bioRxiv Channel: North Carolina State University https://biorxiv.org This feed contains articles for bioRxiv Channel "North Carolina State University" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Genome-wide association study of carbon and nitrogen metabolism in the maize nested association mapping population ]]> https://biorxiv.org/content/10.1101/010785v1?rss=1 Nengyi Zhang Yves Gibon Nicholas Lepak Pinghua Li Lauren Dedow Charles Chen Yoon-Sup So Jason Wallace Karl Kremling Peter Bradbury Thomas Brutnell Mark Stitt Edward Buckler 2014-10-28 doi:10.1101/010785 Cold Spring Harbor Laboratory Press 2014-10-28 <![CDATA[ Settlement, growth and survival of eastern oysters on alternative reef substrates ]]> https://biorxiv.org/content/10.1101/010793v1?rss=1 Seth J. Theuerkauf Russell P. Burke Romuald N. Lipcius 2014-10-28 doi:10.1101/010793 Cold Spring Harbor Laboratory Press 2014-10-28 <![CDATA[ Bayesian priors for tree calibration: Evaluating two new approaches based on fossil intervals ]]> https://biorxiv.org/content/10.1101/014340v1?rss=1 Ryan W Norris Cory L Strope David M McCandlish Arlin Stoltzfus 2015-01-24 doi:10.1101/014340 Cold Spring Harbor Laboratory Press 2015-01-24 <![CDATA[ Genome-wide analysis reveals novel regulators of growth in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/017855v1?rss=1 Sibylle Chantal Vonesch David Lamparter Trudy FC Mackay Sven Bergmann Ernst Hafen 2015-04-10 doi:10.1101/017855 Cold Spring Harbor Laboratory Press 2015-04-10 <![CDATA[ Application of a dense genetic map for assessment of genomic responses to selection and inbreeding in Heliothis virescens. ]]> https://biorxiv.org/content/10.1101/025981v1?rss=1 Megan Fritz Sandra Paa Jennifer Baltzegar Fred Gould 2015-09-02 doi:10.1101/025981 Cold Spring Harbor Laboratory Press 2015-09-02 <![CDATA[ Disruption of endosperm development is a major cause of hybrid seed inviability between Mimulus guttatus and M. nudatus ]]> https://biorxiv.org/content/10.1101/029223v1?rss=1 Elen Oneal John H. Willis Robert Franks 2015-10-15 doi:10.1101/029223 Cold Spring Harbor Laboratory Press 2015-10-15 <![CDATA[ Single molecule targeted sequencing for cancer gene mutation detection ]]> https://biorxiv.org/content/10.1101/029686v1?rss=1 Yan Gao Liwei Deng Qin Yan Yongqian Gao Zengding Wu Jinsen Cai Daorui Ji Gailing Li Ping Wu Huan Jin Luyang Zhao Song Liu Michael W Deem Jiankui He 2015-10-23 doi:10.1101/029686 Cold Spring Harbor Laboratory Press 2015-10-23 <![CDATA[ Sporadic, global linkage disequilibrium between unlinked segregating sites ]]> https://biorxiv.org/content/10.1101/030247v1?rss=1 5%) genetically indistinguishable variants in relatively large datasets. These results clarify a previously underexplored population genetic phenomenon with important implications for association studies, and define conditions under which it is likely to manifest. ]]> Daniel A Skelly Paul M Magwene Eric A Stone 2015-10-30 doi:10.1101/030247 Cold Spring Harbor Laboratory Press 2015-10-30 <![CDATA[ Temporal and spatial domain-specific transcriptomic analysis of a vital reproductive meristem in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/032128v1?rss=1 Gonzalo H Villarino Miguel Flores-Vergara Qiwen Hu Bhupinder Sehra Linda Robles Javier Brumos Anna Stepanova Silvia Manrique Lucia Colombo Eva Sundberg Steffen Heber Robert G Franks 2015-11-18 doi:10.1101/032128 Cold Spring Harbor Laboratory Press 2015-11-18 <![CDATA[ Purifying selection and drift, not life history or RNAi, determine transposable element evolution ]]> https://biorxiv.org/content/10.1101/034884v1?rss=1 Amir Szitenberg Soyeon Cha Charles H Opperman David M Bird Mark Blaxter David H Lunt 2015-12-20 doi:10.1101/034884 Cold Spring Harbor Laboratory Press 2015-12-20 <![CDATA[ Validation of a habitat suitability index for oyster restoration ]]> https://biorxiv.org/content/10.1101/039875v1?rss=1 Seth Theuerkauf Romuald Lipcius 2016-02-17 doi:10.1101/039875 Cold Spring Harbor Laboratory Press 2016-02-17 <![CDATA[ The Genetic Architecture of Quantitative Traits Cannot Be Inferred From Variance Component Analysis ]]> https://biorxiv.org/content/10.1101/041434v1?rss=1 Wen Huang Trudy F.C. Mackay 2016-02-26 doi:10.1101/041434 Cold Spring Harbor Laboratory Press 2016-02-26 <![CDATA[ Functional partitioning of local and distal gene expression regulation in multiple human tissues ]]> https://biorxiv.org/content/10.1101/046383v1?rss=1 Xuanyao Liu Hilary Kiyo Finucane Alexander Gusev Gaurav Bhatia Steven Gazal Luke O'Connor Brendan Bulik-Sullivan Fred Wright Patrick Sullivan Benjamin Neale Alkes Price 2016-03-31 doi:10.1101/046383 Cold Spring Harbor Laboratory Press 2016-03-31 <![CDATA[ The Drosophila genes disconnected and disco-related together specify development of adult legs ]]> https://biorxiv.org/content/10.1101/052811v1?rss=1 Juan Rosario James Mahaffey 2016-05-11 doi:10.1101/052811 Cold Spring Harbor Laboratory Press 2016-05-11 <![CDATA[ Modifications to a LATE MERISTEM IDENTITY-1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.) ]]> https://biorxiv.org/content/10.1101/062612v1?rss=1 Ryan J Andres Viktoriya Coneva Margaret Frank John R Tuttle Sang-Won Han Luis F Samayoa Baljinder Kaur Linglong Zhu Hui Fang Daryl T Bowman Marcela Rojas-Pierce Candace H Haigler Don C Jones James B Holland Daniel H Chitwood Vasu Kuraparthy 2016-07-07 doi:10.1101/062612 Cold Spring Harbor Laboratory Press 2016-07-07 <![CDATA[ Evolutionary dynamics of an epigenetic switch in a fluctuating environment ]]> https://biorxiv.org/content/10.1101/072199v1?rss=1 Mariana Gómez-Schiavon Nicolas E Buchler 2016-08-30 doi:10.1101/072199 Cold Spring Harbor Laboratory Press 2016-08-30 <![CDATA[ Local genetic effects on gene expression across 44 human tissues ]]> https://biorxiv.org/content/10.1101/074450v1?rss=1 Francois Aguet Andrew A Brown Stephane Castel Joe R Davis Pejman Mohammadi Ayellet V Segre Zachary Zappala Nathan S Abell Laure Fresard Eric R Gamazon Ellen Gelfand Machael J Gloudemans Yuan He Farhad Hormozdiari Xiao Li Xin Li Boxiang Liu Diego Garrido-Martin Halit Ongen John J Palowitch YoSon Park Christine B Peterson Gerald Quon Stephan Ripke Andrey A Shabalin Tyler C Shimko Benjamin J Strober Timothy J Sullivan Nicole A Teran Emily K Tsang Hailei Zhang Yi-Hui Zhou Alexis Battle Carlos D Bustamonte Nancy J Cox Barbara E Engelhardt Eleazar Eskin Gad Getz Manolis Kellis Gen Li Daniel G MacArt 2016-09-09 doi:10.1101/074450 Cold Spring Harbor Laboratory Press 2016-09-09 <![CDATA[ Evidence of cryptic incidence in childhood diseases ]]> https://biorxiv.org/content/10.1101/079194v1?rss=1 Christian E Gunning Matthew J Ferrari Erik B Erhardt Helen J Wearing 2016-10-04 doi:10.1101/079194 Cold Spring Harbor Laboratory Press 2016-10-04 <![CDATA[ Incorporating the Rate of Transcriptional Change Improves Construction of Transcription Factor Regulatory Networks ]]> https://biorxiv.org/content/10.1101/093807v1?rss=1 Desai, J. Sartor, R. C. Lawas, L. M. Jagadish SV, K. Doherty, C. J. 2016-12-24 doi:10.1101/093807 Cold Spring Harbor Laboratory Press 2016-12-24 <![CDATA[ Repliscan: a tool for classifying replication timing regions ]]> https://biorxiv.org/content/10.1101/094177v1?rss=1 Zynda, G. J. Song, J. Concia, L. Wear, E. E. Hanley-Bowdoin, L. Thompson, W. F. Vaughn, M. W. 2016-12-14 doi:10.1101/094177 Cold Spring Harbor Laboratory Press 2016-12-14 <![CDATA[ Comparison of one-stage and two-stage genome-wide association studies ]]> https://biorxiv.org/content/10.1101/099291v1?rss=1 Xue, S. Ogut, F. Miller, Z. Verma, J. Bradbury, P. Holland, J. 2017-01-09 doi:10.1101/099291 Cold Spring Harbor Laboratory Press 2017-01-09 <![CDATA[ Estrogen and Soy Isoflavonoids Decrease Sensitivity of Medulloblastoma and Central Nervous System Primitive Neuroectodermal Tumor Cells to Chemotherapeutic Cytotoxicity ]]> https://biorxiv.org/content/10.1101/100107v1?rss=1 10 M. In clonogenic survival assays estradiol decreased the chemosensitivity of D283 Med exposed to cisplatin, lomustine and vincristine. The ER{beta} selective agonist DPN and low physiological concentrations of the soy-derived phytoestrogens genistein, daidzein, and s-equol also decreased sensitivity of D283 Med cells to cisplatin. The protective effects of estradiol were blocked by the antiestrogens 4-hydroxytamoxifen, fulvestrant (ICI 182,780) and the ER{beta} selective antagonist PPHTP. Whereas estradiol also decreased chemosensitivity of PFSK1 cells, estradiol increased sensitivity of Daoy cell to cisplatin, suggesting that ER{beta} mediated effects may vary in different subtypes of MB.nnConclusionsThese findings demonstrate that E2 and environmental estrogens decrease sensitivity of MB to cytotoxic chemotherapeutics, and that ER{beta} selective and non-selective inhibition of estrogen receptor activity blocks these cytoprotective actions. These findings support the therapeutic potential of antiestrogen adjuvant therapies for MB, and findings that soy phytoestrogens also decrease sensitivity of MB cells to cytotoxic chemotherapeutics suggest that decreased exposure to environmental estrogens may benefit MB patient responses to chemotherapy. ]]> Belcher, S. M. Burton, C. C. Cookman, C. J. Kirby, M. Miranda, G. L. L. Saeed, F. Wray, K. E. 2017-01-13 doi:10.1101/100107 Cold Spring Harbor Laboratory Press 2017-01-13 <![CDATA[ Contemporary evolution of a Lepidopteran species, Heliothis virescens, in response to modern agricultural practices ]]> https://biorxiv.org/content/10.1101/103382v1?rss=1 Fritz, M. L. Deyonke, A. M. Papanicolaou, A. Micinski, S. Westbrook, J. Gould, F. 2017-01-26 doi:10.1101/103382 Cold Spring Harbor Laboratory Press 2017-01-26 <![CDATA[ Immune Loss as a Driver of Coexistence During Host-Phage Coevolution ]]> https://biorxiv.org/content/10.1101/105908v1?rss=1 Weissman, J. L. Holmes, R. Barrangou, R. Moineau, S. Fagan, W. F. Levin, B. Johnson, P. L. 2017-02-03 doi:10.1101/105908 Cold Spring Harbor Laboratory Press 2017-02-03 <![CDATA[ Impacts of Bisphenol A and Ethinyl Estradiol on Male and Female CD-1 Mouse Spleen ]]> https://biorxiv.org/content/10.1101/109009v1?rss=1 Gear, R. B. Belcher, S. 2017-02-15 doi:10.1101/109009 Cold Spring Harbor Laboratory Press 2017-02-15 <![CDATA[ Genetic Architecture and Molecular Networks Underlying Leaf Thickness in Desert-Adapted Tomato Solanum pennellii ]]> https://biorxiv.org/content/10.1101/111005v1?rss=1 Coneva, V. Frank, M. H. de Luis Balaguer, M. A. Li, M. Sozzani, R. Chitwood, D. H. 2017-02-22 doi:10.1101/111005 Cold Spring Harbor Laboratory Press 2017-02-22 <![CDATA[ Exact sequence variants should replace operational taxonomic units in marker gene data analysis ]]> https://biorxiv.org/content/10.1101/113597v1?rss=1 Callahan, B. J. McMurdie, P. J. Holmes, S. P. 2017-03-07 doi:10.1101/113597 Cold Spring Harbor Laboratory Press 2017-03-07 <![CDATA[ Assembly Of Whole-Chromosome Pseudomolecules For Polyploid Plant Genomes Using Outcrossed Mapping Populations ]]> https://biorxiv.org/content/10.1101/119271v1?rss=1 Zhou, C. Olukolu, B. Gemenet, D. Wu, S. Gruneberg, W. Cao, M. D. Fei, Z. Zeng, Z.-B. George, A. Khan, A. Yencho, C. Coin, L. 2017-03-22 doi:10.1101/119271 Cold Spring Harbor Laboratory Press 2017-03-22 <![CDATA[ Effects of Bisphenol A on Incidence and Severity of Cardiac Lesions in the NCTR-Sprague-Dawley Rat: A CLARITY-BPA Study ]]> https://biorxiv.org/content/10.1101/128454v1?rss=1 Robin, G. Kendziorski, J. Belcher, S. 2017-04-20 doi:10.1101/128454 Cold Spring Harbor Laboratory Press 2017-04-20 <![CDATA[ A heuristic method to identify runs of homozygosity associated with reduced performance in livestock. ]]> https://biorxiv.org/content/10.1101/131706v1?rss=1 Howard, J. T. Tiezzi, F. Huang, Y. Gray, K. A. Maltecca, C. 2017-04-28 doi:10.1101/131706 Cold Spring Harbor Laboratory Press 2017-04-28 <![CDATA[ An Inference Approach Combines Spatial And Temporal Gene Expression Data To Predict Gene Regulatory Networks In Arabidopsis Stem Cells ]]> https://biorxiv.org/content/10.1101/140269v1?rss=1 de Luis Balaguer, M. A. Fisher, A. P. Clark, N. M. Fernandez-Espinosa, M. G. Moller, B. Weijers, D. Lohmann, J. U. Williams, C. Lorenzo, O. Sozzani, R. 2017-05-19 doi:10.1101/140269 Cold Spring Harbor Laboratory Press 2017-05-19 <![CDATA[ Inter-individual Recovery Of The Microbiota And Metabolome Over Time Following Fecal Microbiota Transplantation In Patients With Recurrent Clostridium difficile Infection ]]> https://biorxiv.org/content/10.1101/141846v1?rss=1 Seekatz, A. Theriot, C. M. Rao, K. Chang, Y.-M. Freeman, A. E. Kao, J. Y. Young, V. B. 2017-05-24 doi:10.1101/141846 Cold Spring Harbor Laboratory Press 2017-05-24 <![CDATA[ Evaluating Strategies For Reversing CRISPR-Cas9 Gene Drives ]]> https://biorxiv.org/content/10.1101/144097v1?rss=1 Vella, M. Gunning, C. Lloyd, A. Gould, F. 2017-05-30 doi:10.1101/144097 Cold Spring Harbor Laboratory Press 2017-05-30 <![CDATA[ Plasticity Of Plant Defense And Its Evolutionary Implications In Wild Populations Of Boechera stricta ]]> https://biorxiv.org/content/10.1101/144626v1?rss=1 Wagner, M. Mitchell-Olds, T. 2017-05-31 doi:10.1101/144626 Cold Spring Harbor Laboratory Press 2017-05-31 <![CDATA[ Persistent homology demarcates a leaf morphospace ]]> https://biorxiv.org/content/10.1101/151712v1?rss=1 Li, M. An, H. Angelovici, R. Bagaza, C. Batushansky, A. Clark, L. Coneva, V. Donoghue, M. Edwards, E. Fajardo, D. Fang, H. Frank, M. Gallaher, T. Gebken, S. Hill, T. Jansky, S. Kaur, B. Klahs, P. Klein, L. Kuraparthy, V. Londo, J. Migicovsky, Z. Miller, A. Mohn, R. Myles, S. Otoni, W. Pires, J. C. Riffer, E. Schmerler, S. Spriggs, E. Topp, C. Van Deynze, A. Zhang, K. Zhu, L. Zink, B. M. Chitwood, D. H. 2017-06-20 doi:10.1101/151712 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ Invasion and migration of self-limiting gene drives: a comparative analysis ]]> https://biorxiv.org/content/10.1101/159855v1?rss=1 Dhole, S. Vella, M. R. Lloyd, A. L. Gould, F. 2017-07-05 doi:10.1101/159855 Cold Spring Harbor Laboratory Press 2017-07-05 <![CDATA[ Rapid and scalable characterization of CRISPR technologies using an E. coli cell-free transcription-translation system ]]> https://biorxiv.org/content/10.1101/169441v1?rss=1 Marshall, R. Maxwell, C. S. Collins, S. P. Luo, M. L. Jacobsen, T. Beisel, C. Noireaux, V. 2017-07-28 doi:10.1101/169441 Cold Spring Harbor Laboratory Press 2017-07-28 <![CDATA[ Anticipating complexity in the deployment of gene drive insects in agriculture ]]> https://biorxiv.org/content/10.1101/169938v1?rss=1 Baltzegar, J. Cavin Barnes, J. Elsensohn, J. E. Gutzmann, N. Jones, M. S. King, S. Sudweeks, J. 2017-07-28 doi:10.1101/169938 Cold Spring Harbor Laboratory Press 2017-07-28 <![CDATA[ Bioinformatics Core Competencies for Undergraduate Life Sciences Education ]]> https://biorxiv.org/content/10.1101/170993v1?rss=1 Wilson Sayres, M. A. Hauser, C. Sierk, M. Robic, S. Rosenwald, A. G. Smith, T. M. Triplett, E. W. Williams, J. J. Dinsdale, E. Morgan, W. Burnette, J. M. Donovan, S. S. Drew, J. C. Elgin, S. C. R. Fowlks, E. R. Galindo-Gonzalez, S. Goodman, A. L. Grandgenett, N. F. Goller, C. C. Jungck, J. Newman, J. D. Pearson, W. R. Ryder, E. Tosado-Acevedo, R. Tapprich, W. Tobin, T. C. Toro-Martinez, A. Welch, L. R. Wright, R. Ebenbach, D. Olney, K. C. McWilliams, M. Pauley, M. A. 2017-08-03 doi:10.1101/170993 Cold Spring Harbor Laboratory Press 2017-08-03 <![CDATA[ The roles of Conserved Domains in DEMETER-Mediated Active DNA Demethylation in planta ]]> https://biorxiv.org/content/10.1101/175091v1?rss=1 Zhang, C. Hung, Y.-H. Zhang, X.-Q. Zhang, D. Xiao, W. Iyer, L. M. Aravind, L. Huh, J. H. Hsieh, T.-F. 2017-08-10 doi:10.1101/175091 Cold Spring Harbor Laboratory Press 2017-08-10 <![CDATA[ Hemimetabolous genomes reveal molecular basis of termite eusociality ]]> https://biorxiv.org/content/10.1101/181909v1?rss=1 Harrison, M. C. Jongepier, E. Robertson, H. M. Arning, N. Bitard-Feildel, T. Chao, H. Childers, C. P. Dinh, H. Doddapaneni, H. Dugan, S. Gowin, J. Greiner, C. Han, Y. Hu, H. Hughes, D. S. T. Huylmans, A.-K. Kemena, C. Kremer, L. P. M. Lee, S. L. Lopez-Ezquerra, A. Mallet, L. Monroy-Kuhn, J. M. Moser, A. Murali, S. C. Muzny, D. M. Otani, S. Piulachs, M.-D. Poelchau, M. Qu, J. Schaub, F. Wada-Katsumata, A. Worley, K. C. Xie, Q. Ylla, G. Poulsen, M. Gibbs, R. A. Schal, C. Richards, S. Belles, X. Korb, J. Bornberg-Bauer, E. 2017-08-29 doi:10.1101/181909 Cold Spring Harbor Laboratory Press 2017-08-29 <![CDATA[ Genetic Analysis of Lodging in Diverse Maize Hybrids ]]> https://biorxiv.org/content/10.1101/185769v1?rss=1 Larsson, S. J. Peiffer, J. A. Edwards, J. W. Ersoz, E. S. Flint-Garcia, S. A. Holland, J. B. McMullen, M. D. Tuinstra, M. R. Romay, C. Buckler, E. S. 2017-09-07 doi:10.1101/185769 Cold Spring Harbor Laboratory Press 2017-09-07 <![CDATA[ Improving the Generation and Selection of Virtual Populations in Quantitative Systems Pharmacology Models ]]> https://biorxiv.org/content/10.1101/196089v1?rss=1 Rieger, T. R. Allen, R. J. Bystricky, L. Chen, Y. Colopy, G. Cui, Y. Gonzalez, A. Liu, Y. White, R. Everett, R. Banks, H. T. Musante, C. J. 2017-09-29 doi:10.1101/196089 Cold Spring Harbor Laboratory Press 2017-09-29 <![CDATA[ Somatic inactivating PTPRJ mutations and dysregulated pathways identified in canine melanoma by integrated comparative genomic analysis ]]> https://biorxiv.org/content/10.1101/196337v1?rss=1 Hendricks, W. P. D. Zismann, V. Sivaprakasam, K. Legendre, C. Poorman, K. Tembe, W. Kiefer, J. Liang, W. DeLuca, V. Stark, M. Ruhe, A. Froman, R. Duesbury, N. Washington, M. Aldrich, J. Neff, M. Huentelman, M. Hayward, N. Brown, K. Thamm, D. Post, G. Khanna, C. Davis, B. Breen, M. Sekulic, A. Trent, J. 2017-09-30 doi:10.1101/196337 Cold Spring Harbor Laboratory Press 2017-09-30 <![CDATA[ A Holistic Analysis of the Intestinal Stem Cell Niche Network ]]> https://biorxiv.org/content/10.1101/2019.12.12.871756v1?rss=1 Hansen, D. M. Meneses Giles, P. I. He, X. C. Chen, S. Paulson, A. Dekaney, C. M. Wang, J. Hu, D. Venkatraman, A. Kim, W. Kaddis, J. Olack, B. J. Dunn, J. C. Y. Kuo, C. Henning, S. Hanash, A. M. Houchen, C. W. Lynch, J. Martin, M. G. Niland, J. C. Stelzner, M. Wong, M. Wang, T. C. Yu, J. Yan, K. Li, L. 2019-12-12 doi:10.1101/2019.12.12.871756 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ Content of xylose, trehalose and L-citrulline in cucumber fermentations and utilization of such compounds by certain lactobacilli ]]> https://biorxiv.org/content/10.1101/2019.12.20.885608v1?rss=1 Ucar, R. A. Perez-Diaz, I. M. Dean, L. L. 2019-12-23 doi:10.1101/2019.12.20.885608 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ Structure-function analysis of interallelic complementation in ROOTY transheterozygotes ]]> https://biorxiv.org/content/10.1101/2020.01.02.893016v1?rss=1 Brumos, J. Bobay, B. G. Clark, C. A. Alonso, J. M. Stepanova, A. N. 2020-01-02 doi:10.1101/2020.01.02.893016 Cold Spring Harbor Laboratory Press 2020-01-02 <![CDATA[ Estimating invasion dynamics with geopolitical-unit level records: performance and similarity of common methods using both simulated data and a real case ]]> https://biorxiv.org/content/10.1101/2020.01.02.893248v1?rss=1 Liang, W. Tran, L. Wiggins, G. Grant, J. 2020-01-02 doi:10.1101/2020.01.02.893248 Cold Spring Harbor Laboratory Press 2020-01-02 <![CDATA[ Evolutionary dynamics of Tomato spotted wilt virus within and between alternate plant hosts and thrips ]]> https://biorxiv.org/content/10.1101/2020.01.13.904250v1?rss=1 Ruark-Seward, C. L. Bonville, B. Kennedy, G. Rasmussen, D. A. 2020-01-14 doi:10.1101/2020.01.13.904250 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Microbiome composition differs in hybrid and inbred maize ]]> https://biorxiv.org/content/10.1101/2020.01.13.904979v1?rss=1 Wagner, M. R. Roberts, J. H. Balint-Kurti, P. J. Holland, J. B. 2020-01-14 doi:10.1101/2020.01.13.904979 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Building the lac operon: A guided-inquiry activity using 3D printed models ]]> https://biorxiv.org/content/10.1101/2020.01.14.904847v1?rss=1 Gordy, C. L. Sandefur, C. I. Lacara, T. Harris, F. R. Ramirez, M. V. 2020-01-20 doi:10.1101/2020.01.14.904847 Cold Spring Harbor Laboratory Press 2020-01-20 <![CDATA[ Urban warming inverse contribution on risk of dengue transmission in the southeastern North America ]]> https://biorxiv.org/content/10.1101/2020.01.15.908020v1?rss=1 Simon, L. M. Pinto-Ledezma, J. N. Dunn, R. R. Rangel, T. F. 2020-01-16 doi:10.1101/2020.01.15.908020 Cold Spring Harbor Laboratory Press 2020-01-16 <![CDATA[ Microbial DNA on the move: sequencing based detection and analysis of transduced DNA in pure cultures and microbial communities ]]> https://biorxiv.org/content/10.1101/2020.01.15.908442v1?rss=1 Kleiner, M. Bushnell, B. Sanderson, K. E. Hooper, L. V. Duerkop, B. A. 2020-01-16 doi:10.1101/2020.01.15.908442 Cold Spring Harbor Laboratory Press 2020-01-16 <![CDATA[ Ursodeoxycholic acid (UDCA) mitigates the host inflammatory response during Clostridioides difficile infection by altering gut bile acids which attenuates NF-κB signaling via bile acid activated receptors ]]> https://biorxiv.org/content/10.1101/2020.01.16.910018v1?rss=1 Winston, J. A. Rivera, A. M. Cai, J. Thanissery, R. M. Montgomery, S. A. Patterson, A. D. Theriot, C. M. 2020-01-21 doi:10.1101/2020.01.16.910018 Cold Spring Harbor Laboratory Press 2020-01-21 <![CDATA[ Establishing Probiotic Saccharomyces boulardii as a Model Organism for Synthesis and Delivery of Biomolecules ]]> https://biorxiv.org/content/10.1101/2020.01.22.915389v1?rss=1 Durmusoglu, D. Al'Abri, I. S. Collins, S. P. Beisel, C. Crook, N. C. 2020-01-23 doi:10.1101/2020.01.22.915389 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Strain-dependent inhibition of Clostridioides difficile by commensal Clostridia encoding the bile acid inducible (bai) operon ]]> https://biorxiv.org/content/10.1101/2020.01.22.916304v1?rss=1 Reed, A. D. Nethery, M. A. Stewart, A. Barrangou, R. Theriot, C. M. 2020-01-23 doi:10.1101/2020.01.22.916304 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots ]]> https://biorxiv.org/content/10.1101/2020.01.24.917914v1?rss=1 Wear, E. E. Song, J. Zynda, G. J. Mickelson-Young, L. LeBlanc, C. Lee, T.-J. Deppong, D. O. Allen, G. C. Martienssen, R. A. Vaughn, M. W. Hanley-Bowdoin, L. Thompson, W. F. 2020-01-24 doi:10.1101/2020.01.24.917914 Cold Spring Harbor Laboratory Press 2020-01-24 <![CDATA[ Heterozygous mutation of Sonic Hedgehog receptor (Ptch) drives cerebellar overgrowth and sex-specifically alters hippocampal and cortical layer structure, activity, and social behavior in female mice ]]> https://biorxiv.org/content/10.1101/2020.01.25.919506v1?rss=1 Jackson, T. W. Bendfeldt, G. A. Beam, K. A. Rock, K. D. Belcher, S. M. 2020-01-25 doi:10.1101/2020.01.25.919506 Cold Spring Harbor Laboratory Press 2020-01-25 <![CDATA[ Beef cattle that respond differently to fescue toxicosis have distinct gastrointestinal tract microbiota ]]> https://biorxiv.org/content/10.1101/2020.02.03.932939v1?rss=1 Koester, L. R. Poole, D. H. Serao, N. V. Schmitz-Esser, S. 2020-02-05 doi:10.1101/2020.02.03.932939 Cold Spring Harbor Laboratory Press 2020-02-05 <![CDATA[ Genome-enabled insights into the biology of thrips as crop pests ]]> https://biorxiv.org/content/10.1101/2020.02.12.941716v1?rss=1 Rotenberg, D. Baumann, A. A. Ben-Mahmoud, S. Christiaens, O. Dermauw, W. Ioannidis, P. Jacobs, C. G. C. Vargas Jentzsch, I. M. Oliver, J. E. Poelchau, M. F. Rajarapu, S. P. Schneweis, D. J. Snoeck, S. Taning, C. N. T. Wei, D. Widana-Gamage, S. M. K. Hughes, D. S. T. Murali, S. C. Bailey, S. Bejerman, N. E. Holmes, C. J. Jennings, E. C. Rosendale, A. J. Rosselot, A. Hervey, K. Schneweis, B. A. Cheng, S. Childers, C. Simao, F. A. Dietzgen, R. G. Chao, H. Dinh, H. Doddapaneni, H. V. Dugan, S. Han, Y. Lee, S. L. Muzny, D. M. Qu, J. Worley, K. C. Benoit, J. B. 2020-02-13 doi:10.1101/2020.02.12.941716 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ A resurrection study reveals limited evolution of thermal performance in response to recent climate change across the geographic range of the scarlet monkeyflower ]]> https://biorxiv.org/content/10.1101/2020.02.14.934166v1?rss=1 Wooliver, R. Sheth, S. N. Tittes, S. B. 2020-02-14 doi:10.1101/2020.02.14.934166 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ Stony coral populations are more sensitive tochanges in vital rates in disturbed environments ]]> https://biorxiv.org/content/10.1101/2020.02.17.952424v1?rss=1 Hall, T. E. Freedman, A. S. de Roos, A. M. Edmunds, P. J. Carpenter, R. C. Gross, K. 2020-02-18 doi:10.1101/2020.02.17.952424 Cold Spring Harbor Laboratory Press 2020-02-18 <![CDATA[ Sequencing depth and genotype quality: Accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops ]]> https://biorxiv.org/content/10.1101/2020.02.23.961383v1?rss=1 Gemenet, D. C. Lindqvist-Kreuze, H. Olukolu, B. A. De Boeck, B. da Silva Pereira, G. Mollinari, M. Zeng, Z.-B. Yencho, G. C. Campos, H. 2020-02-25 doi:10.1101/2020.02.23.961383 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Multidimensional Analysis of Bronchoalveolar Lavage Cytokines and Mast Cell Proteases Reveals Interferon-γ as a Key Biomarker in Equine Asthma Syndrome ]]> https://biorxiv.org/content/10.1101/2020.02.24.956573v1?rss=1 Woodrow, J. S. Hines, M. Sommardahl, C. Flatland, B. Davis, K. Wang, Z. Sheats, M. K. Lo, Y. Lennon, E. M. 2020-02-25 doi:10.1101/2020.02.24.956573 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Characterizing Trabecular Bone Properties near the Glenohumeral Joint Following Brachial Plexus Birth Injury ]]> https://biorxiv.org/content/10.1101/2020.02.26.967224v1?rss=1 Fawcett, E. B. McCormick, C. M. Murray, A. F. Crouch, D. L. Saul, K. R. Cole, J. H. 2020-02-27 doi:10.1101/2020.02.26.967224 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ Forelimb unloading impairs glenohumeral muscle development in growing rats ]]> https://biorxiv.org/content/10.1101/2020.02.26.967273v1?rss=1 Tushak, S. K. Tamburro, M. K. Fawcett, E. B. Merritt, L. E. Saul, K. R. Cole, J. H. 2020-02-27 doi:10.1101/2020.02.26.967273 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ Candidate stress biomarkers for queen failure diagnostics ]]> https://biorxiv.org/content/10.1101/2020.02.27.961847v1?rss=1 McAfee, A. Milone, J. P. Chapman, A. A. Foster, L. J. Tarpy, D. R. Pettis, J. 2020-02-28 doi:10.1101/2020.02.27.961847 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ A lipid metabolic map of the pathogenic fungus Histoplasma capsulatum ]]> https://biorxiv.org/content/10.1101/2020.03.02.973412v1?rss=1 Zamith-Miranda, D. Heyman, H. M. Burnet, M. C. Couvillion, S. P. Zheng, X. Munoz, N. Kyle, J. E. Zink, E. M. Weitz, K. K. Bloodsworth, K. J. Clair, G. C. Zucker, J. D. Teuton, J. R. Payne, S. H. Kim, Y.-M. Reyes Gil, M. Baker, E. S. Bredeweg, E. L. Nosanchuk, J. D. Nakayasu, E. S. 2020-03-03 doi:10.1101/2020.03.02.973412 Cold Spring Harbor Laboratory Press 2020-03-03 <![CDATA[ The combination of mitogenic stimulation and cell cycle arrest induces senescence in equine and human cartilage explants ]]> https://biorxiv.org/content/10.1101/2020.03.05.979872v1?rss=1 Copp, M. E. Flanders, M. C. Gagliardi, R. Gilbertie, J. M. Sessions, G. A. Chubinskaya, S. Loeser, R. F. Schnabel, L. V. Diekman, B. O. 2020-03-06 doi:10.1101/2020.03.05.979872 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ Deep learning-enabled phenotyping reveals distinct patterns of neurodegeneration induced by aging and cold-shock ]]> https://biorxiv.org/content/10.1101/2020.03.08.982074v1?rss=1 Saberi-Bosari, S. Flores, K. B. San-Miguel, A. 2020-03-09 doi:10.1101/2020.03.08.982074 Cold Spring Harbor Laboratory Press 2020-03-09 <![CDATA[ The bacterial community structure dynamics in Meloidogyne incognita infected roots and its role in worm-microbiome interactions ]]> https://biorxiv.org/content/10.1101/2020.03.25.007294v1?rss=1 Yergaliyev, T. Alexander-Shani, R. Dimeretz, H. Pivonia, S. Bird, D. M. Rachmilevitch, S. Szitenberg, A. 2020-03-25 doi:10.1101/2020.03.25.007294 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Genetically encoded live cell sensor for tyrosinated microtubules ]]> https://biorxiv.org/content/10.1101/2020.03.29.013250v1?rss=1 Kesarwani, S. Lama, P. Chandra, A. Reddy, P. P. Jijumon, A. Bodakuntla, S. Rao, B. M. Janke, C. Das, R. Sirajuddin, M. 2020-03-30 doi:10.1101/2020.03.29.013250 Cold Spring Harbor Laboratory Press 2020-03-30 <![CDATA[ Parasites as niche modifiers for the microbiome: A field test with multiple parasites ]]> https://biorxiv.org/content/10.1101/2020.03.31.018713v1?rss=1 O'Keeffe, K. R. Halliday, F. W. Jones, C. D. Carbone, I. Mitchell, C. E. 2020-04-01 doi:10.1101/2020.03.31.018713 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns ]]> https://biorxiv.org/content/10.1101/2020.04.03.024281v1?rss=1 Greenham, K. Sartor, R. C. Zorich, S. Lou, P. Mockler, T. C. McClung, C. R. 2020-04-05 doi:10.1101/2020.04.03.024281 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ Noisy Pooled PCR for Virus Testing ]]> https://biorxiv.org/content/10.1101/2020.04.06.026765v1?rss=1 Zhu, J. Rivera, K. Baron, D. 2020-04-08 doi:10.1101/2020.04.06.026765 Cold Spring Harbor Laboratory Press 2020-04-08 <![CDATA[ Mathematical modeling of genetic pest management through female lethality with independently segregating alleles ]]> https://biorxiv.org/content/10.1101/2020.04.06.028738v1?rss=1 Vella, M. R. Gould, F. Lloyd, A. L. 2020-04-07 doi:10.1101/2020.04.06.028738 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Metabolic differences between symbiont subpopulations in the deep-sea tubeworm Riftia pachyptila ]]> https://biorxiv.org/content/10.1101/2020.04.08.032177v1?rss=1 Hinzke, T. Kleiner, M. Meister, M. Schlueter, R. Hentschker, C. Pane-Farre, J. Hildebrandt, P. Felbeck, H. Sievert, S. M. Bonn, F. Voelker, U. Becher, D. Schweder, T. Markert, S. 2020-04-09 doi:10.1101/2020.04.08.032177 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ Addressable Nanoantennas with Cleared Hotspots for Single-Molecule Detection on a Portable Smartphone Microscope ]]> https://biorxiv.org/content/10.1101/2020.04.09.032037v1?rss=1 Trofymchuk, K. Glembockyte, V. Grabenhorst, L. Steiner, F. Vietz, C. Close, C. Pfeiffer, M. Richter, L. Schütte, M. L. Selbach, F. Yaadav, R. Zähringer, J. Wei, Q. Ozcan, A. Lalkens, B. Acuna, G. P. Tinnefeld, P. 2020-04-09 doi:10.1101/2020.04.09.032037 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ On reproductive and respiratory syndrome virus dissemination across pig production systems in the United States ]]> https://biorxiv.org/content/10.1101/2020.04.09.034181v1?rss=1 Jara, M. Rasmussen, D. Corzo, C. A. Machado, G. 2020-04-10 doi:10.1101/2020.04.09.034181 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ Caspases from Scleractinian Coral Show Unique Regulatory Features ]]> https://biorxiv.org/content/10.1101/2020.04.13.039685v1?rss=1 Shrestha, S. Tung, J. Grinshpon, R. D. Swartz, P. D. Hamilton, P. T. Mydlarz, L. Clark, C. 2020-04-14 doi:10.1101/2020.04.13.039685 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Nairobi Sheep Disease Virus: a historical and epidemiological perspective ]]> https://biorxiv.org/content/10.1101/2020.04.13.040014v1?rss=1 Krasteva, S. Jara, M. Frias-De-Diego, A. F.-D.-D. Machado, G. 2020-04-14 doi:10.1101/2020.04.13.040014 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Isolation of Chemically Cyclized Peptide Binders Using Yeast Surface Display ]]> https://biorxiv.org/content/10.1101/2020.04.16.044438v1?rss=1 Bacon, K. Blain, A. Burroughs, M. McArthur, N. Rao, B. M. Menegatti, S. 2020-04-18 doi:10.1101/2020.04.16.044438 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ What makes Hemidactylus invasions successful? A case study on the island of Curacao. ]]> https://biorxiv.org/content/10.1101/2020.04.17.047209v1?rss=1 Lamb, A. D. Lippi, C. A. Watkins-Colwell, G. J. Jones, A. Warren, D. Iglesias, T. L. Brandley, M. Neagle, C. Dornburg, A. 2020-04-18 doi:10.1101/2020.04.17.047209 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Detection of Gray Mold in Plants Using a Multispectral Imaging System ]]> https://biorxiv.org/content/10.1101/2020.04.23.051300v1?rss=1 Scarboro, C. G. Ruzsa, S. M. Doherty, C. J. Kudenov, M. W. 2020-04-25 doi:10.1101/2020.04.23.051300 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Transcription of intragenic CpG islands influences spatiotemporal host gene pre-mRNA processing ]]> https://biorxiv.org/content/10.1101/2020.05.04.076729v1?rss=1 Amante, S. M. Montibus, B. Cowley, M. Barkas, N. Setiadi, J. Saadeh, H. Giemza, J. Contreras-Castillo, S. Fleischanderl, K. Schulz, R. Oakey, R. J. 2020-05-05 doi:10.1101/2020.05.04.076729 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Microbe-dependent heterosis in maize ]]> https://biorxiv.org/content/10.1101/2020.05.05.078766v1?rss=1 Wagner, M. R. Tang, C. Salvato, F. Clouse, K. M. Bartlett, A. Sermons, S. Hoffmann, M. Balint-Kurti, P. J. Kleiner, M. 2020-05-07 doi:10.1101/2020.05.05.078766 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ K-fiber bundles in the mitotic spindle are mechanically reinforced by Kif15 ]]> https://biorxiv.org/content/10.1101/2020.05.19.104661v1?rss=1 Begley, M. A. Solon, A. L. Davis, E. M. Sherrill, M. G. Ohi, R. Elting, M. W. 2020-05-20 doi:10.1101/2020.05.19.104661 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Transmission and control strategies for porcine reproductive and respiratory syndrome virus ]]> https://biorxiv.org/content/10.1101/2020.05.23.112946v1?rss=1 Galvis, J. A. Prada, J. Jones, C. Machado, G. 2020-05-26 doi:10.1101/2020.05.23.112946 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Elephant genomes reveal insights into differences in disease defense mechanisms between species ]]> https://biorxiv.org/content/10.1101/2020.05.29.124396v1?rss=1 Tollis, M. Ferris, E. Campbell, M. S. Harris, V. K. Rupp, S. M. Harrison, T. M. Kiso, W. K. Schmitt, D. L. Garner, M. M. Aktipis, C. A. Maley, C. C. Boddy, A. M. Yandell, M. Gregg, C. Schiffman, J. D. Abegglen, L. M. 2020-05-31 doi:10.1101/2020.05.29.124396 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Ancient viral genomes reveal introduction of HBV and B19V to Mexico during the transatlantic slave trade. ]]> https://biorxiv.org/content/10.1101/2020.06.05.137083v1?rss=1 Guzman-Solis, A. A. Blanco-Melo, D. Villa-Islas, V. Bravo-Lopez, M. J. Sandoval-Velasco, M. Wesp, J. K. Gomez-Valdes, J. A. Moreno-Cabrera, M. d. l. L. Meraz-Moreno, A. Solis-Pichardo, G. Schaaf, P. tenOever, B. R. Avila-Arcos, M. C. 2020-06-06 doi:10.1101/2020.06.05.137083 Cold Spring Harbor Laboratory Press 2020-06-06 <![CDATA[ A comprehensive framework for handling location error in animal tracking data ]]> https://biorxiv.org/content/10.1101/2020.06.12.130195v1?rss=1 Fleming, C. H. Drescher-Lehman, J. Noonan, M. J. Akre, T. S. B. Brown, D. J. Cochrane, M. M. Dejid, N. DeNicola, V. DePerno, C. S. Dunlop, J. N. Gould, N. P. Hollins, J. Ishii, H. Kaneko, Y. Kays, R. Killen, S. S. Koeck, B. Lambertucci, S. A. LaPoint, S. D. Medici, E. P. Meyburg, B.-U. Miller, T. A. Moen, R. A. Mueller, T. Pfeiffer, T. Pike, K. N. Roulin, A. Safi, K. Sechaud, R. Scharf, A. K. Shephard, J. M. Stabach, J. A. Stein, K. Tonra, C. M. Yamazaki, K. Fagan, W. F. Calabrese, J. M. 2020-06-14 doi:10.1101/2020.06.12.130195 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[ Transposable element mobilization in interspecific yeast hybrids ]]> https://biorxiv.org/content/10.1101/2020.06.16.155218v1?rss=1 Smukowski Heil, C. Patterson, K. Hickey, A. S.-M. Alcantara, E. Dunham, M. J. 2020-06-17 doi:10.1101/2020.06.16.155218 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ Improved neurocognitive performance in FIV infected cats following treatment with the p75 neurotrophin receptor ligand LM11A-31 ]]> https://biorxiv.org/content/10.1101/2020.06.17.156596v1?rss=1 Fogle, J. E. Hudson, L. Thompson, A. Sherman, B. Gruen, M. Lacelles, B. D. Colby, B. M. Clary, G. Longo, F. Meeker, R. 2020-06-17 doi:10.1101/2020.06.17.156596 Cold Spring Harbor Laboratory Press 2020-06-17 <![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[ 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[ Age and genetic background modify hybrid male sterility in house mice ]]> https://biorxiv.org/content/10.1101/2020.06.26.173047v1?rss=1 Widmayer, S. J. Handel, M. A. Aylor, D. L. 2020-06-26 doi:10.1101/2020.06.26.173047 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Trade-offs between sperm viability and immune protein expression in honey bee queens (Apis mellifera) ]]> https://biorxiv.org/content/10.1101/2020.06.29.178913v1?rss=1 McAfee, A. Chapman, A. Pettis, J. Foster, L. Tarpy, D. R. 2020-06-30 doi:10.1101/2020.06.29.178913 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ Evolution of a sex megachromosome ]]> https://biorxiv.org/content/10.1101/2020.07.02.182808v1?rss=1 Conte, M. A. Clark, F. B. Roberts, R. B. Xu, L. Tao, W. Zhou, Q. Wang, D. Kocher, T. D. 2020-07-03 doi:10.1101/2020.07.02.182808 Cold Spring Harbor Laboratory Press 2020-07-03 <![CDATA[ Babesia bovis Rad51 ortholog influences switching of ves genes but is not essential for segmental gene conversion in antigenic variation ]]> https://biorxiv.org/content/10.1101/2020.07.06.189316v1?rss=1 Mack, E. A. Tagliamonte, M. S. Xiao, Y.