren, B. Perrine, C. Pronte 2018-02-01 doi:10.1101/257758 Cold Spring Harbor Laboratory Press 2018-02-01 <![CDATA[ Gene Coregulation and Coexpression in the Aryl Hydrocarbon Receptor-mediated Transcriptional Regulatory Network in the Mouse Liver ]]> https://biorxiv.org/content/10.1101/260018v1?rss=1 Josyula, N. Andersen, M. E. Kaminski, N. Dere, E. Zacharewski, T. R. Bhattacharya, S. 2018-02-05 doi:10.1101/260018 Cold Spring Harbor Laboratory Press 2018-02-05 <![CDATA[ Protein-ligand interfaces are polarized: Discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes ]]> https://biorxiv.org/content/10.1101/260612v1?rss=1 Raschka, S. Wolf, A. J. Bemister-Buffington, J. Kuhn, L. A. 2018-02-05 doi:10.1101/260612 Cold Spring Harbor Laboratory Press 2018-02-05 <![CDATA[ The Atypical Rho GTPase CHW-1 Works With SAX-3/Robo to Mediate Axon Guidance in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/265066v1?rss=1 Alan, J. Robinson, S. Magsig, K. Demarco, R. Lundquist, E. A. 2018-02-13 doi:10.1101/265066 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ ADAR1 A-to-I RNA alters codon usage ]]> https://biorxiv.org/content/10.1101/268813v1?rss=1 Brachova, P. Alvarez, N. S. Hong, X. Vincent, K. A. Latham, K. E. Christenson, L. K. 2018-02-21 doi:10.1101/268813 Cold Spring Harbor Laboratory Press 2018-02-21 <![CDATA[ Factors influencing gene family size variation among related species in a plant family ]]> https://biorxiv.org/content/10.1101/270009v1?rss=1 Wang, P. Moore, B. M. Panchy, N. L. Meng, F. Lehti-Shiu, M. D. Shiu, S.-H. 2018-02-23 doi:10.1101/270009 Cold Spring Harbor Laboratory Press 2018-02-23 <![CDATA[ Sexual stage-induced long noncoding RNAs in the filamentous fungus Fusarium graminearum ]]> https://biorxiv.org/content/10.1101/270298v1?rss=1 Kim, W. Miguel-Rojas, C. Wang, J. Townsend, J. P. Trail, F. 2018-02-23 doi:10.1101/270298 Cold Spring Harbor Laboratory Press 2018-02-23 <![CDATA[ Elongation during segmentation shows axial variability, low mitotic rates, and synchronized cell cycle domains in the crustacean, Thamnocephalus platyurus ]]> https://biorxiv.org/content/10.1101/270728v1?rss=1 Constantinou, S. J. Duan, N. Chipman, A. D. Nagy, L. M. Williams, T. A. 2018-02-23 doi:10.1101/270728 Cold Spring Harbor Laboratory Press 2018-02-23 <![CDATA[ The role of AP-1 in self-sufficient proliferation and migration of cancer cells and its potential impact on an autocrine/paracrine loop. ]]> https://biorxiv.org/content/10.1101/271536v1?rss=1 Abudu, A. Ibrahim, S. Johnson, E. Aftab, N. Fluck, M. 2018-02-25 doi:10.1101/271536 Cold Spring Harbor Laboratory Press 2018-02-25 <![CDATA[ Assessment and refinement of sample preparation methods for deep and quantitative plant proteome profiling ]]> https://biorxiv.org/content/10.1101/273656v1?rss=1 Song, G. Hsu, P. Y. Walley, J. W. 2018-02-28 doi:10.1101/273656 Cold Spring Harbor Laboratory Press 2018-02-28 <![CDATA[ Tripartite chromatin localization of budding yeast Shugoshin involves higher-ordered architecture of mitotic chromosomes ]]> https://biorxiv.org/content/10.1101/274241v1?rss=1 Kuo, M.-H. Deng, X. 2018-03-01 doi:10.1101/274241 Cold Spring Harbor Laboratory Press 2018-03-01 <![CDATA[ Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient ]]> https://biorxiv.org/content/10.1101/276584v1?rss=1 Sorensen, J. W. Dunivin, T. K. Tobin, T. C. Shade, A. 2018-03-05 doi:10.1101/276584 Cold Spring Harbor Laboratory Press 2018-03-05 <![CDATA[ Loss of Peroxisomal Hydroxypyruvate Reductase Inhibits Triose Phosphate Isomerase but Stimulates Cyclic Photosynthetic Electron Flow and the Glc-6P-Phosphate Shunt ]]> https://biorxiv.org/content/10.1101/278580v1?rss=1 Li, J. Weraduwage, S. M. Preiser, A. L. Weise, S. E. Strand, D. D. Froehlich, J. E. Kramer, D. M. Hu, J. Sharkey, T. D. 2018-03-08 doi:10.1101/278580 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ Current production as a rapid response expression reporter under micro-oxic and anoxic conditions ]]> https://biorxiv.org/content/10.1101/289140v1?rss=1 Madsen, C. S. Barvo, N. N. Fromwiller, C. Tyll, S. Amburn, B. Ducat, D. Hamberger, B. TerAvest, M. A. 2018-03-27 doi:10.1101/289140 Cold Spring Harbor Laboratory Press 2018-03-27 <![CDATA[ Non-parametric and semi-parametric support estimation using SEquential RESampling random walks on biomolecular sequences ]]> https://biorxiv.org/content/10.1101/292078v1?rss=1 Wang, W. Smith, J. Hejase, H. Liu, K. J. 2018-03-30 doi:10.1101/292078 Cold Spring Harbor Laboratory Press 2018-03-30 <![CDATA[ Stroke survivors show task-dependent modulation of motor variability during bimanual coordination ]]> https://biorxiv.org/content/10.1101/292193v1?rss=1 Ranganathan, R. Gebara, R. Andary, M. Sylvain, J. 2018-03-30 doi:10.1101/292193 Cold Spring Harbor Laboratory Press 2018-03-30 <![CDATA[ On the deformability of an empirical fitness landscape by microbial evolution ]]> https://biorxiv.org/content/10.1101/293407v1?rss=1 Bajic, D. Vila, J. C. C. Blount, Z. D. Sanchez, A. 2018-04-02 doi:10.1101/293407 Cold Spring Harbor Laboratory Press 2018-04-02 <![CDATA[ Mapping the Peaks: Fitness Landscapes of the Fittest and the Flattest ]]> https://biorxiv.org/content/10.1101/298125v1?rss=1 Franklin, J. LaBar, T. Adami, C. 2018-04-09 doi:10.1101/298125 Cold Spring Harbor Laboratory Press 2018-04-09 <![CDATA[ Monitoring Anti-Pythium insidiosum IgG Antibodies and (1->3)-β-D-Glucan in Vascular Pythiosis ]]> https://biorxiv.org/content/10.1101/300764v1?rss=1 Worasilchai, N. Permpalung, N. Chongsathidkiet, P. Leelahavanichkul, A. Mendoza, L. A. Palaga, T. Reantragoon, R. Finkelman, M. A. Sutcharitchan, P. Chindamporn, A. 2018-04-13 doi:10.1101/300764 3)-β-D-Glucan in Vascular Pythiosis]]> Cold Spring Harbor Laboratory Press 2018-04-13 <![CDATA[ An optimal kernel-based method for gene set association analysis ]]> https://biorxiv.org/content/10.1101/304055v1?rss=1 Cui, Y. He, T. Li, S. Zhong, P.-S. 2018-04-18 doi:10.1101/304055 Cold Spring Harbor Laboratory Press 2018-04-18 <![CDATA[ Robust predictions of specialized metabolism genes through machine learning ]]> https://biorxiv.org/content/10.1101/304873v1?rss=1 Moore, B. M. Wang, P. Fan, P. Leong, B. Schenck, C. A. Lloyd, J. P. Lehti-Shiu, M. Last, R. Pichersky, E. Shiu, S.-H. 2018-04-20 doi:10.1101/304873 Cold Spring Harbor Laboratory Press 2018-04-20 <![CDATA[ SpeciFlex: A Protocol for Mining Binding Site Conformational Selectivity in Structure-Based Inhibitor Discovery ]]> https://biorxiv.org/content/10.1101/304931v1?rss=1 Tonero, M. E. Kuhn, L. A. 2018-04-21 doi:10.1101/304931 Cold Spring Harbor Laboratory Press 2018-04-21 <![CDATA[ Elevated O-GlcNAcylation Enhances Pro-Inflammatory Th17 Function by Altering the Lipid Microenvironment ]]> https://biorxiv.org/content/10.1101/305722v1?rss=1 Machacek, M. Zhang, Z. Tan, E. P. Li, J. Li, T. Villar, M. T. Artigues, A. Lydic, T. Slawson, C. Fields, P. 2018-04-20 doi:10.1101/305722 Cold Spring Harbor Laboratory Press 2018-04-20 <![CDATA[ HIPPO signaling provides a fail-safe for resolving embryonic cell fate conflicts during establishment of pluripotency in vivo ]]> https://biorxiv.org/content/10.1101/316539v1?rss=1 Frum, T. Ralston, A. 2018-05-08 doi:10.1101/316539 Cold Spring Harbor Laboratory Press 2018-05-08 <![CDATA[ The Sheep and the Goats: Distinguishing transcriptional enhancers in a complex chromatin landscape ]]> https://biorxiv.org/content/10.1101/324582v1?rss=1 Sonnenschein, A. Dworkin, I. Arnosti, D. 2018-05-25 doi:10.1101/324582 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Regional neutrality evolves through local adaptive niche evolution ]]> https://biorxiv.org/content/10.1101/326348v1?rss=1 Leibold, M. A. Urban, M. C. De Meester, L. Klausmeier, C. A. Vanoverbeke, J. 2018-05-21 doi:10.1101/326348 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ Investigation of lanthanide-dependent methylotrophy uncovers complementary roles for alcohol dehydrogenase enzymes ]]> https://biorxiv.org/content/10.1101/329011v1?rss=1 Good, N. M. Walser, O. N. Moore, R. S. Suriano, C. Huff, A. F. Martinez-Gomez, N. C. 2018-05-23 doi:10.1101/329011 Cold Spring Harbor Laboratory Press 2018-05-23 <![CDATA[ Biparental inheritance of chloroplasts is controlled by lipid biosynthesis ]]> https://biorxiv.org/content/10.1101/330100v1?rss=1 Sobanski, J. Giavalisco, P. Fischer, A. Walther, D. Schoettler, M. A. Pellizzer, T. Golczyk, H. Obata, T. Bock, R. Sears, B. B. Greiner, S. 2018-05-24 doi:10.1101/330100 Cold Spring Harbor Laboratory Press 2018-05-24 <![CDATA[ Protein Gradients on the Nucleoid Position the Carbon-fixing Organelles of Cyanobacteria ]]> https://biorxiv.org/content/10.1101/334813v1?rss=1 MacCready, J. S. Hakim, P. Young, E. J. Hu, L. Liu, J. Osteryoung, K. W. Vecchiarelli, A. G. Ducat, D. C. 2018-05-30 doi:10.1101/334813 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ Hook length of the bacterial flagellum is controlled to nanometer-scale for optimal motility performance ]]> https://biorxiv.org/content/10.1101/336602v1?rss=1 Spöring, I. Martinez, V. A. Hotz, C. Schwarz-Linek, J. Grady, K. L. Nava-Sedeno, J. M. Vissers, T. Singer, H. M. Rohde, M. Bourquin, C. Hatzikirou, H. Poon, W. C. Dufour, Y. Erhardt, M. 2018-06-02 doi:10.1101/336602 Cold Spring Harbor Laboratory Press 2018-06-02 <![CDATA[ Selecting precise reference normal tissue samples for cancer research using a deep learning approach ]]> https://biorxiv.org/content/10.1101/336909v1?rss=1 Zeng, W. Glicksberg, B. Li, Y. Chen, B. 2018-06-02 doi:10.1101/336909 Cold Spring Harbor Laboratory Press 2018-06-02 <![CDATA[ Evaluating cancer cell lines as models for metastatic breast cancer ]]> https://biorxiv.org/content/10.1101/337287v1?rss=1 Liu, K. Newbury, P. Glicksberg, B. Andrechek, E. Chen, B. 2018-06-02 doi:10.1101/337287 Cold Spring Harbor Laboratory Press 2018-06-02 <![CDATA[ HaploBlocker: Creation of subgroup specific haplotype blocks and libraries ]]> https://biorxiv.org/content/10.1101/339788v1?rss=1 Pook, T. Schlather, M. de los Campos, G. Schoen, C. C. Simianer, H. 2018-06-19 doi:10.1101/339788 Cold Spring Harbor Laboratory Press 2018-06-19 <![CDATA[ Mapping the ligand binding landscape ]]> https://biorxiv.org/content/10.1101/346817v1?rss=1 Dickson, A. 2018-06-13 doi:10.1101/346817 Cold Spring Harbor Laboratory Press 2018-06-13 <![CDATA[ Imputation of Behavioral Candidate Gene Repeat Polymorphisms in 486,551 Publicly-Available UK Biobank Individuals. ]]> https://biorxiv.org/content/10.1101/358267v1?rss=1 0.96 for all four VNTR polymorphisms and one modifying SNP, depending on the reference and target dataset. We describe the imputation procedures of these candidate polymorphisms in 486,551 UK Biobank individuals, and have made the imputed polymorphism data available to UK Biobank researchers. This resource, provided to the community, will allow the most rigorous tests to-date of the roles of these polymorphisms in behavioral and psychiatric phenotypes. ]]> Border, R. Smolen, A. Corley, R. Stallings, M. Brown, S. Conger, R. Derringer, J. Donnellan, M. B. Haberstick, B. C. Hewitt, J. Hopfer, C. Krauter, K. McQueen, M. B. Wall, T. L. Keller, M. C. Evans, L. 2018-06-29 doi:10.1101/358267 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Fast and Robust Deconvolution of Tumor Infiltrating Lymphocyte from Expression Profiles using Least Trimmed Squares ]]> https://biorxiv.org/content/10.1101/358366v1?rss=1 Hao, Y. Yan, M. Lei, Y. L. Xie, Y. 2018-06-29 doi:10.1101/358366 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Mouse Models of GNAO1-Associated Movement Disorder: Allele- and sex-specific differences in phenotypes ]]> https://biorxiv.org/content/10.1101/358614v1?rss=1 Feng, H. Larrivee, C. L. Demireva, E. Xie, H. Leipprandt, J. Neubig, R. R. 2018-06-29 doi:10.1101/358614 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Evolution of Endothelin signaling and diversification of adult pigment pattern in Danio fishes ]]> https://biorxiv.org/content/10.1101/363879v1?rss=1 Spiewak, J. Bain, E. Liu, J. Kou, K. Sturiale, S. Patterson, L. Diba, P. Eisen, J. Braasch, I. Ganz, J. Parichy, D. M. 2018-07-06 doi:10.1101/363879 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ Integrated sequence and gene expression analysis of mouse models of breast cancer reveals critical events with human parallels ]]> https://biorxiv.org/content/10.1101/375154v1?rss=1 Rennhack, J. Swiatnicki, M. Zhang, Y. Li, C. Bylett, E. Ross, C. Szczepanek, K. Hanrahan, W. Jayatissa, M. Hunter, K. Andrechek, E. 2018-07-24 doi:10.1101/375154 Cold Spring Harbor Laboratory Press 2018-07-24 <![CDATA[ De novo mutations in the GTP/GDP-binding region of RALA, a RAS-like small GTPase, cause intellectual disability and developmental delay ]]> https://biorxiv.org/content/10.1101/378349v1?rss=1 Hiatt, S. Neu, M. B. Ramaker, R. C. Hardigan, A. A. Prokop, J. W. Hancarova, M. Prchalova, D. Havlovicova, M. Prchal, J. Stranecky, V. Yim, D. K. Powis, Z. Keren, B. Nava, C. Mignot, C. Rio, M. Revah-Politi, A. Hemati, P. Stong, N. Iglesias, A. D. Suchy, S. F. Willaert, R. Wentzensen, I. M. Wheeler, P. G. Brick, L. Kozenko, M. Hurst, A. C. Wheless, J. W. Lacassie, Y. Sedlacek, Z. Myers, R. M. Barsh, G. S. Cooper, G. M. 2018-07-29 doi:10.1101/378349 Cold Spring Harbor Laboratory Press 2018-07-29 <![CDATA[ A chromosome scale assembly of the model desiccation tolerant grass Oropetium thomaeum ]]> https://biorxiv.org/content/10.1101/378943v1?rss=1 VanBuren, R. Wai, C. M. Keilwagen, J. Pardo, J. 2018-07-31 doi:10.1101/378943 Cold Spring Harbor Laboratory Press 2018-07-31 <![CDATA[ Prospects for enhancing leaf photosynthetic capacity by manipulating mesophyll cell morphology ]]> https://biorxiv.org/content/10.1101/379065v1?rss=1 Ren, T. Weraduwage, S. M. Sharkey, T. D. 2018-07-27 doi:10.1101/379065 Cold Spring Harbor Laboratory Press 2018-07-27 <![CDATA[ Rho-mediated MRTF and YAP1 activation contributes to BRAF inhibitor resistance in Sox9High/Sox10Low melanoma cells. ]]> https://biorxiv.org/content/10.1101/381806v1?rss=1 100-fold increase in Sox9 expression and >100-fold decrease in Sox10 expression. Two transcriptional co-activators downstream of RhoA, MRTF and YAP1, are activated in Sox9High/Sox10Low BRAFi-resistant cells. Pharmacological inhibition of these transcriptional mechanisms re-sensitizes the cells to vemurafenib. Analysis of human BRAFi-resistant tumors reveals that many resistant tumors show gene expression signatures consistent with increased RhoA activation or activation of the transcriptional co-activators MRTF and YAP1. A subset of melanoma tumors in the TCGA dataset with low Sox10 expression also have elevated RhoA, MRTF, and YAP1 activation signatures. Taken together, these results support the concept of targeting RhoA-regulated gene transcription pathways as a promising approach for treating or preventing BRAFi-resistance in melanoma. ]]> Misek, S. A. Appleton, K. M. Dexheimer, T. S. Lisabeth, E. M. Lo, R. Larsen, S. D. Gallo, K. Neubig, R. R. 2018-08-01 doi:10.1101/381806 Cold Spring Harbor Laboratory Press 2018-08-01 <![CDATA[ A galling insect activates plant reproductive programs during gall development ]]> https://biorxiv.org/content/10.1101/383851v1?rss=1 Schultz, J. C. Edger, P. P. Body, M. J. Appel, H. M. 2018-08-02 doi:10.1101/383851 Cold Spring Harbor Laboratory Press 2018-08-02 <![CDATA[ AICM: A Genuine Framework for Correcting Inconsistency Between Large Pharmacogenomics Datasets ]]> https://biorxiv.org/content/10.1101/386896v1?rss=1 Hu, Z. T. Ye, Y. Newbury, P. Huang, H. Chen, B. 2018-08-07 doi:10.1101/386896 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ Predicting cell-cycle expressed genes identifies canonical and non-canonical regulators of time-specific expression in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/387050v1?rss=1 Panchy, N. L. Lloyd, J. Shiu, S.-H. 2018-08-07 doi:10.1101/387050 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ Imperfect Linkage Disequilibrium Generates Phantom Epistasis (& Perils of Big Data) ]]> https://biorxiv.org/content/10.1101/388942v1?rss=1 de los Campos, G. Sorensen, D. A. Toro, M. A. 2018-08-09 doi:10.1101/388942 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ A genus definition for Bacteria and Archaea based on genome relatedness and taxonomic affiliation. ]]> https://biorxiv.org/content/10.1101/392480v1?rss=1 Barco, R. A. Garrity, G. M. Scott, J. J. Amend, J. Nealson, K. H. Emerson, D. 2018-08-16 doi:10.1101/392480 Cold Spring Harbor Laboratory Press 2018-08-16 <![CDATA[ Spatial Structure Can Decrease Symbiotic Cooperation ]]> https://biorxiv.org/content/10.1101/393868v1?rss=1 Vostinar, A. E. Ofria, C. 2018-08-20 doi:10.1101/393868 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ Fluctuating environments select for short-term phenotypic variation leading to long-term exploration ]]> https://biorxiv.org/content/10.1101/394676v1?rss=1 Canino-Koning, R. Ofria, C. Wiser, M. 2018-08-17 doi:10.1101/394676 Cold Spring Harbor Laboratory Press 2018-08-17 <![CDATA[ p38α in CD11c+ cells drives sex-specific differences during progression of autoimmune demyelination ]]> https://biorxiv.org/content/10.1101/396036v1?rss=1 Chechneva, O. Mayrhofer, F. Dariychuk, Z. Zhen, A. Pleasure, D. E. Deng, W. 2018-08-20 doi:10.1101/396036 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ Epigenetic factors coordinate intestinal development ]]> https://biorxiv.org/content/10.1101/399410v1?rss=1 Ganz, J. Melancon, E. Wilson, C. Amores, A. Batzel, P. Strader, M. Braasch, I. Diba, P. Kuhlman, J. A. Postlethwait, J. H. Eisen, J. S. 2018-08-23 doi:10.1101/399410 Cold Spring Harbor Laboratory Press 2018-08-23 <![CDATA[ SPECIES-SPECIFIC ROOT MICROBIOTA DYNAMICS IN RESPONSE TO PLANT-AVAILABLE PHOSPHORUS ]]> https://biorxiv.org/content/10.1101/400119v1?rss=1 Bodenhausen, N. Somerville, V. Desiro, A. Walser, J.-C. Borghi, L. van der Heijden, M. Schlaeppi, K. 2018-08-25 doi:10.1101/400119 Cold Spring Harbor Laboratory Press 2018-08-25 <![CDATA[ Mechanisms of a locally adaptive shift in allocation among growth, reproduction, and herbivore resistance in Mimulus guttatus ]]> https://biorxiv.org/content/10.1101/400523v1?rss=1 Lowry, D. Popovic, D. Brennan, D. J. Holeski, L. M. 2018-08-26 doi:10.1101/400523 Cold Spring Harbor Laboratory Press 2018-08-26 <![CDATA[ Biotransformation of 2,4-dinitrotoluene in a phototrophic co-culture of engineered Synechococcus elongatus and Pseudomonas putida ]]> https://biorxiv.org/content/10.1101/404988v1?rss=1 Fedeson, D. T. Saake, P. Calero, P. Nikel, P. I. Ducat, D. C. 2018-08-31 doi:10.1101/404988 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ OLIVER: A Tool for Visual Data Analysis on Longitudinal Plant Phenomics Data ]]> https://biorxiv.org/content/10.1101/411595v1?rss=1 Tessmer, O. L. Kramer, D. M. Chen, J. 2018-09-08 doi:10.1101/411595 Cold Spring Harbor Laboratory Press 2018-09-08 <![CDATA[ Inhibition of Mycobacterium tuberculosis DosRST two-component regulatory system signaling by targeting response regulator DNA binding and sensor kinase heme ]]> https://biorxiv.org/content/10.1101/411793v1?rss=1 Zheng, H. Aleiwi, B. Ellsworth, E. Abramovitch, R. B. 2018-09-08 doi:10.1101/411793 Cold Spring Harbor Laboratory Press 2018-09-08 <![CDATA[ Systematic analysis of the Myxococcus xanthus developmental gene regulatory network supports posttranslational regulation of FruA by C-signaling ]]> https://biorxiv.org/content/10.1101/415331v1?rss=1 nView larger version (28K):norg.highwire.dtl.DTLVardef@c16410org.highwire.dtl.DTLVardef@909252org.highwire.dtl.DTLVardef@17668a8org.highwire.dtl.DTLVardef@d126c3_HPS_FORMAT_FIGEXP M_FIG C_FIG Abbreviated summaryStarvation promotes MrpC accumulation, whereas nutrients favor proteolysis. MrpC activates transcription of fruA, but FruA protein appears to be activated by short-range C-signaling in a cycle leading to mound formation and lysis of some cells. Activated FruA* and MrpC are proposed to cooperatively stimulate transcription of the dev operon and genes that commit starving rod-shaped cells to form spores, while Dev proteins slow commitment, resulting in a spore-filled fruiting body surrounded by peripheral rods. ]]> Saha, S. Patra, P. Igoshin, O. Kroos, L. 2018-09-12 doi:10.1101/415331 Cold Spring Harbor Laboratory Press 2018-09-12 <![CDATA[ Deciphering the enigmatic role of the amidotransferase LipL in Bacillus subtilis lipoic acid utilization ]]> https://biorxiv.org/content/10.1101/419234v1?rss=1 Rasetto, N. B. Lavatelli, A. Martin, N. Mansilla, M. C. 2018-09-17 doi:10.1101/419234 Cold Spring Harbor Laboratory Press 2018-09-17 <![CDATA[ How phage L capsid decoration protein distinguishes between nearly identical binding sites on an icosahedral virion ]]> https://biorxiv.org/content/10.1101/420992v1?rss=1 Newcomer, R. L. Schrad, J. R. Gilcrease, E. B. Casjens, S. R. Feig, M. Teschke, C. M. Alexandrescu, A. Parent, K. N. 2018-09-18 doi:10.1101/420992 Cold Spring Harbor Laboratory Press 2018-09-18 <![CDATA[ Quantifying Heterogeneity in the Genetic Architecture of Complex Traits Between Ethnically Diverse Groups using Random Effect Interaction Models ]]> https://biorxiv.org/content/10.1101/421149v1?rss=1 Veturi, Y. de los Campos, G. Yi, N. Huang, W. Vazquez, A. I. Kuhnel, B. 2018-09-20 doi:10.1101/421149 Cold Spring Harbor Laboratory Press 2018-09-20 <![CDATA[ Twin Study of Early-Onset Major Depression Finds DNA Methylation Enrichment for Neurodevelopmental Genes ]]> https://biorxiv.org/content/10.1101/422345v1?rss=1 Roberson-Nay, R. Wolen, A. R. Lapato, D. M. Lancaster, E. E. Webb, B. T. Verhulst, B. Hettema, J. M. York, T. P. 2018-09-20 doi:10.1101/422345 Cold Spring Harbor Laboratory Press 2018-09-20 <![CDATA[ Comprehensive transcriptomic analysis of cell lines as models of primary tumor samples across 22 tumor types ]]> https://biorxiv.org/content/10.1101/422592v1?rss=1 Yu, K. Chen, B. Aran, D. Goldstein, T. Sirota, M. 2018-09-20 doi:10.1101/422592 Cold Spring Harbor Laboratory Press 2018-09-20 <![CDATA[ Age-dependent visualization of neural progenitor cells within the rostral migratory stream via MRI and endogenously labeled micron-sized iron oxide particles ]]> https://biorxiv.org/content/10.1101/429787v1?rss=1 Shuboni-Mulligan, D. D. Chakravarty, S. Mallett, C. L. Wolf, A. M. Forton, S. Shapiro, E. M. 2018-09-27 doi:10.1101/429787 Cold Spring Harbor Laboratory Press 2018-09-27 <![CDATA[ Triose phosphate utilization and beyond: from photosynthesis to end-product synthesis ]]> https://biorxiv.org/content/10.1101/434928v1?rss=1 McClain, A. M. Sharkey, T. D. 2018-10-04 doi:10.1101/434928 Cold Spring Harbor Laboratory Press 2018-10-04 <![CDATA[ Comparing faster evolving rplB and rpsC versus SSU rRNA for improved microbial community resolution ]]> https://biorxiv.org/content/10.1101/435099v1?rss=1 Guo, J. Cole, J. R. Brown, C. T. Tiedje, J. M. 2018-10-04 doi:10.1101/435099 Cold Spring Harbor Laboratory Press 2018-10-04 <![CDATA[ RefSoil+: A reference for antimicrobial resistance genes on soil plasmids ]]> https://biorxiv.org/content/10.1101/435107v1?rss=1 Dunivin, T. K. Choi, J. Howe, A. C. Shade, A. 2018-10-04 doi:10.1101/435107 Cold Spring Harbor Laboratory Press 2018-10-04 <![CDATA[ 16S rRNA:rDNA ratios and cell activity staining reveal consistent patterns of soil microbial activity ]]> https://biorxiv.org/content/10.1101/435925v1?rss=1 Bowsher, A. W. Kearns, P. J. Shade, A. 2018-10-05 doi:10.1101/435925 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer. ]]> https://biorxiv.org/content/10.1101/437905v1?rss=1 Fores Martos, J. Catala Lopez, F. Sanchez Valle, J. Ibanez Garikano, K. Tejero, H. Palma Gaudiel, H. Climent Bataller, J. Pancaldi, V. Fananas Saura, L. Arango Lopez, C. Parellada, M. Baudot, A. Vogt, D. Rubenstein, J. Valencia, A. Tabares Seisdedos, R. 2018-10-08 doi:10.1101/437905 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ Evolutionary characteristics of intergenic transcribed regions indicate widespread noisy transcription in the Poaceae ]]> https://biorxiv.org/content/10.1101/440933v1?rss=1 Lloyd, J. P. Bowman, M. J. Azodi, C. B. Moghe, G. D. Childs, K. L. Shiu, S.-H. 2018-10-11 doi:10.1101/440933 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ Supply and consumption of glucose 6-phosphate in the chloroplast stroma ]]> https://biorxiv.org/content/10.1101/442434v1?rss=1 Preiser, A. L. Banerjee, A. Fisher, N. Sharkey, T. D. 2018-10-13 doi:10.1101/442434 Cold Spring Harbor Laboratory Press 2018-10-13 <![CDATA[ Targeting microbial arsenic resistance genes: a new bioinformatic toolkit informs arsenic ecology and evolution in soil genomes and metagenomes ]]> https://biorxiv.org/content/10.1101/445502v1?rss=1 Dunivin, T. K. Yeh, S. Y. Shade, A. 2018-10-17 doi:10.1101/445502 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops ]]> https://biorxiv.org/content/10.1101/446369v1?rss=1 Grady, K. L. Sorensen, J. W. Stopnisek, N. Shade, A. 2018-10-18 doi:10.1101/446369 Cold Spring Harbor Laboratory Press 2018-10-18 <![CDATA[ Evaluation of the causal effect of fibrinogen on incident coronary heart disease via Mendelian randomization ]]> https://biorxiv.org/content/10.1101/448381v1?rss=1 Ward-Caviness, C. K. de Vries, P. S. Wiggins, K. L. Huffman, J. E. Yanek, L. R. Bielak, L. F. Giulianini, F. Guo, X. Kleber, M. E. Kacprowski, T. Gross, S. Petersman, A. Davey Smith, G. Hartwig, F. P. Bowden, J. Hemani, G. Muller-Nuraysid, M. Strauch, K. Koenig, W. Waldenberger, M. Meitinger, T. Pankratz, N. Boerwinkle, E. Tang, W. Fu, Y.-P. Johnson, A. D. Song, C. de Maat, M. P. Uitterlinden, A. G. Franco, O. H. Brody, J. A. McKnight, B. Chen, Y.-D. I. Psaty, B. M. Mathias, R. A. Becker, D. M. Peyser, P. A. Smith, J. A. Bielinski, S. J. Ridker, P. M. Ta 2018-10-19 doi:10.1101/448381 Cold Spring Harbor Laboratory Press 2018-10-19 <![CDATA[ Integrated epigenome, exome and transcriptome analyses reveal molecular subtypes and homeotic transformation in uterine fibroids. ]]> https://biorxiv.org/content/10.1101/452342v1?rss=1 George, J. W. Fan, H. Chatterjee, A. Patterson, A. L. Koeman, J. Adams, M. Madaj, Z. B. Chesla, D. W. Marsh, E. E. Shen, H. Teixeira, J. M. 2018-10-26 doi:10.1101/452342 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ Identifying Emerging Phenomenon in Plant Long Temporal Phenotyping Experiments ]]> https://biorxiv.org/content/10.1101/454686v1?rss=1 Peng, J. Lu, J. Hoh, D. Dina, A. Shang, X. Kramer, D. Chen, J. 2018-10-26 doi:10.1101/454686 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ Extracellular electron uptake by two Methanosarcina species ]]> https://biorxiv.org/content/10.1101/458091v1?rss=1 Yee, M. O. Snoeyenbos-West, O. L. O. Thamdrup, B. Ottosen, L. D. M. Rotaru, A.-E. 2018-10-31 doi:10.1101/458091 Cold Spring Harbor Laboratory Press 2018-10-31 <![CDATA[ Identification of Pirin as a Molecular Target of the CCG-1423/CCG-203971 Series of Anti-Fibrotic and Anti-Metastatic Compounds ]]> https://biorxiv.org/content/10.1101/458554v1?rss=1 Lisabeth, E. M. Kahl, D. Gopallawa, I. Haynes, S. E. Misek, S. A. Campbell, P. L. Dexheimer, T. S. Khanna, D. Fox, D. A. Jin, X. Martin, B. R. Larsen, S. D. Neubig, R. R. 2018-10-31 doi:10.1101/458554 Cold Spring Harbor Laboratory Press 2018-10-31 <![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[ Cis-regulatory code for predicting plant cell-type specific high salinity response ]]> https://biorxiv.org/content/10.1101/466326v1?rss=1 Uygun, S. Azodi, C. B. Shiu, S.-H. 2018-11-08 doi:10.1101/466326 Cold Spring Harbor Laboratory Press 2018-11-08 <![CDATA[ Trust in scientists and rates of noncompliance with a fisheries rule in the Brazilian Pantanal ]]> https://biorxiv.org/content/10.1101/468728v1?rss=1 Gore, M. L. Shirley, E. 2018-11-12 doi:10.1101/468728 Cold Spring Harbor Laboratory Press 2018-11-12 <![CDATA[ A Draft Genome and High-Density Genetic Mapof European Hazelnut (Corylus avellana L.) ]]> https://biorxiv.org/content/10.1101/469015v1?rss=1 Rowley, E. R. VanBuren, R. Bryant, D. W. Priest, H. D. Mehlenbacher, S. A. Mockler, T. C. 2018-12-11 doi:10.1101/469015 Cold Spring Harbor Laboratory Press 2018-12-11 <![CDATA[ Reversing an extracellular electron transfer pathway for electrode-driven NADH generation ]]> https://biorxiv.org/content/10.1101/476481v1?rss=1 Tefft, N. M. TerAvest, M. A. 2018-11-26 doi:10.1101/476481 Cold Spring Harbor Laboratory Press 2018-11-26 <![CDATA[ Reciprocal cybrids reveal how organellar genomes affect plant phenotypes ]]> https://biorxiv.org/content/10.1101/477687v1?rss=1 Flood, P. J. Theeuwen, T. P. J. M. Schneeberger, K. Keizer, P. Kruijer, W. Severing, E. Kouklas, E. Hageman, J. A. Becker, F. F. M. Schnabel, S. K. K. Willems, L. Ligterink, W. van Arkel, J. Mumm, R. Gualberto, J. M. Savage, L. Kramer, D. M. Keurentjes, J. J. B. van Eeuwijk, F. Koornneef, M. Harbinson, J. Aarts, M. G. M. Wijnker, E. 2018-11-24 doi:10.1101/477687 Cold Spring Harbor Laboratory Press 2018-11-24 <![CDATA[ An agent-based framework for improving wildlife disease surveillance: A case study of chronic wasting disease in Missouri white-tailed deer. ]]> https://biorxiv.org/content/10.1101/478610v1?rss=1 Belsare, A. Gompper, M. E. Keller, B. Sumners, J. Hansen, L. Millspaugh, J. 2018-11-29 doi:10.1101/478610 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ Rootstock effects on scion phenotypes in a ‘Chambourcin’ experimental vineyard ]]> https://biorxiv.org/content/10.1101/484212v1?rss=1 Migicovsky, Z. Harris, Z. N. Klein, L. L. Li, M. McDermaid, A. Chitwood, D. H. Fennell, A. Kovacs, L. G. Kwasniewski, M. Londo, J. P. Ma, Q. Miller, A. J. 2018-12-03 doi:10.1101/484212 Cold Spring Harbor Laboratory Press 2018-12-03 <![CDATA[ Developmental Dieldrin Exposure Alters DNA Methylation at Genes Related to Dopaminergic Neuron Development and Parkinson’s Disease in Mouse Midbrain ]]> https://biorxiv.org/content/10.1101/494237v1?rss=1 Kochmanski, J. VanOeveren, S. E. Bernstein, A. I. 2018-12-13 doi:10.1101/494237 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Stratified computational meta-analysis of 2213 acute myeloid leukemia patients reveals age- and sex-dependent gene expression signatures ]]> https://biorxiv.org/content/10.1101/494948v1?rss=1 Roushangar, R. Mias, G. I. 2018-12-13 doi:10.1101/494948 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Genomic footprints of repeated evolution of CAM photosynthesis in tillandsioid bromeliads ]]> https://biorxiv.org/content/10.1101/495812v1?rss=1 de La Harpe, M. Paris, M. Hess, J. Barfuss, M. H. J. Serrano-Serrano, M. L. Ghatak, A. Chaturvedi, P. Weckwerth, W. Till, W. Salamin, N. Wai, C. M. Ming, R. Lexer, C. 2018-12-13 doi:10.1101/495812 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Tissue distribution and tumor concentrations of hydroxychloroquine and quinacrine analogs in mice ]]> https://biorxiv.org/content/10.1101/496018v1?rss=1 MacKeigan, J. P. Solitro, A. R. 2018-12-13 doi:10.1101/496018 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Data-Driven Analysis of Age, Sex, and Tissue Effects on Gene Expression Variability in Alzheimer’s Disease ]]> https://biorxiv.org/content/10.1101/498527v1?rss=1 Brooks, L. R. Mias, G. 2018-12-17 doi:10.1101/498527 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ Diversification of retinoblastoma protein function associated with cis and trans adaptations ]]> https://biorxiv.org/content/10.1101/501866v1?rss=1 Mouawad, R. Prasad, J. Thorley, D. Himadewi, P. Kadiyala, D. Wilson, N. Kapranov, P. Arnosti, D. 2018-12-19 doi:10.1101/501866 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Biological Potencial of Colletotrichum typhae H.C Greene mycoherbicide for Typha domingensis Pers ]]> https://biorxiv.org/content/10.1101/502526v1?rss=1 Maia, C. B. Rodrigues de Melo, P. A. F. Barreto, R. W. Maffia, L. A. Pinto, K. M. S. Rodrigues, A. A. C. de Souza Serra, I. M. R. Mesquita, M. L. R. Mondego, J. M. da Silva, A. P. G. 2018-12-20 doi:10.1101/502526 Cold Spring Harbor Laboratory Press 2018-12-20 <![CDATA[ Evolution of metabolic novelty: a trichome-expressed invertase creates specialized metabolic diversity in wild tomato ]]> https://biorxiv.org/content/10.1101/502971v1?rss=1 Leong, B. J. Lybrand, D. Lou, Y.-R. Fan, P. Schilmiller, A. L. Last, R. L. 2018-12-20 doi:10.1101/502971 Cold Spring Harbor Laboratory Press 2018-12-20 <![CDATA[ Deep evolutionary origin of limb and fin regeneration ]]> https://biorxiv.org/content/10.1101/503011v1?rss=1 Darnet, S. Cutrim Dragalzew, A. Baia Amaral, D. Thompson, A. W. Cass, A. N. Lorena, J. Sousa, J. F. Costa, C. M. Sousa, M. P. Froebisch, N. B. Schneider, P. N. Davis, M. C. Braasch, I. Schneider, I. 2018-12-21 doi:10.1101/503011 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ Visualizing murine placental extracellular vesicle data with tidyNano: a computational framework for analyzing and visualizing nanoparticle data in R ]]> https://biorxiv.org/content/10.1101/503292v1?rss=1 Nguyen, S. L. Greenberg, J. W. Wang, H. Collaer, B. W. Wang, J. Petroff, M. G. 2018-12-20 doi:10.1101/503292 Cold Spring Harbor Laboratory Press 2018-12-20 <![CDATA[ Genomic Prediction of Complex Disease Risk ]]> https://biorxiv.org/content/10.1101/506600v1?rss=1 Lello, L. Raben, T. Yong, S. Y. Tellier, L. C. Hsu, S. D. H. 2018-12-27 doi:10.1101/506600 Cold Spring Harbor Laboratory Press 2018-12-27 <![CDATA[ Hybridisation or Incomplete Lineage Sorting: The convoluted story about the origin of the capped-golden langur lineage (Cercopithecidae: Colobinae) ]]> https://biorxiv.org/content/10.1101/508929v1?rss=1 Arekar, K. Parigi, A. Karanth, K. P. 2018-12-31 doi:10.1101/508929 Cold Spring Harbor Laboratory Press 2018-12-31 <![CDATA[ Remodeling of Mycobacterium tuberculosis lipids regulates prpCD during acid growth arrest ]]> https://biorxiv.org/content/10.1101/509570v1?rss=1 Baker, J. J. Abramovitch, R. B. 2019-01-02 doi:10.1101/509570 Cold Spring Harbor Laboratory Press 2019-01-02 <![CDATA[ Birth-and-death evolution of the fatty acyl-CoA reductase (FAR) gene family and diversification of cuticular hydrocarbon synthesis in Drosophila ]]> https://biorxiv.org/content/10.1101/509588v1?rss=1 Finet, C. Slavik, K. Pu, J. Carroll, S. B. Chung, H. 2019-01-02 doi:10.1101/509588 Cold Spring Harbor Laboratory Press 2019-01-02 <![CDATA[ The Trouble Interpreting fMRI Studies in Populations with Cerebrovascular Risk: The Use of a Subject-Specific Hemodynamic Response Function in a Study of Age, Vascular Risk, and Memory ]]> https://biorxiv.org/content/10.1101/512343v1?rss=1 McDonough, I. M. Bender, A. Patihis, L. Stinson, E. A. Letang, S. K. Miller, W. S. 2019-01-04 doi:10.1101/512343 Cold Spring Harbor Laboratory Press 2019-01-04 <![CDATA[ High-quality, genome-wide SNP genotypic data for pedigreed germplasm of the diploid outbreeding species apple, peach, and sweet cherry through a common workflow ]]> https://biorxiv.org/content/10.1101/514281v1?rss=1 Vanderzande, S. Howard, N. P. Cai, L. Da Silva Linge, C. Antanaviciute, L. Bink, M. C. Kruisselbrink, J. W. Bassil, N. Gasic, K. Iezzoni, A. van de Weg, E. Peace, C. 2019-01-07 doi:10.1101/514281 Cold Spring Harbor Laboratory Press 2019-01-07 <![CDATA[ Feature Design for Protein Interface hotspots using KFC2 and Rosetta ]]> https://biorxiv.org/content/10.1101/514372v1?rss=1 Seeger, F. Little, A. Chen, Y. Woolf, T. Cheng, H. Mitchell, J. C. 2019-01-16 doi:10.1101/514372 Cold Spring Harbor Laboratory Press 2019-01-16 <![CDATA[ Alterations in ion channel expression surrounding implanted microelectrode arrays in the brain ]]> https://biorxiv.org/content/10.1101/518811v1?rss=1 Salatino, J. W. Kale, A. P. Purcell, E. K. 2019-01-11 doi:10.1101/518811 Cold Spring Harbor Laboratory Press 2019-01-11 <![CDATA[ The Regime Shift Detector: a model to identify changes in dynamic rules governing populations ]]> https://biorxiv.org/content/10.1101/522631v1?rss=1 0.8 and those due to sampling error (i.e., erroneous breaks) with weights averaging <0.2. In our case study examining an invasion process, the algorithm identified shifts in population cycling associated with variations in resource availability. The shifts identified for the conservation case study highlight a decline process that generally coincided with changing management practices affecting the availability of hostplant resources.nnWhen interpreted in the context of species biology, the Dynamic Shift Detector algorithm can aid management decisions and identify critical time periods related to species dynamics. In an era of rapid global change, such tools can provide key insights into the conditions under which population parameters, and their corresponding dynamics, can shift.nnAuthor SummaryPopulations naturally fluctuate in abundance, and the rules governing these fluctuations are a result of both internal (density dependent) and external (environmental) processes. For these reasons, pinpointing when changes in populations occur is difficult. In this study, we develop a novel break-point analysis tool for population time series data. Using a density dependent model to describe a populations underlying dynamic process, our tool iterates through all possible break point combinations (i.e., abrupt changes in parameter values) and applies information-theoretic decision tools (i.e. Akaikes Information Criterion corrected for small sample sizes) to determine best fits. Here, we develop the approach, simulate data under a variety of conditions to demonstrate its utility, and apply the tool to two case studies: an invasion of multicolored Asian ladybeetle and declining monarch butterflies. The Dynamic Shift Detector algorithm identified parameter changes that correspond to known environmental change events in both case studies. ]]> Bahlai, C. A. Zipkin, E. F. 2019-01-17 doi:10.1101/522631 Cold Spring Harbor Laboratory Press 2019-01-17 <![CDATA[ Oceanic salt spray and herbivore pressure contribute to local adaptation of coastal perennial and inland annual ecotypes of the Seep Monkeyflower (Mimulus guttatus) ]]> https://biorxiv.org/content/10.1101/523902v1?rss=1 Popovic, D. Lowry, D. B. 2019-01-17 doi:10.1101/523902 Cold Spring Harbor Laboratory Press 2019-01-17 <![CDATA[ Ultra-rare genetic variation in the epilepsies: a whole-exome sequencing study of 17,606 individuals ]]> https://biorxiv.org/content/10.1101/525683v1?rss=1 Epi25 Collaborative, Feng, Y.-C. A. Howrigan, D. P. Abbott, L. E. Tashman, K. Cerrato, F. Singh, T. Heyne, H. Byrnes, A. Churchhouse, C. Lal, D. Heinzen, E. L. Cavalleri, G. L. Hakonarson, H. Helbig, I. Krause, R. May, P. Weckhuysen, S. Petrovski, S. Kamalakaran, S. Sisodiya, S. M. Cossette, P. Cotsapas, C. De Jonghe, P. Dixon-Salazar, T. Guerrini, R. Kwan, P. Marson, A. G. Stewart, R. Depondt, C. Dlugos, D. J. Scheffer, I. E. Striano, P. Freyer, C. McKenna, K. Regan, B. M. Bellows, S. T. Leu, C. Bennett, C. A. Johns, E. M. C. Macdonald, A. Shilling, 2019-01-21 doi:10.1101/525683 Cold Spring Harbor Laboratory Press 2019-01-21 <![CDATA[ Plant growth regulators interact with elevated temperature to alter heat stress signaling via the Unfolded Protein Response ]]> https://biorxiv.org/content/10.1101/532796v1?rss=1 Neill, E. M. Byrd, M. C. R. Billman, T. Brandizzi, F. Stapleton, A. E. 2019-01-29 doi:10.1101/532796 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Translational landscape in tomato revealed by transcriptome assembly and ribosome profiling ]]> https://biorxiv.org/content/10.1101/534677v1?rss=1 Wu, H.-Y. L. Song, G. Walley, J. W. Hsu, P. Y. 2019-01-30 doi:10.1101/534677 Cold Spring Harbor Laboratory Press 2019-01-30 <![CDATA[ Polled Digital Cell Sorter (p-DCS): Automatic identification of hematological cell types from single cell RNA-sequencing clusters ]]> https://biorxiv.org/content/10.1101/539833v1?rss=1 Domanskyi, S. Szedlak, A. Hawkins, N. T. Wang, J. Paternostro, G. Piermarocchi, C. 2019-02-04 doi:10.1101/539833 Cold Spring Harbor Laboratory Press 2019-02-04 <![CDATA[ Graph-to-Signal Transformation Based Classification of Functional Connectivity Brain Networks ]]> https://biorxiv.org/content/10.1101/541532v1?rss=1 Munia, T. T. K. Aviyente, S. 2019-02-05 doi:10.1101/541532 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Identification of circadian rhythms in Nannochloropsis species using bioluminescence reporter lines ]]> https://biorxiv.org/content/10.1101/550954v1?rss=1 Poliner, E. Cummings, C. Newton, L. Farre, E. M. 2019-02-14 doi:10.1101/550954 Cold Spring Harbor Laboratory Press 2019-02-14 <![CDATA[ A global synthesis reveals biodiversity-mediated benefits for crop production ]]> https://biorxiv.org/content/10.1101/554170v1?rss=1 Dainese, M. Martin, E. A. Aizen, M. Albrecht, M. Bartomeus, I. Bommarco, R. Carvalheiro, L. G. Chaplin-Kramer, R. Gagic, V. Garibaldi, L. A. Ghazoul, J. Grab, H. Jonsson, M. Karp, D. S. Kennedy, C. M. Kleijn, D. Kremen, C. Landis, D. A. Letourneau, D. K. Marini, L. Poveda, K. Rader, R. Smith, H. G. Tscharntke, T. Andersson, G. K. S. Badenhausser, I. Baensch, S. Bezerra, A. D. M. Bianchi, F. J. J. A. Boreux, V. Bretagnolle, V. Caballero-Lopez, B. Cavigliasso, P. Cetkovic, A. Chacoff, N. P. Classen, A. Cusser, S. Silva e Silva, F. D. d. de Groot, G. A. Dude 2019-02-20 doi:10.1101/554170 Cold Spring Harbor Laboratory Press 2019-02-20 <![CDATA[ Characterizing grapevine (Vitis spp.) inflorescence architecture using X-ray imaging: implications for understanding cluster density ]]> https://biorxiv.org/content/10.1101/557819v1?rss=1 Li, M. Klein, L. L. Duncan, K. E. Jiang, N. Londo, J. P. Miller, A. Topp, C. 2019-02-22 doi:10.1101/557819 Cold Spring Harbor Laboratory Press 2019-02-22 <![CDATA[ ANP32A and ANP32B are key factors in the Rev dependent CRM1 pathway for nuclear export of HIV-1 unspliced mRNA ]]> https://biorxiv.org/content/10.1101/559096v1?rss=1 Wang, Y. Zhang, H. Na, L. Du, C. Zhang, Z. Zheng, Y. Wang, X. 2019-02-24 doi:10.1101/559096 Cold Spring Harbor Laboratory Press 2019-02-24 <![CDATA[ An oomycete RXLR effector triggers antagonistic plant hormone crosstalk to suppress host immunity ]]> https://biorxiv.org/content/10.1101/561605v1?rss=1 Anderson, R. Deb, D. Withers, J. He, S. Y. McDowell, J. 2019-02-26 doi:10.1101/561605 Cold Spring Harbor Laboratory Press 2019-02-26 <![CDATA[ Challenges and opportunities in population monitoring of cheetahs ]]> https://biorxiv.org/content/10.1101/563122v1?rss=1 20 spatially distinct encounters). We estimated an average cheetah density of ~1.2 cheetahs/100 km2, consistent with the impression that the MMNR provides important habitat for cheetahs in Africa. During most years and seasonal periods, the spatial distribution of vegetation greenness (a proxy for ungulate habitat quality) accounted for important variation in encounter rates. The search-encounter design used here could be applied to other regions for the purposes of cheetah monitoring. While snap-shot estimates of population size across time are useful for wildlife monitoring, open population models could identify the mechanisms behind changes and further facilitate better conservation and management decision making. ]]> Linden, D. W. Green, D. S. Chelysheva, E. V. Mandela, S. Dloniak, S. M. 2019-02-28 doi:10.1101/563122 Cold Spring Harbor Laboratory Press 2019-02-28 <![CDATA[ Parasite histones mediate leak and coagulopathy in cerebral malaria ]]> https://biorxiv.org/content/10.1101/563551v1?rss=1 Moxon, C. A. Alhamdi, Y. Storm, J. Toh, J. Ko, J. Y. Murphy, G. Taylor, T. Seydel, K. Kampondeni, S. Potchen, M. O'Donnell, J. O'Regan, N. Wang, G. Garcia-Cardena, G. Molyneux, M. Craig, A. Abrams, S. Toh, C.-H. 2019-02-28 doi:10.1101/563551 Cold Spring Harbor Laboratory Press 2019-02-28 <![CDATA[ Identification of new MmpL3 inhibitors by untargeted and targeted mutant screens defines MmpL3 domains with differential resistance ]]> https://biorxiv.org/content/10.1101/564245v1?rss=1 Williams, J. T. Haiderer, E. R. Coulson, G. B. Conner, K. N. Ellsworth, E. Chen, C. Dick, T. Abramovitch, R. B. 2019-02-28 doi:10.1101/564245 Cold Spring Harbor Laboratory Press 2019-02-28 <![CDATA[ Differential in vivo biodistribution of 131I-labeled exosomes from diverse cellular origins and its implication in the theranostic application. ]]> https://biorxiv.org/content/10.1101/566323v1?rss=1 Rashid, M. H. Borin, T. F. Ara, R. Angara, K. Cai, J. Achyut, B. Liu, Y. Arbab, A. S. 2019-03-03 doi:10.1101/566323 Cold Spring Harbor Laboratory Press 2019-03-03 <![CDATA[ Dispersal limitation and stage-specific local filtering processes vary with climate across a network of alpine grasslands ]]> https://biorxiv.org/content/10.1101/567586v1?rss=1 Guittar, J. Goldberg, D. Klanderud, K. Berge, A. Boixaderas, M. R. Meineri, E. Topper, J. Vandvik, V. 2019-03-05 doi:10.1101/567586 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ Cell-length heterogeneity: a population-level solution to growth/virulence trade-offs in the plant pathogen Dickeya dadantii ]]> https://biorxiv.org/content/10.1101/577296v1?rss=1 10m). Short cells tended to occur at the interface of healthy and diseased tissues, during the early stage of infection when active attacking and killing is occurring, while filamentous cells tended to form when large amount of nutrients were released at a later stage of infection. Short cells expressed all necessary virulence factors and motility, whereas filamentous cells did not engage in virulence, were non-mobile and more sensitive to environmental stress. However, compared to the short cells, the filamentous cells displayed elevated metabolism and faster growth, which may benefit the pathogens to build up a large population necessary for the secondary infection. The segregation of the two subpopulations was dependent on differential expression of the alarmone guanosine tetraphosphate (ppGpp). When exposed to fresh tuber tissues or freestanding water, filamentous cells quickly transformed to short virulent cells. The pathogen adaptation of cell length heterogeneity identified in this study presents a model for how some necrotrophs balance virulence and vegetative growth to maximize fitness during infection. ]]> Cui, Z. Yang, C.-H. Kharadi, R. R. Yuan, X. Sundin, G. W. Triplett, L. R. Wang, J. Zeng, Q. 2019-03-13 doi:10.1101/577296 Cold Spring Harbor Laboratory Press 2019-03-13 <![CDATA[ SMAUG: Analyzing single-molecule tracks with nonparametric Bayesian statistics ]]> https://biorxiv.org/content/10.1101/578567v1?rss=1 Karslake, J. Donarski, E. D. Shelby, S. A. Demey, L. M. DiRita, V. J. Veatch, S. L. Biteen, J. S. 2019-03-14 doi:10.1101/578567 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ Exceptional subgenome stability and functional divergence in allotetraploid teff, the primary cereal crop in Ethiopia ]]> https://biorxiv.org/content/10.1101/580720v1?rss=1 VanBuren, R. Wai, C. M. Pardo, J. Yocca, A. E. Wang, X. Wang, H. Chaluvadi, S. R. Bryant, D. Edger, P. P. Bennetzen, J. L. Mockler, T. C. Michael, T. P. 2019-03-18 doi:10.1101/580720 Cold Spring Harbor Laboratory Press 2019-03-18 <![CDATA[ Tracking trends in monarch abundances over the 20th century is currently impossible using museum records: a response to Boyle et al. (2019) ]]> https://biorxiv.org/content/10.1101/581801v1?rss=1 Ries, L. Zipkin, E. F. Guralnick, R. P. 2019-03-20 doi:10.1101/581801 Cold Spring Harbor Laboratory Press 2019-03-20 <![CDATA[ Leaf shape is a predictor of fruit quality and cultivar performance in tomato ]]> https://biorxiv.org/content/10.1101/584466v1?rss=1 Rowland, S. D. Zumstein, K. Nakayama, H. Cheng, Z. Flores, A. M. Chitwood, D. H. Maloof, J. N. Sinha, N. R. 2019-03-21 doi:10.1101/584466 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Transcriptome-based prediction of complex traits in maize ]]> https://biorxiv.org/content/10.1101/587121v1?rss=1 Azodi, C. Pardo, J. VanBuren, R. de los Campos, G. Shiu, S.-H. 2019-03-24 doi:10.1101/587121 Cold Spring Harbor Laboratory Press 2019-03-24 <![CDATA[ Impact of initial protein stability on local fitness landscapes ]]> https://biorxiv.org/content/10.1101/590398v1?rss=1 Faber, M. S. Wrenbeck, E. E. Azouz, L. R. Steiner, P. J. Whitehead, T. A. 2019-03-26 doi:10.1101/590398 Cold Spring Harbor Laboratory Press 2019-03-26 <![CDATA[ FGF/MAPK signaling pathway regulates the genome-wide occupancy of Polycomb Repressive Complex 2 in murine embryonic stem cells ]]> https://biorxiv.org/content/10.1101/597674v1?rss=1 Aljazi, M. B. Gao, Y. Wu, Y. Mias, G. I. He, J. 2019-04-03 doi:10.1101/597674 Cold Spring Harbor Laboratory Press 2019-04-03 <![CDATA[ Ultra-local adaptation due to genetic accommodation ]]> https://biorxiv.org/content/10.1101/598292v1?rss=1 Sun, S.-J. Catherall, A. Pascoal, S. Jarrett, B. Miller, S. Sheehan, M. Kilner, R. 2019-04-05 doi:10.1101/598292 Cold Spring Harbor Laboratory Press 2019-04-05 <![CDATA[ Putative cis-regulatory elements predict iron deficiency responses in Arabidopsis roots ]]> https://biorxiv.org/content/10.1101/603290v1?rss=1 100 putative cis-regulatory elements robustly predict Arabidopsis root Fe deficiency-responses in computational models, and shed light on the mechanisms of transcriptional regulation. ]]> Schwarz, B. Azodi, C. B. Shiu, S.-H. Bauer, P. 2019-04-09 doi:10.1101/603290 Cold Spring Harbor Laboratory Press 2019-04-09 <![CDATA[ Environmental drivers define contrasting microbial habitats, diversity and functional redundancy in Lake Baikal, Siberia ]]> https://biorxiv.org/content/10.1101/605899v1?rss=1 Wilburn, P. Shchapov, K. Theriot, E. C. Litchman, E. 2019-04-11 doi:10.1101/605899 Cold Spring Harbor Laboratory Press 2019-04-11 <![CDATA[ Genome annotation of Poly(lactic acid) degrading Pseudomonas aeruginosa and Sphingobacterium sp. ]]> https://biorxiv.org/content/10.1101/609883v1?rss=1 Satti, S. M. Shah, A. A. Auras, R. Marsh, T. 2019-04-23 doi:10.1101/609883 Cold Spring Harbor Laboratory Press 2019-04-23 <![CDATA[ Butterfly abundance declines over 20 years of systematic monitoring in Ohio, USA ]]> https://biorxiv.org/content/10.1101/613786v1?rss=1 Wepprich, T. Adrion, J. Ries, L. Wiedmann, J. Haddad, N. 2019-04-18 doi:10.1101/613786 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Novel engraftment and T cell differentiation of human hematopoietic cells in Art-/- IL2RG-/ SCID pigs ]]> https://biorxiv.org/content/10.1101/614404v1?rss=1 Boettcher, A. Li, Y. Ahrens, A. Kiupel, M. Byrne, K. Loving, C. Cino-Ozuna, A. G. Wiarda, J. Adur, M. Schultz, B. Swanson, J. Snella, E. Ho, C.-S. Charley, S. Kiefer, Z. Cunnick, J. Powell, E. Dell'Anna, G. Jens, J. Sathe, S. Goldman, F. Westin, E. Dekkers, J. Ross, J. Tuggle, C. 2019-05-02 doi:10.1101/614404 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Benchmarking algorithms for genomic prediction of complex traits ]]> https://biorxiv.org/content/10.1101/614479v1?rss=1 Azodi, C. McCarren, A. Roantree, M. de los Campos, G. Shiu, S.-H. 2019-04-20 doi:10.1101/614479 Cold Spring Harbor Laboratory Press 2019-04-20 <![CDATA[ The Vc2 cyclic di-GMP dependent riboswitch of Vibrio cholerae regulates expression of an upstream small RNA by controlling RNA stability ]]> https://biorxiv.org/content/10.1101/617340v1?rss=1 Pursley, B. R. Waters, C. M. 2019-04-24 doi:10.1101/617340 Cold Spring Harbor Laboratory Press 2019-04-24 <![CDATA[ Geographic variation in the genetic basis of resistance to leaf rust in locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum) ]]> https://biorxiv.org/content/10.1101/619148v1?rss=1 VanWallendael, A. Bonnette, J. Juenger, T. E. Fritschi, F. B. Fay, P. A. Mitchell, R. B. Lloyd-Reilley, J. Rouquette, F. Bergstrom, G. C. Lowry, D. B. 2019-04-26 doi:10.1101/619148 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ When does gene flow facilitate evolutionary rescue? ]]> https://biorxiv.org/content/10.1101/622142v1?rss=1 Tomasini, M. Peischl, S. 2019-04-29 doi:10.1101/622142 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ Deceptive combined effects of short allele dominance and stuttering: an example with Ixodes scapularis, the main vector of Lyme disease in the U.S.A. ]]> https://biorxiv.org/content/10.1101/622373v1?rss=1 De Meeus, T. Chan, C. T. Ludwig, J. M. Tsao, J. I. Patel, J. Bhagatwala, J. Beati, M. 2019-05-02 doi:10.1101/622373 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Multiple QTL mapping in autopolyploids: a random-effect model approach with application in a hexaploid sweetpotato full-sib population ]]> https://biorxiv.org/content/10.1101/622951v1?rss=1 da Silva Pereira, G. Gemenet, D. C. Mollinari, M. Olukolu, B. A. Wood, J. C. Diaz, F. Mosquera, V. Gruneberg, W. J. Khan, A. Buell, C. R. Yencho, G. C. Zeng, Z.