-P. Quesada, S. Allred, D. R. 2020-07-06 doi:10.1101/2020.07.06.189316 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ MATHEMATICAL MODELING OF RETINAL DEGENERATION: AEROBIC GLYCOLYSIS IN A SINGLE CONE ]]> https://biorxiv.org/content/10.1101/2020.07.06.190470v1?rss=1 Camacho, E. Dobrovera, A. Larripa, K. Radulescu, A. Schmidt, D. Trejo, I. 2020-07-07 doi:10.1101/2020.07.06.190470 Cold Spring Harbor Laboratory Press 2020-07-07 <![CDATA[ Ultra-accurate Microbial Amplicon Sequencing with Synthetic Long Reads ]]> https://biorxiv.org/content/10.1101/2020.07.07.192286v1?rss=1 Callahan, B. J. Grinevich, D. Thakur, S. Balamotis, M. A. Yehezkel, T. B. 2020-07-07 doi:10.1101/2020.07.07.192286 Cold Spring Harbor Laboratory Press 2020-07-07 <![CDATA[ Using Metacognitive Strategies to Improve Academic Performance in Biochemistry ]]> https://biorxiv.org/content/10.1101/2020.07.08.193649v1?rss=1 Heather B. Miller Melissa C. Srougi 2020-07-09 doi:10.1101/2020.07.08.193649 Cold Spring Harbor Laboratory Press 2020-07-09 <![CDATA[ Ungulate Responses to Unmanned Aerial Vehicles Flying at Different Altitudes in Africas Arid Savanna ]]> https://biorxiv.org/content/10.1101/2020.07.14.202093v1?rss=1 van Vuuren, M. van Vuuren, R. Silverberg, L. Manning, J. Pacifici, K. Dorgeloh, W. Campbell, J. 2020-07-14 doi:10.1101/2020.07.14.202093 Cold Spring Harbor Laboratory Press 2020-07-14 <![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[ Exposure to a mixture of BMAA and MCLR synergistically modulates behavior in larval zebrafish while exacerbating molecular changes related to neurodegeneration. ]]> https://biorxiv.org/content/10.1101/2020.07.15.205617v1?rss=1 Martin, R. M. Bereman, M. S. Marsden, K. C. 2020-07-15 doi:10.1101/2020.07.15.205617 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ Discovery of membrane-permeating cyclic peptides via mRNA display ]]> https://biorxiv.org/content/10.1101/2020.07.20.212142v1?rss=1 Bowen, J. D. Schloop, A. E. Reeves, G. T. Menegatti, S. Rao, B. M. 2020-07-21 doi:10.1101/2020.07.20.212142 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Centennial clonal stability of asexual Daphnia in Greenland lakes despite climate variability ]]> https://biorxiv.org/content/10.1101/2020.07.22.208553v1?rss=1 Dane, M. Anderson, N. J. Osburn, C. L. Colbourne, J. K. Frisch, D. 2020-07-24 doi:10.1101/2020.07.22.208553 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Decadal changes in fire frequencies shift tree communities and functional traits ]]> https://biorxiv.org/content/10.1101/2020.07.22.216226v1?rss=1 Pellegrini, A. Refsland, T. Averill, C. Terrer, C. Staver, C. Brockway, D. Caprio, A. Clatterbuck, W. Coetsee, C. Haywood, J. Hobbie, S. Hoffmann, W. Kush, J. Lewis, T. Moser, W. K. Overby, S. Patterson, W. Peay, K. G. Reich, P. Ryan, C. Sword, M. Scharenbroch, B. Schoennagel, T. Smith, G. Stephan, K. Swanston, C. Turner, M. Varner, M. Jackson, R. B. 2020-07-24 doi:10.1101/2020.07.22.216226 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Inferring the genetic basis of sex determination from the genome of a dioecious nightshade ]]> https://biorxiv.org/content/10.1101/2020.07.23.218370v1?rss=1 Wu, M. Anderson, G. Hahn, M. W. Moyle, L. C. Guerrero, R. F. 2020-07-24 doi:10.1101/2020.07.23.218370 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Computer vision approach to characterize size and shape phenotypes of horticultural crops using high-throughput imagery ]]> https://biorxiv.org/content/10.1101/2020.07.24.199539v1?rss=1 Haque, S. Lobaton, E. Nelson, N. Yencho, G. C. Pecota, K. V. Mierop, R. Kudenov, M. W. Boyette, M. Williams, C. M. 2020-07-26 doi:10.1101/2020.07.24.199539 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ Protective Plant Immune Responses are Elicited by Bacterial Outer Membrane Vesicles ]]> https://biorxiv.org/content/10.1101/2020.07.24.220160v1?rss=1 McMillan, H. M. Zebell, S. G. Ristaino, J. B. Dong, X. Kuehn, M. 2020-07-24 doi:10.1101/2020.07.24.220160 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ From plants to ants: Fungal modification of leaf lipids for nutrition and communication in the leaf-cutter ant fungal garden ecosystem ]]> https://biorxiv.org/content/10.1101/2020.07.28.224139v1?rss=1 Khadempour, L. Kyle, J. E. Webb-Robertson, B.-J. M. Nicora, C. D. Smith, F. B. Smith, R. D. Lipton, M. S. Currie, C. R. Baker, E. S. Burnum-Johnson, K. E. 2020-07-29 doi:10.1101/2020.07.28.224139 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces ]]> https://biorxiv.org/content/10.1101/2020.07.31.227629v1?rss=1 Wang, L. Josephs, E. Lee, K. Roberts, L. Rellan-Alvarez, R. Ross-Ibarra, J. Hufford, M. B. 2020-08-02 doi:10.1101/2020.07.31.227629 Cold Spring Harbor Laboratory Press 2020-08-02 <![CDATA[ Clostridioides difficile exploits toxin-mediated inflammation to alter the host nutritional landscape and exclude competitors from the gut microbiota ]]> https://biorxiv.org/content/10.1101/2020.08.06.238881v1?rss=1 Fletcher, J. R. Pike, C. M. Parsons, R. J. Rivera, A. M. Foley, M. H. McLaren, M. R. Montgomery, S. A. Theriot, C. M. 2020-08-06 doi:10.1101/2020.08.06.238881 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ Remodeling hydrogen bond interactions results in relaxed specificity of Caspase-3 ]]> https://biorxiv.org/content/10.1101/2020.08.07.241620v1?rss=1 Yao, L. Swartz, P. D. Hamilton, P. Clark, C. 2020-08-07 doi:10.1101/2020.08.07.241620 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ Screening of yeast display libraries of enzymatically-cyclized peptides to discover macrocyclic peptide ligands ]]> https://biorxiv.org/content/10.1101/2020.08.08.242537v1?rss=1 Bowen, J. D. Schneible, J. D. Labar, C. R. Menegatti, S. Rao, B. M. 2020-08-10 doi:10.1101/2020.08.08.242537 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Deeply sequenced infectious clones of key cassava begomovirus isolates from Cameroon ]]> https://biorxiv.org/content/10.1101/2020.08.10.244335v1?rss=1 Hoyer, J. S. Fondong, V. N. Dallas, M. M. Aimone, C. D. Deppong, D. O. Duffy, S. Hanley-Bowdoin, L. 2020-08-10 doi:10.1101/2020.08.10.244335 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Tomato spotted wilt virus benefits its thrips vector by modulating metabolic and plant defense pathways in tomato ]]> https://biorxiv.org/content/10.1101/2020.08.10.244665v1?rss=1 Nachappa, P. Challacombe, J. F. Margolies, D. C. Nechols, J. R. Whitfield, A. E. Rotenberg, D. 2020-08-11 doi:10.1101/2020.08.10.244665 Cold Spring Harbor Laboratory Press 2020-08-11 <![CDATA[ Location, location, location: Feeding site affects aphid performance by altering access and quality of nutrients ]]> https://biorxiv.org/content/10.1101/2020.08.10.244954v1?rss=1 Nalam, V. J. Han, J. Pitt, W. J. Acharya, S. Nachappa, P. 2020-08-11 doi:10.1101/2020.08.10.244954 Cold Spring Harbor Laboratory Press 2020-08-11 <![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[ Ever-increasing viral diversity associated with the red imported fire ant Solenopsis invicta (Formicidae: Hymenoptera) ]]> https://biorxiv.org/content/10.1101/2020.08.11.245274v1?rss=1 Xavier, C. A. D. Allen, M. L. Whitfield, A. E. 2020-08-12 doi:10.1101/2020.08.11.245274 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Genomically Complex Human Angiosarcoma and Canine Hemangiosarcoma Establish Convergent Angiogenic Transcriptional Programs ]]> https://biorxiv.org/content/10.1101/2020.08.11.246777v1?rss=1 Kim, J. H. Megquier, K. J. Thomas, R. Sarver, A. L. Song, J. M. Kim, Y. T. Schulte, A. J. Cheng, N. Linden, M. A. Murugan, P. Oseth, L. Foster, C. L. Elvers, I. Swofford, R. Turner-Maier, J. Karlsson, E. K. Breen, M. Lindblad-Toh, K. Modiano, J. F. 2020-08-12 doi:10.1101/2020.08.11.246777 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Quantitative yeast-yeast two hybrid for discovery and binding affinity estimation of protein-protein interactions ]]> https://biorxiv.org/content/10.1101/2020.08.12.247874v1?rss=1 Bacon, K. Blain, A. Bowen, J. Burroughs, M. McArthur, N. Menegatti, S. Rao, B. M. 2020-08-13 doi:10.1101/2020.08.12.247874 Cold Spring Harbor Laboratory Press 2020-08-13 <![CDATA[ Use of target-displaying magnetized yeast in screening mRNA display peptide libraries to identify ligands ]]> https://biorxiv.org/content/10.1101/2020.08.13.249722v1?rss=1 Bowen, J. D. Bacon, K. B. Reese, H. R. Rao, B. M. Menegatti, S. 2020-08-14 doi:10.1101/2020.08.13.249722 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Transcriptomic and epigenomic dynamics of honey bees in response to lethal IAPV viral infection ]]> https://biorxiv.org/content/10.1101/2020.08.14.251769v1?rss=1 Li-Byarlay, H. Boncristiani, H. Howell, G. Herman, J. Clark, L. Strand, M. Tarpy, D. Rueppell, O. 2020-08-14 doi:10.1101/2020.08.14.251769 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Consensus-based somatic variant-calling method correlates FBXW7 mutations with poor prognosis in canine B-cell lymphoma ]]> https://biorxiv.org/content/10.1101/2020.08.16.250100v1?rss=1 White, M. E. Hayward, J. J. E. Hertafeld, S. R. Castelhano, M. G. Leung, W. Dave, S. Bhinder, B. H. Elemento, O. L. Richards, K. L. Suter, S. E. 2020-08-17 doi:10.1101/2020.08.16.250100 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ Estimating encounter location distributions from animal tracking data ]]> https://biorxiv.org/content/10.1101/2020.08.24.261628v1?rss=1 Noonan, M. J. Martinez-Garcia, R. Davis, G. H. Crofoot, M. C. Kays, R. Hirsch, B. T. Payne, E. Sih, A. Sinn, D. L. Spiegel, O. Fagan, W. F. Fleming, C. H. Calabrese, J. 2020-08-25 doi:10.1101/2020.08.24.261628 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ The recombination landscape and multiple QTL mapping in a Solanum tuberosum cv. 'Atlantic'-derived F1 population ]]> https://biorxiv.org/content/10.1101/2020.08.24.265397v1?rss=1 Da Silva Pereira, G. Mollinari, M. Schumann, M. J. Clough, M. E. Zeng, Z.-B. Yencho, C. 2020-08-24 doi:10.1101/2020.08.24.265397 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Reporting to the Convention on Biology Diversity: How are countries assessing and protecting their genetic diversity? ]]> https://biorxiv.org/content/10.1101/2020.08.28.254672v1?rss=1 Hoban, S. Campbell, C. da Silva, J. Ekblom, R. Funk, W. C. Garner, B. Godoy, J. A. Kershaw, F. MacDonald, A. Mergeay, J. Minter, M. O'Brien, D. Paz-Vinas, I. Pearson, S. K. Perez-Espona, S. Potter, K. Russo, I.-R. Segelbacher, G. Vernesi, C. Hunter, M. 2020-08-31 doi:10.1101/2020.08.28.254672 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Integrated omics networks reveal the temporal signaling events of brassinosteroid response in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2020.09.04.283788v1?rss=1 Clark, N. M. Nolan, T. M. Wang, P. Song, G. Montes, C. Guo, H. Sozzani, R. Yin, Y. Walley, J. W. 2020-09-05 doi:10.1101/2020.09.04.283788 Cold Spring Harbor Laboratory Press 2020-09-05 <![CDATA[ The evolution of thermal performance in native and invasive populations of Mimulus guttatus ]]> https://biorxiv.org/content/10.1101/2020.09.10.291252v1?rss=1 Querns, A. Wooliver, R. Vallejo-Marin, M. Sheth, S. N. 2020-09-11 doi:10.1101/2020.09.10.291252 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ Cellular mechanisms of chick limb bud morphogenesis ]]> https://biorxiv.org/content/10.1101/2020.09.10.292359v1?rss=1 Lesnicar-Pucko, G. Belmonte, J. M. Musy, M. Glazier, J. A. Sharpe, J. A. 2020-09-11 doi:10.1101/2020.09.10.292359 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ TIN2 facilitates TRF1-mediated trans- and cis-interactions on physiologically relevant long telomeric DNA ]]> https://biorxiv.org/content/10.1101/2020.09.12.286559v1?rss=1 Pan, H. Kaur, P. Liu, M. Xu, P. Mahn, C. Barnes, R. Tang, Q. Hao, P. Bhattaram, D. You, C. Piehler, J. Weninger, K. Riehn, R. Smith, S. Opersko, P. L. Wang, H. 2020-09-13 doi:10.1101/2020.09.12.286559 Cold Spring Harbor Laboratory Press 2020-09-13 <![CDATA[ Contrasting impacts of urban and farmland cover on flying insect biomass ]]> https://biorxiv.org/content/10.1101/2020.09.16.299404v1?rss=1 Svenningsen, C. S. Bowler, D. E. Hecker, S. Bladt, J. Grescho, V. van Dam, N. M. Dauber, J. Eichenberg, D. Ejrnaes, R. Flojgaard, C. Frenzel, M. Froslev, T. G. Hansen, A. J. Heilmann-Clausen, J. Huang, Y. Larsen, J. C. Menger, J. Nayan, N. L. B. M. Pedersen, L. B. Richter, A. Dunn, R. R. Tottrup, A. P. Bonn, A. 2020-09-16 doi:10.1101/2020.09.16.299404 Cold Spring Harbor Laboratory Press 2020-09-16 <![CDATA[ Processing variables of direct-write, near-field electrospinning impact size and morphology of gelatin fibers ]]> https://biorxiv.org/content/10.1101/2020.09.17.301804v1?rss=1 Davis, Z. G. Hussain, A. F. Fisher, M. B. 2020-09-19 doi:10.1101/2020.09.17.301804 Cold Spring Harbor Laboratory Press 2020-09-19 <![CDATA[ Microbial metabolites of flavanols in urine are associated with enhanced anti-proliferative activity in bladder cancer cells in vitro ]]> https://biorxiv.org/content/10.1101/2020.09.22.308056v1?rss=1 Griffin, L. E. Kohrt, S. E. Rathore, A. Kay, C. D. Grabowska, M. M. Neilson, A. P. 2020-09-23 doi:10.1101/2020.09.22.308056 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Whole genome comparisons reveal panmixia among fall armyworm (Spodoptera frugiperda) from diverse locations ]]> https://biorxiv.org/content/10.1101/2020.09.25.314005v1?rss=1 80 plant species, but two host strains are recognized based on their association with corn (C-strain) or rice and smaller grasses (R-strain). In this study, the population structure and genetic diversity in 55 S. frugiperda samples from Argentina, Brazil, Kenya, Puerto Rico and the United States (USA) were surveyed to further our understanding of whole genome nuclear diversity. Comparisons at the genomic level suggest panmixia in this population, other than a minor reduction in gene flow between the two overwintering populations in the continental USA that also corresponded to genetically distinct host strains. Two maternal lines were detected from analysis of mitochondrial genomes. We found members from the Eastern Hemisphere interspersed within both continental USA overwintering subpopulations, suggesting multiple individuals were likely introduced to Africa. Comparisons between laboratory-reared and field collected S. frugiperda support similar genomic diversity, validating the experimental use of laboratory strains. Our research is the largest diverse collection of United States S. frugiperda whole genome sequences characterized to date, covering eight continental states and a USA territory (Puerto Rico). The genomic resources presented provide foundational information to understand gene flow at the whole genome level among S. frugiperda populations. ]]> Schlum, K. A. Lamour, K. Placidi De Bortoli, C. Banerjee, R. Emrich, S. J. Meagher, R. Pereira, E. Murua, M. G. Sword, G. A. Tessnow, A. E. Dillon, D. V. Linares Ramirez, A. M. Akutse, K. S. Schmidt-Jeffris, R. Huang, F. Reisig, D. Jurat-Fuentes, J. L. 2020-09-26 doi:10.1101/2020.09.25.314005 Cold Spring Harbor Laboratory Press 2020-09-26 <![CDATA[ Effect of sanitation improvements on soil-transmitted helminth eggs in courtyard soil from rural Bangladesh: Evidence from a cluster-randomized controlled trial ]]> https://biorxiv.org/content/10.1101/2020.09.29.318097v1?rss=1 Kwong, L. Sen, D. Islam, S. Shahriar, S. Benjamin-Chung, J. Arnold, B. F. Hubbard, A. Parvez, S. M. Unicomb, L. Rahman, M. Colford, J. M. Luby, S. P. Ercumen, A. 2020-09-29 doi:10.1101/2020.09.29.318097 Cold Spring Harbor Laboratory Press 2020-09-29 <![CDATA[ Enhanced Anticoagulation Activity of Functional RNA Origami ]]> https://biorxiv.org/content/10.1101/2020.09.29.319590v1?rss=1 Krissanaprasit, A. Key, C. M. Froehlich, K. Pontula, S. Mihalko, E. Dupont, D. M. Andersen, E. S. Kjems, J. Brown, A. C. LaBean, T. H. 2020-10-01 doi:10.1101/2020.09.29.319590 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ An improved experimental pipeline for preparing circular ssDNA viruses for next-generation sequencing ]]> https://biorxiv.org/content/10.1101/2020.09.30.321224v1?rss=1 Aimone, C. D. Hoyer, J. S. Dye, A. E. Deppong, D. O. Duffy, S. Carbone, I. Hanley-Bowdoin, L. 2020-10-01 doi:10.1101/2020.09.30.321224 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Single Cell Analysis Reveals Multi-faceted miR-375 Regulation of the Intestinal Crypt ]]> https://biorxiv.org/content/10.1101/2020.10.01.321612v1?rss=1 Shanahan, M. T. Kanke, M. Singh, A. P. Villanueva, J. W. McNairn, A. J. Oyesola, O. O. Bonfini, A. Hung, Y.-H. Sheahan, B. Bloom, J. C. Cubitt, R. L. Curry, E. G. Pitman, W. A. Rinaldi, V. D. Dekaney, C. M. Ding, S. Peck, B. C. E. Schimenti, J. C. Dow, L. E. Buchon, N. Tait-Wojno, E. D. Sethupathy, P. 2020-10-01 doi:10.1101/2020.10.01.321612 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Leveraging High-Throughput Screening Data and Conditional Generative Adversarial Networks to Advance Predictive Toxicology ]]> https://biorxiv.org/content/10.1101/2020.10.02.322917v1?rss=1 Green, A. J. Mohlenkamp, M. J. Das, J. Chaudhari, M. Truong, L. Tanguay, R. L. Reif, D. M. 2020-10-02 doi:10.1101/2020.10.02.322917 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Genome evolution in an agricultural pest following adoption of transgenic crops ]]> https://biorxiv.org/content/10.1101/2020.10.05.326801v1?rss=1 Fritz, M. L. Hamby, K. A. Taylor, K. DeYonke, A. M. Gould, F. 2020-10-07 doi:10.1101/2020.10.05.326801 Cold Spring Harbor Laboratory Press 2020-10-07 <![CDATA[ Automated tracking of S. pombe spindle elongation dynamics ]]> https://biorxiv.org/content/10.1101/2020.10.09.333765v1?rss=1 Uzsoy, A. S. M. Zareiesfandabadi, P. Jennings, J. Kemper, A. F. Elting, M. W. 2020-10-10 doi:10.1101/2020.10.09.333765 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ Mechanical competition alters the cellular interpretation of an endogenous genetic programme ]]> https://biorxiv.org/content/10.1101/2020.10.15.333963v1?rss=1 Bhide, S. Gombalova, D. Stegmaier, J. Mönke, G. Belmonte, J. M. Leptin, M. 2020-10-15 doi:10.1101/2020.10.15.333963 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ A G protein-coupled receptor-like module regulates Cellulose Synthase secretion from the endomembrane system in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2020.10.20.345868v1?rss=1 McFarlane, H. E. Mutwil-Anderwald, D. Verbancic, J. Picard, K. L. Gookin, T. E. Froehlich, A. Trindade, L. M. Alonso, J. M. Assmann, S. M. Persson, S. 2020-10-21 doi:10.1101/2020.10.20.345868 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ The collapse of the spindle following ablation in S. pombe is mediated by microtubules and the motor protein dynein ]]> https://biorxiv.org/content/10.1101/2020.10.20.347922v1?rss=1 Zareiesfandabadi, P. Elting, M. W. 2020-10-21 doi:10.1101/2020.10.20.347922 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Quantitative trait locus mapping for common scab resistance in a tetraploid potato full-sib population ]]> https://biorxiv.org/content/10.1101/2020.10.24.353557v1?rss=1 0.76). Due to large environmental effect, heritability values were zero for all three traits in MN11, but moderate to high in PA11 and ME12 (0.44~0.79). We identified a single quantitative trait locus (QTL) for lesion index in PA11, ME12 and joint analyses on linkage group 3, explaining 22~30% of the total variation. The identification of QTL haplotypes and candidate genes contributing to disease resistance can support genomics-assisted breeding approaches. ]]> da Silva Pereira, G. Mollinari, M. Qu, X. Thill, C. Zeng, Z.-B. Haynes, K. Yencho, G. C. 2020-10-25 doi:10.1101/2020.10.24.353557 Cold Spring Harbor Laboratory Press 2020-10-25 <![CDATA[ A New Paralog Removal Pipeline Resolves Conflict between RAD-seq and Enrichment ]]> https://biorxiv.org/content/10.1101/2020.10.26.355248v1?rss=1 Zhou, W. Soghigian, J. Xiang, Q. J. 2020-10-27 doi:10.1101/2020.10.26.355248 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Root water gates and not changes in root structure provide new insights into plant physiological responses and adaptations to drought, flooding and salinity ]]> https://biorxiv.org/content/10.1101/2020.10.27.357251v1?rss=1 Domec, J.-C. King, J. S. Carmichael, M. J. Treado Overby, A. Wortemann, R. Smith, W. K. Miao, G. Noormets, A. Johnson, D. M. 2020-10-27 doi:10.1101/2020.10.27.357251 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Mating and starvation modulate feeding and host-seeking responses in female bed bugs, Cimex lectularius ]]> https://biorxiv.org/content/10.1101/2020.10.30.362806v1?rss=1 Saveer, A. M. DeVries, Z. C. Santangelo, R. Schal, C. 2020-11-01 doi:10.1101/2020.10.30.362806 Cold Spring Harbor Laboratory Press 2020-11-01 <![CDATA[ Inducible Directed Evolution of Complex Phenotypes in Bacteria ]]> https://biorxiv.org/content/10.1101/2020.10.30.362871v1?rss=1 5-10kb in length, elimination of genomic hitchhiker mutations, and decoupling of diversification and screening steps. To meet these challenges, we developed Inducible Directed Evolution (IDE), which uses a temperate bacteriophage to package large plasmids and transfer them to naive cells after intracellular mutagenesis. To demonstrate IDE, we evolved a 5-gene pathway from Bacillus licheniformis that accelerates tagatose catabolism in Escherichia coli, resulting in clones with 65% shorter lag times during growth on tagatose after only two rounds of evolution. ]]> Al'Abri, I. S. Haller, D. Crook, N. C. 2020-10-31 doi:10.1101/2020.10.30.362871 Cold Spring Harbor Laboratory Press 2020-10-31 <![CDATA[ Artemin and its cognate receptor, GFRα3, play a function role in osteoarthritis pain ]]> https://biorxiv.org/content/10.1101/2020.11.04.368373v1?rss=1 Minnema, L. Mishra, S. K. Lascelles, B. D. X. 2020-11-06 doi:10.1101/2020.11.04.368373 Cold Spring Harbor Laboratory Press 2020-11-06 <![CDATA[ NASA GeneLab RNA-Seq Consensus Pipeline: Standardized Processing of Short-Read RNA-Seq Data ]]> https://biorxiv.org/content/10.1101/2020.11.06.371724v1?rss=1 Overbey, E. G. Saravia-Butler, A. M. Zhang, Z. Rathi, K. S. Fogle, H. da Silveira, W. A. Barker, R. J. Bass, J. J. Beheshti, A. Berrios, D. C. Blaber, E. A. Cekanaviciute, E. Costa, H. A. Davin, L. B. Fisch, K. M. Gebre, S. G. Geniza, M. Gilbert, R. Gilroy, S. Hardiman, G. Herranz, R. Kidane, Y. H. Kruse, C. P. S. Lee, M. D. Liefeld, T. Lewis, N. G. McDonald, J. T. Meller, R. Mishra, T. Perera, I. Ray, S. Reinsch, S. Rosenthal, S. B. Strong, M. Szewczyk, N. J. Tahimic, C. G. T. Taylor, D. M. Vandenbrink, J. P. Villacampa, A. Weging, S. Wolverton, C. Wya 2020-11-10 doi:10.1101/2020.11.06.371724 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ Sulfate import in Salmonella Typhimurium impacts bacterial aggregation and the neutrophil respiratory burst ]]> https://biorxiv.org/content/10.1101/2020.11.06.372433v1?rss=1 Westerman, T. L. Sheats, M. K. Elfenbein, J. R. 2020-11-08 doi:10.1101/2020.11.06.372433 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ Mixing the Message: Do Dung Beetles (Coleoptera: Scarabaeidae) Affect Dung-Generated Greenhouse Gas Emissions? ]]> https://biorxiv.org/content/10.1101/2020.11.19.389601v1?rss=1 Fowler, F. E. Gillespie, C. J. Denning, S. Hu, S. Watson, W. 2020-11-19 doi:10.1101/2020.11.19.389601 Cold Spring Harbor Laboratory Press 2020-11-19 <![CDATA[ Detecting flying insects using mega-nets and meta-barcoding ]]> https://biorxiv.org/content/10.1101/2020.11.19.389742v1?rss=1 Svenningsen, C. S. Froslev, T. G. Bladt, J. Pedersen, L. B. Larsen, J. C. Ejrnaes, R. S. Flojgaard, C. Hansen, A. J. Heilmann-Clausen, J. Dunn, R. R. Tottrup, A. P. 2020-11-20 doi:10.1101/2020.11.19.389742 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Are fleas highly modified Mecoptera? Phylogenomic resolution of Antliophora (Insecta: Holometabola) ]]> https://biorxiv.org/content/10.1101/2020.11.19.390666v1?rss=1 Meusemann, K. Trautwein, M. Friedrich, F. Beutel, R. Wiegmann, B. M. Donath, A. Podsiadlowski, L. Petersen, M. Niehuis, O. Mayer, C. Bayless, K. Shin, S. Liu, S. Hlinka, O. Minh, B. Q. Kozlov, A. M. Morel, B. Peters, R. Bartel, D. Grove, S. Zhou, X. Misof, B. Yeates, D. 2020-11-20 doi:10.1101/2020.11.19.390666 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Exchange of molecular and cellular information: a hybrid model that integrates stem cell divisions and key regulatory interactions ]]> https://biorxiv.org/content/10.1101/2020.11.30.404426v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@abcd10org.highwire.dtl.DTLVardef@123e110org.highwire.dtl.DTLVardef@8d175dorg.highwire.dtl.DTLVardef@f8f498_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Van den Broeck, L. Spurney, R. Fisher, A. Schwartz, M. Clark, N. Nguyen, T. Madison, I. Gobble, M. Long, T. Sozzani, R. 2020-12-01 doi:10.1101/2020.11.30.404426 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ Neuroprotective mechanisms of red clover and soy isoflavones in Parkinson's disease models ]]> https://biorxiv.org/content/10.1101/2020.12.01.391268v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@14446dcorg.highwire.dtl.DTLVardef@1884a7borg.highwire.dtl.DTLVardef@d1ebaborg.highwire.dtl.DTLVardef@1c744b1_HPS_FORMAT_FIGEXP M_FIG The isoflavone-rich extracts red clover and soy and the individual isoflavones daidzein and equol protect neuronal cultures against environmental and genetic triggers of Parkinsons disease, and rescue motor deficits in rats exposed to the neurotoxin 6-OHDA. C_FIG ]]> de Rus Jacquet, A. Ambaw, A. Tambe, M. A. Timmers, M. Ma, S. Y. Wu, Q.-L. Simon, J. E. McCabe, G. P. Lila, M. A. Shi, R. Rochet, J.-C. 2020-12-02 doi:10.1101/2020.12.01.391268 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Electrical synaptic transmission requires a postsynaptic scaffolding protein ]]> https://biorxiv.org/content/10.1101/2020.12.03.410696v1?rss=1 Lasseigne, A. M. Echeverry, F. A. A. Ijaz, S. Michel, J. C. Martin, E. A. Marsh, A. J. Trujillo, E. Marsden, K. C. Pereda, A. E. Miller, A. C. 2020-12-04 doi:10.1101/2020.12.03.410696 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ A neuroprotective locus modulates ischemic stroke infarction independent of collateral vessel anatomy ]]> https://biorxiv.org/content/10.1101/2020.12.04.411397v1?rss=1 Lee, H. K. Wetzel-Strong, S. E. Aylor, D. L. Marchuk, D. A. 2020-12-04 doi:10.1101/2020.12.04.411397 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ fullsibQTL: an R package for QTL mapping in biparental populations of outcrossing species ]]> https://biorxiv.org/content/10.1101/2020.12.04.412262v1?rss=1 Gazaffi, R. Amadeu, R. R. Mollinari, M. Rosa, J. R. B. F. Taniguti, C. H. Margarido, G. R. A. Garcia, A. A. F. 2020-12-07 doi:10.1101/2020.12.04.412262 Cold Spring Harbor Laboratory Press 2020-12-07 <![CDATA[ Baby makes three: maternal, paternal, and zygotic genetic effects shape larval phenotypic evolution ]]> https://biorxiv.org/content/10.1101/2020.12.10.419838v1?rss=1 Zakas, C. Rockman, M. V. 2020-12-14 doi:10.1101/2020.12.10.419838 Cold Spring Harbor Laboratory Press 2020-12-14 <![CDATA[ Physiological and transcriptomic response of Medicago truncatula to high and low benefit mycorrhizal fungi ]]> https://biorxiv.org/content/10.1101/2020.12.11.421693v1?rss=1 Cope, K. R. Kafle, A. Yakha, J. K. Pfeffer, P. E. Strahan, G. D. Garcia, K. Subramanian, S. Bücking, H. 2020-12-12 doi:10.1101/2020.12.11.421693 Cold Spring Harbor Laboratory Press 2020-12-12 <![CDATA[ Decomposing the sources of SARS-CoV-2 fitness variation in the United States ]]> https://biorxiv.org/content/10.1101/2020.12.14.422739v1?rss=1 Kepler, L. Hamins-Puertolas, M. Rasmussen, D. A. 2020-12-14 doi:10.1101/2020.12.14.422739 Cold Spring Harbor Laboratory Press 2020-12-14 <![CDATA[ Genetic variation for plant growth traits in a common wheat population is dominated by known variants and novel QTL ]]> https://biorxiv.org/content/10.1101/2020.12.16.422696v1?rss=1 DeWitt, N. Guedira, M. Lauer, E. Murphy, J. P. Marshall, D. Mergoum, M. Johnson, J. Holland, J. B. Brown-Guedira, G. 2020-12-16 doi:10.1101/2020.12.16.422696 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ A distant pathway-cross regulation designed with transcription factors and JAZ repressors downregulates the biosynthesis of tobacco alkaloids and specific nitrosamines ]]> https://biorxiv.org/content/10.1101/2020.12.20.423678v1?rss=1 Li, M. He, X. La Hovary, C. Zhu, Y. Dong, Y. Liu, S. Xing, H. Liu, Y. Jie, Y. Ma, D. Yuzuak, S. Xie, D.-Y. 2020-12-21 doi:10.1101/2020.12.20.423678 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ Assessment and comparison of two different methods to extract nucleic acids from individual honey bees ]]> https://biorxiv.org/content/10.1101/2020.12.21.423857v1?rss=1 Swami, R. Ganser, B. Tarpy, D. R. Strand, M. K. Li-Byarlay, H. 2020-12-21 doi:10.1101/2020.12.21.423857 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ Mapping the dynamic transfer functions of epigenome editing ]]> https://biorxiv.org/content/10.1101/2021.01.05.425451v1?rss=1 Lee, J. B. Caywood, L. M. Lo, J. Y. Levering, N. B. Keung, A. J. 2021-01-05 doi:10.1101/2021.01.05.425451 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Sustained IL-15 response signature predicts RhCMV/SIV vaccine efficacy ]]> https://biorxiv.org/content/10.1101/2021.01.11.426199v1?rss=1 Barrenäs, F. Hansen, S. G. Law, L. Driscoll, C. Green, R. R. Smith, E. Chang, J. Golez, I. Urion, T. Peng, X. Whitmore, L. Newhouse, D. Hughes, C. M. Morrow, D. Randall, K. T. Selseth, A. Ford, J. C. Gilbride, R. M. Randall, B. Ainslie, E. Oswald, K. Shoemaker, R. Fast, R. Bosche, W. J. Axthelm, M. K. Fukazawa, Y. Pavlakis, G. N. Felber, B. K. Fourati, S. Sekaly, R.-P. Lifson, J. D. Komorowski, J. Kosmider, E. Shao, J. Song, W. Edlefsen, P. T. Picker, L. J. Gale, M. 2021-01-11 doi:10.1101/2021.01.11.426199 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Cooperative Communication with Humans Evolved to Emerge Early in Dogs ]]> https://biorxiv.org/content/10.1101/2021.01.12.425620v1?rss=1 Salomons, H. Smith, K. Callahan-Beckel, M. Callahan, M. Levy, K. Kennedy, B. S. Bray, E. Gnanadesikan, G. E. Horschler, D. J. Gruen, M. Tan, J. White, P. MacLean, E. Hare, B. 2021-01-12 doi:10.1101/2021.01.12.425620 Cold Spring Harbor Laboratory Press 2021-01-12 <![CDATA[ Analysis of phloem trajectory links tissue maturation to cell specialization. ]]> https://biorxiv.org/content/10.1101/2021.01.18.427084v1?rss=1 Roszak, P. Heo, J.-o. Blob, B. Toyokura, K. de Luis Balaguer, M. A. Lau, W. Hamey, F. K. Cirrone, J. Wang, X. Ursache, R. Tavares, H. Verstaen, K. Wendrich, J. Melnyk, C. W. Shasha, D. Ahnert, S. Saeys, Y. De Rybel, B. Heidstra, R. Scheres, B. Mähönen, A. P. Gottgens, B. Sozzani, R. Birnbaum, K. D. Helariutta, Y. 2021-01-19 doi:10.1101/2021.01.18.427084 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ Thermodynamic and Kinetic Characterization of Protein Conformational Dynamics within a Riemannian Framework ]]> https://biorxiv.org/content/10.1101/2021.01.19.427358v1?rss=1 Goolsby, C. Fakharzdeh, A. Moradi, M. 2021-01-20 doi:10.1101/2021.01.19.427358 Cold Spring Harbor Laboratory Press 2021-01-20 <![CDATA[ A brief report of sleep and circadian rhythm quotas in a population of dog owners in North Carolina, USA ]]> https://biorxiv.org/content/10.1101/2021.01.21.427658v1?rss=1 Patel, U. A. Gruen, M. E. Samson, D. R. 2021-01-22 doi:10.1101/2021.01.21.427658 Cold Spring Harbor Laboratory Press 2021-01-22 <![CDATA[ Teosinte introgression modulates phosphatidylcholine levels and induces early maize flowering time ]]> https://biorxiv.org/content/10.1101/2021.01.25.426574v1?rss=1 Rodriguez-Zapata, F. Barnes, A. C. Blocher-Juarez, K. A. Gates, D. J. Kur, A. Wang, L. Jensen, S. E. Estevez-Palmas, J. M. M. Janzen, G. M. Crow, T. M. Aguilar-Rangel, R. Demesa-Arevalo, E. Skopelitis, T. Perez-Limon, S. Stutts, W. L. Thomson, P. M. Chiu, Y.-C. Jackson, D. Fiehn, O. Runcie, D. Buckler, E. S. Ross-Ibarra, J. Hufford, M. Sawers, R. J. Rellan-Alvarez, R. 2021-01-26 doi:10.1101/2021.01.25.426574 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Bidirectional, unlike unidirectional transport, allows transporting axonal cargos against their concentration gradient ]]> https://biorxiv.org/content/10.1101/2021.01.27.428531v1?rss=1 Kuznetsov, I. A. Kuznetsov, A. V. 2021-01-28 doi:10.1101/2021.01.27.428531 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Doxorubicin Induces Senescence in Intestinal Epithelial Cells ]]> https://biorxiv.org/content/10.1101/2021.01.29.428764v1?rss=1 Biruad, M. Cortes, J. Cray, P. Kunzmann, G. Mohammed, J. Dekaney, C. M. 2021-01-29 doi:10.1101/2021.01.29.428764 Cold Spring Harbor Laboratory Press 2021-01-29 <![CDATA[ Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium ]]> https://biorxiv.org/content/10.1101/2021.01.30.428904v1?rss=1 Sato, Y. Wippler, J. Wentrup, C. Ansorge, R. Sadowski, M. Gruber-Vodicka, H. R. Dubilier, N. Kleiner, M. 2021-01-30 doi:10.1101/2021.01.30.428904 Cold Spring Harbor Laboratory Press 2021-01-30 <![CDATA[ CDSeqR: fast complete deconvolution for gene expression data from bulk tissues ]]> https://biorxiv.org/content/10.1101/2021.01.30.428954v1?rss=1 Kang, K. Huang, C. Li, Y. Umbach, D. M. Li, L. 2021-02-01 doi:10.1101/2021.01.30.428954 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Evolution of the bread wheat D-subgenome and enriching it with diversity from Aegilops tauschii ]]> https://biorxiv.org/content/10.1101/2021.01.31.428788v1?rss=1 Gaurav, K. Arora, S. Silva, P. Sanchez-Martin, J. Horsnell, R. Gao, L. Brar, G. S. Widrig, V. Raupp, J. Singh, N. Wu, S. Kale, S. M. Chinoy, C. Nicholson, P. Quiroz-Chavez, J. Simmonds, J. Hayta, S. Smedley, M. A. Harwood, W. Pearce, S. Gilbert, D. Kangara, N. Gardener, C. Forner-Martinez, M. Liu, J. Yu, G. Boden, S. Pascuccci, A. Ghosh, S. Hafeez, A. N. O'Hara, T. Waites, J. Cheema, J. Steuernagel, B. Patpour, M. Justesen, A. F. Liu, S. Rudd, J. Avni, R. Sharon, A. Steiner, B. Kirana, R. P. Buerstmayr, H. Mehrabi, A. A. Nasyrova, F. Y. Chayut, N. 2021-02-01 doi:10.1101/2021.01.31.428788 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ 13C tracer analysis identifies extensive recycling of endogenous CO2 in vivo ]]> https://biorxiv.org/content/10.1101/2021.02.04.429777v1?rss=1 Duan, L. Cooper, D. E. Scheidemantle, G. Locasale, J. Kirsch, D. G. Liu, X. 2021-02-05 doi:10.1101/2021.02.04.429777 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Next-generation sequencing-based bulked segregant analysis without sequencing the parental genomes ]]> https://biorxiv.org/content/10.1101/2021.02.08.430275v1?rss=1 Zhang, J. Panthee, D. R. 2021-02-10 doi:10.1101/2021.02.08.430275 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Relatively Shorter Muscle Lengths Increase the Metabolic Rate of Cyclic Force Production ]]> https://biorxiv.org/content/10.1101/2021.02.10.430661v1?rss=1 Beck, O. N. Schroeder, J. N. Trejo, L. H. Franz, J. R. Sawicki, G. S. 2021-02-11 doi:10.1101/2021.02.10.430661 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ Genomes of gut bacteria from Nasonia wasps shed light on phylosymbiosis and microbe-assisted hybrid breakdown ]]> https://biorxiv.org/content/10.1101/2021.02.13.431100v1?rss=1 Cross, K. L. Leigh, B. A. Hatmaker, E. A. Mikaelyan, A. Miller, A. K. Bordenstein, S. R. 2021-02-14 doi:10.1101/2021.02.13.431100 Cold Spring Harbor Laboratory Press 2021-02-14 <![CDATA[ Effects of early geometric confinement on the transcriptomic profile of human cerebral organoids ]]> https://biorxiv.org/content/10.1101/2021.02.18.431674v1?rss=1 Sen, D. Voulgaropoulos, A. Keung, A. J. 2021-02-19 doi:10.1101/2021.02.18.431674 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Detailed characterization of the UMAMITs provides insight into their evolution, functional properties as amino acid transporters and role in the plant ]]> https://biorxiv.org/content/10.1101/2021.02.18.431885v1?rss=1 Zhao, C. Pratelli, R. Yu, S. Shelley, B. Collakova, E. Pilot, G. 2021-02-18 doi:10.1101/2021.02.18.431885 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ improv: A flexible software platform for adaptive neuroscience experiments ]]> https://biorxiv.org/content/10.1101/2021.02.22.432006v1?rss=1 Draelos, A. Nikitchenko, M. Sriworarat, C. Sprague, D. Loring, M. D. Pnevmatikakis, E. Giovannucci, A. Naumann, E. A. Pearson, J. M. 2021-02-23 doi:10.1101/2021.02.22.432006 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity ]]> https://biorxiv.org/content/10.1101/2021.02.22.432240v1?rss=1 Fabbri, M. C. Dadousis, C. Tiezzi, F. Maltecca, C. Lozada-Soto, E. Biffani, S. Bozzi, R. 2021-02-22 doi:10.1101/2021.02.22.432240 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ REMY: A platform for the rapid interrogation of epigenome modifications on yeast ]]> https://biorxiv.org/content/10.1101/2021.02.24.432679v1?rss=1 Waldman, A. C. Rao, B. M. Keung, A. J. 2021-02-24 doi:10.1101/2021.02.24.432679 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation ]]> https://biorxiv.org/content/10.1101/2021.02.26.433082v1?rss=1 Thomas, H. Van den Broeck, L. Spurney, R. Sozzani, R. Frank, M. 2021-02-27 doi:10.1101/2021.02.26.433082 Cold Spring Harbor Laboratory Press 2021-02-27 <![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[ Modulation of fatty acid elongation generates sexually dimorphic hydrocarbons and female attractiveness in Blattella germanica (L.) ]]> https://biorxiv.org/content/10.1101/2021.03.04.434003v1?rss=1 Pei, X.-J. Fan, Y.-L. Bai, Y. Bai, T.-T. Schal, C. Zhang, Z.-F. Chen, N. Li, S. Liu, T.-X. 2021-03-05 doi:10.1101/2021.03.04.434003 Cold Spring Harbor Laboratory Press 2021-03-05 <![CDATA[ Simulation of a sudden drop-off in distal dense core vesicle concentration in Drosophila type II motoneuron terminals ]]> https://biorxiv.org/content/10.1101/2021.03.04.434010v1?rss=1 Kuznetsov, I. A. Kuznetsov, A. V. 2021-03-05 doi:10.1101/2021.03.04.434010 Cold Spring Harbor Laboratory Press 2021-03-05 <![CDATA[ Critical Assessment of Metaproteome Investigation (CAMPI): a Multi-Lab Comparison of Established Workflows ]]> https://biorxiv.org/content/10.1101/2021.03.05.433915v1?rss=1 Van Den Bossche, T. Kunath, B. J. Schallert, K. Schäpe, S. S. Abraham, P. E. Armengaud, J. Arntzen, M. O. Bassignani, A. Benndorf, D. Fuchs, S. Giannone, R. J. Griffin, T. J. Hagen, L. H. Halder, R. Henry, C. Hettich, R. L. Heyer, R. Jagtap, P. Jehmlich, N. Jensen, M. Juste, C. Kleiner, M. Langella, O. Lehmann, T. Leith, E. May, P. Mesuere, B. Miotello, G. Peters, S. L. Pible, O. Reichl, U. Renard, B. Y. Schiebenhoefer, H. Scryba, A. Tanca, A. Trappe, K. Trezzi, J.-P. Uzzau, S. Verschaffelt, P. von Bergen, M. Wilmes, P. Wolf, M. Martens, L. Muth, T. 2021-03-06 doi:10.1101/2021.03.05.433915 Cold Spring Harbor Laboratory Press 2021-03-06 <![CDATA[ A New Type of Satellite associated with Cassava Mosaic Begomoviruses ]]> https://biorxiv.org/content/10.1101/2021.03.11.434950v1?rss=1 Aimone, C. D. De Leon, L. Dallas, M. M. Ndunguru, J. Ascencio-Ibanez, J. T. Hanley-Bowdoin, L. 2021-03-11 doi:10.1101/2021.03.11.434950 Cold Spring Harbor Laboratory Press 2021-03-11 <![CDATA[ Understanding the Evolution of Nutritive Taste in Animals: Insights from Biological Stoichiometry and Nutritional Geometry ]]> https://biorxiv.org/content/10.1101/2021.03.11.434999v1?rss=1 Demi, L. M. Taylor, B. W. Reading, B. J. Tordoff, M. G. Dunn, R. R. 2021-03-12 doi:10.1101/2021.03.11.434999 Cold Spring Harbor Laboratory Press 2021-03-12 <![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[ Antagonistic effects of chemical mixtures on the oxidative stress response are silenced by heat stress and reversed under dietary restriction ]]> https://biorxiv.org/content/10.1101/2021.03.17.435857v1?rss=1 Suresh Arulalan, K. Huayta, J. Stallrich, J. W. San-Miguel, A. 2021-03-19 doi:10.1101/2021.03.17.435857 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Two-stage Linked Component Analysis for Joint Decomposition of Multiple Biologically Related Data Sets ]]> https://biorxiv.org/content/10.1101/2021.03.22.435728v1?rss=1 Chen, H. Caffo, B. Stein-O'Brien, G. Liu, J. Langmead, B. Colantuoni, C. Xiao, L. 2021-03-22 doi:10.1101/2021.03.22.435728 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation ]]> https://biorxiv.org/content/10.1101/2021.03.22.436436v1?rss=1 Aimone, C. D. Lavington, E. Hoyer, J. S. Deppong, D. O. Mickelson-Young, L. Jacobson, A. Kennedy, G. G. Carbone, I. Hanley-Bowdoin, L. Duffy, S. 2021-03-22 doi:10.1101/2021.03.22.436436 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Extracellular Matrix Hydrogels Promote Expression of Paxillin, a Muscle-Tendon Junction Marker ]]> https://biorxiv.org/content/10.1101/2021.03.24.436805v1?rss=1 Gaffney, L. S. Fisher, M. B. Freytes, D. O. 2021-03-25 doi:10.1101/2021.03.24.436805 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Demonstration of local adaptation of maize landraces by reciprocal transplantation ]]> https://biorxiv.org/content/10.1101/2021.03.25.437076v1?rss=1 Janzen, G. M. Aguilar-Rangel, M. R. Cintora-Martinez, C. Blöcher-Juarez, K. A. Gonzalez-Segovia, E. Studer, A. J. Runcie, D. E. Flint-Garcia, S. A. Rellan-Alvarez, R. Sawers, R. J. H. Hufford, M. B. 2021-03-26 doi:10.1101/2021.03.25.437076 Cold Spring Harbor Laboratory Press 2021-03-26 <![CDATA[ Ultra-sensitive Protein-SIP to quantify activity and substrate uptake in microbiomes with stable isotopes ]]> https://biorxiv.org/content/10.1101/2021.03.29.437612v1?rss=1 Kleiner, M. Kouris, A. Jensen, M. Liu, Y. McCalder, J. Strous, M. 2021-03-30 doi:10.1101/2021.03.29.437612 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ Evolution of Knockdown Resistance Haplotypes in Response to Pyrethroid Selection in Aedes aegypti ]]> https://biorxiv.org/content/10.1101/2021.04.02.438212v1?rss=1 Baltzegar, J. F. Vella, M. Gunning, C. Vasquez, G. Astete, H. Stell, F. Fisher, M. Scott, T. W. Lenhart, A. Lloyd, A. L. Morrison, A. C. GOULD, F. 2021-04-03 doi:10.1101/2021.04.02.438212 Cold Spring Harbor Laboratory Press 2021-04-03 <![CDATA[ Modeling the role of mortality-based response triggers on the effectiveness of African swine fever control strategies ]]> https://biorxiv.org/content/10.1101/2021.04.05.438400v1?rss=1 Machado, G. Farthing, T. Andraud, M. Lopes, F. P. N. Lanzas, C. 2021-04-06 doi:10.1101/2021.04.05.438400 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Predation by protists influences the temperature response of microbial communities ]]> https://biorxiv.org/content/10.1101/2021.04.08.439073v1?rss=1 Rocca, J. D. Yammine, A. Simonin, M. Gibert, J. 2021-04-11 doi:10.1101/2021.04.08.439073 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ The genome of the poecilogonous annelid Streblospio benedicti ]]> https://biorxiv.org/content/10.1101/2021.04.15.440069v1?rss=1 Zakas, C. Harry, N. D. Scholl, E. H. Rockman, M. V. 2021-04-16 doi:10.1101/2021.04.15.440069 Cold Spring Harbor Laboratory Press 2021-04-16 <![CDATA[ Urban tree deaths from invasive alien forest insects in the United States, 2020-2050 ]]> https://biorxiv.org/content/10.1101/2021.04.24.441210v1?rss=1 6000 communities. C_LIO_LIWe define an EAB high-impact zone spanning 902,500km2, largely within the southern and central US, within which we predict the death of 98.8% of all ash trees. "Mortality hotspot cities" include Milwaukee, WI; Chicago, IL; and New York, NY. C_LIO_LIWe identify Asian wood borers of maple and oak trees as the highest risk future invaders, where a new establishment could cost US$ 4.9B over 30 years. C_LIO_LIPolicy implications: To plan effective mitigation, managers must know which tree species in which communities will be at the greatest risk, as well as the highest-risk insects. We provide the first country-wide, spatial forecast of urban tree mortality due to invasive insect pests. This framework identifies dominant pest insects and spatial impact hotspots, which can provide the basis for spatial prioritization of spread control efforts such as quarantines and biological control release sites. Our results highlight the need for EAB early-detection efforts as far from current infestations as Seattle, WA. Further, these findings produce a list of biotic and spatiotemporal risk factors for future high-impact US urban forest insect pests. C_LI ]]> Hudgins, E. J. Koch, F. H. Ambrose, M. J. Leung, B. 2021-04-26 doi:10.1101/2021.04.24.441210 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Honey bee queen health is unaffected by contact exposure to pesticides commonly found in beeswax ]]> https://biorxiv.org/content/10.1101/2021.04.24.441288v1?rss=1 McAfee, A. Milone, J. P. McDermott, E. Metz, B. Foster, L. Tarpy, D. R. 2021-04-26 doi:10.1101/2021.04.24.441288 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Rcompadre and Rage - two R packages to facilitate the use of the COMPADRE and COMADRE databases and calculation of life history traits from matrix population models ]]> https://biorxiv.org/content/10.1101/2021.04.26.441330v1?rss=1 12,000 individual projection matrices for >1,100 species globally. Although these databases represent an unparalleled resource for researchers, land managers, and educators, the current computational tools available to answer questions with MPMs impose significant barriers to potential COM(P)ADRE database users by requiring advanced knowledge to handle diverse data structures and program custom analysis functions. C_LIO_LITo close this knowledge gap, we present two interrelated R packages designed to (i) facilitate the use of these databases by providing functions to acquire, quality control, and manage both the MPM data contained in COMPADRE and COMADRE, and a users own MPM data (Rcompadre), and (ii) present a range of functions to calculate life history traits from MPMs in support of ecological and evolutionary analyses (Rage). We provide examples to illustrate the use of both. C_LIO_LIRcompadre and Rage will facilitate demographic analyses using MPM data and contribute to the improved replicability of studies using these data. We hope that this new functionality will allow researchers, land managers, and educators to unlock the potential behind the thousands of MPMs and ancillary metadata stored in the COMPADRE and COMADRE matrix databases, and in their own MPM data. C_LI ]]> Jones, O. R. Barks, P. Stott, I. M. James, T. D. Levin, S. C. Petry, W. K. Capdevila, P. Che-Castaldo, J. Jackson, J. Römer, G. Schuette, C. Thomas, C. C. Salguero-Gomez, R. 2021-04-26 doi:10.1101/2021.04.26.441330 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Changes in Cellular Crosstalk between Skeletal Muscle Myoblasts and Bone Osteoblasts with Aging ]]> https://biorxiv.org/content/10.1101/2021.04.26.441458v1?rss=1 Doering, J. A. Britt, C. E. Sawicki, G. S. Cole, J. H. 2021-04-27 doi:10.1101/2021.04.26.441458 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Highly variable fidelity drives symbiont community composition in an obligate symbiosis ]]> https://biorxiv.org/content/10.1101/2021.04.28.441735v1?rss=1 Mankowski, A. Kleiner, M. Erseus, C. Leisch, N. Sato, Y. Volland, J.-M. Hüttel, B. Wentrup, C. Woyke, T. Wippler, J. Dubilier, N. Gruber-Vodicka, H. R. 2021-04-28 doi:10.1101/2021.04.28.441735 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice ]]> https://biorxiv.org/content/10.1101/2021.05.03.442460v1?rss=1 Franchini, E. Beretta, V. M. Ud Din, I. Lacchini, E. Van den Broeck, L. Sozzani, R. Orozco-Arroyo, G. Adam, H. Jouannic, S. Gregis, V. Kater, M. M. 2021-05-03 doi:10.1101/2021.05.03.442460 Cold Spring Harbor Laboratory Press 2021-05-03 <![CDATA[ The maize E3 ligase ZmCER9 specifically targets activated NLRs for degradation ]]> https://biorxiv.org/content/10.1101/2021.05.03.442530v1?rss=1 Karre, S. Kim, S.-B. Selote, D. Khangura, R. Dilkes, B. Johal, G. S. Balint-Kurti, P. 2021-05-04 doi:10.1101/2021.05.03.442530 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Cryptic costs of viral infection in a model social insect ]]> https://biorxiv.org/content/10.1101/2021.05.04.442681v1?rss=1 Chapman, A. Amiri, E. Han, B. McDermott, E. Rueppell, O. Tarpy, D. R. Foster, L. McAfee, A. 2021-05-04 doi:10.1101/2021.05.04.442681 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ From theory to experiment and back again -- Challenges in quantifying a trait-based theory of predator-prey dynamics ]]> https://biorxiv.org/content/10.1101/2021.05.06.442910v1?rss=1 Wootton, K. Curtsdotter, A. Jonsson, T. Banks, H. T. Roslin, T. Bommarco, R. Laubmeier, A. 2021-05-06 doi:10.1101/2021.05.06.442910 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Sex-Specific Function and Morphology of the Anterior Cruciate Ligament During Skeletal Growth in a Porcine Model ]]> https://biorxiv.org/content/10.1101/2021.05.10.442986v1?rss=1 Howe, D. Cone, S. G. Piedrahita, J. A. Collins, B. Fordham, L. A. Griffith, E. H. Spang, J. T. Fisher, M. B. 2021-05-10 doi:10.1101/2021.05.10.442986 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ Transcriptional and Functional Activity of Canine Hemangiosarcoma to Support Hematopoiesis Demonstrate Bone Marrow Nurse Cell Ontogeny ]]> https://biorxiv.org/content/10.1101/2021.05.21.445198v1?rss=1 Kim, J. H. Schulte, A. J. Sarver, A. L. Angelos, M. G. Frantz, A. M. Foster, C. L. O'Brien, T. D. Cornax, I. O'Sullivan, M. G. Cheng, N. Lewellen, M. Oseth, L. Kumar, S. Bullman, S. Pedamallu, C. S. Goyal, S. M. Meyerson, M. Lund, T. C. Alfoldi, J. Lindblad-Toh, K. Breen, M. Dickerson, E. B. Kaufman, D. S. Modiano, J. F. 2021-05-23 doi:10.1101/2021.05.21.445198 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ AURKB/Ipl1 restarts replication forks to recover from replication stress. ]]> https://biorxiv.org/content/10.1101/2021.05.27.446025v1?rss=1 Moran, E. Pfister, K. E. Sathyan, K. M. Vignero, B. Burke, D. J. Stukenberg, T. 2021-05-27 doi:10.1101/2021.05.27.446025 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Feasibility of an Inhalable Ultrasound Contrast Agent to Enhance Airway Imaging ]]> https://biorxiv.org/content/10.1101/2021.05.27.446053v1?rss=1 Clapp, P. W. Durham, P. G. Antinori, J. C. Walmer, R. W. Chlebowski, J. G. Velasco, B. Snow, S. J. Dayton, P. A. Caughey, M. C. 2021-05-27 doi:10.1101/2021.05.27.446053 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Experimental demonstration of tethered gene drive systems for confined population modification or suppression ]]> https://biorxiv.org/content/10.1101/2021.05.29.446308v1?rss=1 Metzloff, M. Yang, E. Dhole, S. Clark, A. G. Messer, P. W. Champer, J. 2021-05-30 doi:10.1101/2021.05.29.446308 Cold Spring Harbor Laboratory Press 2021-05-30 <![CDATA[ High Dimensionality Reduction by Matrix Factorization for Systems Pharmacology ]]> https://biorxiv.org/content/10.1101/2021.05.30.446301v1?rss=1 Mehrpooya, A. Saberi-Movahed, F. Azizizadeh, N. Rezaei-Ravari, M. Eftekhari, M. Tavassoly, I. 2021-05-30 doi:10.1101/2021.05.30.446301 Cold Spring Harbor Laboratory Press 2021-05-30 <![CDATA[ Raman spectroscopy reveals phenotype switches in breast cancer metastasis ]]> https://biorxiv.org/content/10.1101/2021.06.02.446487v1?rss=1 Paidi, S. K. Troncoso, J. R. Harper, M. G. Liu, Z. Nguyen, K. G. Ravindranathan, S. Ivers, J. D. Zaharoff, D. A. Rajaram, N. Barman, I. 2021-06-02 doi:10.1101/2021.06.02.446487 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Comparative phylogenomic analysis reveals evolutionary genomic changes and novel toxin families in endophytic Liberibacter pathogens ]]> https://biorxiv.org/content/10.1101/2021.06.02.446850v1?rss=1 Zhang, D. Tan, Y. Wang, C. Schneider, T. Li, H. de Souza, R. F. Tang, X. Hsieh, T.-F. Wang, X. Li, X. 2021-06-05 doi:10.1101/2021.06.02.446850 Cold Spring Harbor Laboratory Press 2021-06-05 <![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[ 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[ Rapid Characterization of Human Serum Albumin Binding for Per- And Polyfluoroalkyl Substances Using Differential Scanning Fluorimetry ]]> https://biorxiv.org/content/10.1101/2021.06.13.448257v1?rss=1 Jackson, T. W. Scheibly, C. M. Polera, M. E. Belcher, S. M. 2021-06-14 doi:10.1101/2021.06.13.448257 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ Evaluation of RNAlater™ as a field-compatible preservation method for metaproteomic analyses of bacteria-animal symbioses ]]> https://biorxiv.org/content/10.1101/2021.06.16.448770v1?rss=1 Jensen, M. Wippler, J. Kleiner, M. 2021-06-17 doi:10.1101/2021.06.16.448770 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Gut microbiota of ring-tailed lemurs (Lemur catta) vary across natural and captive populations and correlate with environmental microbiota ]]> https://biorxiv.org/content/10.1101/2021.06.27.450077v1?rss=1 Bornbusch, S. L. Greene, L. K. Rahobilalaina, S. Calkins, S. Rothman, R. S. Clarke, T. A. LaFleur, M. Drea, C. M. 2021-06-28 doi:10.1101/2021.06.27.450077 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[ Promoting long-term forest landscape resilience in the Lake Tahoe basin ]]> https://biorxiv.org/content/10.1101/2021.06.29.450434v1?rss=1 Abelson, E. S. Reynolds, K. M. White, A. M. Long, J. W. Maxwell, C. Manley, P. N. 2021-07-01 doi:10.1101/2021.06.29.450434 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ Flavonols and dihydroflavonols inhibit the main protease activity of SARS-CoV-2 and the replication of human coronavirus 229E ]]> https://biorxiv.org/content/10.1101/2021.07.01.450756v1?rss=1 Zhu, Y. Scholle, F. Kisthardt, S. C. Xie, D. 2021-07-02 doi:10.1101/2021.07.01.450756 Cold Spring Harbor Laboratory Press 2021-07-02 <![CDATA[ Population-level inference for home-range areas ]]> https://biorxiv.org/content/10.1101/2021.07.05.451204v1?rss=1 Fleming, C. H. Deznabi, I. Alavi, S. Crofoot, M. C. Hirsch, B. T. Medici, E. P. Noonan, M. J. Kays, R. Fagan, W. F. Sheldon, D. Calabrese, J. M. 2021-07-06 doi:10.1101/2021.07.05.451204 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Legionella pneumophila targets autophagosomes and promotes host autophagy during late infection ]]> https://biorxiv.org/content/10.1101/2021.07.08.451723v1?rss=1 Noll, R. R. Pike, C. M. Lehman, S. S. Williamson, C. Neunuebel, R. 2021-07-09 doi:10.1101/2021.07.08.451723 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Beneficial Lactiplantibacillus plantarum promote Drosophila growth by down-regulating the expression of PGRP-SC1 ]]> https://biorxiv.org/content/10.1101/2021.07.16.452638v1?rss=1 Gallo, M. Vento, J. Joncour, P. Quagliariello, A. Maritan, E. Beisel, C. Martino, M. E. 2021-07-16 doi:10.1101/2021.07.16.452638 Cold Spring Harbor Laboratory Press 2021-07-16 <![CDATA[ Evaluation of sample preservation and storage methods for metaproteomics analysis of intestinal microbiomes ]]> https://biorxiv.org/content/10.1101/2021.07.20.453169v1?rss=1 Mordant, A. Kleiner, M. 2021-07-21 doi:10.1101/2021.07.20.453169 Cold Spring Harbor Laboratory Press 2021-07-21 <![CDATA[ Herbarium specimens reveal herbivory patterns across the genus Cucurbita ]]> https://biorxiv.org/content/10.1101/2021.07.21.452357v1?rss=1 Jenny, L. A. Shapiro, L. R. Davis, C. C. Davies, T. J. Pierce, N. E. Meineke, E. 2021-07-23 doi:10.1101/2021.07.21.452357 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Modelling porcine reproductive and respiratory syndrome virus dynamics to quantify the contribution of multiple modes of transmission: between-farm animal and vehicle movements, farm-to-farm proximity, feed ingredients, and re-break ]]> https://biorxiv.org/content/10.1101/2021.07.26.453902v1?rss=1 Galvis, J. A. Corzo, C. Machado, G. 2021-07-27 doi:10.1101/2021.07.26.453902 Cold Spring Harbor Laboratory Press 2021-07-27 <![CDATA[ Mites alight! Sunflower crop area and pollen supplementation enhance honey bee resistance to Varroa destructor ]]> https://biorxiv.org/content/10.1101/2021.08.04.454914v1?rss=1 Palmer-Young, E. C. Malfi, R. Zhou, Y. Joyce, B. Whitehead, H. Van Wyk, J. I. Baylis, K. Grubbs, K. Lopez, D. Evans, J. D. Irwin, R. E. Adler, L. S. 2021-08-06 doi:10.1101/2021.08.04.454914 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Integration of transcriptomics and network analysis reveals co-expressed genes in Frankliniella occidentalis larval guts that respond to tomato spotted wilt virus infection ]]> https://biorxiv.org/content/10.1101/2021.08.14.456355v1?rss=1 Han, J. Rotenberg, D. 2021-08-15 doi:10.1101/2021.08.14.456355 Cold Spring Harbor Laboratory Press 2021-08-15 <![CDATA[ A Novel Power-Amplified Jumping Behavior in Larval Beetles (Coleoptera: Laemophloeidae) ]]> https://biorxiv.org/content/10.1101/2021.08.17.456653v1?rss=1 Bertone, M. A. Gibson, J. C. Seago, A. E. Yoshida, T. Smith, A. A. 2021-08-17 doi:10.1101/2021.08.17.456653 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Single cell based high-throughput Ig and TCR repertoire sequencing analysis in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2021.08.17.456682v1?rss=1 Walsh, E. S. Tollison, T. Brochu, H. Shaw, B. Diveley, K. Chou, H. Law, L. Kirk, A. Gale, M. Peng, X. 2021-08-17 doi:10.1101/2021.08.17.456682 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ brca2-mutant zebrafish exhibit context- and tissue-dependent alterations in cell phenotypes and response to injury ]]> https://biorxiv.org/content/10.1101/2021.08.20.457131v1?rss=1 Kouprianov, V. A. Selmek, A. A. Ferguson, J. L. Mo, X. Shive, H. R. 2021-08-21 doi:10.1101/2021.08.20.457131 Cold Spring Harbor Laboratory Press 2021-08-21 <![CDATA[ Woodsmoke particulates alter expression of antiviral host response genes in human nasal epithelial cells infected with SARS-CoV-2 in a sex-dependent manner ]]> https://biorxiv.org/content/10.1101/2021.08.23.457411v1?rss=1 Brocke, S. A. Billings, G. T. Taft-Benz, S. A. Alexis, N. E. Heise, M. T. Jaspers, I. 2021-08-25 doi:10.1101/2021.08.23.457411 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ Genomic screening of antimicrobial resistance markers in UK and US Campylobacter isolates highlights stability of resistance over an 18 year period ]]> https://biorxiv.org/content/10.1101/2021.08.24.457564v1?rss=1 95% quinolone resistance. This large-scale comparison of AMR prevalence has shown that the prevalence of AMR remains stable for Campylobacter in the UK and the US. This suggests that antimicrobial stewardship and restricted antibiotic usage may help contain further expansion of AMR prevalence in Campylobacter, but are unlikely to reduce it in the short term. ]]> van Vliet, A. H. M. Thakur, S. Prada, J. M. Mehat, J. W. La Ragione, R. 2021-08-24 doi:10.1101/2021.08.24.457564 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ Utilizing Pine Needles to Temporally and Spatially Profile Per- and Polyfluoroalkyl Substances ]]> https://biorxiv.org/content/10.1101/2021.08.24.457570v1?rss=1 Kirkwood, K. I. Fleming, J. Nguyen, H. Reif, D. M. Baker, E. S. Belcher, S. M. 2021-08-26 doi:10.1101/2021.08.24.457570 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ Health assessment of the pink land iguana, Conolophus marthae. ]]> https://biorxiv.org/content/10.1101/2021.08.26.457766v1?rss=1 Lewbart, G. A. Gentile, G. Colosimo, G. Gerber, G. Vera, C. 2021-08-26 doi:10.1101/2021.08.26.457766 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ Drone honey bees (Apis mellifera) are disproportionately sensitive to abiotic stressors despite expressing high levels of stress response proteins ]]> https://biorxiv.org/content/10.1101/2021.08.28.456261v1?rss=1 McAfee, A. Milone, J. P. Metz, B. Tarpy, D. Foster, L. 2021-08-28 doi:10.1101/2021.08.28.456261 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ The polyglutamine amyloid nucleus in living cells is monomeric and has competing dimensions of order ]]> https://biorxiv.org/content/10.1101/2021.08.29.458132v1?rss=1 Kandola, T. Zhang, J. Venkatesan, S. Lerbakken, B. Blanck, J. F. Wu, J. Unruh, J. Berry, P. Lange, J. L. Von Schulze, A. Box, A. Cook, M. Sagui, C. Halfmann, R. 2021-08-31 doi:10.1101/2021.08.29.458132 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ Domestication Reshaped the Genetic Basis of Inbreeding Depression in a Maize Landrace Compared to its Wild Relative, Teosinte ]]> https://biorxiv.org/content/10.1101/2021.09.01.458502v1?rss=1 Holland, J. B. Samayoa, L. F. Olukolu, B. A. Yang, C. J. Chen, Q. Stetter, M. G. York, A. M. Sanchez-Gonzalez, J. d. J. Glaubitz, J. C. Bradbury, P. J. Romay, M. C. Sun, Q. Yang, J. Ross-Ibarra, J. Buckler, E. S. Doebley, J. F. 2021-09-02 doi:10.1101/2021.09.01.458502 Cold Spring Harbor Laboratory Press 2021-09-02 <![CDATA[ Efficient transgenesis and homology-directed gene targeting in monolayers of primary human small intestinal and colonic epithelial stem cells ]]> https://biorxiv.org/content/10.1101/2021.09.08.459297v1?rss=1 Breau, K. A. Ok, M. T. Gomez-Martinez, I. Burclaff, J. Kohn, N. P. Magness, S. T. 2021-09-08 doi:10.1101/2021.09.08.459297 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ Not so local: the population genetics of convergent adaptation in maize and teosinte. ]]> https://biorxiv.org/content/10.1101/2021.09.09.459637v1?rss=1 Tittes, S. Lorant, A. McGinty, S. Doebley, J. F. Holland, J. B. Sanchez-Gonzalez, J. d. J. Seetharam, A. S. Tenaillon, M. I. Ross-Ibarra, J. 2021-09-10 doi:10.1101/2021.09.09.459637 Cold Spring Harbor Laboratory Press 2021-09-10 <![CDATA[ Computation of the mitochondria age distribution along the axon length ]]> https://biorxiv.org/content/10.1101/2021.09.12.459928v1?rss=1 Kuznetsov, I. A. Kuznetsov, A. V. 2021-09-12 doi:10.1101/2021.09.12.459928 Cold Spring Harbor Laboratory Press 2021-09-12 <![CDATA[ A B73 x Palomero Toluqueo mapping population reveals local adaptation in Mexican highland maize ]]> https://biorxiv.org/content/10.1101/2021.09.15.460568v1?rss=1 Perez-Limon, S. Li, M. Cintora-Martinez, G. C. Aguilar-Rangel, M. R. Salazar-Vidal, M. N. Gonzalez-Segovia, E. Blöcher-Juarez, K. A. Guerrero-Zavala, A. Barrales-Gamez, B. Carcano-Macias, J. L. Costich, D. E. Nieto-Sotelo, J. Martinez-De la Vega, O. Simpson, J. Hufford, M. Ross-Ibarra, J. Flint-Garcia, S. Diaz-Garcia, L. Rellan-Alvarez, R. Sawers, R. J. 2021-09-18 doi:10.1101/2021.09.15.460568 Cold Spring Harbor Laboratory Press 2021-09-18 <![CDATA[ Demographic changes of a tropical understory bird in naturally patchy montane habitats in southern India ]]> https://biorxiv.org/content/10.1101/2021.09.17.460862v1?rss=1 Robin, V. V. Hines, J. E. Nichols, J. D. Katti, M. Sinha, A. 2021-09-20 doi:10.1101/2021.09.17.460862 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ A merger between compatible but divergent genomes supports allopolyploidization in the Brassicaceae family ]]> https://biorxiv.org/content/10.1101/2021.09.28.462158v1?rss=1 Shin, H. Park, J. E. Park, H. R. Choi, W. L. Yu, S. H. Koh, W. Kim, S. Soh, H. Y. Waminal, N. E. Belandres, H. R. Lim, J. Y. Yi, G. Ahn, J. H. Kim, J.-S. Kim, Y.-M. Koo, N. Kim, K. Perumal, S. Kang, T. Kim, J. Jang, H. Kang, D. H. Kim, Y. S. Jeong, H.-M. Yang, J. Song, S. Park, S. Kim, J. A. Lim, Y. P. Park, B.-S. Hsieh, T.-F. Yang, T.-J. Choi, D. Kim, H. H. Lee, S.-S. Huh, J. H. 2021-09-28 doi:10.1101/2021.09.28.462158 Cold Spring Harbor Laboratory Press 2021-09-28 <![CDATA[ The exchange of vitamin B1 and its biosynthesis intermediates in synthetic microbial communities shapes the community composition and reveals complexities of nutrient sharing ]]> https://biorxiv.org/content/10.1101/2021.09.29.462401v1?rss=1 Sathe, R. R. M. Paerl, R. W. Hazra, A. B. 2021-09-29 doi:10.1101/2021.09.29.462401 Cold Spring Harbor Laboratory Press 2021-09-29 <![CDATA[ Laminin switches terminal differentiation fate of human trophoblast stem cells under chemically defined culture conditions. ]]> https://biorxiv.org/content/10.1101/2021.09.30.462667v1?rss=1 Karakis, V. McDonald, T. Cordiner, A. Mischler, A. San Miguel, A. Rao, B. M. 2021-10-01 doi:10.1101/2021.09.30.462667 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Genetic basis of body shape variation along the benthic-pelagic axis in cichlid fishes ]]> https://biorxiv.org/content/10.1101/2021.10.02.462884v1?rss=1 975 animals total) along the benthic-pelagic ecomorphological axis to determine the genetic basis of body shape diversification. Using a series of both linear and geometric shape measurements, we identify 55 quantitative trait loci (QTL) that underlie various aspects of body shape variation associated with benthic-pelagic divergence. These QTL are spread throughout the genome, each explain 3.0-7.2% of phenotypic variation, and are largely modular. Further, QTL are distinct both between these two crosses of Lake Malawi cichlids and compared to previously identified QTL for body shape in fishes such as sticklebacks. We find that body shape is controlled by many genes of small effects. In all, we find that convergent benthic and pelagic body phenotypes commonly observed across fish clades are most likely due to distinct genetic and molecular mechanisms. ]]> DeLorenzo, L. Mathews, D. Brandon, A. A. Joglekar, M. Carmona Baez, A. Moore, E. C. Ciccotto, P. J. Roberts, N. B. Roberts, R. B. Powder, K. E. 2021-10-03 doi:10.1101/2021.10.02.462884 Cold Spring Harbor Laboratory Press 2021-10-03 <![CDATA[ A critical assessment of the detailed Aedes aegypti simulation model Skeeter Buster 2 using field experiments of indoor insecticidal control in Iquitos, Peru ]]> https://biorxiv.org/content/10.1101/2021.10.03.462931v1?rss=1 Gunning, C. E. Morrison, A. C. Okamoto, K. W. Scott, T. W. Astete, H. Vasquez, G. M. Gould, F. Lloyd, A. L. 2021-10-04 doi:10.1101/2021.10.03.462931 Cold Spring Harbor Laboratory Press 2021-10-04 <![CDATA[ A proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomics ]]> https://biorxiv.org/content/10.1101/2021.10.05.460818v1?rss=1 Burclaff, J. Bliton, R. J. Breau, K. A. Ok, M. T. Gomez-Martinez, I. Ranek, J. S. Bhatt, A. P. Purvis, J. E. Woosley, J. T. Magness, S. T. 2021-10-06 doi:10.1101/2021.10.05.460818 Cold Spring Harbor Laboratory Press 2021-10-06 <![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[ Polygenic sex determination produces modular sex polymorphism in an African cichlid fish ]]> https://biorxiv.org/content/10.1101/2021.10.09.463756v1?rss=1 Moore, E. C. Ciccotto, P. J. Peterson, E. N. Lamm, M. S. Albertson, R. C. Roberts, R. B. 2021-10-09 doi:10.1101/2021.10.09.463756 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ On the Use of Z-Scores for Fine-Mapping with Related Individuals ]]> https://biorxiv.org/content/10.1101/2021.10.10.463846v1?rss=1 Jiang, J. 2021-10-13 doi:10.1101/2021.10.10.463846 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Phylogenomic analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving the diversifications, with insights into the complex biogeographic history in the Northern Hemisphere ]]> https://biorxiv.org/content/10.1101/2021.10.12.464085v1?rss=1 Liu, B.-B. Ren, C. Kwak, M. Hodel, R. Xu, C. He, J. Zhou, W. Huang, C.-H. Ma, H. Hong, D.-Y. Qian, G.-Z. Wen, J. 2021-10-14 doi:10.1101/2021.10.12.464085 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ Development and Application of Multidimensional Lipid Libraries to Investigate Lipidomic Dysregulation Related to Smoke Inhalation Injury Severity ]]> https://biorxiv.org/content/10.1101/2021.10.13.464246v1?rss=1 Kirkwood, K. I. Christopher, M. W. Burgess, J. L. Littau, S. R. Pratt, B. S. Shulman, N. Tamura, K. MacCoss, M. J. MacLean, B. X. Baker, E. S. 2021-10-15 doi:10.1101/2021.10.13.464246 Cold Spring Harbor Laboratory Press 2021-10-15 <![CDATA[ The cyanotoxin 2,4-DAB enhances mortality and causes behavioral and molecular dysfunctions associated with neurodegeneration in larval zebrafish ]]> https://biorxiv.org/content/10.1101/2021.10.13.464292v1?rss=1 Martin, R. M. Bereman, M. S. Marsden, K. C. 2021-10-15 doi:10.1101/2021.10.13.464292 Cold Spring Harbor Laboratory Press 2021-10-15 <![CDATA[ Super-doses of dietary vitamin D3 intake in aged laying hens illustrates limitation of 24,25-dihydroxycholecalciferol conversion ]]> https://biorxiv.org/content/10.1101/2021.10.14.464328v1?rss=1 Warren, M. F. Pitman, P. M. Hodgson, D. D. Livingston, K. A. 2021-10-15 doi:10.1101/2021.10.14.464328 Cold Spring Harbor Laboratory Press 2021-10-15 <![CDATA[ Survey evaluation of dog owners feeding habits in a household setting and comparison of FDA hygiene protocols on dog bowl bacterial contamination as evaluated by total aerobic cell counts. ]]> https://biorxiv.org/content/10.1101/2021.10.21.465279v1?rss=1 160F) washing decreased TAC (p=0.005) over cold/lukewarm water. In the follow-up survey, 8% of Group A and B respondents reported likely to adhere to protocols long-term. This study suggests a need for pet food handling and dish hygiene guideline education to minimize bacterial contamination of dishes, especially in high-risk households. ]]> Luisana, E. Saker, K. Jaykus, L.-A. Getty, C. 2021-10-21 doi:10.1101/2021.10.21.465279 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ Uterine-specific SIRT1 deficiency confers premature uterine aging and impairs invasion and spacing of blastocyst and stromal cell decidualization in mice. ]]> https://biorxiv.org/content/10.1101/2021.10.25.465671v1?rss=1 Cummings, M. J. Yu, H. Paudel, S. Hu, G. Li, X. Hemberger, M. Wang, X. 2021-10-26 doi:10.1101/2021.10.25.465671 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Gestational Cd Exposure in the CD-1 Mouse Sex-Specifically Disrupts Essential Metal Ion Homeostasis ]]> https://biorxiv.org/content/10.1101/2021.11.06.467551v1?rss=1 Jackson, T. W. Baars, O. Belcher, S. M. 2021-11-07 doi:10.1101/2021.11.06.467551 Cold Spring Harbor Laboratory Press 2021-11-07 <![CDATA[ The Stickland fermentation precursor trans-4-hydroxyproline differentially impacts the metabolism of Clostridioides difficile and commensal Clostridia ]]> https://biorxiv.org/content/10.1101/2021.11.12.468462v1?rss=1 Theriot, C. M. Reed, A. D. Fletcher, J. R. Huang, Y. Thanissery, R. Rivera, A. M. Parsons, R. J. Stewart, A. Kountz, D. J. Shen, A. Balskus, E. P. 2021-11-13 doi:10.1101/2021.11.12.468462 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ Polygalacturonase production enhancement by Piriformospora indica from sugar beet pulp under submerged fermentation using surface methodology ]]> https://biorxiv.org/content/10.1101/2021.11.18.469178v1?rss=1 Kiani, S. Fathi Rezaei, P. Jamalzadegan, S. 2021-11-19 doi:10.1101/2021.11.18.469178 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ A deep learning framework for inference of single-trial neural population activity from calcium imaging with sub-frame temporal resolution ]]> https://biorxiv.org/content/10.1101/2021.11.21.469441v1?rss=1 Zhu, F. Grier, H. A. Tandon, R. Cai, C. Giovannucci, A. Kaufman, M. T. Pandarinath, C. 2021-11-21 doi:10.1101/2021.11.21.469441 Cold Spring Harbor Laboratory Press 2021-11-21 <![CDATA[ Uncovering Xenobiotics in the Dark Metabolome using Ion Mobility Spectrometry, Mass Defect Analysis and Machine Learning ]]> https://biorxiv.org/content/10.1101/2021.11.21.469449v1?rss=1 Foster, M. Rainey, M. Watson, C. Dodds, J. N. Fernandez, F. Baker, E. 2021-11-21 doi:10.1101/2021.11.21.469449 Cold Spring Harbor Laboratory Press 2021-11-21 <![CDATA[ Inferring kinetic rate constants from single-molecule FRET trajectories - a blind benchmark of kinetic analysis tools ]]> https://biorxiv.org/content/10.1101/2021.11.23.469671v1?rss=1 Götz, M. Barth, A. Bohr, S. S.- R. Börner, R. Chen, J. Cordes, T. Erie, D. A. Gebhardt, C. Hadzic, M. C. A. S. Hamilton, G. L. Hatzakis, N. S. Hugel, T. Kisley, L. Lamb, D. C. de Lannoy, C. Mahn, C. Dunukara, D. de Ridder, D. Sanabria, H. Schimpf, J. Seidel, C. A. M. Sigel, R. K. O. Sletfjerding, M. B. Thomsen, J. Vollmar, L. Wanninger, S. Weninger, K. R. Xu, P. Schmid, S. 2021-11-23 doi:10.1101/2021.11.23.469671 Cold Spring Harbor Laboratory Press 2021-11-23 <![CDATA[ A target expression threshold dictates invader defense and autoimmunity by CRISPR-Cas13 ]]> https://biorxiv.org/content/10.1101/2021.11.23.469693v1?rss=1 Vialetto, E. Yu, Y. Collins, S. P. Wandera, K. G. Barquist, L. Beisel, C. L. 2021-11-23 doi:10.1101/2021.11.23.469693 Cold Spring Harbor Laboratory Press 2021-11-23 <![CDATA[ Rapid multilocus adaptation of clonal cabbage leaf curl virus populations to Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2021.11.29.468282v1?rss=1 Hoyer, J. S. Wilkins, O. W. Munshi, A. Wiese, E. Dubey, D. Renard, S. Mortensen, K. R. H. Dye, A. E. Carbone, I. Duffy, S. Ascencio-Ibanez, J. T. 2021-12-01 doi:10.1101/2021.11.29.468282 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Donor Age and Time in Culture Affect Dermal Fibroblast Contraction in a Hydrogel Skin Graft Model ]]> https://biorxiv.org/content/10.1101/2021.11.29.469875v1?rss=1 Detwiler, A. Polkoff, K. Gaffney, L. Freytes, D. Piedrahita, J. 2021-11-30 doi:10.1101/2021.11.29.469875 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ Simulation of pedigree vs. fully-informative marker based relationships matrices in a loblolly pine breeding population ]]> https://biorxiv.org/content/10.1101/2021.11.30.468863v1?rss=1 Festa, A. R. Whetten, R. 2021-12-01 doi:10.1101/2021.11.30.468863 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Heterogeneous Tissue Modulus Improved Prediction of Mechanical Behavior in Osteoporotic Vertebral Cancellous Bone ]]> https://biorxiv.org/content/10.1101/2021.11.30.470675v1?rss=1 Cox, J. M. Smith, J. D. van der Meulen, M. C. H. Cole, J. H. 2021-12-01 doi:10.1101/2021.11.30.470675 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Identifying C. elegans Lifespan Mutants by Screening for Early-Onset Protein Aggregation ]]> https://biorxiv.org/content/10.1101/2021.12.14.472506v1?rss=1 Midkiff, D. F. San Miguel, A. 2021-12-16 doi:10.1101/2021.12.14.472506 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Vandetanib Reduces Inflammatory Cytokines and Ameliorates COVID-19 in Infected Mice ]]> https://biorxiv.org/content/10.1101/2021.12.16.472155v1?rss=1 3 log TCID50/mL for HCoV-229E. The in vivo efficacy of vandetanib was assessed in a mouse model of SARS-CoV-2 infection and statistically significantly reduced the levels of IL-6, IL-10, TNF-, and mitigated inflammatory cell infiltrates in the lungs of infected animals but did not reduce viral load. Vandetanib rescued the decreased IFN-1{beta} caused by SARS-CoV-2 infection in mice to levels similar to that in uninfected animals. Our results indicate that the FDA-approved vandetanib is a potential therapeutic candidate for COVID-19 positioned for follow up in clinical trials either alone or in combination with other drugs to address the cytokine storm associated with this viral infection. ]]> Puhl, A. C. Gomes, G. F. Damasceno, S. Fritch, E. J. Levi, J. A. Johnson, N. J. Scholle, F. Premkumar, L. Hurst, B. L. LeeMontiel, F. Veras, F. P. Batah, S. S. Fabro, A. T. Moorman, N. J. Yount, B. Dickmander, R. Baric, R. S. Pearce, K. H. Cunha, F. Alves-Filho, J. C. Cunha, T. Ekins, S. 2021-12-20 doi:10.1101/2021.12.16.472155 Cold Spring Harbor Laboratory Press 2021-12-20 <![CDATA[ Low Frequency Oscillations drive EEG's complexity changes during wakefulness and sleep ]]> https://biorxiv.org/content/10.1101/2021.12.16.472983v1?rss=1 Gonzalez, J. Mateos, D. M. Cavelli, M. Mondino, A. Pascovich, C. Torterolo, P. Rubido, N. 2021-12-17 doi:10.1101/2021.12.16.472983 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ Leveraging TOPMed Imputation Server and Constructing a Cohort-Specific Imputation Reference Panel to Enhance Genotype Imputation among Cystic Fibrosis Patients ]]> https://biorxiv.org/content/10.1101/2021.12.20.473535v1?rss=1 Sun, Q. Liu, W. Rosen, J. D. Huang, L. Pace, R. G. Dang, H. Gallins, P. J. Blue, E. E. Ling, H. Corvol, H. Strug, L. Bamshad, M. J. Gibson, R. L. Pugh, E. W. Blackman, S. M. Cutting, G. O'Neal, W. K. Zhou, Y.