-B. 2019-04-29 doi:10.1101/622951 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ Genetic image-processing using regularized selection indices ]]> https://biorxiv.org/content/10.1101/625251v1?rss=1 Lopez-Cruz, M. A. Olson, E. Rovere, G. Crossa, J. Dreisigacker, S. Mondal, S. Singh, R. de los Campos, G. 2019-05-02 doi:10.1101/625251 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ The transcriptional correlates of divergent electric organ discharges in Paramormyrops electric fish ]]> https://biorxiv.org/content/10.1101/625475v1?rss=1 Losilla, M. Gallant, J. R. 2019-05-02 doi:10.1101/625475 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Relapse prevention through health technology program reduces hospitalization in schizophrenia ]]> https://biorxiv.org/content/10.1101/626663v1?rss=1 Homan, P. Schooler, N. R. Brunette, M. F. Rotondi, A. Ben-Zeev, D. Gottlieb, J. D. Mueser, K. T. Achtyes, E. D. Gingerich, S. Marcy, P. Meyer-Kalos, P. Hauser, M. John, M. Robinson, D. G. Kane, J. M. 2019-05-03 doi:10.1101/626663 Cold Spring Harbor Laboratory Press 2019-05-03 <![CDATA[ Reconciling Base-Pair Resolution 5-methylcytosine and 5-hydroxymethylcytosine Data in Neuroepigenetics ]]> https://biorxiv.org/content/10.1101/630772v1?rss=1 Kochmanski, J. Savonen, C. Bernstein, A. I. 2019-05-07 doi:10.1101/630772 Cold Spring Harbor Laboratory Press 2019-05-07 <![CDATA[ Strategies for building computing skills to support microbiome analysis: a five-year perspective from the EDAMAME workshop ]]> https://biorxiv.org/content/10.1101/631267v1?rss=1 Shade, A. Dunivin, T. K. Choi, J. Teal, T. Howe, A. C. 2019-05-09 doi:10.1101/631267 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Cyclic di-GMP Increases Catalase Production and Hydrogen Peroxide Tolerance in Vibrio cholerae ]]> https://biorxiv.org/content/10.1101/631275v1?rss=1 Fernandez, N. Waters, C. M. 2019-05-08 doi:10.1101/631275 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ Separation of hemodynamic signals from GCaMP fluorescence measured with widefield imaging ]]> https://biorxiv.org/content/10.1101/634923v1?rss=1 Valley, M. T. Moore, M. Zhuang, J. Mesa, N. Castelli, D. Sullivan, D. Reimers, M. Waters, J. 2019-05-10 doi:10.1101/634923 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Genetic and physiological mechanisms of freezing tolerance in locally adapted populations of a winter annual ]]> https://biorxiv.org/content/10.1101/640763v1?rss=1 Sanderson, B. J. Park, S. Jameel, M. I. Kraft, J. C. Thomashow, M. F. Schemske, D. W. Oakley, C. G. 2019-05-17 doi:10.1101/640763 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Rock the Chalk: A five-year comparative analysis of a large microbiology lecture course reveals improved outcomes of chalk-talk compared to PowerPoint ]]> https://biorxiv.org/content/10.1101/644567v1?rss=1 Waters, C. M. 2019-05-27 doi:10.1101/644567 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ Disease Resistance Genetics and Genomics in Octoploid Strawberry ]]> https://biorxiv.org/content/10.1101/646000v1?rss=1 barbey, C. Lee, S. Verma, S. Bird, K. A. Yocca, A. E. Edger, P. P. Knapp, S. J. Whitaker, V. M. Folta, K. M. 2019-05-23 doi:10.1101/646000 Cold Spring Harbor Laboratory Press 2019-05-23 <![CDATA[ Deconstructing higher-order interactions in the microbiota: A theoretical examination ]]> https://biorxiv.org/content/10.1101/647156v1?rss=1 Yitbarek, S. Guittar, J. L. Knutie, S. A. Ogbunugafor, C. B. 2019-05-24 doi:10.1101/647156 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Lanthanide transport, storage, and beyond: genes and processes contributing to XoxF function in Methylorubrum extorquens AM1 ]]> https://biorxiv.org/content/10.1101/647677v1?rss=1 Roszczenko-Jasinska, P. Vu, H. N. Subuyuj, G. A. Crisostomo, R. V. Cai, J. Raghuraman, C. Ayala, E. M. Clippard, E. J. Lien, N. F. Ngo, R. T. Yarza, F. Hoeber, C. A. Martinez-Gomez, N. C. Skovran, E. 2019-05-24 doi:10.1101/647677 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Locally-adapted Mimulus ecotypes differentially impact rhizosphere bacterial and archaeal communities in an environment-dependent manner ]]> https://biorxiv.org/content/10.1101/652883v1?rss=1 Bowsher, A. W. Kearns, P. J. Popovic, D. Lowry, D. B. Shade, A. 2019-05-30 doi:10.1101/652883 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ Deciphering sex-specific genetic architectures using local Bayesian regressions ]]> https://biorxiv.org/content/10.1101/653386v1?rss=1 Funkhouser, S. A. Vazquez, A. I. Steibel, J. P. Ernst, C. W. de los Campos, G. 2019-05-31 doi:10.1101/653386 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ NADH dehydrogenases contribute to extracellular electron transfer by Shewanella oneidensis MR-1 in bioelectrochemical systems ]]> https://biorxiv.org/content/10.1101/657668v1?rss=1 nView larger version (20K):norg.highwire.dtl.DTLVardef@163db4org.highwire.dtl.DTLVardef@2cf477org.highwire.dtl.DTLVardef@165cb63org.highwire.dtl.DTLVardef@c0bc5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Madsen, C. S. TerAvest, M. A. 2019-06-03 doi:10.1101/657668 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Benchmarking Transposable Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline ]]> https://biorxiv.org/content/10.1101/657890v1?rss=1 Ou, S. Su, W. Liao, Y. Chougule, K. Ware, D. Peterson, T. Jiang, N. Hirsch, C. N. Hufford, M. B. 2019-06-03 doi:10.1101/657890 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ A gall-forming insect manipulates hostplant phytohormone synthesis, concentrations, and signaling ]]> https://biorxiv.org/content/10.1101/658823v1?rss=1 Body, M. J. Appel, H. M. Edger, P. P. Schultz, J. C. 2019-06-03 doi:10.1101/658823 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Transcriptional profiling of the murine airway response to acute ozone exposure ]]> https://biorxiv.org/content/10.1101/660316v1?rss=1 Tovar, A. Smith, G. J. Thomas, J. M. Harkema, J. R. Kelada, S. N. P. 2019-06-05 doi:10.1101/660316 Cold Spring Harbor Laboratory Press 2019-06-05 <![CDATA[ Hippocampal subfields and limbic white matter jointly predict learning rate in older adults ]]> https://biorxiv.org/content/10.1101/661702v1?rss=1 Bender, A. R. Brandmaier, A. M. Düzel, S. Keresztes, A. Pasternak, O. Lindenberger, U. Kühn, S. 2019-06-06 doi:10.1101/661702 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ Mice with GNAO1 R209H Movement Disorder Variant Display Hyperlocomotion Alleviated by Risperidone ]]> https://biorxiv.org/content/10.1101/662031v1?rss=1 A or p.Arg209His (R209H) mutation. We developed heterozygous knock-in Gnao1+/R209H mutant mice using CRISPR/Cas9 methodology to assess whether a mouse model could replicate aspects of the NEDIM clinical pattern. Mice carrying the R209H mutation exhibited increased locomotor activity and a modest gait abnormality at 8-12 weeks. In contrast to mice carrying other mutations in Gnao1, the Gnao1+/R209H mice did not show enhanced seizure susceptibility. Levels of protein expression in multiple brain regions were unchanged from WT mice but the nucleotide exchange rate of mutant R209H Go was 9 times faster than WT. The atypical neuroleptic risperidone has shown efficacy in a patient with the R209H mutation. It also alleviated the hyperlocomotion phenotype observed in our mouse model but suppressed locomotion in WT mice as well. In this study, we show that Gnao1+/R209H mice mirror elements of the patient phenotype and respond to an approved pharmacological agent. ]]> Larrivee, C. L. Feng, H. Leipprandt, J. R. Demireva, E. Y. Xie, H. Neubig, R. R. 2019-06-06 doi:10.1101/662031 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ Intertwined signatures of desiccation and drought tolerance in grasses ]]> https://biorxiv.org/content/10.1101/662379v1?rss=1 Pardo, J. Wai, C. M. Chay, H. Madden, C. F. Hilhorst, H. W. M. Farrant, J. M. VanBuren, R. 2019-06-06 doi:10.1101/662379 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ TEAD4/YAP1/WWTR1 prevent the premature onset of pluripotency prior to the 16-cell stage ]]> https://biorxiv.org/content/10.1101/663005v1?rss=1 Ralston, A. Frum, T. Watts, J. L. 2019-06-06 doi:10.1101/663005 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ Influence of genetic interactions on polygenic prediction ]]> https://biorxiv.org/content/10.1101/667162v1?rss=1 Dai, Z. Long, N. Huang, W. 2019-06-13 doi:10.1101/667162 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ Comparative genomic analyses reveal diverse virulence factors and antimicrobial resistance mechanisms in clinical Elizabethkingia meningoseptica strains ]]> https://biorxiv.org/content/10.1101/668061v1?rss=1 Chen, S. Soehnlen, M. Blom, J. Terrapon, N. Henrissat, B. Walker, E. 2019-06-13 doi:10.1101/668061 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ Highly Genotype- and Tissue-specific Single-Parent Expression Drives Dynamic Gene Expression Complementation in Maize Hybrids ]]> https://biorxiv.org/content/10.1101/668681v1?rss=1 Li, Z. Zhou, P. Della Coletta, R. Zhang, T. Brohammer, A. Vaillancourt, B. Lipzen, A. Daum, C. Barry, K. de Leon, N. Hirsch, C. Buell, C. R. Kaeppler, S. Springer, N. Hirsch, C. 2019-06-12 doi:10.1101/668681 Cold Spring Harbor Laboratory Press 2019-06-12 <![CDATA[ E2F1 Drives Breast Cancer Metastasis by Regulating the Target Gene FGF13 and Altering Cell Migration ]]> https://biorxiv.org/content/10.1101/671149v1?rss=1 Hollern, D. P. Swiatnicki, M. R. Rennhack, J. P. Misek, S. A. Matson, B. C. McAuliff, A. Gallo, K. A. Caron, K. M. Andrechek, E. R. 2019-06-13 doi:10.1101/671149 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ Meta-analysis of Gene Expression Microarray Datasets in Chronic Obstructive Pulmonary Disease ]]> https://biorxiv.org/content/10.1101/671206v1?rss=1 Rogers, L. R. K. Verlinde, M. Mias, G. I. 2019-06-14 doi:10.1101/671206 Cold Spring Harbor Laboratory Press 2019-06-14 <![CDATA[ Elizabethkingia anophelis response to iron stress: physiologic, genomic, and transcriptomic analyses ]]> https://biorxiv.org/content/10.1101/679894v1?rss=1 Chen, S. Johnson, B. K. Yu, T. Nelson, B. Walker, E. 2019-06-22 doi:10.1101/679894 Cold Spring Harbor Laboratory Press 2019-06-22 <![CDATA[ Computational analysis of transcriptome signature repurposes low dose trifluoperazine for the treatment of fragile X syndrome in mouse model ]]> https://biorxiv.org/content/10.1101/683169v1?rss=1 Ding, Q. Sethna, F. Wu, X.-T. Miao, Z. Chen, P. Zhang, Y. Xiao, H. Feng, W. Feng, Y. Li, X. Wang, H. 2019-06-27 doi:10.1101/683169 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Exogenous Protein as an Environmental Stimuli of Biofilm Formation in Select Bacterial Strains ]]> https://biorxiv.org/content/10.1101/683979v1?rss=1 Ye, D. Bapu, L. Cavalcante, M. M. Kato, J. Lauria Sneideman, M. Scribner, K. Loch, T. Marsh, T. L. 2019-06-27 doi:10.1101/683979 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ The Norepinephrine Metabolite DOPEGAL Confers Locus Coeruleus Tau Vulnerability and Propagation via Asparagine Endopeptidase ]]> https://biorxiv.org/content/10.1101/688200v1?rss=1 Kang, S. S. Liu, X. Ahn, E. H. Xiang, J. Manfredsson, F. P. Yang, X. Luo, H. R. Liles, L. C. Weinshenker, D. Ye, K. 2019-07-02 doi:10.1101/688200 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Biased neural coding of feature-based attention in human brain ]]> https://biorxiv.org/content/10.1101/688226v1?rss=1 Gong, M. Liu, T. 2019-07-02 doi:10.1101/688226 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Horse gluteus is a null-sarcolipin muscle with enhanced sarcoplasmic reticulum calcium transport ]]> https://biorxiv.org/content/10.1101/688531v1?rss=1 Autry, J. M. Svensson, B. Carlson, S. F. Chen, Z. Espinoza-Fonseca, L. M. Thomas, D. D. 2019-07-13 doi:10.1101/688531 Cold Spring Harbor Laboratory Press 2019-07-13 <![CDATA[ High density of white-faced capuchins (Cebus capucinus) and habitat quality in the Taboga Forest of Costa Rica ]]> https://biorxiv.org/content/10.1101/692293v1?rss=1 Tinsley Johnson, E. Benitez, M. Fuentes, A. McLean, C. R. Norford, A. B. Ordonez, J. C. Beehner, J. C. Bergman, T. J. 2019-07-04 doi:10.1101/692293 Cold Spring Harbor Laboratory Press 2019-07-04 <![CDATA[ Variation and inheritance of small RNAs in maize inbreds and F1 hybrids ]]> https://biorxiv.org/content/10.1101/692400v1?rss=1 Crisp, P. A. Hammond, R. Zhou, P. Vaillancourt, B. Lipzen, A. Daum, C. Barry, K. de Leon, N. Buell, C. R. Kaeppler, S. M. Meyers, B. C. Hirsch, C. N. Springer, N. M. 2019-07-04 doi:10.1101/692400 Cold Spring Harbor Laboratory Press 2019-07-04 <![CDATA[ Responses of Neurons in the Rostral Ventrolateral Medulla (RVLM) of Conscious Felines to Anticipated and Passive Movements ]]> https://biorxiv.org/content/10.1101/693408v1?rss=1 Miller, D. M. Joshi, A. S. Kambouroglos, E. T. Engstrom, I. C. Bielanin, J. P. Wittman, S. R. McCall, A. A. Barman, S. M. Yates, B. J. 2019-07-05 doi:10.1101/693408 Cold Spring Harbor Laboratory Press 2019-07-05 <![CDATA[ Visualizing the periodic Ribo-seq reads with RiboPlotR ]]> https://biorxiv.org/content/10.1101/694646v1?rss=1 Wu, H.-Y. L. Hsu, P. Y. 2019-07-08 doi:10.1101/694646 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ Historical contingency in the evolution of antibiotic resistance after decades of relaxed selection ]]> https://biorxiv.org/content/10.1101/695767v1?rss=1 Card, K. J. LaBar, T. Gomez, J. B. Lenski, R. E. 2019-07-10 doi:10.1101/695767 Cold Spring Harbor Laboratory Press 2019-07-10 <![CDATA[ Non-rainfall moisture: a key driver of carbon flux from standing litter in arid, semiarid, and mesic grasslands ]]> https://biorxiv.org/content/10.1101/696666v1?rss=1 5% for fine litter and >13% for coarse), and contributed to mass loss, even in the Namib West site that had almost no rain. When we modeled annual mass loss induced by NRM and rain, and extrapolated our characterization of NRM decomposition to a final site with intermediate rainfall (Sevilleta, New Mexico, semiarid grassland), we found that models driven by rainfall alone underestimated mass loss, while including NRM produced estimates within the range of observed mass loss. Together these findings suggest that NRM is an important missing component in quantitative and conceptual models of litter decomposition, but there is nuance involved in modeling NRM at larger scales. Specifically, temperature and physical features of the substrate emerge as factors that affect the common microbial response to litter wetting under NRM across grasslands sites, and require further study. Hourly humidity can provide an adequate proxy of NRM frequency, but site-specific calibration with litter wetness is needed to accurately attribute decomposition to periods when NRM wets litter. Greater recognition of NRM-driven decomposition and its interaction with other processes (e.g. photodegradation) is needed, especially since fog, dew, and humidity are likely to shift under future climates.nnManuscript highlightsO_LINon-rainfall moisture (NRM; humidity, fog, dew) induces decomposition in grasslandsnC_LIO_LINRM decomposition depends on substrate type, and occurs at colder times than rainnC_LIO_LIIncluding NRM (instead of rain alone) improved predictions of litter decompositionnC_LI ]]> Evans, S. E. Todd-Brown, K. Jacobson, K. Jacobson, P. 2019-07-16 doi:10.1101/696666 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ The Tuberous Sclerosis gene, Tsc1, represses parvalbumin+/fast-spiking properties in somatostatin-lineage cortical interneurons ]]> https://biorxiv.org/content/10.1101/699892v1?rss=1 Malik, R. Pai, E. L.-L. Rubin, A. N. Stafford, A. M. Angara, K. Minasi, P. Rubenstein, J. L. Sohal, V. S. Vogt, D. 2019-07-11 doi:10.1101/699892 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ High levels of endemism and local differentiation in the fungal and algal symbionts of saxicolous lecideoid lichens along a latitudinal gradient in southern South America ]]> https://biorxiv.org/content/10.1101/699942v1?rss=1 Ruprecht, U. Fernandez Mendoza, F. Tuerk, R. Fryday, A. 2019-07-22 doi:10.1101/699942 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ Mechanism of processive telomerase catalysis revealed by high-resolution optical tweezers ]]> https://biorxiv.org/content/10.1101/700294v1?rss=1 Patrick, E. M. Slivka, J. Payne, B. Comstock, M. J. Schmidt, J. C. 2019-07-12 doi:10.1101/700294 Cold Spring Harbor Laboratory Press 2019-07-12 <![CDATA[ Genetic rescue without genomic swamping in wild populations ]]> https://biorxiv.org/content/10.1101/701706v1?rss=1 Fitzpatrick, S. W. Bradburd, G. Kremer, C. Salerno, P. Angeloni, L. Funk, W. C. 2019-07-15 doi:10.1101/701706 Cold Spring Harbor Laboratory Press 2019-07-15 <![CDATA[ Microarray Gene Expression DatasetRe-Analysis Reveals Variability in InfluenzaInfection and Vaccination. ]]> https://biorxiv.org/content/10.1101/702068v1?rss=1 Rogers, L. R. de los Campos, G. Mias, G. 2019-07-15 doi:10.1101/702068 Cold Spring Harbor Laboratory Press 2019-07-15 <![CDATA[ A binning tool to reconstruct viral haplotypes from assembled contigs ]]> https://biorxiv.org/content/10.1101/704288v1?rss=1 Chen, J. Shang, J. Wang, J. Sun, Y. 2019-07-16 doi:10.1101/704288 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ Rapid leaf trait response to growing-season meteorology in Vitis: Implications for leaf physiognomic paleoclimate reconstructions ]]> https://biorxiv.org/content/10.1101/706770v1?rss=1 Baumgartner, A. Donahoo, M. Chitwood, D. H. Peppe, D. J. 2019-07-25 doi:10.1101/706770 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ How well do crop models predict phenology, with emphasis on the effect of calibration? ]]> https://biorxiv.org/content/10.1101/708578v1?rss=1 Wallach, D. Palosuo, T. Thorburn, P. Seidel, S. J. Gourdain, E. Asseng, S. Basso, B. Buis, S. Crout, N. Dibari, C. Dumont, B. Ferrise, R. Gaiser, T. Garcia, C. Gayler, S. Ghahramani, A. Hochman, Z. Hoek, S. Horan, H. Hoogenboom, G. Huang, M. Jabloun, M. Jing, Q. Justes, E. Kersebaum, K. C. Klosterhalfen, A. Launay, M. Luo, Q. Maestrini, B. Mielenz, H. Moriondo, M. Nariman Zadeh, H. Olesen, J. E. Poyda, A. Priesack, E. Pullens, J. W. M. Budong, Q. Schuetze, N. Shelia, V. Souissi, A. Specka, X. Srivastava, A. K. Stella, T. Streck, T. Trombi, G. Wallor 2019-07-19 doi:10.1101/708578 Cold Spring Harbor Laboratory Press 2019-07-19 <![CDATA[ PyIOmica: Longitudinal Omics Analysis and Classification ]]> https://biorxiv.org/content/10.1101/708941v1?rss=1 Domanskyi, S. Piermarocchi, C. Mias, G. I. 2019-07-19 doi:10.1101/708941 Cold Spring Harbor Laboratory Press 2019-07-19 <![CDATA[ Drug target discovery via network modeling: a mathematical model of the E. coli folate network response to trimethoprim ]]> https://biorxiv.org/content/10.1101/712257v1?rss=1 Jalli, I. S. Lunt, S. Xu, W. Lopez, C. Contreras, A. Wilmot, C.-S. Nijhout, F. 2019-07-23 doi:10.1101/712257 Cold Spring Harbor Laboratory Press 2019-07-23 <![CDATA[ Dietary vs non-dietary fatty acid profiles of lake trout morphs from Lake Superior and Great Bear Lake: Are fish really what they eat? ]]> https://biorxiv.org/content/10.1101/714352v1?rss=1 Chavarie, L. Hoffmann, J. Muir, A. Krueger, C. Bronte, C. Howland, K. Gallagher, C. Sitar, S. Hansen, M. Vinson, M. Loseto, L. Tonn, W. Swanson, H. 2019-07-25 doi:10.1101/714352 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ Withdraw of prophylactic antimicrobials does not change the pigs’ resistome ]]> https://biorxiv.org/content/10.1101/716597v1?rss=1 Trueba, G. Torres, A. Loayza, F. Zhang, L. 2019-07-26 doi:10.1101/716597 Cold Spring Harbor Laboratory Press 2019-07-26 <![CDATA[ Supervised-learning is an accurate method for network-based gene classification ]]> https://biorxiv.org/content/10.1101/721423v1?rss=1 Liu, R. Mancuso, C. A. Yannakopoulos, A. Johnson, K. A. Krishnan, A. 2019-08-05 doi:10.1101/721423 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ A carbonic anhydrase pseudogene sensitizes select Brucella lineages to low CO2 partial pressure ]]> https://biorxiv.org/content/10.1101/721597v1?rss=1 Varesio, L. M. Willet, J. W. Fiebig, A. Crosson, S. 2019-08-01 doi:10.1101/721597 Cold Spring Harbor Laboratory Press 2019-08-01 <![CDATA[ LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons ]]> https://biorxiv.org/content/10.1101/722736v1?rss=1 Ou, S. Jiang, N. 2019-08-05 doi:10.1101/722736 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ Computational mapping of the differentially expressed gene-lncRNA pairs present at the root nodule developmental stages of Arachis hypogaea ]]> https://biorxiv.org/content/10.1101/724674v1?rss=1 Rizvi, A. Z. Dhusia, K. 2019-08-05 doi:10.1101/724674 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ Cross-continental biogeography of the common bean rhizosphere microbiome reveals a persistent core membership ]]> https://biorxiv.org/content/10.1101/727461v1?rss=1 Stopnisek, N. Shade, A. 2019-08-09 doi:10.1101/727461 Cold Spring Harbor Laboratory Press 2019-08-09 <![CDATA[ Evolution of conserved noncoding sequences in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/727669v1?rss=1 Yocca, A. Lu, Z. Schmitz, R. J. Freeling, M. Edger, P. 2019-08-06 doi:10.1101/727669 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ Feedback control of a two-component signaling system by a 4Fe-4S-binding receiver domain ]]> https://biorxiv.org/content/10.1101/729053v1?rss=1 Stein, B. J. Fiebig, A. Crosson, S. 2019-08-08 doi:10.1101/729053 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ Dormancy dynamics and dispersal contribute to soil microbiome resilience ]]> https://biorxiv.org/content/10.1101/730283v1?rss=1 Sorensen, J. W. Shade, A. 2019-08-08 doi:10.1101/730283 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ High-Accuracy Protein Structures By Combining Machine-Learning With Physics-Based Refinement ]]> https://biorxiv.org/content/10.1101/731521v1?rss=1 Heo, L. Feig, M. 2019-08-10 doi:10.1101/731521 Cold Spring Harbor Laboratory Press 2019-08-10 <![CDATA[ The finger 2 tip loop of Activin A is required for the formation of its non-signaling complex with ACVR1 and type II Bone Morphogenetic Protein receptors ]]> https://biorxiv.org/content/10.1101/733147v1?rss=1 Idone, V. Corpina, R. A. Goebel, E. J. Cunanan, C. J. Dimitriou, A. Kim, H. Zhang, Q. Rafique, A. Leidich, R. Wang, X. McClain, J. Murphy, A. J. Thompson, T. B. Economides, A. N. 2019-08-12 doi:10.1101/733147 Cold Spring Harbor Laboratory Press 2019-08-12 <![CDATA[ Reconstructed protein sequence evolution consistent with the evolution of C4 photosynthesis via a C2 ancestor in the Paniceae ]]> https://biorxiv.org/content/10.1101/733493v1?rss=1 Carvalho, D. S. Kenchanmane Raju, S. K. Zhang, Y. Schnable, J. 2019-08-13 doi:10.1101/733493 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Shared Genetic Risk between Eating Disorder- and Substance-Use-Related Phenotypes: Evidence from Genome-Wide Association Studies ]]> https://biorxiv.org/content/10.1101/741512v1?rss=1 Munn-Chernoff, M. Johnson, E. C. Chou, Y.-L. Coleman, J. R. Thornton, L. M. Walters, R. K. Yilmaz, Z. Baker, J. Hubel, C. Gordon, S. Medland, S. Watson, H. Gaspar, H. A. Bryois, J. Hinney, A. Leppa, V. Mattheisen, M. Ripke, S. Yao, S. Giusti-Rodriguez, P. Hanscombe, K. B. Adan, R. Alredsson, L. Ando, T. Andreassen, O. A. Berrettini, W. Boehm, I. Boni, C. Boraska Perica, V. Buehren, K. Burghardt, R. Cassina, M. Cichon, S. Clementi, M. Cone, R. Courtet, P. Crow, S. Crowley, J. J. Danner, U. Davis, O. de Zwaan, M. Dedoussis, G. Degortes, D. DeSocio, J. 2019-08-23 doi:10.1101/741512 Cold Spring Harbor Laboratory Press 2019-08-23 <![CDATA[ Wheat inositol pyrophosphate kinase (TaVIH2-3B) interacts with Fasciclin-like arabinogalactan (FLA6) protein and alters the plant cell-wall composition ]]> https://biorxiv.org/content/10.1101/743294v1?rss=1 Kaur, M. Shukla, A. Kanwar, S. Shukla, V. Kaur, G. Sharma, S. Kumar, A. Aggarwal, S. Bhati, K. K. Pandey, P. Mazumder, K. Rishi, V. Pandey, A. K. 2019-08-27 doi:10.1101/743294 Cold Spring Harbor Laboratory Press 2019-08-27 <![CDATA[ Modulating cellular cytotoxicity and phototoxicity of fluorescent organic salts through counterion pairing ]]> https://biorxiv.org/content/10.1101/743716v1?rss=1 Broadwater, D. Bates, M. Jayaram, M. Young, M. He, J. Raithel, A. L. Hamann, T. W. Zhang, W. Borhan, B. Lunt, R. R. Lunt, S. Y. 2019-08-22 doi:10.1101/743716 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Nf1 deletion results in depletion of the Lhx6 transcription factor and a specific loss of parvalbumin+ cortical interneurons ]]> https://biorxiv.org/content/10.1101/746214v1?rss=1 Vogt, K. Pai, E. L.-L. Bilinovich, S. M. Stafford, A. M. Nguyen, J. T. Paul, A. Rubenstein, J. L. Vogt, D. 2019-08-24 doi:10.1101/746214 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ Genome sequencing for early-onset dementia: high diagnostic yield and frequent observation of multiple contributory alleles ]]> https://biorxiv.org/content/10.1101/748046v1?rss=1 Cochran, J. N. McKinley, E. C. Cochran, M. Amaral, M. D. Moyers, B. A. Lasseigne, B. N. Gray, D. E. Lawlor, J. M. J. Prokop, J. W. Geier, E. G. Holt, J. M. Thompson, M. L. Newberry, J. S. Yokoyama, J. S. Worthey, E. A. Geldmacher, D. S. Love, M. N. Cooper, G. M. Myers, R. M. Roberson, E. D. 2019-08-28 doi:10.1101/748046 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ Expression and Purification of a Mammalian Protein: Cytosolic Domain of IRE1α from Insect Sf21 Cells ]]> https://biorxiv.org/content/10.1101/750430v1?rss=1 85% pure protein. ]]> Oak, A. Jansen, G. Chan, C. 2019-08-30 doi:10.1101/750430 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data ]]> https://biorxiv.org/content/10.1101/750471v1?rss=1 Jarmusch, A. K. Wang, M. Aceves, C. M. Advani, R. S. Aguire, S. Aksenov, A. A. Aleti, G. Aron, A. T. Bauermeister, A. Bolleddu, S. Bouslimani, A. Caraballo-Rodriguez, A. M. Chaar, R. Coras, R. Elijah, E. O. Ernst, M. Gauglitz, J. M. Gentry, E. C. Husband, M. Jarmusch, S. A. Jones, K. L. Kamenik, Z. Le Gouellec, A. Lu, A. McCall, L.-I. McPhail, K. L. Meehan, M. J. Melnik, A. V. Menezes, R. C. Montoya-Giraldo, Y. A. Nguyen, N. H. Nothias, L. F. Nothias-Esposito, M. Panitchpakdi, M. Petras, D. Quinn, R. Sikora, N. van der Hooft, J. J. J. Vargas, F. Vrbanac, 2019-08-29 doi:10.1101/750471 Cold Spring Harbor Laboratory Press 2019-08-29 <![CDATA[ Genome-wide misexpression associated with hybrid sterility in Mimulus (monkeyflower) ]]> https://biorxiv.org/content/10.1101/750687v1?rss=1 Kerwin, R. E. Sweigart, A. L. 2019-08-30 doi:10.1101/750687 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ Age-related differences in white matter: Comparing fixel based and tensor based analyses ]]> https://biorxiv.org/content/10.1101/751628v1?rss=1 Kelley, S. Plass, J. Bender, A. R. Polk, T. A. 2019-09-02 doi:10.1101/751628 Cold Spring Harbor Laboratory Press 2019-09-02 <![CDATA[ Moderate amounts of epistasis are not evolutionarily stable in small populations ]]> https://biorxiv.org/content/10.1101/752535v1?rss=1 Sydykova, D. K. LaBar, T. O. Adami, C. Wilke, C. O. 2019-08-31 doi:10.1101/752535 Cold Spring Harbor Laboratory Press 2019-08-31 <![CDATA[ Evidence for pre-climacteric activation of AOX transcription during cold-induced conditioning to ripen in European pear (Pyrus communis L.) ]]> https://biorxiv.org/content/10.1101/755686v1?rss=1 Hendrikckson, C. Hewitt, S. Swanson, M. E. Einhorn, T. Dhingra, A. 2019-09-03 doi:10.1101/755686 Cold Spring Harbor Laboratory Press 2019-09-03 <![CDATA[ Charting the native architecture of thylakoid membranes with single-molecule precision ]]> https://biorxiv.org/content/10.1101/759001v1?rss=1 Wietrzynski, W. Schaffer, M. Tegunov, D. Albert, S. Kanazawa, A. Plitzko, J. M. Baumeister, W. Engel, B. D. 2019-09-05 doi:10.1101/759001 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Common genetic variants shape broad patterns of within-population variation in gene expression. ]]> https://biorxiv.org/content/10.1101/763870v1?rss=1 Josephs, E. B. Lee, Y. W. Wood, C. W. Schoen, D. Wright, S. Stinchcombe, J. 2019-09-10 doi:10.1101/763870 Cold Spring Harbor Laboratory Press 2019-09-10 <![CDATA[ Overexpression of Mig-6 in Cartilage Induces An Osteoarthritis-Like Phenotype In Mice. ]]> https://biorxiv.org/content/10.1101/764142v1?rss=1 Bellini, M. Pest, M. A. Miranda-Rodrigues, M. Jeong, J.-W. Beier, F. 2019-09-10 doi:10.1101/764142 Cold Spring Harbor Laboratory Press 2019-09-10 <![CDATA[ Role of Cytosolic, Tyrosine-Insensitive Prephenate Dehydrogenase in Medicago truncatula ]]> https://biorxiv.org/content/10.1101/768317v1?rss=1 Schenck, C. A. Westphal, J. Jayaraman, D. Garcia, K. Wen, J. Mysore, K. S. Anee, J.-M. Sumner, L. W. Maeda, H. A. 2019-09-13 doi:10.1101/768317 Cold Spring Harbor Laboratory Press 2019-09-13 <![CDATA[ Striatal Nurr1 Facilitates the Dyskinetic State and Exacerbates Levodopa-Induced Dyskinesia in a Rat Model of Parkinson’s Disease ]]> https://biorxiv.org/content/10.1101/768374v1?rss=1 Sellnow, R. C. Steece-Collier, K. Altwal, F. Sandoval, I. M. Kordower, J. H. Collier, T. J. Sortwell, C. E. West, A. R. Manfredsson, F. 2019-09-28 doi:10.1101/768374 Cold Spring Harbor Laboratory Press 2019-09-28 <![CDATA[ ASlive: a database for alternative splicing atlas in livestock animals ]]> https://biorxiv.org/content/10.1101/769273v1?rss=1 Liu, J. Tan, S. Huang, S. Huang, W. 2019-09-14 doi:10.1101/769273 Cold Spring Harbor Laboratory Press 2019-09-14 <![CDATA[ Inhibition of the Myocardin-Related Transcription Factor pathway increases efficacy of Trametinib in NRAS-mutant melanoma cell lines ]]> https://biorxiv.org/content/10.1101/773531v1?rss=1 Appleton, K. M. Palsuledesai, C. C. Misek, S. A. Blake, M. Zagorski, J. Dexheimer, T. S. Neubig, R. R. 2019-09-19 doi:10.1101/773531 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Identification of gut microbiome markers for schizophrenia delineates a potential role of Streptococcus ]]> https://biorxiv.org/content/10.1101/774265v1?rss=1 Zhu, F. Ju, Y. Wang, W. Wang, Q. Guo, R. Ma, Q. Sun, Q. Fan, Y. Xie, Y. Yang, Z. Jie, Z. Zhao, B. Xiao, L. Tao, Z. Yang, L. Kristiansen, K. Ma, X. Jia, H. 2019-09-19 doi:10.1101/774265 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Carbon Assimilation Strategies in Ultrabasic Groundwater: Clues from the Integrated Study of a Serpentinization-Influenced Aquifer ]]> https://biorxiv.org/content/10.1101/776849v1?rss=1 Seyler, L. M. Brazelton, W. McLean, C. Putman, L. I. Hyer, A. Kubo, M. Hoehler, T. Cardace, D. Schrenk, M. O. 2019-09-20 doi:10.1101/776849 Cold Spring Harbor Laboratory Press 2019-09-20 <![CDATA[ Boiling Acid Mimics Intracellular Giant Virus Genome Release ]]> https://biorxiv.org/content/10.1101/777854v1?rss=1 Schrad, J. R. Abrahao, J. S. Cortines, J. R. Parent, K. N. 2019-09-20 doi:10.1101/777854 Cold Spring Harbor Laboratory Press 2019-09-20 <![CDATA[ Low E2F2 activity is associated with high genomic instability and PARPi resistance ]]> https://biorxiv.org/content/10.1101/777870v1?rss=1 Rennhack, J. Andrechek, E. R. 2019-10-03 doi:10.1101/777870 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ High-resolution MEMRI characterizes laminar specific ascending and descending spinal cord pathways in rats ]]> https://biorxiv.org/content/10.1101/781823v1?rss=1 Krishnan, V. Xu, J. Mendoza, G. A. Koretsky, A. Anderson, S. Pelled, G. 2019-09-25 doi:10.1101/781823 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Inherited Causes of Clonal Hematopoiesis of Indeterminate Potential in TOPMed Whole Genomes ]]> https://biorxiv.org/content/10.1101/782748v1?rss=1 Bick, A. G. Weinstock, J. Nandakumar, S. K. Fulco, C. P. Leventhal, M. J. Bao, E. L. Nasser, J. Zekavat, S. M. Szeto, M. D. Laurie, C. Taub, M. Mitchell, B. Barnes, K. Moscati, A. Fornage, M. Redline, S. Psaty, B. M. Silverman, E. Weiss, S. Palmer, N. Ramachandran, V. Burchard, E. Kardia, S. He, J. Kaplan, R. Smith, N. L. Arnett, D. Schwartz, D. Correa, A. de Andrade, M. Guo, X. Konkle, B. A. Custer, B. Peralta, J. Gui, H. Meyers, D. McGarvey, S. T. Chen, I. Shoemaker, M. B. Peyser, P. A. Broome, J. Gogarten, S. Wang, F. F. Wong, Q. Montasser, M. Da 2019-09-27 doi:10.1101/782748 Cold Spring Harbor Laboratory Press 2019-09-27 <![CDATA[ High molecular weight DNA isolation method from diverse plant species for use with Oxford Nanopore sequencing ]]> https://biorxiv.org/content/10.1101/783159v1?rss=1 Vaillancourt, B. Buell, C. R. 2019-09-26 doi:10.1101/783159 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Molecular Determinants of Substrate Selectivity of a Pneumococcal Rgg-regulated Peptidase-Containing ABC Transporter. ]]> https://biorxiv.org/content/10.1101/783472v1?rss=1 Wang, C. Y. Medlin, J. S. Nguyen, D. R. Disbennett, W. M. Dawid, S. 2019-09-26 doi:10.1101/783472 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Choosing Your Battles: Which Resistance Genes Warrant Global Action? ]]> https://biorxiv.org/content/10.1101/784322v1?rss=1 Zhang, A.-N. Li, L. Yin, X. Dai, C. L. Groussin, M. Poyet, M. Topp, E. Gillings, M. R. Hanage, W. P. Tiedje, J. M. Alm, E. J. Zhang, T. 2019-10-03 doi:10.1101/784322 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ Longitudinal study of persistence in professional development outcomes of early career biology faculty ]]> https://biorxiv.org/content/10.1101/785857v1?rss=1 Emery, N. C. Maher, J. M. Ebert-May, D. 2019-10-05 doi:10.1101/785857 Cold Spring Harbor Laboratory Press 2019-10-05 <![CDATA[ Long-term research needed to avoid spurious and misleading trends in sustainability attributes of no-till ]]> https://biorxiv.org/content/10.1101/788240v1?rss=1 nView larger version (42K):norg.highwire.dtl.DTLVardef@1e7529eorg.highwire.dtl.DTLVardef@1e11268org.highwire.dtl.DTLVardef@17f8995org.highwire.dtl.DTLVardef@2196fe_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIWe test long-term effects of no-till on yield, soil moisture, and N2O fluxesnC_LIO_LIWe examine 29 years of data with a moving window and relative profitability methodnC_LIO_LIIt takes at least a decade to detect consistent benefits of no-tillnC_LIO_LIShorter studies can produce significant but misleading findingsnC_LIO_LILong studies are essential to reveal the dynamics of agricultural managementnC_LI ]]> Cusser, S. Bahlai, C. Swinton, S. M. Robertson, G. P. Haddad, N. M. 2019-10-08 doi:10.1101/788240 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Phylogeny and Multiple Independent Whole-Genome Duplication Events in the Brassicales ]]> https://biorxiv.org/content/10.1101/789040v1?rss=1 Mabry, M. E. Brose, J. M. Blischak, P. D. Sutherland, B. Dismukes, W. T. Bottoms, C. A. Edger, P. P. Washburn, J. D. An, H. Hall, J. C. McKain, M. R. Al-Shehbaz, I. Barker, M. S. Schranz, M. E. Conant, G. C. Pires, J. C. 2019-10-01 doi:10.1101/789040 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ Self-controlled practice and nudging during structural learning of a novel control interface ]]> https://biorxiv.org/content/10.1101/789644v1?rss=1 Lee, M.-H. Jayasinghe, S. A. L. 2019-10-01 doi:10.1101/789644 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ Factors influencing read coverage variation in a genome assembled using short reads ]]> https://biorxiv.org/content/10.1101/790337v1?rss=1 Wang, P. Meng, F. Moore, B. M. Shiu, S.-H. 2019-10-02 doi:10.1101/790337 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Epigenetic contributions to hemisphere asymmetry in healthy brain, aging, and Parkinson’s disease ]]> https://biorxiv.org/content/10.1101/794255v1?rss=1 Li, P. Ensink, E. Lang, S. Marshall, L. Schilthuis, M. Lamp, J. Vega, I. Labrie, V. 2019-10-07 doi:10.1101/794255 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Light activates the translational regulatory GCN2 kinase via reactive oxygen species emanating from the chloroplast ]]> https://biorxiv.org/content/10.1101/794362v1?rss=1 Lokdarshi, A. Guan, J. Urquidi-Camacho, R. A. Cho, S. K. Morgan, P. W. Leonard, M. Shimono, M. Day, B. von Arnim, A. G. 2019-10-05 doi:10.1101/794362 Cold Spring Harbor Laboratory Press 2019-10-05 <![CDATA[ The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations ]]> https://biorxiv.org/content/10.1101/795005v1?rss=1 Rizzi, A. Jensen, T. Slochower, D. R. Aldeghi, M. Gapsys, V. Ntekoumes, D. Bosisio, S. Papadourakis, M. Henriksen, N. M. de Groot, B. L. Cournia, Z. Dickson, A. Michel, J. Gilson, M. K. Shirts, M. R. Mobley, D. L. Chodera, J. D. 2019-10-07 doi:10.1101/795005 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Metabolomic profiling of mouse mammary tumor derived cell lines reveals targeted therapy options for cancer subtypes ]]> https://biorxiv.org/content/10.1101/796573v1?rss=1 Ogrodzinski, M. P. Lunt, S. Y. 2019-10-07 doi:10.1101/796573 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Saturation mutagenesis genome engineering of infective {Phi}X174 bacteriophage via unamplified oligo pools and golden gate assembly ]]> https://biorxiv.org/content/10.1101/798546v1?rss=1 Faber, M. S. Van Leuven, J. T. Ederer, M. M. Wilson, Z. L. Sapozhnikov, Y. Wichman, H. A. Whitehead, T. A. Miller, C. R. 2019-10-09 doi:10.1101/798546 Cold Spring Harbor Laboratory Press 2019-10-09 <![CDATA[ Switchgrass Rhizosphere Metabolite Chemistry Driven by Nitrogen Availability ]]> https://biorxiv.org/content/10.1101/802926v1?rss=1 Smercina, D. Bowsher, A. W. Evans, S. E. Friesen, M. L. Eder, E. K. Hoyt, D. W. Tiemann, L. K. 2019-10-16 doi:10.1101/802926 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Predicting agronomic traits and associated genomic regions in diverse rice landraces using marker stability ]]> https://biorxiv.org/content/10.1101/805002v1?rss=1 Orhobor, O. I. Alexandrov, N. N. Chebotarov, D. Kretzschmar, T. McNally, K. L. Sanciangco, M. D. King, R. D. 2019-10-15 doi:10.1101/805002 Cold Spring Harbor Laboratory Press 2019-10-15 <![CDATA[ Multi-omic signatures identify pan-cancer classes of tumors beyond tissue of origin. ]]> https://biorxiv.org/content/10.1101/806323v1?rss=1 Gonzalez-Reymundez, A. Vazquez, A. I. 2019-10-31 doi:10.1101/806323 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ Involvement of orexin/hypocretin in the expression of social play behaviour in juvenile rats ]]> https://biorxiv.org/content/10.1101/809475v1?rss=1 Reppucci, C. J. Gergely, C. K. Bredewold, R. Veenema, A. H. 2019-10-17 doi:10.1101/809475 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Trophic variation within a piscivorous lake trout morph from Great Bear Lake, Canada: The initial step toward ecological specialization? ]]> https://biorxiv.org/content/10.1101/811851v1?rss=1 Chavarie, L. B. Howland, K. Harris, L. Gallagher, C. Hansen, M. Tonn, W. Muir, A. Krueger, C. 2019-10-21 doi:10.1101/811851 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Juvenile rank acquisition influences fitness independent of adult rank ]]> https://biorxiv.org/content/10.1101/812362v1?rss=1 Strauss, E. D. Shizuka, D. Holekamp, K. E. 2019-10-21 doi:10.1101/812362 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Feature-based Molecular Networking in the GNPS Analysis Environment ]]> https://biorxiv.org/content/10.1101/812404v1?rss=1 Nothias, L. F. Petras, D. Schmid, R. Duehrkop, K. Rainer, J. Sarvepalli, A. Protsyuk, I. Ernst, M. Tsugawa, H. Fleischauer, M. Aicheler, F. Aksenov, A. Alka, O. Allard, P.-M. Barsch, A. Cachet, X. Caraballo, M. Da Silva, R. Dang, T. Garg, N. Gauglitz, J. M. Gurevich, A. Isaac, G. Jarmusch, A. K. Kamenik, Z. Kang, K. B. Kessler, N. Koester, I. Korf, A. Le Gouellec, A. Ludwig, M. Martin H., C. McCall, L.-I. McSayles, J. Meyer, S. Mohimani, H. Morsy, M. Moyne, O. Neumann, S. Neuweger, H. Nguyen, N. H. Esposito-Nothias, M. Paolini, J. Phelan, V. Pluskal, 2019-10-20 doi:10.1101/812404 Cold Spring Harbor Laboratory Press 2019-10-20 <![CDATA[ Replaying the evolutionary tape to investigate subgenome dominance in allopolyploidBrassica napus ]]> https://biorxiv.org/content/10.1101/814491v1?rss=1 Bird, K. A. Niederhuth, C. Ou, S. A. Gehan, M. A. Pires, J. C. Xiong, Z. VanBuren, R. Edger, P. P. 2019-10-22 doi:10.1101/814491 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Gene Expression Networks in the Drosophila Genetic Reference Panel ]]> https://biorxiv.org/content/10.1101/816579v1?rss=1 Everett, L. J. Huang, W. Zhou, S. Carbone, M. A. Lyman, R. Arya, G. Geisz, M. S. Ma, J. Morgante, F. St. Armour, G. Turlapati, L. Anholt, R. R. H. Mackay, T. F. C. 2019-10-24 doi:10.1101/816579 Cold Spring Harbor Laboratory Press 2019-10-24 <![CDATA[ Haptic assistance that restricts use of redundant solutions is detrimental to motor learning ]]> https://biorxiv.org/content/10.1101/819771v1?rss=1 Lokesh, R. Ranganathan, R. 2019-10-25 doi:10.1101/819771 Cold Spring Harbor Laboratory Press 2019-10-25 <![CDATA[ OCTAD: an open workplace for virtually screening therapeutics targeting precise cancer patient groups using gene expression features ]]> https://biorxiv.org/content/10.1101/821546v1?rss=1 Zeng, B. Glicksberg, B. S. Newbury, P. Xing, J. Liu, K. Wen, A. Chow, C. Chen, B. 2019-11-01 doi:10.1101/821546 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ Enzalutamide-induced PTH1R-mediated TGFBR2 decrease in osteoblasts contributes to resistance in bone-metastatic prostate cancer ]]> https://biorxiv.org/content/10.1101/829044v1?rss=1 Su, S. Cao, J. Meng, X. Liu, R. Vander Ark, A. Woodford, E. Zhang, R. Stiver, I. Zhang, X. Madaj, Z. B. Bowman, M. J. Yu, H. Xu, E. Li, X. 2019-11-04 doi:10.1101/829044 Cold Spring Harbor Laboratory Press 2019-11-04 <![CDATA[ Alpha-synuclein antisense oligonucleotides as a disease-modifying therapy for Parkinson’s disease ]]> https://biorxiv.org/content/10.1101/830554v1?rss=1 Cole, T. A. Zhao, H. Collier, T. J. Sandoval, I. M. Sortwell, C. E. Steece-Collier, K. Daley, B. F. Booms, A. Lipton, J. Welch, M. Berman, M. Jandreski, L. Graham, D. Weihofen, A. Celano, S. Schulz, E. Cole-Strauss, A. Luna, E. Quach, D. Mohan, A. Bennett, C. F. Swayze, E. E. Kordasiewicz, H. B. Luk, K. C. Paumier, K. L. 2019-11-04 doi:10.1101/830554 Cold Spring Harbor Laboratory Press 2019-11-04 <![CDATA[ Metastatic function of METTL18 in breast cancer via actin methylation and Src ]]> https://biorxiv.org/content/10.1101/831701v1?rss=1 Kim, H. G. Kim, J. H. Yang, W. S. Park, J. G. Lee, Y. G. Kim, E. Hong, Y. H. Jo, M. Lee, C. Y. Kim, S. H. Sung, N. Y. Yi, Y.-S. Ratan, Z. A. Kim, S. Yoo, B. C. Kang, S.-U. Kim, Y. B. Kim, S. Paik, H.-J. Lee, J. E. Nam, S. J. Parameswaran, N. Han, J.-W. Cho, J. Y. 2019-11-05 doi:10.1101/831701 Cold Spring Harbor Laboratory Press 2019-11-05 <![CDATA[ Comparative genomic analyses and a novel linkage map for cisco (Coregonus artedi) provides insight into chromosomal evolution and rediploidization across salmonids ]]> https://biorxiv.org/content/10.1101/834937v1?rss=1 Blumstein, D. M. Campbell, M. A. Hale, M. C. Sutherland, B. J. G. McKinney, G. J. Stott, W. Larson, W. A. 2019-11-08 doi:10.1101/834937 Cold Spring Harbor Laboratory Press 2019-11-08 <![CDATA[ Unravelling the genetic architecture of musical rhythm ]]> https://biorxiv.org/content/10.1101/836197v1?rss=1 Niarchou, M. Sathirapongsasuti, J. F. Jacoby, N. Bell, E. McArthur, E. Straub, P. The 23andMe Research Team, McAuley, J. D. Capra, J. A. Ullen, F. Creanza, N. Mosing, M. A. Hinds, D. Davis, L. K. Gordon, R. L. 2019-11-09 doi:10.1101/836197 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Comparative transcriptomics reveal distinct patterns of gene expression conservation through vertebrate embryogenesis ]]> https://biorxiv.org/content/10.1101/840801v1?rss=1 Chan, M. E. Bhamidipati, P. S. Goldsby, H. J. Hintze, A. Hofmann, H. A. Young, R. L. 2019-11-13 doi:10.1101/840801 Cold Spring Harbor Laboratory Press 2019-11-13 <![CDATA[ Phosphate transporter PstSCAB of Campylobacter jejuni is essential for lactate-dependent growth and colonization in chickens ]]> https://biorxiv.org/content/10.1101/843771v1?rss=1 DiRita, V. J. Sinha, R. LeVeque, R. M. Gray, M. J. Bowlin, M. Q. 2019-11-15 doi:10.1101/843771 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ MyD88-Syk axis is a critical determinant for inflammatory response in macrophages ]]> https://biorxiv.org/content/10.1101/844076v1?rss=1 Yi, Y.-S. Kim, J. H. Yang, W. S. Kim, E. Jeong, D. Park, J. G. Aziz, N. Kim, S. Parameswaran, N. Cho, J. Y. 2019-11-15 doi:10.1101/844076 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ Surface Sensing Stimulates Cellular Differentiation in Caulobacter crescentus ]]> https://biorxiv.org/content/10.1101/844324v1?rss=1 Snyder, R. A. Ellison, C. K. Severin, G. B. Waters, C. M. Brun, Y. V. 2019-11-16 doi:10.1101/844324 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ Controlling a robotic arm for functional tasks using a wireless head-joystick: A case study of a child with congenital absence of upper and lower limbs ]]> https://biorxiv.org/content/10.1101/850123v1?rss=1 Aspelund, S. Patel, P. Lee, M.-H. Kagerer, F. Ranganathan, R. Mukherjee, R. 2019-11-20 doi:10.1101/850123 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Dorsal raphe oxytocin receptors regulate the neurobehavioral consequences of social touch ]]> https://biorxiv.org/content/10.1101/850271v1?rss=1 Grieb, Z. Ford, E. Manfredsson, F. Lonstein, J. 2019-11-21 doi:10.1101/850271 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Non-invasive neuromodulation using rTMS and the Electromagnetic-Preceptive Gene (EPG) facilitates plasticity after nerve injury ]]> https://biorxiv.org/content/10.1101/851444v1?rss=1 Cywiak, C. Ashbaugh, R. C. Metto, A. Udpa, L. Qian, C. Gilad, A. A. Zhong, M. Pelled, G. 2019-11-22 doi:10.1101/851444 Cold Spring Harbor Laboratory Press 2019-11-22 <![CDATA[ Genetic Association Study of Childhood Aggression across raters, instruments and age ]]> https://biorxiv.org/content/10.1101/854927v1?rss=1 Ip, H. F. van der Laan, C. M. Brikell, I. Sanchez-Mora, C. Nolte, I. M. St Pourcain, B. Bolhuis, K. Palviainen, T. Zafarmand, H. Colodro-Conde, L. Gordon, S. Zayats, T. Aliev, F. Jiang, C. Wang, C. A. Saunders, G. Karhunen, V. Hammerschlag, A. R. Adkins, D. E. Border, R. Peterson, R. E. Prinz, J. A. Thiering, E. Seppälä, I. Vilor-Tejedor, N. Ahluwalia, T. S. Day, F. R. Hottenga, J.-J. Allegrini, A. G. Krapohl, E. M. L. Rimfeld, K. Chen, Q. Lu, Y. Martin, J. Soler Artigas, M. Rovira, P. Bosch, R. Espanol, G. Ramos Quiroga, J. A. Neumann, A. Ensink, J. 2019-11-29 doi:10.1101/854927 Cold Spring Harbor Laboratory Press 2019-11-29 <![CDATA[ Metastasis is altered through multiple processes regulated by the E2F1 transcription factor ]]> https://biorxiv.org/content/10.1101/858068v1?rss=1 Swiatnicki, M. Andrechek, E. 2019-12-03 doi:10.1101/858068 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ CDK4 as a phytochemical based anticancer drug target ]]> https://biorxiv.org/content/10.1101/859595v1?rss=1 Chando, R. K. Hussain, N. Islam Rana, M. Sayed, S. Alam, S. Ahmed Fakir, T. Sharma, S. Rahman Tanu, A. Mobin, F. Hoque Apu, E. Hasan, M. K. Sayed, M. A. Ashraf, M. A. 2019-11-29 doi:10.1101/859595 Cold Spring Harbor Laboratory Press 2019-11-29 <![CDATA[ Chromosome Evolution of Octoploid Strawberry ]]> https://biorxiv.org/content/10.1101/861526v1?rss=1 Hardigan, M. A. Feldmann, M. J. Lorant, A. Famula, R. Acharya, C. Cole, G. S. Edger, P. P. Knapp, S. J. 2019-12-02 doi:10.1101/861526 Cold Spring Harbor Laboratory Press 2019-12-02 <![CDATA[ Rootstock choice can dramatically affect grapevine growth ]]> https://biorxiv.org/content/10.1101/864850v1?rss=1 Migicovsky, Z. Cousins, P. Jordan, L. M. Myles, S. Striegler, R. K. Verdegaal, P. Chitwood, D. H. 2019-12-05 doi:10.1101/864850 Cold Spring Harbor Laboratory Press 2019-12-05 <![CDATA[ Analysis of Mammalian Succinate Dehydrogenase Kinetics and Reactive Oxygen Species Production ]]> https://biorxiv.org/content/10.1101/870501v1?rss=1 Manhas, N. Duong, Q. Lee, P. Bazil, J. 2019-12-10 doi:10.1101/870501 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Mechanism of perceived duration in artificial brains suggests new model of attentional entrainment ]]> https://biorxiv.org/content/10.1101/870535v1?rss=1 Tehrani-Saleh, A. McAuley, J. D. Adami, C. 2019-12-11 doi:10.1101/870535 Cold Spring Harbor Laboratory Press 2019-12-11 <![CDATA[ Overexpression Of Mig-6 In Limb Mesenchyme Leads To Accelerated Osteoarthritis In Mice ]]> https://biorxiv.org/content/10.1101/871350v1?rss=1 Rodrigues Bellini, M. Pest, M. A. Jeong, J.-W. Beier, F. 2019-12-10 doi:10.1101/871350 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Acidic pH reduces Vibrio cholerae motility in mucus by weakening flagellar motor torque ]]> https://biorxiv.org/content/10.1101/871475v1?rss=1 Dufour, Y. S. Nhu, N. T. Wang, H. J. 2019-12-10 doi:10.1101/871475 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Pharmacological and fasting-induced activation of SIRT1/LXRα signaling alleviates diabetes-induced retinopathy. ]]> https://biorxiv.org/content/10.1101/871822v1?rss=1 Hammer, S. S. Vieira, C. P. McFarland, D. Sandler, M. Levitsky, Y. Dorweiler, T. F. Lydic, T. Asare-Bediako, B. Adu-Agyeiwaah, Y. Sielski, M. S. Dupont, M. Longhini, A. L. Calzi, S. L. Chakraborty, D. Seigel, G. M. Proshlyakov, D. A. Grant, M. B. Busik, J. V. 2019-12-10 doi:10.1101/871822 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Adoption of modern pest control systems associated with declines in butterfly abundance across Midwestern monitoring network ]]> https://biorxiv.org/content/10.1101/2022.07.29.502042v1?rss=1 Van Deynze, B. Swinton, S. M. Hennessy, D. A. Ries, L. 2022-08-02 doi:10.1101/2022.07.29.502042 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Taxonomic, genomic, and functional variation in the gut microbiomes of wild spotted hyenas across two decades of study ]]> https://biorxiv.org/content/10.1101/2022.08.02.502164v1?rss=1 Rojas, C. A. Holekamp, K. E. Jasso, M. V. Souza, V. Eisen, J. A. Theis, K. R. 2022-08-02 doi:10.1101/2022.08.02.502164 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Warming undermines emergence success in a threatened alpine stonefly: a multi-trait perspective on vulnerability to climate change ]]> https://biorxiv.org/content/10.1101/2022.08.01.502337v1?rss=1 Shah, A. A. Hotaling, S. Lapsansky, A. Malison, R. L. Birrell, J. H. Keeley, T. Giersch, J. J. Tronstad, L. M. Woods, H. A. 2022-08-03 doi:10.1101/2022.08.01.502337 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Temporal Regulation of Cold Transcriptional Response in Switchgrass ]]> https://biorxiv.org/content/10.1101/2022.08.01.502344v1?rss=1 Ranaweera, T. Brown, B. N. I. Wang, P. Shiu, S.-H. 2022-08-03 doi:10.1101/2022.08.01.502344 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Recovery of forearm and fine digit function after chronic spinal cord injury by simultaneous blockade of inhibitory matrix CSPG production and the receptor PTPσ. ]]> https://biorxiv.org/content/10.1101/2022.08.01.502398v1?rss=1 Milton, A. Silver, D. J. Kwok, J. C. F. McClellan, J. Warren, P. M. Silver, J. 2022-08-03 doi:10.1101/2022.08.01.502398 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Multifunctional requirements for ERK1/2 signaling in the development of ganglionic eminence derived glia and cortical inhibitory neurons ]]> https://biorxiv.org/content/10.1101/2022.08.02.502073v1?rss=1 Knowles, S. J. Holter, M. C. Li, G. Bjorklund, G. R. Rees, K. P. Martinez-Fuentes, J. S. Nishimura, K. J. Afshari, A. E. Fry, N. Stafford, A. M. Vogt, D. Mangone, M. Anderson, T. Newbern, J. M. 2022-08-04 doi:10.1101/2022.08.02.502073 Cold Spring Harbor Laboratory Press 2022-08-04 <![CDATA[ Systematic Analysis of Autophagy Identifies Atg9 Vesicles as the Origin of the Phagophore ]]> https://biorxiv.org/content/10.1101/2022.08.03.502680v1?rss=1 Broadbent, D. Barnaba, C. Schmidt, J. C. 2022-08-05 doi:10.1101/2022.08.03.502680 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Distinct hyperactive RAS/MAPK alleles converge on common GABAergic interneuron core programs ]]> https://biorxiv.org/content/10.1101/2022.08.04.502867v1?rss=1 Knowles, S. J. Stafford, A. M. Zaman, T. Angara, K. Williams, M. R. Newbern, J. M. Vogt, D. 2022-08-05 doi:10.1101/2022.08.04.502867 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Characterizing Transient Protein-Protein Interactions by Trp-Cys Quenching and Computer Simulations ]]> https://biorxiv.org/content/10.1101/2022.08.05.502984v1?rss=1 Heo, L. Gamage, K. Valdes-Garcia, G. Lapidus, L. J. Feig, M. 2022-08-06 doi:10.1101/2022.08.05.502984 Cold Spring Harbor Laboratory Press 2022-08-06 <![CDATA[ Theoretical and practical refinements of sans spike-in quantitative ChIP-seq with application to p300/CBP inhibition ]]> https://biorxiv.org/content/10.1101/2022.08.09.503331v1?rss=1 Dickson, B. M. Kupai, A. Vaughan, R. M. Rothbart, S. B. 2022-08-11 doi:10.1101/2022.08.09.503331 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Group B streptococcal membrane vesicles induce proinflammatory cytokine production and are sensed in an NLRP3 inflammasome-dependent mechanism in human macrophages ]]> https://biorxiv.org/content/10.1101/2022.08.10.503555v1?rss=1 McCutcheon, C. R. Gaddy, J. Aronoff, D. M. Manning, S. D. Petroff, M. G. 2022-08-12 doi:10.1101/2022.08.10.503555 Cold Spring Harbor Laboratory Press 2022-08-12 <![CDATA[ Characterization of RNA Polymerase II Trigger Loop Mutations using Molecular Dynamics Simulations and Machine Learning ]]> https://biorxiv.org/content/10.1101/2022.08.11.503690v1?rss=1 Dutagaci, B. Duan, B. Qiu, C. Kaplan, C. D. Feig, M. 2022-08-12 doi:10.1101/2022.08.11.503690 Cold Spring Harbor Laboratory Press 2022-08-12 <![CDATA[ Genetic architecture and evolution of color variation in American black bears ]]> https://biorxiv.org/content/10.1101/2022.08.12.503788v1?rss=1 Puckett, E. E. Davis, I. S. Harper, D. C. Wakamatsu, K. Battu, G. Belant, J. L. Beyer, D. E. Carpenter, C. Crupi, A. P. Davidson, M. DePerno, C. S. Forman, N. Fowler, N. L. Garshelis, D. L. Gould, N. Gunther, K. Haroldson, M. Ito, S. Kocka, D. Lackey, C. Leahy, R. Lee-Roney, C. Lewis, T. Lutto, A. McGowan, K. Olfenbuttel, C. Orlando, M. Platt, A. Pollard, M. D. Ramaker, M. Reich, H. Sajecki, J. L. Sell, S. K. Strules, J. Thompson, S. van Manen, F. Whitman, C. Williamson, R. Winslow, F. Kaelin, C. Marks, M. Barsh, G. 2022-08-13 doi:10.1101/2022.08.12.503788 Cold Spring Harbor Laboratory Press 2022-08-13 <![CDATA[ Accurately modeling biased random walks on weighted networks using node2vec+ ]]> https://biorxiv.org/content/10.1101/2022.08.14.503926v1?rss=1 Liu, R. Hirn, M. Krishnan, A. 2022-08-15 doi:10.1101/2022.08.14.503926 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Abiotic conditions alter effectiveness of a key seed defensive trait against granivores similarly across many plant species ]]> https://biorxiv.org/content/10.1101/2022.08.15.504038v1?rss=1 LoPresti, E. F. Stessman, M. E. Warren, S. E. Toll, K. 2022-08-15 doi:10.1101/2022.08.15.504038 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Leveraging prior biological knowledge improves prediction of tocochromanols in maize grain ]]> https://biorxiv.org/content/10.1101/2022.08.16.502005v1?rss=1 Tanaka, R. Wu, D. Li, X. Tibbs-Cortes, L. E. Wood, J. C. Magallanes-Lundback, M. Bornowski, N. Hamilton, J. P. Vaillancourt, B. Li, X. Deason, N. T. Schoenbaum, G. R. Buell, C. R. DellaPenna, D. Yu, J. Gore, M. A. 2022-08-16 doi:10.1101/2022.08.16.502005 Cold Spring Harbor Laboratory Press 2022-08-16 <![CDATA[ Modeling concentration-dependent phase separation processes involving peptides and RNA via residue-based coarse-graining ]]> https://biorxiv.org/content/10.1101/2022.08.19.504518v1?rss=1 Valdes-Garcia, G. Heo, L. Lapidus, L. J. Feig, M. 2022-08-19 doi:10.1101/2022.08.19.504518 Cold Spring Harbor Laboratory Press 2022-08-19 <![CDATA[ Magnetogenetic closed-loop reduction of seizure activity in a rat model of epilepsy ]]> https://biorxiv.org/content/10.1101/2022.08.19.504501v1?rss=1 Metto, A. C. Gilad, A. A. Pelled, G. 2022-08-22 doi:10.1101/2022.08.19.504501 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ Sex-dependent role of hypocretin/orexin neurons in social behavior ]]> https://biorxiv.org/content/10.1101/2022.08.19.504565v1?rss=1 Dawson, M. Terstege, D. J. Jamani, N. Pavlov, D. Tsutsui, M. Bugescu, R. Epp, J. R. Leinninger, G. M. Sargin, D. 2022-08-22 doi:10.1101/2022.08.19.504565 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ C4 Grasses Employ Various Strategies to Acclimate Rubisco Activase to Heat Stress ]]> https://biorxiv.org/content/10.1101/2022.08.24.505184v1?rss=1 Stainbrook, S. C. Aubuchon, L. N. Chen, A. Johnson, E. Si, A. Walton, L. Ahrendt, A. Jez, J. M. 2022-08-26 doi:10.1101/2022.08.24.505184 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Global Phylogeny of the Brassicaceae Provides Important Insights into Gene Discordance ]]> https://biorxiv.org/content/10.1101/2022.09.01.506188v1?rss=1 1,000 genes, almost all 349 genera and 53 tribes) and plastome (60 genes, 79% of the genera, all tribes) data. We found cytonuclear discordance between nuclear and plastome-derived phylogenies, which is likely a result of rampant hybridisation among closely and more distantly related species, and highlight rogue taxa. To evaluate the impact of this rampant hybridisation on the nuclear phylogeny reconstruction, we performed four different sampling routines that increasingly removed variable data and likely paralogs. Our resulting cleaned subset of 297 nuclear genes revealed high support for the tribes, while support for the main lineages remained relatively low. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene icehouse origin of the family. Finally, we propose five new or re-established tribes, including the recognition of Arabidopsideae, a monotypic tribe to accommodate Arabidopsis. With a worldwide community of thousands of researchers working on this family, our new, densely sampled family phylogeny will be an indispensable tool to further highlight Brassicaceae as an excellent model family for studies on biodiversity and plant biology. ]]> Hendriks, K. P. Kiefer, C. Al-Shehbaz, I. A. Bailey, C. D. Hooft van Huysduynen, A. A. C. Nikolov, L. Nauheimer, L. Zuntini, A. R. German, D. A. Franzke, A. Koch, M. A. Lysak, M. A. Toro-Nunez, O. Ozudogru, B. Invernon, V. R. Walden, N. Maurin, O. Hay, N. Sushkov, P. Mandakova, T. Thulin, M. Windham, M. Resetnik, I. Spaniel, S. Ly, E. Pires, J. C. Harkess, A. Neuffer, B. Vogt, R. Braeuchler, C. Rainer, H. Janssens, S. Schmull, M. Forrest, A. Guggisberg, A. Zmarzty, S. Lepschi, B. Scarlett, N. Stauffer, F. W. Schonberger, I. Heenan, P. Baker, W. J. Fore 2022-09-01 doi:10.1101/2022.09.01.506188 Cold Spring Harbor Laboratory Press 2022-09-01 <![CDATA[ A Principal Odor Map Unifies Diverse Tasks in Human Olfactory Perception ]]> https://biorxiv.org/content/10.1101/2022.09.01.504602v1?rss=1 Lee, B. K. Mayhew, E. E. Sanchez-Lengeling, B. Wei, J. N. Qian, W. W. Little, K. Andres, M. Nguyen, B. B. Moloy, T. Parker, J. K. Gerkin, R. C. Mainland, J. D. Wiltschko, A. B. 2022-09-03 doi:10.1101/2022.09.01.504602 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Tumor removal limits prostate cancer cell dissemination in bone cortex and osteoblasts induce cancer cell dormancy ]]> https://biorxiv.org/content/10.1101/2022.09.02.506436v1?rss=1 Liu, R. Su, S. Liu, K. Xing, J. Stangis, M. Jacho, D. P. Yildirim-Ayan, E. D. Yu, H. Chen, B. Li, X. 2022-09-05 doi:10.1101/2022.09.02.506436 Cold Spring Harbor Laboratory Press 2022-09-05 <![CDATA[ Accurate flux predictions using tissue-specific gene expression in plant metabolic modeling ]]> https://biorxiv.org/content/10.1101/2022.09.05.506655v1?rss=1 Kaste, J. A. M. Shachar-Hill, Y. 2022-09-06 doi:10.1101/2022.09.05.506655 Cold Spring Harbor Laboratory Press 2022-09-06 <![CDATA[ 1 Natural Genetic Variation in a Dopamine Receptor is Associated With Variation in Female Fertility in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2022.09.06.506722v1?rss=1 Lyman, R. Lyman, R. Yamamoto, A. Huang, W. Harbison, S. Zhou, S. Anholt, R. Mackay, T. F. C. 2022-09-06 doi:10.1101/2022.09.06.506722 Cold Spring Harbor Laboratory Press 2022-09-06 <![CDATA[ Head and Neck Cancer-derived small extracellular vesicles sensitize TRPV1+ neurons to mediate cancer pain ]]> https://biorxiv.org/content/10.1101/2022.09.06.506411v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@2a13a2org.highwire.dtl.DTLVardef@6f305dorg.highwire.dtl.DTLVardef@1d0417corg.highwire.dtl.DTLVardef@17b36df_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Inyang, K. E. Evans, C. M. Heussner, M. Petroff, M. Reimers, M. Vermer, P. D. Tykocki, N. Folger, J. K. Laumet, G. 2022-09-08 doi:10.1101/2022.09.06.506411 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Multi-Omics Analysis of Magnetically Levitated Plasma Biomolecules ]]> https://biorxiv.org/content/10.1101/2022.09.06.506852v1?rss=1 Ashkarran, A. A. Gharibi, H. Zeki, D. A. Radu, I. Khalighinejad, F. Keyhanian, K. Abrahamsson, C. K. Ionete, C. Saei, A. A. Mahmoudi, M. 2022-09-08 doi:10.1101/2022.09.06.506852 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ HPV E6 upregulates MARCHF8 ubiquitin ligase and inhibits apoptosis by degrading the death receptors in head and neck cancer ]]> https://biorxiv.org/content/10.1101/2022.09.07.507063v1?rss=1 Khalil, M. I. Yang, C. Vu, L. Chadha, S. Welbon, C. James, C. D. Morgan, I. M. Spanos, W. C. Pyeon, D. 2022-09-08 doi:10.1101/2022.09.07.507063 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ The topological shape of gene expression across the evolution of flowering plants ]]> https://biorxiv.org/content/10.1101/2022.09.07.506951v1?rss=1 Palande, S. Kaste, J. A. M. Roberts, M. D. Segura Aba, K. Claucherty, C. Dacon, J. Doko, R. Jayakody, T. B. Jeffery, H. R. Kelly, N. Manousidaki, A. Parks, H. M. Roggenkamp, E. M. Schumacher, A. M. Yang, J. Percival, S. Pardo, J. Husbands, A. Y. Krishnan, A. Montgomery, B. L. Munch, E. Thompson, A. M. Rougon-Cardoso, A. Chitwood, D. H. VanBuren, R. 2022-09-09 doi:10.1101/2022.09.07.506951 Cold Spring Harbor Laboratory Press 2022-09-09 <![CDATA[ X-linked adrenoleukodystrophy patient fibroblast-iPSC-derived astrocytes reveal phenotype-specific metabolic, inflammatory, and microRNA alterations ]]> https://biorxiv.org/content/10.1101/2022.09.09.507263v1?rss=1 PARASAR, P. Kaur, N. Poisson, L. Singh, J. 2022-09-10 doi:10.1101/2022.09.09.507263 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Metadata preservation and stewardship for genomic data is possible, but must happen now ]]> https://biorxiv.org/content/10.1101/2022.09.12.507034v1?rss=1 Crandall, E. D. Toczydlowski, R. H. Liggins, L. Holmes, A. E. Ghoojaei, M. Gaither, M. R. Wham, B. E. Pritt, A. L. Noble, C. Anderson, T. J. Barton, R. L. Berg, J. T. Beskid, S. G. Delgado, A. Farrell, E. Himmelsbach, N. Queeno, S. R. Trinh, T. Weyand, C. A. Bentley, A. Deck, J. Riginos, C. Bradburd, G. S. Toonen, R. J. 2022-09-15 doi:10.1101/2022.09.12.507034 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Structural insights into the elevator-type transport mechanism of a bacterial ZIP metal transporter ]]> https://biorxiv.org/content/10.1101/2022.09.14.508043v1?rss=1 Zhang, Y. Jiang, Y. Gao, K. Sui, D. Yu, P. Su, M. Wei, G. Hu, J. 2022-09-15 doi:10.1101/2022.09.14.508043 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Structural and functional changes of pyramidal neurons at the site of an implanted microelectrode array in rat primary motor cortex ]]> https://biorxiv.org/content/10.1101/2022.09.15.507997v1?rss=1 Gregory, B. A. Thompson, C. H. Salatino, J. W. Railing, M. J. Zimmerman, A. F. Gupta, B. Williams, K. Beatty, J. A. Cox, C. L. Purcell, E. K. 2022-09-17 doi:10.1101/2022.09.15.507997 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Polylactide Degradation Activates Immune Cells by Metabolic Reprogramming ]]> https://biorxiv.org/content/10.1101/2022.09.22.509105v1?rss=1 Maduka, C. V. Alhaj, M. Ural, E. Habeeb, M. O. Kuhnert, M. M. Smith, K. Makela, A. V. Pope, H. Chen, S. Hix, J. M. Mallet, C. L. Chung, S.-J. Hakun, M. Tundo, A. Zinn, K. R. Hankenson, K. D. Goodman, S. B. Narayan, R. Contag, C. H. 2022-09-23 doi:10.1101/2022.09.22.509105 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Continuous directed evolution of a feedback-resistant Arabidopsis arogenate dehydratase in plantized E. coli ]]> https://biorxiv.org/content/10.1101/2022.09.24.509247v1?rss=1 Leong, B. J. Hanson, A. D. 2022-09-24 doi:10.1101/2022.09.24.509247 Cold Spring Harbor Laboratory Press 2022-09-24 <![CDATA[ Genome-wide association study of water use patterns of common bean (Phaseolus vulgaris L.) genotypes in response to drying soil ]]> https://biorxiv.org/content/10.1101/2022.09.23.509270v1?rss=1 Cordoba-Novoa, H. A. Kelly, J. D. Hoyos-Villegas, V. 2022-09-26 doi:10.1101/2022.09.23.509270 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Heterogeneity of burst firing in mouse thalamic reticular nucleus neurons ]]> https://biorxiv.org/content/10.1101/2022.09.25.509400v1?rss=1 Harding-Jackson, L. Beatty, J. A. Cox, C. L. 2022-09-27 doi:10.1101/2022.09.25.509400 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ A national professional development program fills mentoring gaps for postdoctoral researchers ]]> https://biorxiv.org/content/10.1101/2022.09.26.509546v1?rss=1 Sun, T. Drane, D. McGee, R. Campa, H. Goldberg, B. B. Hokanson, S. C. 2022-09-27 doi:10.1101/2022.09.26.509546 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Seasonal models reveal niche changes in Capsella bursa-pastoris ]]> https://biorxiv.org/content/10.1101/2022.09.26.509568v1?rss=1 Wilson Brown, M. Josephs, E. 2022-09-27 doi:10.1101/2022.09.26.509568 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Cross-species predictive modeling reveals conserved drought responses between maize and sorghum ]]> https://biorxiv.org/content/10.1101/2022.09.26.509573v1?rss=1 Pardo, J. Wai, C. M. Harman, M. Nguyen, A. Kremling, K. A. Romay, C. Lepak, N. Bauerle, T. L. Buckler, E. S. Thompson, A. M. VanBuren, R. 2022-09-27 doi:10.1101/2022.09.26.509573 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Profound immunomodulatory effects of 225Ac-NM600 drive enhanced anti-tumor responsein prostate cancer ]]> https://biorxiv.org/content/10.1101/2022.09.26.509374v1?rss=1 de Aguiar Ferreira, C. Potluri, H. K. Massey, C. Grudzinski, J. J. Carston, A. Clemons, N. Thickens, A. S. Rosenkrans, Z. Choi, C. Pinchuk, A. Kwon, O. Jeffery, J. J. Bednarz, B. Morris, Z. Weichert, J. McNeel, D. G. Hernandez, R. 2022-09-28 doi:10.1101/2022.09.26.509374 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Acclimating to degraded environments: The social rationale for swift action on restoration ]]> https://biorxiv.org/content/10.1101/2022.09.27.509807v1?rss=1 Karatayev, V. A. Wilson, R. S. Webster, D. G. Axelrod, M. Bauch, C. T. Anand, M. 2022-09-28 doi:10.1101/2022.09.27.509807 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Predicting partner fitness based on spatial structuring in a light-driven microbial community ]]> https://biorxiv.org/content/10.1101/2022.09.28.510001v1?rss=1 Sakkos, J. K. Santos-Merino, M. Kokarakis, E. J. Li, B. Fuentes-Cabrera, M. Zuliani, P. Ducat, D. C. 2022-09-30 doi:10.1101/2022.09.28.510001 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Clarifying space use concepts in ecology: range vs. occurrence distributions ]]> https://biorxiv.org/content/10.1101/2022.09.29.509951v1?rss=1 Alston, J. M. Fleming, C. H. Noonan, M. J. Tucker, M. A. Silva, I. Folta, C. Akre, T. S. Ali, A. H. Belant, J. L. Beyer, D. Blaum, N. Boehning-Gaese, K. Cunha de Paula, R. Dekker, J. Drescher-Lehman, J. Farwig, N. Fichtel, C. Fischer, C. Ford, A. T. Janssen, R. Jeltsch, F. Kappeler, P. M. LaPoint, S. D. Markham, A. C. Medici, P. Morato, R. G. Nathan, R. Olson, K. Patterson, B. D. Petroelje, T. Ramalho, E. E. Roesner, S. Santos, L. G. R. O. Schabo, D. G. Selva, N. Sergiel, A. Spiegel, O. Ullman, W. Zieba, F. Zwijacz-Kozica, T. Wittemyer, G. Fagan, W. F. 2022-09-30 doi:10.1101/2022.09.29.509951 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Novel inductively-coupled ear-bars (ICEs) for fMRI signal enhancement in rat entorhinal cortex ]]> https://biorxiv.org/content/10.1101/2022.09.30.510293v1?rss=1 Chen, Y. Fernandez, Z. Zhu, D. C. Counts, S. E. Dorrance, A. M. Yu, X. Scheel, N. Qian, W. Gifani, M. Qian, C. 2022-10-03 doi:10.1101/2022.09.30.510293 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ Diversity-stability relationships become decoupled across spatial scales: a synthesis of organism and ecosystem types ]]> https://biorxiv.org/content/10.1101/2022.10.04.510879v1?rss=1 Wisnoski, N. I. Andrade, R. Castorani, M. C. N. Catano, C. P. Compagnoni, A. Lamy, T. Lany, N. K. Marazzi, L. Record, S. Smith, A. C. Swan, C. M. Tonkin, J. D. Voelker, N. M. Zarnetske, P. L. Sokol, E. R. 2022-10-07 doi:10.1101/2022.10.04.510879 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Generative Modeling of Single Cell Gene Expression for Dose-Dependent Chemical Perturbations ]]> https://biorxiv.org/content/10.1101/2022.10.05.510890v1?rss=1 Kana, O. Z. Nault, R. Z. Filipovic, D. Marri, D. K. Zacharewski, T. Bhattacharya, S. 2022-10-07 doi:10.1101/2022.10.05.510890 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Live imaging reveals chromatin compaction transitions and dynamic transcriptional bursting during stem cell differentiation in vivo ]]> https://biorxiv.org/content/10.1101/2022.10.07.511316v1?rss=1 May, D. Yun, S. Gonzalez, D. Park, S. Chen, Y. Lathrop, E. Cai, B. Xin, T. Zhao, H.-y. Wang, S. Gonzalez, L. E. Cockburn, K. Greco, V. 2022-10-07 doi:10.1101/2022.10.07.511316 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Preparing future STEM faculty nationwide through flexible teaching professional development ]]> https://biorxiv.org/content/10.1101/2022.10.06.511090v1?rss=1 Goldberg, B. Bruff, D. Greenler, R. Barnicle, K. Green, N. Campbell, L. Laursen, S. Ford, M. Serafini, A. Mack, C. Carley, T. Maimone, C. Campa, H. 2022-10-11 doi:10.1101/2022.10.06.511090 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ Glycolytic reprogramming underlies immune cell activation by polyethylene wear particles ]]> https://biorxiv.org/content/10.1101/2022.10.14.512318v1?rss=1 Maduka, C. V. Habeeb, O. M. Kuhnert, M. M. Hakun, M. Goodman, S. B. Contag, C. H. 2022-10-18 doi:10.1101/2022.10.14.512318 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Global disparities in plant science: a legacy of colonialism, patriarchy, and exclusion ]]> https://biorxiv.org/content/10.1101/2022.10.15.512190v1?rss=1 Marks, R. A. Amezquita, E. J. Percival, S. Rougon-Cardoso, A. Chibici-Revneanu, C. Tebele, S. M. Farrant, J. M. Chitwood, D. H. VanBuren, R. 2022-10-18 doi:10.1101/2022.10.15.512190 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Ecological drivers of sustained enzootic yellow fever virus transmission in Brazil, 2017-2021 ]]> https://biorxiv.org/content/10.1101/2022.10.19.512702v1?rss=1 Silva, N. I. O. Albery, G. F. Arruda, M. S. Garcia, G. F. O. Costa, T. A. Mello, E. M. Moreira, G. D. Reis, E. V. Silva, S. A. Silva, M. C. Almeida, M. G. Becker, D. Carlson, C. J. Vasilakis, N. Hanley, K. A. Drumond, B. P. 2022-10-19 doi:10.1101/2022.10.19.512702 Cold Spring Harbor Laboratory Press 2022-10-19 <![CDATA[ DANCE: A Deep Learning Library and Benchmark for Single-Cell Analysis ]]> https://biorxiv.org/content/10.1101/2022.10.19.512741v1?rss=1 Ding, J. Wen, H. Tang, W. Liu, R. Li, Z. Venegas, J. Su, R. Molho, D. Jin, W. Zuo, W. Wang, Y. Xie, Y. Tang, J. 2022-10-21 doi:10.1101/2022.10.19.512741 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Elevated oxidative phosphorylation is critical for immune cell activation by polyethylene wear particles ]]> https://biorxiv.org/content/10.1101/2022.10.19.512774v1?rss=1 Maduka, C. V. Kuhnert, M. M. Habeeb, O. M. Tundo, A. Makela, A. V. Goodman, S. B. Contag, C. H. 2022-10-21 doi:10.1101/2022.10.19.512774 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ A comparison of claw removal methods on the post-release survival and claw regeneration of stone crab (Menippe mercenaria) ]]> https://biorxiv.org/content/10.1101/2022.10.24.513277v1?rss=1 Walus, A. M. Schneider, E. V. C. Parker, E. Brittain, C. McGaw, I. J. Hayes, D. Peters, A. K. VanLeeuwen, T. E. 2022-10-25 doi:10.1101/2022.10.24.513277 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Weaker selection on genes with treatment-specific expression may limit plasticity evolution in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2022.10.26.513896v1?rss=1 Roberts, M. D. Josephs, E. 2022-10-27 doi:10.1101/2022.10.26.513896 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Integrated PET and confocal imaging informs a functional timeline for the dynamic process of vascular reconnection during grafting. ]]> https://biorxiv.org/content/10.1101/2022.10.27.513862v1?rss=1 Frank, M. Komarov, S. Wang, Q. Li, K. Hecking, M. Fowler, H. Ravenburg, C. Widmier, A. Johnson, A. Thomas, H. Coneva, V. Chitwood, D. H. Tai, Y.-C. 2022-10-28 doi:10.1101/2022.10.27.513862 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Characterisation of organised smooth endoplasmic reticulum suggests a route towards synthetic compartmentalisation ]]> https://biorxiv.org/content/10.1101/2022.10.27.514093v1?rss=1 Sandor, A. Samalova, M. Brandizzi, F. Kriechbaumer, V. Moore, I. Fricker, M. D. Sweetlove, L. J. 2022-10-28 doi:10.1101/2022.10.27.514093 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Stereochemistry Determines Immune Cellular Responses to Polylactide Implants ]]> https://biorxiv.org/content/10.1101/2022.10.27.514118v1?rss=1 99% L-lactide (PLLA), > 99% D-lactide (PDLA) and a 50/50 melt-blend of PLLA and PDLA (stereocomplex PLA). Stereocomplex PLA breakdown products increased IL-1{beta}, TNF- and IL-6 protein levels but not MCP-1. Expression of these proinflammatory cytokines is mechanistically driven by increases in glycolysis in primary macrophages. In contrast, PLLA and PDLA degradation products selectively increase MCP-1 protein expression. Whereas both oxidative phosphorylation and glycolysis are increased with PDLA, only oxidative phosphorylation is increased with PLLA. For each biomaterial, glycolytic inhibition reduces proinflammatory cytokines and markedly increases anti-inflammatory (IL-10) protein levels; differential metabolic changes in fibroblasts were observed. These findings provide mechanistic explanations for the diverse immune responses to PLA of different stereochemistries, and underscore the pivotal role of immunometabolism on the biocompatibility of biomaterials applied in medicine. ]]> Maduka, C. V. Alhaj, M. Ural, E. Kuhnert, M. M. Habeeb, O. M. Schilmiller, A. L. Hankenson, K. D. Goodman, S. B. Narayan, R. Contag, C. H. 2022-10-28 doi:10.1101/2022.10.27.514118 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ What is an urban bird? Trait-based predictions of urban tolerance for the world's birds are modulated by latitude and human population density ]]> https://biorxiv.org/content/10.1101/2022.10.28.514262v1?rss=1 Neate-Clegg, M. H. C. Tonelli, B. A. Youngflesh, C. Wu, J. X. Montgomery, G. A. Sekercioglu, C. H. Tingley, M. W. 2022-10-28 doi:10.1101/2022.10.28.514262 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Irreversible inactivation of lactate racemase by sodium borohydride reveals reactivity of the nickel-pincer nucleotide cofactor ]]> https://biorxiv.org/content/10.1101/2022.11.09.515893v1?rss=1 Gatreddi, S. Sui, D. Hausinger, R. P. Hu, J. 2022-11-10 doi:10.1101/2022.11.09.515893 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ SUMO2 Protects Against Tau-induced Synaptic and Cognitive Dysfunction ]]> https://biorxiv.org/content/10.1101/2022.11.11.516192v1?rss=1 Orsini, F. Argyrousi, E. K. Restelli, E. Ford, L. K. Takamura, H. Matsuzaki, S. Zentilin, L. Pascente, R. Kanaan, N. M. Soni, R. Katayama, T. Chiesa, R. Forloni, G. Kosik, K. S. Kandel, E. R. Fraser, P. E. Arancio, O. Fioriti, L. 2022-11-13 doi:10.1101/2022.11.11.516192 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ The NDH complex reveals a trade-off that constrains maximising photosynthesis in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2022.11.13.516254v1?rss=1 Theeuwen, T. P. J. M. Lawson, A. W. Tijink, D. Fornaguera, F. Becker, F. F. M. Caracciolo, L. Fisher, N. Kramer, D. M. Wijnker, E. Harbinson, J. Aarts, M. G. M. 2022-11-13 doi:10.1101/2022.11.13.516254 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Plethora of QTLs found in Arabidopsis thaliana reveals complexity of genetic variation for photosynthesis in dynamic light conditions ]]> https://biorxiv.org/content/10.1101/2022.11.13.516256v1?rss=1 Theeuwen, T. P. J. M. Logie, L. L. Put, S. Bagheri, H. Losinski, K. Drouault, J. Flood, P. J. Hanhart, C. Becker, F. F. M. Wijfjes, R. Hall, D. Kramer, D. M. Harbinson, J. Aarts, M. G. M. 2022-11-13 doi:10.1101/2022.11.13.516256 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Integrative Teaching of Metabolic Modeling and Flux Analysis with Interactive Python Modules ]]> https://biorxiv.org/content/10.1101/2022.11.16.516820v1?rss=1 Kaste, J. A. M. Green, A. Shachar-Hill, Y. 2022-11-17 doi:10.1101/2022.11.16.516820 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Phosphatidylserine-exposing medium/large extracellular vesicles: potential cancer biomarkers ]]> https://biorxiv.org/content/10.1101/2022.11.17.516966v1?rss=1 Perez, G. I. Bernard, M. P. Vocelle, D. Zarea, A. A. Schneider, D. Bauzon, M. Hermiston, T. Kanada, M. 2022-11-17 doi:10.1101/2022.11.17.516966 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Approximating carbon fixation - how important is the Calvin-Benson cycle steady-state assumption? ]]> https://biorxiv.org/content/10.1101/2022.11.18.517021v1?rss=1 van Aalst, M. Ebenhoeh, O. Walker, B. J. 2022-11-20 doi:10.1101/2022.11.18.517021 Cold Spring Harbor Laboratory Press 2022-11-20 <![CDATA[ The Effect of Polymer Length in Phase Separation ]]> https://biorxiv.org/content/10.1101/2022.11.21.517354v1?rss=1 Valdes-Garcia, G. Gamage, K. Smith, C. Martirosova, K. Feig, M. Lapidus, L. 2022-11-21 doi:10.1101/2022.11.21.517354 Cold Spring Harbor Laboratory Press 2022-11-21 <![CDATA[ Mapping splice QTLs reveals distinct transcriptional and post-transcriptional regulatory variation of gene expression in pigs ]]> https://biorxiv.org/content/10.1101/2022.11.20.517281v1?rss=1 Zhang, F. Velez-Irizarry, D. Ernst, C. W. Huang, W. 2022-11-22 doi:10.1101/2022.11.20.517281 Cold Spring Harbor Laboratory Press 2022-11-22 <![CDATA[ MerCat2: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from omics data ]]> https://biorxiv.org/content/10.1101/2022.11.22.517562v1?rss=1 Figueroa, J. L. Panyala, A. Colby, S. Friesen, M. L. Tiemann, L. White, R. A. 2022-11-24 doi:10.1101/2022.11.22.517562 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Global Endometrial DNA Multi-omics Analysis Reveals Insights into mQTL Regulation and Associated Endometriosis Disease Risk ]]> https://biorxiv.org/content/10.1101/2022.11.27.518106v1?rss=1 Mortlock, S. Houshdaran, S. Kosti, I. Rahmioglu, N. Nezhat, C. Vitonis, A. F. Andrews, S. V. Grosjean, P. Paranjpe, M. Horne, A. W. Jacoby, A. Lager, J. Opoku-Anane, J. Vo, K. C. Manvelyan, E. Sen, S. Ghukasyan, Z. Collins, F. Santamaria, X. Saunders, P. Kober, K. McRae, A. F. Terry, K. L. Vallve-Juanico, J. Becker, C. Rogers, P. A. W. Irwin, J. C. Zondervan, K. Montgomery, G. W. Missmer, S. Sirota, M. Giudice, L. 2022-11-28 doi:10.1101/2022.11.27.518106 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ Triose phosphate utilization stress during photosynthesis addressed with dynamic assimilation measurements ]]> https://biorxiv.org/content/10.1101/2022.11.27.518113v1?rss=1 McClain, A. M. Sharkey, T. D. 2022-11-28 doi:10.1101/2022.11.27.518113 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ A putative design for electromagnetic activation of split proteins for molecular and cellular manipulation ]]> https://biorxiv.org/content/10.1101/2022.11.30.518522v1?rss=1 Grady, C. J. Schossau, J. Ashbaugh, R. C. Pelled, G. Gilad, A. A. 2022-11-30 doi:10.1101/2022.11.30.518522 Cold Spring Harbor Laboratory Press 2022-11-30 <![CDATA[ Evaluation of EV Storage Buffer for Efficient Preservation of Engineered Extracellular Vesicles ]]> https://biorxiv.org/content/10.1101/2022.12.06.519345v1?rss=1 Kawai-Harada, Y. Komuro, H. Harada, M. 2022-12-07 doi:10.1101/2022.12.06.519345 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ M-Band Wavelet-Based Imputation of scRNA-seq Matrix and Multi-view Clustering of Cell ]]> https://biorxiv.org/content/10.1101/2022.12.05.519090v1?rss=1 Liu, Z. Liu, T. Sun, W. Zhao, Y. Wang, X. 2022-12-08 doi:10.1101/2022.12.05.519090 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ Validation of Fuze IMU system for ergonomics assessments ]]> https://biorxiv.org/content/10.1101/2022.12.05.519202v1?rss=1 Serra-Hsu, E. Taboga, P. 2022-12-08 doi:10.1101/2022.12.05.519202 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ First Biodegradable Bioactive Glass-based Humidity Sensor ]]> https://biorxiv.org/content/10.1101/2022.12.06.519262v1?rss=1 Gharbi, A. Kallel, A. Y. Kanoun, O. Cheikhrouhou-Koubaa, W. H. Contag, C. Antoniac, I. Derbel, N. Ashammakhi, N. 2022-12-08 doi:10.1101/2022.12.06.519262 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ Proposed three-phenylalanine motif involved in magnetoreception signaling of an Actinopterygii protein expressed in mammalian cells ]]> https://biorxiv.org/content/10.1101/2022.12.08.519643v1?rss=1 View larger version (58K): org.highwire.dtl.DTLVardef@19a4f54org.highwire.dtl.DTLVardef@1ce17b2org.highwire.dtl.DTLVardef@175b97borg.highwire.dtl.DTLVardef@1e45294_HPS_FORMAT_FIGEXP M_FIG C_FIG In BriefEPG is a magnetoreceptive GPI anchored protein. Critical to its function is a three-phenylalanine motif which allows EPG to sense and respond to EMF. When expressed in mammalian cell, an increase in intracellular calcium is observed using GCaMP6m. This work represents progress towards understanding magnetoreception for use in future technologies. HighlightsO_LIEPG is associated to the cell membrane via glycosylphosphatidylinositol anchoring C_LIO_LIIn mammalian cells, EPG increases intracellular calcium upon EMF stimulation C_LIO_LIHomologs of EPG from the uPAR/Ly6 family show different responses to EMF C_LIO_LIA three-phenylalanine motif in EPG is critical to its magnetoreceptive ability C_LI ]]> Ricker, B. Mitra, S. Castellanos, E. A. Grady, C. J. Pelled, G. Gilad, A. 2022-12-09 doi:10.1101/2022.12.08.519643 Cold Spring Harbor Laboratory Press 2022-12-09 <![CDATA[ A genome-wide screen in macrophages identifies PTEN as required for myeloid restriction of Listeria monocytogenes infection ]]> https://biorxiv.org/content/10.1101/2022.12.12.520030v1?rss=1 Glover, R. C. Schwardt, N. H. Leano, S.-K. E. Sanchez, M. E. Thomason, M. K. Olive, A. J. Reniere, M. L. 2022-12-12 doi:10.1101/2022.12.12.520030 Cold Spring Harbor Laboratory Press 2022-12-12 <![CDATA[ Long COVID: G Protein-Coupled Receptors (GPCRs) responsible for persistent post-COVID symptoms ]]> https://biorxiv.org/content/10.1101/2022.12.12.520110v1?rss=1 Das, S. Kumar, S. 2022-12-13 doi:10.1101/2022.12.12.520110 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Exploring Viral Communities Associated With Terrestrial Cyanobacteria Metagenomes ]]> https://biorxiv.org/content/10.1101/2022.12.14.520320v1?rss=1 Ettinger, C. L. Paul, S. R. Flores, N. Ward, R. D. Pietrasiak, N. Stajich, J. E. 2022-12-14 doi:10.1101/2022.12.14.520320 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ A patterned human heart tube organoid model generated by pluripotent stem cell self-assembly ]]> https://biorxiv.org/content/10.1101/2022.12.16.519611v1?rss=1 Volmert, B. Aguirre, A. Riggs, A. Wang, F. Juhong, A. Kiselev, A. Kostina, A. O'Hern, C. Muniyandi, P. Wasserman, A. Huang, A. Lewis-Israeli, Y. Park, S. Qiu, Z. Zhou, C. 2022-12-19 doi:10.1101/2022.12.16.519611 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Varying molecular interactions explain crowder-dependent enzyme function of a viral protease ]]> https://biorxiv.org/content/10.1101/2022.12.16.520723v1?rss=1 Ostrowska, N. Feig, M. Trylska, J. 2022-12-19 doi:10.1101/2022.12.16.520723 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Persistent spectral theory-guided protein engineering ]]> https://biorxiv.org/content/10.1101/2022.12.18.520933v1?rss=1 Qiu, Y. Wei, G.-W. 2022-12-19 doi:10.1101/2022.12.18.520933 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ The K+ exchange antiporter 3 senses the chloroplast energy status to synchronize photosynthesis ]]> https://biorxiv.org/content/10.1101/2022.12.19.521033v1?rss=1 Uflewski, M. Rindfleisch, T. Korkmaz, K. Tietz, E. Mielke, S. Galvis, V. C. Duenschede, B. Luzarowski, M. Skirycz, A. Schwarzlaender, M. Strand, D. D. Hertle, A. P. Schuenemann, D. Walther, D. Wolff, M. Thalhammer, A. Armbruster, U. 2022-12-19 doi:10.1101/2022.12.19.521033 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ A genome-wide screen in macrophages defines host genes regulating the uptake of Mycobacterium abscessus. ]]> https://biorxiv.org/content/10.1101/2022.12.20.521338v1?rss=1 Gilliland, H. N. Beckman, O. K. Olive, A. J. 2022-12-21 doi:10.1101/2022.12.20.521338 Cold Spring Harbor Laboratory Press 2022-12-21 <![CDATA[ Techniques for Developing Reliable Machine Learning Classifiers Applied to Understanding and Predicting Protein:Protein Interaction Hot Spots ]]> https://biorxiv.org/content/10.1101/2022.12.26.521948v1?rss=1 Chen, J. Kuhn, L. A. Raschka, S. 2022-12-27 doi:10.1101/2022.12.26.521948 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ The search behavior of terrestrial mammals ]]> https://biorxiv.org/content/10.1101/2022.12.31.521874v1?rss=1 Noonan, M. J. Martinez-Garcia, R. Fleming, C. H. Garcia De Figueiredo, B. Ali, A. H. Attias, N. Belant, J. L. Beyer, D. E. Berteaux, D. Bidner, L. R. Boone, R. B. Boutin, S. Brito, J. Brown, M. Carter, A. Castellanos, A. Castellanos, F. X. Chitwood, M. C. Darlington, S. de la Torre, J. A. Dekker, J. DePerno, C. Droghini, A. Farhadinia, M. Fennessy, J. Fichtel, C. Ford, A. T. Gill, R. Goheen, J. Gustavo R. Oliveira-Santos, L. Hebblewhite, M. Hodges, K. E. Isbell, L. A. Janssen, R. Kappeler, P. M. Kays, R. Kaczensky, P. Kauffman, M. LaPoint, S. Lashley, M. 2023-01-03 doi:10.1101/2022.12.31.521874 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ A Novel Protein for the Bioremediation of Gadolinium Waste ]]> https://biorxiv.org/content/10.1101/2023.01.05.522788v1?rss=1 Lee, H. D. Grady, C. J. Krell, K. Strebeck, C. Good, N. M. Martinez-Gomez, N. C. Gilad, A. 2023-01-06 doi:10.1101/2023.01.05.522788 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Radiopaque Implantable Biomaterials for Nerve Repair ]]> https://biorxiv.org/content/10.1101/2023.01.05.522860v1?rss=1 Pawelec, K. M. Hix, J. M. L. Shapiro, E. M. 2023-01-06 doi:10.1101/2023.01.05.522860 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Durotaxis bridges phase transition as a function of tissue stiffness in vivo ]]> https://biorxiv.org/content/10.1101/2023.01.05.522913v1?rss=1 Zhu, M. Gu, B. Thomas, E. C. Tao, H. Yung, T. Zhang, K. Rossant, J. Sun, Y. Hopyan, S. 2023-01-06 doi:10.1101/2023.01.05.522913 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Gene Expression Changes in Cultured Reactive Rat Astrocyte Models and Comparison to Device-Associated Effects in the Brain ]]> https://biorxiv.org/content/10.1101/2023.01.06.522870v1?rss=1 Riggins, T. E. Whitsitt, Q. A. Saxena, A. Hunter, E. Hunt, B. Thompson, C. H. Moore, M. G. Purcell, E. K. 2023-01-08 doi:10.1101/2023.01.06.522870 Cold Spring Harbor Laboratory Press 2023-01-08 <![CDATA[ Incorporating Radiopacity into Implantable Polymeric Biomedical Devices for Clinical Radiological Monitoring ]]> https://biorxiv.org/content/10.1101/2023.01.06.523025v1?rss=1 Pawelec, K. M. Tu, E. Chakravarty, S. Hix, J. M. L. Buchanan, L. Kenney, L. Buchanan, F. Chatterjee, N. Das, S. Alessio, A. Shapiro, E. 2023-01-08 doi:10.1101/2023.01.06.523025 Cold Spring Harbor Laboratory Press 2023-01-08 <![CDATA[ The identification and analysis of meristematic mutations within the apple tree that developed the RubyMac sport mutation ]]> https://biorxiv.org/content/10.1101/2023.01.10.523380v1?rss=1 AT transitions, while the gene conversions showed the opposite bias for AT=>GC transitions suggesting that GC-biased gene conversions have the potential to counteract the AT-bias of de novo mutations. By comparing the gene expression patterns in fruit skins from mutant and wild-type branches, we found 56 differentially expressed genes including 18 that were involved in anthocyanin biosynthesis. While none of the differently expressed genes harbored a mutation, we found that some of the mutations affected the integrity of candidate genes in regions of the genome that were recently associated with natural variation in fruit coloration. ]]> Sun, H. Abeli, P. Campoy, J. A. Ruetjes, T. Krause, K. Jiao, W.-B. von Korff, M. Beaudry, R. Schneeberger, K. 2023-01-11 doi:10.1101/2023.01.10.523380 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ A chromosome-scale assembly for tetraploid sour cherry (Prunus cerasus L.) 'Montmorency' identifies three distinct ancestral Prunus genomes ]]> https://biorxiv.org/content/10.1101/2023.01.10.523438v1?rss=1 Goeckeritz, C. Z. Rhoades, K. E. Childs, K. L. Iezzoni, A. F. VanBuren, R. Hollender, C. A. 2023-01-11 doi:10.1101/2023.01.10.523438 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ nleval: A Python Toolkit for Generating Benchmarking Datasets for Machine Learning with Biological Networks ]]> https://biorxiv.org/content/10.1101/2023.01.10.523485v1?rss=1 Liu, R. Krishnan, A. 2023-01-12 doi:10.1101/2023.01.10.523485 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ Adrenomedullin 2/intermedin is a slow off-rate, long-acting endogenous agonist of theadrenomedullin2 G protein-coupled receptor ]]> https://biorxiv.org/content/10.1101/2023.01.13.523955v1?rss=1 Babin, K. M. Karim, J. A. Gordon, P. H. Lennon, J. Dickson, A. Pioszak, A. A. 2023-01-13 doi:10.1101/2023.01.13.523955 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts ]]> https://biorxiv.org/content/10.1101/2023.01.13.523990v1?rss=1 Hansen, Z. A. Vasco, K. A. Rudrik, J. T. Scribner, K. T. Zhang, L. Manning, S. D. 2023-01-14 doi:10.1101/2023.01.13.523990 Cold Spring Harbor Laboratory Press 2023-01-14 <![CDATA[ Long term anthropic management and associated loss of plant diversity deeply impact virome richness and composition of Poaceae communities ]]> https://biorxiv.org/content/10.1101/2023.01.12.523554v1?rss=1 Maclot, F. Debue, V. Malmstrom, C. M. Filloux, D. Roumagnac, P. Eck, M. Tamisier, L. Blouin, A. G. Candresse, T. Massart, S. 2023-01-15 doi:10.1101/2023.01.12.523554 Cold Spring Harbor Laboratory Press 2023-01-15 <![CDATA[ A century of sampling at an ecological preserve reveals declining diversity of wild bees ]]> https://biorxiv.org/content/10.1101/2023.01.15.524123v1?rss=1 Graham, K. K. Glaum, P. Hartert, J. Gibbs, J. Tucker, E. Isaacs, R. Valdovinos, F. S. 2023-01-18 doi:10.1101/2023.01.15.524123 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Three-dimensional imaging and quantification of mouse ovarian follicles via optical coherence tomography ]]> https://biorxiv.org/content/10.1101/2023.01.23.525192v1?rss=1 Amaral, M. M. Sun, A. Li, Y. Ren, C. Truong, A. B. Nigam, S. Jiao, Z. Wang, P. Zhou, C. 2023-01-23 doi:10.1101/2023.01.23.525192 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ The Impact of Species Tree Estimation Error on Cophylogenetic Reconstruction ]]> https://biorxiv.org/content/10.1101/2023.01.24.525446v1?rss=1 Zheng, J. Nishida, Y. Okrasinska, A. Bonito, G. M. Heath-Heckman, E. A. Liu, K. J. 2023-01-25 doi:10.1101/2023.01.24.525446 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ The Impact of Multiple Sequence Alignment Error on Phylogenetic Estimation under Variable-Across-Phylogeny Substitution Models ]]> https://biorxiv.org/content/10.1101/2023.01.24.525451v1?rss=1 Doko, R. Liu, K. J. 2023-01-25 doi:10.1101/2023.01.24.525451 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ The worldwide invasion history of a pest ambrosia beetle inferred using population genomics ]]> https://biorxiv.org/content/10.1101/2023.01.25.525497v1?rss=1 Urvois, T. Perrier, C. Roques, A. Saune, L. Courtin, C. Kajimura, H. Hulcr, J. Cognato, A. I. Auger-Rozenberg, M.-A. Kerdelhue, C. 2023-01-25 doi:10.1101/2023.01.25.525497 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ Identification of genes associated with abiotic stress tolerance in sweetpotato using weighted gene co-expression network analysis ]]> https://biorxiv.org/content/10.1101/2023.01.30.526063v1?rss=1 Kitavi, M. N. Gemenet, D. C. Wood, J. Hamilton, J. Wu, S. Fei, Z. C. Khan, A. Buell, C. R. 2023-01-31 doi:10.1101/2023.01.30.526063 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Three dominant Vibrio cholerae lytic phage all require O1 antigen for infection ]]> https://biorxiv.org/content/10.1101/2023.01.31.526503v1?rss=1 Beckman, D. A. Waters, C. M. 2023-01-31 doi:10.1101/2023.01.31.526503 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Evolution of a fatty acyl-CoA elongase underlies desert adaptation in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.02.04.527143v1?rss=1 Wang, Z. Pu, J. Richards, C. Giannetti, E. Cong, H. Lin, Z. Chung, H. 2023-02-05 doi:10.1101/2023.02.04.527143 Cold Spring Harbor Laboratory Press 2023-02-05 <![CDATA[ A Cas9-fusion proximity-based approach generates an Irak1-Mecp2 tandem duplication mouse model for the study of MeCP2 duplication syndrome. ]]> https://biorxiv.org/content/10.1101/2023.02.07.527511v1?rss=1 Maino, E. Scott, O. Rizvi, S. Z. Visuvanathan, S. Ben Zablah, Y. Li, H. Sengar, A. S. Salter, M. W. Jia, Z. Rossant, J. Cohn, R. D. Gu, B. Ivakine, E. A. 2023-02-07 doi:10.1101/2023.02.07.527511 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ Pumping Iron: A Multi-omics Analysis of Two Extremophilic Algae Reveals Mechanisms of Iron Economy ]]> https://biorxiv.org/content/10.1101/2023.02.09.527888v1?rss=1 Davidi, L. Gallaher, S. D. Ben-David, E. Purvine, S. O. Fillmore, T. L. Nicora, C. D. Craig, R. J. Schmollinger, S. Roje, S. Blaby-Haas, C. E. Auber, R. P. Wisecaver, J. Merchant, S. S. 2023-02-09 doi:10.1101/2023.02.09.527888 Cold Spring Harbor Laboratory Press 2023-02-09 <![CDATA[ Protein Fitness Prediction is Impacted by the Interplay of Language Models, Ensemble Learning, and Sampling Methods ]]> https://biorxiv.org/content/10.1101/2023.02.09.527362v1?rss=1 Mardikoraem, M. Woldring, D. 2023-02-10 doi:10.1101/2023.02.09.527362 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Time to lysis determines phage sensitivity to a cytidine deaminase toxin/antitoxin bacterial defense system ]]> https://biorxiv.org/content/10.1101/2023.02.09.527960v1?rss=1 Hsueh, B. Y. Sanath-Kumar, R. Bedore, A. M. Waters, C. M. 2023-02-10 doi:10.1101/2023.02.09.527960 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Rapid lethality of mice lacking the phagocyte oxidase and Caspase1/11 following Mycobacterium tuberculosis infection. ]]> https://biorxiv.org/content/10.1101/2023.02.08.527787v1?rss=1 Thomas, S. M. Olive, A. J. 2023-02-11 doi:10.1101/2023.02.08.527787 Cold Spring Harbor Laboratory Press 2023-02-11 <![CDATA[ Efficient megakaryopoiesis and platelet production require phospholipid remodeling and PUFA uptake through CD36 ]]> https://biorxiv.org/content/10.1101/2023.02.12.527706v1?rss=1 Barrachina, M. N. Pernes, G. Becker, I. C. Allaeys, I. Hirsch, T. I. Groeneveld, D. J. Khan, A. O. Freire, D. Guo, K. Carminita, E. Morgan, P. K. Collins, T. J. Mellett, N. Wei, Z. Almazni, I. Italiano, J. E. Luyendyk, J. Meikle, P. J. Puder, M. Morgan, N. V. Boilard, E. Murphy, A. J. Machlus, K. R. 2023-02-12 doi:10.1101/2023.02.12.527706 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ PyBrOpS: a Python package for breeding program simulation and optimization for multi-objective breeding ]]> https://biorxiv.org/content/10.1101/2023.02.10.528043v1?rss=1 Shrote, R. Z. Thompson, A. M. 2023-02-13 doi:10.1101/2023.02.10.528043 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ Cysteine-Rich Intestinal Protein 1 is a Novel Surface Marker for Myometrial Stem/Progenitor Cells. ]]> https://biorxiv.org/content/10.1101/2023.02.20.529273v1?rss=1 Paul, E. N. Carpenter, T. J. Fitch, S. Sheridan, R. Lau, K. H. Arora, R. Teixeira, J. M. 2023-02-21 doi:10.1101/2023.02.20.529273 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Piscichuviral encephalitis in marine and freshwater chelonians: first evidence of jingchuviral disease ]]> https://biorxiv.org/content/10.1101/2023.02.24.528524v1?rss=1 Laovechprasit, W. Young, K. Stacy, B. A. Tillis, S. B. Ossiboff, R. J. Vann, J. A. Subramaniam, K. Agnew, D. Zhang, J. Whitaker, S. Walker, A. Orgill, A. M. Howell, L. N. Shaver, D. J. Stanton, J. B. 2023-02-27 doi:10.1101/2023.02.24.528524 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Identification of anti-fungal bioactive terpenoids from the bioenergy crop switchgrass (Panicum virgatum) ]]> https://biorxiv.org/content/10.1101/2023.02.24.529965v1?rss=1 Li, X. Chou, M.-Y. Bonito, G. M. Last, R. L. 2023-02-27 doi:10.1101/2023.02.24.529965 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Bulk RNA-Sequencing of small airway cell cultures from IPF and post-COVID lung fibrosis patients illustrates disease signatures and differential responses to TGF-β1 treatment ]]> https://biorxiv.org/content/10.1101/2023.03.01.530431v1?rss=1 Uhl, K. Paithankar, S. Leshchiner, D. Jager, T. Abdelgied, M. Tripp, K. Peraino, A. Kakazu, M. Lawson, C. Chesla, D. Prokop, J. Chen, B. Murphy, E. Girgis, R. Li, X. 2023-03-01 doi:10.1101/2023.03.01.530431 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ A Vibrio cholerae viral satellite maximizes its spread and inhibits phage by remodeling hijacked phage coat proteins into small capsids ]]> https://biorxiv.org/content/10.1101/2023.03.01.530633v1?rss=1 Boyd, C. M. Subramanian, S. Dunham, D. T. Parent, K. N. Seed, K. D. 2023-03-01 doi:10.1101/2023.03.01.530633 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Cat LCA-CRX model, homozygous for an antimorphic mutation has a unique phenotype ]]> https://biorxiv.org/content/10.1101/2023.03.01.530650v1?rss=1 Occelli, L. M. Tran, N. M. Chen, S. Petersen-Jones, S. M. 2023-03-02 doi:10.1101/2023.03.01.530650 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ A critical role of a eubiotic microbiota in gating proper immunocompetence in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2023.03.02.527037v1?rss=1 Paasch, B. C. Sohrabi, R. Kremer, J. M. Nomura, K. Martz, J. Kvitko, B. Tiedje, J. M. He, S. Y. 2023-03-02 doi:10.1101/2023.03.02.527037 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Epigenomic divergence underlies sequence polymorphism and the evolutionary fate of duplicate paralogs in A. thaliana. ]]> https://biorxiv.org/content/10.1101/2023.03.02.530917v1?rss=1 Kenchanmane Raju, S. K. Lensink, M. Kliebenstein, D. J. Niederhuth, C. Monroe, G. 2023-03-03 doi:10.1101/2023.03.02.530917 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Respiration is essential for aerobic growth of Zymomonas mobilis ZM4 ]]> https://biorxiv.org/content/10.1101/2023.03.02.530925v1?rss=1 Felczak, M. M. TerAvest, M. A. 2023-03-03 doi:10.1101/2023.03.02.530925 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Litter Matters: The Importance of Decomposition Products for Soil Bacterial Diversity and abundance of key groups of the N cycle in Tropical Areas ]]> https://biorxiv.org/content/10.1101/2023.03.03.530969v1?rss=1 Diniz, P. P. Borges, B. M. F. Oliveira, A. P. d. Coelho, M. R. Aragao, O. O. d. S. Ribeiro, T. G. Rocha, F. I. Coelho, M. R. R. Dias, E. S. Cole, J. R. R. Howe, A. C. Mui, T. S. Jesus, E. d. C. 2023-03-04 doi:10.1101/2023.03.03.530969 Cold Spring Harbor Laboratory Press 2023-03-04 <![CDATA[ Roles of microbiota in autoimmunity in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2023.03.06.531303v1?rss=1 Cheng, Y. T. Thireault, C. A. Paasch, B. C. Zhang, L. He, S. Y. 2023-03-07 doi:10.1101/2023.03.06.531303 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Targeted development of diagnostic SNP markers for resistance to Fusarium wilt race 4 in Upland cotton (Gossypium hirsutum) ]]> https://biorxiv.org/content/10.1101/2023.03.06.531315v1?rss=1 Zhang, J. Zhu, Y. Wheeler, T. Dever, J. Hake, K. Bissonnette, K. 2023-03-07 doi:10.1101/2023.03.06.531315 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Development of a Synthetic Biosensor for Chemical Exchange MRI Utilizing In Silico Optimized Peptides ]]> https://biorxiv.org/content/10.1101/2023.03.08.531737v1?rss=1 Fillion, A. J. Bricco, A. R. Lee, H. D. Korenchan, D. Farrar, C. T. Gilad, A. A. 2023-03-08 doi:10.1101/2023.03.08.531737 Cold Spring Harbor Laboratory Press 2023-03-08 <![CDATA[ Analysis of histone antibody specificity directly in sequencing data using siQ-ChIP ]]> https://biorxiv.org/content/10.1101/2023.03.08.531745v1?rss=1 Kupai, A. Vaughan, R. M. Rothbart, S. B. Dickson, B. M. 2023-03-08 doi:10.1101/2023.03.08.531745 Cold Spring Harbor Laboratory Press 2023-03-08 <![CDATA[ Pathology of natural infection with highly pathogenic avian influenza virus (H5N1) clade 2.3.4.4b in wild terrestrial mammals in the United States in 2022 ]]> https://biorxiv.org/content/10.1101/2023.03.10.532068v1?rss=1 Elsmo, E. J. Wunschmann, A. Beckmen, K. B. Broughton-Neiswanger, L. B. Buckles, E. L. Ellis, J. Fitzgerald, S. D. Gerlach, R. Hawkins, S. Ip, H. Lankton, J. Lemley, E. M. Lenoch, J. Killian, M. L. Lantz, K. Long, L. Maes, R. Mainenti, M. Melotti, J. Moriarty, M. E. Nakagun, S. Ruden, R. M. Shearn-Bochsler, V. Thompson, D. Torchetti, M. K. Van Wettere, A. J. Wise, A. G. Lim, A. 2023-03-12 doi:10.1101/2023.03.10.532068 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Modulation of Polar Auxin Transport Identifies the Molecular Determinants of Source-Sink Carbon Relationships and Sink Strength in Poplar ]]> https://biorxiv.org/content/10.1101/2023.03.12.532247v1?rss=1 Balasubramanian, V. K. Rivas-Ubach, A. Winkler, T. Mitchell, H. Moran, J. Ahkami, A. H. 2023-03-13 doi:10.1101/2023.03.12.532247 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ Cysteine: an ancestral Cu binding ligand in green algae? ]]> https://biorxiv.org/content/10.1101/2023.03.15.532757v1?rss=1 Strenkert, D. Schmollinger, S. Hu, Y. Hofmann, C. Holbrook, K. Liu, H. W. Purvine, S. O. Nicora, C. D. Chen, S. Lipton, M. S. Northen, T. R. Clemens, S. Merchant, S. S. 2023-03-15 doi:10.1101/2023.03.15.532757 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Distribution of blaCTX-M-gene variants in E. coli from different origins in Ecuador ]]> https://biorxiv.org/content/10.1101/2023.03.15.532797v1?rss=1 Valenzuela, X. Hedman, H. Villagomez, A. Cardenas, P. A. Eisenberg, J. Levy, K. Zhang, L. Trueba, G. 2023-03-15 doi:10.1101/2023.03.15.532797 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Division of labor promotes the entrenchment of multicellularity ]]> https://biorxiv.org/content/10.1101/2023.03.15.532780v1?rss=1 Conlin, P. L. Goldsby, H. J. Libby, E. Skocelas, K. G. Ratcliff, W. C. Ofria, C. Kerr, B. 2023-03-16 doi:10.1101/2023.03.15.532780 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ RHINO restricts MMEJ activity to mitosis ]]> https://biorxiv.org/content/10.1101/2023.03.16.532763v1?rss=1 Sfeir, A. Brambati, A. Sacco, O. Porcella, S. Heyza, J. R. Kareh, M. Schmidt, J. C. 2023-03-16 doi:10.1101/2023.03.16.532763 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ Time-resolved molecular measurements reveal changes in astronauts during spaceflight ]]> https://biorxiv.org/content/10.1101/2023.03.17.530234v1?rss=1 Zheng, M. Charvat, J. Zwart, S. R. Mehta, S. Crucian, B. E. Smith, S. M. He, J. Piermarocchi, C. Mias, G. I. 2023-03-18 doi:10.1101/2023.03.17.530234 Cold Spring Harbor Laboratory Press 2023-03-18 <![CDATA[ Astrocytes control cocaine-induced synaptic plasticity and reward through the matricellular protein hevin ]]> https://biorxiv.org/content/10.1101/2023.03.19.533284v1?rss=1 Mongredien, R. Anesio, A. Fernandes, G. J. D. Eagle, A. L. Maldera, S. Pham, C. Vilette, A. Bianchi, P. C. Franco, C. Louis, F. Gruszczynski, C. Betancur, C. Erdozain, A. M. Robison, A. J. Boucard, A. A. Li, D. J. Cruz, F. C. Gautron, S. Heck, N. Vialou, V. 2023-03-19 doi:10.1101/2023.03.19.533284 Cold Spring Harbor Laboratory Press 2023-03-19 <![CDATA[ Uncovering the Environmental Conditions Required for Phyllachora maydis Infection and Tar Spot Development on Corn in the United States for Use as Predictive Models for Future Epidemics ]]> https://biorxiv.org/content/10.1101/2023.03.18.533264v1?rss=1 Webster, R. W. Nicolli, C. Allen, T. W. Bish, M. D. Bissonette, K. Check, J. C. Chilvers, M. I. Kleczewski, N. Mueller, B. D. Price, P. P. Paul, P. Robertson, A. E. Ross, T. J. Schmidt, C. Schmidt, R. Schmidt, T. Shim, S. Telenko, D. E. P. Wise, K. Smith, D. L. 2023-03-21 doi:10.1101/2023.03.18.533264 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Capturing Spatiotemporal Signaling Patterns in Cellular Data with Geometric Scattering Trajectory Homology ]]> https://biorxiv.org/content/10.1101/2023.03.22.533807v1?rss=1 Bhaskar, D. Moore, J. L. Gao, F. Rieck, B. Khasawneh, F. Munch, E. Greco, V. Krishnaswamy, S. 2023-03-24 doi:10.1101/2023.03.22.533807 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus. ]]> https://biorxiv.org/content/10.1101/2023.03.22.533842v1?rss=1 Mansfeld, B. N. Yocca, A. Ou, S. Harkess, A. Burchard, E. Gutierrez, B. van Nocker, S. Gottschalk, C. 2023-03-24 doi:10.1101/2023.03.22.533842 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Integrative multi-omic sequencing reveals the MMTV-Myc mouse model mimics human breast cancer heterogeneity ]]> https://biorxiv.org/content/10.1101/2023.03.28.534611v1?rss=1 Broeker, C. Ortiz, M. Murillo, M. Andrechek, E. 2023-03-29 doi:10.1101/2023.03.28.534611 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Vasopressin regulates social play behavior in sex-specific ways through glutamate modulation in the lateral septum ]]> https://biorxiv.org/content/10.1101/2023.03.31.535148v1?rss=1 Bredewold, R. Washington, C. Veenema, A. 2023-03-31 doi:10.1101/2023.03.31.535148 Cold Spring Harbor Laboratory Press 2023-03-31 <![CDATA[ Activation of a Vibrio cholerae CBASS anti-phage system by quorum sensing and folate depletion ]]> https://biorxiv.org/content/10.1101/2023.04.04.535582v1?rss=1 Severin, G. B. Ramliden, M. S. Ford, K. C. Van Alst, A. J. Sanath-Kumar, R. Decker, K. A. Hsueh, B. Y. Yoon, S. H. Demey, L. M. O'Hara, B. J. Rhoades, C. R. DiRita, V. J. Ng, W. L. Waters, C. M. 2023-04-04 doi:10.1101/2023.04.04.535582 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ SpatialCTD: a large-scale TME spatial transcriptomic dataset to evaluate cell type deconvolution for immuno-oncology ]]> https://biorxiv.org/content/10.1101/2023.04.11.536333v1?rss=1 Ding, J. Venegas, J. Lu, Q. Wang, Y. Wu, L. Jin, W. Wen, H. Liu, R. Tang, W. Li, Z. Zuo, W. Chang, Y. Lei, Y. Danaher, P. Xie, Y. Tang, J. 2023-04-12 doi:10.1101/2023.04.11.536333 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ Cross regulation in a three-component cell envelope stress signaling system ]]> https://biorxiv.org/content/10.1101/2023.04.15.536747v1?rss=1 Chen, X. Aalakavuklar, M. Fiebig, A. Crosson, S. 2023-04-15 doi:10.1101/2023.04.15.536747 Cold Spring Harbor Laboratory Press 2023-04-15 <![CDATA[ Structural Organization of the Cell Wall of Halophilic Fungi ]]> https://biorxiv.org/content/10.1101/2023.04.15.537024v1?rss=1 Fernando, L. D. Perez-Llano, Y. Dickwella Widanage, M. C. Martinez-Avila, L. Lipton, A. S. Gunde-Cimerman, N. Latge, J.-P. Batista-Garcia, R. A. Wang, T. 2023-04-15 doi:10.1101/2023.04.15.537024 Cold Spring Harbor Laboratory Press 2023-04-15 <![CDATA[ Conserved enhancer logic controls the notochord expression of vertebrate Brachyury ]]> https://biorxiv.org/content/10.1101/2023.04.20.536761v1?rss=1 Kemmler, C. L. Smolikova, J. Moran, H. R. Mannion, B. J. Knapp, D. Lim, F. Czarkwiani, A. Hermosilla Aguayo, V. Rapp, V. Fitch, O. E. Boetschi, S. Selleri, L. Farley, E. Braasch, I. Yun, M. Visel, A. Osterwalder, M. Mosimann, C. Kozmik, Z. Burger, A. 2023-04-20 doi:10.1101/2023.04.20.536761 Cold Spring Harbor Laboratory Press 2023-04-20 <![CDATA[ High-resolution structure of a mercury cross-linked ZIP metal transporter reveals delicate motions and metal relay for regulated zinc transport ]]> https://biorxiv.org/content/10.1101/2023.04.20.537755v1?rss=1 Zhang, T. Zhang, Y. Sui, D. Hu, J. 2023-04-21 doi:10.1101/2023.04.20.537755 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ Genetic basis of aposematic coloration in a mimetic radiation of poison frogs ]]> https://biorxiv.org/content/10.1101/2023.04.20.537757v1?rss=1 Linderoth, T. Aguilar-Gomez, D. White, E. Twomey, E. Stuckert, A. Bi, K. Ko, A. Graham, N. Rocha, J. L. Chang, J. MacManes, M. D. Summers, K. Nielsen, R. 2023-04-21 doi:10.1101/2023.04.20.537757 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ Phylogeny, morphology, virulence, ecology, and host range of Ordospora pajunii (Ordosporidae),a microsporidian symbiont of Daphnia spp. ]]> https://biorxiv.org/content/10.1101/2023.04.21.537887v1?rss=1 Dziuba, M. K. McIntire, K. M. Seto, K. Davenport, E. S. Rogalski, M. A. Gowler, C. D. Baird, E. Vaandrager, M. Huerta, C. Jaye, R. Corcoran, F. E. Withrow, A. Ahrendt, S. Salamov, A. Nolan, M. Tejomurthula, S. Barry, K. Grigoriev, I. James, T. Duffy, M. A. 2023-04-24 doi:10.1101/2023.04.21.537887 Cold Spring Harbor Laboratory Press 2023-04-24 <![CDATA[ Adaptation invariant concentration discrimination in an insect olfactory system ]]> https://biorxiv.org/content/10.1101/2023.05.10.540073v1?rss=1 Ling, D. Zhang, L. Saha, D. Chen, A. B. Raman, B. 2023-05-11 doi:10.1101/2023.05.10.540073 Cold Spring Harbor Laboratory Press 2023-05-11 <![CDATA[ Multi-omics analysis of a Bacteroides fragilis isolate from an ulcerative colitis patient defines genetic determinants of fitness in bile ]]> https://biorxiv.org/content/10.1101/2023.05.11.540287v1?rss=1 50% of the population in ulcerative colitis (UC) patients experiencing inflammation. The mechanisms underlying such microbial blooms are poorly understood, but the gut of UC patients has physicochemical features that differ from healthy patients and likely impact microbial physiology. For example, levels of the secondary bile acid deoxycholate (DC) are highly reduced in the ileoanal J-pouch of UC colectomy patients. We isolated a B. fragilis strain from a UC patient with pouch inflammation (i.e. pouchitis) and developed it as a genetic model system to identify genes and pathways that are regulated by DC and that impact B. fragilis fitness in DC and crude bile. Treatment of B. fragilis with a physiologically relevant concentration of DC reduced cell growth and remodeled transcription of one-quarter of the genome. DC strongly induced expression of chaperones and select transcriptional regulators and efflux systems and downregulated protein synthesis genes. Using a barcoded collection of {approx}50,000 unique insertional mutants, we further defined B. fragilis genes that contribute to fitness in media containing DC or crude bile. Genes impacting cell envelope functions including cardiolipin synthesis, cell surface glycosylation, and systems implicated in sodium-dependent bioenergetics were major bile acid fitness factors. As expected, there was limited overlap between transcriptionally regulated genes and genes that impacted fitness in bile when disrupted. Our study provides a genome-scale view of a B. fragilis bile response and genetic determinants of its fitness in DC and crude bile. ImportanceThe Gram-negative bacterium, Bacteroides fragilis, is a common member of the human gut microbiota that colonizes multiple host niches and can influence human physiology through a variety of mechanisms. Identification of genes that enable B. fragilis to grow across a range of host environments has been impeded in part by the relatively limited genetic tractability of this species. We have developed a high-throughput genetic resource for a B. fragilis strain isolated from a UC pouchitis patient. Bile acids limit microbial growth and are altered in abundance in UC pouches, where B. fragilis often blooms. Using this resource, we uncovered pathways and processes that impact B. fragilis fitness in bile and that may contribute to population expansions during bouts of gut inflammation. ]]> Fiebig, A. Schnizlein, M. Pena-Rivera, S. Trigodet, F. Dubey, A. Hennessy, M. Basu, A. Pott, S. Dalal, S. Rubin, D. Sogin, M. Eren, A. M. Chang, E. Crosson, S. 2023-05-11 doi:10.1101/2023.05.11.540287 Cold Spring Harbor Laboratory Press 2023-05-11 <![CDATA[ SMYD5 is a novel epigenetic gatekeeper of the mild hypothermia response ]]> https://biorxiv.org/content/10.1101/2023.05.11.540170v1?rss=1 Rafnsdottir, S. Jang, K. Halldorsdottir, S. T. Tomasdottir, A. Vinod, M. Moller, K. Reynisdottir, T. Atladottir, L. H. Allison, K. E. He, J. Zhang, L. Northington, F. J. Chavez-Valdez, R. Anderson, K. J. Bjornsson, H. 2023-05-14 doi:10.1101/2023.05.11.540170 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Quantitative flow cytometric selection of tau conformational nanobodies specific for pathological aggregates ]]> https://biorxiv.org/content/10.1101/2023.05.13.540640v1?rss=1 Zupancic, J. M. Smith, M. D. Trzeciakiewicz, H. Skinner, M. E. Ferris, S. P. Makowski, E. K. Lucas, M. J. McArthur, N. Kane, R. S. Paulson, H. L. Tessier, P. M. 2023-05-14 doi:10.1101/2023.05.13.540640 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ P-tau Inflicts Intracellular Stress Responses That Are Mitigated by Apomorphine ]]> https://biorxiv.org/content/10.1101/2023.05.13.540661v1?rss=1 Song, Z. Wang, K.