-H. Wright, F. A. Knowles, M. R. The Cystic Fibrosis Genome Project (CFGP) Consortium, Wen, J. Li, Y. 2021-12-21 doi:10.1101/2021.12.20.473535 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Endogenous DAF-16 Spatiotemporal Activity Quantitatively Predicts Lifespan Extension Induced by Dietary Restriction ]]> https://biorxiv.org/content/10.1101/2021.12.20.473576v1?rss=1 Huayta, J. San-Miguel, A. 2021-12-21 doi:10.1101/2021.12.20.473576 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ An analytical solution simulating growth of Lewy bodies ]]> https://biorxiv.org/content/10.1101/2021.12.22.473938v1?rss=1 Kuznetsov, I. A. Kuznetsov, A. V. 2021-12-23 doi:10.1101/2021.12.22.473938 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ ROOT PENETRATION INDEX 3, a major quantitative trait locus (QTL) associated with root system penetrability in Arabidopsis. ]]> https://biorxiv.org/content/10.1101/2021.12.23.473296v1?rss=1 Bello Bello, E. Rico Cambron, T. Y. Rellan Alvarez, R. Herrera-Estrella, L. R. 2021-12-23 doi:10.1101/2021.12.23.473296 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Strain dependent structural effects and in vivo efficacy of enterovirus-D68 inhibitors ]]> https://biorxiv.org/content/10.1101/2021.12.24.474126v1?rss=1 Lane, T. R. Fu, J. Sherry, B. Tarbet, B. Hurst, B. Riabova, O. Kazakova, E. Egorova, A. Clarke, P. Leser, J. S. Frost, J. Rudy, M. Tyler, K. Klose, T. Kuhn, R. J. Makarov, V. Ekins, S. 2021-12-27 doi:10.1101/2021.12.24.474126 Cold Spring Harbor Laboratory Press 2021-12-27 <![CDATA[ Identifying challenges and opportunities for histone peptides in protein engineering platforms ]]> https://biorxiv.org/content/10.1101/2021.12.28.474372v1?rss=1 Meanor, J. N. Keung, A. J. Rao, B. M. 2021-12-29 doi:10.1101/2021.12.28.474372 Cold Spring Harbor Laboratory Press 2021-12-29 <![CDATA[ Interspecies transfer of syntenic RAMOSA1 orthologs and promoter cis sequences impacts maize inflorescence architecture ]]> https://biorxiv.org/content/10.1101/2022.01.07.475427v1?rss=1 Strable, J. Unger-Wallace, E. Aragon-Raygoza, A. Briggs, S. Vollbrecht, E. 2022-01-09 doi:10.1101/2022.01.07.475427 Cold Spring Harbor Laboratory Press 2022-01-09 <![CDATA[ Engineered cell differentiation and sexual reproduction in probiotic and mating yeasts ]]> https://biorxiv.org/content/10.1101/2022.01.11.475777v1?rss=1 Jensen, E. D. Deichmann, M. Ma, X. Vilandt, R. U. Schiesaro, G. Rojek, M. B. Lengger, B. Eliasson, L. Vento, J. M. Durmusoglu, D. Hovmand, S. P. Al'Abri, I. Zhang, J. Crook, N. C. Jensen, M. K. 2022-01-12 doi:10.1101/2022.01.11.475777 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Espalier: Efficient tree reconciliation and ARG reconstruction using maximum agreement forests ]]> https://biorxiv.org/content/10.1101/2022.01.17.476639v1?rss=1 Rasmussen, D. A. Guo, F. 2022-01-20 doi:10.1101/2022.01.17.476639 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Controlled adhesion, membrane pinning and vesicle transport by Janus particles ]]> https://biorxiv.org/content/10.1101/2022.01.19.474912v1?rss=1 Ewins, E. J. Han, K. Bharti, B. Robinson, T. Velev, O. D. Dimova, R. 2022-01-20 doi:10.1101/2022.01.19.474912 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Transcriptomics informs design of a planar human enterocyte culture system that reveals metformin enhances fatty acid export ]]> https://biorxiv.org/content/10.1101/2022.01.24.477515v1?rss=1 Gomez-Martinez, I. Bliton, R. J. Breau, K. A. Czerwinski, M. J. Williamson, I. A. Wen, J. Rawls, J. F. Magness, S. T. 2022-01-26 doi:10.1101/2022.01.24.477515 Cold Spring Harbor Laboratory Press 2022-01-26 <![CDATA[ Electroencephalographic Signatures of Canine Cognitive Dysfunction ]]> https://biorxiv.org/content/10.1101/2022.01.28.478033v1?rss=1 Mondino, A. Gutierrez, M. Gonzalez, C. Mateos, D. Torterolo, P. Olby, N. Delucchi, L. 2022-02-01 doi:10.1101/2022.01.28.478033 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Identification of interacting proteins of maize mosaic virus glycoprotein in its vector, Peregrinus maidis. ]]> https://biorxiv.org/content/10.1101/2022.02.01.478665v1?rss=1 Alviar, K. B. Rotenberg, D. Martin, K. M. Whitfield, A. E. 2022-02-01 doi:10.1101/2022.02.01.478665 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ In silico structure-based analysis of the predicted protein-protein interaction of Syntaxin-18, a putative receptor of Peregrinus maidis Ashmead (Hemiptera: Delphacidae) with Maize mosaic virus glycoprotein ]]> https://biorxiv.org/content/10.1101/2022.02.02.478912v1?rss=1 Castrosanto, M. A. Clemente, A. J. N. Whitfield, A. E. Alviar, K. 2022-02-03 doi:10.1101/2022.02.02.478912 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ IgD+ Age-Associated B cells are the progenitors of the main T-independent B cell response to infection that generates protective Ab and can be induced by an inactivated vaccine in the aged ]]> https://biorxiv.org/content/10.1101/2022.02.04.479159v1?rss=1 Kugler-Umana, O. A. Zhang, W. Kuang, Y. Liang, J. Castonguay, C. Tonkonogy, S. L. Marshak-Rothstein, A. Devarajan, P. Swain, S. L. 2022-02-05 doi:10.1101/2022.02.04.479159 Cold Spring Harbor Laboratory Press 2022-02-05 <![CDATA[ Finding mutations in all the wrong places: Prevalence of knock-down resistance F1534S 1 mutations among Aedes albopictus (family: Culicidae, order: Diptera) in North Carolina ]]> https://biorxiv.org/content/10.1101/2022.02.08.479572v1?rss=1 Abernathy, H. A. Hollingsworth, B. D. Giandomenico, D. A. Moser, K. A. Juliano, J. J. Bowman, N. M. George, P. J. Reiskind, M. H. Boyce, R. M. 2022-02-08 doi:10.1101/2022.02.08.479572 Cold Spring Harbor Laboratory Press 2022-02-08 <![CDATA[ Recombination-aware Phylogeographic Inference Using the Structured Coalescent with Ancestral Recombination ]]> https://biorxiv.org/content/10.1101/2022.02.08.479599v1?rss=1 Guo, F. Carbone, I. Rasmussen, D. 2022-02-10 doi:10.1101/2022.02.08.479599 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Population genetic structure of the maize weevil, Sitophilus zeamais, in southern Mexico ]]> https://biorxiv.org/content/10.1101/2022.02.11.480163v1?rss=1 Baltzegar, J. F. Jones, M. S. Willcox, M. Ramsey, J. M. Gould, F. 2022-02-11 doi:10.1101/2022.02.11.480163 Cold Spring Harbor Laboratory Press 2022-02-11 <![CDATA[ Experimental and analytical framework for ''mix-and-read'' assays based on split luciferase ]]> https://biorxiv.org/content/10.1101/2022.02.13.480265v1?rss=1 McArthur, N. Cruz-Teran, C. Thatavarty, A. Reeves, G. T. Rao, B. M. 2022-02-15 doi:10.1101/2022.02.13.480265 Cold Spring Harbor Laboratory Press 2022-02-15 <![CDATA[ Blood Concentrations of Per- and Polyfluoroalkyl Substances are Associated with Lupus-like Autoimmunity in the American Alligator ]]> https://biorxiv.org/content/10.1101/2022.02.15.480575v1?rss=1 Guillete, T. Jackson, T. W. Guillette, M. MCCord, J. Belcher, S. M. 2022-02-18 doi:10.1101/2022.02.15.480575 Cold Spring Harbor Laboratory Press 2022-02-18 <![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[ Beyond energy balance in agrivoltaic food production: Emergent crop traits from color selective solar cells ]]> https://biorxiv.org/content/10.1101/2022.03.10.482833v1?rss=1 Charles, M. Edwards, B. Ravishankar, E. Calero, J. Henry, R. Rech, J. Saravitz, C. You, W. Ade, H. O'Connor, B. T. Sederoff, H. 2022-03-13 doi:10.1101/2022.03.10.482833 Cold Spring Harbor Laboratory Press 2022-03-13 <![CDATA[ Asymmetrical lineage introgression and recombination in populations of Aspergillus flavus: implications for biological control ]]> https://biorxiv.org/content/10.1101/2022.03.12.484001v1?rss=1 Molo, M. S. White, J. B. Cornish, V. Gell, R. M. Baars, O. Singh, R. Carbone, M. A. Isakeit, T. Wise, K. A. Woloshuk, C. P. Bluhm, B. H. Horn, B. W. Heiniger, R. W. Carbone, I. 2022-03-14 doi:10.1101/2022.03.12.484001 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Gene expression noise accelerates the evolution of a biological oscillator ]]> https://biorxiv.org/content/10.1101/2022.03.21.485207v1?rss=1 View larger version (44K): org.highwire.dtl.DTLVardef@fdbc9forg.highwire.dtl.DTLVardef@6a8b08org.highwire.dtl.DTLVardef@cdbc7borg.highwire.dtl.DTLVardef@1116812_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Lin, Y. T. Buchler, N. E. 2022-03-23 doi:10.1101/2022.03.21.485207 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ A Rapid, High Throughput, Viral Infectivity Assay using Automated Brightfield Microscopy with Machine Learning ]]> https://biorxiv.org/content/10.1101/2022.03.23.485512v1?rss=1 Dodkins, R. H. Delaney, J. R. Overton, T. Scholle, F. Frias, A. Crisci, E. Huq, N. Jordan, I. Kimata, J. T. Goldberg, I. G. 2022-03-28 doi:10.1101/2022.03.23.485512 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Distinct bile salt hydrolase substrate preferences dictate C. difficile pathogenesis ]]> https://biorxiv.org/content/10.1101/2022.03.24.485529v1?rss=1 Foley, M. H. Walker, M. E. Stewart, A. K. O'Flaherty, S. Gentry, E. C. Allen, G. Patel, S. Pan, M. Beaty, V. V. Vanhoy, M. E. Dougherty, M. K. McGill, S. K. Gulati, A. Dorrestein, P. Baker, E. S. Redinbo, M. R. Barrangou, R. Theriot, C. M. 2022-03-24 doi:10.1101/2022.03.24.485529 Cold Spring Harbor Laboratory Press 2022-03-24 <![CDATA[ Large-bodied ornithomimosaurs inhabited Appalachia during the Late Cretaceous of North America ]]> https://biorxiv.org/content/10.1101/2022.03.25.485782v1?rss=1 Tsogtbaatar, C. Cullen, T. Phillips, G. Rolke, R. Zanno, L. E. 2022-03-25 doi:10.1101/2022.03.25.485782 Cold Spring Harbor Laboratory Press 2022-03-25 <![CDATA[ Establishing a reproducible approach for the controllable deposition and maintenance of plants cells with 3D bioprinting ]]> https://biorxiv.org/content/10.1101/2022.03.25.485804v1?rss=1 Van den Broeck, L. Schwartz, M. F. Krishnamoorthy, S. Spurney, R. J. Abderamane Tahir, M. Melvin, C. Gobble, M. Peters, R. Muhammad, A. Li, B. Stuiver, M. Horn, T. Sozzani, R. 2022-03-27 doi:10.1101/2022.03.25.485804 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ RNA-targeting CRISPR-Cas13 Provides Broad-spectrum Phage Immunity ]]> https://biorxiv.org/content/10.1101/2022.03.25.485874v1?rss=1 Adler, B. A. Hessler, T. Cress, B. F. Mutalik, V. K. Barrangou, R. K. Banfield, J. Doudna, J. A. 2022-03-26 doi:10.1101/2022.03.25.485874 Cold Spring Harbor Laboratory Press 2022-03-26 <![CDATA[ Microgravity enhances the phenotype of Arabidopsis zigzag-1 and reduces the Wortmannin-induced vacuole fusion in root cells ]]> https://biorxiv.org/content/10.1101/2022.04.01.486597v1?rss=1 Wang, M. Danz, K. Ly, V. Rojas-Pierce, M. 2022-04-02 doi:10.1101/2022.04.01.486597 Cold Spring Harbor Laboratory Press 2022-04-02 <![CDATA[ Toward an optimal contraception dosing strategy ]]> https://biorxiv.org/content/10.1101/2022.04.04.486926v1?rss=1 Gavina, B. L. A. de los Reyes, A. A. Olufsen, M. S. Lenhart, S. Ottesen, J. T. 2022-04-06 doi:10.1101/2022.04.04.486926 Cold Spring Harbor Laboratory Press 2022-04-06 <![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[ Tauroursodeoxycholic acid inhibits Clostridioides difficile toxin induced apoptosis ]]> https://biorxiv.org/content/10.1101/2022.04.13.488266v1?rss=1 Pike, C. M. Tam, J. Melnyk, R. Theriot, C. M. 2022-04-14 doi:10.1101/2022.04.13.488266 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ Mitigating pseudoreplication and bias in resource selection functions with autocorrelation-informed weighting ]]> https://biorxiv.org/content/10.1101/2022.04.21.489059v1?rss=1 Alston, J. M. Fleming, C. H. Kays, R. Streicher, J. P. Downs, C. T. Ramesh, T. Calabrese, J. M. 2022-04-22 doi:10.1101/2022.04.21.489059 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ A highly diverse set of novel immunoglobulin-like transcript (NILT) genes in zebrafish indicates a wide range of functions with complex relationships to mammalian receptors ]]> https://biorxiv.org/content/10.1101/2022.04.21.489081v1?rss=1 Wcisel, D. J. Dornburg, A. McConnell, S. C. Hernandez, K. M. Andrade, J. de Jong, J. L. O. Litman, G. W. Yoder, J. A. 2022-04-22 doi:10.1101/2022.04.21.489081 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ De novo phytosterol synthesis in animals ]]> https://biorxiv.org/content/10.1101/2022.04.22.489198v1?rss=1 Michellod, D. Bien, T. Birgel, D. Jensen, M. Kleiner, M. Fearn, S. Zeidler, C. Gruber-Vodicka, H. R. Dubilier, N. Liebeke, M. 2022-04-22 doi:10.1101/2022.04.22.489198 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Effects of axon branching and asymmetry between the branches on transport, mean age, and age density distributions of mitochondria in neurons ]]> https://biorxiv.org/content/10.1101/2022.04.25.489429v1?rss=1 Kuznetsov, I. A. Kuznetsov, A. V. 2022-04-25 doi:10.1101/2022.04.25.489429 Cold Spring Harbor Laboratory Press 2022-04-25 <![CDATA[ Receptor-like kinases FER and SRK mediate Lotus japonicus freezing tolerance and climate adaptation ]]> https://biorxiv.org/content/10.1101/2022.04.27.489728v1?rss=1 Mustamin, Y. Akyol, T. Y. Gordon, M. Manggabarani, A. M. Isomura, Y. Kawamura, Y. Bamba, M. Williams, C. M. Andersen, S. U. Sato, S. 2022-04-28 doi:10.1101/2022.04.27.489728 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Cocoa Extract Exerts Sex-Specific Effects in an Aggressive Hyperglycemia Model: A Pilot Study ]]> https://biorxiv.org/content/10.1101/2022.04.27.489764v1?rss=1 Racine, K. C. Iglesias-carres, L. Herring, J. Ferruzzi, M. Kay, C. Tessem, J. Neilson, A. P. 2022-04-27 doi:10.1101/2022.04.27.489764 Cold Spring Harbor Laboratory Press 2022-04-27 <![CDATA[ A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. Hillquist) ]]> https://biorxiv.org/content/10.1101/2022.04.28.489789v1?rss=1 Bruna, T. Aryal, R. Dudchenko, O. Sargent, D. J. Mead, D. Buti, M. Cavallini, A. Hytönen, T. Andres, J. Pham, M. Weisz, D. Mascagni, F. Usai, G. Natali, L. Bassil, N. Fernandez, G. E. Lomsadze, A. Armour, M. Olukolu, B. A. Poorten, T. J. Britton, C. Davik, J. Ashrafi, H. Aiden, E. L. Borodovsky, M. Worthington, M. L. 2022-04-30 doi:10.1101/2022.04.28.489789 Cold Spring Harbor Laboratory Press 2022-04-30 <![CDATA[ Plasmodium falciparum genetic diversity in coincident human and mosquito hosts ]]> https://biorxiv.org/content/10.1101/2022.05.05.490756v1?rss=1 Lapp, Z. Obala, A. A. Abel, L. Rasmussen, D. A. Sumner, K. M. Freedman, E. Taylor, S. M. Prudhomme-O'Meara, W. 2022-05-05 doi:10.1101/2022.05.05.490756 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Spontaneously produced lysogenic phages are an important component of the soybean Bradyrhizobium mobilome ]]> https://biorxiv.org/content/10.1101/2022.05.06.490963v1?rss=1 Joglekar, P. Ferrell, B. D. Jarvis, T. Haramoto, K. Place, N. Dums, J. T. Polson, S. W. Wommack, K. E. Fuhrmann, J. J. 2022-05-09 doi:10.1101/2022.05.06.490963 Cold Spring Harbor Laboratory Press 2022-05-09 <![CDATA[ Arabidopsis cell suspension culture that lacks circadian rhythms can be recovered by constitutive ELF3 expression ]]> https://biorxiv.org/content/10.1101/2022.05.12.491735v1?rss=1 Laosuntisuk, K. Desai, J. S. Doherty, C. J. 2022-05-13 doi:10.1101/2022.05.12.491735 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Skewness in bee and flower phenological distributions ]]> https://biorxiv.org/content/10.1101/2022.05.17.492369v1?rss=1 Stemkovski, M. Dickson, R. G. Griffin, S. R. Inouye, B. D. Inouye, D. W. Pardee, G. L. Underwood, N. Irwin, R. E. 2022-05-18 doi:10.1101/2022.05.17.492369 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ Assessing epidemiological parameters and dissemination characteristics of the 2000 and 2001 foot-and-mouth disease outbreaks in Rio Grande do Sul, Brazil ]]> https://biorxiv.org/content/10.1101/2022.05.22.492961v1?rss=1 da Costa, J. M. N. Cobellini, L. G. Cardenas, N. C. Groff, F. H. S. Machado, G. 2022-05-24 doi:10.1101/2022.05.22.492961 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ Social Regulation of Egg Size Plasticity in the Honey Bee is Mediated by Cytoskeleton Organizer Rho1 ]]> https://biorxiv.org/content/10.1101/2022.05.22.492980v1?rss=1 Han, B. Wei, Q. Amiri, E. Hu, H. Lifeng, M. Strand, M. Tarpy, D. R. Xu, S. li, J. Rueppell, O. 2022-05-24 doi:10.1101/2022.05.22.492980 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ A multi-functional small molecule alleviates fracture pain and promotes bone healing ]]> https://biorxiv.org/content/10.1101/2022.05.27.493755v1?rss=1 Shih, Y.-R. V. Newman, H. Hoque, J. Lacelles, B. D. Varghese, S. 2022-05-28 doi:10.1101/2022.05.27.493755 Cold Spring Harbor Laboratory Press 2022-05-28 <![CDATA[ Rescue of the first Alphanucleorhabdovirus entirely from cloned complementary DNA: an efficient vector for systemic expression of foreign genes in maize and insect vectors. ]]> https://biorxiv.org/content/10.1101/2022.05.28.493294v1?rss=1 Kanakala, S. Xavier, C. A. D. Martin, K. M. Tran, H. H. Redinbaugh, M. G. Whitfield, A. E. 2022-05-29 doi:10.1101/2022.05.28.493294 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ Leveraging a natural murine meiotic drive to suppress invasive populations ]]> https://biorxiv.org/content/10.1101/2022.05.31.494104v1?rss=1 Gierus, L. Birand, A. Bunting, M. D. Godahewa, G. I. Piltz, S. G. Oh, K. P. Piaggio, A. J. Threadgill, D. W. Godwin, J. Edwards, O. Cassey, P. Ross, J. V. Prowse, T. A. A. Thomas, P. Q. 2022-05-31 doi:10.1101/2022.05.31.494104 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Understanding spatiotemporal effects of food supplementation on host-parasite interactions using community-based science ]]> https://biorxiv.org/content/10.1101/2022.06.02.494595v1?rss=1 Knutie, S. A. Bertone, M. A. Bahouth, R. Webb, C. Mehta, M. Nahom, M. Barta, R. M. Ghai, S. Balenger, S. L. Butler, M. W. Kennedy, A. C. Schultz, E. M. Taff, C. C. Albery, G. F. 2022-06-04 doi:10.1101/2022.06.02.494595 Cold Spring Harbor Laboratory Press 2022-06-04 <![CDATA[ Genetic architecture of trophic adaptations in cichlid fishes ]]> https://biorxiv.org/content/10.1101/2022.06.03.494688v1?rss=1 DeLorenzo, L. DeBrock, V. Carmona Baez, A. Ciccotto, P. J. Peterson, E. N. Stull, C. Roberts, N. B. Roberts, R. B. Powder, K. E. 2022-06-03 doi:10.1101/2022.06.03.494688 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ A discrete-time survival model for porcine epidemic diarrhea virus ]]> https://biorxiv.org/content/10.1101/2022.06.03.494708v1?rss=1 Trostle, P. Corzo, C. A. Reich, B. J. Machado, G. 2022-06-03 doi:10.1101/2022.06.03.494708 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Quantifying the Human Cost of Global Warming ]]> https://biorxiv.org/content/10.1101/2022.06.07.495131v1?rss=1 500 million) outside this niche. By end-of-century (2080-2100), current policies leading to around 2.7 {degrees}C global warming5-9 could leave one third (21-42% or 2-4 billion) of a future 9.5 billion population outside the niche. Limiting global warming to 1.5 {degrees}C could halve this exposure, reducing it by [~]1.5 billion people. For the two countries with the most people affected - India and Nigeria - reducing global warming from 2.7 to 1.5 {degrees}C results in a >6-fold decrease in the population exposed to unprecedented temperatures, MAT [≥]29 {degrees}C. The lifetime emissions of [~]3.5 global average citizens today (or [~]1.2 average US citizens) expose 1 future person to MAT [≥]29 {degrees}C by end-of-century. That person comes from a place where emissions today are around half of the global average. These results highlight the need for more decisive policy action to limit the human costs and inequities of climate change. ]]> Lenton, T. M. Xu, C. Abrams, J. F. Ghadiali, A. Loriani, S. Sakschewski, B. Zimm, C. Ebi, K. L. Dunn, R. R. Svenning, J.-C. Scheffer, M. 2022-06-09 doi:10.1101/2022.06.07.495131 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Genomic analyses provide new insights into the evolutionary history and reproduction of the Paleogene relictual Kingdonia (Circaeasteraceae, Ranunculales) ]]> https://biorxiv.org/content/10.1101/2022.06.07.495209v1?rss=1 Sun, Y. Zhang, X. Zhang, A. Landis, J. B. Zhang, H. Sun, H. Xiang, J. Wang, H. 2022-06-12 doi:10.1101/2022.06.07.495209 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Modeling foot-and-mouth disease dissemination in Brazil and evaluating the effectiveness of control measures ]]> https://biorxiv.org/content/10.1101/2022.06.14.496159v1?rss=1 Cardenas, N. Lopes, F. Machado, G. 2022-06-16 doi:10.1101/2022.06.14.496159 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ Dynein dysfunction prevents maintenance of high concentrations of slow axonal transport cargos at the axon terminal ]]> https://biorxiv.org/content/10.1101/2022.06.19.496644v1?rss=1 Kuznetsov, I. A. Kuznetsov, A. V. 2022-06-19 doi:10.1101/2022.06.19.496644 Cold Spring Harbor Laboratory Press 2022-06-19 <![CDATA[ Enteric glial cells of the two plexi of the enteric nervous system exhibit phenotypic and functional inter-and intra-heterogeneity ]]> https://biorxiv.org/content/10.1101/2022.06.28.497986v1?rss=1 Touvron, M. Wieland, B. A. Mariant, C. L. Hattenhauer, A. R. Van Landeghem, L. 2022-07-02 doi:10.1101/2022.06.28.497986 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Dehydration and infection elicit increased feeding in the western flower thrips, Frankliniella occidentalis, likely triggered by glycogen depletion ]]> https://biorxiv.org/content/10.1101/2022.07.14.499040v1?rss=1 Bailey, S. T. Kondragunta, A. Choi, H. A. Han, J. Rotenberg, D. Ullmann, D. E. Benoit, J. B. 2022-07-15 doi:10.1101/2022.07.14.499040 Cold Spring Harbor Laboratory Press 2022-07-15 <![CDATA[ Morphological and sensorimotor phenotypes in a zebrafish CHARGE syndrome model are domain-dependent ]]> https://biorxiv.org/content/10.1101/2022.07.14.499979v1?rss=1 Hodorovich, D. R. Lindsley, P. M. Berry, A. A. Burton, D. F. Marsden, K. C. 2022-07-14 doi:10.1101/2022.07.14.499979 Cold Spring Harbor Laboratory Press 2022-07-14 <![CDATA[ Allele-specific expression reveals multiple paths to highland adaptation in maize ]]> https://biorxiv.org/content/10.1101/2022.07.15.500250v1?rss=1 Hu, H. Crow, T. M. Nojoomi, S. Schulz, A. J. Estevez-Palmas, J. M. Hufford, M. Flint-Garcia, S. Sawers, R. Rellan-Alvarez, R. Ross-Ibarra, J. Runcie, D. E. 2022-07-16 doi:10.1101/2022.07.15.500250 Cold Spring Harbor Laboratory Press 2022-07-16 <![CDATA[ Sex-biased proteomic response to tomato spotted wilt virus infection of the salivary glands of Frankliniella occidentalis, the western flower thrips ]]> https://biorxiv.org/content/10.1101/2022.07.18.500439v1?rss=1 Rajarapu, S. P. Ben-Mahmoud, S. Benoit, J. B. Ullman, D. E. Whitfield, A. E. Rotenberg, D. 2022-07-19 doi:10.1101/2022.07.18.500439 Cold Spring Harbor Laboratory Press 2022-07-19 <![CDATA[ Optimal mating of Pinus taeda L. under different scenarios using differential evolution algorithm ]]> https://biorxiv.org/content/10.1101/2022.07.18.500513v1?rss=1 Goda, K. Isik, F. 2022-07-19 doi:10.1101/2022.07.18.500513 Cold Spring Harbor Laboratory Press 2022-07-19 <![CDATA[ Fusing an agent-based model of mosquito population dynamics with a statistical reconstruction of spatio-temporal abundance patterns ]]> https://biorxiv.org/content/10.1101/2022.07.25.501354v1?rss=1 Cavany, S. M. Espana, G. Lloyd, A. L. Vazquez-Prokopec, G. Astete, H. Waller, L. Kitron, U. Scott, T. W. Morrison, A. C. Reiner, R. Perkins, T. A. 2022-07-26 doi:10.1101/2022.07.25.501354 Cold Spring Harbor Laboratory Press 2022-07-26 <![CDATA[ Why slow axonal transport is bidirectional - can axonal transport of tau protein rely only on motor-driven anterograde transport? ]]> https://biorxiv.org/content/10.1101/2022.07.31.502201v1?rss=1 Kuznetsov, I. A. Kuznetsov, A. V. 2022-08-02 doi:10.1101/2022.07.31.502201 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ An open-access T-BAS phylogeny for Emerging Phytophthora species ]]> https://biorxiv.org/content/10.1101/2022.08.06.503053v1?rss=1 Coomber, A. Saville, A. Carbone, I. Ristaino, J. B. 2022-08-07 doi:10.1101/2022.08.06.503053 Cold Spring Harbor Laboratory Press 2022-08-07 <![CDATA[ CCS Predictor 2.0: An Open-Source Jupyter Notebook Tool for Filtering Out False Positives in Metabolomics ]]> https://biorxiv.org/content/10.1101/2022.08.09.503345v1?rss=1 Rainey, M. A. Watson, C. A. Asef, C. K. Foster, M. R. Baker, E. Fernandez, F. M. 2022-08-09 doi:10.1101/2022.08.09.503345 Cold Spring Harbor Laboratory Press 2022-08-09 <![CDATA[ Structural and Dynamic Basis of DNA Capture and Translocation by Mitochondrial Twinkle Helicase ]]> https://biorxiv.org/content/10.1101/2022.08.11.503323v1?rss=1 Li, Z. Kaur, P. Lo, C.-Y. Chopra, N. Smith, J. K. Wang, H. Gao, Y. 2022-08-12 doi:10.1101/2022.08.11.503323 Cold Spring Harbor Laboratory Press 2022-08-12 <![CDATA[ A rapid alkalinization factor-like peptide EaF82 impairs tapetum degeneration during pollen development ]]> https://biorxiv.org/content/10.1101/2022.08.11.503650v1?rss=1 Hung, C.-Y. Kittur, F. Wharton, K. Chen, J. Umstead, M. Burwell, D. Thomas, M. Qi, Q. Zhang, J. Oldham, C. E. Burkey, K. O. Xie, J. J. 2022-08-11 doi:10.1101/2022.08.11.503650 Cold Spring Harbor Laboratory Press 2022-08-11 <![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[ Disease decreases variation in host community structure in an old-field grassland ]]> https://biorxiv.org/content/10.1101/2022.08.15.503989v1?rss=1 Grunberg, R. L. Halliday, F. W. Heckman, R. W. Joyner, B. N. O'Keeffe, K. R. Mitchell, C. E. 2022-08-16 doi:10.1101/2022.08.15.503989 Cold Spring Harbor Laboratory Press 2022-08-16 <![CDATA[ DNA capture and loop extrusion dynamics by cohesin-NIPBL ]]> https://biorxiv.org/content/10.1101/2022.08.18.504320v1?rss=1 Kaur, P. Shi, z. Lu, X. Zhang, H. Finkelstein, I. J. Tao, Y. J. Yu, H. Wang, H. 2022-08-19 doi:10.1101/2022.08.18.504320 Cold Spring Harbor Laboratory Press 2022-08-19 <![CDATA[ Implications of taxonomic bias for microbial differential-abundance analysis ]]> https://biorxiv.org/content/10.1101/2022.08.19.504330v1?rss=1 McLaren, M. R. Nearing, J. T. Willis, A. D. Lloyd, K. G. Callahan, B. J. 2022-08-19 doi:10.1101/2022.08.19.504330 Cold Spring Harbor Laboratory Press 2022-08-19 <![CDATA[ The ecology of cancer prevalence across species: Cancer prevalence is highest in desert species and high trophic levels ]]> https://biorxiv.org/content/10.1101/2022.08.23.504890v1?rss=1 Kapsetaki, S. E. Compton, Z. Rupp, S. M. Garner, M. M. Duke, E. G. Boddy, A. M. Harrison, T. M. Aktipis, A. Maley, C. C. 2022-08-23 doi:10.1101/2022.08.23.504890 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ Screening cell-cell communication in spatial transcriptomics via collective optimal transport ]]> https://biorxiv.org/content/10.1101/2022.08.24.505185v1?rss=1 Cang, Z. Zhao, Y. Almet, A. A. Stabell, A. Ramos, R. Plikus, M. Atwood, S. X. Nie, Q. 2022-08-26 doi:10.1101/2022.08.24.505185 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Vector acquisition and co-inoculation of two plant viruses influences transmission, infection, and replication in new hosts ]]> https://biorxiv.org/content/10.1101/2022.08.27.505557v1?rss=1 McLaughlin, A. A. Hanley-Bowdoin, L. Kennedy, G. G. Jacobson, A. 2022-08-27 doi:10.1101/2022.08.27.505557 Cold Spring Harbor Laboratory Press 2022-08-27 <![CDATA[ Cardiomyocyte alpha-1A adrenergic receptors mitigate post-infarct remodeling and mortality by constraining necroptosis ]]> https://biorxiv.org/content/10.1101/2022.08.29.505687v1?rss=1 Zhang, J. Sandroni, P. B. Huang, W. Oswalt, L. Smith, A. J. Ash, T. Lee, S.-H. Shih, Y.-Y. I. Huang, H.-Y. S. Myagmar, B.-E. Schisler, J. C. Jensen, B. C. 2022-08-29 doi:10.1101/2022.08.29.505687 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Combining phenotypic and genomic data to improve prediction of binary traits ]]> https://biorxiv.org/content/10.1101/2022.08.30.505948v1?rss=1 Jarquin, D. Roy, A. Clarke, B. Ghosal, S. 2022-09-01 doi:10.1101/2022.08.30.505948 Cold Spring Harbor Laboratory Press 2022-09-01 <![CDATA[ Chitosan diet alters the microbiome of adult house flies ]]> https://biorxiv.org/content/10.1101/2022.08.31.502951v1?rss=1 Schaal, H. Choudoir, M. Diwanji, V. Stoffolano, J. DeAngelis, K. M. 2022-08-31 doi:10.1101/2022.08.31.502951 Cold Spring Harbor Laboratory Press 2022-08-31 <![CDATA[ Diversity, Phylogenetic Relationships, And Expression Profiles Of Invertase Inhibitor Genes In Sweetpotato ]]> https://biorxiv.org/content/10.1101/2022.08.31.505262v1?rss=1 Acheampong, S. Sederoff, H. Olukolu, B. A. Asare, A. Yencho, G. 2022-08-31 doi:10.1101/2022.08.31.505262 Cold Spring Harbor Laboratory Press 2022-08-31 <![CDATA[ Estimating the effectiveness of control and eradication actions on African swine fever transmission in commercial swine populations in the United States ]]> https://biorxiv.org/content/10.1101/2022.09.04.506538v1?rss=1 Sykes, A. Galvis, J. A. O'Hara, K. C. Corzo, C. Machado, G. 2022-09-08 doi:10.1101/2022.09.04.506538 Cold Spring Harbor Laboratory Press 2022-09-08 <![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[ A multiplexed plant-animal SNP array for selective breeding and species conservation applications ]]> https://biorxiv.org/content/10.1101/2022.09.07.507051v1?rss=1 Montanari, S. Deng, C. Koot, E. Bassil, N. V. Zurn, J. D. Morrison-Whittle, P. Worthington, M. L. Aryal, R. Ashrafi, H. Pradelles, J. Wellenreuther, M. Chagne, D. 2022-09-11 doi:10.1101/2022.09.07.507051 Cold Spring Harbor Laboratory Press 2022-09-11 <![CDATA[ Extensions of mean-field approximations for environmentally-transmitted pathogen networks ]]> https://biorxiv.org/content/10.1101/2022.09.13.507803v1?rss=1 Davies, K. Lenhart, S. Day, J. Lloyd, A. L. Lanzas, C. 2022-09-13 doi:10.1101/2022.09.13.507803 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Development of the First High-Density Linkage Map in the Maize Weevil, Sitophilus zeamais ]]> https://biorxiv.org/content/10.1101/2022.09.16.508320v1?rss=1 Baltzegar, J. F. Gould, F. 2022-09-19 doi:10.1101/2022.09.16.508320 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Experimental Parameters-Based Monte-Carlo Simulation of Single-Molecule Localization Microscopy of Nuclear Pore Complex to Evaluate Clustering Algorithms ]]> https://biorxiv.org/content/10.1101/2022.09.21.508613v1?rss=1 Yeo, W.-H. Zhang, Y. Neely, A. E. Bao, X. Sun, C. Zhang, H. F. 2022-09-22 doi:10.1101/2022.09.21.508613 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Evolutionary and biomedical implications of sex differences in the primate brain transcriptome ]]> https://biorxiv.org/content/10.1101/2022.10.03.510711v1?rss=1 DeCasien, A. R. Chiou, K. L. Testard, C. Mercer, A. Negron-Del Valle, J. E. Surratt, S. E. B. Gonzalez, O. Stock, M. K. Ruiz-Lambides, A. V. Martinez, M. I. Cayo Biobank Research Unit, Anton, S. Walker, C. S. Sallet, J. Wilson, M. A. Brent, L. J. N. Montague, M. J. N. Sherwood, C. C. Platt, M. L. Higham, J. P. Snyder-Mackler, N. 2022-10-04 doi:10.1101/2022.10.03.510711 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ Maternal patterns of inheritance alter transcript expression in eggs ]]> https://biorxiv.org/content/10.1101/2022.10.10.511534v1?rss=1 Zakas, C. Harry, N. D. 2022-10-11 doi:10.1101/2022.10.10.511534 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ Uterine histotroph and conceptus development. III. Adrenomedullin stimulates proliferation, migration and adhesion of porcine trophectoderm cells via AKT-TSC2-MTOR cell signaling pathway. ]]> https://biorxiv.org/content/10.1101/2022.10.10.511652v1?rss=1 Liu, B. Paudel, S. Flowers, W. L. Piedrahita, J. A. Wang, X. 2022-10-11 doi:10.1101/2022.10.10.511652 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ Computational investigation of the effect of reduced dynein velocity and reduced cargo diffusivity on slow axonal transport ]]> https://biorxiv.org/content/10.1101/2022.10.14.512302v1?rss=1 Kuznetsov, I. A. Kuznetsov, A. V. 2022-10-14 doi:10.1101/2022.10.14.512302 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ A unified model for the dynamics of ATP-independent ultrafast contraction ]]> https://biorxiv.org/content/10.1101/2022.10.14.512304v1?rss=1 Floyd, C. Molines, A. T. Lei, X. Honts, J. E. Chang, F. Elting, M. W. Vaikuntanathan, S. Dinner, A. R. Bhamla, M. S. 2022-10-16 doi:10.1101/2022.10.14.512304 Cold Spring Harbor Laboratory Press 2022-10-16 <![CDATA[ Loss of Linker Histone H1 in the Maternal Genome Influences DEMETER-Mediated Demethylation and Affects the Endosperm DNA Methylation Landscape ]]> https://biorxiv.org/content/10.1101/2022.10.17.512625v1?rss=1 Hsieh, T.-F. Han, Q. Hung, Y.-H. Zhang, C. Bartels, A. Rea, M. Yang, H. Park, C. Zhang, X.-Q. Fsicher, R. L. Xiao, W. 2022-10-20 doi:10.1101/2022.10.17.512625 Cold Spring Harbor Laboratory Press 2022-10-20 <![CDATA[ Dynamics of BMP signaling in the early Drosophila embryo ]]> https://biorxiv.org/content/10.1101/2022.10.20.513072v1?rss=1 Al Asafen, H. Y. Beseli, A. Hiremath, S. V. Reeves, G. T. Williams, C. M. 2022-10-21 doi:10.1101/2022.10.20.513072 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Sign-epistatic centromere drive in panmictic populations ]]> https://biorxiv.org/content/10.1101/2022.10.24.513597v1?rss=1 Brud, E. 2022-10-26 doi:10.1101/2022.10.24.513597 Cold Spring Harbor Laboratory Press 2022-10-26 <![CDATA[ A Model of High-Speed Endovascular Sonothrombolysis with Vortex Ultrasound-Induced Shear Stress to Treat Cerebral Venous Sinus Thrombosis ]]> https://biorxiv.org/content/10.1101/2022.11.02.514936v1?rss=1 Zhang, B. Wu, H. Kim, H. Welch, P. J. Cornett, A. Stocker, G. Nogueira, R. G. Kim, J. Owens, G. Dayton, P. A. Xu, Z. Shi, C. Jiang, X. 2022-11-03 doi:10.1101/2022.11.02.514936 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ Enteric Glial Cell Network Function is Required for Epithelial Barrier Restitution following Intestinal Ischemic Injury in the Early Postnatal Period ]]> https://biorxiv.org/content/10.1101/2022.11.04.514575v1?rss=1 Ziegler, A. L. Erwin, S. J. Caldwell, M. L. Touvron, M. Pridgen, T. A. Magness, S. T. Odle, J. Van Landeghem, L. L. Blikslager, A. T. 2022-11-04 doi:10.1101/2022.11.04.514575 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Structured Joint Decomposition (SJD) identifies conserved molecular dynamics across collections of biologically related multi-omics data matrices ]]> https://biorxiv.org/content/10.1101/2022.11.07.515489v1?rss=1 Chen, H. Liu, J. Sonthalia, S. Stein-OBrien, G. Xiao, L. Caffo, B. Colantuoni, C. 2022-11-08 doi:10.1101/2022.11.07.515489 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ A compendium of genetic regulatory effects across pig tissues ]]> https://biorxiv.org/content/10.1101/2022.11.11.516073v1?rss=1 Jinyan, T. Gao, Y. Yin, H. Bai, Z. Liu, S. Zeng, H. Bai, L. Cai, Z. Zhao, B. Li, X. Xu, Z. Lin, Q. Pan, Z. Yang, W. Yu, X. Guan, D. Hou, Y. Keel, B. N. Rohrer, G. A. Lindholm-Perry, A. K. Oliver, W. T. Ballester, M. Crespo-Piazuelo, D. Quintanilla, R. Canela-Xandri, O. Rawlik, K. Xia, C. Yao, Y. Zhao, Q. Yao, W. Yang, L. Li, H. Zhang, H. Liao, W. Chen, T. Karlskov-Mortensen, P. Fredholm, M. Amills, M. Clop, A. Giuffra, E. Wu, J. Cai, X. Diao, S. Pan, X. Wei, C. Li, J. Cheng, H. Wang, S. Su, G. Sahana, G. Lund, M. S. Dekkers, J. C. M. Kramer, 2022-11-11 doi:10.1101/2022.11.11.516073 Cold Spring Harbor Laboratory Press 2022-11-11 <![CDATA[ Degenerative changes are associated with severity of anterior cruciate ligament injury within the skeletally immature joint ]]> https://biorxiv.org/content/10.1101/2022.11.12.516262v1?rss=1 Howe, D. Thompson, J. D. Teeter, S. D. Barlow, O. Griffith, E. H. Schnabel, L. V. Spang, J. T. Fisher, M. B. 2022-11-13 doi:10.1101/2022.11.12.516262 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Developing best practices for genotyping-by-sequencing analysis using linkage maps as benchmarks ]]> https://biorxiv.org/content/10.1101/2022.11.24.517847v1?rss=1 Taniguti, C. H. Taniguti, L. M. Amadeu, R. R. Mollinari, M. Pereira, G. d. S. Riera-Lizarazu, O. Lau, J. Byrne, D. Gesteira, G. d. S. Oliveira, T. d. P. Ferreira, G. C. Garcia, A. A. F. 2022-11-25 doi:10.1101/2022.11.24.517847 Cold Spring Harbor Laboratory Press 2022-11-25 <![CDATA[ Assortative mating and mate-choice contributes to a developmental dimorphism in Streblospio benedicti ]]> https://biorxiv.org/content/10.1101/2022.11.27.518082v1?rss=1 Ruskie, E. L. Zakas, C. 2022-11-28 doi:10.1101/2022.11.27.518082 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ Long-term fertilization modifies the composition of slow-growing oligotrophs more than fast-growing copiotrophs in a nutrient poor coastal plain wetland ]]> https://biorxiv.org/content/10.1101/2022.11.28.518233v1?rss=1 Walker, A. Stephens, D. Garcia, A. Peralta, A. L. 2022-11-29 doi:10.1101/2022.11.28.518233 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ Non-redundant dimethyl sulfoxide reductases influence Salmonella enterica serotype Typhimurium anaerobic growth and virulence ]]> https://biorxiv.org/content/10.1101/2022.11.29.517730v1?rss=1 Cruz, E. Haeberle, A. L. Westerman, T. L. Durham, M. E. Suyemoto, M. M. Knodler, L. A. Elfenbein, J. R. 2022-11-30 doi:10.1101/2022.11.29.517730 Cold Spring Harbor Laboratory Press 2022-11-30 <![CDATA[ Assessing the Nucleotide-Level Impact of Spaceflight Stress using RNA-Sequencing Data ]]> https://biorxiv.org/content/10.1101/2022.12.01.518235v1?rss=1 Knight, M. S. Nielsen, D. M. Doherty, C. J. 2022-12-02 doi:10.1101/2022.12.01.518235 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ Effect of mitochondrial circulation on mitochondrial age density distribution ]]> https://biorxiv.org/content/10.1101/2022.12.01.518783v1?rss=1 Kuznetsov, I. A. Kuznetsov, A. V. 2022-12-03 doi:10.1101/2022.12.01.518783 Cold Spring Harbor Laboratory Press 2022-12-03 <![CDATA[ Parameter estimation and identifiability analysis for a bivalent analyte model of monoclonal antibody-antigen binding ]]> https://biorxiv.org/content/10.1101/2022.12.05.519088v1?rss=1 Nguyen, K. Li, K. Flores, K. Tomaras, G. Dennison, S. M. McCarthy, J. 2022-12-08 doi:10.1101/2022.12.05.519088 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ Integrated Single-Dose Kinome Profiling Data is Predictive of Cancer Cell Line Sensitivity to Kinase Inhibitors ]]> https://biorxiv.org/content/10.1101/2022.12.06.519165v1?rss=1 Joisa, C. U. Chen, K. A. Berginski, M. E. Golitz, B. T. Jenner, M. R. Loeza, S. G. H. Yeh, J. J. Gomez, S. M. 2022-12-10 doi:10.1101/2022.12.06.519165 Cold Spring Harbor Laboratory Press 2022-12-10 <![CDATA[ COMBINe: Automated Detection and Classification of Neurons and Astrocytes in Tissue Cleared Mouse Brains ]]> https://biorxiv.org/content/10.1101/2022.12.06.519291v1?rss=1 Cai, Y. Zhang, X. Li, C. Ghashghaei, T. Greenbaum, A. 2022-12-06 doi:10.1101/2022.12.06.519291 Cold Spring Harbor Laboratory Press 2022-12-06 <![CDATA[ Transgenic porcine model reveals two roles for LGR5 during lung development and homeostasis ]]> https://biorxiv.org/content/10.1101/2022.12.09.516617v1?rss=1 Polkoff, K. Gupta, N. K. Murphy, Y. Lampe, R. Chung, J. Carter, A. Simon, J. M. Moatti, A. Kadur Lakshminarasimha Murthy, P. Gleason, K. Edwards, L. Greenbaum, A. Tata, A. Tata, P. R. Piedrahita, J. A. 2022-12-11 doi:10.1101/2022.12.09.516617 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Transport of ATP by diffusion is sufficient to provide high ATP concentration in presynaptic boutons lacking mitochondria ]]> https://biorxiv.org/content/10.1101/2022.12.09.519840v1?rss=1 Kuznetsov, I. A. Kuznetsov, A. V. 2022-12-10 doi:10.1101/2022.12.09.519840 Cold Spring Harbor Laboratory Press 2022-12-10 <![CDATA[ Bulk and Mosaic Deletions of Egfr Reveal Regionally Defined Gliogenesis in the Developing Mouse Forebrain ]]> https://biorxiv.org/content/10.1101/2022.12.10.519926v1?rss=1 Zhang, X. Xiao, G. Johnson, C. A. Cai, Y. Horowitz, Z. Mennicke, C. Coffey, R. Haider, M. Threadgill, D. W. Eliscu, R. Oldham, M. C. Greenbaum, A. C. Ghashghaei, H. T. 2022-12-11 doi:10.1101/2022.12.10.519926 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Genome and Genetic Engineering of the House Cricket (Acheta domesticus) Applications for Sustainable Agriculture ]]> https://biorxiv.org/content/10.1101/2022.12.14.520443v1?rss=1 Dossey, A. T. Oppert, B. Chu, F.-C. Lorenzen, M. D. Scheffler, B. Simpson, S. Koren, S. Johnston, J. S. Kataoka, K. Ide, K. 2022-12-16 doi:10.1101/2022.12.14.520443 Cold Spring Harbor Laboratory Press 2022-12-16 <![CDATA[ A chromosome level genome assembly of longnose gar, Lepisosteus osseus ]]> https://biorxiv.org/content/10.1101/2022.12.21.521478v1?rss=1 Mallik, R. Carlson, K. Wcisel, D. J. Fisk, M. Yoder, J. A. Dornburg, A. 2022-12-22 doi:10.1101/2022.12.21.521478 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Uncovering Changes in Microbiome Profiles Across Commercial and Backyard Poultry Farming Systems ]]> https://biorxiv.org/content/10.1101/2022.12.22.521647v1?rss=1 Muyyarikkandy, M. S. Parzygnat, J. Thakur, S. 2022-12-23 doi:10.1101/2022.12.22.521647 Cold Spring Harbor Laboratory Press 2022-12-23 <![CDATA[ Pushing the envelope: force balance in fission yeast closed mitosis ]]> https://biorxiv.org/content/10.1101/2022.12.28.522145v1?rss=1 Begley, M. A. Pagan Medina, C. Zareiesfandabadi, P. Rapp, M. B. Elting, M. W. 2022-12-29 doi:10.1101/2022.12.28.522145 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ Improving Therapeutic Protein Secretion in the Probiotic Yeast Saccharomyces boulardii using a Multifactorial Engineering Approach ]]> https://biorxiv.org/content/10.1101/2022.12.30.522352v1?rss=1 10-fold over wild-type Sb. Overall, this work systematically explores a broad collection of engineering strategies to improve protein secretion in Sb and highlights the ability of proteomics to highlight under-explored mediators of this process. In doing so, we created a set of probiotic strains that are capable of delivering a wide range of protein titers and therefore furthers the ability of Sb to deliver therapeutics to the gut and other settings to which it is adapted. ]]> Durmusoglu, D. Al'Abri, I. Williams, T. Collins, L. B. Martinez, J. L. Crook, N. C. 2022-12-31 doi:10.1101/2022.12.30.522352 Cold Spring Harbor Laboratory Press 2022-12-31 <![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[ Transfer Learning with False Negative Control Improves Polygenic Risk Prediction ]]> https://biorxiv.org/content/10.1101/2023.01.02.522532v1?rss=1 Jeng, X. J. Hu, Y. Tzeng, J.-Y. 2023-01-03 doi:10.1101/2023.01.02.522532 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Metabolic engineering of anthocyanin pathway in Artemisia annua cells does not exclude the expression of artemisinin pathway ]]> https://biorxiv.org/content/10.1101/2023.01.05.522882v1?rss=1 Judd, R. Dong, Y. Sun, X. Zhu, Y. Li, M. Xie, D.-Y. 2023-01-06 doi:10.1101/2023.01.05.522882 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ The probability of edge existence due to node degree: a baseline for network-based predictions ]]> https://biorxiv.org/content/10.1101/2023.01.05.522939v1?rss=1 Zietz, M. Himmelstein, D. S. Kloster, K. Williams, C. Nagle, M. W. Greene, C. S. 2023-01-06 doi:10.1101/2023.01.05.522939 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Hetnet connectivity search provides rapid insights into how two biomedical entities are related ]]> https://biorxiv.org/content/10.1101/2023.01.05.522941v1?rss=1 Himmelstein, D. S. Zietz, M. Rubinetti, V. Kloster, K. Heil, B. J. Alquaddoomi, F. Hu, D. Nicholson, D. N. Hao, Y. Sullivan, B. D. Nagle, M. W. Greene, C. S. 2023-01-07 doi:10.1101/2023.01.05.522941 Cold Spring Harbor Laboratory Press 2023-01-07 <![CDATA[ H2A.X mutants exhibit enhanced DNA demethylation in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2023.01.08.523178v1?rss=1 Frost, J. M. Lee, J. Hsieh, P.-H. Lin, S. J. Min, Y. Bauer, M. Runkel, A. Cho, H.-T. Hsieh, T.-F. Choi, Y. Fischer, R. L. 2023-01-09 doi:10.1101/2023.01.08.523178 Cold Spring Harbor Laboratory Press 2023-01-09 <![CDATA[ Design of 8-mer Peptides that Block Clostridioides difficile Toxin A in Intestinal Cells ]]> https://biorxiv.org/content/10.1101/2023.01.10.523493v1?rss=1 Sarma, S. Catella, C. M. Pedro, E. T. S. Xiao, X. Durmusoglu, D. Menegatti, S. Crook, N. Magness, S. T. Hall, C. 2023-01-12 doi:10.1101/2023.01.10.523493 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ Evolutionarily diverse origins of honey bee deformed wing viruses ]]> https://biorxiv.org/content/10.1101/2023.01.21.525007v1?rss=1 Hasegawa, N. Techer, M. al-Hissnawi, M. Adjlane, N. Antunez, K. Beaurepaire, A. Christmon, K. Delatte, H. Dukku, U. Eliash, N. El-Niweir, M. Esnault, O. Evans, J. Haddad, N. Locke, B. Munoz, I. Noel, G. Panziera, D. Roberts, J. De la Rua, P. Shebl, M. Stanimirovic, Z. Rasmussen, D. Mikheyev, A. 2023-01-21 doi:10.1101/2023.01.21.525007 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ A cathepsin C-like protease post-translationally modifies Toxoplasma gondii secretory proteins for optimal invasion and egress. ]]> https://biorxiv.org/content/10.1101/2023.01.21.525043v1?rss=1 Thornton, L. B. Key, M. Micchelli, C. Stasic, A. J. Kwain, S. Floyd, K. Moreno, S. N. J. Dominy, B. N. Whitehead, D. C. Dou, Z. 2023-01-22 doi:10.1101/2023.01.21.525043 Cold Spring Harbor Laboratory Press 2023-01-22 <![CDATA[ Conformationally Adaptive Dyes Enable Protein-Adaptive Differential Scanning Fluorometry ]]> https://biorxiv.org/content/10.1101/2023.01.23.525251v1?rss=1 Wu, T. S. Yu, J. C. Suresh, A. Gale-Day, Z. J. Alteen, M. G. Woo, A. S. Millbern, Z. Johnson, O. T. Carroll, E. C. Partch, C. L. Fourches, D. Vilnueza, N. R. Vocadlo, D. J. Gestwicki, J. E. 2023-01-24 doi:10.1101/2023.01.23.525251 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ Neo-natal castration leads to subtle differences in porcine anterior cruciate ligament morphology and function in adolescence ]]> https://biorxiv.org/content/10.1101/2023.01.24.524954v1?rss=1 0.05). The barrows had smaller temporal increases in AM bundle percent function than boars, but these data were highly variable. Thus, early and sustained loss in testosterone leads to subtle differences in ACL morphology, but may not influence measures associated with increased injury risk, such as CSA or bundle forces in response to applied loads. ]]> Thompson, J. D. Howe, D. Griffith, E. H. Schnabel, L. V. Fisher, M. B. 2023-01-25 doi:10.1101/2023.01.24.524954 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ TGF-β downregulates antigen processing and presentation genes and MHC I surface expression through a Smad3-dependent mechanism. ]]> https://biorxiv.org/content/10.1101/2023.01.30.526196v1?rss=1 Berglund, A. K. Hinson, A. L. Schnabel, L. V. 2023-02-01 doi:10.1101/2023.01.30.526196 Cold Spring Harbor Laboratory Press 2023-02-01 <![CDATA[ Microtubule competition and cell growth recenter the nucleus after anaphase in fission yeast. ]]> https://biorxiv.org/content/10.1101/2023.01.31.526443v1?rss=1 Bellingham-Johnstun, K. Thorn, A. Belmonte, J. M. Laplante, C. 2023-02-01 doi:10.1101/2023.01.31.526443 Cold Spring Harbor Laboratory Press 2023-02-01 <![CDATA[ An unbiased, automated platform for scoring dopaminergic neurodegeneration in C. elegans ]]> https://biorxiv.org/content/10.1101/2023.02.02.526781v1?rss=1 Clark, A. S. Kalmanson, Z. Morton, K. Hartman, J. Meyer, J. San-Miguel, A. 2023-02-03 doi:10.1101/2023.02.02.526781 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Gardnerella Diversity and Ecology in Pregnancy and Preterm Birth ]]> https://biorxiv.org/content/10.1101/2023.02.03.527032v1?rss=1 Berman, H. L. Goltsman, D. S. A. Anderson, M. Relman, D. A. Callahan, B. J. 2023-02-04 doi:10.1101/2023.02.03.527032 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Insights into substrate coordination and glycosyl transfer of poplar cellulose synthase-8 ]]> https://biorxiv.org/content/10.1101/2023.02.07.527505v1?rss=1 Verma, P. Kwansa, A. L. Ho, R. Yingling, Y. G. Zimmer, J. 2023-02-07 doi:10.1101/2023.02.07.527505 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ Assessing changes in global fire regimes ]]> https://biorxiv.org/content/10.1101/2023.02.07.527551v1?rss=1 Sayedi, S. S. Global group of fire experts, 2023-02-08 doi:10.1101/2023.02.07.527551 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels ]]> https://biorxiv.org/content/10.1101/2023.02.09.527947v1?rss=1 Zvi-Kedem, T. Vintila, S. Kleiner, M. Tchernov, D. Rubin-Blum, M. 2023-02-10 doi:10.1101/2023.02.09.527947 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Life history and cancer in birds: clutch size predicts cancer ]]> https://biorxiv.org/content/10.1101/2023.02.11.528100v1?rss=1 Kapsetaki, S. E. Compton, Z. Dolan, J. Harris, V. K. Rupp, S. M. Duke, E. G. Harrison, T. M. Aksoy, S. Giraudeau, M. Vincze, O. McGraw, K. J. Aktipis, A. Tollis, M. Boddy, A. M. Maley, C. C. 2023-02-13 doi:10.1101/2023.02.11.528100 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ Cancer Prevalence Across Vertebrates ]]> https://biorxiv.org/content/10.1101/2023.02.15.527881v1?rss=1 Compton, Z. T. Harris, V. Mellon, W. Rupp, S. Mallo, D. Kapsetaki, S. Wilmot, M. Kennington, R. Noble, K. Baciu, C. Ramirez, L. Peraza, A. Martins, B. Sudhakar, S. Aksoy, S. Furukawa, G. Vincze, O. Giraudeau, M. T. Duke, E. Spiro, S. Flach, E. Davidson, H. Zehnder, A. Graham, T. A. Troan, B. Harrison, T. Tollis, M. Schiffman, J. Aktipis, A. Abegglen, L. Maley, C. Boddy, A. 2023-02-16 doi:10.1101/2023.02.15.527881 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ UTILIZATION OF A PUBLICLY AVAILABLE DIVERSITY PANEL IN GENOMIC PREDICTION OF FUSARIUM HEAD BLIGHT RESISTANCE TRAITS IN WHEAT ]]> https://biorxiv.org/content/10.1101/2023.02.15.528729v1?rss=1 Winn, Z. J. Lyerly, J. Brown-Guedira, G. J. Murphy, J. P. Mason, E. 2023-02-16 doi:10.1101/2023.02.15.528729 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Mitochondrial Transport in Axons with Multiple Branching Junctions: A Computational Study ]]> https://biorxiv.org/content/10.1101/2023.02.22.529604v1?rss=1 Kuznetsov, I. A. Kuznetsov, A. V. 2023-02-23 doi:10.1101/2023.02.22.529604 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ Bearded or Smooth? Awns Improve Yield when Wheat Experiences Heat Stress During Grain Fill ]]> https://biorxiv.org/content/10.1101/2023.02.27.530138v1?rss=1 DeWitt, N. Lyerly, J. Guedira, M. Holland, J. B. Murphy, J. P. Ward, B. P. Boyles, R. E. Mergoum, M. Babar, M. A. Shakiba, E. Sutton, R. Ibrahim, A. Tiwari, V. K. Santantonio, N. Van Sanford, D. A. Howell, K. Smith, J. H. Harrison, S. A. Brown-Guedira, G. 2023-03-01 doi:10.1101/2023.02.27.530138 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Biosynthesis of plant papanridins -A group of novel oligomeric flavonoids ]]> https://biorxiv.org/content/10.1101/2023.03.01.530648v1?rss=1 Zhu, Y. Yuzuak, S. Sun, X. Xie, D. 2023-03-02 doi:10.1101/2023.03.01.530648 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Human Vascularized Bile Duct-on-a Chip: A multi-cellular micro-physiological system for studying Primary Sclerosing Cholangitis ]]> https://biorxiv.org/content/10.1101/2023.03.02.530888v1?rss=1 Du, Y. Gupta, K. Waisbourd-Zinman, O. Har-Zahav, A. Soroka, C. J. Boyer, J. L. Llewellyn, J. Liu, C. Naji, A. Polacheck, W. J. Wells, R. G. 2023-03-03 doi:10.1101/2023.03.02.530888 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Simulations suggest walking with reduced propulsive force would not mitigate the energetic consequences of lower tendon stiffness ]]> https://biorxiv.org/content/10.1101/2023.03.03.530931v1?rss=1 Pimentel, R. Sawicki, G. Franz, J. R. 2023-03-03 doi:10.1101/2023.03.03.530931 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Re-engineering a lost trait: IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss ]]> https://biorxiv.org/content/10.1101/2023.03.06.531368v1?rss=1 Hornstein, E. D. Charles, M. Franklin, M. Edwards, B. Vintila, S. Kleiner, M. Sederoff, H. 2023-03-07 doi:10.1101/2023.03.06.531368 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Smart Lattice Light Sheet Microscopy for imaging rare and complex cellular events ]]> https://biorxiv.org/content/10.1101/2023.03.07.531517v1?rss=1 Shi, Y. Tabet, J. S. Milkie, D. E. Daugird, T. A. Yang, C. Q. Giovannucci, A. Legant, W. R. 2023-03-09 doi:10.1101/2023.03.07.531517 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Improvements in the detection power of algorithms for analyzing next-generation sequencing based bulked segregant analysis data via estimating thresholds at the genomic region level ]]> https://biorxiv.org/content/10.1101/2023.03.12.532308v1?rss=1 Zhang, J. Panthee, D. 2023-03-13 doi:10.1101/2023.03.12.532308 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ B12-dependent virioplankton demonstrate interseasonal dynamics and associate with a diversity of pelagic bacterioplankton ]]> https://biorxiv.org/content/10.1101/2023.03.13.532061v1?rss=1 Wu, L.-Y. Piedade, G. J. Moore, R. M. Harrison, A. O. Martins, A. M. Bidle, K. D. Polson, S. W. Sakowski, E. Nissimov, J. I. Dums, J. T. Ferrell, B. D. Wommack, K. E. 2023-03-14 doi:10.1101/2023.03.13.532061 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms ]]> https://biorxiv.org/content/10.1101/2023.03.13.532449v1?rss=1 Luu, G. T. Little, J. C. Pierce, E. C. Morin, M. Ertekin, C. A. Wolfe, B. E. Baars, O. Dutton, R. J. Sanchez, L. M. 2023-03-13 doi:10.1101/2023.03.13.532449 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ Glycome profiling and immunohistochemistry uncover spaceflight-induced changes in non-cellulosic cell wall components in Arabidopsis thaliana seedling roots ]]> https://biorxiv.org/content/10.1101/2023.03.14.532448v1?rss=1 Nakashima, J. Pattathil, S. Avci, U. Chin, S. Sparks, J. A. Hahn, M. G. Gilroy, S. Blancaflor, E. B. 2023-03-15 doi:10.1101/2023.03.14.532448 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Pangenomes reveal genomic signatures of microbial adaptation to chronic soil warming ]]> https://biorxiv.org/content/10.1101/2023.03.16.532972v1?rss=1 Choudoir, M. J. Narayanan, A. Rodriguez-Ramos, D. Simoes, R. Efroni, A. Sondrini, A. DeAngelis, K. M. 2023-03-17 doi:10.1101/2023.03.16.532972 Cold Spring Harbor Laboratory Press 2023-03-17 <![CDATA[ Molecular understanding of anthocyanin biosynthesis activated by PAP1 in engineered red Artemisia annua cells and regulation of 2, 4-dichlorophenoxyacetic acid ]]> https://biorxiv.org/content/10.1101/2023.03.17.533196v1?rss=1 Dong, Y. Li, M. Cruz, B. Ye, E. Zhu, Y. Li, L. Xu, Z. Xie, D.-Y. 2023-03-20 doi:10.1101/2023.03.17.533196 Cold Spring Harbor Laboratory Press 2023-03-20 <![CDATA[ Phyllosphere fungal diversity generates pervasive non-additive effects on plant performance ]]> https://biorxiv.org/content/10.1101/2023.03.17.533234v1?rss=1 1000% increase in productivity above the additive expectation), 2) interactions among commensal fungi were responsible for this non-additivity in diverse communities, 3) synergistic interactions were ~4 times stronger than antagonistic effects, 4) fungal diversity affected the magnitude but not frequency or direction of non-additivity, and 5) diversity affected plant performance nonlinearly with highest performance in low microbial diversity treatments. C_LIO_LIThese findings highlight the importance of interpreting plant-microbial interactions under a framework that incorporates intermicrobial interactions and non-additive outcomes to understand natural complexity. C_LI ]]> Almeida, B. K. Tran, E. Afkhami, M. E. 2023-03-21 doi:10.1101/2023.03.17.533234 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal ]]> https://biorxiv.org/content/10.1101/2023.03.20.533418v1?rss=1 Kandola, T. Venkatesan, S. Zhang, J. Lerbakken, B. T. Von Schulze, A. Blanck, J. F. Wu, J. Unruh, J. R. Berry, P. Lange, J. J. Box, A. C. Cook, M. Sagui, C. Halfmann, R. 2023-03-21 doi:10.1101/2023.03.20.533418 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Transcriptomic Prediction of Breeding Values in Loblolly Pine ]]> https://biorxiv.org/content/10.1101/2023.03.21.533546v1?rss=1 Festa, A. R. Whetten, R. 2023-03-24 doi:10.1101/2023.03.21.533546 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Ancient Fish Lineages Illuminate Toll-Like Receptor Diversification in Early Vertebrate Evolution ]]> https://biorxiv.org/content/10.1101/2023.04.05.535752v1?rss=1 Carlson, K. B. Nguyen, C. Wcisel, D. J. Yoder, J. A. Dornburg, A. 2023-04-06 doi:10.1101/2023.04.05.535752 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Embryo-specific epigenetic mechanisms reconstitute the CHH methylation landscape during Arabidopsis embryogenesis ]]> https://biorxiv.org/content/10.1101/2023.04.06.535361v1?rss=1 Hsieh, P.-H. Frost, J. M. Choi, Y. Hsieh, T.-F. Zilberman, D. Fischer, R. L. 2023-04-08 doi:10.1101/2023.04.06.535361 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ Evolutionary druggability: leveraging low-dimensional fitness landscapes towards new metrics for antimicrobial applications ]]> https://biorxiv.org/content/10.1101/2023.04.08.536116v1?rss=1 Guerrero, R. F. Dorji, T. Harris, R. M. Shoulders, M. D. Ogbunugafor, C. B. 2023-04-08 doi:10.1101/2023.04.08.536116 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ Epistasis meets pleiotropy in shaping biophysical protein subspaces associated with antimicrobial resistance ]]> https://biorxiv.org/content/10.1101/2023.04.09.535490v1?rss=1 Ogbunugafor, C. B. Guerrero, R. F. Shakhnovich, E. I. Shoulders, M. D. 2023-04-09 doi:10.1101/2023.04.09.535490 Cold Spring Harbor Laboratory Press 2023-04-09 <![CDATA[ Legacy effects of precipitation and land use impact maize growth and microbiome assembly under drought stress ]]> https://biorxiv.org/content/10.1101/2023.04.11.536405v1?rss=1 Swift, J. F. Kolp, M. R. Carmichael, A. Ford, N. E. Hansen, P. M. Sikes, B. A. Kleiner, M. Wagner, M. R. 2023-04-12 doi:10.1101/2023.04.11.536405 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ Genetic Mapping of SNP Markers and Candidate Genes Associated with Day-Neutral Flowering in Cannabis sativa L. ]]> https://biorxiv.org/content/10.1101/2023.04.17.537043v1?rss=1 Garfinkel, A. R. Wilkerson, D. G. Chen, H. Smart, L. B. Rojas, B. M. Getty, B. A. Michael, T. P. Crawford, S. 2023-04-18 doi:10.1101/2023.04.17.537043 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ Barley HvNIP2;1 aquaporin permeates water, metalloids, saccharides, and ion pairs due to structural plasticity and diversification ]]> https://biorxiv.org/content/10.1101/2023.04.17.537278v1?rss=1 Venkataraghavan, A. Kim, H. Schwerdt, J. G. Gulyuk, A. V. Singh, A. Yingling, Y. G. Tyerman, S. D. Hrmova, M. 2023-04-18 doi:10.1101/2023.04.17.537278 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ Relationship of maternal cytomegalovirus-specific antibody responses and viral load to vertical transmission risk following primary maternal infection in a rhesus macaque model ]]> https://biorxiv.org/content/10.1101/2023.04.21.537769v1?rss=1 Otero, C. E. Barfield, R. Scheef, E. Nelson, C. S. Rodgers, N. Wang, H.-Y. Moström, M. Manuel, T. D. Sass, J. Schmidt, K. Taher, H. Papen, C. Sprehe, L. Kendall, S. Davalos, A. Barry, P. A. Früh, K. Pollara, J. Malouli, D. Chan, C. Kaur, A. Permar, S. R. 2023-04-21 doi:10.1101/2023.04.21.537769 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ Dietary phenolics and their microbial metabolites are poor inhibitors of trimethylamine oxidation to trimethylamine N-oxide by hepatic flavin monooxygenase 3 ]]> https://biorxiv.org/content/10.1101/2023.04.21.537826v1?rss=1 Iglesias-Carres, L. Chadwick-Corbin, S. A. Sweet, M. G. Neilson, A. P. 2023-04-22 doi:10.1101/2023.04.21.537826 Cold Spring Harbor Laboratory Press 2023-04-22 <![CDATA[ Analysis of Gene Expression Differences Between Eastern and Western Loblolly Pine Seed Sources ]]> https://biorxiv.org/content/10.1101/2023.04.24.538124v1?rss=1 Festa, A. R. Whetten, R. 2023-04-28 doi:10.1101/2023.04.24.538124 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ SARS-CoV-2 Spike Protein Reduces Burst Activities in Neurons Measured by Micro-Electrode Arrays ]]> https://biorxiv.org/content/10.1101/2023.04.24.538161v1?rss=1 Salvador, M. Tseng, N. Park, C. Williams, G. Vethan, A. Thomas, G. Baker, J. Hemry, J. Hammond, E. Freeburg, P. Chou, G.-W. Taylor, N. Lu, Y.-F. 2023-04-25 doi:10.1101/2023.04.24.538161 Cold Spring Harbor Laboratory Press 2023-04-25 <![CDATA[ Protective effects of polyphenol-rich extracts against neurotoxicity elicited by paraquat or rotenone in cellular models of Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2023.04.26.538474v1?rss=1 Tambe, M. A. Jacquet, A. d. R. Strathearn, K. E. Yousef, G. G. Grace, M. H. Ferruzzi, M. G. Wu, Q. Simon, J. E. Lila, M. A. Rochet, J.-C. 2023-04-27 doi:10.1101/2023.04.26.538474 Cold Spring Harbor Laboratory Press 2023-04-27 <![CDATA[ Single cell assessment of human stem cell derived mesolimbic models and their responses to substances of abuse. ]]> https://biorxiv.org/content/10.1101/2023.05.12.540534v1?rss=1 Rudibaugh, T. Tam, R. Estridge, R. C. Keung, A. J. 2023-05-14 doi:10.1101/2023.05.12.540534 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Opening a can of worms: a test of the coinfection facilitation hypothesis ]]> https://biorxiv.org/content/10.1101/2023.05.18.541347v1?rss=1 Rodgers, M. L. Bolnick, D. I. 2023-05-19 doi:10.1101/2023.05.18.541347 Cold Spring Harbor Laboratory Press 2023-05-19 <![CDATA[ Allosteric site variants affect GTP hydrolysis on RAS ]]> https://biorxiv.org/content/10.1101/2023.05.29.542740v1?rss=1 Johnson, C. W. Fetics, S. K. Davis, K. P. Rodrigues, J. A. Mattos, C. 2023-05-29 doi:10.1101/2023.05.29.542740 Cold Spring Harbor Laboratory Press 2023-05-29 <![CDATA[ Optimizing Cell Therapy by Sorting Cells with High Extracellular Vesicle Secretion ]]> https://biorxiv.org/content/10.1101/2023.05.29.542772v1?rss=1 Koo, D. Cheng, X. Udani, S. Zhu, D. Li, J. Hall, B. Tsubamoto, N. Hu, S. Ko, J. Cheng, K. Di Carlo, D. 2023-05-30 doi:10.1101/2023.05.29.542772 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ Offline Two-dimensional Liquid Chromatography-Mass Spectrometry for Deep Annotation of the Fecal Metabolome ]]> https://biorxiv.org/content/10.1101/2023.05.31.543178v1?rss=1 Anderson, B. G. Raskind, A. Theriot, C. M. Kennedy, R. T. Evans, C. R. 2023-06-05 doi:10.1101/2023.05.31.543178 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Utilizing Aggregated Molecular Phenotype (AMP) Scores to Visualize Simultaneous Molecular Changes in Mass Spectrometry Imaging Data ]]> https://biorxiv.org/content/10.1101/2023.06.01.543306v1?rss=1 Chappel, J. R. King, M. E. Fleming, J. Eberlin, L. S. Reif, D. M. Baker, E. 2023-06-05 doi:10.1101/2023.06.01.543306 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Engineering the Maize Root Microbiome: A Rapid MoClo Toolkit and Identification of Potential Bacterial Chassis for studying Plant-Microbe Interactions ]]> https://biorxiv.org/content/10.1101/2023.06.05.543168v1?rss=1 Van Schaik, J. Li, Z. Cheadle, J. B. Crook, N. C. 2023-06-05 doi:10.1101/2023.06.05.543168 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ The microbial derived bile acid lithocholate and its epimers inhibit Clostridioides difficile growth and pathogenicity while sparing members of the gut microbiota ]]> https://biorxiv.org/content/10.1101/2023.06.06.543867v1?rss=1 Kisthardt, S. C. Thanissery, R. Pike, C. M. Foley, M. H. Theriot, C. M. 2023-06-07 doi:10.1101/2023.06.06.543867 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ Evaluating the ileal and cecal microbiota composition of a 1940 heritage genetic line and a 2016 commercial line of white leghorns fed representative diets from 1940 and 2016 ]]> https://biorxiv.org/content/10.1101/2023.06.08.544207v1?rss=1 0.05; Q > 0.05). The beta diversity between the ileum and ceca, as well as between the genetic lines (1940 vs. 2016) were significantly different from one another (P = 0.001; Q = 0.001). Using ANCOM, Proteobacteria and Actinobacteriota were significantly different than other phyla (P 0.05) with a higher relative abundance of Proteobacteria being observed among treatment groups 2 and 3, while Actinobacteriota had higher relative abundance in treatment groups 1 and 4. Among the significantly different genera in the ileum, Pseudomonas, Rhizobiaceae, Leuconostoc, and Aeriscardovia were different (P 0.05) with treatment groups 1 and 4 having a higher relative abundance of Aeriscardovia, while treatment groups 2 and 3 had higher relative abundance in both Pseudomonas and Leuconostoc. In the ceca, Proteobacteria, Firmicutes, Actinobacteriota, and Euryarchaeota were significantly different phyla (P 0.05) with Firmicutes having the highest relative abundance across all treatment groups. Among the significantly different genera (Pseudomonas, Leuconostoc, Alloprevotella, and Aeriscardovia), Alloprevotella had the highest relative abundance across all treatment groups 1 and 2, while Leuconostoc and Pseudomonas had the highest relative abundance in treatment group 4. Results from this study suggest that genetic makeup in conjunction with the nutritional composition of laying hens influences the cecal and ileal microbiota of corresponding hens. ]]> Wall, D. C. Dittoe, D. Mahlerios, R. D. Anderson, K. E. Anthony, N. B. 2023-06-08 doi:10.1101/2023.06.08.544207 Cold Spring Harbor Laboratory Press 2023-06-08 <![CDATA[ An intranuclear bacterial parasite of deep-sea musselsexpresses apoptosis inhibitors acquired from its host ]]> https://biorxiv.org/content/10.1101/2023.06.11.544495v1?rss=1 Gonzalez Porras, M. A. Assie, A. Tietjen, M. Violette, M. Kleiner, M. Gruber-Vodicka, H. R. Dubilier, N. Leisch, N. 2023-06-11 doi:10.1101/2023.06.11.544495 Cold Spring Harbor Laboratory Press 2023-06-11 <![CDATA[ Construction of a multi-tissue cell atlas reveals cell-type-specific regulation of molecular and complex phenotypes in pigs ]]> https://biorxiv.org/content/10.1101/2023.06.12.544530v1?rss=1 Chen, L. Li, H. Teng, J. Wang, Z. Qu, X. Chen, Z. Cai, X. Zeng, H. Bai, Z. Li, J. Pan, X. Yan, L. Wang, F. Lin, L. Luo, Y. Sahana, G. Lund, M. Ballester, M. Crespo-Piazuelo, D. Karlskov-Mortensen, P. Fredholm, M. Clop, A. Amills, M. Loving, C. Tuggle, C. Madsen, O. Li, J. Zhang, Z. Liu, G. Jiang, J. Fang, L. Yi, G. 2023-06-13 doi:10.1101/2023.06.12.544530 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ Cytoplasmic Male Sterility and Abortive Seed Traits Generated through Mitochondrial Genome Editing Coupled with Allotopic Expression of atp1 in Tobacco ]]> https://biorxiv.org/content/10.1101/2023.06.12.544621v1?rss=1 Dewey, R. E. Selote, D. Griffin, H. C. Dickey, A. N. Jantz, D. Smith, J. J. Matthiadis, A. Strable, J. Kestell, C. Smith, W. A. 2023-06-12 doi:10.1101/2023.06.12.544621 Cold Spring Harbor Laboratory Press 2023-06-12 <![CDATA[ Reactive Oxygen Species Mediate Transcriptional Responses to Dopamine and Cocaine in Human Cerebral Organoids ]]> https://biorxiv.org/content/10.1101/2023.06.13.544782v1?rss=1 Rudibaugh, T. Keung, A. J. 2023-06-13 doi:10.1101/2023.06.13.544782 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ High-fat diet-induced obesity increases susceptibility to endogenous and ethyl carbamate-induced somatic mutagenesis ]]> https://biorxiv.org/content/10.1101/2023.06.14.543760v1?rss=1 Lichtler, R. Wilson, M. J. Wickliffe, J. K. 2023-06-14 doi:10.1101/2023.06.14.543760 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ Characterizing the power spectrum dynamics of the NREM to REM sleep transition ]]> https://biorxiv.org/content/10.1101/2023.06.14.544943v1?rss=1 Serantes, D. Cavelli, M. Gonzalez, J. Mondino, A. Benedetto, L. Torterolo, P. 2023-06-15 doi:10.1101/2023.06.14.544943 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ Characterizing Adeno-Associated Virus Capsids with both Denaturing and Intact Analysis Methods ]]> https://biorxiv.org/content/10.1101/2023.06.20.543103v1?rss=1 Ryan, J. P. Kostelic, M. M. Hsieh, C.-C. Powers, J. B. Aspinwall, C. A. Dodds, J. N. Schiel, J. E. Marty, M. T. Baker, E. S. 2023-06-20 doi:10.1101/2023.06.20.543103 Cold Spring Harbor Laboratory Press 2023-06-20 <![CDATA[ Virome analysis of irrigation water sources provides extensive insights into the diversity and distribution of plant viruses in agroecosystems ]]> https://biorxiv.org/content/10.1101/2023.06.20.545696v1?rss=1 Maksimovic, O. Bacnik, K. Selda Rivarez, M. P. Vucurovic, A. Mehle, N. Ravnikar, M. Gutierrez Aguirre, I. Kutnjak, D. 2023-06-20 doi:10.1101/2023.06.20.545696 Cold Spring Harbor Laboratory Press 2023-06-20 <![CDATA[ Loss of Bacteroides thetaiotaomicron bile acid altering enzymes impact bacterial fitness and the global metabolic transcriptome ]]> https://biorxiv.org/content/10.1101/2023.06.27.546749v1?rss=1 McMillan, A. S. Foley, M. H. Perkins, C. E. Theriot, C. M. 2023-06-27 doi:10.1101/2023.06.27.546749 Cold Spring Harbor Laboratory Press 2023-06-27 <![CDATA[ Serovar-level Identification of Bacterial Foodborne Pathogens From Full-length 16S rRNA Gene Sequencing ]]> https://biorxiv.org/content/10.1101/2023.06.28.546915v1?rss=1 Grinevich, D. Harden, L. Grinevich, D. O. Callahan, B. J. 2023-06-28 doi:10.1101/2023.06.28.546915 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ Distinct genetic origins of eumelanin intensity and barring patterns in cichlid fishes ]]> https://biorxiv.org/content/10.1101/2023.07.02.547430v1?rss=1 Brandon, A. A. Michael, C. Baez, A. C. Moore, E. C. Ciccotto, P. J. Roberts, N. B. Roberts, R. B. Powder, K. E. 2023-07-03 doi:10.1101/2023.07.02.547430 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Allelic variation in the wheat homolog of topoisomerase II is associated with crossover rate ]]> https://biorxiv.org/content/10.1101/2023.07.06.548017v1?rss=1 Jordan, K. W. Fernandez-de Soto, M. Korol, A. Akhunova, A. Akhunov, E. 2023-07-07 doi:10.1101/2023.07.06.548017 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ Multiple TonB Homologs are Important for Carbohydrate Utilization by Bacteroides thetaiotaomicron ]]> https://biorxiv.org/content/10.1101/2023.07.07.548152v1?rss=1 Pollet, R. M. Foley, M. H. Kumar, S. S. Elmore, A. Jabara, N. T. Venkatesh, S. Vasconcelos Pereira, G. Martens, E. Koropatkin, N. M. 2023-07-07 doi:10.1101/2023.07.07.548152 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ Ten Years of Using Key Characteristics of Human Carcinogens to Organize and Evaluate Mechanistic Evidence in IARC Monographs on the Identification of Carcinogenic Hazards to Humans: Patterns and Associations ]]> https://biorxiv.org/content/10.1101/2023.07.11.548354v1?rss=1 Rusyn, I. Wright, F. A. 2023-07-12 doi:10.1101/2023.07.11.548354 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ An epigenome-wide association study of child appetitive traits and DNA methylation ]]> https://biorxiv.org/content/10.1101/2023.07.17.549289v1?rss=1 Harris, H. A. Friedman, C. Starling, A. Dabelea, D. Johnson, S. L. Fuemmeler, B. F. Jima, D. Murphy, S. K. Hoyo, C. Jansen, P. W. Felix, J. Mulder, R. H. 2023-07-18 doi:10.1101/2023.07.17.549289 Cold Spring Harbor Laboratory Press 2023-07-18 <![CDATA[ HaploCatcher: An R Package for Prediction of Haplotypes ]]> https://biorxiv.org/content/10.1101/2023.07.20.549744v1?rss=1 Winn, Z. J. Hudson-Arns, E. Hammers, M. DeWitt, N. D. Lyerly, J. Bai, G. St Amand, P. Nachappa, P. Haley, S. D. Mason, E. 2023-07-24 doi:10.1101/2023.07.20.549744 Cold Spring Harbor Laboratory Press 2023-07-24 <![CDATA[ Chromosome-scale genome assembly of Tinospora sagittata (Oliv.) Gagnep. enhances identifying genes involved in the biosynthesis of jatrorrhizine ]]> https://biorxiv.org/content/10.1101/2023.07.20.549971v1?rss=1 Alami, M. M. Shu, S. Liu, S. Ouyang, Z. Zhang, Y. Lv, M. Sang, Y. Gong, D. Yang, G. Feng, S. Mei, Z. Xie, D.-Y. Wang, X. 2023-07-21 doi:10.1101/2023.07.20.549971 Cold Spring Harbor Laboratory Press 2023-07-21 <![CDATA[ Effects of 4 testing arena sizes and 11 types of embryo media on sensorimotor behaviors in wild-type and chd7 mutant zebrafish larvae ]]> https://biorxiv.org/content/10.1101/2023.07.31.551330v1?rss=1 Hodorovich, D. R. Harris, T. F. Burton, D. F. Neese, K. M. Bieler, R. A. Chudasama, V. Marsden, K. C. 2023-08-01 doi:10.1101/2023.07.31.551330 Cold Spring Harbor Laboratory Press 2023-08-01 <![CDATA[ Effect of diffusivity of amyloid beta monomers on the formation of senile plaques ]]> https://biorxiv.org/content/10.1101/2023.07.31.551367v1?rss=1 Kuznetsov, A. V. 2023-08-02 doi:10.1101/2023.07.31.551367 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ The relationship between diet, plasma glucose, and cancer prevalence across vertebrates ]]> https://biorxiv.org/content/10.1101/2023.07.31.551378v1?rss=1 Kapsetaki, S. E. Basile, A. J. Compton, Z. T. Rupp, S. M. Duke, E. G. Boddy, A. M. Harrison, T. M. Sweazea, K. L. Maley, C. C. 2023-08-02 doi:10.1101/2023.07.31.551378 Cold Spring Harbor Laboratory Press 2023-08-02 <![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[ Combined kinome inhibition states are predictive of cancer cell line sensitivity to kinase inhibitor combination therapies ]]> https://biorxiv.org/content/10.1101/2023.08.01.551346v1?rss=1 Joisa, C. U. Chen, K. A. Berginski, M. Beville, S. Stuhlmiller, T. Okumu, D. Golitz, B. T. Johnson, G. L. Gomez, S. M. 2023-08-03 doi:10.1101/2023.08.01.551346 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ RACER-m Leverages Structural Features for Sparse T Cell Specificity Prediction ]]> https://biorxiv.org/content/10.1101/2023.08.06.552190v1?rss=1 Wang, A. T. Lin, X. Chau, K. N. Onuchic, J. N. Levine, H. George, J. T. 2023-08-07 doi:10.1101/2023.08.06.552190 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Germline mutation rate predicts cancer mortality across 37 vertebrate species ]]> https://biorxiv.org/content/10.1101/2023.08.13.553123v1?rss=1 Kapsetaki, S. E. Compton, Z. T. Mellon, W. Vincze, O. Giraudeau, M. T. Harrison, T. Abegglen, L. Boddy, A. Maley, C. C. Schiffman, J. 2023-08-15 doi:10.1101/2023.08.13.553123 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ Season, not long-term warming, affects the relationship between ecosystem function and microbial diversity ]]> https://biorxiv.org/content/10.1101/2023.08.14.553264v1?rss=1 Shinfuku, M. S. Domeignoz-Horta, L. A. Choudoir, M. J. Frey, S. DeAngelis, K. M. 2023-08-15 doi:10.1101/2023.08.14.553264 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ Automated, high-throughput quantification of EGFP-expressing neutrophils in zebrafish by machine learning and a highly-parallelized microscope ]]> https://biorxiv.org/content/10.1101/2023.08.16.553550v1?rss=1 Efromson, J. Ferrero, G. Begue, A. Doman, T. J. J. Dugo, C. Barker, A. Saliu, V. Reamey, P. Kim, K. Harfouche, M. Yoder, J. A. 2023-08-18 doi:10.1101/2023.08.16.553550 Cold Spring Harbor Laboratory Press 2023-08-18 <![CDATA[ The role of heterochronic gene expression and regulatory architecture in early developmental divergence ]]> https://biorxiv.org/content/10.1101/2023.08.18.553877v1?rss=1 Harry, N. D. Zakas, C. 2023-08-18 doi:10.1101/2023.08.18.553877 Cold Spring Harbor Laboratory Press 2023-08-18 <![CDATA[ Longevity Bottlenecks ]]> https://biorxiv.org/content/10.1101/2023.08.18.553936v1?rss=1 Florea, M. Hamalainen, M. Seebold, P. Cheng, N. Murray, P. Colville, A. J. Zheng, S. Ingham, D. Kantelal, R. De Sicilia, R. 2023-08-21 doi:10.1101/2023.08.18.553936 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Regulatory variation controlling architectural pleiotropy in maize ]]> https://biorxiv.org/content/10.1101/2023.08.19.553731v1?rss=1 Bertolini, E. Rice, B. R. Braud, M. Yang, J. Hake, S. Strable, J. Lipka, A. E. Eveland, A. L. 2023-08-21 doi:10.1101/2023.08.19.553731 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Morphological hallmarks of dopaminergic neurodegeneration are associated with altered neuron function in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2023.08.22.554364v1?rss=1 Clark, A. S. Huayta, J. Morton, K. S. Meyer, J. N. San-Miguel, A. 2023-08-23 doi:10.1101/2023.08.22.554364 Cold Spring Harbor Laboratory Press 2023-08-23 <![CDATA[ Genomic insights into post-domestication expansion and selection of body size in ponies ]]> https://biorxiv.org/content/10.1101/2023.08.25.554910v1?rss=1 Li, X. Wang, Z. Zhu, M. Wang, B. Teng, S. Yan, J. Yuan, P. Cao, S. Qu, X. Wang, Z. Choudhury, M. P. Yang, X. Bao, Q. He, S. Liu, L. Zhao, P. Jiang, J. Xiang, H. Fang, L. Tang, Z. Liao, Y. Yi, G. 2023-08-27 doi:10.1101/2023.08.25.554910 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Metagenomic analysis of the honey bee queen microbiome reveals low bacterial diversity and Caudoviricetes phages ]]> https://biorxiv.org/content/10.1101/2023.08.29.555332v1?rss=1 Caesar, L. Rice, D. W. McAfee, A. Underwood, R. Tarpy, D. R. J Foster, L. Newton, I. L. G. 2023-09-01 doi:10.1101/2023.08.29.555332 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Advances in genomic characterization of Urochloa humidicola: exploring polyploid inheritance and apomixis ]]> https://biorxiv.org/content/10.1101/2023.08.31.555743v1?rss=1 Moraes, A. d. C. L. Mollinari, M. Ferreira, R. U. Aono, A. H. Lara, L. A. d. C. Pessoa-Filho, M. Barrios, S. C. L. Garcia, A. A. F. do Valle, C. B. de Souza, A. P. Vigna, B. B. Z. 2023-09-03 doi:10.1101/2023.08.31.555743 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ Assessing Per- and Polyfluoroalkyl Substances (PFAS) in Fish Fillet Using Non-Targeted Analyses ]]> https://biorxiv.org/content/10.1101/2023.09.01.555938v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@b3084org.highwire.dtl.DTLVardef@9e69bborg.highwire.dtl.DTLVardef@2f9628org.highwire.dtl.DTLVardef@2b33c8_HPS_FORMAT_FIGEXP M_FIG C_FIG For use in table of contents only ]]> Boatman, A. K. Chappel, J. R. Polera, M. E. Dodds, J. N. Belcher, S. M. Baker, E. S. 2023-09-05 doi:10.1101/2023.09.01.555938 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ The role of fruitless in specifying courtship behaviors differs across Drosophila species ]]> https://biorxiv.org/content/10.1101/2023.09.01.556001v1?rss=1 Baker, C. A. Guan, X.