-W. Hagar, H.-T. C. Chen, H.-R. Kuan, C.-Y. Zhang, K. Kuo, M.-H. 2023-05-14 doi:10.1101/2023.05.13.540661 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Retinoblastoma protein activity revealed by CRISPRi study of divergent Rbf1 and Rbf2 paralogs ]]> https://biorxiv.org/content/10.1101/2023.05.19.541454v1?rss=1 Raicu, A.-M. Castanheira, P. H. Arnosti, D. N. 2023-05-19 doi:10.1101/2023.05.19.541454 Cold Spring Harbor Laboratory Press 2023-05-19 <![CDATA[ A regulatory role for the unstructured C-terminal domain of the CtBP transcriptional corepressor ]]> https://biorxiv.org/content/10.1101/2023.05.19.541472v1?rss=1 Raicu, A.-M. Suresh, M. Arnosti, D. N. 2023-05-20 doi:10.1101/2023.05.19.541472 Cold Spring Harbor Laboratory Press 2023-05-20 <![CDATA[ Plasmid-free cheater cells commonly evolve during laboratory growth ]]> https://biorxiv.org/content/10.1101/2023.05.19.541508v1?rss=1 Bedore, A. M. Waters, C. M. 2023-05-20 doi:10.1101/2023.05.19.541508 Cold Spring Harbor Laboratory Press 2023-05-20 <![CDATA[ Nighthawk: acoustic monitoring of nocturnal bird migration in the Americas ]]> https://biorxiv.org/content/10.1101/2023.05.22.541336v1?rss=1 Van Doren, B. M. Farnsworth, A. Stone, K. Osterhaus, D. M. Drucker, J. Van Horn, G. 2023-05-23 doi:10.1101/2023.05.22.541336 Cold Spring Harbor Laboratory Press 2023-05-23 <![CDATA[ One particle per residue is sufficient to describe all-atom protein structures ]]> https://biorxiv.org/content/10.1101/2023.05.22.541652v1?rss=1 Heo, L. Feig, M. 2023-05-23 doi:10.1101/2023.05.22.541652 Cold Spring Harbor Laboratory Press 2023-05-23 <![CDATA[ Long-range repression by ecdysone receptor on complex enhancers of the insulin receptor gene. ]]> https://biorxiv.org/content/10.1101/2023.05.23.541945v1?rss=1 Thompson, K. Suber, W. Nicholas, R. Arnosti, D. 2023-05-23 doi:10.1101/2023.05.23.541945 Cold Spring Harbor Laboratory Press 2023-05-23 <![CDATA[ The transcription factor OsbZIP48 governs rice responses to zinc deficiency ]]> https://biorxiv.org/content/10.1101/2023.05.18.541251v1?rss=1 Zheng, L. Hu, S. Du, B. Mu, G. jiang, Z. Li, H. Song, Y. Zhang, B. Xia, J. Rouached, H. 2023-05-24 doi:10.1101/2023.05.18.541251 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ The phycobilisome linker protein ApcG interacts with photosystem II and regulates energy transfer to photosystem I in Synechocystis sp. PCC 6803 ]]> https://biorxiv.org/content/10.1101/2023.05.22.541798v1?rss=1 espinoza-corral, R. Iwai, M. Zavrel, T. Lechno-Yossef, S. Sutter, M. Cerveny, J. Niyogi, K. K. Kerfeld, C. 2023-05-24 doi:10.1101/2023.05.22.541798 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Urbanisation generates multiple trait syndromes for terrestrial taxa worldwide ]]> https://biorxiv.org/content/10.1101/2023.05.24.541105v1?rss=1 Hahs, A. K. Fournier, B. Aronson, M. F. J. Nilon, C. H. Herrera-Montes, A. Salisbury, A. Threlfall, C. G. Rega-Brodsky, C. C. Lepczyk, C. A. La Sorte, F. A. MacGregor-Fors, I. MacIvor, J. S. Jung, K. Piana, M. R. Williams, N. S. G. Knapp, S. Acevedo, A. A. Gainsbury, A. M. Rainho, A. Hamer, A. J. Shwartz, A. Voigt, C. C. Lewanzik, D. Lowenstein, D. M. O'Brien, D. Tommasi, D. Pineda, E. Sita Carpenter, E. Belskaya, E. Lovei, G. Makinson, J. C. Castaneda-Oviedo, J. Coleman, J. Sadler, J. P. Shroyer, J. Shapiro, J. T. Baldock, K. C. R. Ksiazek-Mikenas, K. Mat 2023-05-24 doi:10.1101/2023.05.24.541105 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Liquid plug propagation in computer-controlled microfluidic airway-on-a-chip with semi-circular microchannels ]]> https://biorxiv.org/content/10.1101/2023.05.24.542177v1?rss=1 Viola, H. Vasani, V. Washington, K. Lee, J. H. Selva, C. Li, A. Llorente, C. J. Murayama, Y. Grotberg, J. B. Romano, F. Takayama, S. 2023-05-25 doi:10.1101/2023.05.24.542177 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Extensive DNA methylome rearrangement during early lamprey embryogenesis ]]> https://biorxiv.org/content/10.1101/2023.05.25.542242v1?rss=1 30% of the embryonic genome and is predominantly associated with partially methylated domains (PMDs). We further demonstrate that sequences eliminated during programmed genome rearrangement (PGR), a hallmark of lamprey embryogenesis, are hypermethylated in sperm prior to the onset of PGR. Our study thus unveils important insights into the evolutionary origins of vertebrate 5mC reprogramming, and how this process might participate in diverse developmental strategies. ]]> Angeloni, A. Fissette, S. Kaya, D. Hammond, J. M. Gamaarachchi, H. Deveson, I. W. Klose, R. J. Li, W. Zhang, X. Bogdanovic, O. 2023-05-25 doi:10.1101/2023.05.25.542242 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Accounting for active populations provides a new perspective on the degree and mechanisms of soil microbiome resilience ]]> https://biorxiv.org/content/10.1101/2023.05.25.542271v1?rss=1 Barnett, S. E. Shade, A. 2023-05-25 doi:10.1101/2023.05.25.542271 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Defying Gravity: WEEP promotes negative gravitropism in Prunus persica (peach) shoots and roots by establishing asymmetric auxin gradients ]]> https://biorxiv.org/content/10.1101/2023.05.26.542472v1?rss=1 Kohler, A. R. Scheil, A. Hill, J. L. Allen, J. R. Al-Haddad, J. M. Goeckeritz, C. Z. Strader, L. C. Telewski, F. W. Hollender, C. A. 2023-05-28 doi:10.1101/2023.05.26.542472 Cold Spring Harbor Laboratory Press 2023-05-28 <![CDATA[ Kit Ligand and Kit receptor tyrosine kinase sustain synaptic inhibition of Purkinje Cells ]]> https://biorxiv.org/content/10.1101/2023.05.30.542885v1?rss=1 View larger version (54K): org.highwire.dtl.DTLVardef@1d53d9eorg.highwire.dtl.DTLVardef@c05c4borg.highwire.dtl.DTLVardef@eb58eeorg.highwire.dtl.DTLVardef@11b8431_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Zaman, T. Vogt, D. Prokop, J. Alsabia, Q. A. Simms, G. Stafford, A. Luikart, B. Williams, M. R. 2023-05-30 doi:10.1101/2023.05.30.542885 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ Lipid Bilayer Strengthens the Cooperative Network of a Membrane-Integral Enzyme ]]> https://biorxiv.org/content/10.1101/2023.05.30.542905v1?rss=1 Muhammednazaar, S. Yao, J. Guo, R. Rhee, M. S. Kim, K. H. Kang, S.-g. Hong, H. 2023-05-31 doi:10.1101/2023.05.30.542905 Cold Spring Harbor Laboratory Press 2023-05-31 <![CDATA[ CRISPRi-TnSeq: A genome-wide high-throughput tool for bacterial essential-nonessential genetic interaction mapping ]]> https://biorxiv.org/content/10.1101/2023.05.31.543074v1?rss=1 van Opijnen, T. Jana, B. Liu, X. Denereaz, J. Park, H. Leshchiner, D. Liu, B. Gallay, C. Veening, J.-W. 2023-06-01 doi:10.1101/2023.05.31.543074 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Accelerometer-based predictions of behaviour elucidate factors affecting the daily activity patterns of spotted hyenas ]]> https://biorxiv.org/content/10.1101/2023.05.31.543053v1?rss=1 Minasandra, P. Jensen, F. H. Gersick, A. S. Holekamp, K. E. Strauss, E. D. Strandburg-Peshkin, A. 2023-06-03 doi:10.1101/2023.05.31.543053 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ Trading acyls and swapping sugars: metabolic innovations in Solanum trichomes ]]> https://biorxiv.org/content/10.1101/2023.06.05.542877v1?rss=1 1200 species in the phenotypically megadiverse Solanum genus, with a handful containing inositol and glycosylated inositol cores. The current study sampled several dozen species across subclades of the Solanum to get a more detailed view of acylsugar chemodiversity. In depth characterization of acylsugars from the Clade II species Solanum melongena (brinjal eggplant) led to the identification of eight unusual structures with inositol or inositol glycoside cores, and hydroxyacyl chains. Liquid chromatography-mass spectrometry analysis of 31 additional species in the Solanum genus revealed striking acylsugar diversity with some traits restricted to specific clades and species. Acylinositols and inositol-based acyldisaccharides were detected throughout much of the genus. In contrast, acylglucoses and acylsucroses were more restricted in distribution. Analysis of tissue-specific transcriptomes and interspecific acylsugar acetylation differences led to the identification of the S. melongena AcylSugar AcylTransferase 3-Like 1 (SmASAT3-L1; SMEL4.1_12g015780) enzyme. This enzyme is distinct from previously characterized acylsugar acetyltransferases, which are in the ASAT4 clade, and appears to be a functionally divergent ASAT3. This study provides a foundation for investigating the evolution and function of diverse Solanum acylsugar structures and harnessing this diversity in breeding and synthetic biology. ]]> Fiesel, P. D. Kerwin, R. A. Jones, A. D. Last, R. L. 2023-06-05 doi:10.1101/2023.06.05.542877 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Mutator transposon insertions within maize genes often provide a novel outward reading promoter ]]> https://biorxiv.org/content/10.1101/2023.06.05.543741v1?rss=1 Ellison, E. E. Zhou, P. Hermanson, P. J. Read, A. Chu, Y.-H. Hirsch, C. N. Grotewold, E. Springer, N. M. 2023-06-05 doi:10.1101/2023.06.05.543741 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ The VR Billboard Paradigm: Using VR and Eye-tracking to Examine the Exposure-Reception-Retention Link in Realistic Communication Environments ]]> https://biorxiv.org/content/10.1101/2023.06.03.543559v1?rss=1 Schmaelzle, R. Lim, S. Cho, H. J. Wu, J. Bente, G. 2023-06-06 doi:10.1101/2023.06.03.543559 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ Disentangling plant- and environment-mediated drivers of active rhizosphere bacterial community dynamics during short-term drought ]]> https://biorxiv.org/content/10.1101/2023.06.06.543716v1?rss=1 Bandopadhyay, S. Li, X. Bowsher, A. W. Last, R. L. Shade, A. 2023-06-07 doi:10.1101/2023.06.06.543716 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ The Caulobacter NtrB-NtrC two-component system bridges nitrogen assimilation and cell development ]]> https://biorxiv.org/content/10.1101/2023.06.06.543975v1?rss=1 North, H. McLaughlin, M. Fiebig, A. Crosson, S. 2023-06-07 doi:10.1101/2023.06.06.543975 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ ER stress and lipid imbalance drive embryonic cardiomyopathy in a human heart organoid model of pregestational diabetes ]]> https://biorxiv.org/content/10.1101/2023.06.07.544081v1?rss=1 Kostina, A. Lewis-Israeli, Y. Abdelhamid, M. Gabalski, M. Volmert, B. Lankerd, H. Huang, A. Wasserman, A. Lydic, T. Chan, C. Olomu, I. Aguirre, A. 2023-06-08 doi:10.1101/2023.06.07.544081 Cold Spring Harbor Laboratory Press 2023-06-08 <![CDATA[ Tonic Meningeal Interleukin-10 Upregulates Delta Opioid Receptor to Prevent Relapse to Pain ]]> https://biorxiv.org/content/10.1101/2023.06.08.544200v1?rss=1 Inyang, K. E. Sim, J. Clark, K. B. Matan, G. Monahan, K. Evans, C. Beng, P. Ma, J. Heijnen, C. J. Dantzer, R. Scherrer, G. Kavelaars, A. Bernard, M. Aldhamen, Y. Folger, J. K. Laumet, G. 2023-06-09 doi:10.1101/2023.06.08.544200 Cold Spring Harbor Laboratory Press 2023-06-09 <![CDATA[ The Genetics of Aerotolerant Growth in a Naturally Reduced Genome Alphaproteobacterium ]]> https://biorxiv.org/content/10.1101/2023.06.12.544693v1?rss=1 Enright, A. L. Banta, A. B. Ward, R. D. Rivera Vazquez, J. Felczak, M. M. Wolfe, M. B. TerAvest, M. A. Amador-Noguez, D. Peters, J. M. 2023-06-13 doi:10.1101/2023.06.12.544693 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis ]]> https://biorxiv.org/content/10.1101/2023.06.14.544965v1?rss=1 Saul, F. Scharmann, M. Wakatake, T. Rajaraman, S. Marques, A. Freund, M. Bringmann, G. Channon, L. Becker, D. Carroll, E. Low, Y. W. Lindqvist, C. Gilbert, K. J. Renner, T. Masuda, S. Richter, M. Vogg, G. Shirasu, K. Michael, T. P. Hedrich, R. Albert, V. A. Fukushima, K. 2023-06-14 doi:10.1101/2023.06.14.544965 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis ]]> https://biorxiv.org/content/10.1101/2023.06.16.545386v1?rss=1 Samelson, A. J. Ariqat, N. McKetney, J. Rohanitazangi, G. Parra Bravo, C. Goodness, D. Tian, R. Grosjean, P. Abskharon, R. Eisenberg, D. Kanaan, N. M. Gan, L. Condello, C. Swaney, D. L. Kampmann, M. 2023-06-17 doi:10.1101/2023.06.16.545386 Cold Spring Harbor Laboratory Press 2023-06-17 <![CDATA[ Rational engineering of an elevator-type metal transporter ZIP8 reveals a conditional selectivity filter critically involved in determining substrate specificity ]]> https://biorxiv.org/content/10.1101/2023.06.19.545588v1?rss=1 Jiang, Y. Li, Z. Sui, D. Sharma, G. Wang, T. MacRenaris, K. Takahashi, H. Merz, K. Hu, J. 2023-06-19 doi:10.1101/2023.06.19.545588 Cold Spring Harbor Laboratory Press 2023-06-19 <![CDATA[ Polyploidy enhances desiccation tolerance in the grass Microchloa caffra ]]> https://biorxiv.org/content/10.1101/2023.06.20.545583v1?rss=1 Marks, R. A. Delgado, P. Makonya, G. M. Cooper, K. VanBuren, R. Farrant, J. M. 2023-06-22 doi:10.1101/2023.06.20.545583 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Single-molecule imaging reveals the kinetics of non-homologous end-joining in living cells ]]> https://biorxiv.org/content/10.1101/2023.06.22.546088v1?rss=1 Mikhova, M. Heyza, J. R. Meek, K. Schmidt, J. C. 2023-06-22 doi:10.1101/2023.06.22.546088 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Developmental exposure to the Parkinson's disease-associated organochlorine pesticide dieldrin alters dopamine neurotransmission in α-synuclein pre-formed fibril (PFF)-injected mice ]]> https://biorxiv.org/content/10.1101/2023.06.21.545967v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@d679deorg.highwire.dtl.DTLVardef@db0d70org.highwire.dtl.DTLVardef@14f368dorg.highwire.dtl.DTLVardef@1868894_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Boyd, S. L. Kuhn, N. C. Patterson, J. R. Stoll, A. C. Zimmerman, S. A. Kolanowski, M. R. Neubecker, J. J. Luk, K. C. Ramsson, E. S. Sortwell, C. E. Bernstein, A. I. 2023-06-24 doi:10.1101/2023.06.21.545967 Cold Spring Harbor Laboratory Press 2023-06-24 <![CDATA[ Wildlife vaccination strategies for eliminating bovine tuberculosis at the wildlife-livestock interface ]]> https://biorxiv.org/content/10.1101/2023.06.22.546040v1?rss=1 Pandey, A. Feuka, A. B. Cosgrove, M. Moriarty, M. Duffiney, A. VerCauteren, K. C. Campa, H. Pepin, K. M. 2023-06-25 doi:10.1101/2023.06.22.546040 Cold Spring Harbor Laboratory Press 2023-06-25 <![CDATA[ Characterization of a phyllosphere methylotroph community isolated with lanthanides ]]> https://biorxiv.org/content/10.1101/2023.06.28.546956v1?rss=1 Govindaraju, A. Friel, C. A. Good, N. M. Wayne, K. S. Martinez-Gomez, N. C. 2023-06-28 doi:10.1101/2023.06.28.546956 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ The ChickenGTEx pilot analysis: a reference of regulatory variants across 28 chicken tissues ]]> https://biorxiv.org/content/10.1101/2023.06.27.546670v1?rss=1 Guan, D. Bai, Z. Zhu, X. Zhong, C. Hou, Y. Lan, F. Diao, S. Yao, Y. Zhao, B. Zhu, D. Li, X. Pan, Z. Gao, Y. Wang, Y. Zou, D. Wang, R. Xu, T. Sun, C. Yin, H. Teng, J. Xu, Z. Lin, Q. Shi, S. Shao, D. Degalez, F. Lagarrigue, S. Wang, Y. Wang, M. Peng, M. Rocha, D. Charles, M. Smith, J. Watson, K. Buitenhuis, A. J. Sahana, G. Lund, M. S. Warren, W. Frantz, L. Larson, G. Lamont, S. J. Si, W. Zhao, X. Li, B. Zhang, H. Luo, C. Shu, D. Qu, H. Luo, W. Li, Z. Nie, Q. Zhang, X. Zhang, Z. Zhang, Z. Liu, G. E. Cheng, H. Yang, N. Hu, X. Zhou, H. Fang 2023-06-29 doi:10.1101/2023.06.27.546670 Cold Spring Harbor Laboratory Press 2023-06-29 <![CDATA[ Implementing a framework of carbon and nitrogen feedback responses into a plant resource allocation model ]]> https://biorxiv.org/content/10.1101/2023.06.27.546727v1?rss=1 Holland, B. L. Monk, N. A. M. Clayton, R. H. Osborne, C. P. 2023-06-29 doi:10.1101/2023.06.27.546727 Cold Spring Harbor Laboratory Press 2023-06-29 <![CDATA[ Immunologically mediated trade-offs shaping transmission of sylvatic dengue and Zika viruses in native and novel non-human primate hosts ]]> https://biorxiv.org/content/10.1101/2023.06.30.547187v1?rss=1 Hanley, K. A. Cecilia, H. Azar, S. R. Moehn, B. Yu, W. Yun, R. Althouse, B. M. Vasilakis, N. Rossi, S. L. 2023-06-30 doi:10.1101/2023.06.30.547187 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Flow cytometric isolation of drug-like conformational antibodies specific for amyloid fibrils ]]> https://biorxiv.org/content/10.1101/2023.07.04.547698v1?rss=1 Desai, A. A. Zupancic, J. M. Trzeciakiewicz, H. Gerson, J. E. DuBois, K. N. Skinner, M. E. Sharkey, L. M. McArthur, N. Ferris, S. P. Bhatt, N. N. Makowski, E. K. Smith, M. D. Chen, H. Huang, J. Jerez, C. Kane, R. S. Kanaan, N. M. Paulson, H. L. Tessier, P. M. 2023-07-04 doi:10.1101/2023.07.04.547698 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ Exogenous corticosterone administration during pregnancy alters placental and fetal thyroid hormone availability in females. ]]> https://biorxiv.org/content/10.1101/2023.07.05.547278v1?rss=1 Paul, E. N. Shubitidze, S. Rahim, R. Rucker, I. Valin, L. Apostle, S. Pospisilik, J. A. Racicot, K. E. Smith, A. L. 2023-07-05 doi:10.1101/2023.07.05.547278 Cold Spring Harbor Laboratory Press 2023-07-05 <![CDATA[ Flagellar motor remodeling during swarming requires FliL ]]> https://biorxiv.org/content/10.1101/2023.07.14.549092v1?rss=1 Harshey, R. M. Partridge, J. D. Dufour, Y. Hwang, Y. 2023-07-14 doi:10.1101/2023.07.14.549092 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ Topological data analysis reveals a core heteroblastic program embedded in leaves of grapevine and maracuya ]]> https://biorxiv.org/content/10.1101/2023.07.14.549010v1?rss=1 Percival, S. Chitwood, D. H. Husbands, A. Y. 2023-07-15 doi:10.1101/2023.07.14.549010 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ Distinct ossification trade-offs illuminate the shoulder girdle reconfiguration at the water-to-land transition. ]]> https://biorxiv.org/content/10.1101/2023.07.17.547998v1?rss=1 Wei, J. Wood, T. W. P. Flaherty, K. Enny, A. Andrescavage, A. Brazer, D. Navon, D. Stewart, T. A. Cohen, H. Shanabag, A. Kuroda, S. Braasch, I. Nakamura, T. 2023-07-17 doi:10.1101/2023.07.17.547998 Cold Spring Harbor Laboratory Press 2023-07-17 <![CDATA[ Persistent effects of intramammary ceftiofur treatment on the gut microbiome and antibiotic resistance in dairy cattle ]]> https://biorxiv.org/content/10.1101/2023.07.17.549362v1?rss=1 Vasco, K. A. Carbonell, S. Sloup, R. E. Bowcutt, B. Colwell, R. R. Graubics, K. Erskine, R. Norby, B. Ruegg, P. L. Zhang, L. Manning, S. D. 2023-07-17 doi:10.1101/2023.07.17.549362 Cold Spring Harbor Laboratory Press 2023-07-17 <![CDATA[ Syntactic Constructions Drive Cortical Tracking in the Absence of Lexical Content: An Electrophysiological Investigation of Sentence Processing During Reading ]]> https://biorxiv.org/content/10.1101/2023.07.17.549412v1?rss=1 Rafferty, M. B. Saltuklaroglu, T. Paek, E. J. Reilly, K. J. Jenson, D. Thornton, D. Casenhiser, D. M. 2023-07-19 doi:10.1101/2023.07.17.549412 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ The International Weed Genomics Consortium: Community Resources for Weed Genomics Research ]]> https://biorxiv.org/content/10.1101/2023.07.19.549613v1?rss=1 Montgomery, J. S. Morran, S. MacGregor, D. R. McElroy, J. S. Neve, P. Neto, C. Vila-Aiub, M. M. Sandoval, M. V. Menendez, A. I. Kreiner, J. Fan, L. Caicedo, A. L. Maughan, P. J. Martins, B. A. B. Mika, J. Collavo, A. Merotto, A. Subramanian, N. K. Bagavathiannan, M. V. Cutti, L. Islam, M. M. Gill, B. S. Cicchillo, R. Gast, R. Soni, N. Wright, T. R. Zastrow-Hayes, G. May, G. Malone, J. M. Sehgal, D. Kaundun, S. S. Dale, R. P. Vorster, B. J. Peters, B. Lerchl, J. Tranel, P. J. Beffa, R. Jugulam, M. Fengler, K. Llaca, V. Patterson, E. L. Gaines, T. A. 2023-07-20 doi:10.1101/2023.07.19.549613 Cold Spring Harbor Laboratory Press 2023-07-20 <![CDATA[ Detection of viral infection in cell lines using ViralCellDetector ]]> https://biorxiv.org/content/10.1101/2023.07.21.550094v1?rss=1 Chen, B. Paithankar, S. Gupta, S. Shankar, R. 2023-07-25 doi:10.1101/2023.07.21.550094 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Ribosome Heterogeneity in Development and Disease ]]> https://biorxiv.org/content/10.1101/2023.07.25.550527v1?rss=1 Gao, Y. Wang, H. 2023-07-25 doi:10.1101/2023.07.25.550527 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ A cline within an ecotype of the yellow monkeyflower, Mimulus guttatus ]]> https://biorxiv.org/content/10.1101/2023.07.24.550335v1?rss=1 Zambiasi, T. Lowry, D. B. 2023-07-26 doi:10.1101/2023.07.24.550335 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Regulation of late-acting operons by three transcription factors and a CRISPR-Cas component during Myxococcus xanthus development ]]> https://biorxiv.org/content/10.1101/2023.07.26.550624v1?rss=1 Saha, S. Kroos, L. 2023-07-26 doi:10.1101/2023.07.26.550624 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Bacterial pathogens deliver water/solute-permeable channels as a virulence strategy ]]> https://biorxiv.org/content/10.1101/2023.07.29.547699v1?rss=1 Nomura, K. Andreazza, F. Cheng, J. Dong, K. Zhou, P. He, S. Y. 2023-07-29 doi:10.1101/2023.07.29.547699 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ Brd4-Nutm1 fusion gene initiates NUT carcinoma in vivo ]]> https://biorxiv.org/content/10.1101/2023.07.29.551125v1?rss=1 Zheng, D. El Negiry, A. A. M. Bendahou, M. A. Xie, L. Tsoi, M. F. Gu, B. 2023-07-30 doi:10.1101/2023.07.29.551125 Cold Spring Harbor Laboratory Press 2023-07-30 <![CDATA[ Mining threats in high-level biodiversity conservation policies ]]> https://biorxiv.org/content/10.1101/2023.07.30.550308v1?rss=1 Torres, A. zu Ermgassen, S. O. S. E. Navarro, L. M. Ferri-Yanez, F. Teixeira, F. Z. Wittkopp, C. Rosa, I. M. D. Liu, J. 2023-07-30 doi:10.1101/2023.07.30.550308 Cold Spring Harbor Laboratory Press 2023-07-30 <![CDATA[ Immunometabolic cues recompose and reprogram the microenvironment around biomaterials ]]> https://biorxiv.org/content/10.1101/2023.07.30.551180v1?rss=1 Maduka, C. V. Schmitter-Sanchez, A. D. Makela, A. V. Ural, E. Stivers, K. B. Pope, H. Kuhnert, M. M. Habeeb, O. M. Tundo, A. Alhaj, M. Kiselev, A. Chen, S. Olive, A. J. Hankenson, K. D. D. Narayan, R. Park, S. Elisseeff, J. H. Contag, C. H. 2023-07-31 doi:10.1101/2023.07.30.551180 Cold Spring Harbor Laboratory Press 2023-07-31 <![CDATA[ Flavinated SDHA Underlies the Change in Intrinsic Optical Properties of Oral Cancers ]]> https://biorxiv.org/content/10.1101/2023.07.30.551184v1?rss=1 Marumo, T. Maduka, C. V. Ural, E. Apu, E. H. Chung, S.-J. van den Berg, N. S. Zhou, Q. Martin, B. A. Rosenthal, E. L. Shibahara, T. Contag, C. H. 2023-07-31 doi:10.1101/2023.07.30.551184 Cold Spring Harbor Laboratory Press 2023-07-31 <![CDATA[ Interdependence of a kinase and its cognate substrate plasma membrane nanoscale dynamics underlies Arabidopsis response to viral infection ]]> https://biorxiv.org/content/10.1101/2023.07.31.551174v1?rss=1 JOLIVET, M.-D. Deroubaix, A.-F. Boudsocq, M. Abel, N. B. Rocher, M. Robbe, T. Wattelet, V. Huard, J. Lefebvre, D. Lu, Y.-J. Day, B. Saias, G. Ahmed, J. Cotelle, V. Giovinazzo, N. Gallois, J.-L. Yamaji, Y. German-Retana, S. Gronnier, J. Ott, T. MONGRAND, S. Germain, V. 2023-08-01 doi:10.1101/2023.07.31.551174 Cold Spring Harbor Laboratory Press 2023-08-01 <![CDATA[ Multiple host targets of Pseudomonas effector protein HopM1 form a protein complex regulating apoplastic immunity and water homeostasis ]]> https://biorxiv.org/content/10.1101/2023.07.31.551310v1?rss=1 He, S. Y. 2023-08-01 doi:10.1101/2023.07.31.551310 Cold Spring Harbor Laboratory Press 2023-08-01 <![CDATA[ Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts ]]> https://biorxiv.org/content/10.1101/2023.07.31.551392v1?rss=1 Yocca, A. E. Platts, A. Alger, E. Teresi, S. Mengist, M. F. Benevenuto, J. Felipe V. Ferrao, L. Jacobs, M. Babinski, M. Magallanes-Lundback, M. Bayer, P. Golicz, A. Humann, J. L. Main, D. Espley, R. V. Chagne, D. Albert, N. W. Montanari, S. Vorsa, N. Polashock, J. Diaz-Garcia, L. Zalapa, J. Bassil, N. V. Munoz, P. R. Iorizzo, M. Edger, P. P. 2023-08-02 doi:10.1101/2023.07.31.551392 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ CDDO-Methyl Ester Inhibits BRAF Inhibitor Resistance and Remodels the Myeloid Compartment in BRAF-mutant Melanoma ]]> https://biorxiv.org/content/10.1101/2023.08.01.551524v1?rss=1 Torres, G. M. Jarnagin, H. C. Park, C. Yang, H. Kosarek, N. N. Bhandari, R. Wang, C.-Y. Kolling, F. W. Whitfield, M. L. Turk, M. J. Liby, K. T. Pioli, P. A. 2023-08-03 doi:10.1101/2023.08.01.551524 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ MRI-based cell tracking of OATP-expressing cell transplants by pre-labeling with Gd-EOB-DTPA ]]> https://biorxiv.org/content/10.1101/2023.08.04.552007v1?rss=1 Bhattacharyya, T. Mallett, C. L. Shapiro, E. M. 2023-08-07 doi:10.1101/2023.08.04.552007 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Nutrient levels control root growth responses to high ambient temperature in plants ]]> https://biorxiv.org/content/10.1101/2023.08.04.552051v1?rss=1 Lee, S. Showalter, J. Zhang, L. Cassin-Ross, G. Rouached, H. Busch, W. 2023-08-07 doi:10.1101/2023.08.04.552051 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ MRI of OATP-expressing transplanted cells using clinical doses of gadolinium contrast agent ]]> https://biorxiv.org/content/10.1101/2023.08.07.552326v1?rss=1 Bhattacharyya, T. Mallett, C. L. Hix, J. M.- L. Shapiro, E. M. 2023-08-08 doi:10.1101/2023.08.07.552326 Cold Spring Harbor Laboratory Press 2023-08-08 <![CDATA[ Structural Remodeling of Fungal Cell Wall Promotes Resistance to Echinocandins ]]> https://biorxiv.org/content/10.1101/2023.08.09.552708v1?rss=1 Dickwella Widanage, M. C. Gautam, I. Sarkar, D. Mentink-Vigier, F. Vermaas, J. V. Fontaine, T. Latge, J.-P. Wang, P. Wang, T. 2023-08-12 doi:10.1101/2023.08.09.552708 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ The Electron Transport Chain of Shewanella oneidensis MR-1 can Operate Bidirectionally to Enable Microbial Electrosynthesis ]]> https://biorxiv.org/content/10.1101/2023.08.11.553014v1?rss=1 Ford, K. C. TerAvest, M. A. 2023-08-12 doi:10.1101/2023.08.11.553014 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ Does urbanization lead to parallel demographic shifts across the world in a cosmopolitan plant? ]]> https://biorxiv.org/content/10.1101/2023.08.14.552623v1?rss=1 Caizergues, A. E. Santangelo, J. S. Ness, R. W. Angeoletto, F. Anstett, D. N. Anstett, J. Baena-Diaz, F. Carlen, E. J. Chaves, J. A. Comerford, M. S. Dyson, K. Falahati-Anbaran, M. Fellowes, M. D. E. Hodgins, K. A. Hood, G. R. Iniguez-Armijos, C. Kooyers, N. J. Lazaro-Lobo, A. Moles, A. T. Munshi-South, J. Paule, J. Porth, I. M. Santiago-Rosario, L. Y. Stack Whitney, K. Tack, A. J. M. Johnson, M. T. J. 2023-08-14 doi:10.1101/2023.08.14.552623 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Intra-leaf modeling of Cannabis leaflet shape produces synthetic leaves that predict genetic and developmental identities ]]> https://biorxiv.org/content/10.1101/2023.08.15.553356v1?rss=1 Balant, M. Garnatje, T. Vitales, D. Hidalgo, O. Chitwood, D. H. 2023-08-16 doi:10.1101/2023.08.15.553356 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ GSK3α/β restrains IFNγ-inducible costimulatory molecule expression in alveolar macrophages, limiting CD4+ T cell activation ]]> https://biorxiv.org/content/10.1101/2023.08.16.553574v1?rss=1 Ankley, L. M. Conner, K. N. Vielma, T. E. Thapa, M. Olive, A. J. 2023-08-18 doi:10.1101/2023.08.16.553574 Cold Spring Harbor Laboratory Press 2023-08-18 <![CDATA[ Warming alters cascading effects of a dominant arthropod predator on microbial community composition in the Arctic ]]> https://biorxiv.org/content/10.1101/2023.08.16.553601v1?rss=1 Koltz, A. M. Koyama, A. Wallenstein, M. D. 2023-08-18 doi:10.1101/2023.08.16.553601 Cold Spring Harbor Laboratory Press 2023-08-18 <![CDATA[ Loss of Carnitine Palmitoyltransferase 1a Reduces Docosahexaenoic Acid-Containing Phospholipids and Drives Sexually Dimorphic Liver Disease in Mice ]]> https://biorxiv.org/content/10.1101/2023.08.17.553705v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@f42ea0org.highwire.dtl.DTLVardef@12135f2org.highwire.dtl.DTLVardef@15cd9d0org.highwire.dtl.DTLVardef@e0106b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Zelows, M. M. Cady, C. Dharanipragada, N. Mead, A. E. Kipp, Z. A. Bates, E. A. Venkateshwari, V. Banerjee, R. Park, S.-H. Shelman, N. R. Clarke, H. A. Hawkinson, T. R. Medina, T. Sun, R. C. Lydic, T. A. Hinds, T. D. Brown, J. M. Softic, S. Graf, G. A. Helsley, R. N. 2023-08-18 doi:10.1101/2023.08.17.553705 Cold Spring Harbor Laboratory Press 2023-08-18 <![CDATA[ XRE Transcription Factors Conserved in Caulobacter and {varphi}CbK Modulate Adhesin Development and Phage Production ]]> https://biorxiv.org/content/10.1101/2023.08.20.554034v1?rss=1 McLaughlin, M. Fiebig, A. Crosson, S. 2023-08-20 doi:10.1101/2023.08.20.554034 Cold Spring Harbor Laboratory Press 2023-08-20 <![CDATA[ Phenotypic lags influence rapid evolution throughout a drought cycle ]]> https://biorxiv.org/content/10.1101/2023.08.18.553905v1?rss=1 Branch, H. A. Anstett, D. N. Angert, A. L. 2023-08-21 doi:10.1101/2023.08.18.553905 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Development and Validation of the Mentoring in Undergraduate Research Survey ]]> https://biorxiv.org/content/10.1101/2023.08.19.553952v1?rss=1 Limeri, L. B. Carter, N. T. Hess, R. A. Tuma, T. T. Koscik, I. Morrison, A. J. Outlaw, B. Royston, K. S. Bridges, B. H. T. Dolan, E. L. 2023-08-21 doi:10.1101/2023.08.19.553952 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ A data-driven evaluation of Arabidopsis-centric research and the model species concept ]]> https://biorxiv.org/content/10.1101/2023.08.20.554029v1?rss=1 Palande, S. Arsenault, J. Basurto-Lozada, P. Bleich, A. Brown, B. N. I. Buysse, S. F. Connors, N. A. Das Adhikari, S. Dobson, K. C. Guerra-Castillo, F. X. Guerrero-Carrillo, M. F. Harlow, S. Herrera-Orozco, H. Hightower, A. T. Izquierdo, P. Jacobs, M. Johnson, N. A. Leuenberger, W. Lopez-Hernandez, A. Luckie-Duque, A. Martinez-Avila, C. Mendoza-Galindo, E. Plancarte, D. Schuster, J. M. Shomer, H. Sitar, S. C. Steensma, A. K. Thomson, J. E. Villasenor-Amador, D. Waterman, R. Webster, B. M. Whyte, M. Zorrilla-Azcue, S. Montgomery, B. L. Husbands, A. Y. Krishnan 2023-08-21 doi:10.1101/2023.08.20.554029 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ A deep learning phenotyping method for genetic analysis of 3D micro-CT data ]]> https://biorxiv.org/content/10.1101/2023.08.24.554725v1?rss=1 Karshenas, A. Linderoth, T. P. Zatha, R. RusuWa, B. Durbin, R. 2023-08-26 doi:10.1101/2023.08.24.554725 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ Uncovering the Infection Strategy of Phyllachora maydis during Maize Colonization: A Comprehensive Analysis ]]> https://biorxiv.org/content/10.1101/2023.08.26.554799v1?rss=1 Caldwell, D. L. Da Silva, C. R. McCoy, A. G. Avila, H. Bonkowski, J. C. Chilvers, M. Helm, M. Telenko, D. E. Iyer-Pascuzzi, A. S. 2023-08-27 doi:10.1101/2023.08.26.554799 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Enhanced metabolic detoxification is associated with fluroxypyr resistance in Bassia scoparia ]]> https://biorxiv.org/content/10.1101/2023.08.29.554743v1?rss=1 Todd, O. E. Patterson, E. Westra, E. P. Simoes Araujo, A. L. Kramer, W. B. Dayan, F. E. Gaines, T. A. 2023-08-31 doi:10.1101/2023.08.29.554743 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ Deep Whole-Genome Resequencing of Marek's Disease Virus Strains Reveals Intrastrain Variation ]]> https://biorxiv.org/content/10.1101/2023.09.04.556264v1?rss=1 2% read support for alternative alleles in two ultra-deeply sequenced samples. We were able to confirm that both populations of CVI988 and Md5 were mixed, exhibiting a total of 29 and 27 high-confidence minor variant positions, respectively. We did not find any evidence of minor variants in the positions corresponding to the 19 SNPs in the unique regions of CVI988GenBank.BAC. Taken together, our findings confirm that consensus genomes of the same strain of MDV can vary and suggest that multiple consensus genomes per strain are needed in order to maximize the accuracy of interstrain genomic comparisons. ]]> Ortigas-Vasquez, A. Pandey, U. Renner, D. W. Bowen, C. D. Baigent, S. Dunn, J. Cheng, H. Yao, Y. Read, A. F. Nair, V. Kennedy, D. A. Szpara, M. L. 2023-09-04 doi:10.1101/2023.09.04.556264 Cold Spring Harbor Laboratory Press 2023-09-04 <![CDATA[ Improved Super-Resolution Ribosome Profiling Revealed Prevalent Translation of Upstream ORFs and Small ORFs in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2023.09.08.556947v1?rss=1 Wu, L. Ai, Q. Teixeira, R. T. Song, G. Montes-Serey, C. Elmore, J. M. Walley, J. Hsu, P. Y. 2023-09-11 doi:10.1101/2023.09.08.556947 Cold Spring Harbor Laboratory Press 2023-09-11 <![CDATA[ Temperature, phenology, and plant defenses predict fitness near colder range limit ]]> https://biorxiv.org/content/10.1101/2023.09.11.557202v1?rss=1 Anstett, D. N. 2023-09-14 doi:10.1101/2023.09.11.557202 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ Predicting photosynthetic pathway from anatomy using machine learning ]]> https://biorxiv.org/content/10.1101/2023.09.11.557216v1?rss=1 Gilman, I. S. Heyduk, K. Maya-Lastra, C. A. Hancock, L. P. Edwards, E. J. 2023-09-15 doi:10.1101/2023.09.11.557216 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Genomic analysis reveals limited hybridization among three giraffe species in Kenya ]]> https://biorxiv.org/content/10.1101/2023.09.12.557229v1?rss=1 Coimbra, R. T. F. Winter, S. Muneza, A. Fennessy, S. Otiende, M. Mijele, D. Masiaine, S. Stacy-Dawes, J. Fennessy, J. Janke, A. 2023-09-15 doi:10.1101/2023.09.12.557229 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Mate choice in the brain: Species differ in how male traits 'turn on' gene expression in female brains ]]> https://biorxiv.org/content/10.1101/2023.09.15.557962v1?rss=1 Keagy, J. Hofmann, H. A. Boughman, J. W. 2023-09-15 doi:10.1101/2023.09.15.557962 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Pyruvate Kinase Activity Regulates Cystine Starvation Induced Ferroptosis through Malic Enzyme 1 in Pancreatic Cancer Cells ]]> https://biorxiv.org/content/10.1101/2023.09.15.557984v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@fa23c2org.highwire.dtl.DTLVardef@41c01dorg.highwire.dtl.DTLVardef@abc283org.highwire.dtl.DTLVardef@6f53ef_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIPKM2KO in pancreatic ductal adenocarcinoma (PDAC) cells produces enhanced defense against cystine starvation induced ferroptosis. C_LIO_LIPharmacologic activation of pyruvate kinase (PK) activity promotes ferroptosis under cystine starvation, while inhibition promotes ferroptosis survival in PDAC cells. C_LIO_LIDecrease in PK activity reprograms glutamine metabolism to increase use of malic enzyme 1 and promote survival under cystine starvation in PDAC cells. C_LIO_LICystine starvation and activation of pyruvate kinase synergistically decreases progression of pancreatic cancer in vivo. C_LI ]]> Ensink, E. M. Jordan, T. Dias de Medeiros, H. C. Thurston, G. Pardal, A. Yu, L. Lunt, S. 2023-09-17 doi:10.1101/2023.09.15.557984 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ bamSliceR: cross-cohort variant and allelic bias analysis for rare variants and rare diseases ]]> https://biorxiv.org/content/10.1101/2023.09.15.558026v1?rss=1 Huang, Y. P. Harmon, L. M. Gardner, E. Ma, X. Harsh, J. Xue, Z. Wen, H. Ramos, M. Davis, S. R. Triche, T. J. 2023-09-17 doi:10.1101/2023.09.15.558026 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ An accurate probabilistic step finder for time-series analysis ]]> https://biorxiv.org/content/10.1101/2023.09.19.558535v1?rss=1 Rojewski, A. Schweiger, M. Sgouralis, I. Comstock, M. Presse, S. 2023-09-22 doi:10.1101/2023.09.19.558535 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Structural basis of transcription: RNA Polymerase II substrate binding and metal coordination at 3.0 A using a free-electron laser ]]> https://biorxiv.org/content/10.1101/2023.09.22.559052v1?rss=1 Guowu, L. Barnes, C. O. Weiss, S. Dutagaci, B. Qiu, C. Feig, M. Lyubimov, A. Song, J. Cohen, A. E. Kaplan, C. D. Calero, G. 2023-09-22 doi:10.1101/2023.09.22.559052 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Microbially-catalyzed conjugation of GABA and tyramine to bile acids ]]> https://biorxiv.org/content/10.1101/2023.09.25.559407v1?rss=1 Mullowney, M. Fiebig, A. Schnizlein, M. McMillin, M. Koval, J. Rubin, D. Dalal, S. Sogin, M. Chang, E. Sidebottom, A. Crosson, S. 2023-09-25 doi:10.1101/2023.09.25.559407 Cold Spring Harbor Laboratory Press 2023-09-25 <![CDATA[ From buds to shoots: Insights into grapevine development from the Witch's Broom bud sport ]]> https://biorxiv.org/content/10.1101/2023.09.25.559343v1?rss=1 Ritter, E. J. Cousins, P. Quigley, M. Kile, A. Raju, S. K. K. Chitwood, D. H. Niederhuth, C. 2023-09-26 doi:10.1101/2023.09.25.559343 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Virulence and transmission biology of the widespread, ecologically important pathogen of zooplankton, Spirobacillus cienkowskii ]]> https://biorxiv.org/content/10.1101/2023.09.26.557596v1?rss=1 Wale, N. Freimark, C. B. Ramirez, J. Kafri, A. Dziuba, M. K. Bilich, R. Duffy, M. A. 2023-09-26 doi:10.1101/2023.09.26.557596 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Science abhors a surveillance vacuum: detection of ticks and tick-borne bacteria in southern New Mexico through passive surveillance ]]> https://biorxiv.org/content/10.1101/2023.09.25.559416v1?rss=1 Harman, P. R. Mendell, N. L. Harman, M. M. Draney, P. A. Boyle, A. T. Gompper, M. E. Orr, T. J. Bouyer, D. H. Teel, P. D. Hanley, K. 2023-09-28 doi:10.1101/2023.09.25.559416 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ Non-destructive, whole-plant phenotyping reveals dynamic changes in water use efficiency, photosynthetic efficiency, and rhizosphere acidification of sorghum cultivars under osmotic stress ]]> https://biorxiv.org/content/10.1101/2023.09.26.559576v1?rss=1 Ginzburg, D. Cox, J. A. Rhee, S. Y. 2023-09-28 doi:10.1101/2023.09.26.559576 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ The shape and volume of air, kernels, and cracks, in a nutshell ]]> https://biorxiv.org/content/10.1101/2023.09.26.559651v1?rss=1 Amezquita, E. J. Quigley, M. Y. Brown, P. J. Munch, E. Chitwood, D. H. 2023-09-28 doi:10.1101/2023.09.26.559651 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ AMPK Regulates Phagophore-to-Autophagosome Maturation ]]> https://biorxiv.org/content/10.1101/2023.09.28.559981v1?rss=1 Schmidt, J. C. Barnaba, C. Broadbent, D. G. Perez, G. I. 2023-09-28 doi:10.1101/2023.09.28.559981 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ Novel Epidermal Oxysterols Function as Alarm Substances in Zebrafish ]]> https://biorxiv.org/content/10.1101/2023.09.26.559639v1?rss=1 Li, Y. Yan, Z. Lin, A. Yang, X. Li, X. Yin, X. Li, W. Li, K. 2023-09-29 doi:10.1101/2023.09.26.559639 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ An amphipathic helix drives interaction of Fibrillins with plastoglobule lipid droplets ]]> https://biorxiv.org/content/10.1101/2023.09.28.559984v1?rss=1 Shivaiah, K.-K. Boren, D. M. Herrera-Tequia, A. Vermaas, J. Lundquist, P. K. 2023-09-29 doi:10.1101/2023.09.28.559984 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes ]]> https://biorxiv.org/content/10.1101/2023.09.30.560311v1?rss=1 Sauer, P. V. Cupellini, L. Sutter, M. Bondanza, M. Dominguez Martin, M. A. Kirst, H. Bina, D. Koh, A. F. Kotecha, A. Greber, B. J. Nogales, E. Polivka, T. Mennucci, B. Kerfeld, C. A. 2023-09-30 doi:10.1101/2023.09.30.560311 Cold Spring Harbor Laboratory Press 2023-09-30 <![CDATA[ Cytochrome P450 and Epoxide Hydrolase Metabolites in Aβ and tau-induced Neurodegeneration: Insights from Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2023.10.02.560527v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@8fd3fdorg.highwire.dtl.DTLVardef@a6c4e1org.highwire.dtl.DTLVardef@c7a5a7org.highwire.dtl.DTLVardef@14c8ce2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sarparast, M. Hinman, J. Pourmand, E. Vonarx, D. Ramirez, L. Ma, W. Liachko, N. F. Alan, J. Lee, K. S. S. 2023-10-02 doi:10.1101/2023.10.02.560527 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Gut metabolite L-lactate supports Campylobacter jejuni population expansion during acute infection ]]> https://biorxiv.org/content/10.1101/2023.10.02.560557v1?rss=1 Sinha, R. LeVeque, R. M. Callahan, S. M. Stopnisek, N. Kuipel, M. Johnson, J. G. DiRita, V. J. 2023-10-02 doi:10.1101/2023.10.02.560557 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Non-canonical activation of IRE1α during Candida albicans infection enhances macrophage fungicidal activity ]]> https://biorxiv.org/content/10.1101/2023.10.02.560560v1?rss=1 McFadden, M. J. Reynolds, M. B. Michmerhuizen, B. C. Anderson, F. M. O'Riordan, M. X. D. O'Meara, T. R. 2023-10-02 doi:10.1101/2023.10.02.560560 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Evolution of research topics and paradigms in plant sciences ]]> https://biorxiv.org/content/10.1101/2023.10.02.560457v1?rss=1 Shiu, S.-H. Lehti-Shiu, M. D. 2023-10-03 doi:10.1101/2023.10.02.560457 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Spiral NeuroString: High-Density Soft Bioelectronic Fibers for Multimodal Sensing and Stimulation ]]> https://biorxiv.org/content/10.1101/2023.10.02.560482v1?rss=1 Khatib, M. Zhao, E. T. Wei, S. Abramson, A. Bishop, E. B. Chen, C.-H. Thomas, A.-L. Xu, C. Park, J. Lee, Y. Hamnett, R. Yu, W. Root, S. E. Yuan, L. Chakhtoura, D. Kim, K. K. Zhong, D. Nishio, Y. Zhao, C. Wu, C. Jiang, Y. Zhang, A. Li, J. Wang, W. Salimi-Jazi, F. Rafeeqi, T. A. Hemed, N. M. Tok, J. B.-H. Chen, X. Kaltschmidt, J. A. Dunn, J. Bao, Z. 2023-10-03 doi:10.1101/2023.10.02.560482 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Quantitative Profiling Method for Oxylipins in Neurodegenerative Diseases by Liquid Chromatography Coupled with Tandem Mass Spectrometry ]]> https://biorxiv.org/content/10.1101/2023.10.02.560544v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@415035org.highwire.dtl.DTLVardef@1f8d81eorg.highwire.dtl.DTLVardef@34a9f8org.highwire.dtl.DTLVardef@182de04_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pourmand, E. Zhang, F. Sarparast, M. Alan, J. K. Lee, K. S. S. 2023-10-03 doi:10.1101/2023.10.02.560544 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Establishment and comparative genomics of a high-quality collection of mosquito-associated bacterial isolates -- MosAIC (Mosquito-Associated Isolate Collection) ]]> https://biorxiv.org/content/10.1101/2023.10.04.560816v1?rss=1 Foo, A. Brettell, L. E. Nichols, H. L. 2022 UW-Madison Capstone in Microbiology Students, Medina Munoz, M. Lysne, J. Dhokiya, V. Hoque, A. F. Brackney, D. E. Caragata, E. P. Hutchinson, M. Jacobs-Lorena, M. Lampe, D. J. Martin, E. Valiente Moro, C. Povelones, M. Short, S. M. Steven, B. Xu, J. Paustian, T. D. Rondon, M. R. Hughes, G. L. Coon, K. L. Heinz, E. 2023-10-04 doi:10.1101/2023.10.04.560816 Cold Spring Harbor Laboratory Press 2023-10-04 <![CDATA[ CellPLM: Pre-training of Cell Language Model Beyond Single Cells ]]> https://biorxiv.org/content/10.1101/2023.10.03.560734v1?rss=1 Wen, H. Tang, W. Dai, X. Ding, J. Jin, W. Xie, Y. Tang, J. 2023-10-05 doi:10.1101/2023.10.03.560734 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Employing a honeybee olfactory neural circuit as a novel gas sensor for the detection of human lung cancer biomarkers ]]> https://biorxiv.org/content/10.1101/2023.10.04.560899v1?rss=1 Parnas, M. Cox, E. Sanchez, S. Farnum, A. Lefevre, N. Miller, S. Saha, D. 2023-10-06 doi:10.1101/2023.10.04.560899 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Population-specific responses to developmental temperature in the arboviral vector <Aedes albopictus>: implications for climate change ]]> https://biorxiv.org/content/10.1101/2023.10.06.561151v1?rss=1 Carlassara, M. Khorramnejad, A. Oker, H. Bahrami, R. Lozada-Chavez, A. N. Mancini, M. V. Body, M. J. Lahondere, C. Bonizzoni, M. 2023-10-06 doi:10.1101/2023.10.06.561151 : implications for climate change]]> Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Mimetic butterfly wings through mimetic butterfly eyes: Evidence that brightness vision helps Adelpha fessonia identify potential mates ]]> https://biorxiv.org/content/10.1101/2023.10.05.561098v1?rss=1 Dang, A. Bernard, G. D. Yuan, F. Macias-Munoz, A. Hill, R. I. Lawrence, J. P. Olguin, A. R. G. Luis-Martinez, A. Mullen, S. P. Llorente-Bousquets, J. Briscoe, A. D. 2023-10-07 doi:10.1101/2023.10.05.561098 Cold Spring Harbor Laboratory Press 2023-10-07 <![CDATA[ A Cell Atlas of Thoracic Aortic Perivascular Adipose Tissue: a focus on mechanotransducers ]]> https://biorxiv.org/content/10.1101/2023.10.09.561581v1?rss=1 Thompson, J. M. Watts, S. W. Terrian, L. Contreras, G. A. Rockwell, C. Rendon, C. J. Wabel, E. Lockwood, L. Bhattacharya, S. Nault, R. 2023-10-09 doi:10.1101/2023.10.09.561581 Cold Spring Harbor Laboratory Press 2023-10-09 <![CDATA[ AP-LASR: Automated Protein Libraries from Ancestral Sequence Reconstruction ]]> https://biorxiv.org/content/10.1101/2023.10.09.561537v1?rss=1 VanAntwerp, J. Mardikoraem, M. Pascual, N. Woldring, D. 2023-10-12 doi:10.1101/2023.10.09.561537 Cold Spring Harbor Laboratory Press 2023-10-12 <![CDATA[ Cross-sector collaboration reduces SARS-CoV-2 risk in deer ]]> https://biorxiv.org/content/10.1101/2023.10.13.562192v1?rss=1 Cook, J. D. Rosenblatt, E. DiRenzo, G. V. Campbell Grant, E. H. Mosher, B. Arce, F. Christensen, S. Ghai, R. Runge, M. 2023-10-17 doi:10.1101/2023.10.13.562192 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Five amino acid mismatches in the zinc-finger domains of CELLULOSE SYNTHASE 5 and CELLULOSE SYNTHASE 6 modulate their incorporation into cellulose synthase complexes in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2023.10.13.562211v1?rss=1 Park, S. Ding, S.-Y. 2023-10-17 doi:10.1101/2023.10.13.562211 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ A General Single-Cell Analysis Framework via Conditional Diffusion Generative Models ]]> https://biorxiv.org/content/10.1101/2023.10.13.562243v1?rss=1 Tang, W. Liu, R. Wen, H. Dai, X. Ding, J. Li, H. Fan, W. Xie, Y. Tang, J. 2023-10-17 doi:10.1101/2023.10.13.562243 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Chronic social defeat stress induces a depression-relevant outcome in male prairie voles ]]> https://biorxiv.org/content/10.1101/2023.10.16.562541v1?rss=1 Rodriguez, M. Themann, A. Garcia-Carachure, I. Lira, O. Robison, A. J. Cushing, B. Iniguez, S. D. 2023-10-17 doi:10.1101/2023.10.16.562541 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ BUMBLE BEE RESPONSES TO CLIMATE AND LANDSCAPES: INVESTIGATING HABITAT ASSOCIATIONS AND SPECIES ASSEMBLAGES ACROSS GEOGRAPHIC REGIONS IN THE UNITED STATES OF AMERICA ]]> https://biorxiv.org/content/10.1101/2023.10.16.562230v1?rss=1 Christman, M. E. Spears, L. R. Burchfield, E. K. Pearse, W. D. Strange, J. P. Ramirez, R. A. 2023-10-19 doi:10.1101/2023.10.16.562230 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Conflicts in natural selection constrain adaptation to climate change in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2023.10.16.562583v1?rss=1 Ruffley, M. R. Levanthal, L. Hateley, S. Rhee, S. Y. Exposito-Alonso, M. 2023-10-19 doi:10.1101/2023.10.16.562583 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Computational discovery of co-expressed antigens as dual targeting candidates for cancer therapy through bulk, single-cell, and spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2023.10.17.562711v1?rss=1 Chekalin, E. Paithankar, S. Shankar, R. Xing, J. Xu, W. Chen, B. 2023-10-19 doi:10.1101/2023.10.17.562711 Cold Spring Harbor Laboratory Press 2023-10-19 <![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[ BayesKAT: Bayesian Optimal Kernel-based Test for genetic association studies reveals joint genetic effects in complex diseases ]]> https://biorxiv.org/content/10.1101/2023.10.18.562824v1?rss=1 Das Adhikari, S. Cui, Y. Wang, J. 2023-10-20 doi:10.1101/2023.10.18.562824 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ CONE: COntext-specific Network Embedding via Contextualized Graph Attention ]]> https://biorxiv.org/content/10.1101/2023.10.21.563390v1?rss=1 Liu, R. Yuan, H. Johnson, K. A. Krishnan, A. 2023-10-24 doi:10.1101/2023.10.21.563390 Cold Spring Harbor Laboratory Press 2023-10-24 <![CDATA[ Regulating the proinflammatory response to implanted composite biomaterials comprising polylactide and hydroxyapatite by targeting immunometabolism ]]> https://biorxiv.org/content/10.1101/2023.10.21.563447v1?rss=1 Maduka, C. V. Makela, A. V. Ural, E. Stivers, K. B. Kuhnert, M. M. Tundo, A. Alhaj, M. Hoque Apu, E. Ashammakhi, N. Hankenson, K. D. Narayan, R. Elisseeff, J. H. Contag, C. H. 2023-10-25 doi:10.1101/2023.10.21.563447 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ Effect of Human Infant Gut Microbiota on Mouse Behavior, Dendritic Complexity, and Myelination ]]> https://biorxiv.org/content/10.1101/2023.10.24.563309v1?rss=1 DUBEY, H. Roychoudhury, R. Alex, A. Best, C. Liu, S. White, A. Carlson, A. Azcarate-Peril, M. A. Mansfield, L. Knickmeyer, R. C. 2023-10-27 doi:10.1101/2023.10.24.563309 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Apple and banana fruits produce anteiso- and iso-branched-chain esters from newly synthesized precursors ]]> https://biorxiv.org/content/10.1101/2023.10.26.564239v1?rss=1 Engelgau, P. Wendakoon, S. K. DuBois, A. Mayhew, E. J. Beaudry, R. 2023-10-28 doi:10.1101/2023.10.26.564239 Cold Spring Harbor Laboratory Press 2023-10-28 <![CDATA[ Untangling the Role of Pathobionts from Bacteroides Species in Inflammatory Bowel Diseases ]]> https://biorxiv.org/content/10.1101/2023.10.29.564605v1?rss=1 Shan, Y. Lake, J. Cham, C. M. Zhu, M. Kaur, D. Ringus, D. Fei, N. Weber, C. R. Spedale, M. Theriault, B. Dalal, S. Rubin, D. T. Fiebig, A. Crosson, S. Lolans, K. Comstock, L. Eren, A. M. Basu, A. Pott, S. Sogin, M. Liu, C. Chang, E. B. 2023-10-29 doi:10.1101/2023.10.29.564605 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ Identification of Hub Genes and Functional Annotation of Glaucoma Using Bioinformatic Analysis ]]> https://biorxiv.org/content/10.1101/2023.10.25.563916v1?rss=1 Venkataramanan, S. 2023-10-30 doi:10.1101/2023.10.25.563916 Cold Spring Harbor Laboratory Press 2023-10-30 <![CDATA[ In vivo Biomedical Imaging of Immune Tolerant, Radiopaque Nanoparticle-Embedded Polymeric Device Degradation ]]> https://biorxiv.org/content/10.1101/2023.10.26.564238v1?rss=1 Pawelec, K. Hix, J. M. L. Troia, A. Kiupel, M. Shapiro, E. 2023-10-30 doi:10.1101/2023.10.26.564238 Cold Spring Harbor Laboratory Press 2023-10-30 <![CDATA[ Deployment of a Vibrio cholerae ordered transposon mutant library in a quorum-competent genetic background ]]> https://biorxiv.org/content/10.1101/2023.10.31.564941v1?rss=1 Grant, N. A. Sontz, J. T. Waters, C. M. 2023-11-01 doi:10.1101/2023.10.31.564941 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Population level gene expression can repeatedly link genes to functions in maize ]]> https://biorxiv.org/content/10.1101/2023.10.31.565032v1?rss=1 Torres-Rodriguez, J. V. Li, D. Turkus, J. Newton, L. Davis, J. Lopez-Corona, L. Ali, W. Sun, G. Mural, R. V. Grzybowski, M. W. Thompson, A. M. Schnable, J. C. 2023-11-01 doi:10.1101/2023.10.31.565032 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Small but significant genetic differentiation among populations of Phyllachora maydis in the midwestern United States revealed by microsatellite (SSR) markers. ]]> https://biorxiv.org/content/10.1101/2023.10.31.563566v1?rss=1 0.001). Structure analysis showed the samples were not geographically structured but rather grouped into two genetic clusters (k =2) of severe genetic admixture suggesting possible long-distance dispersal of aerial spores or infected corn materials among the five Midwest states. Both principal coordinate analysis (PCoA) and discriminate analysis of principal component (DAPC) supported the STRUCTURE analysis of the two clusters. These 13 highly polymorphic molecular markers could be used for future investigations of this pathogens population dynamics within the U.S., and possibly populations outside. ]]> Ross, T. J. Jumbam, B. Bonkowski, J. Chaky, J. Chilvers, M. Goodwin, S. B. Kleczewski, N. M. Mueller, D. S. Robertson, A. E. Smith, D. L. Telenko, D. E. P. 2023-11-02 doi:10.1101/2023.10.31.563566 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Murine uterine gland branching is necessary for gland function in implantation ]]> https://biorxiv.org/content/10.1101/2023.11.01.565233v1?rss=1 Granger, K. Fitch, S. Shen, M. Lloyd, J. Bhurke, A. Hancock, J. Ye, X. Arora, R. 2023-11-04 doi:10.1101/2023.11.01.565233 Cold Spring Harbor Laboratory Press 2023-11-04 <![CDATA[ The membrane-associated ubiquitin ligase MARCHF8 stabilizes the human papillomavirus oncoprotein E7 by degrading CUL1 and UBE2L3 in head and neck cancer ]]> https://biorxiv.org/content/10.1101/2023.11.03.565564v1?rss=1 Khalil, M. I. Yang, C. Vu, L. Chadha, S. Nabors, H. James, C. D. Morgan, I. M. Pyeon, D. 2023-11-04 doi:10.1101/2023.11.03.565564 Cold Spring Harbor Laboratory Press 2023-11-04 <![CDATA[ Interleukin-10-producing monocytes contribute to sex differences in pain resolution in mice and humans. ]]> https://biorxiv.org/content/10.1101/2023.11.03.565129v1?rss=1 View larger version (46K): org.highwire.dtl.DTLVardef@6e158corg.highwire.dtl.DTLVardef@148c8b5org.highwire.dtl.DTLVardef@1711d2dorg.highwire.dtl.DTLVardef@132a755_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sim, J. O'Guin, E. Monahan, K. Sugimoto, C. McLean, S. Albertorio-Saez, L. Zhao, Y. Dagenais, A. Laumet, S. Bernard, M. Folger, J. K. Robison, A. J. Linnstaedt, S. D. Laumet, G. 2023-11-05 doi:10.1101/2023.11.03.565129 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Human Endogenous Retrovirus Expression is Dynamically Regulated in Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2023.11.03.565438v1?rss=1 Gordevicius, J. Goralski, T. Bergsma, A. Parham, A. Kuhn, E. Meyerdirk, L. McDonald, M. Milciute, M. Putten, E. V. Marshall, L. Brundin, P. Brundin, L. Labrie, V. Henderson, M. Pospisilik, J. A. 2023-11-05 doi:10.1101/2023.11.03.565438 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Tick extracellular vesicles impair epidermal homeostasis through immune-epithelial networks during hematophagy ]]> https://biorxiv.org/content/10.1101/2023.11.10.566612v1?rss=1 Marnin, L. Bogale, H. Laukaitis-Yousey, H. Valencia, L. Rolandelli, A. O'Neal, A. Ferraz, C. Schmitter-Sanchez, A. Bencosme Cuevas, E. Nguyen, T.