-J. Choi, M. Murthy, M. 2023-09-03 doi:10.1101/2023.09.01.556001 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ Distilling Mechanistic Models From Multi-Omics Data ]]> https://biorxiv.org/content/10.1101/2023.09.06.556597v1?rss=1 Erwin, S. Fletcher, J. R. Sweeney, D. C. Theriot, C. M. Lanzas, C. 2023-09-06 doi:10.1101/2023.09.06.556597 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Barriers to Integration of Bioinformatics into Undergraduate Life Sciences Education ]]> https://biorxiv.org/content/10.1101/204420v1?rss=1 Williams, J. Drew, J. Galindo-Gonzalez, S. Robic, S. Dinsdale, E. Morgan, W. Triplett, E. Burnette, J. Donovan, S. Elgin, S. Fowlks, E. Goodman, A. Grandgenett, N. Goller, C. Hauser, C. Jungck, J. R. Newman, J. Pearson, W. Ryder, E. Wilson Sayres, M. Sierk, M. Smith, T. Tosado-Acevedo, R. Tapprich, W. Tobin, T. Toro-Martinez, A. Welch, L. Wright, R. Ebenbach, D. McWilliams, M. Rosenwald, A. Pauley, M. 2017-10-19 doi:10.1101/204420 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ The Basic Reproductive Number for Disease Systems with Multiple Coupled Heterogeneities ]]> https://biorxiv.org/content/10.1101/220004v1?rss=1 Lloyd, A. Kitron, U. Perkins, A. Vazquez Prokopec, G. Waller, L. 2017-11-16 doi:10.1101/220004 Cold Spring Harbor Laboratory Press 2017-11-16 <![CDATA[ Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data ]]> https://biorxiv.org/content/10.1101/221499v1?rss=1 Davis, N. M. Proctor, D. Holmes, S. P. Relman, D. A. Callahan, B. J. 2017-11-17 doi:10.1101/221499 Cold Spring Harbor Laboratory Press 2017-11-17 <![CDATA[ Bacterial adaptation to host diet is a key evolutionary force shaping host-microbe symbiosis ]]> https://biorxiv.org/content/10.1101/222364v1?rss=1 Martino, M. E. Joncour, P. Leenay, R. Gervais, H. Shaw, M. Hughes, S. Gillet, B. Beisel, C. Leulier, F. 2017-11-20 doi:10.1101/222364 Cold Spring Harbor Laboratory Press 2017-11-20 <![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[ A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities ]]> https://biorxiv.org/content/10.1101/245290v1?rss=1 Kleiner, M. Dong, X. Hinzke, T. Wippler, J. Thorson, E. Mayer, B. Strous, M. 2018-01-09 doi:10.1101/245290 Cold Spring Harbor Laboratory Press 2018-01-09 <![CDATA[ A folded viral noncoding RNA blocks host cell exoribonucleases through programmed remodeling of RNA structure ]]> https://biorxiv.org/content/10.1101/262683v1?rss=1 Steckelberg, A.-L. Akiyama, B. M. Costantino, D. A. Sit, T. L. Nix, J. C. Kieft, J. S. 2018-02-09 doi:10.1101/262683 Cold Spring Harbor Laboratory Press 2018-02-09 <![CDATA[ PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer ]]> https://biorxiv.org/content/10.1101/264010v1?rss=1 Lin, X. Roy, S. Jolly, M. K. Bocci, F. Schafer, N. Tsai, M.-Y. Kulkarni, P. Chen, Y. He, Y. Orban, J. Grishaev, A. Weninger, K. Rangarajan, G. Levine, H. Onuchic, J. N. 2018-02-14 doi:10.1101/264010 Cold Spring Harbor Laboratory Press 2018-02-14 <![CDATA[ A Cross-Platform Comparison of Student’s Perceptions of the Learning Environment in an Introductory Microbiology Course ]]> https://biorxiv.org/content/10.1101/274571v1?rss=1 Ramirez, M. V. Lee, V. S. Hamm, L. Taveirne, M. E. Lee, A. M. 2018-03-03 doi:10.1101/274571 Cold Spring Harbor Laboratory Press 2018-03-03 <![CDATA[ American Gut: an Open Platform for Citizen-Science Microbiome Research ]]> https://biorxiv.org/content/10.1101/277970v1?rss=1 McDonald, D. Hyde, E. R. Debelius, J. W. Morton, J. T. Gonzalez, A. Ackermann, G. Aksenov, A. A. Behsaz, B. Brennan, C. Chen, Y. DeRight Goldasicha, L. Dorrestein, P. C. Dunn, R. R. Fahimipourg, A. K. Gaffney, J. Gilbert, J. A. Gogul, G. Green, J. L. Hugenholtz, P. Humphrey, G. Huttenhower, C. Jackson, M. A. Janssen, S. Jeste, D. V. Jiang, L. Kelley, S. T. Knights, D. Kosciolek, T. Ladau, J. Leach, J. Marotz, C. Meleshko, D. Melnik, A. V. Metcalf, J. L. Mohimani, H. Montassier, E. Navas-Molina, J. Nguyen, T. T. Peddada, S. Pevzner, P. Pollard, K. S. Rah 2018-03-07 doi:10.1101/277970 Cold Spring Harbor Laboratory Press 2018-03-07 <![CDATA[ Altered Bile Acid Profile Associates with Cognitive Impairment in Alzheimer’s Disease – An Emerging Role for Gut Microbiome ]]> https://biorxiv.org/content/10.1101/281956v1?rss=1 Mahmoudiandehkordi, S. Arnold, M. Nho, K. Ahmad, S. Jia, W. Xia, G. Louie, G. Kueider, A. Moseley, M. A. Thompson, J. W. St. John Williams, L. Tenenbaum, J. D. Blach, C. Baillie, R. Han, X. Bhattacharyya, S. Toledo, J. B. Schafferer, S. Klein, S. Koal, T. Risacher, S. L. Kling, M. A. Motsinger-Reif, A. Rotroff, D. M. Jack, J. Hankemeier, T. Bennett, D. A. De Jager, P. L. Trojanowski, J. Q. Shaw, L. M. Weiner, M. W. Doraiswamy, P. M. van Duijn, C. M. Saykin, A. Kastenmueller, G. Kaddurah-Daouk, R. Alzheimers Disease Neuroimaging Initiative, Alzheimers Dise 2018-03-17 doi:10.1101/281956 Cold Spring Harbor Laboratory Press 2018-03-17 <![CDATA[ Expanded view of the ecological genomics of ant responses to climate change ]]> https://biorxiv.org/content/10.1101/302679v1?rss=1 16,000 species), mostly from tropical and sub-tropical species. To address this limited sampling, we sequenced genomes of temperate-latitude species from the genus Aphaenogaster, a genus with important seed dispersers. In total, we sampled seven colonies of six species: A. ashmeadi, A. floridana, A. fulva, A. miamiana, A. picea, and A. rudis. The geographic ranges of these species collectively span eastern North America from southern Florida to southern Canada, which encompasses a latitudinal gradient in which many climatic variables are changing rapidly. For the six genomes, we assembled an average of 271,039 contigs into 47,337 scaffolds. The mean genome size was 370.5 Mb, ranging from 310.3 to 429.7, which is comparable to that of other sequenced ant genomes (212.8 to 396.0 Mb) and flow cytometry estimates (210.7 to 690.4 Mb). In an analysis of currently sequenced ant genomes and the new Aphaenogaster sequences, we found that after controlling for both spatial autocorrelation and phylogenetics ant genome size was marginally correlated with sample site climate similarity. Of all examined climate variables, minimum temperature showed the strongest correlation with genome size, with ants from locations with colder minimum temperatures having larger genomes. These results suggest that temperature extremes could be a selective force acting on ant genomes and point to the need for more extensive sequencing of ant genomes. ]]> Lau, M. Ellison, A. M. Nguyen, A. D. Penick, C. DeMarco, B. Gotelli, N. J. Sanders, N. Dunn, R. Helms Cahan, S. 2018-04-17 doi:10.1101/302679 Cold Spring Harbor Laboratory Press 2018-04-17 <![CDATA[ One-step assembly of large CRISPR arrays enables multi-functional targeting and reveals constraints on array design ]]> https://biorxiv.org/content/10.1101/312421v1?rss=1 Liao, C. Ttofali, F. Slotkowski, R. A. Denny, S. R. Cecil, T. D. Leenay, R. T. Keung, A. J. Beisel, C. L. 2018-05-02 doi:10.1101/312421 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ Determination of novel members in the Drosophila melanogaster anterior-posterior patterning system using natural variation ]]> https://biorxiv.org/content/10.1101/319434v1?rss=1 Jermusyk, A. A. Gharavi, S. E. Tingare, A. S. Reeves, G. T. 2018-05-10 doi:10.1101/319434 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ Dorsal/NF-κB exhibits a dorsal-to-ventral mobility gradient in the Drosophila embryo ]]> https://biorxiv.org/content/10.1101/320754v1?rss=1 Al Asafen, H. Clark, N. M. Jacobsen, T. Sozzani, R. Reeves, G. 2018-05-11 doi:10.1101/320754 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Coral: Clear and customizable visualization of human kinome data ]]> https://biorxiv.org/content/10.1101/330274v1?rss=1 Metz, K. Deoudes, E. M. Berginski, M. E. Jimenez-Ruiz, I. Aksoy, B. A. Hammerbacher, J. Gomez, S. M. Phanstiel, D. H. 2018-05-25 doi:10.1101/330274 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Identifying individual risk rare variants using protein structure-guided local tests (POINT) ]]> https://biorxiv.org/content/10.1101/333245v1?rss=1 Marceau West, R. Lu, W. Rotroff, D. M. Kuenemann, M. Chang, S.-M. Wagner, M. J. Buse, J. B. Motsinger-Reif, A. Fourches, D. Tzeng, J.-Y. 2018-05-29 doi:10.1101/333245 Cold Spring Harbor Laboratory Press 2018-05-29 <![CDATA[ TuxNet: A simple interface to process RNA sequencing data and infer gene regulatory networks ]]> https://biorxiv.org/content/10.1101/337147v1?rss=1 de Luis Balaguer, M. A. Spurney, R. J. Clark, N. Fisher, A. P. Sozzani, R. 2018-06-03 doi:10.1101/337147 Cold Spring Harbor Laboratory Press 2018-06-03 <![CDATA[ Canine transmissible venereal tumor genome reveals ancient introgression from coyotes to arctic sled dogs ]]> https://biorxiv.org/content/10.1101/350512v1?rss=1 Wang, X. Zhou, B.-W. Yin, T.-T. Chen, F.-L. Esmailizadeh, A. Turner, M. M. Poyarkov, A. D. Savolainen, P. Wang, G.-D. Fu, Q. Zhang, Y.-P. 2018-06-19 doi:10.1101/350512 Cold Spring Harbor Laboratory Press 2018-06-19 <![CDATA[ Streamlined, recombinase-free genome editing with CRISPR-Cas9 in Lactobacillus plantarum reveals barriers to efficient editing ]]> https://biorxiv.org/content/10.1101/352039v1?rss=1 Leenay, R. T. Vento, J. M. Shah, M. Martino, M. E. Leulier, F. Beisel, C. L. 2018-06-20 doi:10.1101/352039 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ Lysophosphatidic acid provokes fibroblast chemotaxis through combinatorial regulation of myosin II ]]> https://biorxiv.org/content/10.1101/355610v1?rss=1 Asokan, S. Johnson, H. Sondek, J. Shutova, M. Svitkina, T. Haugh, J. Bear, J. 2018-06-25 doi:10.1101/355610 Cold Spring Harbor Laboratory Press 2018-06-25 <![CDATA[ Redesign of an Undergraduate General Microbiology Lab to Include Authentic Discovery-Driven Research on Cucumber Fermentations ]]> https://biorxiv.org/content/10.1101/356261v1?rss=1 Greenstein, J. Ford, B. Gove, S. Breidt, F. Lee, A. Taveirne, M. E. 2018-07-05 doi:10.1101/356261 Cold Spring Harbor Laboratory Press 2018-07-05 <![CDATA[ Within-host infectious disease models accommodating cellular coinfection, with an application to influenza ]]> https://biorxiv.org/content/10.1101/359067v1?rss=1 Koelle, K. Farrell, A. Brooke, C. Ke, R. 2018-06-29 doi:10.1101/359067 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Comparative Biochemical and Structural Analysis of Novel Cellulose Binding Proteins (Tapirins) from Extremely Thermophilic Caldicellulosiruptor Species ]]> https://biorxiv.org/content/10.1101/359786v1?rss=1 Lee, L. L. Hart, W. S. Lunin, V. V. Alahuhta, M. Bomble, Y. J. Himmel, M. E. Blumer-Schuette, S. E. Adams, M. W. W. Kelly, R. M. 2018-06-30 doi:10.1101/359786 Cold Spring Harbor Laboratory Press 2018-06-30 <![CDATA[ Epithelial restitution defect in neonatal jejunum is rescued by juvenile mucosal homogenate in a pig model of intestinal ischemic injury and repair ]]> https://biorxiv.org/content/10.1101/361352v1?rss=1 Ziegler, A. L. Pridgen, T. A. Mills, J. K. Gonzalez, L. M. Van Landeghem, L. Odle, J. Blikslager, A. T. 2018-07-03 doi:10.1101/361352 Cold Spring Harbor Laboratory Press 2018-07-03 <![CDATA[ Predicting Growth and Carcass Traits in Swine Using Metagenomic Data and Machine Learning Algorithms ]]> https://biorxiv.org/content/10.1101/363309v1?rss=1 Maltecca, C. Lu, D. Schillebeeckx, C. McNulty, N. Schawb, C. Schull, C. Tiezzi, F. 2018-07-06 doi:10.1101/363309 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ Genetic evidence for two carbon fixation pathways in symbiotic and free-living bacteria: The Calvin-Bassham cycle and the reverse tricarboxylic acid cycle ]]> https://biorxiv.org/content/10.1101/363564v1?rss=1 Rubin Blum, M. Dubilier, N. Kleiner, M. 2018-07-06 doi:10.1101/363564 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ Adaptive strategies of the candidate probiotic E. coli Nissle in the mammalian gut ]]> https://biorxiv.org/content/10.1101/364505v1?rss=1 Crook, N. Ferreiro, A. Gasparrini, A. Pesesky, M. Gibson, M. Wang, B. Sun, X. Condiotte, Z. Dobrowolski, S. Peterson, D. Dantas, G. 2018-07-08 doi:10.1101/364505 Cold Spring Harbor Laboratory Press 2018-07-08 <![CDATA[ Ecological analyses of mycobacteria in showerhead biofilms and their relevance to human health ]]> https://biorxiv.org/content/10.1101/366088v1?rss=1 Gebert, M. Delgado-Baquerizo, M. Oliverio, A. Webster, T. Nichols, L. Honda, J. Chan, E. Adjemian, J. Dunn, R. Fierer, N. 2018-07-10 doi:10.1101/366088 Cold Spring Harbor Laboratory Press 2018-07-10 <![CDATA[ Distinct timescales of RNA regulators enable the construction of a genetic pulse generator ]]> https://biorxiv.org/content/10.1101/377572v1?rss=1 Westbrook, A. Tang, X. Marshall, R. Maxwell, C. Chappell, J. Agrawal, D. Dunlop, M. Noireaux, V. Beisel, C. Lucks, J. Franco, E. 2018-07-25 doi:10.1101/377572 Cold Spring Harbor Laboratory Press 2018-07-25 <![CDATA[ Age and genetic background determine hybrid male sterility in house mice ]]> https://biorxiv.org/content/10.1101/382382v1?rss=1 Aylor, D. L. Widmayer, S. J. 2018-08-01 doi:10.1101/382382 Cold Spring Harbor Laboratory Press 2018-08-01 <![CDATA[ The Genomic Basis of Arthropod Diversity ]]> https://biorxiv.org/content/10.1101/382945v1?rss=1 Thomas, G. W. C. Dohmen, E. Hughes, D. S. T. Murali, S. C. Poelchau, M. Glastad, K. Anstead, C. A. Ayoub, N. A. Batterham, P. Bellair, M. Binford, G. J. Chao, H. Chen, Y. H. Childers, C. Dinh, H. Doddapaneni, H. Duan, J. J. Dugan, S. Esposito, L. A. Friedrich, M. Garb, J. Gasser, R. B. B. Goodisman, M. A. D. Gundersen-Rindal, D. E. Han, Y. Handler, A. M. Hatakeyama, M. Hering, L. Hunter, W. B. Ioannidis, P. Jayaseelan, J. C. Kalra, D. Khila, A. Korhonen, P. K. Lee, C. E. Lee, S. L. Li, Y. Lindsey, A. R. I. Mayer, G. McGregor, A. P. McKenna, D. D. Misof, 2018-08-04 doi:10.1101/382945 Cold Spring Harbor Laboratory Press 2018-08-04 <![CDATA[ Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes ]]> https://biorxiv.org/content/10.1101/383992v1?rss=1 Conte, M. A. Joshi, R. Moore, E. C. Nandamuri, S. P. Gammerdinger, W. J. Roberts, R. B. Carleton, K. L. Lien, S. Kocher, T. D. 2018-08-03 doi:10.1101/383992 Cold Spring Harbor Laboratory Press 2018-08-03 <![CDATA[ High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution ]]> https://biorxiv.org/content/10.1101/392332v1?rss=1 Callahan, B. J. Wong, J. Heiner, C. Oh, S. Theriot, C. M. Gulati, A. S. McGill, S. K. Dougherty, M. K. 2018-08-15 doi:10.1101/392332 Cold Spring Harbor Laboratory Press 2018-08-15 <![CDATA[ Filter paper-based spin column for low throughput nucleic acid purification ]]> https://biorxiv.org/content/10.1101/392696v1?rss=1 Shi, R. Lewis, R. R. Panthee, D. 2018-08-15 doi:10.1101/392696 Cold Spring Harbor Laboratory Press 2018-08-15 <![CDATA[ Adaptive evolution of sperm proteins depends on sperm competition in a pair of Lepidoptera ]]> https://biorxiv.org/content/10.1101/404236v1?rss=1 Mongue, A. J. Hansen, M. E. Gu, L. Sorenson, C. E. Walters, J. R. 2018-08-31 doi:10.1101/404236 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models ]]> https://biorxiv.org/content/10.1101/415232v1?rss=1 Mollinari, M. Garcia, A. A. F. 2018-09-12 doi:10.1101/415232 Cold Spring Harbor Laboratory Press 2018-09-12 <![CDATA[ Discovery of novel thrips vector proteins that bind to the plant bunyavirus, tomato spotted wilt virus. ]]> https://biorxiv.org/content/10.1101/416560v1?rss=1 Badillo-Vargas, I. E. Chen, Y. Martin, K. M. Rotenberg, D. Whitfield, A. E. 2018-09-23 doi:10.1101/416560 Cold Spring Harbor Laboratory Press 2018-09-23 <![CDATA[ Computational estimation of ms-sec atomistic folding times ]]> https://biorxiv.org/content/10.1101/427393v1?rss=1 Adhikari, U. Mostofian, B. Petersen, A. Zuckerman, D. M. 2018-09-29 doi:10.1101/427393 Cold Spring Harbor Laboratory Press 2018-09-29 <![CDATA[ Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria) ]]> https://biorxiv.org/content/10.1101/437616v1?rss=1 Assie, A. Leisch, N. Meier, D. V. Gruber Vodicka, H. Tegetmeyer, H. E. Meyerdirks, A. Kleiner, M. Hinzke, T. Joye, S. Saxton, M. Dubilier, N. Petersen, J. M. 2018-10-08 doi:10.1101/437616 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ Cell type-specific differences in protein complex stoichiometry and transcriptional regulation affect the timing of stem cell division ]]> https://biorxiv.org/content/10.1101/439331v1?rss=1 Clark, N. M. Fisher, A. P. Berckmans, B. Zebell, S. G. Simon, R. Gallagher, K. Sozzani, R. 2018-10-09 doi:10.1101/439331 Cold Spring Harbor Laboratory Press 2018-10-09 <![CDATA[ Positive feedback and feedforward loops between PERIANTHIA, WUSCHEL-RELATED HOMEOBOX5 and GRF-INTERACTING FACTOR 1 modulate gene expression and function in the Arabidopsis root ]]> https://biorxiv.org/content/10.1101/439851v1?rss=1 Fisher, A. P. Clark, N. M. Sozzani, R. 2018-10-11 doi:10.1101/439851 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ Variation in pigmentation gene expression is associated with distinct aposematic color morphs in the poison frog, Dendrobates auratus ]]> https://biorxiv.org/content/10.1101/445684v1?rss=1 Stuckert, A. Moore, E. Coyle, K. P. Davison, I. MacManes, M. D. Roberts, R. Summers, K. 2018-10-17 doi:10.1101/445684 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Tethered homing gene drives: a new design for spatially restricted population replacement and suppression ]]> https://biorxiv.org/content/10.1101/457564v1?rss=1 Dhole, S. Loyd, A. L. Gould, F. 2018-10-31 doi:10.1101/457564 Cold Spring Harbor Laboratory Press 2018-10-31 <![CDATA[ Exploring neighborhoods in large metagenome assembly graphs reveals hidden sequence diversity ]]> https://biorxiv.org/content/10.1101/462788v1?rss=1 Brown, C. T. Moritz, D. O'Brien, M. Reidl, F. Reiter, T. Sullivan, B. 2018-11-05 doi:10.1101/462788 Cold Spring Harbor Laboratory Press 2018-11-05 <![CDATA[ Genetics of Cocaine and Methamphetamine Consumption and Preference in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/470906v1?rss=1 Highfill, C. Baker, B. Stevens, S. Anholt, R. R. H. Mackay, T. 2018-11-14 doi:10.1101/470906 Cold Spring Harbor Laboratory Press 2018-11-14 <![CDATA[ Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia ]]> https://biorxiv.org/content/10.1101/471656v1?rss=1 Ward, B. Brown-Guedira, G. Kolb, F. Van Sanford, D. Tyagi, P. Sneller, C. Griffey, C. 2018-11-15 doi:10.1101/471656 Cold Spring Harbor Laboratory Press 2018-11-15 <![CDATA[ BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis ]]> https://biorxiv.org/content/10.1101/474296v1?rss=1 Bouckaert, R. Vaughan, T. G. Barido-Sottani, J. Duchene, S. Fourment, M. Gavryushkina, A. Heled, J. Jones, G. Kuhnert, D. de Maio, N. Matschiner, M. Mendes, F. K. Muller, N. Ogilvie, H. A. du Plessis, L. Popinga, A. Rambaut, A. Rasmussen, D. Siveroni, I. Suchard, M. Wu, C.-H. Xie, D. Zhang, C. Stadler, T. Drummond, A. J. 2018-11-19 doi:10.1101/474296 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ IgG is differentially and selectively transferred across the placenta in HIV-infected women ]]> https://biorxiv.org/content/10.1101/479121v1?rss=1 Martinez, D. R. Fong, Y. Li, S. H. Yang, F. Jennewein, M. Weiner, A. Harrell, E. Mangold, J. Goswami, R. Seage, G. Alter, G. Ackerman, M. Peng, X. Fouda, G. Permar, S. 2018-11-30 doi:10.1101/479121 Cold Spring Harbor Laboratory Press 2018-11-30 <![CDATA[ Stress, novel sex genes and epigenetic reprogramming orchestrate socially-controlled sex change ]]> https://biorxiv.org/content/10.1101/481143v1?rss=1 Todd, E. V. Ortega-Recalde, O. Liu, H. Lamm, M. S. Rutherford, K. M. Cross, H. Black, M. A. Kardailsky, O. Graves, J. A. Hore, T. A. Godwin, J. R. Gemmell, N. J. 2018-12-03 doi:10.1101/481143 Cold Spring Harbor Laboratory Press 2018-12-03 <![CDATA[ Accelerated Bayesian inference of gene expression models from snapshots of single-cell transcripts ]]> https://biorxiv.org/content/10.1101/489880v1?rss=1 Lin, Y. T. Buchler, N. E. 2018-12-07 doi:10.1101/489880 Cold Spring Harbor Laboratory Press 2018-12-07 <![CDATA[ Queen and king recognition in the subterranean termite, Reticulitermes flavipes: Evidence for royal recognition pheromones ]]> https://biorxiv.org/content/10.1101/496240v1?rss=1 Funaro, C. F. Schal, C. Vargo, E. L. 2018-12-13 doi:10.1101/496240 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Global invasion history of the world’s most abundant pest butterfly: a citizen science population genomics study ]]> https://biorxiv.org/content/10.1101/506162v1?rss=1 1,000 specimens from 13 countries), demonstrating the power of the public to aid scientists in collections-based research addressing important questions in ecology and evolutionary biology.nnNon-technical summaryWe provide genetic evidence that the success of the small cabbage white butterfly--its rise to one of the most widespread and abundant butterflies on the planet-- was largely facilitated by human activities, through the domestication of its food plants and the accidental movement of the butterfly by means of trade and human movement (migration). Through an international citizen science project--Pieris Project--people from around the world helped to unravel the global invasion history of this agricultural pest butterfly by collecting samples for DNA analysis. The success of this citizen science project demonstrates the power of the public to aid in collections-based research that address important questions related to ecology and evolutionary biology. ]]> Ryan, S. F. Lombaert, E. Espeset, A. Vila, R. Talavera, G. Dinca, V. Renshaw, M. A. Eng, M. W. Doellman, M. M. Hornett, E. A. Li, Y. Pfrender, M. E. Shoemaker, D. 2018-12-26 doi:10.1101/506162 Cold Spring Harbor Laboratory Press 2018-12-26 <![CDATA[ Locally Fixed Alleles: A method to localize gene drive to island populations ]]> https://biorxiv.org/content/10.1101/509364v1?rss=1 Sudweeks, J. Hollingsworth, B. Blondel, D. V. Campbell, K. J. Dhole, S. Eisemann, J. D. Edwards, O. Godwin, J. Howald, G. R. Oh, K. Piaggio, A. J. Prowse, T. A. A. Ross, J. V. Saah, J. R. Shiels, A. B. Thomas, P. Threadgill, D. W. Vella, M. R. Gould, F. Lloyd, A. 2019-01-02 doi:10.1101/509364 Cold Spring Harbor Laboratory Press 2019-01-02 <![CDATA[ Bacterial Diversity in Feces of Wild Bald Eagles, Turkey Vultures and Common Ravens from the Pacific Northwest Coast, U.S.A. ]]> https://biorxiv.org/content/10.1101/511147v1?rss=1 Crespo, R. Dowd, S. E. Varland, D. E. Ford, S. Hamer, T. E. 2019-01-03 doi:10.1101/511147 Cold Spring Harbor Laboratory Press 2019-01-03 <![CDATA[ Effects of water, sanitation, handwashing and nutritional interventions on soil-transmitted helminth infections in young children: a cluster-randomized controlled trial in rural Bangladesh ]]> https://biorxiv.org/content/10.1101/512509v1?rss=1 1.5 billion people. Mass drug administration (MDA) reduces infection; however, drug resistance is emerging and reinfection occurs rapidly. We conducted a randomized controlled trial in Bangladesh (WASH Benefits, NCT01590095) to assess whether water, sanitation, hygiene and nutrition interventions, alone and combined, reduce STH in a setting with ongoing MDA. Methodology/Principal FindingsWe randomized clusters of pregnant women into water treatment, sanitation, handwashing, combined water+sanitation+handwashing (WSH), nutrition, nutrition+WSH (N+WSH) or control arms. After 2.5 years of intervention, we enumerated STH infections in children aged 2-12 years with Kato-Katz. We estimated intention-to-treat intervention effects on infection prevalence and intensity. Participants and field staff were not blinded; laboratory technicians and data analysts were blinded. In 2012-2013, we randomized 5551 women in 720 clusters. In 2015-2016, we enrolled 7795 children of 4102 available women for STH follow-up and collected stool from 7187. Prevalence among controls was 36.8% for A. lumbricoides, 9.2% for hookworm and 7.5% for T. trichiura. Most infections were low-intensity. Compared to controls, the water intervention reduced hookworm (prevalence ratio [PR]=0.69 (0.50, 0.95), prevalence difference [PD]=-2.83 (-5.16, -0.50)) but did not affect other STH. Sanitation improvements reduced T. trichiura (PR=0.71 (0.52, 0.98), PD=-2.17 (-4.03, -0.38)), had a similar borderline effect on hookworm and no effect on A. lumbricoides. Handwashing and nutrition interventions did not reduce any STH. WSH and N+WSH reduced hookworm prevalence by 29-33% (2-3 percentage points) and marginally reduced A. lumbricoides. Effects on infection intensity were similar. Conclusions/SignificanceIn a low-intensity infection setting with MDA, we found modest but sustained hookworm reduction from water treatment, sanitation and combined WSH interventions. Interventions more effectively reduced STH species with no persistent environmental reservoirs. Our findings highlight waterborne transmission for hookworm and suggest that water treatment and sanitation improvements can augment MDA programs to interrupt STH transmission. Author summarySoil-transmitted helminths (STH) infect >1.5 billion people worldwide. Mass-administration of deworming drugs is the cornerstone of global strategy for STH control but treated individuals often rapidly get reinfected and there is also concern about emerging drug resistance. Interventions to treat drinking water, wash hands at critical times and isolate human feces from the environment through improved sanitation could reduce STH transmission by reducing the spread of ova from the feces of infected individuals into the environment and subsequently to new hosts, while nutrition improvements could reduce host susceptibility to infection. Existing evidence on the effect of these interventions on STH is scarce. In a setting with ongoing mass-drug administration, we assessed the effect of individual and combined water, sanitation, handwashing and nutrition interventions on STH infection in children. Approximately 2.5 years after delivering interventions, we found reductions in STH infection from water treatment and sanitation interventions; there was no reduction from the handwashing and nutrition interventions. While the reductions were modest in magnitude compared to cure rates achieved by deworming drugs, they indicated sustained reduction in environmental transmission. The reductions were more pronounced for STH species that do not have persistent environmental reservoirs. These findings suggest that water treatment and sanitation interventions can augment mass-drug administration programs in striving toward elimination of STH. ]]> Ercumen, A. Benjamin-Chung, J. Arnold, B. F. Lin, A. Hubbard, A. E. Stewart, C. Rahman, Z. Parvez, S. M. Unicomb, L. Rahman, M. Haque, R. Colford, J. M. Luby, S. P. 2019-01-12 doi:10.1101/512509 Cold Spring Harbor Laboratory Press 2019-01-12 <![CDATA[ Stem-cell-ubiquitous genes spatiotemporally coordinate division through regulation of stem-cell-specific gene networks ]]> https://biorxiv.org/content/10.1101/517250v1?rss=1 Clark, N. M. Buckner, E. Fisher, A. P. Nelson, E. C. Nguyen, T. T. Simmons, A. R. de Luis Balaguer, M. A. Butler-Smith, T. Sheldon, P. J. Bergmann, D. C. Williams, C. M. Sozzani, R. 2019-01-10 doi:10.1101/517250 Cold Spring Harbor Laboratory Press 2019-01-10 <![CDATA[ Sequence based mapping identifies AWNS1, a candidate transcription repressor underlying awn suppression at the B1 locus in wheat ]]> https://biorxiv.org/content/10.1101/519264v1?rss=1 DeWitt, N. Guedira, M. Lauer, E. Sarinelli, M. Tyagi, P. Hao, Q. Fu, D. Murphy, J. P. Marshall, D. Akhunova, A. Jordan, K. Akhunov, E. Brown-Guedira, G. 2019-01-18 doi:10.1101/519264 Cold Spring Harbor Laboratory Press 2019-01-18 <![CDATA[ A novel technique for mapping viscosity in discrete subcellular locations with a BODIPY based fluorescent probe ]]> https://biorxiv.org/content/10.1101/522532v1?rss=1 Pytowski, L. Foley, A. C. Hernandez, Z. Moon, N. Donohoe, T. Vaux, D. J. 2019-01-16 doi:10.1101/522532 Cold Spring Harbor Laboratory Press 2019-01-16 <![CDATA[ Microhabitat predicts species differences in exploratory behavior in Lake Malawi cichlids ]]> https://biorxiv.org/content/10.1101/525378v1?rss=1 Johnson, Z. V. Moore, E. C. Wong, R. Y. Godwin, J. R. Streelman, J. T. Roberts, R. B. 2019-01-22 doi:10.1101/525378 Cold Spring Harbor Laboratory Press 2019-01-22 <![CDATA[ Mapping changes in the spatiotemporal distribution of lumpy skin disease virus ]]> https://biorxiv.org/content/10.1101/531343v1?rss=1 Machado, G. Korennoy, F. Alvarez, J. Picasso-Risso, C. Perez, A. VanderWaal, K. 2019-02-01 doi:10.1101/531343 Cold Spring Harbor Laboratory Press 2019-02-01 <![CDATA[ Coupling adaptive molecular evolution to phylodynamics using fitness-dependent birth-death models ]]> https://biorxiv.org/content/10.1101/531525v1?rss=1 Rasmussen, D. A. Stadler, T. 2019-01-26 doi:10.1101/531525 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Same-Species Contamination Detection with Variant Calling Information from Next Generation Sequencing ]]> https://biorxiv.org/content/10.1101/531558v1?rss=1 Jiang, T. Buchkovich, M. Motsinger-Reif, A. 2019-01-26 doi:10.1101/531558 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Sulfur-oxidizing symbionts without canonical genes for autotrophic CO2 fixation ]]> https://biorxiv.org/content/10.1101/540435v1?rss=1 Seah, B. Antony, C. P. Huettel, B. Zarzycki, J. Schada von Borzyskowski, L. Erb, T. Kouris, A. Kleiner, M. Liebeke, M. Dubilier, N. Gruber-Vodicka, H. 2019-02-05 doi:10.1101/540435 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Coinfection of semi-infectious particles can contribute substantially to influenza infection dynamics ]]> https://biorxiv.org/content/10.1101/547349v1?rss=1 Farrell, A. Brooke, C. Koelle, K. Ke, R. 2019-02-12 doi:10.1101/547349 Cold Spring Harbor Laboratory Press 2019-02-12 <![CDATA[ Window to the Fluorescence: The White Eye-Color Gene of Western Corn Rootworm, Diabrotica virgifera virgifera ]]> https://biorxiv.org/content/10.1101/552935v1?rss=1 Grubbs, N. Chu, F.-C. Lorenzen, M. 2019-02-18 doi:10.1101/552935 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ Report on the spatial spread of defective interfering particles and its role in suppressing infectious particles ]]> https://biorxiv.org/content/10.1101/558932v1?rss=1 Ali, Q. Ke, R. 2019-03-06 doi:10.1101/558932 Cold Spring Harbor Laboratory Press 2019-03-06 <![CDATA[ Spatial distribution and spread potential of sixteen Leptospira serovars in a subtropical region of Brazil ]]> https://biorxiv.org/content/10.1101/559609v1?rss=1 Jara, M. Escobar, L. Rodriges, R. O. Frias, A. Sanhueza, J. Machado, G. 2019-02-28 doi:10.1101/559609 Cold Spring Harbor Laboratory Press 2019-02-28 <![CDATA[ Consistent and correctable bias in metagenomic sequencing measurements ]]> https://biorxiv.org/content/10.1101/559831v1?rss=1 McLaren, M. R. Willis, A. D. Callahan, B. J. 2019-02-25 doi:10.1101/559831 Cold Spring Harbor Laboratory Press 2019-02-25 <![CDATA[ Major QTLs for resistance to early and late leaf spot diseases are identified on chromosomes 3 and 5 in peanut (Arachis hypogaea) ]]> https://biorxiv.org/content/10.1101/567206v1?rss=1 Chu, Y. Chee, P. Culbreath, A. K. Isleib, T. G. Holbrook, C. C. Ozias-Akins, P. 2019-03-04 doi:10.1101/567206 Cold Spring Harbor Laboratory Press 2019-03-04 <![CDATA[ The Trichoplax microbiome: the simplest animal lives in an intimate symbiosis with two intracellular bacteria ]]> https://biorxiv.org/content/10.1101/568287v1?rss=1 Gruber-Vodicka, H. R. Leisch, N. Kleiner, M. Hinzke, T. Liebeke, M. McFall-Ngai, M. Hadfield, M. G. Dubilier, N. 2019-03-05 doi:10.1101/568287 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ How to make more from exposure data? An integrated machine learning pipeline to predict pathogen exposure ]]> https://biorxiv.org/content/10.1101/569012v1?rss=1 Fountain-Jones, N. Machado, G. Carver, S. Packer, C. Mendoza, M. Craft, M. E. 2019-03-06 doi:10.1101/569012 Cold Spring Harbor Laboratory Press 2019-03-06 <![CDATA[ Genomic analysis reveals shared genes and pathways in human and canine angiosarcoma ]]> https://biorxiv.org/content/10.1101/570879v1?rss=1 Megquier, K. Turner-Maier, J. Swofford, R. Kim, J.-H. Sarver, A. L. Wang, C. Sakthikumar, S. Johnson, J. Koltookian, M. Lewellen, M. Scott, M. C. Graef, A. J. Borst, L. Tonomura, N. Alfoldi, J. Painter, C. Thomas, R. Karlsson, E. K. Breen, M. Modiano, J. F. Elvers, I. Lindblad-Toh, K. 2019-03-08 doi:10.1101/570879 Cold Spring Harbor Laboratory Press 2019-03-08 <![CDATA[ Differences in proteome response to cold acclimation in Zoysia japonica cultivars with different levels of freeze tolerance ]]> https://biorxiv.org/content/10.1101/581488v1?rss=1 Brown, J. M. Holloway, M. P. Dacosta, M. A. Bernstein, R. P. Lu, J. H. Tuong, T. D. Patton, A. J. Dunne, J. C. Arellano, C. Livingston, D. P. Milla-Lewis, S. R. 2019-03-19 doi:10.1101/581488 Cold Spring Harbor Laboratory Press 2019-03-19 <![CDATA[ Functional diversification enabled grassy biomes to fill global climate space ]]> https://biorxiv.org/content/10.1101/583625v1?rss=1 50% of the ground layer is covered by grasses) occupy almost every part of Earths vegetated climate space, characterising over 40% of the land surface. Major evolutionary lineages of grasses have specialised in different environments, but species from only three grass lineages occupy 88% of the land area of grassy vegetation, segregating along gradients of temperature, rainfall and fire. The environment occupied by each lineage is associated with unique plant trait combinations, including C3 and C4 photosynthesis, maximum plant height, and adaptations to fire and aridity. There is no single global climatic limit where C4 grasses replace C3 grasses. Instead this ecological transition varies biogeographically, with continental disjunctions arising through contrasting evolutionary histories.nnSignificance statementWorldviews of vegetation generally focus on trees and forests but grasses characterize the ground layer over 40% of the Earths vegetated land surface. This omission is important because grasses transform surface-atmosphere exchanges, biodiversity and disturbance regimes. We looked beneath the trees to produce the first global map of grass-dominated biomes. Grassy biomes occur in virtually every climate on Earth. However, three lineages of grasses are much more successful than others, characterizing 88% of the land area of grassy biomes. Each of these grass lineages evolved ecological specializations related to aridity, freezing and fire. Recognizing the extent and causes of grass dominance beneath trees is important because grassy vegetation plays vital roles in the dynamics of our biosphere and human wellbeing. ]]> Lehmann, C. Griffith, D. Simpson, K. Anderson, M. Archibald, S. Beerling, D. Bond, W. Denton, E. Edwards, E. Forrestel, E. Fox, D. Georges, D. Hoffmann, W. Kluyver, T. Mucina, L. Pau, S. Ratnam, J. Salamin, N. Santini, B. Smith, M. Spriggs, E. Westley, R. Still, C. Stromberg, C. Osborne, C. 2019-03-21 doi:10.1101/583625 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Hemimetabolous insects elucidate the origin of sexual development via alternative splicing ]]> https://biorxiv.org/content/10.1101/587964v1?rss=1 Wexler, J. Delaney, E. Belles, X. Schal, C. Wada-Katsumata, A. Amicucci, M. Kopp, A. 2019-03-26 doi:10.1101/587964 Cold Spring Harbor Laboratory Press 2019-03-26 <![CDATA[ Driving the scalability of DNA-based information storage systems ]]> https://biorxiv.org/content/10.1101/591594v1?rss=1 Tomek, K. J. Volkel, K. Simpson, A. Hass, A. G. Indermaur, E. W. Tuck, J. Keung, A. J. 2019-03-29 doi:10.1101/591594 Cold Spring Harbor Laboratory Press 2019-03-29 <![CDATA[ Identification of novel neuroprotective loci modulating ischemic stroke volume in a cross between wild-derived inbred mouse strains ]]> https://biorxiv.org/content/10.1101/591669v1?rss=1 Lee, H. K. Widmayer, S. J. Aylor, D. L. Marchuk, D. 2019-03-28 doi:10.1101/591669 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ A Bile Duct-on-a-Chip with Organ-Level Functions ]]> https://biorxiv.org/content/10.1101/594291v1?rss=1 Du, Y. Khandekar, G. Llewellyn, J. Polacheck, W. Chen, C. S. Wells, R. G. 2019-03-30 doi:10.1101/594291 Cold Spring Harbor Laboratory Press 2019-03-30 <![CDATA[ Managing congestion at visitor hotspots using park-level use level data: Case study of a Chinese World Heritage site ]]> https://biorxiv.org/content/10.1101/596031v1?rss=1 Guo, J.-H. Guo, T. Lin, K.-M. Leung, Y.-F. Chen, Q.-H. 2019-04-02 doi:10.1101/596031 Cold Spring Harbor Laboratory Press 2019-04-02 <![CDATA[ Additive genetic variance for lifetime fitness and the capacity for adaptation in the wild ]]> https://biorxiv.org/content/10.1101/601682v1?rss=1 Kulbba, M. W. Sheth, S. N. Pain, R. E. Eckhart, V. M. Shaw, R. G. 2019-04-07 doi:10.1101/601682 Cold Spring Harbor Laboratory Press 2019-04-07 <![CDATA[ Genomic prediction accuracies and abilities for growth and wood quality traits of Scots pine, using genotyping-by-sequencing (GBS) data ]]> https://biorxiv.org/content/10.1101/607648v1?rss=1 Calleja-Rodriguez, A. Pan, J. Funda, T. Chen, Z.-q. Baison, J. Isik, F. Abrahamsson, S. Wu, H. X. 2019-04-12 doi:10.1101/607648 Cold Spring Harbor Laboratory Press 2019-04-12 <![CDATA[ A shared core microbiome in soda lakes separated by large distances ]]> https://biorxiv.org/content/10.1101/608471v1?rss=1 8,000 km apart. We present evidence for (very rare) dispersion of some core microbiome members from Canadian mats to Central Asian soda lake sediments. The close similarity between distant microbial communities indicates that these communities share common design principles, that reproducibly lead to a high and robust productivity. We unravel a few examples of such principles and speculate that these might be applied to create robust biotechnology for carbon dioxide conversion, to mitigate of global climate change. ]]> Zorz, J. K. Sharp, C. E. Kleiner, M. Gordon, P. M. Pon, R. T. Dong, X. Strous, M. 2019-04-13 doi:10.1101/608471 Cold Spring Harbor Laboratory Press 2019-04-13 <![CDATA[ After the Honeymoon, the Divorce: Unexpected Outcomes of Disease Control Measures Against Endemic Infections ]]> https://biorxiv.org/content/10.1101/608653v1?rss=1 Hollingsworth, B. Okamoto, K. Lloyd, A. 2019-04-19 doi:10.1101/608653 Cold Spring Harbor Laboratory Press 2019-04-19 <![CDATA[ Microclimate and larval habitat density predict adult Aedes albopictus abundance in urban areas ]]> https://biorxiv.org/content/10.1101/615625v1?rss=1 Evans, M. V. Hintz, C. W. Jones, L. Shiau, J. Solano, N. Drake, J. M. Murdock, C. C. 2019-04-22 doi:10.1101/615625 Cold Spring Harbor Laboratory Press 2019-04-22 <![CDATA[ The continuing impact of an ancient polyploidy on the genomes of teleosts ]]> https://biorxiv.org/content/10.1101/619205v1?rss=1 Conant, G. 2019-04-26 doi:10.1101/619205 Cold Spring Harbor Laboratory Press 2019-04-26 <![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[ The Catalytic Core of DEMETER Guides Active DNA Demethylation in Arabidopsis ]]> https://biorxiv.org/content/10.1101/623843v1?rss=1 Zhang, C. Hung, Y.