-T. Leal-Galvan, B. Rickert, D. Bruno, V. M. Mendes, M. T. Samaddar, S. Butler, L. R. Singh, N. Cabrera Paz, F. Oliver, J. Jameson, J. Munderloh, U. Oliva Chavez, A. Mulenga, A. Park, S. Serre, D. Pedra, J. H. F. 2023-11-10 doi:10.1101/2023.11.10.566612 Cold Spring Harbor Laboratory Press 2023-11-10 <![CDATA[ MEM-GAN: A Pseudo Membrane Generator for Single-cell Imaging in Fluorescent Microscopy ]]> https://biorxiv.org/content/10.1101/2023.11.08.566343v1?rss=1 Wang, Y. Ding, J. Wu, L. Wardhani, A. Danaher, P. Lu, Q. Wen, H. Tang, W. Chang, Y. Lei, Y. L. Tang, J. Xie, Y. 2023-11-13 doi:10.1101/2023.11.08.566343 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Genetic factors acting prior to dormancy in sour cherry influence bloom time the following spring ]]> https://biorxiv.org/content/10.1101/2023.11.09.566501v1?rss=1 Goeckeritz, C. Z. Grabb, C. Grumet, R. Iezzoni, A. F. Hollender, C. A. 2023-11-14 doi:10.1101/2023.11.09.566501 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ Prediction of plant complex traits via integration of multi-omics data ]]> https://biorxiv.org/content/10.1101/2023.11.14.566971v1?rss=1 Wang, P. Lehti-Shiu, M. D. Lotreck, S. Segura Aba, K. Shiu, S.-H. 2023-11-14 doi:10.1101/2023.11.14.566971 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ Translocations spur population growth but exacerbate inbreeding in an imperiled species ]]> https://biorxiv.org/content/10.1101/2023.11.11.566550v1?rss=1 Linderoth, T. Deaner, L. Chen, N. Bowman, R. Boughton, R. Fitzpatrick, S. W. 2023-11-15 doi:10.1101/2023.11.11.566550 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Genome of the North American wild apple species Malus angustifolia ]]> https://biorxiv.org/content/10.1101/2023.11.16.567428v1?rss=1 Mansfeld, B. N. Ou, S. Burchard, E. Yocca, A. Harkess, A. Gutierrez, B. van Nocker, S. Tang, L. Gottschalk, C. 2023-11-17 doi:10.1101/2023.11.16.567428 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Quantifying potential abiotic drivers of the nurse-plant effect in two dominant shrub species of the northern Chihuahuan Desert ]]> https://biorxiv.org/content/10.1101/2023.11.16.567462v1?rss=1 Ferrenberg, S. Faist, A. Osborne, B. Lee, S. 2023-11-17 doi:10.1101/2023.11.16.567462 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Aalbo1200: global genetic differentiation and variability of the mosquito Aedes albopictus ]]> https://biorxiv.org/content/10.1101/2023.11.21.568070v1?rss=1 Crawford, J. E. Beebe, N. Bonizzoni, M. Caputo, B. Carter, B. H. Chen, C.-H. Cosme, L. De Marco, C. M. della Torre, A. Estallo, E. L. Guo, X. Liu, W.-L. Maringer, K. Mains, J. Maynard, A. Mogi, M. Livdahl, T. Rose, N. H. Scarafia, P. Y. Severson, D. Stein, M. Surendran, S. N. Tuno, N. Wahid, I. Wang, X. Xu, J. Yan, G. Yee, D. Armbruster, P. A. Caccone, A. White, B. 2023-11-22 doi:10.1101/2023.11.21.568070 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Phenology across scales: an intercontinental analysis of leaf-out dates in temperate deciduous tree communities ]]> https://biorxiv.org/content/10.1101/2023.11.21.568089v1?rss=1 Delpierre, N. Garnier, S. Treuil-Dussouet, H. Hufkens, K. Lin, J. Beier, C. Bell, M. Berveiller, D. Cuntz, M. Curioni, G. Dahlin, K. Denham, S. O. Desai, A. R. Domec, J.-C. Hart, K. M. Ibrom, A. Joetzjer, E. King, J. Klosterhalfen, A. Koebsch, F. McHale, P. Morfin, A. Munger, J. W. Noormets, A. Pilegaard, K. Pohl, F. Rebmann, C. Richardson, A. D. Rothstein, D. Schwartz, M. D. Wilkinson, M. Soudani, K. 2023-11-22 doi:10.1101/2023.11.21.568089 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ QTL analysis of floral morphology polymorphisms between Gilia yorkii and G. capitata ]]> https://biorxiv.org/content/10.1101/2023.11.22.568340v1?rss=1 DeTemple, J. M. Chitwood, D. H. Mosquera, V. Whipple, C. J. 2023-11-23 doi:10.1101/2023.11.22.568340 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ The formation of ubiquitin rich condensates triggers recruitment of the ATG9A lipid transfer complex to initiate basal autophagy ]]> https://biorxiv.org/content/10.1101/2023.11.28.569058v1?rss=1 Broadbent, D. G. McEwan, C. M. Tsang, T.-M. Poole, D. M. Naylor, B. C. Price, J. C. Schmidt, J. C. Andersen, J. L. 2023-11-29 doi:10.1101/2023.11.28.569058 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Morphometrics and phylogenomics of coca (Erythroxylum spp.) illuminate its reticulate evolution, with implications for taxonomy ]]> https://biorxiv.org/content/10.1101/2023.11.28.569066v1?rss=1 Przelomska, N. Diaz, R. Avila, F. A. Ballen, G. A. Cortes-B, R. Kistler, L. Chitwood, D. H. Charitonidou, M. Renner, S. S. Perez-Escobar, O. A. Antonelli, A. 2023-11-29 doi:10.1101/2023.11.28.569066 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Origin and evolution of the bread wheat D genome ]]> https://biorxiv.org/content/10.1101/2023.11.29.568958v1?rss=1 Cavalet-Giorsa, E. Gonzalez-Munoz, A. Athiyannan, N. Holden, S. Salhi, A. Gardener, C. Quiroz-Chavez, J. Rustamova, S. M. Elkot, A. F. Patpour, M. Rasheed, A. Mao, L. Lagudah, E. S. Periyannan, S. K. Sharon, A. Himmelbach, A. Reif, J. C. Knauft, M. Mascher, M. Stein, N. Chayut, N. Ghosh, S. Perovic, D. Putra, A. Perera, A. B. Hu, C.-Y. Yu, G. Ahmed, H. I. Laquai, K. D. Rivera, L. F. Chen, R. Wang, Y. Gao, X. Liu, S. Raupp, W. J. Olson, E. L. Lee, J.-Y. Chhuneja, P. Kaur, S. Zhang, P. Park, R. F. Ding, Y. Liu, D.-C. Li, W. Nasyrova, F. Y. Dvorak, J. 2023-11-29 doi:10.1101/2023.11.29.568958 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Imitating the 'breeder's eye': predicting grain yield from measurements of non-yield traits ]]> https://biorxiv.org/content/10.1101/2023.11.29.568906v1?rss=1 Jin, H. Tross, M. C. Tan, R. Newton, L. Mural, R. V. Yang, J. Thompson, A. M. Schnable, J. C. 2023-12-01 doi:10.1101/2023.11.29.568906 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Convergent evolution of desiccation tolerance in grasses ]]> https://biorxiv.org/content/10.1101/2023.11.29.569285v1?rss=1 Marks, R. A. Van Der Pas, L. Schuster, J. VanBuren, R. 2023-12-01 doi:10.1101/2023.11.29.569285 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Molecular dynamics simulations provide insights into ULK-101 potency and selectivity toward autophagic kinases ULK1/2 ]]> https://biorxiv.org/content/10.1101/2023.12.01.569261v1?rss=1 Vaughan, R. M. Dickson, B. M. Martin, K. R. Mackeigan, J. P. 2023-12-03 doi:10.1101/2023.12.01.569261 Cold Spring Harbor Laboratory Press 2023-12-03 <![CDATA[ Quantitative Analysis of Autophagy in Single Cells: Differential Response to Amino Acid and Glucose Starvation ]]> https://biorxiv.org/content/10.1101/2023.12.01.569679v1?rss=1 Martin, K. R. Celano, S. L. Sheldon, R. D. Jones, R. G. MacKeigan, J. P. 2023-12-03 doi:10.1101/2023.12.01.569679 Cold Spring Harbor Laboratory Press 2023-12-03 <![CDATA[ Imaging the dynamics of uterine contractions in early pregnancy ]]> https://biorxiv.org/content/10.1101/2023.12.06.570447v1?rss=1 Dawson, M. Flores, D. Zou, L. Anandhasenthil, S. Mahesh, R. Zavala, O. Arora, R. 2023-12-08 doi:10.1101/2023.12.06.570447 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ The role of breakpoint mutations, supergene effects, and ancient nested rearrangements in the evolution of adaptive chromosome inversions in the yellow monkey flower, Mimulus guttatus ]]> https://biorxiv.org/content/10.1101/2023.12.06.570460v1?rss=1 Kollar, L. M. Stanley, L. E. Kenchanmane Raju, S. K. M. Lowry, D. Niederhuth, C. E. 2023-12-08 doi:10.1101/2023.12.06.570460 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ The dysregulated IL-23/TH17 axis in endometriosis pathophysiology ]]> https://biorxiv.org/content/10.1101/2023.12.07.570652v1?rss=1 Sisnett, D. J. Zutautas, K. B. Miller, J. E. Lingegowda, H. Ahn, S. H. McCallion, A. Bougie, O. Lessey, B. A. Tayade, C. 2023-12-08 doi:10.1101/2023.12.07.570652 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Adapting to changing methodology in a long-term experiment ]]> https://biorxiv.org/content/10.1101/2023.12.07.570659v1?rss=1 McNamara Manning, K. Perrone, J. Petrycki, S. Landis, D. A. Bahlai, C. 2023-12-08 doi:10.1101/2023.12.07.570659 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Large-Scale Information Retrieval and Correction of Noisy Pharmacogenomic Datasets through Residual Thresholded Deep Matrix Factorization ]]> https://biorxiv.org/content/10.1101/2023.12.07.570723v1?rss=1 Hu, Z. T. Yu, Y. Chen, R. Yeh, S.-J. Chen, B. Huang, H. 2023-12-08 doi:10.1101/2023.12.07.570723 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ PNLDC1 catalysis and postnatal germline function are required for piRNA trimming, LINE1 silencing, and spermatogenesis in mice ]]> https://biorxiv.org/content/10.1101/2023.12.26.573375v1?rss=1 Wei, C. Yan, X. Mann, J. M. Geng, R. Xie, H. Demireva, E. Y. Sun, L. Ding, D. Chen, C. 2023-12-27 doi:10.1101/2023.12.26.573375 Cold Spring Harbor Laboratory Press 2023-12-27 <![CDATA[ Transcriptomic Analysis Identifies Candidate Genes for Differential Expression during Xenopus laevis Inner Ear Development ]]> https://biorxiv.org/content/10.1101/2023.12.29.573599v1?rss=1 Virk, S. M. Trujillo-Provencio, C. Serrano, E. E. 2024-01-01 doi:10.1101/2023.12.29.573599 Cold Spring Harbor Laboratory Press 2024-01-01 <![CDATA[ pGpG-signaling regulates virulence and global transcriptomic targets in Erwinia amylovora ]]> https://biorxiv.org/content/10.1101/2024.01.12.575434v1?rss=1 Kharadi, R. R. Hsueh, B. Y. Waters, C. M. Sundin, G. W. 2024-01-14 doi:10.1101/2024.01.12.575434 Cold Spring Harbor Laboratory Press 2024-01-14 <![CDATA[ Behavioral sequences across multiple animal species in the wild share common structural features ]]> https://biorxiv.org/content/10.1101/2024.01.20.576411v1?rss=1 Minasandra, P. Grout, E. M. Crofoot, M. C. Demartsev, V. Gersick, A. S. Hirsch, B. T. Holekamp, K. E. Johnson-Ulrich, L. Nayak, A. Ortega, J. Roch, M. A. Strauss, E. D. Strandburg-Peshkin, A. 2024-01-21 doi:10.1101/2024.01.20.576411 Cold Spring Harbor Laboratory Press 2024-01-21 <![CDATA[ Parasite contingency loci and the evolution of host specificity: Simple sequence repeats mediate Bartonella adaptation to a wild rodent host ]]> https://biorxiv.org/content/10.1101/2024.01.18.576196v1?rss=1 Rodriguez-Pastor, R. Knossow, N. Shahar, N. Hasik, A. Z. Deatherage, D. E. Gutierrez, R. Harrus, S. Zaman, L. E. Lenski, R. E. Barrick, J. E. Hawlena, H. 2024-01-22 doi:10.1101/2024.01.18.576196 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Geographic variation in resistance of the invasive Drosophila suzukii to parasitism by the biological control agent, Ganaspis brasiliensis ]]> https://biorxiv.org/content/10.1101/2024.01.18.576198v1?rss=1 Istas, O. Szucs, M. 2024-01-22 doi:10.1101/2024.01.18.576198 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ OCT4 is expressed in extraembryonic endoderm stem (XEN) cell progenitors during somatic cell reprogramming ]]> https://biorxiv.org/content/10.1101/2024.01.22.576724v1?rss=1 Moauro, A. Hickey, S. L. Halbisen, M. A. Parenti, A. Ralston, A. 2024-01-22 doi:10.1101/2024.01.22.576724 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Smad4 is essential for epiblast scaling and morphogenesis after implantation, but nonessential prior to implantation in the mouse ]]> https://biorxiv.org/content/10.1101/2024.01.23.576717v1?rss=1 Kruger, R. Frum, T. Brumm, A. S. Hickey, S. L. Niakan, K. Aziz, F. Shammami, M. Roberts, J. Ralston, A. 2024-01-24 doi:10.1101/2024.01.23.576717 Cold Spring Harbor Laboratory Press 2024-01-24 <![CDATA[ MR-SPLIT: a novel method to address selection and weak instrument bias in one-sample Mendelian randomization studies ]]> https://biorxiv.org/content/10.1101/2024.02.11.579683v1?rss=1 Shi, R. Wang, L. Burgess, S. Cui, Y. 2024-02-12 doi:10.1101/2024.02.11.579683 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ Functional dynamics and selectivity of two parallel corticocortical pathways from motor cortex to layer 5 circuits in somatosensory cortex ]]> https://biorxiv.org/content/10.1101/2024.02.11.579810v1?rss=1 Kim, H.-H. Bonekamp, K. E. Gillie, G. R. Autio, D. M. Keller, T. Crandall, S. R. 2024-02-12 doi:10.1101/2024.02.11.579810 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation ]]> https://biorxiv.org/content/10.1101/2024.02.13.580169v1?rss=1 Tiedemann, R. Hrit, J. Du, Q. Wiseman, A. K. Eden, H. E. Dickson, B. M. Kong, X. Chomiak, A. Vaughan, R. M. Hebert, J. M. David, Y. Zhou, W. M. Baylin, S. Jones, P. A. Clark, S. Rothbart, S. B. 2024-02-16 doi:10.1101/2024.02.13.580169 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ Engineering the cyanobacterial ATP-driven BCT1 bicarbonate transporter for functional targeting to C3 plant chloroplasts ]]> https://biorxiv.org/content/10.1101/2024.02.14.580295v1?rss=1 Rottet, S. Rourke, L. M. Pabuayon, I. C. M. Phua, S. Y. Yee, S. Weerasooriya, H. N. Wang, X. Mehra, H. S. Nguyen, N. D. Long, B. M. Moroney, J. V. Price, G. D. 2024-02-16 doi:10.1101/2024.02.14.580295 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ Functional brain imaging predicts population-level visits to urban spaces ]]> https://biorxiv.org/content/10.1101/2024.02.16.580650v1?rss=1 Kaur, A. Rodrigues, A. L. Hoogstraten, S. Blanco-Mora, D. A. Miranda, B. Morgado, P. Meshi, D. 2024-02-18 doi:10.1101/2024.02.16.580650 Cold Spring Harbor Laboratory Press 2024-02-18 <![CDATA[ Arabidopsis thaliana RHAMNOSE 1 condensate formation drives UDP-rhamnose synthesis ]]> https://biorxiv.org/content/10.1101/2024.02.15.580454v1?rss=1 Field, S. Dorone, Y. Dwyer, W. P. Cox, J. A. Raba, D. Froehlich, J. Blea, M. Carmo, O. M. S. Wallace, I. S. Hastings, R. Boeynaems, S. Rhee, S. Y. 2024-02-19 doi:10.1101/2024.02.15.580454 Cold Spring Harbor Laboratory Press 2024-02-19 <![CDATA[ Convergent evolution of plant prickles is drivenby repeated gene co-option over deep time ]]> https://biorxiv.org/content/10.1101/2024.02.21.581474v1?rss=1 Satterlee, J. W. Alonso, D. Gramazio, P. Jenike, K. M. He, J. Arrones, A. Villanueva, G. Plazas, M. Ramakrishnan, S. Benoit, M. Gentile, I. Hendelman, A. Shohat, H. Fitzgerald, B. Robitaille, G. M. Green, Y. Swartwood, K. Passalacqua, M. J. Gagnon, E. Hilgenhof, R. Huggins, T. D. Eizenga, G. C. Gur, A. Rutten, T. Stein, N. Yao, S. Bellot, C. Bendahmane, M. Frary, A. Knapp, S. Sarkinen, T. Gillis, J. Van Eck, J. Schatz, M. C. Eshed, Y. Prohens, J. Vilanova, S. Lippman, Z. B. 2024-02-22 doi:10.1101/2024.02.21.581474 Cold Spring Harbor Laboratory Press 2024-02-22 <![CDATA[ Biomaterial Degradation Products affect Regenerating Glia Independently of Surface Properties ]]> https://biorxiv.org/content/10.1101/2024.02.20.581223v1?rss=1 Pawelec, K. Hix, J. M. L. Shapiro, E. 2024-02-23 doi:10.1101/2024.02.20.581223 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Computed Tomography of Polymeric Biomedical Implants from Bench to Bedside ]]> https://biorxiv.org/content/10.1101/2024.02.20.581229v1?rss=1 Pawelec, K. Schoborg, T. Shapiro, E. 2024-02-23 doi:10.1101/2024.02.20.581229 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ NFixDB (Nitrogen Fixation DataBase) - A Comprehensive Integrated Database for Robust 'Omics Analysis of Diazotrophs ]]> https://biorxiv.org/content/10.1101/2024.03.04.583350v1?rss=1 Bellanger, M. Figueroa, J. L. Tiemann, L. Friesen, M. L. White, R. A. 2024-03-06 doi:10.1101/2024.03.04.583350 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ CD47 is Required for Mesenchymal Progenitor Proliferation and Fracture Repair ]]> https://biorxiv.org/content/10.1101/2024.03.06.583756v1?rss=1 Zondervan, R. L. Capobianco, C. A. Jenkins, D. C. Reicha, J. D. Fredrick, L. M. Lam, C. Isenberg, J. S. Ahn, J. Marcucio, R. S. Hankenson, K. D. 2024-03-06 doi:10.1101/2024.03.06.583756 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Atypical Cell Cycle Regulation Promotes Mammary Stem Cell Expansion and Therapeutic Resistance ]]> https://biorxiv.org/content/10.1101/2024.03.05.583524v1?rss=1 Fifield, B.-A. Vusich, J. Haberfellner, E. Andrechek, E. R. Porter, L. A. 2024-03-08 doi:10.1101/2024.03.05.583524 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ Conformational switch of a peptide provides a novel strategy to design peptide loaded porous organic polymer for Pyroptosis pathway mediated cancer therapy ]]> https://biorxiv.org/content/10.1101/2024.03.05.583621v1?rss=1 Chattopahyay, K. Mishra, S. Sannigrahi, A. Ruidas, S. Chatterjee, S. Roy, K. Mishra, D. Maity, B. K. Paul, R. Das Saha, K. Bhaumik, A. 2024-03-08 doi:10.1101/2024.03.05.583621 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ Deep Plasma Proteome Profiling by Modulating Single Nanoparticle Protein Corona with Small Molecules ]]> https://biorxiv.org/content/10.1101/2024.03.06.582595v1?rss=1 Ashkarran, A. A. Gharibi, H. Modaresi, S. M. Sayadi, M. Jafari, M. Lin, Z. Ritz, D. Kakhniashvili, D. Sun, L. Landry, M. P. Dibavar, A. S. Mahmoudi, M. 2024-03-08 doi:10.1101/2024.03.06.582595 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ Sacbrood viruses and select Lake Sinai virus variants dominated Apis mellifera colonies symptomatic for European foulbrood ]]> https://biorxiv.org/content/10.1101/2024.03.11.584375v1?rss=1 Hesketh-Best, P. J. Fowler, P. D. Odogwu, N. M. Milbrath, M. O. Schroeder, D. C. 2024-03-11 doi:10.1101/2024.03.11.584375 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ A high resolution model of the grapevine leaf morphospace predicts synthetic leaves ]]> https://biorxiv.org/content/10.1101/2024.03.08.584086v1?rss=1 Chitwood, D. H. Torres-Lomas, E. Hadi, E. S. Peterson, W. L. G. Fischer, M. F. Rogers, S. E. He, C. Acierno, M. G. F. Azumaya, S. Benjamin, S. W. Chalise, D. P. Chess, E. E. Engelsma, A. J. Fu, Q. Jaikham, J. Knight, B. M. Kodjak, N. S. Lengyel, A. Munoz, B. L. Patterson, J. T. Rincon, S. I. Schumann, F. L. Shi, Y. Smith, C. C. St. Clair, M. K. Sweeney, C. S. Whitaker, P. Wu, J. Diaz-Garcia, L. 2024-03-13 doi:10.1101/2024.03.08.584086 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Graph Contrastive Learning of Subcellular-resolution Spatial Transcriptomics Improves Cell Type Annotation and Reveals Critical Molecular Pathways ]]> https://biorxiv.org/content/10.1101/2024.03.08.584192v1?rss=1 Lu, Q. Ding, J. Li, L. Chang, Y. Tang, J. Qiu, X. 2024-03-13 doi:10.1101/2024.03.08.584192 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Magnetic particle imaging reveals that iron-labeled extracellular vesicles accumulate in brains of mice with metastases ]]> https://biorxiv.org/content/10.1101/2024.03.12.584146v1?rss=1 View larger version (20K): org.highwire.dtl.DTLVardef@8cf21org.highwire.dtl.DTLVardef@56b6f0org.highwire.dtl.DTLVardef@104626eorg.highwire.dtl.DTLVardef@da60cd_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Toomajian, V. A. Tundo, A. Ural, E. E. Greeson, E. M. Contag, C. H. Makela, A. V. 2024-03-13 doi:10.1101/2024.03.12.584146 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Unveiling shared genetic regulators for plant architectural and biomass yield traits in sorghum ]]> https://biorxiv.org/content/10.1101/2024.03.13.584802v1?rss=1 Singh, A. Newton, L. A. Schnable, J. C. Thompson, A. M. 2024-03-14 doi:10.1101/2024.03.13.584802 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ The transcription factor ATML1 maintains giant cell identity by inducing synthesis of its own (very) long-chain fatty acid-containing ligands ]]> https://biorxiv.org/content/10.1101/2024.03.14.584694v1?rss=1 Vadde, B. V. L. Russell, N. J. Bagde, S. R. Askey, B. Saint-Antoine, M. M. Brownfield, B. A. Mughal, S. Apprill, L. E. Khosla, A. Clark, F. K. Schwarz, E. M. Alseekh, S. Fernie, A. R. Singh, A. Schrick, K. Fromme, J. C. Skirycz, A. Formosa-Jordan, P. Roeder, A. H. K. 2024-03-16 doi:10.1101/2024.03.14.584694 Cold Spring Harbor Laboratory Press 2024-03-16 <![CDATA[ Orthogonality of shell proteins across BMC subclasses in cyanobacteria ]]> https://biorxiv.org/content/10.1101/2024.03.19.585794v1?rss=1 MacCready, J. S. Dwyer, M. E. Kerfeld, C. A. Ducat, D. C. 2024-03-20 doi:10.1101/2024.03.19.585794 Cold Spring Harbor Laboratory Press 2024-03-20 <![CDATA[ Spatial Transcriptomic Analysis Identifies Epithelium-Macrophage Crosstalk in Endometriotic Lesions ]]> https://biorxiv.org/content/10.1101/2024.03.23.586434v1?rss=1 Burns, G. W. Fu, Z. Vegter, E. L. Madaj, Z. B. Greaves, E. Flores, I. Fazleabas, A. T. 2024-03-24 doi:10.1101/2024.03.23.586434 Cold Spring Harbor Laboratory Press 2024-03-24 <![CDATA[ Mass spectrometry-based top-down proteomics in nanomedicine: proteoform-specific measurement of protein corona ]]> https://biorxiv.org/content/10.1101/2024.03.22.586273v1?rss=1 Sadeghi, S. A. Ashkarran, A. A. Mahmoudi, M. sun, l. 2024-03-27 doi:10.1101/2024.03.22.586273 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Mutation of negative regulatory gene CEHC1 encoding an FBXO3 protein results in normoxic expression of HYDA genes in Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.1101/2024.03.22.586359v1?rss=1 Sun, X. LaVoie, M. Lefebvre, P. Gallaher, S. D. Glaesener, A. G. Strenkert, D. Mehta, R. Merchant, S. S. Silflow, C. D. 2024-03-27 doi:10.1101/2024.03.22.586359 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Nutrient Sensing Receptor GPRC6A Regulates mTORC1 Signaling and Tau Biology ]]> https://biorxiv.org/content/10.1101/2024.03.24.586459v1?rss=1 Ma, C. Campbell, K. Kovalenko, A. Sandusky-Beltran, L. A. Liang, H. Hunt, J. B. Calahatian, J. Kallupurackal, M. Pandey, S. Vasisht, M. Walter, M. Quadri, Z. Michalski, C. Fahnestock, M. Papangelis, A. Pedersen, D. S. Ulven, T. Nash, K. Selenica, M.-L. B. Morgan, D. Bickford, P. C. Lee, D. C. 2024-03-27 doi:10.1101/2024.03.24.586459 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Analysis Pipeline to Quantify Uterine Gland Structural Variations ]]> https://biorxiv.org/content/10.1101/2024.03.24.586502v1?rss=1 Khan, S. Alessio, A. Arora, R. 2024-03-27 doi:10.1101/2024.03.24.586502 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Thermotherapy has Sexually Dimorphic Responses in APP/PS1 Mice ]]> https://biorxiv.org/content/10.1101/2024.03.26.586836v1?rss=1 McFadden, S. A. Peck, M. R. Sime, L. N. Cox, M. F. Ikiz, E. D. Findley, C. A. Quinn, K. Fang, Y. Bartke, A. Hascup, E. R. Hascup, K. N. 2024-03-29 doi:10.1101/2024.03.26.586836 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Pitfalls and windfalls of detecting demographic declines using population genetics in long-lived species ]]> https://biorxiv.org/content/10.1101/2024.03.27.586886v1?rss=1 Clark, M. I. Fitzpatrick, S. W. Bradburd, G. S. 2024-03-30 doi:10.1101/2024.03.27.586886 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ Carbohydrate Hydrolytic Activity, Antibiotic Resistance and Stress Tolerance of Lacticaseibacillus paracasei BCRC-16100 and Lacticaseibacillus paracasei ZFM54 for Probiotics Using Genomic and Biochemical Approaches ]]> https://biorxiv.org/content/10.1101/2024.03.31.587454v1?rss=1 Gann, P. J. I. Fabia, J. Z. P. Baranda, S. M. Olivar, M. P. Agcaoili, M. J. T. Racho, A. J. J. 2024-04-01 doi:10.1101/2024.03.31.587454 Cold Spring Harbor Laboratory Press 2024-04-01 <![CDATA[ Identification of cell-type-specific response to silicon treatment in soybean leaves through single nucleus RNA-sequencing ]]> https://biorxiv.org/content/10.1101/2024.04.01.587592v1?rss=1 Devkar, V. Dagostino, L. Kshetry, A. O. Yong, L. Nadaf, A. B. Thirumlaikumar, V. P. Skirycz, A. Ma, J. Stupar, R. Herrera Estrella, L. Deshmukh, R. Patil, G. B. 2024-04-01 doi:10.1101/2024.04.01.587592 Cold Spring Harbor Laboratory Press 2024-04-01 <![CDATA[ Intrapartum antibiotic prophylaxis selects for mutators in group B streptococci among persistently colonized patients ]]> https://biorxiv.org/content/10.1101/2024.04.01.587590v1?rss=1 Pell, M. E. Blankenship, H. M. Gaddy, J. A. Davies, H. D. Manning, S. D. 2024-04-02 doi:10.1101/2024.04.01.587590 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Terroir and rootstock effects on leaf shape in California Central Valley vineyards ]]> https://biorxiv.org/content/10.1101/2024.04.02.587833v1?rss=1 Migicovsky, Z. Swift, J. F. Awale, M. Helget, Z. Klein, L. L. Pinkner, L. Woodhouse, K. Cousins, P. Fennell, A. Y. Miller, A. Chitwood, D. H. 2024-04-03 doi:10.1101/2024.04.02.587833 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Reduced selection during sweeps lead to adaptive momentum on rugged landscapes ]]> https://biorxiv.org/content/10.1101/2024.04.08.588357v1?rss=1 Bohm, C. Ragusa, V. R. Ofria, C. Lenski, R. E. Adami, C. 2024-04-11 doi:10.1101/2024.04.08.588357 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ Remote sensing for estimating genetic parameters of biomass accumulation and modeling stability of growth curves in alfalfa ]]> https://biorxiv.org/content/10.1101/2024.04.08.588572v1?rss=1 Thapa, R. Kunze, K. Hansen, J. Pierce, C. Moore, V. Ray, I. Wickes-Do, L. Morales, N. Sabadin, F. Santantonio, N. Gore, M. A. Robbins, K. R. 2024-04-11 doi:10.1101/2024.04.08.588572 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ Modeling With Uncertainty Quantification Identifies Essential Features of a Non-Canonical Algal Carbon-Concentrating Mechanism ]]> https://biorxiv.org/content/10.1101/2024.04.12.589284v1?rss=1 Steensma, A. K. Kaste, J. A. M. Heo, J. Orr, D. Sung, C.-L. Shachar-Hill, Y. Walker, B. J. 2024-04-15 doi:10.1101/2024.04.12.589284 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ Estimation of Species Abundance Based on the Number of Segregating Sites using Environmental DNA (eDNA) ]]> https://biorxiv.org/content/10.1101/2024.04.15.589638v1?rss=1 0.9; P < 0.01). Results from the in situ experiment further validated the correlation (R2 = 0.70, P < 0.01), and such correlation was not affected by biotic factors, including body size and feeding behavior (P > 0.05). Results of the cross-validation test also showed that the number of segregating sites predicted species abundance with less bias and variability than the eDNA concentration. Overall, the number of segregating sites correlates stronger with species abundance and also provides a better estimate than eDNA concentration. This advancement can significantly enhance the quantitative capabilities of eDNA technology. ]]> Ai, Q. Yuan, H. Wang, Y. Li, C. 2024-04-20 doi:10.1101/2024.04.15.589638 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Global patterns in the evolutionary relations between seed mass and germination traits ]]> https://biorxiv.org/content/10.1101/2024.04.16.589747v1?rss=1 Maleki, K. Vandelook, F. Saatkamp, A. Maleki, K. Heshmati, S. Soltani, E. 2024-04-20 doi:10.1101/2024.04.16.589747 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Effects of Repetitive Mild Traumatic Brain Injury on Corticotropin-Releasing Factor Modulation of Lateral Habenula Excitability and Motivated Behavior ]]> https://biorxiv.org/content/10.1101/2024.04.16.589760v1?rss=1 Flerlage, W. J. Simmons, S. C. Thomas, E. H. Gouty, S. Tsuda, M. C. Wu, T. J. Armstrong, R. S. Cox, B. M. Nugent, F. S. 2024-04-20 doi:10.1101/2024.04.16.589760 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Native proteomics by capillary zone electrophoresis-mass spectrometry ]]> https://biorxiv.org/content/10.1101/2024.04.24.590970v1?rss=1 Wang, Q. Wang, Q. Qi, Z. Moeller, W. Wysocki, V. H. Sun, L. 2024-04-28 doi:10.1101/2024.04.24.590970 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Standardizing protein corona characterization in nanomedicine: a multi-center study to enhance reproducibility and data homogeneity ]]> https://biorxiv.org/content/10.1101/2024.04.25.591109v1?rss=1 Ashkarran, A. A. Gharibi, H. Modaresi, S. M. Saei, A. A. Mahmoudi, M. 2024-04-28 doi:10.1101/2024.04.25.591109 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Dispersed Transcription Start Sites Modulate uORF-Mediated Regulation in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2024.04.25.591216v1?rss=1 Wu, H.-Y. L. Hsu, P. Y. 2024-04-28 doi:10.1101/2024.04.25.591216 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Reversible host cell surface remodelling limits immune recognition and maximizes transmission of Plasmodium falciparum gametocytes ]]> https://biorxiv.org/content/10.1101/2024.04.30.591837v1?rss=1 Ngotho, P. Dantzler Press, K. Peedell, M. Muasya, W. Omondi, B. R. Otoboh, S. O. Seydel, K. B. Kapulu, M. Laufer, M. Taylor, T. E. Bousema, T. Marti, M. 2024-04-30 doi:10.1101/2024.04.30.591837 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ Proteomic Dynamics and Heat Stress Response in Arabidopsis Seedlings ]]> https://biorxiv.org/content/10.1101/2024.04.30.591943v1?rss=1 Fan, K.-T. Xu, Y. 2024-04-30 doi:10.1101/2024.04.30.591943 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ Forest edge landscape context affects mosquito community composition and risk of pathogen emergence ]]> https://biorxiv.org/content/10.1101/2024.04.30.591911v1?rss=1 Hendy, A. Fe, N. F. Pedrosa, I. Girao, A. Figueira dos Santos, T. N. Mendonca, C. R. Andes Junior, J. T. Assuncao, F. P. Costa, E. R. Sluydts, V. Gordo, M. Scarpassa, V. M. Buenemann, M. Lacerda, M. V. G. d. Mourao, M. P. G. Vasilakis, N. Hanley, K. A. 2024-05-03 doi:10.1101/2024.04.30.591911 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Repeat modules and N-linked glycans define structure and antigenicity of a critical enterotoxigenic E. coli adhesin ]]> https://biorxiv.org/content/10.1101/2024.05.08.593125v1?rss=1 Berndsen, Z. T. Akhtar, M. Thapa, M. Vickers, T. J. Schmitz, A. Torres, J. Kumar, P. Khatoon, N. Sheikh, A. Hamrick, M. Diedrich, J. Martinez-Bartolome, S. Garrett, P. Yates, J. Turner, J. Laird, R. M. Porter, C. K. Poly, F. Copps, J. Ellebedy, A. Ward, A. Fleckenstein, J. M. 2024-05-08 doi:10.1101/2024.05.08.593125 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ Post-translational Modification of α-Synuclein Modifies Monomer Dynamics and Aggregation Kinetics ]]> https://biorxiv.org/content/10.1101/2024.05.06.592473v1?rss=1 Gamage, K. Wang, B. Hard, E. Van, T. Galesic, A. Phillips, G. Pratt, M. R. Lapidus, L. 2024-05-09 doi:10.1101/2024.05.06.592473 Cold Spring Harbor Laboratory Press 2024-05-09 <![CDATA[ Activity-dependent FosB gene expression negatively regulates mast cell functions. ]]> https://biorxiv.org/content/10.1101/2024.05.06.592755v1?rss=1 View larger version (48K): org.highwire.dtl.DTLVardef@190be2corg.highwire.dtl.DTLVardef@1b53f9borg.highwire.dtl.DTLVardef@631997org.highwire.dtl.DTLVardef@250bc7_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Duque-Wilckens, N. Maradiaga, N. Yeh, S.-Y. Joseph, D. Srinavasan, V. Thelen, K. Sotomayor, F. Durga, K. Nestler, E. J. Moeser, A. Robison, A. J. 2024-05-10 doi:10.1101/2024.05.06.592755 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Complete list of canonical post-transcriptional modifications in the Bacillus subtilis ribosome and their link to RbgA driven large subunit assembly ]]> https://biorxiv.org/content/10.1101/2024.05.10.593627v1?rss=1 Popova, A. M. Jain, N. Dong, X. Abdollah-Nia, F. Britton, R. A. Williamson, J. R. 2024-05-11 doi:10.1101/2024.05.10.593627 Cold Spring Harbor Laboratory Press 2024-05-11 <![CDATA[ LAGOS-US LANDSAT: Remotely sensed water quality estimates for U.S. lakes over 4 ha from 1984 to 2020 ]]> https://biorxiv.org/content/10.1101/2024.05.10.593626v1?rss=1 4 ha (1984-2020). WQ estimates use machine-learning models with Landsat imagery and ground-truthed Water Quality Portal data (LAGOS-US LIMNO). The dataset includes: (a) 45.9 million whole-lake water reflectance (six bands and 15 band ratios); (b) 740,627 matchups from 13,756 lakes with in situ data for six WQ variables: chlorophyll, Secchi depth, true color, dissolved organic carbon, total suspended solids, or turbidity; and (c) predictions for each WQ variable across lake-time combinations with quality imagery. Two random forest models were fit for each variable: Holdout-data (75/25 spatially representative train-test split) and Full-data (trained on all data). Variance explained for the Full-data predictions ranged from 20.7% for TSS to 63.7% for Secchi depth. Imagery underwent cloud and pixel quality control, and workflow components were validated guiding future research. ]]> Hanly, P. J. Webster, K. E. Soranno, P. A. 2024-05-14 doi:10.1101/2024.05.10.593626 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Climate resilience conserved in global germplasm repositories: Picking the most promising parents for agile plant breeding ]]> https://biorxiv.org/content/10.1101/2024.05.11.593573v1?rss=1 Campbell, Q. Castaneda-Alvarez, N. Domingo, R. Bishop-von Wettberg, E. Runck, B. Nandkangre, H. McCormick, A. Fumia, N. Neyhart, J. Kilian, B. Wambugu, P. Nyamongo, D. Hubner, S. Sitar, S. Thompson, A. Rieseberg, L. Gore, M. A. Kantar, M. B. 2024-05-14 doi:10.1101/2024.05.11.593573 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Phenotype and function of IL-10 producing NK cells in individuals with malaria experience. ]]> https://biorxiv.org/content/10.1101/2024.05.11.593687v1?rss=1 McNitt, S. A. Dick, J. K. Hernandez Castaneda, M. Sangala, J. A. Pierson, M. Macchietto, M. Burrack, K. S. Crompton, P. D. Seydel, K. B. Hamilton, S. E. Hart, G. T. 2024-05-14 doi:10.1101/2024.05.11.593687 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Acceleration of genome rearrangement in clitellate annelids ]]> https://biorxiv.org/content/10.1101/2024.05.12.593736v1?rss=1 Schultz, D. T. Heath-Heckman, E. A. C. Winchell, C. J. Kuo, D.-H. T. Yu, Y.-s. Oberauer, F. Kocot, K. Cho, S.-J. Simakov, O. Weisblat, D. A. 2024-05-14 doi:10.1101/2024.05.12.593736 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ De novo pyrimidine biosynthesis inhibition synergizes with BCL-XL targeting in pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2024.05.17.594738v1?rss=1 Zhang, H. Yu, Q. Santana-Codina, N. Poupault, C. Campos, C. Qin, X. Padhye, A. Sindoni, N. Kuljanin, M. Wang, J. Dorman, M. J. Aguirre, A. J. Dougan, S. K. Sarosiek, K. A. Mancias, J. D. 2024-05-21 doi:10.1101/2024.05.17.594738 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Parkinson's disease-associated shifts between DNA methylation and DNA hydroxymethylation in human brain ]]> https://biorxiv.org/content/10.1101/2024.05.21.595193v1?rss=1 Choza, J. I. Virani, M. Kuhn, N. C. Adams, M. Kochmanski, J. Bernstein, A. I. 2024-05-22 doi:10.1101/2024.05.21.595193 Cold Spring Harbor Laboratory Press 2024-05-22 <![CDATA[ A simple active fluid model unites cytokinesis, cell crawling, and axonal outgrowth ]]> https://biorxiv.org/content/10.1101/2024.05.22.595337v1?rss=1 Craig, E. M. Oprea, F. Alam, S. Grodsky, A. Miller, K. E. 2024-05-23 doi:10.1101/2024.05.22.595337 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ Quantification of rose rosette emaravirus (RRV) titers in eriophyoid mites: insights into viral dynamics and vector competency ]]> https://biorxiv.org/content/10.1101/2024.05.23.595398v1?rss=1 Druciarek, T. Z. Rojas, A. Tzanetakis, I. 2024-05-25 doi:10.1101/2024.05.23.595398 Cold Spring Harbor Laboratory Press 2024-05-25 <![CDATA[ A reference-free algorithm discovers regulation in the plant transcriptome ]]> https://biorxiv.org/content/10.1101/2024.05.23.595613v1?rss=1 Meyer, E. Saldivar, E. Kokot, M. Xue, B. Deorowicz, S. Rhee, S. Y. Salzman, J. 2024-05-25 doi:10.1101/2024.05.23.595613 Cold Spring Harbor Laboratory Press 2024-05-25 <![CDATA[ Complimentary vertebrate Wac models exhibit phenotypes relevant to DeSanto-Shinawi Syndrome ]]> https://biorxiv.org/content/10.1101/2024.05.26.595966v1?rss=1 Lee, K.-H. Stafford, A. M. Pacheco-Vergara, M. Cichewicz, K. Canales, C. P. Seban, N. Corea, M. Rahbarian, D. Bonekamp, K. E. Gillie, G. R. Pacheco-Cruz, D. Gill, A. M. Hwang, H.-E. Uhl, K. Shinawi, M. Li, X. Obenaus, A. Crandall, S. R. Jeong, J. Nord, A. S. Kim, C.-H. Vogt, D. 2024-05-26 doi:10.1101/2024.05.26.595966 Cold Spring Harbor Laboratory Press 2024-05-26 <![CDATA[ Plant hormone manipulation impacts salt spray tolerance, which preempts herbivory as a driver of local adaptation in the yellow monkeyflower, Mimulus guttatus ]]> https://biorxiv.org/content/10.1101/2024.05.23.595619v1?rss=1 Toll, K. Blanchard, M. Scharnagl, A. Lowry, D. Holeski, L. 2024-05-28 doi:10.1101/2024.05.23.595619 Cold Spring Harbor Laboratory Press 2024-05-28 <![CDATA[ Active E. coli heteromeric acetyl-CoA carboxylase forms polymorphic helical tubular filaments ]]> https://biorxiv.org/content/10.1101/2024.05.28.596234v1?rss=1 Xu, X. Silva de Sousa, A. Boram, T. J. Jiang, W. Lohman, J. R. 2024-05-28 doi:10.1101/2024.05.28.596234 Cold Spring Harbor Laboratory Press 2024-05-28 <![CDATA[ Detection of neutralizing antibodies against arboviruses from liver homogenates ]]> https://biorxiv.org/content/10.1101/2024.05.28.596289v1?rss=1 Costa, T. A. Arruda, M. S. Garcia-Oliveira, G. F. Reis, E. V. S. Guimaraes, A. C. D. S. Moreira, G. D. Arias, N. E. C. Beirao, M. d. V. Vasilakis, N. Hanley, K. A. Drumond, B. P. 2024-05-28 doi:10.1101/2024.05.28.596289 Cold Spring Harbor Laboratory Press 2024-05-28 <![CDATA[ Circulating miR-126-3p is a mechanistic biomarker for knee osteoarthritis ]]> https://biorxiv.org/content/10.1101/2024.05.31.596603v1?rss=1 Wilson, T. G. Baghel, M. Kaur, N. Datta, I. Loveless, I. Potla, P. Mendez, D. Hansen, L. Baker, K. C. Lynch, T. S. Moutzouros, V. Davis, J. Ali, S. A. 2024-06-03 doi:10.1101/2024.05.31.596603 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Early life adversity promotes gastrointestinal dysfunction through a sex-dependent phenotypic switch in enteric glia ]]> https://biorxiv.org/content/10.1101/2024.05.31.596805v1?rss=1 Gonzales, J. A. Dharshika, C. Mazhar, K. Morales-Soto, W. McClain, J. L. Moeser, A. J. Nault, R. Price, T. J. Gulbransen, B. D. 2024-06-03 doi:10.1101/2024.05.31.596805 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Insights into Immune Gene Prediction and Function Through the Evolutionary History of ADF Gene Family ]]> https://biorxiv.org/content/10.1101/2024.05.31.596878v1?rss=1 Chen, H. Day, B. 2024-06-03 doi:10.1101/2024.05.31.596878 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Annotating publicly-available samples and studies using interpretable modeling of unstructured metadata ]]> https://biorxiv.org/content/10.1101/2024.06.03.597206v1?rss=1 Yuan, H. Hicks, P. Ahmadian, M. Johnson, K. Krishnan, A. 2024-06-04 doi:10.1101/2024.06.03.597206 Cold Spring Harbor Laboratory Press 2024-06-04 <![CDATA[ Unifying the Research Landscape of Desiccation Tolerance to Identify Trends, Gaps, and Opportunities ]]> https://biorxiv.org/content/10.1101/2024.06.06.597802v1?rss=1 Lotreck, S. G. Ghassemi, M. VanBuren, R. 2024-06-07 doi:10.1101/2024.06.06.597802 Cold Spring Harbor Laboratory Press 2024-06-07 <![CDATA[ Functional Changes to Achilles Tendon and Enthesis in a Mouse Model of an Adolescent Masculine Gender-Affirming Hormone Treatment ]]> https://biorxiv.org/content/10.1101/2024.06.10.598308v1?rss=1 Hold, L. A. Phillips, T. Cordts, P. Steltzer, S. Bae, S.-H. Henry, B. W. Migotsky, N. Grossman, S. Cruz, C. D. Padmanabhan, V. Moravek, M. Shikanov, A. Abraham, A. C. Killian, M. L. 2024-06-12 doi:10.1101/2024.06.10.598308 Cold Spring Harbor Laboratory Press 2024-06-12 <![CDATA[ Local adaptation of both plant and pathogen: an arms-race compromise in switchgrass rust ]]> https://biorxiv.org/content/10.1101/2024.06.11.595169v1?rss=1 VanWallendael, A. Wijewardana, C. Bonnette, J. Vormwald, L. Fritschi, F. B. Boe, A. Chambers, S. Mitchell, R. Rouquette, F. M. Wu, Y. Fay, P. A. Jastrow, J. D. Lovell, J. Juenger, T. Lowry, D. B. 2024-06-13 doi:10.1101/2024.06.11.595169 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Large-scale genotyping and meta-analysis of PIEZO1 short tandem repeat alleles suggest a modest association with malaria susceptibility ]]> https://biorxiv.org/content/10.1101/2024.06.12.598682v1?rss=1 Leffler, E. M. Band, G. Jeffreys, A. E. Rowlands, K. Hubbart, C. Bojang, K. A. Conway, D. J. Jallow, M. Sisay-Joof, F. D'Alessandro, U. Ndila, C. M. Macharia, A. W. Marsh, K. Williams, T. N. Kachala, D. Molyneux, M. Nyirongo, V. Taylor, T. E. Rockett, K. A. Kwiatkowski, D. P. 2024-06-13 doi:10.1101/2024.06.12.598682 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Genotypic and Phenotypic Analyses Show Ralstonia solanacearum Cool Virulence is a Quantitative Trait Not Restricted to 'Race 3 biovar 2' ]]> https://biorxiv.org/content/10.1101/2024.06.13.598915v1?rss=1 Dewberry, R. J. Sharma, P. Prom, J. L. Kinscherf, N. A. Lowe-Power, T. Mazloom, R. Zhang, X. Arif, M. Stulberg, M. Heath, L. S. Eversole, K. Beattie, G. A. Vinatzer, B. Allen, C. 2024-06-13 doi:10.1101/2024.06.13.598915 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ The Roles of Drift and Selection on Short Stamen Loss in Arabidopsis thaliana along an Elevational Gradient in the Spanish Pyrenees ]]> https://biorxiv.org/content/10.1101/2024.06.12.598645v1?rss=1 Buysse, S. F. Perez, S. G. Puzey, J. R. Garrison, A. Bradburd, G. S. Oakley, C. G. Pico, X. Tonsor, S. J. Josephs, E. B. Conner, J. K. 2024-06-14 doi:10.1101/2024.06.12.598645 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ Unravelling biological processess and EGFR pathway regulation by the receptor-like protein tyrosine phosphatase PTPRH in non-small cell lung cancer ]]> https://biorxiv.org/content/10.1101/2024.06.13.598886v1?rss=1 Ortiz, M. M. O. Patel, D. M. Swiatnicki, M. Andrechek, E. R. 2024-06-16 doi:10.1101/2024.06.13.598886 Cold Spring Harbor Laboratory Press 2024-06-16 <![CDATA[ Chromosome-scale Salvia hispanica L. (Chia) genome assembly reveals rampant Salvia interspecies introgression ]]> https://biorxiv.org/content/10.1101/2024.06.14.598901v1?rss=1 Brose, J. Hamilton, J. P. Schlecht, N. Zhao, D. Mejia-Ponce, P. M. Cruz Perez, A. Vaillancourt, B. Wood, J. C. Edger, P. P. Montes-Hernandez, S. Orozco de Rosas, G. Hamberger, B. Cibrian Jaramillo, A. Buell, C. R. 2024-06-17 doi:10.1101/2024.06.14.598901 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Structural variants contribute to phenotypic variation in maize ]]> https://biorxiv.org/content/10.1101/2024.06.14.599082v1?rss=1 Catlin, N. S. Agha, H. I. Platts, A. E. Munasinghe, M. Hirsch, C. S. Jospehs, E. B. 2024-06-17 doi:10.1101/2024.06.14.599082 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Impact of genome assemblies, genotyping methods, variant types, ploidy levels and population structures on genomic prediction in switchgrass ]]> https://biorxiv.org/content/10.1101/2024.06.17.599440v1?rss=1 Wang, P. Meng, F. Azodi, C. B. D. Ab, K. S. Casler, M. D. Shiu, S.-H. 2024-06-19 doi:10.1101/2024.06.17.599440 Cold Spring Harbor Laboratory Press 2024-06-19 <![CDATA[ Interdisciplinarity through internationality: results from a US-Mexico graduate course bridging computational and plant science ]]> https://biorxiv.org/content/10.1101/2024.06.19.599776v1?rss=1 Chitwood, D. H. Rougon-Cardoso, A. VanBuren, R. 2024-06-21 doi:10.1101/2024.06.19.599776 Cold Spring Harbor Laboratory Press 2024-06-21 <![CDATA[ PKA Activity-Driven Modulation of Bidirectional Long-Distance transport of Lysosomal vesicles During Synapse Maintenance ]]> https://biorxiv.org/content/10.1101/2024.06.28.601272v1?rss=1 Badal, K. K. Zhao, Y. Raveendra, B. L. Lozano-Villada, S. Miller, K. E. Puthanveettil, S. 2024-06-30 doi:10.1101/2024.06.28.601272 Cold Spring Harbor Laboratory Press 2024-06-30 <![CDATA[ Camelina CircRNA Landscape: Implications for Gene Regulation and Fatty Acid Metabolism ]]> https://biorxiv.org/content/10.1101/2024.07.02.601705v1?rss=1 Utley, D. Edwards, B. Budnick, A. Grotewold, E. Sederoff, H. 2024-07-03 doi:10.1101/2024.07.02.601705 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ A pilot study for deciphering post-translational modifications and proteoforms of tau protein by capillary electrophoresis-mass spectrometry ]]> https://biorxiv.org/content/10.1101/2024.07.04.602093v1?rss=1 Fang, F. Xu, T. Chien Hagar, H.-T. Hovde, S. Kuo, M.-H. Sun, L. 2024-07-08 doi:10.1101/2024.07.04.602093 Cold Spring Harbor Laboratory Press 2024-07-08 <![CDATA[ Impacts of Antiretroviral Therapy on the Oral Microbiome and Periodontal Health of Feline Immunodeficiency Virus Positive Cats ]]> https://biorxiv.org/content/10.1101/2024.07.10.602918v1?rss=1 Bashor, L. Rawlinson, J. E. Kozakiewicz, C. P. Behzadi, E. Miller, C. Kim, J. Conry, M. Nehring, M. Carver, S. Abdo, Z. VandeWoude, S. 2024-07-11 doi:10.1101/2024.07.10.602918 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Quantifying seed rain patterns in a remnant and a chronosequence of restored tallgrass prairies in north central Missouri ]]> https://biorxiv.org/content/10.1101/2024.07.10.602969v1?rss=1 Wynne, K. C. Parker-Smith, M. J. Murdock, E. M. Sullivan, L. L. 2024-07-16 doi:10.1101/2024.07.10.602969 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Effects of clinically relevant radionuclides on the activation of a type I interferon response by radiopharmaceuticals in syngeneic murine tumor models ]]> https://biorxiv.org/content/10.1101/2024.07.10.602990v1?rss=1 Kerr, C. P. Sheehan-Klenk, J. Grudzinski, J. J. Adam, D. P. Nguyen, T. P. T. de Aguiar Ferreira, C. Bates, A. M. Jin, W. J. Kwon, O. Olson, A. P. Lin, W. Hyun, M. Jagodinsky, J. C. Powers, M. Sriramaneni, R. N. Clark, P. A. Shea, A. G. Comas Rojas, H. Choi, C. Massey, C. F. Zangl, L. M. Pinchuk, A. N. Aluicio-Sarduy, E. Kim, K. Engle, J. W. Hernandez, R. Bednarz, B. P. Weichert, J. P. Morris, Z. S. 2024-07-16 doi:10.1101/2024.07.10.602990 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Species wide inventory of Arabidopsis thaliana organellar variation reveals ample phenotypic variation for photosynthetic performance ]]> https://biorxiv.org/content/10.1101/2024.07.12.603232v1?rss=1 Theeuwen, T. P. J. M. Wijfjes, R. Y. Dorussen, D. Lawson, A. W. Lind, J. Jin, K. Boekeloo, J. Tijink, D. Hall, D. Hanhart, C. Becker, F. F. M. van Eeuwijk, F. A. Kramer, D. M. Wijnker, E. Harbinson, J. Koornneef, M. Aarts, M. G. M. 2024-07-16 doi:10.1101/2024.07.12.603232 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Engineered endosymbionts that modulate primary macrophage function and attenuate tumor growth by shifting the tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2024.07.18.604190v1?rss=1 Madsen, C. S. Makela, A. V. Maduka, C. V. Greeson, E. M. Tundo, A. Ural, E. Kulkarni, S. H. Zarea, A. Kiupel, M. Sayadi, M. Contag, C. H. 2024-07-19 doi:10.1101/2024.07.18.604190 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ Eyes on VR: Unpacking the Causal Chain Between Exposure, Reception, and Retention for Emotional Billboard Messages ]]> https://biorxiv.org/content/10.1101/2024.07.19.604208v1?rss=1 Cho, H. J. Lim, S. Turner, M. M. Bente, G. Schmalzle, R. 2024-07-19 doi:10.1101/2024.07.19.604208 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ A transposable element insertion in IAA16 interrupts normal splicing and generates a novel dicamba resistance allele in Bassia scoparia ]]> https://biorxiv.org/content/10.1101/2024.07.19.604363v1?rss=1 Montgomery, J. S. Soni, N. Marques Hill, S. Morran, S. Patterson, E. Edwards, S. Ratnayake, S. Hung, Y.-H. Pandesha, P. H. Slotkin, R. K. Dayan, F. E. Gaines, T. A. 2024-07-23 doi:10.1101/2024.07.19.604363 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Toward improved uncertainty quantification in predictions of forest dynamics: A dynamical model of forest change ]]> https://biorxiv.org/content/10.1101/2024.07.22.604669v1?rss=1 Itter, M. S. Finley, A. O. 2024-07-23 doi:10.1101/2024.07.22.604669 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ A novel method for integrating genomic and Tn-Seq data to identify common in vivo fitness mechanisms across multiple bacterial species ]]> https://biorxiv.org/content/10.1101/2024.07.24.604993v1?rss=1 Fouts, D. E. Clarke, T. H. Brown, A. N. Ottosen, E. N. Holmes, C. L. Moricz, B. S. Mason, S. Sinha, R. Severin, G. B. Anderson, M. T. DiRita, V. Bachman, M. A. Mobley, H. L. T. 2024-07-25 doi:10.1101/2024.07.24.604993 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ Introgression dynamics of sex-linked chromosomal inversions shape the Malawi cichlid adaptive radiation ]]> https://biorxiv.org/content/10.1101/2024.07.28.605452v1?rss=1 Blumer, L. M. Burskaia, V. Artiushin, I. Saha, J. Camacho Garcia, J. Elkin, J. Fischer, B. Zhou, C. Gresham, S. Malinsky, M. Linderoth, T. Sawasawa, W. Bista, I. Hickey, A. Kucka, M. Louzada, S. Zatha, R. Yang, F. Rusuwa, B. Santos, M. E. Chan, Y. F. Joyce, D. A. Böhne, A. Miska, E. A. Ngochera, M. Turner, G. F. Durbin, R. Svardal, H. 2024-07-29 doi:10.1101/2024.07.28.605452 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ K-mer Genome-wide Association Study for Anthracnose and BCMV Resistance in the Andean Diversity Panel ]]> https://biorxiv.org/content/10.1101/2024.07.29.605481v1?rss=1 Wiersma, A. Hamilton, J. P. Vaillanoucrt, B. Brose, J. Awale, H. E. Wright, E. M. Kelly, J. D. Buell, C. R. 2024-07-30 doi:10.1101/2024.07.29.605481 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ Transcriptome profiling of maize transcription factor mutants to probe gene regulatory network predictions ]]> https://biorxiv.org/content/10.1101/2024.07.30.605884v1?rss=1 Ellison, E. L. Zhou, P. Chu, Y.-H. Hermanson, P. Gomez-Cano, L. Myers, Z. A. Abnave, A. Gray, J. Hirsch, C. N. Grotewold, E. Springer, N. M. 2024-07-31 doi:10.1101/2024.07.30.605884 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ Imputing abundance of over 2500 surface proteins from single-cell transcriptomes with context-agnostic zero-shot deep ensembles ]]> https://biorxiv.org/content/10.1101/2024.07.31.605432v1?rss=1 2500 proteins from single-cell transcriptomes, we demonstrate the broad applications of SPIDER including cell type annotation, biomarker/target identification, and cell-cell interaction analysis in hepatocellular carcinoma and colorectal cancer. ]]> Chen, R. Zhou, J. Chen, B. 2024-07-31 doi:10.1101/2024.07.31.605432 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ IDENTIFICATION OF IMMUNE RESPONSE AND RNA NETWORK OF RHEUMATOID ARTHRITIS AND MOLECULAR DOCKING OF CELASTRUS PANICULATUS AS POTENTIAL THERAPEUTIC AGENT ]]> https://biorxiv.org/content/10.1101/2024.07.30.605947v1?rss=1 SWAMINATHAN, V. 2024-08-01 doi:10.1101/2024.07.30.605947 Cold Spring Harbor Laboratory Press 2024-08-01 <![CDATA[ A novel hybrid Wireless Integrated Sensing Detector for simultaneous EEG and MRI (WISDEM) ]]> https://biorxiv.org/content/10.1101/2024.07.31.606016v1?rss=1 Chen, Y. Qian, W. Razansky, D. Yu, X. Qian, C. 2024-08-01 doi:10.1101/2024.07.31.606016 Cold Spring Harbor Laboratory Press 2024-08-01 <![CDATA[ Sustained Strain Applied at High Rates Drives Dynamic Tensioning in Epithelial Cells ]]> https://biorxiv.org/content/10.1101/2024.07.31.606021v1?rss=1 Safa, B. T. Rosenbohm, J. Esfahani, A. M. Minnick, G. Moghaddam, A. O. Lavrik, N. V. Huang, C. Charras, G. Kabla, A. Yang, R. 2024-08-01 doi:10.1101/2024.07.31.606021 Cold Spring Harbor Laboratory Press 2024-08-01 <![CDATA[ Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans ]]> https://biorxiv.org/content/10.1101/2024.08.01.606178v1?rss=1 300 P. agglomerans strains associated with symptomatic onion plants and bulbs from public culture collections, research laboratories, and a multi-year survey in 11 states in the USA. Genome assemblies were generated for 87 P. agglomerans strains that showed a range in onion virulence phenotypes. Combining the 87 genome assemblies with 100 high-quality, public P. agglomerans genome assemblies identified two well-represented and well-supported P. agglomerans phylogroups. Strains causing severe symptoms on onion leaves and bulbs were only identified in Phylogroup II and encoded the HiVir biosynthetic cluster for the phytotoxin pantaphos, supporting the role of HiVir as a crucial pathogenicity factor. Using a MASH-based plasmid classification system, the P. agglomerans HiVir cluster was determined to be encoded in two distinct plasmid contexts: 1) as an accessory gene cluster on a conserved P. agglomerans plasmid (pAggl), or 2) on a mosaic cluster of plasmids common among onion strains (pOnion). Analysis of closed genomes of P. agglomerans revealed that the pOnion plasmids harbored alt genes responsible for encoding tolerance to the thiosulfinate defensive chemistry in Allium spp. Additionally, many of these pOnion plasmids harbored cop gene clusters, which confer resistance to copper. However, the pOnion plasmids encoded the HiVir cluster less frequently. We demonstrated that the pOnion plasmid pCB1C, encoding HiVir and alt clusters as well as an intact conjugative type IV secretion system (T4SS), can act as a natively mobilizable pathogenicity plasmid that transforms P. agglomerans Phylogroup I strains, including environmental strains, into virulent pathogens of onion. This work indicates a central role for plasmids and plasmid ecology in mediating P. agglomerans interactions with onion plants, with potential implications for onion bacterial disease management. ]]> Shin, G. Y. Asselin, J. A. Smith, A. Aegerter, B. Coutinho, T. Zhao, M. Dutta, B. Mazzone, J. Neupane, R. Gugino, B. Hoepting, C. Khanal, M. Malla, S. Nischwitz, C. Sidhu, J. Burke, A. M. Davey, J. Uchanski, M. Derie, M. L. du Toit, L. J. Stresow, S. Bonasera, J. M. Stodghill, P. Kvitko, B. H. 2024-08-01 doi:10.1101/2024.08.01.606178 Cold Spring Harbor Laboratory Press 2024-08-01 <![CDATA[ Varietal screening of newly developed blackgram genotypes against Cercospora Leaf Spot (Cercospora canescens) in the Terai region of Nepal. ]]> https://biorxiv.org/content/10.1101/2024.08.12.607552v1?rss=1 Shrestha, S. Bohara, S. Oli, S. Nainabasti, A. Bohara, K. R. Upadhyaya, K. Banet, I. 2024-08-12 doi:10.1101/2024.08.12.607552 Cold Spring Harbor Laboratory Press 2024-08-12 <![CDATA[ The role of mitochondrial complex I in the proinflammatory response to polylactide implants ]]> https://biorxiv.org/content/10.1101/2024.08.12.607680v1?rss=1 Maduka, C. V. Makela, A. V. Tundo, A. Ural, E. Stivers, K. B. Alhaj, M. Narayan, R. Goodman, S. B. Ashammakhi, N. Elisseeff, J. H. Hankenson, K. D. Contag, C. H. 2024-08-15 doi:10.1101/2024.08.12.607680 Cold Spring Harbor Laboratory Press 2024-08-15 <![CDATA[ Allopolyploidy expanded gene content but not pangenomic variation in the hexaploid oilseed Camelina sativa ]]> https://biorxiv.org/content/10.1101/2024.08.13.607619v1?rss=1 Bird, K. A. Brock, J. R. Grabowski, P. P. Harder, A. M. Shu, S. Barry, K. Boston, L. Daum, C. Guo, J. Lipzen, A. Walstead, R. Grimwood, J. Schmutz, J. Lu, C. Edger, P. P. Lovell, J. T. Kliebenstein, D. J. 2024-08-16 doi:10.1101/2024.08.13.607619 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ Comparative Analysis of Polysaccharide and Cell Wall Structure in Aspergillus nidulans and Aspergillus fumigatus by Solid-State NMR ]]> https://biorxiv.org/content/10.1101/2024.08.13.607833v1?rss=1 Gautam, I. Yarava, J. R. Xu, Y. Li, R. Scott, F. J. Mentink-Vigier, F. Momany, M. Latge, J.-P. Wang, T. 2024-08-16 doi:10.1101/2024.08.13.607833 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ Prediction of Oligomeric Status of Quaternary Protein Structure by using Sequential Minimal Optimization for Support Vector Machine ]]> https://biorxiv.org/content/10.1101/2024.08.15.608027v1?rss=1 Kumar, S. 2024-08-17 doi:10.1101/2024.08.15.608027 Cold Spring Harbor Laboratory Press 2024-08-17 <![CDATA[ The heat sensitivity of sperm in the lizard Anolis sagrei ]]> https://biorxiv.org/content/10.1101/2024.08.14.607821v1?rss=1 Wang, W. W.-Y. Gunderson, A. R. Page, N. R. Strickler, A. M. Kusaka, A. K. 2024-08-19 doi:10.1101/2024.08.14.607821 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Using VR and eye-tracking to study attention to and retention of AI-generated ads in outdoor advertising environments ]]> https://biorxiv.org/content/10.1101/2024.08.15.607684v1?rss=1 Lim, S. Cho, H. J. Jeon, M. Cui, X. Schmaelzle, R. 2024-08-19 doi:10.1101/2024.08.15.607684 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Title: 4-week GLP immunotoxicity assessment of lactoferrin alpha produced by Komagataella phaffii in Sprague Dawley rats ]]> https://biorxiv.org/content/10.1101/2024.08.16.608335v1?rss=1 Peterson, R. Crawford, R. B. Blevins, L. K. Kaminski, N. E. Clark, A. J. Malinczak, C.-A. 2024-08-19 doi:10.1101/2024.08.16.608335 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Phased chromosome-level genome assembly provides insight into the origin of hexaploid sweetpotato ]]> https://biorxiv.org/content/10.1101/2024.08.17.608395v1?rss=1 Wu, S. Sun, H. Hamilton, J. P. Mollinari, M. Gesteira, G. D. S. Kitavi, M. Yan, M. Wang, H. Yang, J. Yencho, G. C. Buell, C. R. Fei, Z. 2024-08-19 doi:10.1101/2024.08.17.608395 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ UnigeneFinder: An automated pipeline for gene calling from transcriptome assemblies without a reference genome ]]> https://biorxiv.org/content/10.1101/2024.08.19.608648v1?rss=1 Xue, B. Prado, K. Rhee, S. Y. Stata, M. 2024-08-19 doi:10.1101/2024.08.19.608648 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ EEG Biomarkers of Age-Related Memory Change ]]> https://biorxiv.org/content/10.1101/2024.08.20.608804v1?rss=1 Broitman, A. W. Healey, M. K. Kahana, M. J. 2024-08-21 doi:10.1101/2024.08.20.608804 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ Playtime for Cephalopods: Understanding the Significance of Play Behavior inOctopus bimaculoides ]]> https://biorxiv.org/content/10.1101/2024.08.23.609397v1?rss=1 Jarmoluk, K. Pelled, G. 2024-08-26 doi:10.1101/2024.08.23.609397 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Flanker task parameters are related to the strength of association between the ERN and anxiety: a meta-analysis ]]> https://biorxiv.org/content/10.1101/2024.08.27.609944v1?rss=1 Buzzell, G. A. Niu, Y. Machado, E. Dickinson, R. Moser, J. S. Morales, S. Troller-Renfree, S. V. 2024-08-28 doi:10.1101/2024.08.27.609944 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ Charting the Silent Signals of Social Gaze: Automating Eye Contact Assessment in Face-to-Face Conversations ]]> https://biorxiv.org/content/10.1101/2024.08.28.610064v1?rss=1 Schmaelzle, R. Jahn, N. T. Bente, G. M. 2024-08-29 doi:10.1101/2024.08.28.610064 Cold Spring Harbor Laboratory Press 2024-08-29 <![CDATA[ The Impact of Brain-Derived Neurotrophic Factor rs6265 (Val66Met) Polymorphism on Therapeutic Electrical Stimulation for Peripheral Nerve Regeneration: A Preclinical Study of Therapy-Genotype Interactions ]]> https://biorxiv.org/content/10.1101/2024.08.29.610333v1?rss=1 Walters, J. B. Quezada, M. J. He, S. Steece-Collier, K. Collier, T. J. Sortwell, C. E. Franz, C. 2024-08-30 doi:10.1101/2024.08.29.610333 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Mechanistic insights into gene expression changes and electric organ discharge elongation in mormyrid electric fish ]]> https://biorxiv.org/content/10.1101/2024.09.02.610879v1?rss=1 Losilla, M. Gallant, J. R. 2024-09-03 doi:10.1101/2024.09.02.610879 Cold Spring Harbor Laboratory Press 2024-09-03 <![CDATA[ Effect of Genotype and Age on a Defined Microbiota in Gnotobiotic SCID Piglets ]]> https://biorxiv.org/content/10.1101/2024.09.03.611011v1?rss=1 Widmer, K. M. Rahic-Seggerman, F. Forster, A. Ahrens-Kress, A. Sauer, M. Mooyottu, S. Vinithakumari, A. Dunkerson-Kurzhumov, A. Sponseller, B. Kiupel, M. Schmitz-Esser, S. Tuggle, C. K. 2024-09-07 doi:10.1101/2024.09.03.611011 Cold Spring Harbor Laboratory Press 2024-09-07 <![CDATA[ TGFβ primes alveolar-like macrophages to induce type I IFN following TLR2 activation ]]> https://biorxiv.org/content/10.1101/2024.09.04.611226v1?rss=1 Thomas, S. M. Ankley, L. M. Conner, K. N. Rapp, A. W. McGee, A. P. LeSage, F. Tanner, C. D. Vielma, T. E. Scheeres, E. C. Obar, J. J. Olive, A. J. 2024-09-08 doi:10.1101/2024.09.04.611226 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ Human microRNA-153-3p targets specific neuronal genes and is associated with the risk of Alzheimer's disease. ]]> https://biorxiv.org/content/10.1101/2024.09.07.611728v1?rss=1 Wang, R. Maloney, B. Nho, K. Beck, J. Counts, S. E. Lahiri, D. K. 2024-09-14 doi:10.1101/2024.09.07.611728 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ Causality Analysis of Protein Corona Composition: Phosphatidylcholine-Enhances Plasma Proteome Profiling by Proteomics ]]> https://biorxiv.org/content/10.1101/2024.09.10.612356v1?rss=1 Rafieioskouei, A. Rogale, K. Dibavar, A. S. Mahmoudi, M. Bonakdarpour, B. 2024-09-14 doi:10.1101/2024.09.10.612356 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ Dual-format attentional template during preparation in human visual cortex ]]> https://biorxiv.org/content/10.1101/2024.09.12.602176v1?rss=1 Chen, Y. Liu, T. Jia, K. Theeuwes, J. Gong, M. 2024-09-14 doi:10.1101/2024.09.12.602176 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ The new phycobilisome linker protein ApcI regulates high light adaptation in Synechocystis sp. PCC 6803 ]]> https://biorxiv.org/content/10.1101/2024.09.09.612062v1?rss=1 Espinoza-Corral, R. Zavrel, T. Sutter, M. Leslie, C. H. Yang, K. Beck, W. F. Cerveny, J. Kerfeld, C. A. 2024-09-15 doi:10.1101/2024.09.09.612062 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Attention and Retention Effects of Culturally Targeted Billboard Messages: An Eye-Tracking Study Using Immersive Virtual Reality ]]> https://biorxiv.org/content/10.1101/2024.09.10.610975v1?rss=1 Jeon, M. Lim, S. Lapinski, M. K. Bente, G. Spates, S. A. Schmaezle, R. 2024-09-16 doi:10.1101/2024.09.10.610975 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ Single unit electrophysiology recordings and computational modeling can predict octopus arm movement ]]> https://biorxiv.org/content/10.1101/2024.09.13.612676v1?rss=1 Gedela, N. S. S. Salim, S. Radawiec, R. D. Richie, J. M. Chestek, C. A. Draelos, A. Pelled, G. 2024-09-19 doi:10.1101/2024.09.13.612676 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Molecular insights into substrate translocation in an elevator-type metal transporter ]]> https://biorxiv.org/content/10.1101/2024.09.18.613805v1?rss=1 Jafari, M. Zhang, T. Sui, D. Sagresti, L. Merz, K. Hu, J. 2024-09-19 doi:10.1101/2024.09.18.613805 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Global Genotype by Environment Prediction Competition Reveals That Diverse Modeling Strategies Can Deliver Satisfactory Maize Yield Estimates ]]> https://biorxiv.org/content/10.1101/2024.09.13.612969v1?rss=1 Washburn, J. D. Varela, J. I. Xavier, A. Chen, Q. Ertl, D. Gage, J. L. Holland, J. B. Lima, D. C. Romay, M. C. Lopez-Cruz, M. de los Campos, G. Barber, W. Zimmer, C. Trucillo Silva, I. Rocha, F. Rincent, R. Ali, B. Hu, H. Runcie, D. E. Gusev, K. Slabodkin, A. Bax, P. Aubert, J. Gangloff, H. Mary-Huard, T. Vanrenterghem, T. Quesada-Traver, C. Yates, S. Ariza-Suarez, D. Ulrich, A. Wyler, M. Kick, D. R. Bellis, E. S. Causey, J. L. Soriano Chavez, E. Wang, Y. Piyush, V. Fernando, G. D. Hu, R. K. Kumar, R. Timon, A. J. Venkatesh, R. Segura Aba, K. Chen, H. 2024-09-20 doi:10.1101/2024.09.13.612969 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Chromosome-level assemblies of Amaranthus palmeri, Amaranthus retroflexus, and Amaranthus hybridus allow for genomic comparisons and identification of a sex-determining region ]]> https://biorxiv.org/content/10.1101/2024.09.18.613719v1?rss=1 Raiyemo, D. A. Montgomery, J. S. Cutti, L. Abdollahi, F. Llaca, V. Fengler, K. Lopez, A. J. Morran, S. Saski, C. A. Nelson, D. R. Patterson, E. Gaines, T. A. Tranel, P. J. 2024-09-22 doi:10.1101/2024.09.18.613719 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ How interactions between temperature and resources scale from populations to communities ]]> https://biorxiv.org/content/10.1101/2024.09.19.613936v1?rss=1 Kremer, C. T. Thomas, M. K. Klausmeier, C. A. Litchman, E. 2024-09-23 doi:10.1101/2024.09.19.613936 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ Mechanistic insights into Rho/MRTF inhibition-induced apoptotic events and prevention of drug resistance in melanoma: Implications for the involvement of pirin ]]> https://biorxiv.org/content/10.1101/2024.09.19.614009v1?rss=1 Foda, B. Baker, A. Joachimiak, L. Mazur, M. Neubig, R. R. 2024-09-24 doi:10.1101/2024.09.19.614009 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ STANCE: a unified statistical model to detect cell-type-specific spatially variable genes in spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2024.09.22.614385v1?rss=1 Su, H. Wu, Y. Chen, B. Cui, Y. 2024-09-24 doi:10.1101/2024.09.22.614385 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Carbapenem-Resistant Enterobacter hormaechei Uses Mucus Metabolism to Facilitate Gastrointestinal Colonization ]]> https://biorxiv.org/content/10.1101/2024.09.25.615021v1?rss=1 Sinha, R. Ottosen, E. N. Ngwaga, T. Shames, S. R. DiRita, V. J. 2024-09-25 doi:10.1101/2024.09.25.615021 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ Aspergillus nidulans cell wall integrity kinase, MpkA, impacts cellular phenotypes that alter mycelial-material mechanical properties ]]> https://biorxiv.org/content/10.1101/2024.09.28.615565v1?rss=1 Gray, K. Edwards, H. Doan, A. G. Huso, W. Lee, J. Pan, W. Bolima, N. Morse, M. E. Yoda, S. Gautam, I. Harris, S. Zupan, M. Wang, T. deCarvalho, T. Marten, M. R. 2024-09-30 doi:10.1101/2024.09.28.615565 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ A molecular representation system with a common reference frame for natural products pathway discovery and structural diversity tasks. ]]> https://biorxiv.org/content/10.1101/2024.10.01.616173v1?rss=1 Babineau, N. Nguyen, L. T. D. Mathieu, D. McCue, C. Schlecht, N. Abrahamson, T. Hamberger, B. Busta, L. 2024-10-01 doi:10.1101/2024.10.01.616173 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Predicting Inhibitors of OATP1B1 via Heterogeneous OATP-Ligand Interaction Graph Neural Network (HOLI-GNN) ]]> https://biorxiv.org/content/10.1101/2024.10.01.615464v1?rss=1 Mardikoraem, M. Eaves, J. N. Belecciu, T. Pascual, N. S. Aljets, A. Orlando, B. J. Shapiro, E. M. Woldring, D. R. 2024-10-02 doi:10.1101/2024.10.01.615464 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Proton channel inactivation results in loss of chloroplast NDH complex activity ]]> https://biorxiv.org/content/10.1101/2024.10.01.616091v1?rss=1 Strand, D. D. Ruf, S. Sandoval-Ibanez, O. Bock, R. 2024-10-02 doi:10.1101/2024.10.01.616091 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Transcriptome-based identification of long noncoding RNAs (lncRNAs) across the genome of Anopheles gambiae ]]> https://biorxiv.org/content/10.1101/2024.10.02.616138v1?rss=1 Xu, J. Hu, K. Riehle, M. M. Khadka, V. 2024-10-02 doi:10.1101/2024.10.02.616138 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Differential composition of lymphocyte subpopulations and activation between the hypertensive Bph/2 and normotensive Bpn/3 mouse strains ]]> https://biorxiv.org/content/10.1101/2024.10.01.616072v1?rss=1 Dattmore, D. A. McDonald, P. Chowdhury, A. Awali, S. Boss, A. P. Jin, Y. Sather, L. Lauver, D. A. Rockwell, C. E. 2024-10-03 doi:10.1101/2024.10.01.616072 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Microplate micromilling: A customizable platform to support the prototyping, development and testing of microphysiological culture models ]]> https://biorxiv.org/content/10.1101/2024.10.02.615399v1?rss=1 2.5-fold increase in cell growth after three days. Machines were tested on their ability to create common device features including a traditional microfluidic device as well as a custom design incorporating complex geometries. Features were measured by confocal microscopy. We found that features including 1000{micro}m ports, 800{micro}m microchannels, 200{micro}m phase-guides, and 500{micro}m post arrays were machined and the range of CVs for features were 1.02-4.42, 1.32-3.50, 2.34-16.58, 6.25-16.40 respectively, while the 3D printed features exhibited maximal CVs of 20.98, 11.68, 23.60, and 10.01 for the same features. Predictably, more expensive machines generally showed higher accuracy and lower variation, but many features could be created accurately and precisely by inexpensive (<$3000) machines facilitating the broader use of this technology to create a user customizable platform to support the prototyping, development, and testing of human relevant models with broad applications across the life sciences. Graphical abstractMultiple CNC mills are assessed on accuracy and precision of microfluidic features of interest for microphysiological model development creation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/615399v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1be08eorg.highwire.dtl.DTLVardef@33b0a4org.highwire.dtl.DTLVardef@192167borg.highwire.dtl.DTLVardef@200b7_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Reynolds, J. I. Adams, M. Jimenez, J. Johnson, B. P. 2024-10-03 doi:10.1101/2024.10.02.615399 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ EvoSeq-ML: Advancing Data-Centric Machine Learning with Evolutionary-Informed Protein Sequence Representation and Generation ]]> https://biorxiv.org/content/10.1101/2024.10.02.616302v1?rss=1 Mardikoraem, M. Pascual, N. S. Finneran, P. Woldring, D. R. 2024-10-03 doi:10.1101/2024.10.02.616302 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Single-Cell Data Integration and Cell Type Annotation through Contrastive Adversarial Open-set Domain Adaptation ]]> https://biorxiv.org/content/10.1101/2024.10.04.616599v1?rss=1 Aminzadeh, F. Wu, J. He, J. Saberi, M. Vafaee, F. 2024-10-04 doi:10.1101/2024.10.04.616599 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Targeted Degradation of MYC2 through MPK6 Phosphorylation Reveals Mechanisms and Implications for JA Signaling ]]> https://biorxiv.org/content/10.1101/2024.10.04.616682v1?rss=1 Han, K.-H. Im, J. H. Son, S. Jung, M.-Y. Ko, J.-H. 2024-10-04 doi:10.1101/2024.10.04.616682 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Testing for the genomic footprint of conflict between life stages in an angiosperm and a moss species ]]> https://biorxiv.org/content/10.1101/2024.10.04.613734v1?rss=1 Yuan, M. Kollar, L. M. Sacchi, B. M. Carey, S. B. Choudhury, B. I. Jones, T. Grimwood, J. Barrett, S. C. McDaniel, S. F. Wright, S. I. Stinchcombe, J. R. 2024-10-05 doi:10.1101/2024.10.04.613734 Cold Spring Harbor Laboratory Press 2024-10-05 <![CDATA[ Diffusion and Viscosity in Mixed Protein Solutions ]]> https://biorxiv.org/content/10.1101/2024.10.10.617612v1?rss=1 Wozniak, S. Feig, M. 2024-10-11 doi:10.1101/2024.10.10.617612 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ The fire blight pathogen Erwinia amylovora enters apple leaves through naturally-occurring wounds from the abscission of trichomes ]]> https://biorxiv.org/content/10.1101/2024.10.10.617712v1?rss=1 Millett, F. Standish, J. Scanley, J. Miller, K. Inguagiato, J. Zuverza-Mena, N. Abril, M. Robinson, V. Li, Y. Sundin, G. W. Zeng, Q. 2024-10-11 doi:10.1101/2024.10.10.617712 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ A Novel Genomic Rearrangement in the Amaranthus palmeri Extrachromosomal Circular DNA Provides Dual Herbicide Resistance to Glyphosate and Glufosinate ]]> https://biorxiv.org/content/10.1101/2024.10.08.617243v1?rss=1 Carvalho-Moore, P. Borgato, E. A. Cutti, L. Porri, A. Meiners, I. Lerchl, J. Norsworthy, J. K. Patterson, E. L. 2024-10-12 doi:10.1101/2024.10.08.617243 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Data-Driven Image Analysis to Determine Antibody-Induced Dissociation of Cell-Cell Adhesion and Antibody Pathogenicity in Pemphigus Vulgaris ]]> https://biorxiv.org/content/10.1101/2024.10.09.617446v1?rss=1 Moghaddam, A. O. Jin, X. Zhai, H. Safa, B. T. Seiffert-Sinha, K. Leiker, M. Rosenbohm, J. Meng, F. Sinha, A. A. Yang, R. 2024-10-13 doi:10.1101/2024.10.09.617446 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ Late Quaternary climatic impact on the woodland strawberry genome: a perennial herb's tale ]]> https://biorxiv.org/content/10.1101/2024.10.09.617376v1?rss=1 Toivainen, T. Salonen, J. S. Kirshner, J. Lembinen, S. De Kort, H. Lyyski, A. Edger, P. P. Hilmarsson, H. S. Hallsson, J. H. Sargent, D. J. Olbricht, K. Sanchez-Sevilla, J. F. Jaakola, L. Stenberg, J. A. Duralija, B. Labokas, J. Vare, H. Salojarvi, J. Auvinen, P. Pose, D. Albert, V. A. Hytonen, T. 2024-10-14 doi:10.1101/2024.10.09.617376 Cold Spring Harbor Laboratory Press 2024-10-14 <![CDATA[ Maximum vertical height during wing flapping of laying hens captured with a depth camera ]]> https://biorxiv.org/content/10.1101/2024.10.12.617995v1?rss=1 0.05). Hens in this study were from a single strain, were old enough to have keel damage, and were cage-reared and housed, preventing us from generalizing the results too far. However, depth cameras provide a useful approach to measure how much space laying hens of varying strains, ages, and rearing/housing methods need to perform dynamic behaviors. ]]> Grebey, T. Bongiorno, V. Han, J. Steibel, J. Siegford, J. M. 2024-10-14 doi:10.1101/2024.10.12.617995 Cold Spring Harbor Laboratory Press 2024-10-14 <![CDATA[ Metabolic interplay drives population cycles in a cross-feeding microbial community ]]> https://biorxiv.org/content/10.1101/2024.10.14.618235v1?rss=1 Ross, T. Klausmeier, C. A. Venturelli, O. 2024-10-17 doi:10.1101/2024.10.14.618235 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ A co-conserved gene pair supports Caulobacter iron homeostasis during chelation stress ]]> https://biorxiv.org/content/10.1101/2024.10.16.618771v1?rss=1 Ortiz, S. H. Ok, K. O'Halloran, T. V. Fiebig, A. Crosson, S. 2024-10-17 doi:10.1101/2024.10.16.618771 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Controlled enzyme cargo loading in engineered bacterial microcompartment shells ]]> https://biorxiv.org/content/10.1101/2024.10.21.619467v1?rss=1 Tefft, N. M. Wang, Y. Jussupow, A. Feig, M. TerAvest, M. A. 2024-10-24 doi:10.1101/2024.10.21.619467 Cold Spring Harbor Laboratory Press 2024-10-24 <![CDATA[ Maintenance of parasite species diversity: Spatiotemporal niche partitioning and aggregation facilitate species coexistence ]]> https://biorxiv.org/content/10.1101/2024.10.21.619552v1?rss=1 Ramesh, A. McDermott-Sipe, O. Bashey-Visser, F. 2024-10-24 doi:10.1101/2024.10.21.619552 Cold Spring Harbor Laboratory Press 2024-10-24 <![CDATA[ 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) elicited dose-dependent shifts in the murine urinary metabolome associated with hepatic AHR-mediated differential gene expression ]]> https://biorxiv.org/content/10.1101/2024.10.22.619714v1?rss=1 Sink, W. J. Fling, R. Yilmaz, A. Nault, R. Goniwiecha, D. Harkema, J. Graham, S. Zacharewski, T. 2024-10-25 doi:10.1101/2024.10.22.619714 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Uterine stromal but not epithelial PTGS2 is critical for murine pregnancy success ]]> https://biorxiv.org/content/10.1101/2024.10.24.620133v1?rss=1 Massri, N. Arora, R. 2024-10-26 doi:10.1101/2024.10.24.620133 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ Complex system modelling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria ]]> https://biorxiv.org/content/10.1101/2024.10.28.620613v1?rss=1 Mukherjee, S. D. Batagello, C. Adler, A. Agudelo, J. Zampini, A. Suryavanshi, M. Nguyen, A. Orr, T. Dearing, D. Monga, M. Miller, A. W. 2024-10-28 doi:10.1101/2024.10.28.620613 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ COCOMO2: A coarse-grained model for interacting folded and disordered proteins ]]> https://biorxiv.org/content/10.1101/2024.10.29.620916v1?rss=1 View larger version (15K): org.highwire.dtl.DTLVardef@32d74forg.highwire.dtl.DTLVardef@1d5aa9eorg.highwire.dtl.DTLVardef@b47a5forg.highwire.dtl.DTLVardef@ce0f08_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Jussupow, A. Bartley, D. Lapidus, L. J. Feig, M. 2024-11-01 doi:10.1101/2024.10.29.620916 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Isoprene deters insect herbivory by priming plant hormone responses ]]> https://biorxiv.org/content/10.1101/2024.11.01.621578v1?rss=1 Sahu, A. Mostofa, M. G. Xu, Y. Serda, B. O'Keefe, J. Sharkey, T. D. 2024-11-02 doi:10.1101/2024.11.01.621578 Cold Spring Harbor Laboratory Press 2024-11-02 <![CDATA[ Species-specific phyllosphere responses to external pH change ]]> https://biorxiv.org/content/10.1101/2024.11.01.621601v1?rss=1 Lopez Gonzalez, C. Floc'h, J.-B. Renner, T. Gilbert, K. J. 2024-11-02 doi:10.1101/2024.11.01.621601 Cold Spring Harbor Laboratory Press 2024-11-02 <![CDATA[ Platelets are Protective in Early Abdominal Aortic Aneurysm Formation ]]> https://biorxiv.org/content/10.1101/2024.10.29.616205v1?rss=1 Russell, H. M. Spuzzillo, A. Benson, T. W. Jaworski, J. Clement, M. Boulaftali, Y. Saum, K. Conrad, K. A. Howatt, D. A. Luyendyk, J. P. Cameron, S. J. Nieswandt, B. Steinhubl, S. R. Daugherty, A. Bergmeier, W. Tong, W. Damrauer, S. Tsao, P. Mallat, Z. Edwards, T. L. Mackman, N. Owens, A. P. 2024-11-03 doi:10.1101/2024.10.29.616205 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ MARVEL: Microenvironment Annotation by Supervised Graph Contrastive Learning ]]> https://biorxiv.org/content/10.1101/2024.10.29.620828v1?rss=1 CUI, Y. Wen, H. Yang, R. Luo, X. Liu, H. Xie, Y. 2024-11-03 doi:10.1101/2024.10.29.620828 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Gene expression divergence between locally adapted inland annual and coastal perennial ecotypes of Mimulus guttatus across developmental stages ]]> https://biorxiv.org/content/10.1101/2024.11.04.621855v1?rss=1 Olsen, J. D. Gould, B. A. Chen, Y. Lowry, D. B. 2024-11-05 doi:10.1101/2024.11.04.621855 Cold Spring Harbor Laboratory Press 2024-11-05 <![CDATA[ Cocaine, via ΔFosB, remodels gene expression and excitability in ventral hippocampus ]]> https://biorxiv.org/content/10.1101/2024.11.06.621895v1?rss=1 Eagle, A. L. Doyle, M. A. Sugimoto, C. Dykstra, M. M. Kuhn, H. M. Murray, B. R. Bastle, R. M. He, J. Maze, I. Mazei-Robison, M. Robison, A. J. 2024-11-07 doi:10.1101/2024.11.06.621895 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ Characterizing gene expression profiles of various tissue states in stony coral tissue loss disease using a feature selection algorithm ]]> https://biorxiv.org/content/10.1101/2024.11.05.622084v1?rss=1 Beavers, K. M. Gutierrez-Andrade, D. Van Buren, E. W. Emery, M. A. Brandt, M. E. Apprill, A. Mydlarz, L. D. 2024-11-08 doi:10.1101/2024.11.05.622084 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Whole-genome sequencing across space and time reveals impact of population decline and reduced gene flow in Florida Scrub-Jays ]]> https://biorxiv.org/content/10.1101/2024.11.05.622154v1?rss=1 Nguyen, T. N. Cosgrove, E. J. Chen, N. Lehr, N. Lokey, M. Beaudry, F. E. G. Fitzpatrick, S. W. Miller, K. E. Fitzpatrick, J. W. Clark, A. G. 2024-11-08 doi:10.1101/2024.11.05.622154 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ An algal nutrient-replete, optimized medium for fast growth and high triacylglycerol accumulation ]]> https://biorxiv.org/content/10.1101/2024.11.07.622501v1?rss=1 Jeffers, T. L. McCombs, R. Schmollinger, S. Merchant, S. S. Niyogi, K. K. Roth, M. S. 2024-11-08 doi:10.1101/2024.11.07.622501 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ From Quantitative Trait Loci towards Mechanisms: Linkage Integration Hypothesis Testing (LIgHT) Sheds Light on the Mechanisms of Genetically Modulated Stress Tolerance ]]> https://biorxiv.org/content/10.1101/2024.11.07.622539v1?rss=1 Hoh, D. Osei-Bonsu, I. Kanazawa, A. Fisher, N. Cruz, J. Roberts, P. A. Huynh, B.-L. Kramer, D. M. 2024-11-08 doi:10.1101/2024.11.07.622539 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Small molecule oxybutynin rescues proliferative capacity of complex III-defective MPCs ]]> https://biorxiv.org/content/10.1101/2024.11.08.622694v1?rss=1 Qu, Y. Edwards, K. Li, M. Liu, Y. Tsai, P.-Y. Cheng, C. Blum, J. Acor, N. Oshoe, T. Rooney, K. Walter, C. Thirumlaikumar, V. P. Thalacker-Mercer, A. Skirycz, A. Barrow, J. 2024-11-09 doi:10.1101/2024.11.08.622694 Cold Spring Harbor Laboratory Press 2024-11-09 <![CDATA[ Ecological synchrony in human-modified landscapes under a changing climate ]]> https://biorxiv.org/content/10.1101/2024.11.09.621137v1?rss=1 Song, Y. Barnes, M. Browning, D. M. Bybee-Finley, K. A. Dahlin, K. M. Munch, S. B. Ponce-Campos, G. E. Youngflesh, C. Zuckerberg, B. Zhu, K. 2024-11-11 doi:10.1101/2024.11.09.621137 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Inter-individual gene expression variability implies stable regulation of brain-biased genes across organs ]]> https://biorxiv.org/content/10.1101/2024.11.11.623020v1?rss=1 Bucao, C. F. Aletti, C. Moretti, S. Thompson, A. W. Racicot, B. L. Wilson, C. A. Bobe, J. Braasch, I. Guigen, Y. Postlethwait, J. H. Robinson-Rechavi, M. 2024-11-12 doi:10.1101/2024.11.11.623020 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Accumulation of Dietary and Non-Enzymatic Oxysterols in Preeclamptic Placentas: Insights into Cholesterol Dynamics in Pregnancy Complications ]]> https://biorxiv.org/content/10.1101/2024.11.13.623499v1?rss=1 Zou, L. Maldonado-Pereira, L. Ticiani, E. Sethuraman, V. Olomu, N. Long, R. Veiga-Lopez, A. Medina-Meza, I. G. 2024-11-14 doi:10.1101/2024.11.13.623499 Cold Spring Harbor Laboratory Press 2024-11-14 <![CDATA[ Volumetric and Diffusion Tensor Imaging biomarkers indicating long lasting post-concussion abnormalities in a youth pig model of mild Traumatic Brain Injury ]]> https://biorxiv.org/content/10.1101/2024.11.12.623259v1?rss=1 Islam, S. Netzley, A. Chenyang, L. Zhang, J. Montero, B. D. Vazquez, A. Subbaiah, S. Meoded, A. Munoz, K. Colbath, A. Huang, J. Mejia-Alvarez, R. Manfredi, J. Pelled, G. 2024-11-15 doi:10.1101/2024.11.12.623259 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Human heart assembloids with autologous tissue-resident macrophages recreate physiological immuno-cardiac interactions ]]> https://biorxiv.org/content/10.1101/2024.11.13.623051v1?rss=1 O'Hern, C. Caywood, S. Aminova, S. Kiselev, A. Volmert, B. Wang, F. Sewavi, M.-L. Cao, W. Dionise, M. Muniyandi, P. Popa, M. Basrai, H. Skoric, M. Boulos, G. Huang, A. Nunez-Regueiro, I. Chalfoun, N. Park, S. Zhou, C. Contag, C. H. Aguirre, A. 2024-11-15 doi:10.1101/2024.11.13.623051 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Structure Characterization of Bacterial Microcompartment Shells via X-ray Scattering and Coordinate Modeling: Evidence for adventitious capture of cytoplasmic proteins ]]> https://biorxiv.org/content/10.1101/2024.11.13.623460v1?rss=1 Zuo, X. Jussupow, A. Ponomarenko, N. S. Tefft, N. M. Yadav, N. S. Range, K. L. Ralston, C. Y. TerAvest, M. A. Sutter, M. Kerfeld, C. A. Vermaas, J. V. Feig, M. Tiede, D. M. 2024-11-15 doi:10.1101/2024.11.13.623460 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ To Play or Not to Play? Effects of Playmate Familiarity and Social Isolation on Social Play Engagement in Three Laboratory Rat Strains ]]> https://biorxiv.org/content/10.1101/2024.11.14.623692v1?rss=1 Orsucci, I. C. Becker, K. D. Lee, J. D. A. Bowden, S. M. Ham, J. R. Veenema, A. 2024-11-15 doi:10.1101/2024.11.14.623692 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ A TORC1-PHR1 signaling axis regulates phosphorus starvation and immunity signaling network in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2024.11.18.624151v1?rss=1 Awasthi, P. Jamsheer K, M. Kumar, M. Mishra, S. Tiwari, A. Jindal, S. Saksena, H. B. Singh, D. Vadassery, J. Rouached, H. Meyer, C. Laxmi, A. 2024-11-20 doi:10.1101/2024.11.18.624151 Cold Spring Harbor Laboratory Press 2024-11-20 <![CDATA[ The N-terminal Domain of cpTatC Protein Interacts with the Precursor Mature Domain in Chloroplast TAT Translocation ]]> https://biorxiv.org/content/10.1101/2024.11.24.625085v1?rss=1 Maddethalawe, T. Hird, K. Dabney-Smith, C. 2024-11-26 doi:10.1101/2024.11.24.625085 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Transcriptional Regulation of Mammary Alveolar Proliferation and Differentiation during Early Pregnancy ]]> https://biorxiv.org/content/10.1101/2024.11.27.625731v1?rss=1 Garcia-Lerena, J. Vusich, J. Schulte, A. Corfixsen, R. Andrechek, E. 2024-11-27 doi:10.1101/2024.11.27.625731 Cold Spring Harbor Laboratory Press 2024-11-27 <![CDATA[ Drone-Based Identification of Flood-Tolerant Maize via Multispectral Imaging: A Real-World Case Study ]]> https://biorxiv.org/content/10.1101/2024.11.26.625493v1?rss=1 Mitchell, M. N. Sidberry, G. Mathison, M. DeSalvio, A. J. Kick, D. R. Washburn, J. D. 2024-11-28 doi:10.1101/2024.11.26.625493 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Structural Basis for Catalysis and Substrate Specificity of a LarA Racemase with a Broad Substrate Spectrum ]]> https://biorxiv.org/content/10.1101/2024.11.28.625916v1?rss=1 Gatreddi, S. Urdiain-Arraiza, J. Desguin, B. Hausinger, R. P. Hu, J. 2024-11-28 doi:10.1101/2024.11.28.625916 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Evolution of thermal tolerance in marine diatoms: Metabolic strategies under heat stress. ]]> https://biorxiv.org/content/10.1101/2024.11.27.625584v1?rss=1 Aranguren-Gassis, M. Diz, A. P. Huete-Ortega, M. Allen, A. Litchman, E. 2024-12-02 doi:10.1101/2024.11.27.625584 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ Unveiling Cell Wall Structure and Echinocandin Response in Candida auris and Candida albicans via Solid-State NMR ]]> https://biorxiv.org/content/10.1101/2024.12.02.626508v1?rss=1 Dickwella Widanage, M. C. Singh, K. Li, J. Reddy Yarava, J. Scott, F. J. Xu, Y. Gow, N. A. R. Mentink-Vigier, F. Wang, P. Lamoth, F. Wang, T. 2024-12-03 doi:10.1101/2024.12.02.626508 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Conserved effectors underpin the virulence of liverwort-isolated Pseudomonas in divergent plants ]]> https://biorxiv.org/content/10.1101/2024.12.03.626388v1?rss=1 Robinson, K. Buric, L. Grenz, K. Chia, K.-S. Hulin, M. T. Ma, W. Carella, P. 2024-12-03 doi:10.1101/2024.12.03.626388 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Trehalose supports the growth of Aedes aegypti cells and modifies gene expression and dengue virus replication ]]> https://biorxiv.org/content/10.1101/2024.12.03.626538v1?rss=1 Conway, M. J. Marten, A. D. Haslitt, D. P. Martin, C. A. Swanson, D. H. Kalera, K. Johnson, U. G. Swarts, B. M. 2024-12-03 doi:10.1101/2024.12.03.626538 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Pirin does not bind to p65 or regulate NFkappaB-dependent gene expression ]]> https://biorxiv.org/content/10.1101/2024.12.03.626411v1?rss=1 Meschkewitz, M. Lisabeth, E. M. Cab-Gomez, A. D. Leipprandt, J. Neubig, R. R. 2024-12-04 doi:10.1101/2024.12.03.626411 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ A photorespiratory glyoxylate shunt in the cytosol supports photosynthesis and plant growth under high light conditions in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2024.12.03.626664v1?rss=1 Jiang, X. Koenig, A. M. Walker, B. J. Hu, J. 2024-12-04 doi:10.1101/2024.12.03.626664 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ The membrane-associated ubiquitin ligase MARCHF8 promotes cancer immune evasion by degrading MHC class I proteins ]]> https://biorxiv.org/content/10.1101/2024.11.29.626106v1?rss=1 Khalil, M. I. Wang, J. Yang, C. Vu, L. Yin, C. Chadha, S. Nabors, H. Vocelle, D. May, D. G. Chrisopolus, R. J. Zhou, L. Roux, K. G. Bernard, M. P. Mi, Q.-S. Pyeon, D. 2024-12-06 doi:10.1101/2024.11.29.626106 Cold Spring Harbor Laboratory Press 2024-12-06 <![CDATA[ Modulation of Purkinje Cell Inhibition by Stem Cell Factor ]]> https://biorxiv.org/content/10.1101/2024.12.09.627581v1?rss=1 Zaman, T. Lahr, J. Cherian, S. Pozzo-Miller, L. Williams, M. R. 2024-12-10 doi:10.1101/2024.12.09.627581 Cold Spring Harbor Laboratory Press 2024-12-10 <![CDATA[ Root-pore interactions, the underestimated driver for rhizosphere structure and rhizosheath development ]]> https://biorxiv.org/content/10.1101/2024.12.06.627175v1?rss=1 Geers-Lucas, M. Guber, A. Kravchenko, A. 2024-12-12 doi:10.1101/2024.12.06.627175 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Accurate Predictions of Molecular Properties of Proteins via Graph Neural Networks and Transfer Learning ]]> https://biorxiv.org/content/10.1101/2024.12.10.627714v1?rss=1 Wozniak, S. Janson, G. Feig, M. 2024-12-12 doi:10.1101/2024.12.10.627714 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Jan and mini-Jan, a model system for potato functional genomics ]]> https://biorxiv.org/content/10.1101/2024.12.10.627817v1?rss=1 Xin, H. Strickland, L. W. Hamilton, J. P. Trusky, J. K. Fang, C. Butler, N. M. Douches, D. S. Buell, C. R. Jiang, J. 2024-12-12 doi:10.1101/2024.12.10.627817 Cold Spring Harbor Laboratory Press 2024-12-12 <![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[ Image Processing in the Acute to Chronic Pain Signatures (A2CPS) Project ]]> https://biorxiv.org/content/10.1101/2024.12.19.627509v1?rss=1 Sadil, P. Arfanakis, K. Bhuiyan, E. H. Caffo, B. Calhoun, V. D. Clauw, D. J. DeLano, M. C. Ford, J. C. Gattu, R. Guo, X. Harris, R. E. Ichesco, E. Johnson, M. A. Jung, H. Kahn, A. B. Kaplan, C. M. Leloudas, N. Lindquist, M. A. Luo, Q. Mulderink, T. A. Peltier, S. J. Prasad, P. V. Sica, C. Urrutia, J. Vance, C. G. Wager, T. D. Xuan, Y. Zhou, X. J. Zhou, Y. Shu, D. C. The Acute to Chronic Pain Signatures Consortium, 2024-12-20 doi:10.1101/2024.12.19.627509 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Detecting mtDNA effects with an Extended Pedigree Model: An Analysis of Statistical Power and Estimation Bias ]]> https://biorxiv.org/content/10.1101/2024.12.19.629449v1?rss=1 Lyu, X. Hunter, M. D. Burt, S. A. Good, R. Carroll, S. L. Garrison, S. M. 2024-12-22 doi:10.1101/2024.12.19.629449 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ TRF1 and TRF2 form distinct shelterin subcomplexes at telomeres ]]> https://biorxiv.org/content/10.1101/2024.12.23.630076v1?rss=1 Janovic, T. Perez, G. Schmidt, J. C. 2024-12-23 doi:10.1101/2024.12.23.630076 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ Rule-Based Deconstruction and Reconstruction of Diterpene Libraries: Categorizing Patterns & Unravelling the Structural Landscape ]]> https://biorxiv.org/content/10.1101/2024.12.20.629783v1?rss=1 Mathieu, D. Schlecht, N. van Aalst, M. Shebek, K. Busta, L. Babineau, N. Ebenhoeh, O. Hamberger, B. 2024-12-24 doi:10.1101/2024.12.20.629783 Cold Spring Harbor Laboratory Press 2024-12-24 <![CDATA[ Priming versus propagating: distinct immune effects of an alpha- versus beta-particle emitting radiopharmaceutical when combined with immune checkpoint inhibition ]]> https://biorxiv.org/content/10.1101/2024.12.26.630430v1?rss=1 Kerr, C. P. Jin, W. J. Liu, P. Grudzinski, J. J. de Aguiar Ferreira, C. Comas Rojas, H. Onate, A. J. Kwon, O. Hyun, M. Bio Idrissou, M. Welch Schwartz, R. Vera, J. M. Clark, P. A. Takashima, M. Erbe, A. K. Shea, A. G. Powers, M. Pinchuk, A. N. Massey, C. F. Choi, C. Hernandez, R. T. Bednarz, B. P. Ong, I. M. Weichert, J. P. Morris, Z. S. 2024-12-27 doi:10.1101/2024.12.26.630430 Cold Spring Harbor Laboratory Press 2024-12-27 <![CDATA[ Structure and Post-Translational Modification of the Prostaglandin Transporter ]]> https://biorxiv.org/content/10.1101/2024.12.31.630934v1?rss=1 Yu, P. Orlando, M. A. Orlando, B. J. 2025-01-02 doi:10.1101/2024.12.31.630934 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Differences in apple fruit shape are independent of fruit size ]]> https://biorxiv.org/content/10.1101/2025.01.01.631017v1?rss=1 DeViller, K. Chitwood, D. H. Myles, S. Li, M. Migicovsky, Z. 2025-01-02 doi:10.1101/2025.01.01.631017 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Comparative immuno-biology at clinical recognition of early multiple organ dysfunction syndrome in pediatric and adult patients using single-cell transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.01.02.630924v1?rss=1 Shankar, R. Goodyke, A. J. Koirala, S. Paithankar, S. Chen, R.-Q. Hartog, N. L. Chesla, D. Rajasekaran, S. Chen, B. 2025-01-02 doi:10.1101/2025.01.02.630924 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Phosphorus Availability Modulates Flowering Time Through Subcellular Reprogramming of bGLU25 and GRP7 in Flowering Plants ]]> https://biorxiv.org/content/10.1101/2025.01.02.631137v1?rss=1 Cho, H. Choi, I. Bouain, N. Nawaz, A. Zheng, L. Shahzad, Z. Brandizzi, F. Rhee, S. Y. Rouached, H. 2025-01-03 doi:10.1101/2025.01.02.631137 Cold Spring Harbor Laboratory Press 2025-01-03 <![CDATA[ Toward a privacy-preserving predictive foundation model of single-cell transcriptomics with federated learning and tabular modeling ]]> https://biorxiv.org/content/10.1101/2025.01.06.631427v1?rss=1 Ding, J. Lin, J. Jiang, S. Wang, Y. Mao, Z. Fang, Z. Tang, J. Li, M. Qiu, X. 2025-01-06 doi:10.1101/2025.01.06.631427 Cold Spring Harbor Laboratory Press 2025-01-06 <![CDATA[ Memory Inception through Gaze-Contingent Message Exposure: Using Virtual Reality to Study Media Influence ]]> https://biorxiv.org/content/10.1101/2025.01.08.631803v1?rss=1 Cho, H. J. Lim, S. Saenz, M. Schmaelzle, R. 2025-01-08 doi:10.1101/2025.01.08.631803 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ The MAP kinase scaffold MORG1 shapes cell death in unresolved ER stress in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2025.01.08.632046v1?rss=1 KIM, J. Y. Ko, D. K. Brandizzi, F. 2025-01-13 doi:10.1101/2025.01.08.632046 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ The PST repeat region of MDC1 is a tunable multivalent chromatin tethering domain ]]> https://biorxiv.org/content/10.1101/2025.01.10.632395v1?rss=1 Heyza, J. R. Mikhova, M. Perez, G. I. Broadbent, D. G. Schmidt, J. C. 2025-01-13 doi:10.1101/2025.01.10.632395 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Euprymna berryi as a comparative model host for Vibrio fischeri light organ symbiosis ]]> https://biorxiv.org/content/10.1101/2025.01.10.632448v1?rss=1 Imes, A. M. Pavelsky, M. Badal, K. Kamp, D. L. Briseno, J. L. Sakmar, T. Vogt, M. A. Nyholm, S. V. Heath-Heckman, E. Grasse, B. Septer, A. N. Mandel, M. J. 2025-01-13 doi:10.1101/2025.01.10.632448 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Autoimmune regulator deficiency causes sterile epididymitis and impacts male fertility through disruption of inorganic physiology ]]> https://biorxiv.org/content/10.1101/2025.01.11.632558v1?rss=1 Ahn, S. H. Halgren, K. Grzesiak, G. MacRenaris, K. W. Sue, A. Xie, H. Demireva, E. O'Halloran, T. V. Petroff, M. G. 2025-01-15 doi:10.1101/2025.01.11.632558 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Harnessing Extracellular Vesicles for Stabilized and Functional IL-10 Delivery in Macrophage Immunomodulation ]]> https://biorxiv.org/content/10.1101/2025.01.14.633016v1?rss=1 Saleh, N. A. Gagea, M. A. Vitija, X. Janovic, T. Schmidt, J. C. Deng, C. X. Kanada, M. 2025-01-18 doi:10.1101/2025.01.14.633016 Cold Spring Harbor Laboratory Press 2025-01-18 <![CDATA[ A field-focused systems approach reveals mRNA covalent modifications linked to sorghum growth and development under drought stress ]]> https://biorxiv.org/content/10.1101/2025.01.17.633510v1?rss=1 Yu, L. Melandri, G. Dittrich, A. C. Calleja, S. Palos, K. Srinivasan, A. Brewer, E. K. Henderson, R. Garcia, C. D. Zhang, X. Rozzi, B. Eveland, A. Schroeder, S. J. Stern, D. Skirycz, A. Lyons, E. Arnold, E. A. Gregory, B. D. Nelson, A. D. L. Pauli, D. 2025-01-22 doi:10.1101/2025.01.17.633510 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Multifunctional bending magnet beamline with a capillary optic for X-ray fluorescence studies of metals in tissue sections ]]> https://biorxiv.org/content/10.1101/2025.01.18.633695v1?rss=1 Roter, B. Crawford, A. M. Jin, Q. Glowacki, A. T. Lai, B. Marin, F. S. Maxey, E. R. Shi, X. Culotta, V. C. Wildeman, A. S. Patel, N. K. O'Halloran, T. V. Jacobsen, C. 2025-01-22 doi:10.1101/2025.01.18.633695 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Plastoquinone redox status influences carboxysome integrity via a RpaA- and ROS-dependent regulatory network ]]> https://biorxiv.org/content/10.1101/2025.01.24.634715v1?rss=1 Santos-Merino, M. Nikkanen, L. Kokarakis, E. J. Allahverdiyeva, Y. Ducat, D. C. 2025-01-24 doi:10.1101/2025.01.24.634715 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ The evolution of robustness and fragility during long-term bacterial adaptation ]]> https://biorxiv.org/content/10.1101/2025.01.24.632760v1?rss=1 Chihoub, D. Pintard, C. Lenski, R. E. Tenaillon, O. Couce, A. 2025-01-27 doi:10.1101/2025.01.24.632760 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ Dynamics of biofilm-forming Bacillus subtilis in Caenorhabditis elegans gut ]]> https://biorxiv.org/content/10.1101/2025.01.26.634914v1?rss=1 Saitoh, Y. Qiu, T. 2025-01-27 doi:10.1101/2025.01.26.634914 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ Emergence of Lignin-Carbohydrate Interactions During Plant Stem Maturation Visualized by Solid-State NMR ]]> https://biorxiv.org/content/10.1101/2025.01.27.635099v1?rss=1 Xiao, P. Pfaff, S. A. Zhao, W. Debnath, D. Liu, C.-J. Cosgrove, D. J. Wang, T. 2025-01-28 doi:10.1101/2025.01.27.635099 Cold Spring Harbor Laboratory Press 2025-01-28 <![CDATA[ Females use multiple cues to assess competition for egg-laying decisions ]]> https://biorxiv.org/content/10.1101/2025.01.28.635106v1?rss=1 Sharma, M. Ramesh, A. Nagaraj, N. Isvaran, K. 2025-01-29 doi:10.1101/2025.01.28.635106 Cold Spring Harbor Laboratory Press 2025-01-29 <![CDATA[ Metabolic modeling reveals synergistic growth benefits of engineering maize symbiosis with rhizobia and arbuscular mycorrhizal fungi ]]> https://biorxiv.org/content/10.1101/2025.01.28.635303v1?rss=1 Kaste, J. A. M. Ji, R. Sydow, P. W. Sawers, R. J. H. Matthews, M. L. 2025-02-01 doi:10.1101/2025.01.28.635303 Cold Spring Harbor Laboratory Press 2025-02-01 <![CDATA[ Comparative transcriptional analysis reveals gene expression changes in spore germination of opportunistic pathogenic fungi ]]> https://biorxiv.org/content/10.1101/2025.02.03.636182v1?rss=1 Kim, D.-W. Ebert, M. K. Moonjely, S. Wang, Z. Yarden, O. Townsend, J. P. Trail, F. 2025-02-03 doi:10.1101/2025.02.03.636182 Cold Spring Harbor Laboratory Press 2025-02-03 <![CDATA[ ggRibo: a ggplot-based single-gene viewer for visualizing Ribo-seq and related omics datasets ]]> https://biorxiv.org/content/10.1101/2025.01.30.635743v1?rss=1 Wu, H.-Y. L. Kaufman, I. D. Hsu, P. Y. 2025-02-05 doi:10.1101/2025.01.30.635743 Cold Spring Harbor Laboratory Press 2025-02-05 <![CDATA[ A Multi-Model Ensemble Reveals Soil Carbon Gains from Regenerative Practices in the U.S. Midwest Cropland ]]> https://biorxiv.org/content/10.1101/2025.02.04.636509v1?rss=1 Basso, B. Tadiello, T. Millar, N. Maureira, F. Albarenque, S. Baer, B. Price, L. Sharma, P. Villalobos, C. Paustian, K. Fowler, A. Delandmeter, M. Acutis, M. Archontoulis, S. Covey, K. Doro, L. Dumont, B. Grace, P. Hoogenboom, G. Jones, J. W. Perego, A. Robertson, G. P. Ruane, A. Stockle, C. Zhang, Y. 2025-02-08 doi:10.1101/2025.02.04.636509 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Overexpression of GITRL by B cell IgD low (BDL) B cells is a therapeutic strategy to increase endogenous CD4+Foxp3+ T regulatory cells for the treatment of autoimmunity ]]> https://biorxiv.org/content/10.1101/2025.02.04.636512v1?rss=1 Khalil, M. I. Gurski, C. J. Burns, R. Zander, R. Sommers, K. C. Beltrame, A. K. Dittel, B. N. 2025-02-08 doi:10.1101/2025.02.04.636512 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Single-nucleus analysis of thoracic perivascular adipose tissue reveals critical changes in cell composition, communication, and gene regulatory networks induced by a high fat hypertensive diet ]]> https://biorxiv.org/content/10.1101/2025.02.13.636878v1?rss=1 Terrian, L. Thompson, J. M. Bowman, D. E. Panda, V. Contreras, G. A. Rockwell, C. E. Sather, L. Fink, G. D. Lauver, D. A. Nault, R. Watts, S. W. Bhattacharya, S. 2025-02-14 doi:10.1101/2025.02.13.636878 Cold Spring Harbor Laboratory Press 2025-02-14 <![CDATA[ ClusterApp to visualize, organize, and navigate metabolomics data ]]> https://biorxiv.org/content/10.1101/2025.02.12.637912v1?rss=1 Hansel, V. Karunarathne, P. Borelli, T. C. Quinn, R. da Silva, R. R. 2025-02-17 doi:10.1101/2025.02.12.637912 Cold Spring Harbor Laboratory Press 2025-02-17 <![CDATA[ The Legionella pneumophila type IVb secretion system effector BinA subverts amino acid transport to sensitize TORC1 signaling in macrophages ]]> https://biorxiv.org/content/10.1101/2025.02.20.639245v1?rss=1 Circu, M. Castore, R. Latimer, B. Shames, S. Roy, C. Dragoi, A.-M. Ivanov, S. S. 2025-02-20 doi:10.1101/2025.02.20.639245 Cold Spring Harbor Laboratory Press 2025-02-20 <![CDATA[ In vitro cellular phenotypes of cortical neurons from R255X MECP2 knock-in mice are improved by either expression of wildtype MeCP2 or read-through with G418 ]]> https://biorxiv.org/content/10.1101/2025.02.17.638700v1?rss=1 Xu, X. Merritt, J. K. Gray, S. J. Neul, J. Pozzo-Miller, L. 2025-02-21 doi:10.1101/2025.02.17.638700 Cold Spring Harbor Laboratory Press 2025-02-21 <![CDATA[ Coaxial line-scanning Brillouin microscopy ]]> https://biorxiv.org/content/10.1101/2025.02.25.640150v1?rss=1 Shi, C. Zhang, J. 2025-03-01 doi:10.1101/2025.02.25.640150 Cold Spring Harbor Laboratory Press 2025-03-01 <![CDATA[ Cell jamming transitions shape regulatory protein gradients and prime evolutionary divergence ]]> https://biorxiv.org/content/10.1101/2025.03.05.641736v1?rss=1 Badyaev, A. V. Lee, C. A. Gleason, M. J. Semenov, G. A. Britton, S. E. Moreno, C. S. Duckworth, R. A. 2025-03-06 doi:10.1101/2025.03.05.641736 Cold Spring Harbor Laboratory Press 2025-03-06 <![CDATA[ Rho2 regulates granulocyte-triggered stress adaptation and cell wall remodeling in Aspergillus fumigatus ]]> https://biorxiv.org/content/10.1101/2025.03.10.642427v1?rss=1 Ruf, D. Striegler, K. Brazil, S. Elsaman, H. Singh, K. Lepas, M. Fernando, L. D. Brantl, V. Hess, P. Dichtl, K. Aimanianda, V. Wang, T. Wagener, J. 2025-03-11 doi:10.1101/2025.03.10.642427 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Solid-State NMR Analysis of Schizosaccharomyces pombe Reveals Role of α-Amylase Family Enzymes in Cell Wall Structure and Function ]]> https://biorxiv.org/content/10.1101/2025.03.10.642465v1?rss=1 Jacob, A. Willet, A. H. Igarashi, M. G. El Nokab, M. E. H. Turner, L. A. Alsanad, A. K. A. Wang, T. Gould, K. L. 2025-03-11 doi:10.1101/2025.03.10.642465 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Deep generative modeling of temperature-dependent structural ensembles of proteins ]]> https://biorxiv.org/content/10.1101/2025.03.09.642148v1?rss=1 Janson, G. Jussupow, A. Feig, M. 2025-03-13 doi:10.1101/2025.03.09.642148 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Probing the substrate binding-induced conformational change of a ZIP metal transporter using a sandwich ELISA ]]> https://biorxiv.org/content/10.1101/2025.03.09.642161v1?rss=1 Zhang, Y. Hu, R. Su, M. Hu, J. 2025-03-13 doi:10.1101/2025.03.09.642161 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Proton-Detected Solid-State NMR for Deciphering Structural Polymorphism and Dynamic Heterogeneity of Cellular Carbohydrates in Pathogenic Fungi ]]> https://biorxiv.org/content/10.1101/2025.03.09.642223v1?rss=1 Yarava, J. R. Gautam, I. Jacob, A. Fu, R. Wang, T. 2025-03-13 doi:10.1101/2025.03.09.642223 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ From smartphones to satellites: Uniting crowdsourced biodiversity monitoring and Earth observation to fill the gaps in global plant trait mapping ]]> https://biorxiv.org/content/10.1101/2025.03.10.641660v1?rss=1 Lusk, D. Wolf, S. Svidzinska, D. Dormann, C. F. Kattge, J. Bruelheide, H. Sabatini, F. M. Damasceno, G. Moreno Martinez, A. Violle, C. Hending, D. Hähn, G. J. A. Tabeni, S. Phartyal, S. Goncalves, F. Kreft, H. Schmidt, M. Chen, H. Güler, B. Dolezal, J. Pielech, R. Guido, A. Dwyer, C. Napoleone, F. Willie, J. Gasper, A. L. Macia, M. J. Chytry, M. Lenoir, J. Thakur, D. Dengler, J. Swierszcz, S. Altman, J. Mucina, L. Nerlekar, A. N. Kakinuma, K. Rawat, P. Stancic, Z. Testolin, R. Hatim, M. Z. Rodrigues, F. Homeier, J. Marques, M. C. M. McCarthy, J. K. 2025-03-13 doi:10.1101/2025.03.10.641660 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Intrahippocampal delivery of hyperphosphorylated human tau oligomers induces neurodegeneration in non-transgenic wildtype mice ]]> https://biorxiv.org/content/10.1101/2025.03.10.642468v1?rss=1 Chen, H.-R. Hagar, H. T. Kuo, M.-H. KUAN, C.-Y. 2025-03-13 doi:10.1101/2025.03.10.642468 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Burnout in nurses and biomarkers of stress, inflammation and neuroplasticity. ]]> https://biorxiv.org/content/10.1101/2025.03.11.642730v1?rss=1 Arnetz, B. B. Iseler, J. Pena, M. Evola, N. vanSchagen, J. Beck, J. S. Counts, S. E. Arble, E. Arnetz, J. E. 2025-03-13 doi:10.1101/2025.03.11.642730 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Molecular Insights into Cell Wall Architecture and Xylan-Bound Cellulose Fibrils in the Wheat Straw ]]> https://biorxiv.org/content/10.1101/2025.03.11.642666v1?rss=1 Hu, Y. Yu, S. Ling, Z. Xiao, P. Zhu, Y. Miao, G. He, Y. Li, H. Chen, S. You, T. Wang, T. Xu, F. 2025-03-14 doi:10.1101/2025.03.11.642666 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Connecting growth and yield models to continuous forest inventory data to better account for uncertainty ]]> https://biorxiv.org/content/10.1101/2025.03.14.643281v1?rss=1 Itter, M. S. Finley, A. O. Weiskittel, A. 2025-03-17 doi:10.1101/2025.03.14.643281 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ Transcriptomic analysis of whole staged ovarian follicles reveals stage-specific folliculogenesis signatures in mice ]]> https://biorxiv.org/content/10.1101/2025.03.20.644278v1?rss=1 VanBenschoten, H. Chen, Y.