-H. Zhang, X.-Q. Zhang, D. Frost, J. M. Liu, F. Xiao, W. Iyer, L. M. Aravind, L. Huh, J. H. Fischer, R. L. Hsieh, T.-F. 2019-05-01 doi:10.1101/623843 Cold Spring Harbor Laboratory Press 2019-05-01 <![CDATA[ Queen honey bees combat heat stress-induced loss of stored sperm viability with ATP-independent heat shock proteins ]]> https://biorxiv.org/content/10.1101/627729v1?rss=1 McAfee, A. Higo, H. Underwood, R. M. Milone, J. P. Foster, L. J. Guarna, M. M. Pettis, J. S. Tarpy, D. R. 2019-05-05 doi:10.1101/627729 Cold Spring Harbor Laboratory Press 2019-05-05 <![CDATA[ Comparison of multi-parallel qPCR and Kato-Katz for detection of soil-transmitted helminth infection among children in rural Bangladesh ]]> https://biorxiv.org/content/10.1101/629501v1?rss=1 Benjamin-Chung, J. Pilotte, N. Ercumen, A. Grant, J. R. Maasch, J. R. M. A. Gonzales, A. M. Abrams, B. P. Ester, A. C. Arnold, B. F. Rahman, M. Haque, R. Hubbard, A. E. Luby, S. P. Williams, S. A. Colford, J. M. 2019-05-10 doi:10.1101/629501 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Factors affecting pathogenicity of the turfgrass dollar spot pathogen in natural and model hosts ]]> https://biorxiv.org/content/10.1101/630582v1?rss=1 Rioux, R. A. Stephens, C. Kerns, J. P. 2019-05-07 doi:10.1101/630582 Cold Spring Harbor Laboratory Press 2019-05-07 <![CDATA[ Environmental, social, management and health factors associated with within- and between-individual variability in fecal glucocorticoid metabolite concentrations in zoo-housed Asian and African elephants ]]> https://biorxiv.org/content/10.1101/634691v1?rss=1 Brown, J. L. Bray, J. Carlstead, K. L. Dickey, D. Farin, C. Ange, K. 2019-05-10 doi:10.1101/634691 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ From morphogenesis to pathogenesis: A cellulose loosening protein is one of the most widely distributed tools in nature ]]> https://biorxiv.org/content/10.1101/637728v1?rss=1 Chase, W. R. Zhaxybayeva, O. Rocha, J. Cosgrove, D. J. Shapiro, L. R. 2019-05-16 doi:10.1101/637728 Cold Spring Harbor Laboratory Press 2019-05-16 <![CDATA[ Genomics of clinal local adaptation in Pinus sylvestris under continuous environmental and spatial genetic setting ]]> https://biorxiv.org/content/10.1101/647412v1?rss=1 Tyrmi, J. S. Vuosku, J. Acosta, J. J. Li, Z. Sterck, L. Savolainen, O. Pyhajarvi, T. 2019-05-24 doi:10.1101/647412 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Reconsidering the management paradigm of fragmented populations ]]> https://biorxiv.org/content/10.1101/649129v1?rss=1 Kolodny, O. McLaren, M. R. Greenbaum, G. Ramakrishnan, U. Feldman, M. W. Petrov, D. Taylor, R. W. 2019-05-24 doi:10.1101/649129 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Host-microbe interactions in the chemosynthetic Riftia pachyptila symbiosis ]]> https://biorxiv.org/content/10.1101/651323v1?rss=1 Hinzke, T. Kleiner, M. Breusing, C. Felbeck, H. Haesler, R. Sievert, S. M. Schlueter, R. Rosenstiel, P. Reusch, T. B. H. Schweder, T. Markert, S. 2019-05-27 doi:10.1101/651323 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ PyBSASeq: a novel, simple, and effective algorithm for BSA-Seq data analysis ]]> https://biorxiv.org/content/10.1101/654137v1?rss=1 Zhang, J. Panthee, D. 2019-05-29 doi:10.1101/654137 Cold Spring Harbor Laboratory Press 2019-05-29 <![CDATA[ Untargeted Metabolomic Profiling Identifies Disease-specific Profiles in Food Allergy ]]> https://biorxiv.org/content/10.1101/657866v1?rss=1 Crestani, E. Harb, H. Charbonnier, L. M. Leirer, J. Motsinger-Reif, A. Rachid, R. Phipatanakul, W. Kaddurah-Daouk, R. Chatila, T. A. 2019-06-03 doi:10.1101/657866 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Community turnover by composition and climate affinity across scales in an alpine system ]]> https://biorxiv.org/content/10.1101/659169v1?rss=1 Smithers, B. V. Oldfather, M. F. Koontz, M. J. Bishop, J. Bishop, C. Nachlinger, J. Sheth, S. N. 2019-06-19 doi:10.1101/659169 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ On the Effectiveness of UAS for Anti-Poaching in the African Arid Savanna ]]> https://biorxiv.org/content/10.1101/660126v1?rss=1 Silverberg, L. M. vanVuuren, M. vanVuuren, R. Lutz, G. 2019-06-05 doi:10.1101/660126 Cold Spring Harbor Laboratory Press 2019-06-05 <![CDATA[ Association Tests Using Copy Number Profile Curves (CONCUR) Enhances Power in Rare Copy Number Variant Analysis ]]> https://biorxiv.org/content/10.1101/666875v1?rss=1 Brucker, A. R. Lu, W. Marceau West, R. Yu, Q.-Y. Hsiao, C. K. Hsiao, T.-H. Lin, C.-H. Magnusson, P. K. E. Sullivan, P. F. Szatkiewicz, J. Lu, T.-P. Tzeng, J.-Y. 2019-06-10 doi:10.1101/666875 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Modeling cross-regulatory influences on monolignol transcripts and proteins under single and combinatorial gene knockdowns in Populus trichocarpa ]]> https://biorxiv.org/content/10.1101/677047v1?rss=1 Matthews, M. L. Wang, J. P. Sederoff, R. Chiang, V. L. Williams, C. 2019-06-19 doi:10.1101/677047 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ Development and testing of a novel Killer-Rescue self-limiting gene drive system in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/680629v1?rss=1 Webster, S. H. Vella, M. R. Scott, M. 2019-06-23 doi:10.1101/680629 Cold Spring Harbor Laboratory Press 2019-06-23 <![CDATA[ Exploring the Relationship between Geomagnetic Activity and Human Heart Rate Variability ]]> https://biorxiv.org/content/10.1101/684035v1?rss=1 Mattoni, M. Ahn, S. Frohlich, C. Frohlich, F. 2019-06-26 doi:10.1101/684035 Cold Spring Harbor Laboratory Press 2019-06-26 <![CDATA[ Tissue-specific changes in size and shape of the ligaments and tendons of the porcine knee during post-natal growth ]]> https://biorxiv.org/content/10.1101/688820v1?rss=1 Cone, S. G. Piercy, H. E. Lambeth, E. P. Ru, H. Piedrahita, J. A. Spang, J. T. Fordham, L. A. Fisher, M. 2019-07-01 doi:10.1101/688820 Cold Spring Harbor Laboratory Press 2019-07-01 <![CDATA[ Unraveling the hexaploid sweetpotato inheritance using ultra-dense multilocus mapping ]]> https://biorxiv.org/content/10.1101/689638v1?rss=1 Mollinari, M. Olukolu, B. A. Da Silva Pereira, G. Khan, A. Gemenet, D. C. Yencho, G. C. Zeng, Z.-B. 2019-07-02 doi:10.1101/689638 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Bacterial communities of herbivores and pollinators that have co-evolved Cucurbita spp. ]]> https://biorxiv.org/content/10.1101/691378v1?rss=1 Shapiro, L. R. Youngblom, M. Scully, E. D. Rocha, J. Paulson, J. N. Klepac-Ceraj, V. Cibrian-Jaramillo, A. Lopez-Uribe, M. M. 2019-07-03 doi:10.1101/691378 Cold Spring Harbor Laboratory Press 2019-07-03 <![CDATA[ Inoculation with the mycorrhizal fungus Rhizophagus irregulars increases nutrient uptake in maize (Zea mays) through hyphal foraging and promotion of root growth ]]> https://biorxiv.org/content/10.1101/695411v1?rss=1 Ramirez Flores, M. R. Bello-Bello, E. Rellan Alvarez, R. Sawers, R. J. H. Olalde-Portugal, V. 2019-07-08 doi:10.1101/695411 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ Secondary bile acid ursodeoxycholic acid (UDCA) alters weight, the gut microbiota, and the bile acid pool in conventional mice ]]> https://biorxiv.org/content/10.1101/698795v1?rss=1 Winston, J. A. Rivera, A. Cai, J. Patterson, A. D. Theriot, C. M. 2019-07-11 doi:10.1101/698795 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ Warm nights disrupt global transcriptional rhythms in field-grown rice panicles ]]> https://biorxiv.org/content/10.1101/702183v1?rss=1 Desai, J. S. Lawas, L. M. F. Valente, A. M. Leman, A. R. Grinevich, D. O. Jagadish, S. K. Doherty, C. 2019-07-16 doi:10.1101/702183 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ Single-gene resolution of locally adaptive genetic variation in Mexican maize ]]> https://biorxiv.org/content/10.1101/706739v1?rss=1 Gates, D. J. Runcie, D. Janzen, G. M. Romero Navarro, A. Willcox, M. Sonder, K. Snodgrass, S. Rodriguez-Zapata, F. Sawers, R. J. Rellan-Alvarez, R. Buckler, E. S. Hearne, S. Hufford, M. B. Ross-Ibarra, J. 2019-07-18 doi:10.1101/706739 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ International lineages of Salmonella enterica serovars isolated from chicken farms, Wakiso District, Uganda ]]> https://biorxiv.org/content/10.1101/707372v1?rss=1 Ball, T. Fedorka-cray, P. J. Farias Marinho do Monte, D. Aidara-Kane, A. Ru, H. Thakur, S. Ejobi, F. Matheu, J. 2019-07-18 doi:10.1101/707372 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ Thermodynamic and Kinetic Characterization of Protein Conformational Dynamics within a Riemannian Diffusion Formalism ]]> https://biorxiv.org/content/10.1101/707711v1?rss=1 Goolsby, C. Fakharzadeh, A. Moradi, M. 2019-07-26 doi:10.1101/707711 Cold Spring Harbor Laboratory Press 2019-07-26 <![CDATA[ Stroke prevents exercise-induced gains in bone microstructure but not composition in mice ]]> https://biorxiv.org/content/10.1101/708388v1?rss=1 Hanne, N. J. Steward, A. J. Sessions, M. R. Thornburg, H. L. Sheng, H. Cole, J. H. 2019-07-19 doi:10.1101/708388 Cold Spring Harbor Laboratory Press 2019-07-19 <![CDATA[ Validating Minimally Invasive Laser Doppler Flowmetry for Serial Bone Perfusion Measurements in Mice ]]> https://biorxiv.org/content/10.1101/708412v1?rss=1 Hanne, N. J. Easter, E. D. Cole, J. H. 2019-07-19 doi:10.1101/708412 Cold Spring Harbor Laboratory Press 2019-07-19 <![CDATA[ A Minimally Invasive Technique for Serial Intraosseous Perfusion Measurements in the Murine Tibia Using Laser Doppler Flowmetry ]]> https://biorxiv.org/content/10.1101/708453v1?rss=1 Hanne, N. J. Easter, E. D. Stangeland-Molo, S. Cole, J. H. 2019-07-22 doi:10.1101/708453 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ Improving yield and fruit quality traits in sweet passion fruit: evidence for genotype by environment interaction and cross-compatibility in selected genotypes ]]> https://biorxiv.org/content/10.1101/714162v1?rss=1 Chavarria-Perez, L. M. Giordani, W. Dias, K. O. G. Costa, Z. P. Ribeiro, C. A. M. Benedetti, A. R. Cauz-Santos, L. A. Pereira, G. S. Rosa, J. R. B. F. Garcia, A. A. F. Vieira, M. L. C. 2019-07-25 doi:10.1101/714162 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ Heterospecific aggression differs predominately by species, rather than sex, in Lake Malawi cichlid fish ]]> https://biorxiv.org/content/10.1101/720375v1?rss=1 Moore, E. C. Roberts, R. B. 2019-07-30 doi:10.1101/720375 Cold Spring Harbor Laboratory Press 2019-07-30 <![CDATA[ Pedigree-based measurement of the de novo mutation rate in the gray mouse lemur reveals a high mutation rate, few mutations in CpG sites, and a weak sex bias ]]> https://biorxiv.org/content/10.1101/724880v1?rss=1 Campbell, C. R. Tiley, G. P. Poelstra, J. W. Hunnicutt, K. E. Larsen, P. A. dos Reis, M. Yoder, A. D. 2019-08-05 doi:10.1101/724880 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ Inositol Trisphosphate Kinase and Diphosphoinositol Pentakisphosphate Kinase Enzymes Constitute the Inositol Pyrophosphate Synthesis Pathway in Plants ]]> https://biorxiv.org/content/10.1101/724914v1?rss=1 Adepoju, O. Williams, S. P. Craige, B. Cridland, C. A. Sharp, A. K. Brown, A. M. Land, E. Perera, I. Y. Mena, D. Sobrado, P. Gillaspy, G. E. 2019-08-05 doi:10.1101/724914 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ A Fyn - specific biosensor reveals localized, pulsatile kinase activity and spatially regulated signaling crosstalk ]]> https://biorxiv.org/content/10.1101/726133v1?rss=1 Mukherjee, A. Singh, R. Udayan, S. Biswas, S. Pothula, P. Manmadhan, S. George, G. Dilip Kumar, S. Das, R. Rao, B. M. Gulyani, A. 2019-08-05 doi:10.1101/726133 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ Screening yeast display libraries against magnetized yeast cell targets enables efficient isolation of membrane protein binders. ]]> https://biorxiv.org/content/10.1101/728436v1?rss=1 100-fold, in a single round of screening, suggesting feasibility of screening combinatorial libraries. Subsequently, we screened yeast display libraries of Sso7d and nanobody variants against yeast displayed targets to isolate binders specific to the cytosolic domain of the mitochondrial membrane protein TOM22 (KD ~ 271-2009 nM) and the extracellular domain of the c-Kit receptor (KD ~ 131 to KD >2000 nM). Additional studies showed that the TOM22 binders identified using this approach could be used for the enrichment of mitochondria from cell lysates, thereby confirming binding to the native mitochondrial protein. The ease of expressing a membrane protein or a domain thereof as a yeast cell surface fusion - in contrast to recombinant soluble expression - makes the use of yeast-displayed targets particularly attractive. Therefore, we expect the use of magnetized yeast cell targets will enable efficient isolation of binders to membrane proteins.nnO_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY ]]> Bacon, K. Burroughs, M. Blain, A. Menegatti, S. Rao, B. M. 2019-08-07 doi:10.1101/728436 Cold Spring Harbor Laboratory Press 2019-08-07 <![CDATA[ High Fat Diet-Induced Obesity Negatively Affects Whole Bone Bending Strength but not Cortical Structure in the Femur ]]> https://biorxiv.org/content/10.1101/729624v1?rss=1 Hanne, N. J. Steward, A. J. Cox, J. M. Easter, E. D. Thornburg, H. L. Sessions, M. R. Pinnamaraju, S. V. Cole, J. H. 2019-08-08 doi:10.1101/729624 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ Ischemic Stroke Reduces Bone Perfusion and Alters Osteovascular Structure ]]> https://biorxiv.org/content/10.1101/729632v1?rss=1 Hanne, N. J. Steward, A. J. Geeroms, C. Easter, E. D. Thornburg, H. L. Kerckhofs, G. Parac-Vogt, T. Sheng, H. Cole, J. H. 2019-08-08 doi:10.1101/729632 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ Natural genetic variation underlying tiller development in barley (Hordeum vulgare L) ]]> https://biorxiv.org/content/10.1101/730945v1?rss=1 Haaning, A. M. Smith, K. P. Brown-Guedira, G. Chao, S. Tyagi, P. Muehlbauer, G. J. 2019-08-09 doi:10.1101/730945 Cold Spring Harbor Laboratory Press 2019-08-09 <![CDATA[ Engineered cartilage from human chondrocytes with homozygous knockout of cell cycle inhibitor p21 ]]> https://biorxiv.org/content/10.1101/731216v1?rss=1 D'Costa, S. Rich, M. J. Diekman, B. O. 2019-08-09 doi:10.1101/731216 Cold Spring Harbor Laboratory Press 2019-08-09 <![CDATA[ Transcriptome-based Analysis of Tomato Genotypes Resistant to Bacterial spot (Xanthomonas perforans) Race T4 ]]> https://biorxiv.org/content/10.1101/736660v1?rss=1 Shi, R. Panthee, D. R. 2019-08-15 doi:10.1101/736660 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Genetic analysis of seed and pod traits in a set of Recombinant Inbred Lines (RILs) in peanut (Arachis hypogaea L.) ]]> https://biorxiv.org/content/10.1101/738914v1?rss=1 20% variance) were attributed to NC 3033 and located in a single linkage group, LG B06_1. In contrast, the most consistent QTL for kernel percentage were located on A07/B07 and derived from Tifrunner. ]]> Chavarro, C. Chu, Y. Holbrook, C. C. Isleib, T. Bertioli, D. Hovav, R. Butts, C. Marshall, L. Sorensen, R. Jackson, S. A. Ozias-Akins, P. 2019-08-18 doi:10.1101/738914 Cold Spring Harbor Laboratory Press 2019-08-18 <![CDATA[ Shuttling of Dorsal by Cactus: mechanism and implications ]]> https://biorxiv.org/content/10.1101/739284v1?rss=1 Schloop, A. E. Carrell-Noel, S. Reeves, G. T. 2019-08-19 doi:10.1101/739284 Cold Spring Harbor Laboratory Press 2019-08-19 <![CDATA[ Robustness of the Dorsal morphogen gradient with respect to morphogen dosage ]]> https://biorxiv.org/content/10.1101/739292v1?rss=1 Al Asafen, H. Y. Bandodkar, P. U. Carrell-Noel, S. Reeves, G. T. 2019-08-19 doi:10.1101/739292 Cold Spring Harbor Laboratory Press 2019-08-19 <![CDATA[ Tunable self-cleaving ribozymes for modulating gene expression in eukaryotic systems ]]> https://biorxiv.org/content/10.1101/739326v1?rss=1 Jacobsen, T. Yi, G. Al Asafen, H. Y. Jermusyk, A. A. Beisel, C. L. Reeves, G. T. 2019-08-18 doi:10.1101/739326 Cold Spring Harbor Laboratory Press 2019-08-18 <![CDATA[ Short-term effects of GPS collars on the activity, behavior, and adrenal response of scimitar-horned oryx (Oryx dammah) ]]> https://biorxiv.org/content/10.1101/740191v1?rss=1 3 days post-collaring). Similarly, FGM concentrations (i.e., stress hormones) increased after GPS collars were fitted on animals but returned to pre-collaring levels within 5 days of collaring. Lastly, tri-axial accelerometers, collecting data at eight positions per second, indicated a > 480 percent increase in the amount of hourly headshaking immediately after collaring. This post-collaring increase in headshaking was estimated to decline in magnitude within 4 hours after GPS collar fitting. These effects constitute a handling and/or habituation response (model dependent), with animals showing short-term responses in activity, behavior, and stress that dissipated within several hours to several days of being fitted with GPS collars. Importantly, none of our analyses indicated any long-term effects that would have more pressing animal welfare concerns. ]]> Stabach, J. A. Cunningham, S. A. Connette, G. Mota, J. L. Reed, D. Byron, M. Songer, M. Wacher, T. Mertes, K. Brown, J. L. Comizzoli, P. Newby, J. Monfort, S. Leimgruber, P. 2019-08-19 doi:10.1101/740191 Cold Spring Harbor Laboratory Press 2019-08-19 <![CDATA[ Human cerebral organoids capture the spatiotemporal complexity and disease dynamics of UBE3A ]]> https://biorxiv.org/content/10.1101/742213v1?rss=1 Sen, D. Voulgaropoulos, A. Drobna, Z. Keung, A. J. 2019-08-22 doi:10.1101/742213 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ The relevance of dominance and functional annotations to predict agronomic traits in hybrid maize ]]> https://biorxiv.org/content/10.1101/745208v1?rss=1 Ramstein, G. P. Larsson, S. J. Cook, J. P. Edwards, J. Ersoz, E. S. Flint-Garcia, S. Gardner, C. A. Holland, J. B. Lorenz, A. J. McMullen, M. D. Millard, M. J. Rocheford, T. R. Tuinstra, M. R. Bradbury, P. Buckler, E. S. Romay, M. C. 2019-08-24 doi:10.1101/745208 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ When a phenotype is not the genotype: Implications of phenotype misclassification and pedigree errors in genomics-assisted breeding of sweetpotato ]]> https://biorxiv.org/content/10.1101/747469v1?rss=1 Gemenet, D. C. De Boeck, B. Pereira, G. D. S. Kitavi, M. N. Ssali, R. T. Utoblo, O. Swanckaert, J. Carey, E. Gruneberg, W. Yada, B. Yencho, C. Mwanga, R. O. M. 2019-08-28 doi:10.1101/747469 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ Replicated Umbilical Cord Blood DNA Methylation Loci Associated with Gestational Age at Birth ]]> https://biorxiv.org/content/10.1101/749135v1?rss=1 York, T. Latendresse, S. J. Jackson-Cook, C. Lapato, D. Moyer, S. Wolen, A. R. Roberson-Nay, R. Do, E. K. Murphy, S. K. Hoyo, C. Fuemmeler, B. F. Strauss, J. F. 2019-09-03 doi:10.1101/749135 Cold Spring Harbor Laboratory Press 2019-09-03 <![CDATA[ Resurrection of ancestral effector caspases identifies novel networks for evolution of substrate specificity ]]> https://biorxiv.org/content/10.1101/749143v1?rss=1 Grinshpon, R. D. Shrestha, S. Titus-McQuillan, J. Hamilton, P. T. Swartz, P. D. Clark, A. C. 2019-08-28 doi:10.1101/749143 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ Ultra-Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea) ]]> https://biorxiv.org/content/10.1101/761874v1?rss=1 cruaud, a. Delvare, G. Nidelet, S. Saune, L. Ratnasingham, S. Chartois, M. Blaimer, B. B. Gates, M. Brady, S. G. Faure, S. van Noort, S. Rossi, J.-P. Rasplus, j.-y. 2019-09-09 doi:10.1101/761874 Cold Spring Harbor Laboratory Press 2019-09-09 <![CDATA[ Two distinct trophectoderm lineage stem cells from human pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/762542v1?rss=1 Mischler, A. Karakis, V. Mahinthakumar, J. Carberry, C. San Miguel, A. Rager, J. Fry, R. Rao, B. M. 2019-09-08 doi:10.1101/762542 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ Environmental decomposition of cuticular hydrocarbons generates a volatile pheromone that guides insect social behavior ]]> https://biorxiv.org/content/10.1101/773937v1?rss=1 Hatano, E. Wada-Katsumata, A. Schal, C. 2019-09-19 doi:10.1101/773937 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ GWAS and Fine-Mapping of Livability and Six Disease Traits in Holstein Cattle ]]> https://biorxiv.org/content/10.1101/775098v1?rss=1 Freebern, E. Santos, D. Fang, L. Jiang, J. Parker Gaddis, K. Liu, G. VanRaden, P. Maltecca, C. Cole, J. Ma, L. 2019-09-19 doi:10.1101/775098 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Systematic profiling of full-length immunoglobulin and T-cell receptor repertoire diversity in rhesus macaque through long read transcriptome sequencing ]]> https://biorxiv.org/content/10.1101/782938v1?rss=1 Brochu, H. Tseng, E. Smith, E. Thomas, M. J. Jones, A. Diveley, K. Law, L. Hansen, S. G. Picker, L. Gale, M. Peng, X. 2019-09-26 doi:10.1101/782938 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Genetic transformation and live-cell nuclear and actin dynamics during the life cycle of a chytrid ]]> https://biorxiv.org/content/10.1101/787945v1?rss=1 Medina, E. M. Robinson, K. A. Bellingham-Johnstun, K. Ianiri, G. Laplante, C. Fritz-Laylin, L. K. Buchler, N. E. 2019-09-30 doi:10.1101/787945 Cold Spring Harbor Laboratory Press 2019-09-30 <![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[ Insights from a survey-based analysis of the academic job market ]]> https://biorxiv.org/content/10.1101/796466v1?rss=1 Fernandes, J. D. Sarabipour, S. Smith, C. T. Niemi, N. M. Jadavji, N. M. Kozik, A. J. Holehouse, A. S. Pejaver, V. Symmons, O. Bisson Filho, A. W. Haage, A. 2019-10-09 doi:10.1101/796466 Cold Spring Harbor Laboratory Press 2019-10-09 <![CDATA[ A Mechanical Model of Early Somite Segmentation ]]> https://biorxiv.org/content/10.1101/804203v1?rss=1 Adhyapok, P. Piatkowska, A. M. Clendenon, S. G. Stern, C. D. Glazier, J. A. Belmonte, J. M. 2019-10-13 doi:10.1101/804203 Cold Spring Harbor Laboratory Press 2019-10-13 <![CDATA[ Association between DNA methylation and ADHD symptoms from birth to school age: A prospective meta-analysis ]]> https://biorxiv.org/content/10.1101/806844v1?rss=1 Neumann, A. Walton, E. Alemany, S. Cecil, C. Gonzalez, J. R. Jima, D. D. Lahti, J. Tuominen, S. T. Barker, E. D. Binder, E. Caramaschi, D. Carracedo, A. Czamara, D. Evandt, J. Felix, J. F. Fuemmeler, B. F. Gutzkow, K. B. Hoyo, C. Julvez, J. Kajantie, E. Laivuori, H. Maguire, R. Maitre, L. Murphy, S. K. Murcia, M. Villa, P. M. Sharp, G. Sunyer, J. Raikkonen, K. Bakermans-Kranenburg, M. van IJzendoorn, M. Guxens, M. Relton, C. L. Tiemeier, H. 2019-10-16 doi:10.1101/806844 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Learning Your Heart Actions From Pulse: ECG Waveform Reconstruction From PPG ]]> https://biorxiv.org/content/10.1101/815258v1?rss=1 Zhu, Q. Tian, X. Wong, C.-W. Wu, M. 2019-10-22 doi:10.1101/815258 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ The Toxin Cercosporin is a Virulence Factor for Infection of Coffee by Cercospora coffeicola ]]> https://biorxiv.org/content/10.1101/818328v1?rss=1 Souza, A. Herrero, S. Daub, M. 2019-10-25 doi:10.1101/818328 Cold Spring Harbor Laboratory Press 2019-10-25 <![CDATA[ Characterization of C. difficile strains isolated from companion animals and the associated changes in the host fecal microbiota ]]> https://biorxiv.org/content/10.1101/822577v1?rss=1 Thanissery, R. McLaren, M. R. Rivera, A. Reed, A. D. Betrapally, N. S. Burdette, T. Winston, J. A. Jacob, M. Callahan, B. J. Theriot, C. M. 2019-10-29 doi:10.1101/822577 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ Leveraging multiple layers of data to predict Drosophila complex traits ]]> https://biorxiv.org/content/10.1101/824896v1?rss=1 Morgante, F. Huang, W. Sorensen, P. Maltecca, C. Mackay, T. 2019-10-30 doi:10.1101/824896 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ Development of diagnostic SNP markers for quality assurance and control in sweetpotato breeding programs ]]> https://biorxiv.org/content/10.1101/826792v1?rss=1 Gemenet, D. C. Kitavi, M. N. David, M. Ndege, D. Ssali, R. T. Swanckaert, J. Makunde, G. Yencho, C. Gruneberg, W. Carey, E. Mwanga, R. O. Andrade, M. I. Heck, S. Campos, H. 2019-10-31 doi:10.1101/826792 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ Inference of Population Genetic Structure and High Linkage Disequilibrium AmongAlternaria spp. Collected from Tomato and Potato Using Genotyping by Sequencing ]]> https://biorxiv.org/content/10.1101/827790v1?rss=1 0.8). To measure the strength of the linkage disequilibrium (LD), we also calculated the allelic association between pairs of loci. Lewontins D (measures the fraction of allelic variations) and physical distances provided evidence of linkage throughout the entire genome, consistent with the hypothesis of non-random association of alleles among loci. Our findings provide new insights into the understanding of clonal populations on a genome-wide scale and microevolutionary factors that might play an important role in population structure. Although we found limited genetic diversity, the three Alternaria spp. studied here are genetically distinct and each species is preferentially associated with one host. ]]> Adhikari, T. Knaus, B. Grünwald, N. Halterman, D. Louws, F. 2019-11-01 doi:10.1101/827790 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ Immunoglobulin J chain as a non-invasive indicator of pregnancy in the cheetah (Acinonyx jubatus) ]]> https://biorxiv.org/content/10.1101/831628v1?rss=1 Byron, M. J. Koester, D. C. Edwards, K. L. Mozdziak, P. E. Farin, C. E. Crosier, A. E. 2019-11-05 doi:10.1101/831628 Cold Spring Harbor Laboratory Press 2019-11-05 <![CDATA[ Microbiability of meat quality and carcass composition traits in swine ]]> https://biorxiv.org/content/10.1101/833731v1?rss=1 KHANAL, P. Maltecca, C. Schwab, C. Fix, J. Tiezzi, F. 2019-11-07 doi:10.1101/833731 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ Dynamic DNA-based information storage ]]> https://biorxiv.org/content/10.1101/836429v1?rss=1 Lin, K. Tuck, J. M. Keung, A. J. 2019-11-09 doi:10.1101/836429 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Marker-Trait Complete Analysis ]]> https://biorxiv.org/content/10.1101/836494v1?rss=1 Zhou, Y.-H. Gallins, P. Wright, F. 2019-11-09 doi:10.1101/836494 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa ]]> https://biorxiv.org/content/10.1101/842351v1?rss=1 Qi, X. An, H. Hall, T. E. Di, C. Blischak, P. Pires, J. C. Barker, M. S. 2019-11-14 doi:10.1101/842351 Cold Spring Harbor Laboratory Press 2019-11-14 <![CDATA[ The microRNA476a/RFL module regulates adventitious root formation through a mitochondria-dependent pathway in Populus ]]> https://biorxiv.org/content/10.1101/852178v1?rss=1 Luo, K. Xu, C. Tao, Y. Fu, X. Guo, L. Xing, H. Li, C. Wang, X. Su, H. Hu, J. Fan, D. Chiang, V. L. 2019-11-22 doi:10.1101/852178 Cold Spring Harbor Laboratory Press 2019-11-22 <![CDATA[ Differences in in vitro responses of the hypothalamo-pituitary-gonadal hormonal axis between low and high egg producing turkey hens ]]> https://biorxiv.org/content/10.1101/854679v1?rss=1 Brady, K. Long, J. A. Liu, H.-C. Porter, T. E. 2019-11-25 doi:10.1101/854679 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ clustifyr: An R package for automated single-cell RNA sequencing cluster classification ]]> https://biorxiv.org/content/10.1101/855064v1?rss=1 Fu, R. Gillen, A. E. Sheridan, R. M. Tian, C. Daya, M. Hao, Y. Hesselberth, J. R. Riemondy, K. A. 2019-11-26 doi:10.1101/855064 Cold Spring Harbor Laboratory Press 2019-11-26 <![CDATA[ Gene regulatory effects of a large chromosomal inversion in highland maize ]]> https://biorxiv.org/content/10.1101/861583v1?rss=1 Crow, T. M. Ta, J. Nojoomi, S. Aguilar-Rangel, M. R. Torres Rodriguez, J. V. Gates, D. Rellan-Alvarez, R. Sawers, R. Runcie, D. E. 2019-12-02 doi:10.1101/861583 Cold Spring Harbor Laboratory Press 2019-12-02 <![CDATA[ Phylogeography of equine infectious anemia virus ]]> https://biorxiv.org/content/10.1101/867747v1?rss=1 Jara, M. Frias-De-Diego, A. Machado, G. 2019-12-06 doi:10.1101/867747 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ Holsteins Favor Heifers, Not Bulls: Biased Milk Production Programmed during Pregnancy as a Function of Fetal Sex ]]> https://biorxiv.org/content/10.1101/002063v1?rss=1 Katie Hinde Abigail J Carpenter John C Clay Barry J Bradford 2014-01-24 doi:10.1101/002063 Cold Spring Harbor Laboratory Press 2014-01-24 <![CDATA[ RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing ]]> https://biorxiv.org/content/10.1101/010116v1?rss=1 Vikas Gupta April Dawn Estrada Ivory Clabaugh Blakley Rob Reid Ketan Patel Mason D. Meyer Stig Uggerhoj Andersen Allan F. Brown Mary Ann Lila Ann Loraine 2014-10-08 doi:10.1101/010116 Cold Spring Harbor Laboratory Press 2014-10-08 <![CDATA[ The origins of a novel butterfly wing patterning gene from within a family of conserved cell cycle regulators ]]> https://biorxiv.org/content/10.1101/016006v1?rss=1 Nicola Nadeau Carolina Pardo-Diaz Annabel Whibley Megan Ann Supple Richard Wallbank Grace C. Wu Luana Maroja Laura Ferguson Heather Hines Camilo Salazar Richard ffrench-Constant Mathieu Joron William Owen McMillan Chris Jiggins 2015-03-05 doi:10.1101/016006 Cold Spring Harbor Laboratory Press 2015-03-05 <![CDATA[ Genetic Basis of Transcriptome Diversity in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/018325v1?rss=1 Wen Huang Mary Anna Carbone Michael Magwire Jason Peiffer Richard Lyman Eric Stone Robert Anholt Trudy Mackay 2015-04-21 doi:10.1101/018325 Cold Spring Harbor Laboratory Press 2015-04-21 <![CDATA[ Arabidopsis late blight: Infection of a nonhost plant by Albugo laibachii enables full colonization by Phytophthora infestans ]]> https://biorxiv.org/content/10.1101/035006v1?rss=1 Khaoula Belhaj Liliana M. Cano David C. Prince Ariane Kemen Kentaro Yoshida Yasin F. Dagdas Graham J. Etherington Henk-jan Schoonbeek H. Peter van Esse Jonathan DG Jones Sophien Kamoun Sebastian Schornack 2015-12-23 doi:10.1101/035006 Cold Spring Harbor Laboratory Press 2015-12-23 <![CDATA[ Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi ]]> https://biorxiv.org/content/10.1101/038372v1?rss=1 Edgar M. Medina Jonathan J. Turner Raluca Gordan Jan M. Skotheim Nicolas E. Buchler 2016-02-01 doi:10.1101/038372 Cold Spring Harbor Laboratory Press 2016-02-01 <![CDATA[ A Facilitated Diffusion Mechanism Establishes the Drosophila Dorsal Gradient ]]> https://biorxiv.org/content/10.1101/057091v1?rss=1 Sophia N Carrell MIchael D O'Connell Amy E Allen Stephanie M Smith Gregory Reeves 2016-06-03 doi:10.1101/057091 Cold Spring Harbor Laboratory Press 2016-06-03 <![CDATA[ Construction of a high-density American cranberry (Vaccinium macrocarpon Ait.) composite map using genotyping-by-sequencing for multi-pedigree linkage mapping ]]> https://biorxiv.org/content/10.1101/088419v1?rss=1 0.99) between the LGs of the parental maps demonstrates the utility of GBS in cranberry for identifying polymorphic SNP loci that are transferable between pedigrees and populations in future trait-association studies. Furthermore, the high-density of markers anchored within the component maps allowed identification of segregation distortion regions, placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results represent an important contribution to the current understanding of cranberry genomic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry. ]]> Schlautman, B. Covarrubias-Pazaran, G. Diaz-Garcia, L. Iorizzo, M. Polashock, J. Grygleski, E. Vorsa, N. Zalapa, J. 2016-11-17 doi:10.1101/088419 Cold Spring Harbor Laboratory Press 2016-11-17 <![CDATA[ Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells ]]> https://biorxiv.org/content/10.1101/109603v1?rss=1 Gomez-Schiavon, M. Chen, L.-F. West, A. E. Buchler, N. E. 2017-02-18 doi:10.1101/109603 Cold Spring Harbor Laboratory Press 2017-02-18 <![CDATA[ Naturally-segregating Variation at Ugt86Dd Contributes to Nicotine Resistance in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/134429v1?rss=1 Highfill, C. Tran, J. Nguyen, S. Moldenhauer, T. Wang, X. Macdonald, S. J. 2017-05-05 doi:10.1101/134429 Cold Spring Harbor Laboratory Press 2017-05-05 <![CDATA[ Genome-Wide Characterization Of Isoform Switching In Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/136770v1?rss=1 Vaneechoutte, D. Estrada, A. R. Lin, Y.-C. Loraine, A. Vandepoele, K. 2017-05-11 doi:10.1101/136770 Cold Spring Harbor Laboratory Press 2017-05-11 <![CDATA[ Directly Estimating Epidemic Curves From Genomic Data ]]> https://biorxiv.org/content/10.1101/142570v1?rss=1 Vaughan, T. G. Leventhal, G. E. Rasmussen, D. A. Drummond, A. J. Welch, D. Stadler, T. 2017-05-30 doi:10.1101/142570 Cold Spring Harbor Laboratory Press 2017-05-30 <![CDATA[ Cadmium Disrupts Vestibular Function by Interfering with Otolith Formation ]]> https://biorxiv.org/content/10.1101/162347v1?rss=1 Green, A. J. Mattingly, C. J. Planchart, A. 2017-07-13 doi:10.1101/162347 Cold Spring Harbor Laboratory Press 2017-07-13 <![CDATA[ Cadmium Exposure Increases The Risk Of Juvenile Obesity: A Human And Zebrafish Comparative Study ]]> https://biorxiv.org/content/10.1101/172346v1?rss=1 Green, A. J. Hoyo, C. Mattingly, C. J. Luo, Y. Tzeng, J.-Y. Murphy, S. Planchart, A. 2017-08-18 doi:10.1101/172346 Cold Spring Harbor Laboratory Press 2017-08-18 <![CDATA[ Genome-wide expression analysis of immune receptors in hot pepper reveals an autonomous NLR cluster in higher plants ]]> https://biorxiv.org/content/10.1101/2019.12.16.878959v1?rss=1 Lee, H.-Y. Mang, H. Seo, Y.-E. Oh, S. Kim, S.-B. Park, E. Choi, D. 2019-12-17 doi:10.1101/2019.12.16.878959 Cold Spring Harbor Laboratory Press 2019-12-17 <![CDATA[ Quantifying the dynamics of pig movements improve targeted disease surveillance and control plans ]]> https://biorxiv.org/content/10.1101/2019.12.29.886408v1?rss=1 Machado, G. Galvis, J. A. Lopes, F. P. N. Voges, J. Medeiros, A. A. R. Cardenas, N. 2019-12-30 doi:10.1101/2019.12.29.886408 Cold Spring Harbor Laboratory Press 2019-12-30 <![CDATA[ Online analysis of microendoscopic 1-photon calcium imaging data streams ]]> https://biorxiv.org/content/10.1101/2020.01.31.929141v1?rss=1 Friedrich, J. Giovannucci, A. Pnevmatikakis, E. A. 2020-01-31 doi:10.1101/2020.01.31.929141 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ Insecticide-free trapping bed-net can mitigate insecticide resistance threat in malaria vector control strategies ]]> https://biorxiv.org/content/10.1101/2020.02.06.937623v1?rss=1 Mouhamadou, C. Luan, K. Fodjo, B. K. West, A. McCord, M. Apperson, C. Roe, M. 2020-02-07 doi:10.1101/2020.02.06.937623 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Climate and urbanization drive mosquito preference for humans ]]> https://biorxiv.org/content/10.1101/2020.02.12.939041v1?rss=1 Rose, N. H. Sylla, M. Badolo, A. Lutomiah, J. Ayala, D. Aribodor, O. B. Ibe, N. Akorli, J. Otoo, S. Mutebi, J.-P. Kriete, A. L. Ewing, E. G. Sang, R. Gloria-Soria, A. Powell, J. R. Baker, R. E. White, B. J. Crawford, J. E. McBride, C. S. 2020-02-13 doi:10.1101/2020.02.12.939041 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Loss of α7 nicotinic acetylcholine receptors in GABAergic interneurons causes sex-dependent impairments in postnatal neurogenesis and cognitive and social behavior ]]> https://biorxiv.org/content/10.1101/2020.03.16.994111v1?rss=1 Nacer, S. A. Otto, S. Letsinger, A. C. Strauss DeFilipp, J. Stevanovic, K. D. Riddick, N. V. Nikolova, V. Cushman, J. D. Yakel, J. L. 2020-03-18 doi:10.1101/2020.03.16.994111 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ An 1,4-α-glucosyltransferase defines a new maltodextrin catabolism scheme in Lactobacillus acidophilus ]]> https://biorxiv.org/content/10.1101/2020.03.17.996314v1?rss=1 Andersen, S. Moeller, M. S. Poulsen, J.-C. N. Pichler, M. J. Svensson, B. Goh, Y.