-Y. Kholod, O. Russo, D. D. Shalek, A. K. Duncan, F. E. Woodruff, T. K. Goods, B. A. 2025-03-22 doi:10.1101/2025.03.20.644278 Cold Spring Harbor Laboratory Press 2025-03-22 <![CDATA[ New Insights into Microbial Nitrogen Utilization in the Rumen Enabled by Genome-Resolved Multi-Omics ]]> https://biorxiv.org/content/10.1101/2025.03.23.644819v1?rss=1 Yan, M. Firkins, J. Guo, J. Relling, A. Yu, Z. 2025-03-23 doi:10.1101/2025.03.23.644819 Cold Spring Harbor Laboratory Press 2025-03-23 <![CDATA[ Population and adaptation history of 739 Thlaspi arvense natural accessions ]]> https://biorxiv.org/content/10.1101/2025.03.21.644658v1?rss=1 Wu, X. Epstein, R. Esfahanian, M. Gautam, B. Griffiths, M. Perez, J. Barry, K. Lipzen, A. Daum, C. Yoshinaga, Y. Abeyratne, C. R. Akhmetov, Z. Arana, S. T. Bayliss, R. Borphukan, B. Brusa, A. Chhetri, H. Combs-Giroir, R. Czech, L. Dyderski, M. K. Gjesvold, E. S. Grzejszczak, G. Hateley, S. Heller, N. Hoffmann, D. Jaikumar, N. Jarvis, B. A. Jawahir, V. Klisz, M. Kruse, P. Lane, M. Lima, A. Liu, A. Madrid, G. Marlino, M. McGinn, M. Pavicic, M. Perry, W. Shah, M. Thomas, J. Townsend, A. Wanigarathna, T. L. Wesley, T. Connolly, B. Lim, Y. P. Puchałka, R 2025-03-25 doi:10.1101/2025.03.21.644658 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ Microbiome responses to natural Fusarium infection in field-grown soybean plants ]]> https://biorxiv.org/content/10.1101/2025.03.27.645697v1?rss=1 van Bentum, S. O'Banion, B. S. Gates, A. D. van Pelt, H. A. Bakker, P. A. H. M. Pieterse, C. M. J. Lebeis, S. L. Berendsen, R. L. 2025-03-28 doi:10.1101/2025.03.27.645697 Cold Spring Harbor Laboratory Press 2025-03-28 <![CDATA[ Archaeological Bolivian maize genomes suggest Inca cultural expansion augmented maize diversity in South America ]]> https://biorxiv.org/content/10.1101/2025.03.31.646424v1?rss=1 Chen, H. Baetsen-Young, A. Thompson, A. Day, B. Madzima, T. Wasef, S. Rivera Casanovas, C. Lovis, W. Wrobel, G. 2025-04-01 doi:10.1101/2025.03.31.646424 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ The impact of fungal developmental structures on mechanical properties of mycelial materials. ]]> https://biorxiv.org/content/10.1101/2025.04.01.644731v1?rss=1 Gray, K. J. Edwards, H. Doan, A. G. Huso, W. Lee, J. Pan, W. Bolima, N. Gautam, I. Wang, T. Srivastava, R. Zupan, M. Harris, S. Marten, M. R. 2025-04-01 doi:10.1101/2025.04.01.644731 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Autoinduction expression systems by AHL-mediated quorum-sensing circuits in Synechococcus elongatus PCC 7942 ]]> https://biorxiv.org/content/10.1101/2025.04.03.647055v1?rss=1 Kokarakis, E. Santos-Merino, M. Ghaffarinasab, S. Vocelle, D. Ducat, D. 2025-04-03 doi:10.1101/2025.04.03.647055 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Evidence of Gait Impairment After mTBI in an Adolescent Pig Model ]]> https://biorxiv.org/content/10.1101/2025.03.31.646330v1?rss=1 Vizzeswarapu, N. Kanat, S. Bush, T. R. Pelled, G. 2025-04-04 doi:10.1101/2025.03.31.646330 Cold Spring Harbor Laboratory Press 2025-04-04 <![CDATA[ Regional species coexistence despite local priority effects: the overlooked role of dispersal-community feedback ]]> https://biorxiv.org/content/10.1101/2025.03.31.646410v1?rss=1 Nell, L. A. Klausmeier, C. A. Fukami, T. 2025-04-04 doi:10.1101/2025.03.31.646410 Cold Spring Harbor Laboratory Press 2025-04-04 <![CDATA[ Immune phenotype-guided identification of disease-associated pathobionts in Crohn's disease ]]> https://biorxiv.org/content/10.1101/2025.04.01.646605v1?rss=1 Nagao-Kitamoto, H. Sugihara, K. Kitamoto, S. Ebihara, S. Kim, Y. Newman, K. L. Alonso, U. Suzuki, T. Kioi, Y. Yunesi, A. Inohara, N. Alteri, C. J. Minar, P. Denson, L. A. Higgins, P. Kao, J. Y. Bishu, S. Xie, Y. Lei, Y. L. Kamada, N. 2025-04-07 doi:10.1101/2025.04.01.646605 Cold Spring Harbor Laboratory Press 2025-04-07 <![CDATA[ Rapid High-Resolution Analysis of Polysaccharide-Lignin Interactions via Proton-Detected Solid-State NMR with Application to Eucalyptus and Spruce ]]> https://biorxiv.org/content/10.1101/2025.04.06.647447v1?rss=1 Xiao, P. Yarava, J. R. Debnath, D. Sahu, P. Xu, Y. Xie, L. Holmes, D. Wang, T. 2025-04-07 doi:10.1101/2025.04.06.647447 Cold Spring Harbor Laboratory Press 2025-04-07 <![CDATA[ Differential activation of NF-κB and HIF-1α between alveolar-like macrophages and myeloid-derived macrophages drive inflammatory differences following Mycobacterium abscessus infection. ]]> https://biorxiv.org/content/10.1101/2025.04.03.647026v1?rss=1 Gilliland, H. N. Soverina, S. Conner, K. N. Vielma, T. E. Olive, A. J. 2025-04-08 doi:10.1101/2025.04.03.647026 Cold Spring Harbor Laboratory Press 2025-04-08 <![CDATA[ Multiple evolutionary events in host plant adaptation in Lepidoptera ]]> https://biorxiv.org/content/10.1101/2025.04.05.647383v1?rss=1 Luo, M. Li, B. Ma, L. Jia, Z. Shi, Z. Liu, H. Wang, Z. Zhang, B. Yu, S. Qi, J. Xiao, Y. Zhou, S. Chung, H. Wang, G. 2025-04-09 doi:10.1101/2025.04.05.647383 Cold Spring Harbor Laboratory Press 2025-04-09 <![CDATA[ Sperm meet the elevated energy demands to attain fertilization competence by increasing flux through aldolase ]]> https://biorxiv.org/content/10.1101/2025.04.09.647926v1?rss=1 Violante, S. Kyaw, A. Kouatli, L. Paladugu, K. Apostolakis, L. Jenks, M. Johnson, A. Sheldon, R. Schilmiller, A. Visconti, P. Cross, J. Levin, L. Buck, J. Balbach, M. 2025-04-10 doi:10.1101/2025.04.09.647926 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ Recognition-dependent activation of the RRS1-R/RPS4 immune receptor complex ]]> https://biorxiv.org/content/10.1101/2025.04.11.646618v1?rss=1 Ahn, H.-K. Guo, G. Sklenar, J. Keh, S. P. Y. Huh, S. U. Hulin, M. T. Burdett, H. Sindalovskaya, M. Choi, J. Mukhi, N. Zhao, H. Knorr, L. Banfield, M. J. Menke, F. Ma, W. Jones, J. D. 2025-04-14 doi:10.1101/2025.04.11.646618 Cold Spring Harbor Laboratory Press 2025-04-14 <![CDATA[ Measuring the selective packaging of RNA molecules by viral coat proteins in cells ]]> https://biorxiv.org/content/10.1101/2025.04.14.648219v1?rss=1 Rastandeh, A. Makasarashvili, N. Dhaliwal, H. K. Subramanian, S. Villarreal, D. A. Baker, S. Gamez, E. I. Parent, K. N. Garmann, R. F. 2025-04-17 doi:10.1101/2025.04.14.648219 Cold Spring Harbor Laboratory Press 2025-04-17 <![CDATA[ High-Dimensional Protein Analysis Uncovers Distinct Immunological and Stromal Signatures Between Primary and Metastatic Pancreatic Ductal Adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2025.04.18.649381v1?rss=1 Greene, E. Horvat, N. K. Doxie, D. B. Parihar, V. C. Kim, J. Herting, C. J. Grundy, E. E. Ruffin, A. T. Krasinskas, A. M. Maithel, S. K. Sarmiento, J. M. Shah, M. M. Zaidi, M. Y. Diab, M. Alese, O. B. Dhodapkar, K. Kissick, H. T. El-Rayes, B. F. Paulos, C. M. Lesinski, G. B. 2025-04-18 doi:10.1101/2025.04.18.649381 Cold Spring Harbor Laboratory Press 2025-04-18 <![CDATA[ The Effects of Antidepressants on the Hippocampus: A Meta-Analysis of Public Transcriptional Profiling Data ]]> https://biorxiv.org/content/10.1101/2025.04.21.648805v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@8b41b1org.highwire.dtl.DTLVardef@85d600org.highwire.dtl.DTLVardef@a4bc1eorg.highwire.dtl.DTLVardef@13a8723_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Geoghegan, E. M. Hagenauer, M. H. Hernandez, E. Espinoza, S. Flandreau, E. I. Nguyen, P. T. Bhuiyan, M. R. Mensch, S. Watson, S. J. Akil, H. 2025-04-23 doi:10.1101/2025.04.21.648805 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ VasoTracker 2: An Open-source Platform for Quantitative Analysis of Vascular Reactivity and Function ]]> https://biorxiv.org/content/10.1101/2025.04.23.648411v1?rss=1 Lee, M. D. Osborne, C. Stevenson, R. MacDonald, A. Ebner, G. Jeffrey, D. A. MacDonald, M. A. Zhang, X. Buckley, C. Dabertrand, F. Machin, D. R. Au, J. Harraz, O. F. Tykocki, N. McCarron, J. G. Wilson, C. 2025-04-23 doi:10.1101/2025.04.23.648411 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ High resolution diel transcriptomes of autotetraploid potato reveal expression and sequence conservation among rhythmic genes ]]> https://biorxiv.org/content/10.1101/2025.04.22.650056v1?rss=1 Feke, A. Vaillancourt, B. Acheson, K. Brose, J. Hamilton, J. P. Martin, D. Wang, Y.-W. Wood, J. C. Buell, C. R. Farre, E. M. 2025-04-24 doi:10.1101/2025.04.22.650056 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ A role of villin-dependent F-actin organization in peroxisome motility in Arabidopsis cells ]]> https://biorxiv.org/content/10.1101/2025.04.23.650090v1?rss=1 Huang, C. Koenig, A. Lee, Y.-R. J. Shi, Y. Hu, J. Liu, B. 2025-04-24 doi:10.1101/2025.04.23.650090 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Inside-Out: Modeling the link between Zika virus viral dynamics within hosts and transmission to vectors across host species and virus strains ]]> https://biorxiv.org/content/10.1101/2025.04.23.650178v1?rss=1 Cecilia, H. Althouse, B. M. Azar, S. R. Rossi, S. L. Vasilakis, N. Hanley, K. A. 2025-04-29 doi:10.1101/2025.04.23.650178 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Neuroanatomical and behavioral characterization of corticotropin releasing factor-expressing lateral Habenula neurons in mice ]]> https://biorxiv.org/content/10.1101/2025.04.29.651264v1?rss=1 Flerlage, W. J. Gouty, S. C. Thomas, E. H. Simmons, S. C. Tsuda, M. C. Rujan, O. Iyer, L. Petrus, E. S. Cox, B. M. Wu, T. J. Nugent, F. S. 2025-04-30 doi:10.1101/2025.04.29.651264 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ Baseline State for Pulmonary Vasculature with Pulmonary Arterial Hypertension: Effect of Geometric Remodeling and Metabolic Shift ]]> https://biorxiv.org/content/10.1101/2025.04.30.651520v1?rss=1 Mullagura, H. N. Gharahi, H. Figueroa, C. A. Baek, S. 2025-05-06 doi:10.1101/2025.04.30.651520 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ Loss of age-associated increase in m6A-modified RNA contributes to GABAergic dysregulation in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2025.05.02.651974v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@995c55org.highwire.dtl.DTLVardef@7d0619org.highwire.dtl.DTLVardef@1b6a20org.highwire.dtl.DTLVardef@1d47dce_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Libera, J. L. Hu, J. Nguyen, T.-A. Wang, Z. van der Spek, S. J. F. Schult, K. Dorrian, L. Majka, J. Tobunluepop, K. Puri, S. Kynshov, A. Kanaan, N. M. Nelson, P. T. Meyer, K. Hou, L. Zhang, X. Wolozin, B. 2025-05-06 doi:10.1101/2025.05.02.651974 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ Endocytosis of a zinc transceptor ZIP4 is mediated by AP2 through an atypical dileucine motif ]]> https://biorxiv.org/content/10.1101/2025.05.03.652025v1?rss=1 Wang, T. Zhang, C. Zhang, Y. Hu, J. 2025-05-06 doi:10.1101/2025.05.03.652025 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ Phylogenetic Analysis and Machine Learning Identify Signatures of Selection and Predict Deleterious Mutations in Common Bean ]]> https://biorxiv.org/content/10.1101/2025.05.05.652309v1?rss=1 Cordoba-Novoa, H. A. Buckler, E. S. Romay, C. Berthel, A. Johnson, L. Balasubramanian, P. Hoyos Villegas, V. 2025-05-06 doi:10.1101/2025.05.05.652309 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ Persistent endotoxin exposure in macrophages elicits an immunometabolic profile susceptible to NF-kB and p53 perturbation ]]> https://biorxiv.org/content/10.1101/2025.04.30.651567v1?rss=1 Maduka, C. V. Xie, X. Makela, A. V. Ural, E. Contag, C. H. 2025-05-07 doi:10.1101/2025.04.30.651567 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Repetitive Neuronal Activation Regulates Cellular Maturation State via Nuclear Reprogramming ]]> https://biorxiv.org/content/10.1101/2025.05.02.651848v1?rss=1 Murano, T. Hagihara, H. Tajinda, K. Takao, K. Takamiya, Y. Katoh, K. Robison, A. J. Matsumoto, M. Namihira, M. Miyakawa, T. 2025-05-08 doi:10.1101/2025.05.02.651848 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ Acute session of three endurance exercise intensities alters subcutaneous adipose tissue transcriptome in regular exercisers ]]> https://biorxiv.org/content/10.1101/2025.05.02.651890v1?rss=1 Ahn, C. Zhang, T. Rode, T. Yang, G. Chugh, O. K. Ellis, S. Ghayur, S. J. Mehta, S. Salzman, R. Jiang, H. Parker, S. Burant, C. Horowitz, J. F. 2025-05-08 doi:10.1101/2025.05.02.651890 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ In vivo production of an anti-HIV antibody from primate hematopoietic cells by non-viral knock-in ]]> https://biorxiv.org/content/10.1101/2025.05.02.651933v1?rss=1 Castelli, J. M. Poljakov, K. Youngseo, J. Cassidy, M. E. Gray, M. D. Sanchez Gaytan, J. N. Enstrom, M. R. Linton, J. D. Rongvaux, A. Taylor, J. J. Adair, J. E. 2025-05-08 doi:10.1101/2025.05.02.651933 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ An All-In-One Software Solution for Automated Processing of LA-ICP-TOF-MS datasets ]]> https://biorxiv.org/content/10.1101/2025.05.09.653091v1?rss=1 Crawford, A. M. Zee, D. Z. Jin, Q. Sue, A. Sinha, N. Ahn, S. H. MacRenaris, K. W. O'Halloran, T. 2025-05-12 doi:10.1101/2025.05.09.653091 Cold Spring Harbor Laboratory Press 2025-05-12 <![CDATA[ Targeting the selectivity filter to drastically alter the activity and substrate spectrum of a promiscuous metal transporter ]]> https://biorxiv.org/content/10.1101/2025.05.07.652779v1?rss=1 Jiang, Y. Nikolovski, M. Wang, T. MacRenaris, K. O'Halloran, T. V. Hu, J. 2025-05-13 doi:10.1101/2025.05.07.652779 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Non-redundant cardiolipin synthases support membrane integrity and stress resilience in Bacteroides fragilis ]]> https://biorxiv.org/content/10.1101/2025.05.12.653583v1?rss=1 Schnizlein, M. K. Hong, B. J. Nguyen, J. N. T. Jones, K. Rodriguez, A. I. Fiebig, A. Campagna, S. R. Balunas, M. J. O'Halloran, T. V. Crosson, S. 2025-05-13 doi:10.1101/2025.05.12.653583 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Sex differences in DNA methylation in bats ]]> https://biorxiv.org/content/10.1101/2025.05.13.653776v1?rss=1 Rayner, J. G. Bock, S. L. Lonski, A. J. Riddle, N. C. Wilkinson, G. S. 2025-05-15 doi:10.1101/2025.05.13.653776 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Entry Steps in the Biosynthetic Pathway to DiterpenoidAlkaloids in Delphinium grandiflorum and Aconitum plicatum ]]> https://biorxiv.org/content/10.1101/2025.05.15.654307v1?rss=1 Miller, G. P. Mutabdzija-Nedelcheva, L. Andersen, T. Pascoe, I. Van Winkle, K. Pluskal, T. Hamberger, B. 2025-05-17 doi:10.1101/2025.05.15.654307 Cold Spring Harbor Laboratory Press 2025-05-17 <![CDATA[ Inorganic profiles of preimplantation embryos reveal a role for zinc in blastocyst development ]]> https://biorxiv.org/content/10.1101/2025.05.14.654061v1?rss=1 Balough, J. L. O'Halloran, T. V. Duncan, F. E. Woodruff, T. K. 2025-05-18 doi:10.1101/2025.05.14.654061 Cold Spring Harbor Laboratory Press 2025-05-18 <![CDATA[ Robust inference and widespread genetic correlates from a large-scale genetic association study of human personality ]]> https://biorxiv.org/content/10.1101/2025.05.16.648988v1?rss=1 Schwaba, T. Clapp Sullivan, M. L. Akingbuwa, W. A. Ilves, K. Tanksley, P. T. Williams, C. M. Dragostinov, Y. Liao, W. Ackerman, L. S. Fealy, J. C. M. Hemani, G. de la Fuente, J. Gupta, P. Stein, M. B. Gelernter, J. Levey, D. F. Vosa, U. Ausmees, L. Realo, A. Estonian Biobank Research Team, Vaht, M. Allik, J. Esko, T. Mottus, R. Vainik, U. Jonsdottir, G. A. Thorleifsson, G. Gunnarsson, A. F. Bjornsdottir, G. Thorgeirsson, T. E. Steffansson, H. Stefansson, K. Cheesman, R. Qin, Q. Corfield, E. C. Ask, H. Ask Torvik, F. Ystrom, E. Tesli, M. Boomsma, D. I. 2025-05-20 doi:10.1101/2025.05.16.648988 Cold Spring Harbor Laboratory Press 2025-05-20 <![CDATA[ Estradiol treatment enhances neurovascular coupling independent of metabolic health status in a mouse model of menopause ]]> https://biorxiv.org/content/10.1101/2025.05.21.655189v1?rss=1 Plumley, Z. M. Calvo Iglesias, J. Fernandez Ugidos, I. Walker, A. B. Pires dos Santos, I. Taylor, H. Mostany, R. 2025-05-21 doi:10.1101/2025.05.21.655189 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Variation in responses to temperature across admixed genotypes of Populus trichocarpa x P. balsamifera predict geographic shifts in regions where hybrids are favored ]]> https://biorxiv.org/content/10.1101/2025.05.16.654548v1?rss=1 Mead, A. Beasley-Bennett, J. R. Bleich, A. C. Fischer, D. G. Flint, S. Golightly, J. Klopf, S. K. Kulbaba, M. W. Lasky, J. LeBoldus, J. M. Lowry, D. B. Mitchell, N. Moran, E. V. Sexton, J. P. Sondreli, K. L. Worthing, B. W. Zavala-Paez, M. Fitzpatrick, M. C. Holliday, J. A. Keller, S. R. Hamilton, J. A. 2025-05-22 doi:10.1101/2025.05.16.654548 Cold Spring Harbor Laboratory Press 2025-05-22 <![CDATA[ Everything, everywhere, all at once - Surveillance and molecular epidemiology reveal Melissococcus plutonius is endemic among Michigan, US beekeeping operations of all sizes and present in some honey bee colonies year-round ]]> https://biorxiv.org/content/10.1101/2025.05.22.655465v1?rss=1 Fowler, P. D. Dhakal, U. Chang, J. H. Milbrath, M. O. 2025-05-23 doi:10.1101/2025.05.22.655465 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ Simple, rapid, and sensitive assay for the quantification of total polysaccharides to estimate extracellular polymeric substances (EPS) in soil ]]> https://biorxiv.org/content/10.1101/2025.05.22.654594v1?rss=1 Bogar, G. Lennon, J. T. Vander Stel, H. M. Evans, S. E. 2025-05-27 doi:10.1101/2025.05.22.654594 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Dynamic changes to the plastoglobule lipidome and proteome in water-deficient maize ]]> https://biorxiv.org/content/10.1101/2025.05.26.656201v1?rss=1 Devadasu, E. Schilmiller, A. L. Gonzalez, N. Lundquist, P. K. 2025-05-30 doi:10.1101/2025.05.26.656201 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ An intermediate activation state primes Langerhans cell migration from the epidermis ]]> https://biorxiv.org/content/10.1101/2025.05.29.656912v1?rss=1 Kiselev, A. Schmitter-Sanchez, A. D. Williams, S. Park, S. 2025-05-30 doi:10.1101/2025.05.29.656912 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ Developmentally-specific physiological and metabolic responses support drought resilience in switchgrass and constrains biofuel yield ]]> https://biorxiv.org/content/10.1101/2025.05.29.656847v1?rss=1 Basyal, B. Li, X. Pargulski, V. Fu, X. Nightingale, N. Overmyer, K. Coon, J. Zhang, Y. Benucci, G. M. N. Last, R. Sato, T. Walker, B. 2025-06-01 doi:10.1101/2025.05.29.656847 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Transplantation of GABAergic Interneuron Progenitors Restores Cortical Circuit Function in an Alzheimer's Disease Mouse Model ]]> https://biorxiv.org/content/10.1101/2025.05.31.656412v1?rss=1 Yokomizo, S. Maci, M. Stafford, A. M. Miller, M. R. Perle, S. J. Takahashi, S. Brown-Harding, H. Liang, L. Lovely, A. Algamal, M. Gillani, R. L. Zwang, T. J. Richardson, D. Naegele, J. R. Vogt, D. Kastanenka, K. V. 2025-06-01 doi:10.1101/2025.05.31.656412 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ HIGH CO2 LEVELS OVERCOME THE NIGHTTIME LETHALITY OF CIRCADIAN MUTANTS IN CYANOBACTERIA ]]> https://biorxiv.org/content/10.1101/2025.06.01.657271v1?rss=1 Mendana, A. Santos-Merino, M. Dominguez-Quintero, M. Gutierrez-Lanza, R. Ducat, D. Fernandez-Lopez, R. 2025-06-01 doi:10.1101/2025.06.01.657271 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Revealing Spatial Heterogeneity across the Gut Tissue-Lumen Interface through MALDI Mass Spectrometry Imaging ]]> https://biorxiv.org/content/10.1101/2025.06.01.657309v1?rss=1 Haffner, J. J. Ahn, S. H. Qiu, T. 2025-06-02 doi:10.1101/2025.06.01.657309 Cold Spring Harbor Laboratory Press 2025-06-02 <![CDATA[ Integrating multiple transcriptome-based methods for drug repurposing in tuberculosis ]]> https://biorxiv.org/content/10.1101/2025.06.02.657296v1?rss=1 Samart, K. Buskirk, L. R. Tonielli, A. P. Krishnan, A. Ravi, J. 2025-06-02 doi:10.1101/2025.06.02.657296 Cold Spring Harbor Laboratory Press 2025-06-02 <![CDATA[ γ-glutamyl-cysteine is a critical intermediate in glutathione-led amelioration of PFOS-neurotoxicity ]]> https://biorxiv.org/content/10.1101/2025.06.01.657248v1?rss=1 Sammi, S. R. Boonpraman, N. Kuhn, N. C. Cannon, J. R. 2025-06-03 doi:10.1101/2025.06.01.657248 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ The Neurofibrillary Tangle Maturity Scale: A Novel Framework for Tangle Pathology Evaluation in Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2025.06.02.657435v1?rss=1 Moloney, C. M. Rutledge, M. H. Labuzan, S. A. Peng, Z. Tranovich, J. F. Wood, A. C. Rothberg, D. M. Duara, R. Lachner, C. Graff-Radford, N. R. Dickson, D. W. Kanaan, N. M. Carter, R. E. Murray, M. E. 2025-06-06 doi:10.1101/2025.06.02.657435 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ The architecture of resilience: a genome assembly of Myrothamnus flabellifolia sheds light on desiccation tolerance and sex determination ]]> https://biorxiv.org/content/10.1101/2025.06.02.657439v1?rss=1 Marks, R. Lovell, J. T. Carey, S. B. Van Der Pas, L. Chimukuche, N. M. Bruna, T. Plott, C. Webber, J. Lipzen, A. Yan, J. Bauer, D. Bentley, J. Talag, J. Barry, K. Grimwood, J. Jenkins, J. W. Schmutz, J. Harkess, A. VanBuren, R. Leebens-Mack, J. Farrant, J. M. 2025-06-06 doi:10.1101/2025.06.02.657439 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ An insect brain-based bioelectronic neural sensor for the systemic detection and precise classification of endometriosis ]]> https://biorxiv.org/content/10.1101/2025.06.03.657650v1?rss=1 Saha, D. Sanchez, S. W. Vegter, E. L. Parnas, M. Song, Y. Fazleabas, A. T. 2025-06-06 doi:10.1101/2025.06.03.657650 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ FLOE1 maintains cellular viscosity in rehydrating Arabidopsis embryos ]]> https://biorxiv.org/content/10.1101/2025.06.03.657678v1?rss=1 Field, S. Ramirez, J. F. Dorone, Y. Cox, J. A. Boothby, T. C. Rhee, S. Y. 2025-06-06 doi:10.1101/2025.06.03.657678 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Constitutive expression of full-length or partial of SOC1 genes for yield enhancement in tomato ]]> https://biorxiv.org/content/10.1101/2025.06.03.657751v1?rss=1 Danial, G. H. Jaikham, J. Song, G.-q. 2025-06-06 doi:10.1101/2025.06.03.657751 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ PP2A METHYLESTERASE, PME-1, AND PP2A METHYLTRANSFERASE, LCMT-1, CONTROL SENSITIVITY TO IMPAIRMENTS CAUSED BY INJURY-RELATED OLIGOMERIC TAU ]]> https://biorxiv.org/content/10.1101/2025.06.05.657660v1?rss=1 Sundaresh, S. N. Vogel, E. W. Hue, C. D. Zhang, H. Staniszewski, A. Berman, H. L. Gill, Z. Asam, K. Liang, S. Shen, L. Gnanaprakash, M. Acquarone, E. Fa, M. Kanaan, N. M. Morrison, B. Arancio, O. Nicholls, R. E. 2025-06-06 doi:10.1101/2025.06.05.657660 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Single-cell imaging reveals spontaneous phenotypic sorting and bet-hedging in developing biofilms ]]> https://biorxiv.org/content/10.1101/2025.06.03.657734v1?rss=1 Tai, J.-S. B. Nam, K.-M. Li, C. Nijjer, J. Zhang, S. Waters, C. M. Yan, J. 2025-06-07 doi:10.1101/2025.06.03.657734 Cold Spring Harbor Laboratory Press 2025-06-07 <![CDATA[ Generation and characterization of a mouse model of conditional Chd4 knockout in the endometrial epithelium. ]]> https://biorxiv.org/content/10.1101/2025.06.05.658183v1?rss=1 Chandler, R. L. Harkins, S. K. Skalski, H. J. Bennett, A. Z. Pavliscak, L. Arendt, A. R. Wood, L. Moldovan, G. E. 2025-06-09 doi:10.1101/2025.06.05.658183 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ G1 and G2 ApolipoproteinL1 modulate macrophage inflammation and lipid accumulation through the polyamine pathway ]]> https://biorxiv.org/content/10.1101/2025.06.06.658371v1?rss=1 Liu, E. Wright, M. Kearney, A. O. Caza, T. Yang, J. Y. Garcia, V. Dadi, A. O. Ishibe, S. Chandel, N. S. Zhang, H. Benjamin Thorp, E. Lin, J. 2025-06-09 doi:10.1101/2025.06.06.658371 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Unraveling the diversity and functional potential of cyanosphere microbiomes assembled from terrestrial cyanobacteria ]]> https://biorxiv.org/content/10.1101/2025.06.10.658773v1?rss=1 Palmer, B. Couradeau, E. Johansen, J. Kurbessoian, T. Ortega Carranza, J. Stajich, J. E. Ward, R. Pietrasiak, N. 2025-06-15 doi:10.1101/2025.06.10.658773 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Generalizing animal movement predictions across landscapes: a scalable framework grounded in empirical telemetry data ]]> https://biorxiv.org/content/10.1101/2025.06.12.658668v1?rss=1 Chalkowski, K. Sack, A. Wittemyer, G. Miller, R. S. Boughton, R. K. Snow, N. P. Beasley, J. C. Ditchkoff, S. S. Evans, T. S. Gray, S. M. Lewis, J. S. Parsons, M. A. Vercauteren, K. C. Webb, S. L. Young, J. K. Pepin, K. M. 2025-06-15 doi:10.1101/2025.06.12.658668 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Use of a specific set of learner-centered evidence-based teaching practices correlates with higher exam performance across seven STEM departments ]]> https://biorxiv.org/content/10.1101/2025.06.13.659643v1?rss=1 Jackson, M. A. Liu, H. Moon, S. Doherty, J. H. Wenderoth, M. P. 2025-06-16 doi:10.1101/2025.06.13.659643 Cold Spring Harbor Laboratory Press 2025-06-16 <![CDATA[ Omega-3 Fatty Acid Synergy with Glucocorticoid in Lupus Macrophages: Targeting Pathogenic Pathways to Reduce Steroid Dependence ]]> https://biorxiv.org/content/10.1101/2025.06.12.658906v1?rss=1 Heine, L. K. Nault, R. Jackson, J. Anderson, A. N. Harkema, J. R. Olive, A. J. Pestka, J. J. McDonald, O. F. 2025-06-17 doi:10.1101/2025.06.12.658906 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Immune pathways and perinatal environmental exposures contribute to epigenetic gestational age prediction and acceleration ]]> https://biorxiv.org/content/10.1101/2025.06.13.659090v1?rss=1 Eapen, A. A. Loveless, I. M. Pan, M. Liang, X. Straughen, J. Cassidy-Bushrow, A. Sitarik, A. R. Simmerman, N. Thompson, E. E. Kottyan, L. Ober, C. Johnson, C. C. Zoratti, E. Levin, A. M. 2025-06-18 doi:10.1101/2025.06.13.659090 Cold Spring Harbor Laboratory Press 2025-06-18 <![CDATA[ YAP signaling promotes resistance to MEK and AKT inhibition in NF1-related MPNSTs ]]> https://biorxiv.org/content/10.1101/2025.06.16.659334v1?rss=1 McGee, L. E. Grit, J. L. Essenburg, C. J. Agrusa, S. Turner, L. Becker, K. Dey, A. Klomp, J. E. Klomp, J. A. Adams, M. Beddows, I. Wolfrum, E. Fu, D. Hirbe, A. C. Graveel, C. R. Steensma, M. R. 2025-06-20 doi:10.1101/2025.06.16.659334 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ Multi-Omics Analysis of Heat Stress-Induced Memory in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2025.06.19.660594v1?rss=1 Thirumlaikumar, V. P. P. Yu, L. Arora, D. Mubeen, U. Wisniewski, A. Walther, D. Giavalisco, P. Alseekh, S. DL Nelson, A. Skirycz, A. Balazadeh, S. 2025-06-23 doi:10.1101/2025.06.19.660594 Cold Spring Harbor Laboratory Press 2025-06-23 <![CDATA[ Vocal convergence during formation of social relationships in vampire bats ]]> https://biorxiv.org/content/10.1101/2025.06.21.660856v1?rss=1 Vrtilek, J. Smith-Vidaurre, G. Fosler-Lussier, E. Page, R. A. Carter, G. G. 2025-06-23 doi:10.1101/2025.06.21.660856 Cold Spring Harbor Laboratory Press 2025-06-23 <![CDATA[ Quantifying impacts of natural gas development on forest carbon ]]> https://biorxiv.org/content/10.1101/2025.06.23.661107v1?rss=1 Shannon, E. S. Finley, A. O. May, P. B. 2025-06-24 doi:10.1101/2025.06.23.661107 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ Biocatalytic Construction of a CEST MRI Nucleoside Probe: Synthesis and Evaluation of 5-Methyl-5,6-dihydrothymidine ]]> https://biorxiv.org/content/10.1101/2025.06.25.661137v1?rss=1 Al-Hilfi, A. Franco, E. A. C. Grady, C. J. Mohanta, Z. McMahon, M. T. Bazayeva, M. Li, Z. Merz, K. M. Gilad, A. A. 2025-06-25 doi:10.1101/2025.06.25.661137 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ New niches for larger phytoplankton in a warmer, more resource-limited ocean ]]> https://biorxiv.org/content/10.1101/2025.06.22.660956v1?rss=1 Leles, S. G. Breithaupt, L. Krinos, A. Alexander, H. Moeller, H. V. Flanjak, L. Laufkoetter, C. Litchman, E. Aranguren-Gassis, M. Levine, N. M. 2025-06-27 doi:10.1101/2025.06.22.660956 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Targeted ablation and regeneration of enteric nervous system neurons in zebrafish ]]> https://biorxiv.org/content/10.1101/2025.07.01.660701v1?rss=1 Shah, M. A. Moran, K. K. Rueckert, H. Sharrock, A. V. Ackerley, D. F. Mumm, J. S. Ganz, J. 2025-07-04 doi:10.1101/2025.07.01.660701 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Attention robustly dissociates objective performance and subjective visibility reports ]]> https://biorxiv.org/content/10.1101/2025.07.03.661972v1?rss=1 Tian, K. J. Maniscalco, B. Epstein, M. L. Shen, A. Castaneda, O. G. Kurosawa, T. Motzer, J. A. Olsson, E. Russell, E. E. Walsh, M. E. Wang, J. Zeb, T. B. A. Brown, R. Lamme, V. A. Lau, H. He, B. J. Brascamp, J. W. Block, N. Chalmers, D. Peters, M. A. Denison, R. N. 2025-07-04 doi:10.1101/2025.07.03.661972 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Analysis of a Rpb2 mutant in Schizosaccharomyces pombe reveals a non-canonical role for Elp1 in regulating RNAi-dependent heterochromatin assembly ]]> https://biorxiv.org/content/10.1101/2025.07.02.662331v1?rss=1 Nirmal, M. B. Pearce, M. E. Liu, C. T. Finkel, J. M. Darrow, K. S. Vo, T. V. 2025-07-05 doi:10.1101/2025.07.02.662331 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ From sequence to signature: Uncovering multiscale AMR features across bacterial pathogens with supervised machine learning ]]> https://biorxiv.org/content/10.1101/2025.07.03.663053v1?rss=1 Ghosh, A. Brenner, E. P. Vang, C. K. Wolfe, E. P. Burke, J. T. Lesiyon, R. L. Manpearl, K. R. Sridhar, V. Krol, J. D. Boyer, E. Bilodeaux, J. M. Jongnarangsin, K. Majlessi, E. J. Ravi, J. 2025-07-07 doi:10.1101/2025.07.03.663053 Cold Spring Harbor Laboratory Press 2025-07-07 <![CDATA[ Warm-loving species perform well under limiting resources:trait combinations for future climate ]]> https://biorxiv.org/content/10.1101/2025.07.04.662912v1?rss=1 Levasseur, S. A. Y. Weber de Melo, V. Hille Ris Lambers, J. Klausmeier, C. A. Kremer, C. T. Litchman, E. Reyes, M. Thomas, M. K. Narwani, A. 2025-07-07 doi:10.1101/2025.07.04.662912 Cold Spring Harbor Laboratory Press 2025-07-07 <![CDATA[ Identification of functional neural networks of human brains with fMRI ]]> https://biorxiv.org/content/10.1101/2025.07.07.663492v1?rss=1 Huang, J. 2025-07-10 doi:10.1101/2025.07.07.663492 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ Deep Learning for Sorghum Yield Forecasting using Uncrewed Aerial Systems and Lab-Derived Imagery ]]> https://biorxiv.org/content/10.1101/2025.07.11.663520v1?rss=1 Bari, M. A. Bakshi, A. Choton, J. C. A. Pramanik, S. Witt, T. D. Caragea, D. Bean, S. Jagadish, K. Felderhoff, T. 2025-07-12 doi:10.1101/2025.07.11.663520 Cold Spring Harbor Laboratory Press 2025-07-12 <![CDATA[ SOX2 is a dispensable modulator of NUT carcinoma oncogenesis in mouse ]]> https://biorxiv.org/content/10.1101/2025.07.09.664010v1?rss=1 Gu, B. Luo, C. Zheng, D. Elnegiry, A. Bhatara, S. Mias, G. I. Tsoi, M. F. Yu, J. 2025-07-14 doi:10.1101/2025.07.09.664010 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ Using spatial statistics to infer game-theoretic interactions in an agent-based model of cancer cells ]]> https://biorxiv.org/content/10.1101/2025.07.09.664005v1?rss=1 Leither, S. Strobl, M. Scott, J. G. Dolson, E. 2025-07-15 doi:10.1101/2025.07.09.664005 Cold Spring Harbor Laboratory Press 2025-07-15 <![CDATA[ Controlling treatment toxicity in ovarian cancer to prime the patient for tumor extinction therapy ]]> https://biorxiv.org/content/10.1101/2025.07.10.664235v1?rss=1 50%), most eventually succumb to their disease due to high recurrence rates, acquired resistance, and cumulative toxicity. This report summarizes work from the 12th IMO Workshop in which we explored an alternative "extinction therapy" strategy for frontline treatment of HGSOC. Inspired by ecological principles, this multi-strike approach aims to eradicate tumors not through a singular "magic bullet" but through a series of therapies after standard frontline treatment when the tumor is still, and perhaps most, vulnerable. We present a framework leveraging mathematical modeling (MM) to develop personalized multi-strike protocols for HGSOC. Key contributions include: 1) An "IMOme" score using liquid biopsy data to assess patient-specific hematopoietic toxicity risk, guiding the timing and selection of subsequent therapies, 2) MM strategies to design effective lowdose combinations of targeted agents to achieve synthetic lethality while managing toxicity, and 3) A MM framework to analyze the interplay between chemotherapy, gut microbiome toxicity, and immunotherapy, demonstrating how mitigating microbiome damage could enhance immune response. Overall, the computational approaches presented herein aim to support the design of personalized, multi-strike regimens in the frontline setting that proactively target tumor extinction while managing toxicity, ultimately seeking to deliver cures for patients with HGSOC. ]]> Gallagher, K. Sousa, R. S. Gatenbee, C. D. Schenck, R. Chen, P. Citak, T. Leither, S. Mazzacurati, L. Xella, A. Zhou, Z. Lemanne, D. Rodriguez, P. George, E. Strobl, M. A. R. 2025-07-16 doi:10.1101/2025.07.10.664235 Cold Spring Harbor Laboratory Press 2025-07-16 <![CDATA[ Response to "No evidence that transmissible cancer has shifted from emergence to endemism in Tasmanian devils" ]]> https://biorxiv.org/content/10.1101/2025.07.14.664746v1?rss=1 Storfer, A. Margres, M. J. Kozakiewicz, C. P. Hamede, R. Ruiz-Aravena, M. Hamilton, D. G. Comte, S. Stadler, T. Leache, A. McCallum, H. Jones, M. E. Hohenlohe, P. A. 2025-07-16 doi:10.1101/2025.07.14.664746 Cold Spring Harbor Laboratory Press 2025-07-16 <![CDATA[ Mouse Adapted Omicron BA.5 Induces A Fibrotic Lung Disease Phenotype in BALB/c Mice ]]> https://biorxiv.org/content/10.1101/2025.07.16.665104v1?rss=1 Powers, J. M. Leist, S. R. Suryadevara, N. Zost, S. Binshtein, E. Abdelgadir, A. Mallory, M. L. Edwards, C. E. Gully, K. L. Hubbard, M. L. Zweigart, M. R. Bailey, A. B. Sheahan, T. P. Crowe, J. E. Montgomery, S. A. Harkema, J. R. Baric, R. S. 2025-07-16 doi:10.1101/2025.07.16.665104 Cold Spring Harbor Laboratory Press 2025-07-16 <![CDATA[ Graph pangenome reveals structural variation dynamics during cucumber breeding ]]> https://biorxiv.org/content/10.1101/2025.07.17.665377v1?rss=1 Zhao, X. Yu, J. Zhang, J. Sun, H. Wu, S. Zhao, J. Zhou, Y. Hammar, S. Lin, Y.-C. Zhang, Z. Huang, S. Dymerski, R. Chen, F. Weng, Y. Grumet, R. Xu, Y. Fei, Z. 2025-07-21 doi:10.1101/2025.07.17.665377 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ DANCE 2.0: Transforming single-cell analysis from black box to transparent workflow ]]> https://biorxiv.org/content/10.1101/2025.07.17.665427v1?rss=1 Ding, J. Xing, Z. Wang, Y. Liu, R. Liu, S. Huang, Z. Tang, W. Xie, Y. Zou, J. Qiu, X. Ma, J. Yu, G. Tang, J. 2025-07-22 doi:10.1101/2025.07.17.665427 Cold Spring Harbor Laboratory Press 2025-07-22 <![CDATA[ The Tricuspid Valve is Transcriptionally Active During Prolonged Pressure Overload, Right-Sided Heart Failure, and Valve Regurgitation ]]> https://biorxiv.org/content/10.1101/2025.07.21.666043v1?rss=1 Goodyke, A. Gaweda, B. Piekarska, M. Arora, S. Westgate, M. Loyaga-Rendon, R. Jani, M. Rausch, M. K. Aguirre, A. Prokop, J. Timek, T. A. 2025-07-25 doi:10.1101/2025.07.21.666043 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ A comparison of tools and read depth criteria for genuine single nucleotide polymorphism identification in ancient maize samples ]]> https://biorxiv.org/content/10.1101/2025.07.22.666096v1?rss=1 = 5X is optimal for inferring the closest relative of the aDNA maize samples used in this study. Our study aims to improve the current standardized approach, including optimal approaches, tools and read depth criteria, to improve the accuracy of aDNA data interpretation. Furthermore, our results offer a practical guideline for researchers seeking to improve the quality of their aDNA data for downstream analysis. ]]> Chen, H. Madzima, T. 2025-07-25 doi:10.1101/2025.07.22.666096 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon ]]> https://biorxiv.org/content/10.1101/2025.07.25.666869v1?rss=1 Sun, H. Zhang, J. Liao, S. Guo, S. Zhou, Z. Zhao, X. Wu, S. Zhao, J. Gong, G. Wang, J. Li, M. Yu, Y. Ren, Y. Tian, S. Li, S. Zhang, H. Hammar, S. A. McGregor, C. Jarret, R. Wechter, P. Branham, S. E. Kousik, C. Levi, A. Grumet, R. Xu, Y. Fei, Z. 2025-07-27 doi:10.1101/2025.07.25.666869 Cold Spring Harbor Laboratory Press 2025-07-27 <![CDATA[ Bacterial metabolites induce cell wall remodeling, antifungal resistance, and immune recognition of commensal fungi ]]> https://biorxiv.org/content/10.1101/2025.07.26.666966v1?rss=1 Davis, F. A. Singh, K. Krampen, J. M. Bryant, J. A. Ost, K. S. Righi, S. E. Balunas, M. J. Wang, T. O'Meara, T. R. 2025-07-27 doi:10.1101/2025.07.26.666966 Cold Spring Harbor Laboratory Press 2025-07-27 <![CDATA[ Myelin Decompaction in Mice Given Anesthetics during Magnetic Resonance Imaging ]]> https://biorxiv.org/content/10.1101/2025.07.29.667499v1?rss=1 Best, C. DUBEY, H. Liu, S. White, A. Jayam, S. Mallett, C. L. Knickmeyer, R. C. 2025-08-01 doi:10.1101/2025.07.29.667499 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Various Optimization Strategies for the Isolation of Mitochondria from Sprague-Dawley Rat Liver Tissue ]]> https://biorxiv.org/content/10.1101/2025.07.30.667653v1?rss=1 Roth, C. Vadovsky, A. Xia, T. Bazil, J. N. 2025-08-01 doi:10.1101/2025.07.30.667653 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Noninvasive detection of bacterial biofilms using an insect olfactory brain-based gas sensor ]]> https://biorxiv.org/content/10.1101/2025.08.01.668178v1?rss=1 Parnas, M. Mclane-Svoboda, A. K. Shahab, M. Stout, C. McLane-Svoboda, S. B. Cox, E. Hardy, J. Saha, D. 2025-08-01 doi:10.1101/2025.08.01.668178 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Oxytocin neurons in the anterior and posterior paraventricular nucleus have distinct behavioral functions and electrophysiological profiles ]]> https://biorxiv.org/content/10.1101/2025.08.03.668226v1?rss=1 Chrisman, A. N. Sugimoto, C. Butler-Struben, H. Minie, V. A. Anderson, D. Eagle, A. L. Duque-Wilckens, N. Ramos, A. Lewis, Y. I. Archdeacon, S. C. Robison, A. J. Trainor, B. C. 2025-08-04 doi:10.1101/2025.08.03.668226 Cold Spring Harbor Laboratory Press 2025-08-04 <![CDATA[ Secreted Protein Production is Improved by Controlling Endoplasmic Reticulum Stress Associated Protein Degradation ]]> https://biorxiv.org/content/10.1101/2025.08.05.666879v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@9139c3org.highwire.dtl.DTLVardef@673bc1org.highwire.dtl.DTLVardef@1842210org.highwire.dtl.DTLVardef@1d86903_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG Therapeutic proteins are produced frequently by mammalian cells in large-scale bioreactors. As a result, producer cells are exposed to a chemically (nutrients, gas exchange, target protein overexpression) and physically (shear due to mixing) stressful environment, which can lead to loss of proteostasis and endoplasmic reticulum (ER) stress. In response, cells activate the unfolded protein response (UPR). The UPR includes activation of autophagy and proteasomes, both of which target unfolded/misfolded proteins for degradation. To investigate the impacts of autophagy and proteasome activity on secreted protein production in ER-stressed cells, we used HeLa and MDA-MB-231 cells transfected to express Gaussia luciferase (as a model for therapeutic protein production) and exposed to tunicamycin (TM) (to activate ER stress). As expected, TM exposure decreased protein production and secretion. Inhibiting autophagy improved secretion in stressed cells as expected. However, counterintuitively, increasing proteasomal degradation improved secretion while inhibiting proteasomal activity decreased secretion, that is proteasomal activity was directly correlated to secretion. Taken together, our results demonstrate that protein secretion can be improved through control of autophagy and proteasomal activity, providing insight into strategies for improving yield from protein production bioprocesses. Key PointsO_LITunicamycin induced ER stress reduced protein production. C_LIO_LIAutophagy inhibition improved secretion in ER stressed cells. C_LIO_LIActivation of proteasomal degradation improved secretion in ER stressed cells. C_LI ]]> Splichal, R. C. Chan, C. Walton, S. P. 2025-08-07 doi:10.1101/2025.08.05.666879 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Potato dihaploids uncover diverse alleles to facilitate diploid potato breeding ]]> https://biorxiv.org/content/10.1101/2025.08.06.668948v1?rss=1 Coronejo, S. Vaillancourt, B. Hamilton, J. P. Meng, X. Mailloux, K. Christiansen, G. Huege, J. Shaw, K. M. Agha, H. Brown-Donovan, K. Busse, J. S. Hamernik, A. J. Caraza-Harter, M. V. Heroux, L. Kardile, H. B. Knoeck, E. Sorensen, P. L. Spencer, D. Yilma, S. Bethke, P. C. Douches, D. S. Parsons, J. Sathuvalli, V. R. Tan, E. H. Endelman, J. B. Buell, C. R. Shannon, L. M. 2025-08-07 doi:10.1101/2025.08.06.668948 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Procrustean pseudo-landmark methods in Python to measure massive quantities of leaf shape data ]]> https://biorxiv.org/content/10.1101/2025.08.08.669192v1?rss=1 Hightower, A. T. Hall, S. Camacho, R. U. Papamichail, A. Adamski, E. Colligan, C. Deneen, A. Dunn, G. Haziza, J. Henley, C. Pawawongsak, A. Simms, L. Ward, S. Balant, M. Blackwood, C. Cannon, C. Case, A. Husbands, A. Josephs, E. H. Migicovsky, Z. Naegele, R. Patterson, E. Saavedra-Rojas, Y.-A. Chitwood, D. H. 2025-08-09 doi:10.1101/2025.08.08.669192 Cold Spring Harbor Laboratory Press 2025-08-09 <![CDATA[ Identification of perrhenate-binding peptides by phage display ]]> https://biorxiv.org/content/10.1101/2025.08.12.669540v1?rss=1 Takyi, S. Feliciano, M. A. M. Dulanjali, S. S. Gold, B. Walker, M. C. 2025-08-12 doi:10.1101/2025.08.12.669540 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Control of Chloroplast Integrity by the Jasmonate Signaling Pathway is Linked to Growth-Defense Balance ]]> https://biorxiv.org/content/10.1101/2025.08.15.670541v1?rss=1 Howe, G. A. Johnson, L. Y. Major, I. T. Guo, Q. Yoshida, Y. Kramer, D. M. 2025-08-20 doi:10.1101/2025.08.15.670541 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ CIA5 INTERACTS WITH THE ZINC CHAPERONE ZNG3 TO BALANCECARBON AND ZINC METABOLISM ]]> https://biorxiv.org/content/10.1101/2025.08.16.670667v1?rss=1 Kusi-Appiah, G. Schmollinger, S. Mamo, A. Stainbrook, S. C. O'Halloran, T. V. Strenkert, D. 2025-08-20 doi:10.1101/2025.08.16.670667 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ Structures of two LarA-like nickel-pincer nucleotide cofactor-utilizing enzymes with a single catalytic histidine residue ]]> https://biorxiv.org/content/10.1101/2025.08.19.671153v1?rss=1 Gatreddi, S. Subramanian, S. Sui, D. Wang, T. Urdiain-Arraiza, J. Desguin, B. Hausinger, R. Parent, K. N. Hu, J. 2025-08-21 doi:10.1101/2025.08.19.671153 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ Tracking blaKPC Plasmid Dissemination within and between Enterobacterales across Michigan Over a Decade ]]> https://biorxiv.org/content/10.1101/2025.08.18.670900v1?rss=1 Shankar, C. Narayanan, D. B. Miihlbach, A. McNamara, S. Brennan, B. Miles-Jay, A. Blankenship, H. M. Bahr, A. Snitkin, E. S. 2025-08-22 doi:10.1101/2025.08.18.670900 Cold Spring Harbor Laboratory Press 2025-08-22 <![CDATA[ Closed-Loop Connectivity Best Supports Angular Tuning and Sleep Dynamics in a Biophysical Thalamocortical Circuit Model ]]> https://biorxiv.org/content/10.1101/2025.08.18.670921v1?rss=1 Moreira, J. V. Borges, F. d. S. Atherton, Z. Crandall, S. R. Varela, C. Dura-Bernal, S. 2025-08-22 doi:10.1101/2025.08.18.670921 Cold Spring Harbor Laboratory Press 2025-08-22 <![CDATA[ Sorghum Metabolic Atlas: Large-Scale Mapping of Subcellular Enzyme Localization in Sorghum bicolor ]]> https://biorxiv.org/content/10.1101/2025.08.24.672047v1?rss=1 Karia, P. Dwyer, W. Kloss-schmidt, A. Hawkins, C. Xue, B. Ginzburg, D. Gutierrez, M. L. Mewalal, R. Blaby, I. Ehrhardt, D. W. Rhee, S. Y. 2025-08-27 doi:10.1101/2025.08.24.672047 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Developmental expression of risk genes implicates the age of onset for neuropsychiatric disorders ]]> https://biorxiv.org/content/10.1101/2025.08.27.672343v1?rss=1 Xue, C. Yu, X. Ye, L. Luo, Y. Zhang, L. Tang, B. Gui, H. Jiang, L. Li, M. 2025-08-28 doi:10.1101/2025.08.27.672343 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ Single-cell-level response to drought in Sorghum bicolor reveals novel targets for improving water use efficiency ]]> https://biorxiv.org/content/10.1101/2025.08.28.671794v1?rss=1 Stata, M. Greenblum, S. Yoshinaga, Y. Koriabine, M. Keymanesh, K. Karia, P. Zhao, C. O'Malley, R. C. Rhee, S. Y. 2025-08-28 doi:10.1101/2025.08.28.671794 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ gnSPADE: a reference-free deconvolution method incorporating gene network structures in spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.08.26.672457v1?rss=1 Xie, A. Cui, Y. 2025-08-31 doi:10.1101/2025.08.26.672457 Cold Spring Harbor Laboratory Press 2025-08-31 <![CDATA[ BMP9 regulates the endothelial secretome to drive pulmonary hypertension ]]> https://biorxiv.org/content/10.1101/2025.08.29.673113v1?rss=1 Zhong, Y. Yang, P. Troncone, L. Kovalenko, O. V. Fast, E. M. Rajesh, S. Lavoie, S. Tumelty, K. E. Shin, E. Covington, T. Zeghibe, A. Wadsworth, M. H. Christensen, S. M. Nathans, R. Benard, S. A. Tang, X. Quazi, S. A. Worst, L. R. McNeil, M. E. Kim, S. S. J. Bocobo, G. D. Szulcek, R. Bogaard, H. J. Hart, K. M. Martinez-Hackert, E. M. Berasi, S. P. Huard, C. Yu, P. B. 2025-09-04 doi:10.1101/2025.08.29.673113 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ When does temporal resolution matter? Including detection covariates in discrete- versus continuous-time occupancy and N-mixture models ]]> https://biorxiv.org/content/10.1101/2025.08.31.673411v1?rss=1 Pautrel, L. Moulherat, S. Charrasse, B. Debat, G. Gendron, L. Kellner, K. Etienne, M.-P. Gimenez, O. 2025-09-04 doi:10.1101/2025.08.31.673411 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Cellular mechanism linking endoplasmic reticulum inheritance and cell cycle regulation of the nuclear genome ]]> https://biorxiv.org/content/10.1101/2025.09.04.674221v1?rss=1 Lai, Y.-S. Chao, J. Niwa, M. 2025-09-04 doi:10.1101/2025.09.04.674221 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Speaker responses to audience-induced social-evaluative threat: Evidence from scientific presentation tasks in immersive virtual reality ]]> https://biorxiv.org/content/10.1101/2025.09.03.673376v1?rss=1 Lim, S. Schmaelzle, R. Bente, G. 2025-09-05 doi:10.1101/2025.09.03.673376 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ Distributional Data Analysis Uncovers Hundreds of Novel and Heritable Phenomic Features from Temporal Cotton and Maize Drone Imagery ]]> https://biorxiv.org/content/10.1101/2025.09.05.674557v1?rss=1 DeSalvio, A. J. Matabuena, M. Adak, A. Arik, M. A. DeSalvio, S. M. Murray, S. C. Wong, R. K. W. Edwards, J. de Leon, N. Kaeppler, S. M. Lima, D. C. Hirsch, C. N. Thompson, A. Stelly, D. M. 2025-09-07 doi:10.1101/2025.09.05.674557 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ TESSA: A unified model to detect trajectory-preserved and spatially-variable genes in spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.09.06.674654v1?rss=1 Wu, Y. Su, H. Steele, N. Xie, Y. Cui, Y. 2025-09-11 doi:10.1101/2025.09.06.674654 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Courtship choreography is stabilised among genetically isolated populations ]]> https://biorxiv.org/content/10.1101/2025.09.08.675024v1?rss=1 Butterworth, N. J. White, T. E. Dawson, B. M. Appleton, J. McDonald, C. McGaughran, A. Markowsky, G. Bayless, K. M. 2025-09-11 doi:10.1101/2025.09.08.675024 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Origin, domestication, and diversity of the climate resilient Ethiopian cereal teff ]]> https://biorxiv.org/content/10.1101/2025.09.07.674720v1?rss=1 Wai, C. M. Wilson, M. L. Braun, E. Baczkowski, J. Chanyalew, S. Del Acqua, M. Grotewold, E. Thompson, A. VanBuren, R. 2025-09-12 doi:10.1101/2025.09.07.674720 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ The nucleus accumbens to ventral pallidum pathway regulates social play behavior via sex-specific mechanisms in juvenile rats ]]> https://biorxiv.org/content/10.1101/2025.09.06.674638v1?rss=1 Lee, J. D. A. Anderson, D. N. Orsucci, I. C. Bowden, S. M. Veenema, A. H. 2025-09-13 doi:10.1101/2025.09.06.674638 Cold Spring Harbor Laboratory Press 2025-09-13 <![CDATA[ Uncovering the Design Rules for Sustainable Growth of Mineralized Mycomaterials ]]> https://biorxiv.org/content/10.1101/2025.09.12.675881v1?rss=1 Moss, D. H. Pear, O. Guio, J. Libonati, A. Ducat, D. Bay, K. Khakhar, A. 2025-09-13 doi:10.1101/2025.09.12.675881 Cold Spring Harbor Laboratory Press 2025-09-13 <![CDATA[ Microscopical and molecular characterization of the infection cycle of Phytophthora betacei during disease development on tree tomato (Solanum betaceum). ]]> https://biorxiv.org/content/10.1101/2025.09.11.675658v1?rss=1 Palacios, N. G. Gonzalez-Tobon, J. Buitrago, M. C. Bautista, D. Gonzalez, L. N. Toquica, M. C. Mideros, M. F. Schornack, S. Restrepo, S. 2025-09-17 doi:10.1101/2025.09.11.675658 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ SpatialESD: spatial ensemble domain detection in spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.09.11.675735v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@1344724org.highwire.dtl.DTLVardef@12ab936org.highwire.dtl.DTLVardef@1e59d57org.highwire.dtl.DTLVardef@1bcd55f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cao, H. Liu, G. Xia, J. Chen, R. Wang, T. Yang, X. Fang, R. Luo, Y. zeng, p. Yu, H. Zhang, Y. Cui, Y. 2025-09-17 doi:10.1101/2025.09.11.675735 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Sampling bias obscures biodiversity patterns, reveals data gaps in priority conservation areas: a call for improved documentation ]]> https://biorxiv.org/content/10.1101/2025.09.13.676052v1?rss=1 Pitogo, K. M. E. Meneses, C. G. Decena, S. C. P. Supsup, C. E. Som, H. E. Bernstein, J. M. Chan, K. O. Herr, M. W. Brown, R. M. 2025-09-17 doi:10.1101/2025.09.13.676052 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Identification of a novel CLPX variant in a mixed breed dog with anemia and spinocerebellar ataxia ]]> https://biorxiv.org/content/10.1101/2025.09.15.676223v1?rss=1 de Cecco, B. S. Blake, J. M. Kim, N. J. Coffey, M. C. Johnston, A. Miller, A. D. Ekenstedt, K. J. Lee, J. 2025-09-18 doi:10.1101/2025.09.15.676223 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Evaluating the legacy of drought exposure on root and rhizosphere bacterial microbiomes over two plant generations ]]> https://biorxiv.org/content/10.1101/2025.09.19.677321v1?rss=1 Bintarti, A. F. Sulesky-Grieb, A. Colovas, J. Marolleau, B. Boureau, T. SIMONIN, M. BARRET, M. Shade, A. 2025-09-19 doi:10.1101/2025.09.19.677321 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Detection of multiple per- and polyfluoroalkyl substances (PFAS) using a biological brain-based gas sensor ]]> https://biorxiv.org/content/10.1101/2025.09.17.676814v1?rss=1 McLane-Svoboda, S. B. Joshi, S. McLane-Svoboda, A. K. Stout, C. Bazhenov, M. Saha, D. 2025-09-20 doi:10.1101/2025.09.17.676814 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Invasive plants affect native plant pollination through pollinator-mediated cross-boundary effects ]]> https://biorxiv.org/content/10.1101/2025.09.18.677159v1?rss=1 Nelson, R. A. Williams, N. Valdovinos, F. Harrison, S. 2025-09-20 doi:10.1101/2025.09.18.677159 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Disturbance increases soil microbiome functional redundancy but decreases capacity for insurance via winnowed environmental responsiveness ]]> https://biorxiv.org/content/10.1101/2025.09.19.677300v1?rss=1 Barnett, S. E. Shade, A. 2025-09-21 doi:10.1101/2025.09.19.677300 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ RIP3 and MLKL regulate Hepatic ER stress in alcohol-associated liver disease and pharmacological ER stress models: insights beyond necroptosis ]]> https://biorxiv.org/content/10.1101/2025.09.24.677754v1?rss=1 Arya, R. Huang, E. McMullen, M. R. Poulsen, K. L. Wu, J. Travers, J. Paouri, E. Davalos, D. Nagy, L. E. 2025-09-25 doi:10.1101/2025.09.24.677754 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ CRISPR/Cas9 screenings reveal the role of STX1A and CDK1 in Cathepsin G entering and killing colorectal cancer cells ]]> https://biorxiv.org/content/10.1101/2025.09.24.678097v1?rss=1 Wang, Y. Rozen, V. Dinh, T. Li, H. Li, Y. Wang, Z. 2025-09-26 doi:10.1101/2025.09.24.678097 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome ]]> https://biorxiv.org/content/10.1101/2025.09.26.678720v1?rss=1 Bird, K. A. Rifkin, J. L. McLaughlin, C. M. Harder, A. M. Basnet, P. Katz, E. Bruna, T. Barry, K. Boston, L. Daum, C. Guo, J. Lipzen, A. Plott, C. Jenkins, J. W. Walstead, R. N. Rajasekar, S. Talag, J. Frels, K. Greenham, K. Ellison, S. Grimwood, J. Schmutz, J. Edger, P. P. Pires, J. C. Lovell, J. T. Kliebenstein, D. J. 2025-09-28 doi:10.1101/2025.09.26.678720 Cold Spring Harbor Laboratory Press 2025-09-28 <![CDATA[ Nutrient enrichment intensifies plant competitive effects, favouring monocultures: a global meta-analysis ]]> https://biorxiv.org/content/10.1101/2025.09.26.678566v1?rss=1 Petri, L. Ramesh, A. Martinez-Blancas, A. Deep Tiwari, A. Bills, P. Sullivan, L. L. Zarnetske, P. 2025-09-29 doi:10.1101/2025.09.26.678566 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Magnetically Controlled Microrobots for In Vivo Non-Invasive Embryo Transfer ]]> https://biorxiv.org/content/10.1101/2025.09.29.679217v1?rss=1 35). However, these methods have declined due to advancements in IVF and the variability in laparoscopy procedures used for GIFT/ZIFT. To address these challenges, we propose a non-invasive microrobotic embryo transfer ({micro}ET) technique using remotely controlled microcarriers comparable in size to embryos. We demonstrate the capabilities of magnetically actuated spiral microrobots, fabricated using laser direct writing for capturing, transporting, and releasing embryos into murine uteri. Additionally, we characterize their motion performance and implement image-guided closed-loop control and dual ultrasound (US)/photoacoustic (PA) tracking for deep-tissue interventions. Recognizing the importance of clinical translation, we present preliminary studies on gelatin-based microrobots, a biodegradable alternative, and explore endometrial remodeling after the in vivo transfer of microrobots carrying embryo-like structures. Our findings show that these microrobots can effectively transport embryos, support their development, and enable minimally invasive delivery, providing a more natural, targeted, and non-invasive strategy for in vivo assisted reproduction. One-Sentence SummaryWe propose a non-invasive {micro}ET technique using magnetically actuated microcarriers to improve embryo cargo-delivery in assisted reproduction, addressing challenges in infertility treatments by enabling precise, image-guided embryo delivery with minimal invasiveness. ]]> Aziz, A. Castellanos-Robles, D. Chen, Z. Naumann, R. Raghu Kumar, H. Nauber, R. Ribeiro, C. Arora, R. Medina Sanchez, M. 2025-09-30 doi:10.1101/2025.09.29.679217 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ scLinguist: A pre-trained hyena-based foundation model for cross-modality translation in single-cell multi-omics ]]> https://biorxiv.org/content/10.1101/2025.09.30.679123v1?rss=1 Fang, Z. Miao, Z. Lin, J. Xie, Y. Tang, J. Ding, J. Li, M. 2025-10-01 doi:10.1101/2025.09.30.679123 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Predicting complex phenotypes using multi-omics data in maize ]]> https://biorxiv.org/content/10.1101/2025.09.30.679283v1?rss=1 Creach, M. Webster, B. Newton, L. Turkus, J. Schnable, J. Thompson, A. VanBuren, R. 2025-10-01 doi:10.1101/2025.09.30.679283 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Sex differences in cytokine induction by activated T cells from hypertensive BPH/2 and normotensive BPN/3 mice ]]> https://biorxiv.org/content/10.1101/2025.09.30.679479v1?rss=1 Dattmore, D. A. Leipprandt, J. R. Awali, S. Fu, T. Mahlmeister, M. Garver, H. Onunkun, A. Lauver, D. A. Rockwell, C. E. 2025-10-01 doi:10.1101/2025.09.30.679479 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Generation of Cellular Biofactories for Scalable Production of Surface-Engineered Extracellular Vesicles via CRISPR Genome Editing ]]> https://biorxiv.org/content/10.1101/2025.09.30.679598v1?rss=1 Kawai-Harada, Y. Scarborough, T. Siraj, N. Yedla, J. Rennells, T. Walton, S. P. Chan, C. Harada, M. 2025-10-02 doi:10.1101/2025.09.30.679598 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Angiotensin II Infusion Promotes Activation and Selective Cytokine Responses in Activated CD4 and CD8 T cells ]]> https://biorxiv.org/content/10.1101/2025.10.01.679792v1?rss=1 Dattmore, D. A. Leipprandt, J. R. Awali, S. Mahlmeister, M. Lauver, D. A. Rockwell, C. E. 2025-10-03 doi:10.1101/2025.10.01.679792 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Seed vernalization and gibberellic acid interact to affect life cycle type in facultative winter annual Canadian horseweed (Erigeron canadensis) ]]> https://biorxiv.org/content/10.1101/2025.10.06.680458v1?rss=1 Waterman, R. Catlett, B. Bhatt, I. Edmonds, G. Conner, J. K. 2025-10-06 doi:10.1101/2025.10.06.680458 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Mycoelectronics: Bioprinted Living Fungal Bioelectronics for Artificial Sensation ]]> https://biorxiv.org/content/10.1101/2025.10.06.680560v1?rss=1 Li, J. Cai, Y. Ronders, C. Mottini, V. Yuan, H. Singh, K. Xing, L. Singh, I. Fu, D. Zhao, K. Heller, L. Nguyen, K. Waller, B. Wang, T. Bonito, G. 2025-10-07 doi:10.1101/2025.10.06.680560 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Diurnal plant and Rhizophagus irregularis transcriptional patterns are linked to shifts in cassava tissue partitioning in the field ]]> https://biorxiv.org/content/10.1101/2025.10.08.681086v1?rss=1 McGale, E. Robbins, C. Pena-Quemba, D. C. Ceballos, I. C. Rodriguez, A. Sanders, I. R. 2025-10-08 doi:10.1101/2025.10.08.681086 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ BC-Predict Database: A Curated Resource of Experimentally Validated Markers in Multidrug Resistance in Breast Cancer ]]> https://biorxiv.org/content/10.1101/2025.10.09.681460v1?rss=1 15 drugs, 5-15 drugs, and 2-4 drugs. Analysis of patient profiles in the database revealed that the number of proteins contributing to drug resistance was high in the poor prognosis category compared to the good prognosis category. ConclusionsOur study highlights the probable gaps in breast cancer drug resistance research, as only a small subset of overexpressed mRNA candidates found in patients are studied in vitro or in vivo experiments focusing on drug resistance. We also identified candidates involved in multidrug resistance, whose role in drug resistance has not been studied in more than 15 drugs. After further validations, this will benefit the clinicians and upcoming CRISPR gene therapeutics. ]]> Parate, S. S. Rehas, R. Gupta, S. George, L. S. Mahammad, N. Unni, A. TR, S. Manuel, S. Shaji, V. Krishna S.V, A. George, M. R, B. Dev, R. R. B, P. Ayeraselvan, S. S. Krishna S.V, M. TK, A. Chatterjee, R. VG, R. Jogy, M. PG, R. Prakash, C. Muralidharan, A. Prakash, A. Upadhyay, S. S. Anilkumar, A. Rehman, N. Manavalan, V. Shetty, R. Codi, J. A. K. Prasad, T. S. K. Velikkakath, A. K. G. Raju, R. 2025-10-10 doi:10.1101/2025.10.09.681460 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ Mechanisms of sex differences in acute and long COVID sequelae in mice ]]> https://biorxiv.org/content/10.1101/2025.10.13.682101v1?rss=1 Liu, J. A. Chaulagain, S. Creisher, P. S. Zhong, W. Zhang, T. Taddese, M. Shi, K. Park, H.-S. Hcnir, H. Arnold, A. P. Baric, R. S. Barahona, N. B. Engler-Chiurazzi, E. B. Zwezdaryk, K. J. Thio, C. L. Balagopal, A. Harkema, J. R. Thompson, E. A. Pekosz, A. Cox, A. L. Klein, S. L. 2025-10-14 doi:10.1101/2025.10.13.682101 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Isomer-specific distribution of perfluorooctane sulfonate (PFOS) in hepatic zonation in mouse ]]> https://biorxiv.org/content/10.1101/2025.10.13.682167v1?rss=1 Reynolds, A. J. Mickel, J. A. Nault, R. Qiu, T. 2025-10-14 doi:10.1101/2025.10.13.682167 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Oxidation of ΔFOSB at Cys172 Controls Hippocampal Gene Targets and Learning ]]> https://biorxiv.org/content/10.1101/2025.10.14.682315v1?rss=1 Lynch, H. Anderson, D. Hughes, B. Aglyamova, G. Yeh, S.-Y. Ohnishi, Y. Estill, M. Granger, B. Cates, H. Berto, S. Chin, J. Nestler, E. J. Rudenko, G. Robison, A. J. 2025-10-15 doi:10.1101/2025.10.14.682315 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Skin-conformal electronics for wearable electrogastrography monitoring ]]> https://biorxiv.org/content/10.1101/2025.10.14.682324v1?rss=1 Xing, L. Cai, Y. Zhang, Y. Mottini, V. Heller, L. Li, J. 2025-10-15 doi:10.1101/2025.10.14.682324 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Highly Adaptive Conductive Polymer Electronics Enhance Neural Data and Learning Accuracy ]]> https://biorxiv.org/content/10.1101/2025.10.14.682347v1?rss=1 Mottini, V. Xing, L. Meilinger, C. Inamdar, S. Chen, X. C. Wang, J. Xing, Y. Darbonne, J. Tang, Z. Zhang, Y. Contag, C. H. Zhang, M. Li, J. 2025-10-15 doi:10.1101/2025.10.14.682347 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Acute oral toxicity and angiotensin-converting enzyme (ACE) inhibitory activity of the aqueous fractions of the methanol leaf extract of Psychotria luzoniensis ]]> https://biorxiv.org/content/10.1101/2025.10.14.681951v1?rss=1 Ramil, M. D. Heralde, F. M. Sasaki, K. Kobayashi, K. 2025-10-16 doi:10.1101/2025.10.14.681951 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ Moderated designs can balance between batch-effect mitigation and cell loss due to hashtag-assisted pooling in single-cell experiments ]]> https://biorxiv.org/content/10.1101/2025.10.16.682943v1?rss=1 Chatterjee, B. Gorga, K. Blair, C. Ohta, Y. Hill, E. M. Boughter, C. T. Meier-Schellersheim, M. Singh, N. J. 2025-10-17 doi:10.1101/2025.10.16.682943 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Predictive models of the genetic bases underlying budding yeast fitness in multiple environments ]]> https://biorxiv.org/content/10.1101/2025.10.20.683436v1?rss=1 Aba, K. E. S. Izquierdo, P. de Los Campos, G. Lehti-Shiu, M. Shiu, S.-H. 2025-10-20 doi:10.1101/2025.10.20.683436 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Phages use contingency loci as a bet-hedging strategy ]]> https://biorxiv.org/content/10.1101/2025.10.21.683753v1?rss=1 Gomez, J. B. Barrick, J. Waters, C. M. 2025-10-21 doi:10.1101/2025.10.21.683753 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Discovery of Small Molecules and a Druggable Groove That Regulate DNA Binding and Release of the AP1 Transcription Factor DeltaFOSB ]]> https://biorxiv.org/content/10.1101/2025.10.21.683675v1?rss=1 McNeme, S. Yim, Y. Y. Kumar, A. Li, Y. Hughes, B. W. St. Romain, C. P. Aglyamova, G. Chen, J. Nguyen, N. D. Fan, S. Stephens, G. S. Zhao, W.-N. Kruzshak, S. Estill, M. Brener, C. Tofani, S. Kumar, A. Chen, E. P. Takatka, N. Robison, A. J. Chen, H. Powell, R. T. Haggarty, S. J. Stephan, C. Nestler, E. J. Chin, J. Machius, M. Zhou, J. Rudenko, G. 2025-10-23 doi:10.1101/2025.10.21.683675 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Efficient in vivo pharmacological inhibition of deltaFOSB, an AP1 transcription factor, in brain ]]> https://biorxiv.org/content/10.1101/2025.10.21.683721v1?rss=1 McNeme, S. Kumar, A. Yim, Y. Y. Hughes, B. W. St. Romain, C. P. Li, Y. Kumar, A. Bao, Q. Estill, M. Fan, S. Takatka, N. Rivera, M. Chen, E. P. Chen, H. Robison, A. J. Machius, M. Haggarty, S. J. Chin, J. Nestler, E. J. Zhou, J. Rudenko, G. 2025-10-23 doi:10.1101/2025.10.21.683721 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Crystal structure of the Legionella pneumophila effector SidL (Lpg0437) in complex with its metaeffector LegA11 (Lpg0436) ]]> https://biorxiv.org/content/10.1101/2025.10.23.683979v1?rss=1 Machtens, D. A. Hutchison, C. A. Stein, A. M. Eberhage, J. Willerding, J. M. Eschenburg, S. Shames, S. R. Reubold, T. F. 2025-10-23 doi:10.1101/2025.10.23.683979 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Island Biogeography Theory of coevolution in pollination networks ]]> https://biorxiv.org/content/10.1101/2025.10.22.684063v1?rss=1 Birskis-Barros, I. Yeakel, J. D. 2025-10-24 doi:10.1101/2025.10.22.684063 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ A scalable filtration-based method for isolating exomeres and other nanoscale extracellular particles ]]> https://biorxiv.org/content/10.1101/2025.10.23.684032v1?rss=1 Scarborough, T. Kawai-Harada, Y. Brennan, O. Chan, C. Harada, M. Walton, S. P. 2025-10-24 doi:10.1101/2025.10.23.684032 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ Distinct Roles of Surface Nanostructure and Polymer Degradation in Fibroblast Response to Device Design ]]> https://biorxiv.org/content/10.1101/2025.10.24.684439v1?rss=1 Pawelec, K. Shapiro, E. 2025-10-25 doi:10.1101/2025.10.24.684439 Cold Spring Harbor Laboratory Press 2025-10-25 <![CDATA[ Identification of dehydrin protein complexes in vivo reveals functional interactions of LEA5 with OSCA3, PIP2B and PLDα1 in plant water-deficit stress ]]> https://biorxiv.org/content/10.1101/2025.10.27.684818v1?rss=1 Fabregas, N. Rivas, F. J. M. Hernandez-Sanchez, I. E. Lozano-Elena, F. Arabi, F. Sokolowska, E. Skirycz, A. Fernie, A. R. 2025-10-27 doi:10.1101/2025.10.27.684818 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ IRE1 Regulates TOR Signaling via RIDD of RAPTOR1b to Coordinate Growth and Stress Adaptation ]]> https://biorxiv.org/content/10.1101/2025.10.30.685559v1?rss=1 Reagan, B. C. KIM, J. Y. Angelos, E. Vermaas, J. V. Brandizzi, F. 2025-10-31 doi:10.1101/2025.10.30.685559 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16 ]]> https://biorxiv.org/content/10.1101/2025.11.03.685595v1?rss=1 Kretsch, R. C. Posani, E. Baulin, E. F. Bujnicki, J. M. Bussi, G. Cheatham, T. E. Chen, S.-J. Elofsson, A. Farsani, M. A. Fisher, O. N. Gromiha, M. M. Gupta, A. Hamada, M. Harini, K. Hu, G. Huang, D. Iwakiri, J. Jain, A. Kagaya, Y. Kihara, D. Kmiecik, S. Krishnan, S. R. Kurisaki, I. Languin-Cattoen, O. Li, J. Li, S. Malekzadeh, K. Nakamura, T. Ni, W. Nithin, C. Palo, M. Z. Park, J. H. Pilla, S. P. Poblete, S. Pucci, F. Punuru, P. Saha, A. Sato, K. Srivastava, A. Terashi, G. Tugolukova, E. Verburgt, J. Wuyun, Q. Zerze, G. H. Zhang, K. Zhang, S. Zhen 2025-11-03 doi:10.1101/2025.11.03.685595 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Defining the Mycobacterium tuberculosis Pangenome and Suggestions for a New Composite Reference Sequence ]]> https://biorxiv.org/content/10.1101/2025.11.03.686283v1?rss=1 Chitale, P. Ocke, E. Odom, A. R. Fan, H. Henoch, A. Vasco, K. Fogarty, E. C. Grady, C. Lemenze, A. D. Kumar, P. Manning, S. Eren, A. M. Johnson, W. E. Alland, D. 2025-11-03 doi:10.1101/2025.11.03.686283 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Spatiotemporal control of PIWI compartmentalization by mitochondrial scaffolds defines pachytene piRNA pathway organization ]]> https://biorxiv.org/content/10.1101/2025.11.02.684826v1?rss=1 Wei, C. Yan, X. Mann, J. M. Shang, G. Wang, Q. Xie, H. Demireva, E. Y. Sun, L. Ding, D. Chen, C. 2025-11-04 doi:10.1101/2025.11.02.684826 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Pre-implantation non-steroidal anti-inflammatory drug treatment disrupts mouse embryo spacing and post-implantation chamber morphogenesis ]]> https://biorxiv.org/content/10.1101/2025.11.02.686054v1?rss=1 Massri, N. LaBuda, S. E. Oltean, M. Arora, R. 2025-11-04 doi:10.1101/2025.11.02.686054 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Understanding the Mechanisms Behind the Annuloplasty Effect in Tricuspid Valve TEER: A Computational Study ]]> https://biorxiv.org/content/10.1101/2025.11.04.686540v1?rss=1 Haese, C. E. Dubey, V. Mathur, M. Kreidel, F. Fuhg, J. N. Moussa, I. Timek, T. Rausch, M. K. 2025-11-05 doi:10.1101/2025.11.04.686540 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Bridging Language Markers and Pathology: Correlations Between Digital Speech Measures and Surrogate CSF Biomarkers in Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2025.11.05.686472v1?rss=1 Pang, Y. Chen, L. Dodge, H. H. Zhou, J. 2025-11-06 doi:10.1101/2025.11.05.686472 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ Restraint Stress Prolongs Diestrus Phase of Mouse Estrous Cycle ]]> https://biorxiv.org/content/10.1101/2025.11.07.687283v1?rss=1 Urbain, G. R. Chapman, A. D. Van Loh, B. Folger, J. K. Laumet, G. 2025-11-10 doi:10.1101/2025.11.07.687283 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Sex-specific regulation of social play in juvenile rats by oxytocin neurons in the hypothalamus and oxytocin signaling in the nucleus accumbens ]]> https://biorxiv.org/content/10.1101/2025.11.11.687699v1?rss=1 Bowden, S. M. Becker, K. D. Grinevich, V. Lee, J. D. Veenema, A. 2025-11-12 doi:10.1101/2025.11.11.687699 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Screening for residues in Atg11, a central organizer of selective autophagy in yeast, important for binding with Atg9 ]]> https://biorxiv.org/content/10.1101/2025.11.14.688473v1?rss=1 Sherpa, C. D. Woghiren, P. Leonello, E. Abdel-Khalek, M. Schuessler, B. J. Vermaas, J. V. Backues, S. K. 2025-11-14 doi:10.1101/2025.11.14.688473 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Hunger, displacement, or play? Object manipulation behaviour in Asian small-clawed otters (Aonyx cinereus) ]]> https://biorxiv.org/content/10.1101/2025.11.14.688474v1?rss=1 Evans, I. Cooke, A. S. Cooper, J. Ventura, B. 2025-11-17 doi:10.1101/2025.11.14.688474 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Ku limits aberrant mRNA splicing promoted by intronic antisense Alu elements ]]> https://biorxiv.org/content/10.1101/2025.11.20.689478v1?rss=1 Pascarella, G. C. Mikhova, M. Parkhi, G. Godfrey, J. Heyza, J. Janovic, T. Olive, A. Carninci, P. Schmidt, J. C. Meek, K. 2025-11-20 doi:10.1101/2025.11.20.689478 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ Magneto-Photonic Gene Circuit for Minimally Invasive Control of Gene Expression in Mammalian Cells ]]> https://biorxiv.org/content/10.1101/2025.11.21.688514v1?rss=1 Franco, E. A. C. Radawiec, R. Slaviero, A. Grady, C. J. Ricker, B. Pelled, G. Hochgeschwender, U. Kim, T. Gilad, A. 2025-11-23 doi:10.1101/2025.11.21.688514 Cold Spring Harbor Laboratory Press 2025-11-23 <![CDATA[ Distinct NIR Reflectance Spectra Associated with Foliar Symptoms of Beech Leaf Disease ]]> https://biorxiv.org/content/10.1101/2025.11.22.689946v1?rss=1 Moore, E. G. Dabydeen, L. C. Salha, R. Bichler, J. Borsuk, A. M. 2025-11-25 doi:10.1101/2025.11.22.689946 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ GC3 codons enhance protein production in diverse GC- and AT-rich plant species ]]> https://biorxiv.org/content/10.1101/2025.11.25.690434v1?rss=1 Kaufman, I. D. Wu, H.-Y. L. Hsu, P. Y. 2025-11-25 doi:10.1101/2025.11.25.690434 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Tuning Yeast Glycosylation Proximal to the FLS2-flg22 Binding Interface enables Functional Yeast Surface Display under Induced ER Stress ]]> https://biorxiv.org/content/10.1101/2025.11.25.690463v1?rss=1 View larger version (42K): org.highwire.dtl.DTLVardef@7c4ef7org.highwire.dtl.DTLVardef@1245f4eorg.highwire.dtl.DTLVardef@ed279aorg.highwire.dtl.DTLVardef@1c32233_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Dolgikh, B. Schulte, S. Woldring, D. R. 2025-11-26 doi:10.1101/2025.11.25.690463 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ Reconnecting food production and consumption through redesigning food systems to support healthy diets ]]> https://biorxiv.org/content/10.1101/2025.11.25.690428v1?rss=1 De Clerck, C. Desmarez, T. Delandmeter, M. de Faccio Carvalho, P. C. Dumont, B. Bindelle, J. 2025-11-28 doi:10.1101/2025.11.25.690428 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ Neuronal innervation of breast cancer promotes metastatic dissemination ]]> https://biorxiv.org/content/10.1101/2025.11.25.690523v1?rss=1 Schulte, A. J. Andrechek, E. 2025-11-29 doi:10.1101/2025.11.25.690523 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ A Functional Resting-State Network Atlas Based on 420 Older Adults with Hypertension ]]> https://biorxiv.org/content/10.1101/2025.11.26.690831v1?rss=1 Scheel, N. Fernandez, Z. Baker, J. Yanev, P. Keller, J. N. Binder, E. F. Vidoni, E. Burns, J. M. Stowe, A. M. Kerwin, D. R. Cullum, C. M. Hynan, L. S. Vongpatanasin, W. Zhang, R. Zhu, D. C. 2025-12-01 doi:10.1101/2025.11.26.690831 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Widespread sex-biased gene expression reflects female-biased longevity in a species with environmental sex determination ]]> https://biorxiv.org/content/10.1101/2025.11.26.690843v1?rss=1 Bock, S. Hoekstra, L. A. Hagerty, K. Schmidt, R. E. Judson, J. Adorsoo, M. Singh, R. Janzen, F. J. Bronikowski, A. M. 2025-12-01 doi:10.1101/2025.11.26.690843 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Intracellular C. neoformans infection stimulates increased glycolytic activity in fetal liver-derived alveolar-like macrophages ]]> https://biorxiv.org/content/10.1101/2025.11.28.690224v1?rss=1 Wiggins, D. A. Griggs, J. B. England, A. M. Callison, E. N. Kamel, C. H. Hasan, C. A. Davis, A. E. Chappell, M. E. Conner-Halim, K. N. Olive, A. J. McClelland, E. E. Leander, R. N. Seipelt-Thiemann, R. L. Nelson, D. E. 2025-12-03 doi:10.1101/2025.11.28.690224 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ Dordaviprone/ONC201 Activation of the ClpP Mitochondrial Protease Inhibits the Growth of KRAS-Mutant Pancreatic Cancer and Overcomes RAS Inhibitor Resistance ]]> https://biorxiv.org/content/10.64898/2025.12.01.691471v1?rss=1 Drizyte-Miller, K. Degan, S. E. Mouery, R. D. Amparo, A. M. Mouery, B. L. Chang, W.-H. Yang, R. Nicewarner Pena, S. R. Baldelli, E. Klomp, J. A. Iwanowicz, E. J. Graves, L. M. Petricoin, E. Cox, A. D. Stalnecker, C. A. Bryant, K. L. Der, C. J. 2025-12-03 doi:10.64898/2025.12.01.691471 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ A Microstructurally-Motivated Framework to Study Autoregulation in the Coronary Circulation ]]> https://biorxiv.org/content/10.64898/2025.12.02.691683v1?rss=1 Eden, M. J. Gharahi, H. Sturgess, V. E. Uceda, D. E. Baek, S. Beard, D. A. Tune, J. D. Figueroa, C. A. 2025-12-05 doi:10.64898/2025.12.02.691683 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Native catalase expression in Arabidopsis thaliana is more than sufficient to limit excess decarboxylation from photorespiratory intermediates ]]> https://biorxiv.org/content/10.64898/2025.12.06.692765v1?rss=1 Gregory, L. M. Scott, K. F. Twinamaani, F. Strand, D. D. Bao, H. Weber, A. P. M. Walker, B. J. 2025-12-09 doi:10.64898/2025.12.06.692765 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Natural competence promotes high rates of DNA transfer between strains of the core bee gut bacterium Snodgrassella alvi ]]> https://biorxiv.org/content/10.64898/2025.12.12.693966v1?rss=1 Ashraf, A. H. M. Z. Weaver, K. K. Lariviere, P. J. Barrick, J. E. 2025-12-12 doi:10.64898/2025.12.12.693966 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Sex- and age-differences in cellular hallmarks of aging in a species with female-biased longevity and environmental sex determination ]]> https://biorxiv.org/content/10.64898/2025.12.10.693506v1?rss=1 Marks, J. R. Janzen, F. J. Reinke, B. A. Addis, E. A. Adesioye, O. Bock, S. Clark, M. Crowther, C. Hoekstra, L. A. Judson, J. Krueger, C. Sills, A. P. Bronikowski, A. M. 2025-12-13 doi:10.64898/2025.12.10.693506 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ Chemical modulation of chloroplast de- and re-differentiation reveals a role for the SAL1-PAP retrograde pathway in facilitating plastid transitions ]]> https://biorxiv.org/content/10.64898/2025.12.11.693750v1?rss=1 PEREZ-COLAO, P. CRUCES, J. PEREZ-RODRIGUEZ, S. KOPRIVOVA, A. Kopriva, S. Skirycz, A. Lozano-Juste, J. Rodriguez-Concepcion, M. 2025-12-15 doi:10.64898/2025.12.11.693750 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ Adaptation of an herbivorous arthropod to green tea plants by overcoming catechin defenses ]]> https://biorxiv.org/content/10.64898/2025.12.13.694159v1?rss=1 Takeda, N. Abiskaroon, B. Arriaza, R. H. Murakami, R. Sasaki, S. Yamamoto, M. Zhurov, V. Grbic, V. Chruszcz, M. Suzuki, T. 2025-12-16 doi:10.64898/2025.12.13.694159 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Rapid High-Throughput Analysis of Bovine Skeletal Muscle Fiber Morphology via Automated Fluorescent Microscopy and MuscleBos software ]]> https://biorxiv.org/content/10.64898/2025.12.18.695234v1?rss=1 Rehman, H. Gouveia, K. M. Coombe, R. K. Boerman, J. P. Pasternak, J. A. Markworth, J. F. 2025-12-22 doi:10.64898/2025.12.18.695234 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Leveraging species-wide variation and patterns of adaptation to inform pecan crop improvement efforts ]]> https://biorxiv.org/content/10.64898/2025.12.19.695279v1?rss=1 Grabowski, P. P. McLaughlin, C. M. Rifkin, J. Jenkins, J. J. Hilton, A. Shadgou Rhein, H. Cervantes, K. Ishimori, M. Sreedasyam, A. Plott, C. Webber, J. Bentley, N. Bhattarai, G. Gabriel, P. O. Harmon, A. Kubenka, K. Bock, C. Chatwin, W. Conner, P. Grauke, L. Grimwood, J. Iwata, H. Klein, P. Mattison, C. P. Pisani, C. Schmutz, J. Udall, J. Wang, X. Randall, J. Lovell, J. T. 2025-12-22 doi:10.64898/2025.12.19.695279 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Spatially precise neuron formation via hydrogel mediated modulation of the host astrocyte response ]]> https://biorxiv.org/content/10.64898/2025.12.20.695501v1?rss=1 View larger version (65K): org.highwire.dtl.DTLVardef@397e41org.highwire.dtl.DTLVardef@90047forg.highwire.dtl.DTLVardef@1175831org.highwire.dtl.DTLVardef@19f30eb_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Mahmoudi, N. Harvey, A. Moriarty, N. Mahmoudi, M. Tong, W. Goris, T. Reynolds, N. Ahmed, N. Dehorter, N. Lisowski, L. Parish, C. Williams, R. Nisbet, D. R. 2025-12-22 doi:10.64898/2025.12.20.695501 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Abundance redistribution increases predator-prey interaction potentials among North American birds ]]> https://biorxiv.org/content/10.64898/2025.12.19.695589v1?rss=1 Zou, H.-X. Hsieh, C. Zarnetske, P. L. Zhu, K. Weeks, B. C. 2025-12-23 doi:10.64898/2025.12.19.695589 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Lipid nanoparticle protein coronas form via lipoprotein fusion rather than shell-like adsorption ]]> https://biorxiv.org/content/10.64898/2025.12.21.695162v1?rss=1 Grumelot, S. Mohammed, N. Colonrosado, J. Sadeghi, S. A. Fang, F. Hilsen, K. Shango, B. Saei, A. A. Murray, A. M. Mitchell, M. J. Borhan, B. Sun, L. Vali, H. Whitehead, K. Mahmoudi, M. 2025-12-23 doi:10.64898/2025.12.21.695162 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Gene-by-Environment Interaction Significantly Drives Bacterial Endophyte Communities in Maize Stalks ]]> https://biorxiv.org/content/10.64898/2025.12.23.696053v1?rss=1 Li, H. Griffis, H. K. Edwards, J. Flint-Garcia, S. Hirsch, C. N. Holland, J. B. Knoll, J. E. Lima, D. C. de Leon, N. Murray, S. C. Singh, M. P. Schnable, J. C. Sekhon, R. S. Thomison, P. Thompson, A. M. Wallace, J. G. 2025-12-24 doi:10.64898/2025.12.23.696053 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ Oxidative Stress-Responsive Cell Wall Remodeling Depends on Phosphate in Candida albicans ]]> https://biorxiv.org/content/10.64898/2025.12.23.696271v1?rss=1 Jacob, A. Qi, W. Yarava, J. R. Barkarar, M. Karai, A. Vermaas, J. V. Kohler, J. R. Wang, T. 2025-12-24 doi:10.64898/2025.12.23.696271 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ Colibactin produced by a honeybee symbiont defends against pathogens and shapes the gut community ]]> https://biorxiv.org/content/10.64898/2025.12.27.695564v1?rss=1 Song, Y. Powell, J. E. Wong, J. Liu, Y. Aguilar Ramos, M. A. de Jong, T. Lariviere, P. J. Maganti, J. Balskus, E. P. Moran, N. A. 2025-12-27 doi:10.64898/2025.12.27.695564 Cold Spring Harbor Laboratory Press 2025-12-27 <![CDATA[ Dispersal transiently modifies the temperature dependence of ecosystem productivity after an extreme thermal fluctuation ]]> https://biorxiv.org/content/10.64898/2025.12.29.695627v1?rss=1 Stark, K. Thompson, P. L. Bernhardt, J. R. Forbes, C. Davis, K. E. Yangel, E. Jackman, A. Heinrichs, M. Parfrey, L. O'Connor, M. I. 2025-12-30 doi:10.64898/2025.12.29.695627 Cold Spring Harbor Laboratory Press 2025-12-30 <![CDATA[ Murine implantation chamber formation precedes natural and artificial decidualization ]]> https://biorxiv.org/content/10.64898/2025.12.30.697086v1?rss=1 Raghu Kumar, H. Massri, N. Bhurke, A. V. Kapur, A. Gadhiya, P. Arora, R. 2025-12-31 doi:10.64898/2025.12.30.697086 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Histone Demethylase KDM6B Promotes Postnatal Oligodendrocyte Development and Cortical Myelination ]]> https://biorxiv.org/content/10.64898/2025.12.30.697092v1?rss=1 Lambries, R. Shen, Z. Mias, G. I. He, J. 2025-12-31 doi:10.64898/2025.12.30.697092 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ α-1,3-Glucan-Driven Remodeling of the Conidial Cell Wall in an Aspergillus fumigatus Vaccine Strain Alters Innate Immune Recognition ]]> https://biorxiv.org/content/10.64898/2025.12.31.697239v1?rss=1 Singh, K. Ankur, A. Yarava, J. R. Fernandes, C. M. Vascelli, G. Sulla, A. Zelante, T. Del Poeta, M. Wang, T. 2026-01-02 doi:10.64898/2025.12.31.697239 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ Conformation Driven Enhancement of Neurolysin Activity in Presence of a Small Molecule Activator ]]> https://biorxiv.org/content/10.64898/2026.01.05.697776v1?rss=1 Bose, S. Aly, A. Karamyan, V. T. Orlando, B. J. Dickson, A. 2026-01-06 doi:10.64898/2026.01.05.697776 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ Reducing Glucocorticoid Burden in Lupus with Omega-3 Fatty Acids: Docosahexaenoic Acid Augments Prednisone Efficacy in Maintaining Cyclophosphamide-Induced Remission of Preclinical Lupus Nephritis ]]> https://biorxiv.org/content/10.64898/2026.01.07.698195v1?rss=1 Anderson, A. N. McDonald, O. F. Johnson, S.-R. Liddle, J. J. Estrada, V. Jackson, J. T. Lewandowski, R. P. Wagner, J. G. Harkema, J. R. Pestka, J. J. 2026-01-08 doi:10.64898/2026.01.07.698195 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Differentiation for drought strategy but conserved plasticity to heat and drought in locally adapted populations of Arabidopsis thaliana ]]> https://biorxiv.org/content/10.64898/2026.01.07.698234v1?rss=1 Buysse, S. F. Nicholes, V. Conner, J. K. Josephs, E. B. 2026-01-08 doi:10.64898/2026.01.07.698234 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ On-slide Preparation of Caenorhabditis elegans Towards Quantitative, High-Resolution LA-ICP-TOF Mass Spectrometry Imaging ]]> https://biorxiv.org/content/10.64898/2026.01.08.698490v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@7c66c5org.highwire.dtl.DTLVardef@13f4934org.highwire.dtl.DTLVardef@1df3215org.highwire.dtl.DTLVardef@512fd2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Reynolds, A. J. Sue, A. MacRenaris, K. O'Halloran, T. V. Qiu, T. 2026-01-09 doi:10.64898/2026.01.08.698490 Cold Spring Harbor Laboratory Press 2026-01-09 <![CDATA[ The Genomic Basis of Electric Signal Diversity ]]> https://biorxiv.org/content/10.64898/2026.01.14.699493v1?rss=1 Gallant, J. R. Picq, S. Koenig, L. Aba'a, N. N. Nzigou, F. Mipounga, H. K. 2026-01-14 doi:10.64898/2026.01.14.699493 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Client distribution between Chlamydomonas FDX1 and FDX2 in carbon, nitrogen and sulfur assimilation ]]> https://biorxiv.org/content/10.64898/2026.01.14.699543v1?rss=1 Schmollinger, S. Kusi-Appiah, G. Villegas, D. Stainbrook, S. O'Halloran, T. V. Strenkert, D. 2026-01-15 doi:10.64898/2026.01.14.699543 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ X-ray fluorescence microscopy exposure estimates using a single excitation energy ]]> https://biorxiv.org/content/10.64898/2026.01.15.699668v1?rss=1 Roter, B. Crawford, A. O'Halloran, T. Jacobsen, C. 2026-01-15 doi:10.64898/2026.01.15.699668 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ NON-REDUNDANT ROLES OF COPPER TRANSPORTERS ATP7A AND ATP7B IN NORADRENERGIC SIGNALING ]]> https://biorxiv.org/content/10.64898/2026.01.15.699802v1?rss=1 ROY, S. Wang, Y. Aja, S. Sinha, N. Crawford, A. MacRenaris, K. Wade, A. Kim, K. Muchenditsi, A. Torres-Hernandez, L. Na, C.-H. Kralli, A. Petris, M. Taylor, A. O'Halloran, T. Tressler, C. Glunde, K. lutsenko, S. 2026-01-16 doi:10.64898/2026.01.15.699802 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ Phosphorylation of Cyclophilin-D is Not Required for Regulation of The Mitochondrial Permeability Transition Pore by GSK3β ]]> https://biorxiv.org/content/10.64898/2026.01.15.699680v1?rss=1 Alex, L. Klutho, P. Song, L. Gutierrez-Aguilar, M. Baines, C. 2026-01-19 doi:10.64898/2026.01.15.699680 Cold Spring Harbor Laboratory Press 2026-01-19 <![CDATA[ From SCUBA to spectra: Broadly applicable methods for coral metabolomics research ]]> https://biorxiv.org/content/10.64898/2026.01.19.700417v1?rss=1 Rosset, S. L. Cline, T. J. B. Shivaiah, K.-K. Ashley, I. Smith, K. Tortorelli, G. Rapid Resilient Reefs Consortium, Walling, L. K. Parkinson, J. E. Vermeij, M. J. A. Bouhaddou, M. Drury, C. Roach, T. N. F. Quinn, R. A. 2026-01-19 doi:10.64898/2026.01.19.700417 Cold Spring Harbor Laboratory Press 2026-01-19 <![CDATA[ Wildfire, restoration, and post-wildfire rehabilitation effects on wind erosion in the Great Basin ]]> https://biorxiv.org/content/10.64898/2026.01.16.699976v1?rss=1 Treminio, R. Webb, N. P. Edwards, B. L. Newingham, B. A. Garbowski, M. Brungard, C. Dubois, D. Faist, A. Kachergis, E. Houdeshell, C.-A. 2026-01-20 doi:10.64898/2026.01.16.699976 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Refactored genetic parts for modular assembly of the E. coli MccV type I secretion system used to screen class II microcin candidates from plant-associated bacteria ]]> https://biorxiv.org/content/10.64898/2026.01.19.700402v1?rss=1 Morton, A. K. Chaudhari, K. Matibag, B. D. Iyengar, V. B. Dullen, K. E. VanDieren, A. J. Parker, J. K. Mishler, D. M. Barrick, J. E. 2026-01-20 doi:10.64898/2026.01.19.700402 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Precursor-Dependent Routing of Aromatic Amino Acids Determines Lignin Structure in Grasses by Sensitivity-Enhanced Solid-State NMR ]]> https://biorxiv.org/content/10.64898/2026.01.17.700116v1?rss=1 Sahu, P. Debnath, D. Xiao, P. Gunaga, S. S. Scott, F. J. Bentelspacher, M. Xu, Y. Mentink-Vigier, F. Barros, J. Wang, T. 2026-01-21 doi:10.64898/2026.01.17.700116 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Chaotropic Ions Reshape the Cell Wall of the Obligate Halophile Aspergillus atacamensis: Insight from Solid-State NMR ]]> https://biorxiv.org/content/10.64898/2026.01.18.700186v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@a38e89org.highwire.dtl.DTLVardef@1e2f7fdorg.highwire.dtl.DTLVardef@71a94org.highwire.dtl.DTLVardef@61f2c4_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LISolid-state NMR reveals salt-dependent remodeling of fungal cell wall polysaccharides C_LIO_LIKosmotropic and chaotropic salts drive distinct cell wall adaptation strategies C_LIO_LINaCl stress promotes dehydration and compaction of the {beta}-1,3-glucan-chitin framework C_LIO_LIMgCl2 induces chitosan emergence and alters mannan organization in the rigid phase C_LIO_LIPolysaccharide hydration and dynamics encode fungal adaptation to extreme environments C_LI ]]> Gautam, I. Munoz, G. V. Karai, A. Paul-Latge, J. Llano, Y. P. Gunde-Cimerman, N. Batista-Garcia, R. A. Wang, T. 2026-01-21 doi:10.64898/2026.01.18.700186 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Gravid Anopheles stephensi Detects Indole for Oviposition Despite Ablation of Antennae and Maxillary Palps ]]> https://biorxiv.org/content/10.64898/2026.01.19.700218v1?rss=1 Agbetsi, J. Xu, J. 2026-01-22 doi:10.64898/2026.01.19.700218 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ A dynamic RNA hub facilitates activation induced cytidine deaminase recruitment to the immunoglobulin heavy chain locus ]]> https://biorxiv.org/content/10.64898/2026.01.19.700375v1?rss=1 Mikhova, M. Kapanka, M. Han, L. Schmidt, J. C. Yu, K. 2026-01-22 doi:10.64898/2026.01.19.700375 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Biosynthesis of 14-membered cyclopeptide alkaloids via non-heme-iron- and 2-oxoglutarate-dependent oxidative decarboxylation ]]> https://biorxiv.org/content/10.64898/2026.01.20.700549v1?rss=1 Hungerford, J. Mydy, L. S. Wang, X. Mendoza-Perez, L. Ousley, D. A. Shafiq, K. McDonough, K. M. Li, W. May, G. Chigumba, D. Yao, S. Kersten, R. D. 2026-01-23 doi:10.64898/2026.01.20.700549 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ N-terminal phosphorylation inhibits Arabidopsis katanin and affects vegetative and reproductive development in opposite ways ]]> https://biorxiv.org/content/10.64898/2026.01.20.700631v1?rss=1 Ambastha, V. Burkart, G. Balkunde, R. Dixit, R. 2026-01-23 doi:10.64898/2026.01.20.700631 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Assessing the Stability of Molecular Glues with Weighted Ensemble Simulations ]]> https://biorxiv.org/content/10.64898/2026.01.23.701371v1?rss=1 Atik, S. B. Dickson, A. 2026-01-26 doi:10.64898/2026.01.23.701371 Cold Spring Harbor Laboratory Press 2026-01-26 <![CDATA[ Global Proteomic Analysis of Colorectal Cancers Stratified by Microsatellite Instability Subtype Reveals Protein Differences ]]> https://biorxiv.org/content/10.64898/2026.01.28.702312v1?rss=1 Tobias, F. Sekera, E. R. Xiong, X. Fang, F. Hampel, H. Pearlman, R. Liu, X. Sun, L. Hummon, A. B. 2026-01-29 doi:10.64898/2026.01.28.702312 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ Encapsulation in a bacterial microcompartment shell improves thermal stability of a glycolytic enzyme ]]> https://biorxiv.org/content/10.64898/2026.01.28.702358v1?rss=1 Tefft, N. M. Yadav, N. S. Cross, M. C. G. Swiggett, C. D. Parent, K. N. Vermaas, J. V. TerAvest, M. A. 2026-01-29 doi:10.64898/2026.01.28.702358 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ Global population structures and demographic history of Suillus luteus, a pine co-introduced ectomycorrhizal fungus associated with exotic forestry and invasion. ]]> https://biorxiv.org/content/10.64898/2026.01.27.699563v1?rss=1 Ke, Y.-H. Bazzicalupo, A. Ruytinx, J. Lofgren, L. A. Bruns, T. D. Branco, S. Looney, B. P. Hirose, D. Tedersoo, L. Peintner, U. Rojas, J. A. Liao, H.-L. Plett, J. M. Anderson, I. Lipzen, A. M. Kuo, A. Barry, K. W. Grigoriev, I. Hoeksema, J. D. Nguyen, N. H. Kennedy, P. Vilgalys, R. 2026-01-30 doi:10.64898/2026.01.27.699563 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ A Robust Chemical-free Platform for Age-Synchronized Caenorhabditis elegans Populations Maintenance for High-Throughput Screening in Aging Studies ]]> https://biorxiv.org/content/10.64898/2026.01.27.702075v1?rss=1 Yousefsaber, F. Sarparast, M. Johnson, B. Alan, J. Lee, K. S. S. 2026-01-30 doi:10.64898/2026.01.27.702075 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Normal table of post-embryonic larval development for the California newt, Taricha torosa ]]> https://biorxiv.org/content/10.64898/2026.01.30.702904v1?rss=1 Westcott, S. M. Bucciarelli, G. M. Heath-Heckman, E. A. Eisthen, H. L. 2026-02-02 doi:10.64898/2026.01.30.702904 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Polyploid cardiomyocytes define disease-specific transcriptional states in the mammalian heart ]]> https://biorxiv.org/content/10.64898/2026.01.31.701472v1?rss=1 Kiessling, P. Joodaki, M. Pikulska, D. Scheidereit, E. Cesaro, G. Ruiz, M. Kuehn, D. Peng, K. Goni, O. Foecking, S. Samiei, S. Liao, X. Li, K. Feng, Z. Wang, D. Mavrommatis, L. Vllaho, A.-M. Rombach, M. Cucinella, G. Cheng, M. Lautenschlaeger, T. Morales, D. R. Veltrop, R. J. A. Schurgers, L. J. von Scheidt, M. Klinkhammer, B. M. Kahles, F. Kranz, J. Aguirre, A. Loft, A. Kluemper, N. Eckstein, M. Seidel, T. Forte, G. Westland, R. Zhang, M. Zhao, H. Ren, F. Hayat, S. Amrute, J. M. Kopecky, B. Schneider, R. Medyouf, H. Tharaux, P.-L. Boor, P. Kramann, 2026-02-03 doi:10.64898/2026.01.31.701472 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Intra-annual precipitation variability mutes or magnifies the impact of wet and dry years on plant biomass. ]]> https://biorxiv.org/content/10.64898/2026.02.03.703587v1?rss=1 Terry, T. Higgins, S. Hammer, A. Adler, P. Brudvig, L. Bakker, J. Borer, E. Bugalho, M. Caldeira, M. Catford, J. Chen, Q. Collins, S. Dickman, C. Hagenah, N. Komatsu, K. Knops, J. Niu, Y. Raynaud, X. Risch, A. Seabloom, E. Wardle, G. Yost, J. Jentsch, A. 2026-02-06 doi:10.64898/2026.02.03.703587 Cold Spring Harbor Laboratory Press 2026-02-06 <![CDATA[ The Signal in the Noise: Hierarchy and Robustness of Physiological Audience Alignment during Narrative Media ]]> https://biorxiv.org/content/10.64898/2026.02.05.703516v1?rss=1 Schmaelzle, R. Cho, H. J. Turner, M. 2026-02-07 doi:10.64898/2026.02.05.703516 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ A Large-Scale Cryo-EM RNA Motif Dataset and Benchmark for Machine Learning-Based Structure Modeling ]]> https://biorxiv.org/content/10.64898/2026.02.06.704425v1?rss=1 Murugadass, C. Rana, H. Znosko, B. M. Hou, J. Si, D. 2026-02-09 doi:10.64898/2026.02.06.704425 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Large language models unlock the ecology of species interactions ]]> https://biorxiv.org/content/10.64898/2026.02.06.704115v1?rss=1 Zou, H.-X. Yang, X. Hajamaideen, T. H. Stein, O. J. Beltran, R. S. Freeman, B. G. Lindquist, M. Miller, E. T. Mengarelli, S. Probst, C. M. Valdovinos, F. S. Van Berkel, D. B. Zarnetske, P. L. Weeks, B. C. Zhu, K. 2026-02-10 doi:10.64898/2026.02.06.704115 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ Biotic modulators of global change effects on plant communities ]]> https://biorxiv.org/content/10.64898/2026.02.11.704804v1?rss=1 Eskelinen, A. Andrzejak, M. Harpole, S. Harrison, S. Classen, A. Laine, A.-L. Pichon, N. Risch, A. Alexander, J. Jessen, M.-T. Zarnetske, P. Korell, L. 2026-02-12 doi:10.64898/2026.02.11.704804 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ Summary statistics and approximate bayesian computation are comparable to convolutional neural networks for inferring times to fixation ]]> https://biorxiv.org/content/10.64898/2026.02.17.706432v1?rss=1 Roberts, M. Josephs, E. B. 2026-02-18 doi:10.64898/2026.02.17.706432 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ TAZ (Wwtr1) deficiency leads to ER stress and mitochondrial dysfunction in a mouse model of Fuchs' endothelial corneal dystrophy ]]> https://biorxiv.org/content/10.64898/2026.02.17.706456v1?rss=1 Park, S. Ramarapu, R. Lim, J. Khan, S. Khan, M. J. Stoehr, W. R. Leonard, B. C. Thomasy, S. M. 2026-02-19 doi:10.64898/2026.02.17.706456 Cold Spring Harbor Laboratory Press 2026-02-19 <![CDATA[ A Glucan Synthase-Remodeler Module Organizes Branched Glucan Assembly in the Fungal Cell Wall ]]> https://biorxiv.org/content/10.64898/2026.02.18.706439v1?rss=1 Willet, A. H. Jacob, A. Turner, L. A. Alsanad, A. K. A. Wang, T. Gould, K. L. 2026-02-19 doi:10.64898/2026.02.18.706439 Cold Spring Harbor Laboratory Press 2026-02-19 <![CDATA[ Recalibrating Nanoparticle Protein Corona Analysis for Accurate Biological Identity and Soluble Plasma Proteome Profiling ]]> https://biorxiv.org/content/10.64898/2026.02.19.706828v1?rss=1 Ghaffari, B. Grumelot, S. Sadeghi, S. A. Alpaydin, A. Hilsen, K. Shango, B. Ritz, D. Schmidt, A. Vali, H. Sun, L. Saei, A. A. Borhan, B. Mahmoudi, M. 2026-02-20 doi:10.64898/2026.02.19.706828 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Landrace and bred accessions of allotetraploid sour cherry (Prunus cerasus L.) reveal variation in subgenome dosage and subgenome expression bias ]]> https://biorxiv.org/content/10.64898/2026.02.19.706907v1?rss=1 Rhoades, K. E. B. Goeckeritz, C. Z. Bird, K. A. Yocca, A. E. Edger, P. P. Iezzoni, A. 2026-02-20 doi:10.64898/2026.02.19.706907 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Exploring the Influence of Chemical Exposures in Breast Cancer Disparities: High-Throughput Transcriptomic Analysis in Normal Breast Cells from Diverse Donors ]]> https://biorxiv.org/content/10.64898/2026.02.23.707203v1?rss=1 Zhao, N. Zhao, P. Tapaswi, A. Polemi, K. M. Thong, T. Sexton, J. Z. Charles, S. Wicha, M. S. Svoboda, L. Zhou, X. Colacino, J. 2026-02-24 doi:10.64898/2026.02.23.707203 Cold Spring Harbor Laboratory Press 2026-02-24 <![CDATA[ Longitudinal modality prediction learns gene regulatory patterns: insights from a single-cell competition ]]> https://biorxiv.org/content/10.64898/2026.02.24.707614v1?rss=1 Lance, C. Shitov, V. A. Wen, H. Ji, Y. Holderrieth, P. Wu, Y. Liu, R. Cannoodt, R. Tang, W. Waldrant, K. DeMeo, B. Cortes, M. Kotlarz, D. Tang, J. Xie, Y. Theis, F. J. Burkhardt, D. B. Luecken, M. D. 2026-02-25 doi:10.64898/2026.02.24.707614 Cold Spring Harbor Laboratory Press 2026-02-25 <![CDATA[ Convergent evolution of red pigmentation in extrafloral nectaries: global patterns and mechanisms ]]> https://biorxiv.org/content/10.64898/2026.02.24.707775v1?rss=1 Martin-Eberhardt, S. Pan, V. S. Gilbert, K. J. Weber, M. 2026-02-25 doi:10.64898/2026.02.24.707775 Cold Spring Harbor Laboratory Press 2026-02-25 <![CDATA[ Nonlinear Impacts of Herbivory on Plants Explain the Herbivory Paradox ]]> https://biorxiv.org/content/10.64898/2026.02.24.707788v1?rss=1 Pan, V. S. Adam, J. Anstett, D. N. Carvajal Acosta, A. N. Cornelissen, T. Galman, A. Haslup, P. Karp, J. Lopez-Goldar, X. Martin-Eberhardt, S. Ritter, K. Santos Lopes, H. D. Wonderlin, N. E. Wetzel, W. C. 2026-02-25 doi:10.64898/2026.02.24.707788 Cold Spring Harbor Laboratory Press 2026-02-25 <![CDATA[ Multi-tissue metabolic GWAS and drought-responsive multi-omics reveal the genetic basis of the quinoa metabolome ]]> https://biorxiv.org/content/10.64898/2026.02.25.706111v1?rss=1 von Steimker, J. Rey, E. L. Stanschewski, C. Wendenburg, R. Klemmer, A. Macho, M. Thirumlaikumar, V. Saber, N. O. Skirycz, A. Fernie, A. R. Tester, M. Alseekh, S. 2026-02-25 doi:10.64898/2026.02.25.706111 Cold Spring Harbor Laboratory Press 2026-02-25 <![CDATA[ Phytochemical Characterization and In Vitro Antidiabetic Activity of Aruncus dioicus from Vietnam ]]> https://biorxiv.org/content/10.64898/2026.02.26.707872v1?rss=1 Thuc, B. T. Tung, N. V. D. Trang, V. T. H. 2026-02-28 doi:10.64898/2026.02.26.707872 Cold Spring Harbor Laboratory Press 2026-02-28 <![CDATA[ Not all mantra meditations are equal: Emergence of divergent alpha oscillatory dynamics across mantras ]]> https://biorxiv.org/content/10.64898/2026.02.26.707862v1?rss=1 Li, A. Rodriguez Larios, J. Zhang, M. Liu, T. Cohen, B. H. Ravishankar, S. 2026-03-02 doi:10.64898/2026.02.26.707862 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ ProPrep: An Interactive and Instructional Interface for Proper Protein Preparation with AMBER ]]> https://biorxiv.org/content/10.64898/2026.02.26.708365v1?rss=1 Walker, a. Guberman-Pfeffer, M. J. 2026-03-02 doi:10.64898/2026.02.26.708365 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ mPFC pyramidal neuron synchrony during social competition to form social rankings is disrupted in male Mecp2 knockout mice ]]> https://biorxiv.org/content/10.64898/2026.03.02.709145v1?rss=1 Acevedo-Triana, C. Tuscher, J. Day, J. J. Perez-Ortega, J. Pozzo-Miller, L. 2026-03-04 doi:10.64898/2026.03.02.709145 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Neurobehavioral impacts of the autism risk gene, WAC: Studies involving C. elegans and Mice ]]> https://biorxiv.org/content/10.64898/2026.03.02.709202v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@1771dc4org.highwire.dtl.DTLVardef@1434b4eorg.highwire.dtl.DTLVardef@10525ecorg.highwire.dtl.DTLVardef@fcd8a9_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Boonpraman, N. Kim, D.-W. Tislerics, E. Barot, J. Pacheco-Cruz, D. Kuhn, N. C. Vogt, D. Sammi, S. R. 2026-03-05 doi:10.64898/2026.03.02.709202 Cold Spring Harbor Laboratory Press 2026-03-05 <![CDATA[ RRTF1 promotes touch-responses in Arabidopsis shoots independent of jasmonic acid ]]> https://biorxiv.org/content/10.64898/2026.03.08.710212v1?rss=1 Park, S. Finlayson, S. A. Li, C. 2026-03-09 doi:10.64898/2026.03.08.710212 Cold Spring Harbor Laboratory Press 2026-03-09 <![CDATA[ Mature Citrus Leaves Undergo Coordinated Photosynthetic Downregulation to Support Flush-Driven Carbon and Nitrogen Sink Demand ]]> https://biorxiv.org/content/10.64898/2026.03.09.710566v1?rss=1 Hussain, S. B. Meng, Q. Li, S. Wang, Y. Vincent, C. I. 2026-03-11 doi:10.64898/2026.03.09.710566 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Structure and conformational dynamics of the Pseudomonas CbrA transceptor ]]> https://biorxiv.org/content/10.64898/2026.03.10.710862v1?rss=1 Orlando, M. A. Shah, T. Faber, M. W. Bose, S. Orlando, B. J. 2026-03-11 doi:10.64898/2026.03.10.710862 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Heat alters fruit morphology and severely limits reproduction but not growth in a widespread urban weed. ]]> https://biorxiv.org/content/10.64898/2026.03.10.710864v1?rss=1 Hightower, A. T. Henley, C. Colligan, C. Josephs, E. B. 2026-03-12 doi:10.64898/2026.03.10.710864 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ A Knock-in Ntsr1-Flp Driver Enables Intersectional and Systemic Targeting of Heterogeneous Midbrain Dopamine Circuits ]]> https://biorxiv.org/content/10.64898/2026.03.11.711093v1?rss=1 Garcia, F. Villa, A. Wong, J. Fenno, L. Leinninger, G. Steele, A. 2026-03-12 doi:10.64898/2026.03.11.711093 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ A systematic analysis of brain tissue response to microelectrode material and size with single-cell spatial transcriptomics ]]> https://biorxiv.org/content/10.64898/2026.03.12.711361v1?rss=1 Thompson, C. Chakraborty, A. Wade-Kleyn, L. Reimers, M. Purcell, E. 2026-03-16 doi:10.64898/2026.03.12.711361 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ Mapping frog genomic diversity on a continental scale ]]> https://biorxiv.org/content/10.64898/2026.03.13.711368v1?rss=1 Barrow, L. N. McDaniels, C. X. Bishop, A. P. Amador, L. Wiley, D. L. F. Eberle, C. M. Mason, N. M. Rosario Sanchez, E. O. Giermakowski, J. T. Hoffman, E. A. Jongsma, G. F. M. Michelsohn, M. J. Nava Martinez, M. Omlor, K. N. Rivera, S. R. Torres Lopez, A. S. Warwick, A. R. Webster, K. C. 2026-03-17 doi:10.64898/2026.03.13.711368 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Functional impact of PCSK9 variants on LDL uptake in a knockout hepatic model ]]> https://biorxiv.org/content/10.64898/2026.03.13.711724v1?rss=1 Li, H. Liu, H. Xu, W. Zeng, Y. Huang, P. Guo, J. Cai, B. Chen, Y. Lin, Y. Zhang, C. 2026-03-17 doi:10.64898/2026.03.13.711724 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Impaired motor activity in a CRISPR SCA5 L253P knock-in mouse is associated with selective beta-III-spectrin subcellular redistribution in the cerebellum ]]> https://biorxiv.org/content/10.64898/2026.03.14.711824v1?rss=1 Avery, A. W. O'Callaghan, B. L. Thiel, M. T. Denha, S. A. O'Callaghan, D. G. Cismas, E. M. Lamp, J. Orr, H. T. Hays, T. S. 2026-03-17 doi:10.64898/2026.03.14.711824 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ ULK1 drives NDP52-mediated selective autophagic degradation of MHC-I to promote immune evasion in HPV-positive head and neck cancer ]]> https://biorxiv.org/content/10.64898/2026.03.14.711071v1?rss=1 Vu, L. Giacobbi, N. S. Khalil, M. I. Yang, C. Eckerman, W. J. Gomez Recinos, E. Garber, J. D. Son, H. Chahal, P. Villa, D. M. Srivastava, T. Bennett, A. Z. Martin, K. R. Welbon, C. Williamson, C. Spanos, W. C. MacKeigan, J. P. Olive, A. J. Pyeon, D. 2026-03-18 doi:10.64898/2026.03.14.711071 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Introgression across ploidies contributes to genetic diversity in introduced urban Capsella bursa-pastoris ]]> https://biorxiv.org/content/10.64898/2026.03.17.712489v1?rss=1 Wilson Brown, M. K. Panko, R. Platts, A. E. Josephs, E. B. 2026-03-19 doi:10.64898/2026.03.17.712489 Cold Spring Harbor Laboratory Press 2026-03-19 <![CDATA[ Multi-lab, Multi-enzyme Study Demonstrates the Versatility of Bacterial Microcompartment Shells as a Modular Platform for Confined Biocatalysis ]]> https://biorxiv.org/content/10.64898/2026.03.18.712704v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@2c7548org.highwire.dtl.DTLVardef@c7f524org.highwire.dtl.DTLVardef@1af2887org.highwire.dtl.DTLVardef@8deb38_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Retnadhas, S. Tefft, N. M. Wang, Y. Range, K. L. Pramanik, A. Singh, K. Chiang, T. K. Nigrelli, K. Hausinger, R. P. Hegg, E. L. TerAvest, M. A. Sutter, M. Kerfeld, C. 2026-03-19 doi:10.64898/2026.03.18.712704 Cold Spring Harbor Laboratory Press 2026-03-19 <![CDATA[ Phenotypic plasticity evolved for climate variability constrains performance under climate warming ]]> https://biorxiv.org/content/10.64898/2026.03.15.711905v1?rss=1 Mead, A. Zavala-Paez, M. Beasley-Bennett, J. R. Bleich, A. C. Clancy-Mallue, I. P. Fischer, D. G. Golightly, J. M. Hufford, K. M. Kalcsits, L. A. Klopf, S. K. Lasky, J. R. LeBoldus, J. M. Lowry, D. B. Mitchell, N. Moran, E. V. Sexton, J. P. Sondreli, K. L. Fitzpatrick, M. C. Holliday, J. Keller, S. R. Hamilton, J. 2026-03-20 doi:10.64898/2026.03.15.711905 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Endometrial Hyperplasia Risk Is Increased by High-Fat Diet Via Estrogen-Driven Stromal Fibroblast Reprogramming Toward a Pro-Fibrotic State ]]> https://biorxiv.org/content/10.64898/2026.03.20.713224v1?rss=1 View larger version (47K): org.highwire.dtl.DTLVardef@195aceborg.highwire.dtl.DTLVardef@18b8a8dorg.highwire.dtl.DTLVardef@354b78org.highwire.dtl.DTLVardef@edc8ee_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO HFD-induced estrogen dominance disrupts endometrial fibroblast homeostasis to predispose the endometrium to diseaseThis study demonstrates that HFD drives estrogen-dependent reprogramming of stromal fibroblasts, characterized by inflammation, stromal ECM accumulation and fibrosis, and a post-ovulatory shift from PGR-network-associated Aldh1a2+ Fibroblasts toward increasing ER-network-associated Gsn+ Fibroblasts. These fibroblast changes are accompanied by a reduction in endometrial macrophages and a transcriptomic shift of HFD epithelium toward hyperplastic epithelium seen in a mouse model of EH. Figure made with BioRender. C_FIG ]]> Skalski, H. J. Bennett, A. Z. Wood, L. E. Harkins, S. K. Arendt, A. R. Lopez Espinosa, A. G. Burns, G. W. Paul, E. N. Hostetter, G. Becker, K. Wegener, M. Adams, M. Teixeira, J. M. Lau, K. Chandler, R. L. 2026-03-24 doi:10.64898/2026.03.20.713224 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Host-mediated pH influences microbiome assembly and function on the phylloplane ]]> https://biorxiv.org/content/10.64898/2026.03.21.713394v1?rss=1 Floc'h, J.-B. Lopez-Gonzalez, C. Renner, T. Gilbert, K. J. 2026-03-24 doi:10.64898/2026.03.21.713394 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Global synthesis of aquatic insect heat tolerance reveals oxygen availability as a key driver of climate vulnerability ]]> https://biorxiv.org/content/10.64898/2026.03.23.713664v1?rss=1 Bristow, S. A. Verberk, W. C. E. P. Stoks, R. Kefford, B. J. Dewenter, B. S. Shah, A. A. 2026-03-25 doi:10.64898/2026.03.23.713664 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Molecular design principles for Photosystem I-based biohybrid solar fuel catalysts ]]> https://biorxiv.org/content/10.64898/2026.03.23.713776v1?rss=1 Emerson, M. D. Damaraju, S. N. S. Short, A. H. Alvord, Z. B. Palmer, Z. A. Mehra, H. S. Brininger, C. M. Vermaas, J. V. Utschig, L. M. Gisriel, C. J. 2026-03-25 doi:10.64898/2026.03.23.713776 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Regulation of PDGF-BB Signaling in Placental Pericytes by Soluble PDGFRβ Isoforms: Implications for Fetoplacental Vascular Development ]]> https://biorxiv.org/content/10.64898/2026.03.24.713995v1?rss=1 Barnes, A. Duggan, E. C. Dunkenberger, R. Lessard, C. Cosma, C. Steele, C. Taylor, S. V. Whitham, M. D. Durica, A. R. Chappell, J. C. 2026-03-27 doi:10.64898/2026.03.24.713995 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Cerebral Oxygen Budgeting: Network-Level BOLD Dynamics During Acute Hypoxia ]]> https://biorxiv.org/content/10.64898/2026.03.27.713294v1?rss=1 Kang, D. Uchida, K. Haider, C. R. Campeau, N. G. In, M.-H. Gray, E. M. Trzasko, J. D. Welker, K. M. Wiggins, C. C. Senefeld, J. W. Bernstein, M. A. Holmes, D. R. Joyner, M. J. Curry, T. B. Huston, J. Shu, Y. 2026-03-31 doi:10.64898/2026.03.27.713294 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Estimation of chloroplast macromolecular complex copy numbers and subunit stoichiometries during the Chlamydomonas reinhardtii cell cycle ]]> https://biorxiv.org/content/10.64898/2026.03.30.715394v1?rss=1 Schmollinger, S. Strenkert, D. Purvine, S. O. Nicora, C. D. Soubeyrand, E. Basset, G. J. Merchant, S. 2026-04-01 doi:10.64898/2026.03.30.715394 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Microbe-mediated plant acclimation to drought may be rare in agriculture ]]> https://biorxiv.org/content/10.64898/2026.04.02.715620v1?rss=1 Howard, M. M. Bolin, L. G. Bogar, G. D. Evans, S. E. Lennon, J. T. Marquart-Pyatt, S. T. Lau, J. A. 2026-04-04 doi:10.64898/2026.04.02.715620 Cold Spring Harbor Laboratory Press 2026-04-04 <![CDATA[ Humanization of the rpb9 locus in fission yeast reveals conserved and divergent roles of rpb9 and human POLR2I ]]> https://biorxiv.org/content/10.64898/2026.04.02.716003v1?rss=1 Finkel, J. M. Williams, M. G. Nirmal, M. B. Pandey, S. Howe, E. D. Liu, C. T. Lohman, J. R. Sharma, N. Vo, T. V. 2026-04-04 doi:10.64898/2026.04.02.716003 Cold Spring Harbor Laboratory Press 2026-04-04 <![CDATA[ Depletion of Chloroplast HSP70B Triggers Proteostasis Collapse and Compromises Thylakoid Membrane Integrity in Chlamydomonas ]]> https://biorxiv.org/content/10.64898/2026.04.02.716084v1?rss=1 Probst, A. Schmollinger, S. Berg, J. Unger, A.-K. Strenkert, D. Geimer, S. Sommer, F. Schroda, M. 2026-04-06 doi:10.64898/2026.04.02.716084 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ Ancient IL-6-STAT5 signaling orchestrates inflammation in jawless vertebrates ]]> https://biorxiv.org/content/10.64898/2026.04.02.716188v1?rss=1 Fontenla-Iglesias, F. Boulay, J.-L. Rast, J. P. Hirano, M. Au-Yeung, B. B. Lamas, J. Li, W. Boehm, T. Cooper, M. D. DAS, S. 2026-04-06 doi:10.64898/2026.04.02.716188 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ Screening metatranscriptomes for ultrastable RNA secondary structures reveals hidden bacteriophages and novel capsid nanomaterials ]]> https://biorxiv.org/content/10.64898/2026.04.05.716407v1?rss=1 Villarreal, D. A. Makasarashvili, N. Kapoor, A. Root, M. Campbell, M. Gibson, S. Schiveley, C. Rastandeh, A. Baker, S. Subramanian, S. Neri, U. Mills, C. E. McNair, K. Segall, A. M. Gophna, U. Parent, K. N. Garmann, R. F. 2026-04-07 doi:10.64898/2026.04.05.716407 Cold Spring Harbor Laboratory Press 2026-04-07