-J. Lo Leggio, L. Abou Hachem, M. 2020-03-18 doi:10.1101/2020.03.17.996314 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ Renewable Fatty Acid Ester Production in Clostridium ]]> https://biorxiv.org/content/10.1101/2020.03.29.014746v1?rss=1 Feng, J. Zhang, J. Wang, P. Jimenez-Bonilla, P. Gu, Y. Zhou, J. Cao, M. Shao, Z. Borovok, I. Wang, Y. 2020-03-30 doi:10.1101/2020.03.29.014746 Cold Spring Harbor Laboratory Press 2020-03-30 <![CDATA[ Impact of Advanced Maternal Age on Physiologic Adaptations to Pregnancy in Vervet Monkeys ]]> https://biorxiv.org/content/10.1101/2020.04.06.027771v1?rss=1 Plant, M. Armstrong, C. Ruggiero, A. Sherrill, C. Uberseder, B. Jeffries, R. Nevarez, J. Jorgensen, M. J. Kavanagh, K. Quinn, M. A. 2020-04-07 doi:10.1101/2020.04.06.027771 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Computationally-guided exchange of substrate selectivity motifs in a modular polyketide synthase acyltransferase ]]> https://biorxiv.org/content/10.1101/2020.04.23.058214v1?rss=1 Kalkreuter, E. Bingham, K. S. Keeler, A. M. Lowell, A. Schmidt, J. J. Sherman, D. H. Williams, G. J. 2020-04-25 doi:10.1101/2020.04.23.058214 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Iron Chelator-Mediated Anoxic Biotransformation of Lignin by Novel sp., Tolumonas lignolytica BRL6-1 ]]> https://biorxiv.org/content/10.1101/2020.05.14.095802v1?rss=1 Chaput, G. Billings, A. F. DeDiego, L. Orellana, R. Adkins, J. N. Chu, R. Simmons, B. DeAngelis, K. M. 2020-05-14 doi:10.1101/2020.05.14.095802 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Machine Learning Models Identify Inhibitors of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.06.16.154765v1?rss=1 Gawriljuk, V. O. Kyaw Zin, P. P. Foil, D. H. Bernatchez, J. Beck, S. Beutler, N. Ricketts, J. Yang, L. Rogers, T. Puhl, A. C. Zorn, K. M. Lane, T. R. Godoy, A. S. Olivia, G. Siqueira-Neto, J. L. Madrid, P. Ekins, S. 2020-06-16 doi:10.1101/2020.06.16.154765 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ A forward genetic screen identifies Dolk as a regulator of startle magnitude through the potassium channel subunit Kv1.1 ]]> https://biorxiv.org/content/10.1101/2020.06.19.161240v1?rss=1 Meserve, J. H. Nelson, J. C. Marsden, K. C. Hsu, J. Echeverry, F. A. Jain, R. A. Wolman, M. A. Pereda, A. E. Granato, M. 2020-06-19 doi:10.1101/2020.06.19.161240 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Evolutionary dynamics of bipartite begomoviruses revealed by complete genome analysis ]]> https://biorxiv.org/content/10.1101/2020.06.25.171728v1?rss=1 Xavier, C. A. Godinho, M. T. Mar, T. B. Ferro, C. G. Sande, O. F. Silva, J. C. Ramos-Sobrinho, R. Nascimento, R. N. Assuncao, I. Lima, G. S. Lima, A. T. Zerbini, F. M. 2020-06-25 doi:10.1101/2020.06.25.171728 Cold Spring Harbor Laboratory Press 2020-06-25 <![CDATA[ Towards genetic modification of plant-parasitic nematodes: delivery of macromolecules to adults and expression of exogenous mRNA in second stage juveniles. ]]> https://biorxiv.org/content/10.1101/2020.07.15.193052v1?rss=1 Kranse, O. Beasley, H. Adams, S. Pires da Silva, A. Bell, C. Lilley, C. Urwin, P. E. Bird, D. Miska, E. A. Smant, G. Gheysen, G. Jones, J. Viney, M. Abad, P. Maier, T. R. Baum, T. J. Siddique, S. Williamson, V. Akay, A. Eves-van den Akker, S. 2020-07-15 doi:10.1101/2020.07.15.193052 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ Visual effort moderates postural cascade dynamics ]]> https://biorxiv.org/content/10.1101/2020.07.17.209486v1?rss=1 Mangalam, M. Lee, I.-C. Newell, K. M. Kelty-Stephen, D. G. 2020-07-19 doi:10.1101/2020.07.17.209486 Cold Spring Harbor Laboratory Press 2020-07-19 <![CDATA[ Visual effort moderates a self-correcting nonlinear postural control policy ]]> https://biorxiv.org/content/10.1101/2020.07.17.209502v1?rss=1 Kelty-Stephen, D. G. Lee, I.-C. Carver, N. S. Newell, K. M. Mangalam, M. 2020-07-19 doi:10.1101/2020.07.17.209502 Cold Spring Harbor Laboratory Press 2020-07-19 <![CDATA[ Natural Antisense Transcript of Period2, Per2AS, regulates the amplitude of the mouse circadian clock ]]> https://biorxiv.org/content/10.1101/2020.07.27.222760v1?rss=1 Mosig, R. A. Castaneda, A. N. Deslauriers, J. C. Frazier, L. P. He, K. L. Maghzian, N. Pokharel, A. Schrier, C. T. Zhu, L. Koike, N. Tyson, J. J. Green, C. B. Takahashi, J. S. Kojima, S. 2020-07-28 doi:10.1101/2020.07.27.222760 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ Global historic pandemics caused by the FAM-1 genotype of the Irish potato pathogen Phytophthora infestans ]]> https://biorxiv.org/content/10.1101/2020.08.25.266759v1?rss=1 Saville, A. Ristaino, J. B. 2020-08-25 doi:10.1101/2020.08.25.266759 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ Insulin potentiates the synchronous firing of arcuate nucleus Kiss1 neurons that protects against diet-induced obesity ]]> https://biorxiv.org/content/10.1101/2020.09.09.289017v1?rss=1 Qiu, J. Stincic, T. L. Bosch, M. A. Connors, A. M. Petrie, S. K. Ronnekleiv, O. K. Kelly, M. J. 2020-09-11 doi:10.1101/2020.09.09.289017 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ Direct Continuous EMG control of a Powered Prosthetic Ankle for Improved Postural Control after Guided Physical Training: a Case Study ]]> https://biorxiv.org/content/10.1101/2020.09.11.293373v1?rss=1 Fleming, A. Huang, S. Buxton, E. Hodges, F. Huang, H. 2020-09-14 doi:10.1101/2020.09.11.293373 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ Assessing whitefly diversity to infer about begomovirus dynamics in cassava in Brazil ]]> https://biorxiv.org/content/10.1101/2020.09.22.309187v1?rss=1 Xavier, C. A. Zerbini, F. M. 2020-09-23 doi:10.1101/2020.09.22.309187 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Perilipin2 down-regulation in beta cells impairs insulin secretion under nutritional stress and damages mitochondria ]]> https://biorxiv.org/content/10.1101/2020.10.01.322974v1?rss=1 Mishra, A. Liu, S. Promes, J. Harata, M. Sivitz, W. Fink, B. Bhardwaj, G. O'Neill, B. Kang, C. Sah, R. Strack, S. Stephens, S. King, T. Jackson, L. Greenberg, A. Anokye-Danso, F. Ahima, R. Ankrum, J. A. Imai, Y. 2020-10-01 doi:10.1101/2020.10.01.322974 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Trade-offs between risks of predation and starvation in larvae make the shelf break an optimal spawning location for Atlantic Bluefin tuna ]]> https://biorxiv.org/content/10.1101/2020.11.01.363465v1?rss=1 Shropshire, T. A. Morey, S. L. Chassignet, E. P. Karnauskas, M. Coles, V. J. Malca, E. Laiz-Carrion, R. Fiksen, O. Reglero, P. Shiroza, A. Maria Quintanilla Hervas, J. Gerard, T. Lamkin, J. Stukel, M. R. 2020-11-02 doi:10.1101/2020.11.01.363465 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ Repurposing the Ebola and Marburg Virus Inhibitors Tilorone, Quinacrine and Pyronaridine: In vitro Activity Against SARS-CoV-2 and Potential Mechanisms ]]> https://biorxiv.org/content/10.1101/2020.12.01.407361v1?rss=1 Puhl, A. C. Fritch, E. J. Lane, T. R. Tse, L. V. Yount, B. Sacramento, C. Q. Tavella, T. A. Costa, F. T. M. Weston, S. Logue, J. Frieman, M. Premkumar, L. Pearce, K. H. Hurst, B. L. Andrade, C. H. Levi, J. A. Johnson, N. J. Kisthardt, S. C. Scholle, F. Souza, T. M. Moorman, N. J. Baric, R. S. Madrid, P. Ekins, S. 2020-12-02 doi:10.1101/2020.12.01.407361 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ A conserved regulatory module regulates receptor kinase signaling in immunity and development ]]> https://biorxiv.org/content/10.1101/2021.01.19.427293v1?rss=1 DeFalco, T. A. Anne, P. James, S. R. Willoughby, A. Johanndrees, O. Genolet, Y. Pullen, A.-M. zipfel, c. Hardtke, C. Nimchuk, Z. L. 2021-01-20 doi:10.1101/2021.01.19.427293 Cold Spring Harbor Laboratory Press 2021-01-20 <![CDATA[ Tristetraprolin prevents gastric metaplasia in mice by suppressing pathogenic inflammation ]]> https://biorxiv.org/content/10.1101/2021.01.21.427435v1?rss=1 Busada, J. T. Kadka, S. Peterson, K. N. Stumpo, D. J. Zhou, L. Cidlowski, J. A. Blackshear, P. J. 2021-01-21 doi:10.1101/2021.01.21.427435 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Home range and movement patterns of the Andean Fox Lycalopex culpaeus (Molina 1782) in Cotopaxi National Park, Ecuador ]]> https://biorxiv.org/content/10.1101/2021.02.10.430628v1?rss=1 Castellanos, A. Castellanos, F. X. Kays, R. Brito, J. 2021-02-11 doi:10.1101/2021.02.10.430628 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ A Programmable Toolkit to Dynamically Signal Cells using Peptide Strand Displacement ]]> https://biorxiv.org/content/10.1101/2021.02.17.431719v1?rss=1 Riker, K. Daly, M. L. Papanikolas, M. Jian, T. Klawa, S. J. Sahin, J. S. Liu, D. Singh, A. Miller, A. G. Freeman, R. 2021-02-18 doi:10.1101/2021.02.17.431719 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Structural basis for the tryptophan sensitivity of TnaC-mediated ribosome stalling ]]> https://biorxiv.org/content/10.1101/2021.03.31.437805v1?rss=1 van der Stel, A.-X. Gordon, E. R. Sengupta, A. Martinez, A. K. Klepacki, D. Perry, T. N. Herrero del Valle, A. Vazquez-Laslop, N. Sachs, M. S. Cruz-Vera, L. R. Innis, C. A. 2021-03-31 doi:10.1101/2021.03.31.437805 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Repair of critical-size porcine craniofacial bone defects using a collagen-polycaprolactone composite biomaterial ]]> https://biorxiv.org/content/10.1101/2021.04.19.440506v1?rss=1 Dewey, M. J. Milner, D. J. Weisgerber, D. Flanagan, C. Rubessa, M. Lotti, S. Polkoff, K. Crotts, S. Hollister, S. J. Wheeler, M. B. Harley, B. 2021-04-20 doi:10.1101/2021.04.19.440506 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Ozone sensitivity of diverse maize genotypes is associated with differences in gene regulation, not gene content ]]> https://biorxiv.org/content/10.1101/2021.05.06.442991v1?rss=1 Nanni, A. V. Morse, A. M. Newman, J. R. Choquette, N. E. Wedow, J. M. Liu, Z. Leakey, A. D. Conesa, A. Ainsworth, E. A. McIntyre, L. 2021-05-07 doi:10.1101/2021.05.06.442991 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ Engineering a thixotropic and biochemically tunable hyaluronan and collagen bioink for biofabrication of multiple tissue construct types ]]> https://biorxiv.org/content/10.1101/2021.09.01.458584v1?rss=1 Aleman, J. Sivakumar, H. DePalma, T. Zhou, Y. Mazzocchi, A. Huntwork, R. C. Yoo, K. M. Banks, S. Clark, C. Maycock, A. Leaks, K. Enck, K. Opara, E. Gatenholm, P. Welker, M. Soker, S. Herberg, S. Criswell, T. Skardal, A. 2021-09-03 doi:10.1101/2021.09.01.458584 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ Dopamine biases sensitivity to personal goals and social influence in self-control over everyday desires ]]> https://biorxiv.org/content/10.1101/2021.09.10.459829v1?rss=1 Castrellon, J. J. Young, J. S. Dang, L. C. Smith, C. T. Cowan, R. L. Zald, D. H. Samanez-Larkin, G. R. 2021-09-11 doi:10.1101/2021.09.10.459829 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ Clostridioides difficile infection increases circulating p-cresol levels and dysregulates brain dopamine metabolism: linking gut-brain axis to autism and other neurologic disorders? ]]> https://biorxiv.org/content/10.1101/2021.10.22.465382v1?rss=1 A. Vinithakumari, A. Padhi, P. G. Hernandez, B. Je-Han Lin, S. Dunkerson-Kurzhumov, A. Showman, L. Breitzman, M. Stokes, C. Sulaiman, Y. Tangudu, C. Kuttappan, D. A. Muyyarikkandy, M. S. Phillips, G. J. Anantharam, V. Perera, A. Sponseller, B. Kanthasamy, A. Mooyottu, S. 2021-10-24 doi:10.1101/2021.10.22.465382 Cold Spring Harbor Laboratory Press 2021-10-24 <![CDATA[ Enterotoxigenic Escherichia coli degrades the host MUC2 mucin barrier to facilitate critical pathogen-enterocyte interactions in human small intestine. ]]> https://biorxiv.org/content/10.1101/2021.10.22.465536v1?rss=1 Sheikh, A. Wangdi, T. Vickers, T. J. Aaron, B. Palmer, M. P. Miller, M. Kim, S. Herring, C. Simoes, R. Crainic, J. A. Gildersleeve, J. van der Post, S. Hansson, G. C. Fleckenstein, J. M. 2021-10-23 doi:10.1101/2021.10.22.465536 Cold Spring Harbor Laboratory Press 2021-10-23 <![CDATA[ Estimating the Designability of Protein Structures ]]> https://biorxiv.org/content/10.1101/2021.11.03.467111v1?rss=1 Pan, F. Zhang, Y. Liu, X. Zhang, J. 2021-11-04 doi:10.1101/2021.11.03.467111 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Protein loop modeling and refinement using deep learning models ]]> https://biorxiv.org/content/10.1101/2021.11.03.467148v1?rss=1 Pan, F. Zhang, Y. Lo, C.-C. Mandal, A. Liu, X. Zhang, J. 2021-11-04 doi:10.1101/2021.11.03.467148 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Applications of AlphaFold beyond Protein Structure Prediction ]]> https://biorxiv.org/content/10.1101/2021.11.03.467194v1?rss=1 Zhang, Y. Li, P. PAN, F. Liu, H. Hong, P. Liu, X. Zhang, J. 2021-11-04 doi:10.1101/2021.11.03.467194 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ ProDCoNN-server: a web server for protein sequence prediction and design from a three-dimensional structure ]]> https://biorxiv.org/content/10.1101/2021.11.04.467289v1?rss=1 Zhang, Y. Mandal, A. Cui, K. Liu, X. Zhang, J. 2021-11-05 doi:10.1101/2021.11.04.467289 Cold Spring Harbor Laboratory Press 2021-11-05 <![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[ Variability of in vivo sarcomere length measures in the upper limb obtained with second harmonic generation microendoscopy ]]> https://biorxiv.org/content/10.1101/2021.11.17.468984v1?rss=1 Adkins, A. N. Fong, R. Dewald, J. P. A. Murray, W. M. 2021-11-18 doi:10.1101/2021.11.17.468984 Cold Spring Harbor Laboratory Press 2021-11-18 <![CDATA[ Host exposure to symbionts and ecological drift generate divergence in parasite community assembly ]]> https://biorxiv.org/content/10.1101/2021.11.19.469294v1?rss=1 Grunberg, R. L. Joyner, B. N. Mitchell, C. E. 2021-11-20 doi:10.1101/2021.11.19.469294 Cold Spring Harbor Laboratory Press 2021-11-20 <![CDATA[ Considering decoupled phenotypic diversification between ontogenetic phases in macroevolution: An example using Triggerfishes (Balistidae) ]]> https://biorxiv.org/content/10.1101/2022.01.11.475856v1?rss=1 Dornburg, A. Zapfe, K. Williams, R. Alfaro, M. Morris, R. Adachi, H. Flores, J. Santini, F. Near, T. Frederich, B. 2022-01-12 doi:10.1101/2022.01.11.475856 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ MoveApps - a serverless no-code analysis platform for animal tracking data ]]> https://biorxiv.org/content/10.1101/2022.02.15.480513v1?rss=1 Koelzsch, A. Davidson, S. C. Gauggel, D. Hahn, C. Hirt, J. Kays, R. Lang, I. Lohr, A. K. Russell, B. Scharf, A. K. Schneider, G. Vinciguerra, C. Wikelski, M. Safi, K. 2022-02-19 doi:10.1101/2022.02.15.480513 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Apiaceae FNS I originated from F3H through tandem gene duplication ]]> https://biorxiv.org/content/10.1101/2022.02.16.480750v1?rss=1 Pucker, B. Iorizzo, M. 2022-02-19 doi:10.1101/2022.02.16.480750 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ SELF PRUNING 3C is a flowering repressor that modulates seed germination, root architecture and drought responses ]]> https://biorxiv.org/content/10.1101/2022.03.10.483842v1?rss=1 Moreira, J. d. R. Quinones, A. Lira, B. S. Robledo, J. M. Curtin, S. J. Vicente, M. H. Ribeiro, D. M. Ryngajllo, M. Jimenez-Gomez, J. M. Peres, L. E. P. Rossi, M. M. Zsögön, A. 2022-03-11 doi:10.1101/2022.03.10.483842 Cold Spring Harbor Laboratory Press 2022-03-11 <![CDATA[ Rapid evolution of the fine-scale recombination landscape in wild house mouse (Mus musculus) populations ]]> https://biorxiv.org/content/10.1101/2022.06.08.495013v1?rss=1 100 alleles identified to date, and pose a particularly powerful system for addressing this open question. We employed a coalescent-based approach to construct fine-scale, sex-averaged recombination maps from contemporary patterns of linkage disequilibrium in nine geographically isolated wild house mouse populations, including multiple populations from each of three subspecies. Comparing maps between wild mouse populations and subspecies reveals several themes. First, we report weak fine- and broad-scale recombination map conservation across subspecies and populations, with genetic divergence offering no clear prediction for recombination map divergence. Second, most hotspots are unique to one population, an outcome consistent with minimal sharing of Prdm9 alleles between surveyed populations. Finally, by contrasting aggregate hotspot activity on the X versus autosomes, we uncover evidence for population-specific differences in the degree and direction of sex-dimorphism for recombination. Overall, our findings illuminate the variability of both the broad- and fine-scale recombination landscape in Mus musculus and underscore the functional impact of Prdm9 allelic variation in wild mouse populations. ]]> Wooldridge, L. K. Dumont, B. L. 2022-06-08 doi:10.1101/2022.06.08.495013 Cold Spring Harbor Laboratory Press 2022-06-08 <![CDATA[ Cooperation between Imp2p and Cdc15p imparts stiffness to the constricting contractile ring in fission yeast. ]]> https://biorxiv.org/content/10.1101/2022.06.11.495753v1?rss=1 Bellingham-Johnstun, K. Commer, B. E. Levesque, B. Tyree, Z. L. Laplante, C. 2022-06-12 doi:10.1101/2022.06.11.495753 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Regulation of urea cycle by reversible high stoichiometry lysine succinylation ]]> https://biorxiv.org/content/10.1101/2022.06.24.497535v1?rss=1 Zhang, R. Xie, X. Carrico, C. Meyer, J. G. Wei, L. Bons, J. Rose, J. Riley, R. Kwok, R. Kumaar, P. A. He, W. Nishida, Y. Liu, X. Locasale, J. Schilling, B. Verdin, E. 2022-06-26 doi:10.1101/2022.06.24.497535 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Holographic stimulation of opposing amygdala ensembles bidirectionally modulates valence-specific behavior ]]> https://biorxiv.org/content/10.1101/2022.07.11.499499v1?rss=1 Piantadosi, S. C. Zhou, Z. C. Pizzano, C. M. Pedersen, C. E. Nguyen, T. K. Thai, S. Stuber, G. D. Bruchas, M. R. 2022-07-12 doi:10.1101/2022.07.11.499499 Cold Spring Harbor Laboratory Press 2022-07-12 <![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[ Enterotoxigenic Escherichia coli heat-labile toxin drives enteropathic changes in small 1intestinal epithelia ]]> https://biorxiv.org/content/10.1101/2022.08.24.504189v1?rss=1 Sheikh, A. Tumala, B. Vickers, T. J. Martin, J. C. Rosa, B. A. Sabui, S. Simoes, R. D. Mitreva, M. Storer, C. Tyksen, E. Head, R. D. Beatty, W. Said, H. M. Fleckenstein, J. M. 2022-08-24 doi:10.1101/2022.08.24.504189 Cold Spring Harbor Laboratory Press 2022-08-24 <![CDATA[ Phosphorylation chemistry of the Bordetella PlrSR TCS and its contribution to bacterial persistence in the lower respiratory tract ]]> https://biorxiv.org/content/10.1101/2022.10.06.511181v1?rss=1 Barr, S. A. Kennedy, E. N. McKay, L. S. Johnson, R. M. Ohr, R. J. Cotter, P. A. Bourret, R. B. 2022-10-06 doi:10.1101/2022.10.06.511181 Cold Spring Harbor Laboratory Press 2022-10-06 <![CDATA[ Dietary sugar and protein exert opposing effects on key larval growth and metabolic regulators, the Drosophila insulin-like peptides Dilp2 and Dilp6. ]]> https://biorxiv.org/content/10.1101/2022.12.01.518785v1?rss=1 Suzawa, M. McPherson, W. K. Van Gorder, E. E. Reddy, S. Hilovsky, D. L. Keliinui, C. N. Jamali, L. A. Bland, M. L. 2022-12-03 doi:10.1101/2022.12.01.518785 Cold Spring Harbor Laboratory Press 2022-12-03 <![CDATA[ Nanofluidic Device for Manipulation and Modification of DNA by Proteins ]]> https://biorxiv.org/content/10.1101/2022.12.29.521498v1?rss=1 Dangi, S. Liu, M. Azad, Z. Countryman, P. J. Roushan, M. Livshits, G. I. Kaur, P. Pan, H. Shi, Z. Detwiler, A. C. Opresko, P. L. Yu, H. Wang, H. Riehn, R. 2022-12-30 doi:10.1101/2022.12.29.521498 Cold Spring Harbor Laboratory Press 2022-12-30 <![CDATA[ A new microphysiological system shows hypoxia primes human ISCs for interleukin-dependent rescue of stem cell activity ]]> https://biorxiv.org/content/10.1101/2023.01.31.524747v1?rss=1 Rivera, K. R. Bliton, R. J. Burclaff, J. Czerwinski, M. J. Liu, J. Trueblood, J. M. Hinesley, C. Breau, K. A. Joshi, S. Pozdin, V. A. Yao, M. Ziegler, A. L. Blikslager, A. T. Daniele, M. Magness, S. 2023-02-01 doi:10.1101/2023.01.31.524747 Cold Spring Harbor Laboratory Press 2023-02-01 <![CDATA[ Peptide ligands for the affinity purification of adeno-associated viruses from HEK 293 cell lysates ]]> https://biorxiv.org/content/10.1101/2023.02.19.529155v1?rss=1 1013 vp per mL of resin) and product yields ([~]50-80%) on par with commercial adsorbents. The peptide-based adsorbents were finally utilized to purify AAV2 from a HEK 293 cell lysate, affording high recovery (50-80%), 80-to-400-fold reduction of host cell proteins (HCPs), and high transduction activity (up to 80%) of the purified viruses. ]]> Chu, W. Barbieri, E. Prodromou, R. Greback-Clarke, P. Smith, W. K. Moore, B. D. Kilgore, R. E. Cummings, C. L. Pancorbo, J. Gilleskie, G. L. Daniele, M. A. Menegatti, S. 2023-02-21 doi:10.1101/2023.02.19.529155 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Actin-microtubule crosstalk imparts stiffness to the contractile ring in fission yeast. ]]> https://biorxiv.org/content/10.1101/2023.03.01.530611v1?rss=1 Bellingham-Johnstun, K. Tyree, Z. L. Martinez-Baird, J. Thorn, A. Laplante, C. 2023-03-02 doi:10.1101/2023.03.01.530611 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Pharmacokinetic considerations for optimizing inhaled spray-dried pyrazinoic acid formulations ]]> https://biorxiv.org/content/10.1101/2023.04.01.534965v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@c548fforg.highwire.dtl.DTLVardef@3b8efborg.highwire.dtl.DTLVardef@281d94org.highwire.dtl.DTLVardef@1ae07a2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yeshwante, S. B. Hanafin, P. Miller, B. Rank, L. Murcia, S. Xander, C. Annis, A. Baxter, V. Anderson, E. Jermain, B. Konicki, R. Schmalstig, A. Stewart, I. Braunstein, M. Hickey, A. Rao, G. G. 2023-04-03 doi:10.1101/2023.04.01.534965 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ Isolation of Actinomyces cricetomyis sp. nov from orocervicofacial abscesses of African giant pouched rats (Cricetomys ansorgei) ]]> https://biorxiv.org/content/10.1101/2023.04.04.535624v1?rss=1 Franklin-Guild, R. J. Labitt, R. N. McQueary, H. C. Llanos-Soto, S. Mitchell, P. K. Tallmadge, R. L. Anderson, R. R. Flint, J. F. Ophir, A. G. Thachil, A. Singh, B. Goodman, L. B. 2023-04-04 doi:10.1101/2023.04.04.535624 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ HISTONE DEACETYLASE 19 REGULATES SHOOT MERISTEMLESS EXPRESSION IN THE CARPEL MARGIN MERISTEM CONTRIBUTING TO OVULE NUMBER DETERMINATION AND TRANSMITTING TRACT DIFFERENTIATION ]]> https://biorxiv.org/content/10.1101/2023.05.08.537343v1?rss=1 Manrique, S. Cavalleri, A. Guazzotti, A. Villarino, G. H. Simonini, S. Bombarely, A. Higashiyama, T. Grossniklaus, U. Mizzotti, C. Pereira, A. M. Coimbra, S. Onelli, E. Masiero, S. Franks, R. G. Colombo, L. 2023-05-09 doi:10.1101/2023.05.08.537343 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Evaluation of ready-to-use freezer stocks of a synthetic microbial community for maize root colonization ]]> https://biorxiv.org/content/10.1101/2023.05.10.540175v1?rss=1 Parnell, J. J. Vintila, S. Tang, C. Wagner, M. R. Kleiner, M. 2023-05-10 doi:10.1101/2023.05.10.540175 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ Efficacy of Aedes aegypti control by indoor Ultra Low Volume (ULV) insecticide spraying in Iquitos, Peru ]]> https://biorxiv.org/content/10.1101/231134v1?rss=1 Gunning, C. Okamoto, K. Astete, H. Vasquez, G. Erhardt, E. Aguila, C. D. Pinedo, R. Cardenas, R. Pacheco, C. Chalco, E. Rodriguez-Ferruci, H. Scott, T. W. Lloyd, A. L. Gould, F. Morrison, A. 2017-12-08 doi:10.1101/231134 Cold Spring Harbor Laboratory Press 2017-12-08 <![CDATA[ Agricultural fungicides inadvertently influence the fitness of Colorado potato beetles, Leptinotarsa decemlineata, and their susceptibility to insecticides ]]> https://biorxiv.org/content/10.1101/286377v1?rss=1 Clements, J. Schoville, S. Clements, A. Amezian, D. Davis, T. Sanchez-Sedillo, B. Bradfield, C. Huseth, A. Groves, R. 2018-03-22 doi:10.1101/286377 Cold Spring Harbor Laboratory Press 2018-03-22 <![CDATA[ Antigen receptor control of methionine metabolism in T cells ]]> https://biorxiv.org/content/10.1101/499095v1?rss=1 Sinclair, L. V. Howden, A. J. Brenes-Murillo, A. J. Spinelli, L. Hukelmann, J. L. Macintyre, A. N. Liu, X. Thomson, S. Taylor, P. M. Rathmell, J. C. Locasale, J. W. Lamond, A. I. Cantrell, D. A. 2018-12-18 doi:10.1101/499095 Cold Spring Harbor Laboratory Press 2018-12-18 <![CDATA[ Structural basis for activation of Dot1L methyltransferase on the nucleosome by histone H2BK120 ubiquitylation ]]> https://biorxiv.org/content/10.1101/503128v1?rss=1 Anderson, C. J. Baird, M. R. Hsu, A. Barbour, E. H. Koyama, Y. Borgnia, M. J. McGinty, R. K. 2018-12-20 doi:10.1101/503128 Cold Spring Harbor Laboratory Press 2018-12-20 <![CDATA[ Global phylogeographical patterns in the spread of foot-and-mouth disease virus ]]> https://biorxiv.org/content/10.1101/590612v1?rss=1 0.45). Furthermore, we identified the key centers of dispersal of the virus, being China, India and Uganda the most important ones. Bayes factor analysis revealed cattle as the major source of the virus for most of the serotypes (RSPP> 0.63), where the most important host-species transition route for serotypes O, A, and Asia1 was from cattle Bos taurus to swine Sus scrofa domesticus (BF>500), while, for SAT serotypes was from B. taurus to African buffalo Syncerus caffer. This study provides significant insights into the spatiotemporal dynamics of the global circulation of FMDV serotypes, by characterizing the viral routes of spread at serotype level, especially uncovering the importance of host species for each serotype in the evolution and spread of FMDV which further improve future decisions for more efficient control and eradication. ]]> Jara, M. Frias-De-Diego, A. Dellicour, S. Baele, G. Machado, G. 2019-03-28 doi:10.1101/590612 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ Lipidome profiles of postnatal day 2 vaginal swabs reflect fat composition of gilts postnatal diet ]]> https://biorxiv.org/content/10.1101/593392v1?rss=1 1.3 kg) were selected at birth across 8 litters and assigned to treatments: colostrum suckled (S, n=8); S plus fat supplement (SF, n=5); bottle-fed milk replacer (B, n=8); or B plus fat supplement (BF, n=7). At 48 h postnatal, vaginal swabs were taken with a cytology brush, immersed in ultrapure water to burst cells, and lipids extracted for analysis using multiple reaction monitoring (MRM)-profiling. Lipids extracted from serum collected at 48 h from gilts and milk collected from sows at 24 h were also analyzed with MRM-profiling. Receiver operating characteristic curve analysis found 18 lipids highly distinguished [area-under-the-curve (AUC) > 0.9] between S and B gilts, including phosphatidylethanolamine with 34 carbon and four unsaturations in the fatty acyl residues [PE(34:4)]. Twelve lipids from vaginal swabs highly correlated (r > 0.6; p < 0.01) with nutrition source. Lipids more abundant in milk replacer drove association. For example, mean intensity of PE (34:4) was 149-fold higher in milk replacer than colostrum, with 1.6- and 2.12-fold higher levels in serum and vaginal swab samples (p < 0.001), respectively, of B versus S gilts. Findings support that vaginal swabs can be used to noninvasively study effects of perinatal nutrition on tissue composition.nnSummary sentenceVaginal swab lipidome profiles at 48 h reflect the fat composition of neonatal diet during first two days postnatal. ]]> Harlow, K. Ferreira, C. R. Sobreira, T. J. P. Casey, T. M. Stewart, K. 2019-03-29 doi:10.1101/593392 Cold Spring Harbor Laboratory Press 2019-03-29 <![CDATA[ Quantitative evaluation of a high resolution lipidomics platform ]]> https://biorxiv.org/content/10.1101/627687v1?rss=1 Liu, J. Liu, X. Xiao, Z. Locasale, J. W. 2019-05-04 doi:10.1101/627687 Cold Spring Harbor Laboratory Press 2019-05-04 <![CDATA[ An improved plant toolset for high-throughput recombineering ]]> https://biorxiv.org/content/10.1101/659276v1?rss=1 Brumos, J. Zhao, C. Gong, Y. Soriano, D. Patel, A. Perez-Amador, M. A. Stepanova, A. N. Alonso, J. M. 2019-06-03 doi:10.1101/659276 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Slow changes in seizure pathways in individual patients with focal epilepsy ]]> https://biorxiv.org/content/10.1101/661371v1?rss=1 Schroeder, G. M. Diehl, B. Chowdhury, F. A. Duncan, J. S. de Tisi, J. Trevelyan, A. J. Forsyth, R. Jackson, A. Taylor, P. N. Wang, Y. 2019-06-06 doi:10.1101/661371 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ Comparing the microbial communities of natural and supplemental nests of an endangered ecosystem engineer ]]> https://biorxiv.org/content/10.1101/727966v1?rss=1 Thoemmes, M. S. Cove, M. V. 2019-08-07 doi:10.1101/727966 Cold Spring Harbor Laboratory Press 2019-08-07 <![CDATA[ Transcriptomic Stratification of Late-Onset Alzheimer’s Cases Reveals Novel Genetic Modifiers of Disease Pathology ]]> https://biorxiv.org/content/10.1101/763516v1?rss=1 Milind, N. Preuss, C. Haber, A. Ananda, G. Mukherjee, S. John, C. Shapley, S. Tyler, A. L. Logsdon, B. A. Crane, P. K. Carter, G. W. 2019-09-11 doi:10.1101/763516 Cold Spring Harbor Laboratory Press 2019-09-11 <![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[ TLR5 participates in the TLR4 receptor complex and biases towards MyD88-dependent signaling in environmental lung injury ]]> https://biorxiv.org/content/10.1101/792705v1?rss=1 Hussain, S. Johnson, C. C. Sciurba, J. Meng, X. Stober, V. P. Liu, C. Cypher-Daly, J. Bulek, K. Qian, W. Solis, A. Sakamachi, Y. Trempus, C. Aloor, J. J. Gowdy, K. Foster, W. M. Hollingsworth, J. W. Tighe, R. M. Li, X. Fessler, M. B. Garantziotis, S. 2019-10-03 doi:10.1101/792705 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ Spatiotemporal control of gene expression boundaries using a feedforward loop ]]> https://biorxiv.org/content/10.1101/806620v1?rss=1 Bandodkar, P. Al Asafen, H. Reeves, G. T. 2019-10-16 doi:10.1101/806620 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Orexin signaling in GABAergic lateral habenula neurons modulates aggressive behavior ]]> https://biorxiv.org/content/10.1101/811265v1?rss=1 Flanigan, M. Aleyasin, H. Li, L. Burnett, C. J. Chan, K. LeClair, K. Lucas, E. Matikainen-Ankney, B. Janssen, W. Takahashi, A. Menard, C. Pfau, M. Golden, S. Bouchard, S. Calipari, E. S. Nestler, E. J. DiLeone, R. Yamanaka, A. Huntley, G. Clem, R. Russo, S. 2019-10-21 doi:10.1101/811265 Cold Spring Harbor Laboratory Press 2019-10-21 <![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[ Chromosomal length reference assembly for Diaphorina citri using single-molecule sequencing and Hi-C proximity ligation with manually curated genes in developmental, structural and immune pathways ]]> https://biorxiv.org/content/10.1101/869685v1?rss=1 Hosmani, P. S. Flores-Gonzalez, M. Shippy, T. Vosburg, C. Massimino, C. Tank, W. Reynolds, M. Tamayo, B. Miller, S. Norus, J. Kercher, K. Grace, B. Jernigan, M. Harper, D. Adkins, S. DeLaFlor, Y. Paris, T. Vandervoort, S. Adams, R. Norman, S. Ventura, J. Perry, M. Weirauch, M. Benoit, J. Hunter, W. Wiersma-Koch, H. D'elia, T. Brown, S. J. Mueller, L. Saha, S. 2019-12-10 doi:10.1101/869685 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Large-scale phenotypic and genomic characterization of Listeria monocytogenes susceptibility to quaternary ammonium compounds ]]> https://biorxiv.org/content/10.1101/2023.09.07.556668v1?rss=1 Ivanova, M. Laage Kragh, M. Szarvas, J. Tosun, E. S. Holmud, N. F. Gmeiner, A. Amar, C. F. L. Guldimann, C. Huynh, T. N. Karpiskova, R. Garcia, C. R. Gomez, D. Aboagye, E. Etter, A. J. Centorame, P. Torresi, M. De Angelis, M. E. Pomilio, F. Okholm, A. H. Xiao, Y. Kleta, S. Lüth, S. Pietzka, A. T. Pagotto, F. Kovacevic, J. Rychli, K. Zdovc, I. Papic, B. Heir, E. Langsrud, S. Moretro, T. Roger, S. Brown, P. Kathariou, S. Tasara, T. Aarestrup, F. M. Njage, P. M. K. Fagerlund, A. Truelstrup Hansen, L. Leekitcharoenphon, P. 2023-09-11 doi:10.1101/2023.09.07.556668 Cold Spring Harbor Laboratory Press 2023-09-11 <![CDATA[ A Need for Stronger Regulation: Commercially Sold Probiotics for Honey Bees Do Not Live Up to Their Claims ]]> https://biorxiv.org/content/10.1101/2023.09.13.557574v1?rss=1 Damico, M. E. Beasley, B. Greenstein, D. Raymann, K. 2023-09-13 doi:10.1101/2023.09.13.557574 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Numerical and analytical simulation of the growth of amyloid-β plaques ]]> https://biorxiv.org/content/10.1101/2023.09.11.557187v1?rss=1 Kuznetsov, A. V. 2023-09-15 doi:10.1101/2023.09.11.557187 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ A cell-free transcription-translation pipeline for recreating methylation patterns boosts DNA transformation in bacteria ]]> https://biorxiv.org/content/10.1101/2023.09.16.557782v1?rss=1 Vento, J. M. Durmusoglu, D. Li, T. Sullivan, S. M. Ttofali, F. van Schaik, J. Yu, Y. Barquist, L. Crook, N. Beisel, C. L. 2023-09-16 doi:10.1101/2023.09.16.557782 Cold Spring Harbor Laboratory Press 2023-09-16 <![CDATA[ Deep autoencoder-based behavioral pattern recognition outperforms standard statistical methods in high-dimensional zebrafish studies ]]> https://biorxiv.org/content/10.1101/2023.09.13.557544v1?rss=1 Green, A. J. Truong, L. Thunga, P. Leong, C. Hancock, M. Tanguay, R. L. Reif, D. M. 2023-09-17 doi:10.1101/2023.09.13.557544 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Transposable element abundance subtly contributes to lower fitness in maize ]]> https://biorxiv.org/content/10.1101/2023.09.18.557618v1?rss=1 Stitzer, M. C. Khaipho-Burch, M. B. Hudson, A. I. Song, B. Valdes-Franco, J. A. Ramstein, G. P. Feschotte, C. Buckler, E. S. 2023-09-18 doi:10.1101/2023.09.18.557618 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ Genome-wide Characterization of Diverse Bacteriophages Enabled by RNA-Binding CRISPRi ]]> https://biorxiv.org/content/10.1101/2023.09.18.558157v1?rss=1 Adler, B. A. Al-Shimary, M. J. Patel, J. R. Ambruster, E. Colognori, D. Charles, E. J. Miller, K. V. Lahiri, A. Trinidad, M. Boger, R. Nomburg, J. Beurnier, S. Cui, M. L. Barrangou, R. Mutalik, V. K. Schoeniger, J. S. Pogliano, J. A. Savage, D. F. Doudna, J. A. Cress, B. F. 2023-09-18 doi:10.1101/2023.09.18.558157 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ Plant-based production of diverse human milk oligosaccharides ]]> https://biorxiv.org/content/10.1101/2023.09.18.558286v1?rss=1 Barnum, C. R. Paviani, B. Couture, G. Masarweh, C. Chen, Y. Huang, Y.-P. Mills, D. A. Lebrilla, C. B. Barile, D. Yang, M. Shih, P. 2023-09-20 doi:10.1101/2023.09.18.558286 Cold Spring Harbor Laboratory Press 2023-09-20 <![CDATA[ Exportin 1 is required for the reproduction and maize mosaic virus accumulation in its insect vector Peregrinus maidis ]]> https://biorxiv.org/content/10.1101/2023.09.19.558515v1?rss=1 Xavier, C. A. D. Tyson, C. Kerner, L. M. Whitfield, A. E. 2023-09-20 doi:10.1101/2023.09.19.558515 Cold Spring Harbor Laboratory Press 2023-09-20 <![CDATA[ Multi-omics analysis reveals signatures of selection and loci associated with complex traits in pigs ]]> https://biorxiv.org/content/10.1101/2023.09.19.558553v1?rss=1 Yi, G. Liu, L. Yao, Y. Liu, Y. Li, J. Yang, Y. Fang, L. Mo, D. Zhang, L. Liu, Y. Niu, Y. Wang, L. Qu, X. Pan, Z. Wang, L. Chen, M. Fan, X. Chen, Y. Zhang, Y. Li, X. Wang, Z. Tang, Y. Huang, H. Yuan, P. Liao, Y. Li, X. Yin, Z. Liu, D. Zhang, D. Zhou, Q. Wu, W. Jiang, J. Gao, Y. Liu, G. E. Wang, L. Chen, Y. Groenen, M. Tang, Z. 2023-09-21 doi:10.1101/2023.09.19.558553 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Context-dependent hyperactivity in syngap1a and syngap1b zebrafish autism models. ]]> https://biorxiv.org/content/10.1101/2023.09.20.557316v1?rss=1 Sumathipala, S. H. Khan, S. Kozol, R. A. Araki, Y. Syed, S. Huganir, R. L. Dallman, J. 2023-09-21 doi:10.1101/2023.09.20.557316 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Into the Wild: A novel wild-derived inbred strain resource expands the genomic and phenotypic diversity of laboratory mouse models ]]> https://biorxiv.org/content/10.1101/2023.09.21.558738v1?rss=1 90% of 1119 surveyed traits and expand the range of phenotypic diversity captured in classical inbred strain panels alone. Taken together, our work introduces a novel wild-derived inbred mouse strain resource that will enable new discoveries in basic and preclinical research. These strains are currently available through The Jackson Laboratory Repository under laboratory code NachJ. ]]> Dumont, B. L. Gatti, D. M. Ballinger, M. A. Lin, D. Phifer-Rixey, M. Sheehan, M. J. Suzuki, T. Wooldridge, L. K. Opoku Frempong, H. Churchill, G. A. Lutz, C. M. Rosenthal, N. White, J. K. Nachman, M. 2023-09-21 doi:10.1101/2023.09.21.558738 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Testing Adaptive Therapy Protocols using Gemcitabine and Capecitabine on a Mouse Model of Endocrine-Resistant Breast Cancer ]]> https://biorxiv.org/content/10.1101/2023.09.18.558136v1?rss=1 SEYEDI, S. Teo, R. Foster, L. Saha, D. Mina, L. Northfelt, D. Anderson, K. S. Shibata, D. Gatenby, R. Cisneros, L. Troan, B. Anderson, A. R. A. Maley, C. C. 2023-09-22 doi:10.1101/2023.09.18.558136 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Multi-signal regulation of the GSK-3β homolog Rim11 governs meiosis entry in yeast ]]> https://biorxiv.org/content/10.1101/2023.09.21.558844v1?rss=1 Kociemba, J. Joergensen, A. C. S. Tadic, N. Harris, A. Sideri, T. Chan, W. Y. Ibrahim, F. Unal, E. Skehel, M. Shahrezaei, V. Arguello-Miranda, O. van Werven, F. J. 2023-09-22 doi:10.1101/2023.09.21.558844 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Variability in the phytoplankton response to upwelling across an iron limitation mosaic within the California Current System ]]> https://biorxiv.org/content/10.1101/2023.09.22.558967v1?rss=1 Lin, Y. Torano, O. Whitehouse, L. Pierce, E. Till, C. P. Hurst, M. Freiberger, R. Mellett, T. Maldonado, M. T. Guo, J. Sutton, M. Zeitz, D. Marchetti, A. 2023-09-23 doi:10.1101/2023.09.22.558967 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ Sex differences in avoidance behavior and cued threat memory dynamics in mice: Interactions between estrous cycle and genetic background ]]> https://biorxiv.org/content/10.1101/2023.09.23.559127v1?rss=1 Ryherd, G. L. Bunce, A. L. Edwards, H. A. Baumgartner, N. E. Lucas, E. K. 2023-09-24 doi:10.1101/2023.09.23.559127 Cold Spring Harbor Laboratory Press 2023-09-24 <![CDATA[ Programming dynamic division of labor using horizontal gene transfer ]]> https://biorxiv.org/content/10.1101/2023.10.03.560696v1?rss=1 Hamrick, G. S. Maddamsetti, R. Son, H.-I. Wilson, M. L. Davis, H. M. You, L. 2023-10-03 doi:10.1101/2023.10.03.560696 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Rapid evolution of pesticide resistance via adaptation and interspecific introgression in a major North American crop pest ]]> https://biorxiv.org/content/10.1101/2023.10.04.560869v1?rss=1 North, H. L. Fu, Z. Metz, R. Stull, M. A. Johnson, C. D. Shirley, X. Crumley, K. Reisig, D. Kerns, D. L. Gilligan, T. Walsh, T. Jiggins, C. D. Sword, G. 2023-10-06 doi:10.1101/2023.10.04.560869 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Climate warming suppresses soil abundant fungal taxa and reduces soil carbon efflux in a semi-arid grassland ]]> https://biorxiv.org/content/10.1101/2023.10.08.561373v1?rss=1 Qiu, Y. Zhang, K. Zhao, Y. Zhao, Y. Wang, B. Wang, Y. He, T. Xu, X. Bai, T. Zhang, Y. Hu, S. 2023-10-10 doi:10.1101/2023.10.08.561373 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ An in vitro platform for quantifying cell cycle phase lengths in primary human intestinal stem cells ]]> https://biorxiv.org/content/10.1101/2023.10.09.561410v1?rss=1 Cotton, M. J. Ariel, P. Chen, K. Walcott, V. A. Dixit, M. Breau, K. A. Hinesley, C. M. Kedziora, K. Tang, C. Y. Zheng, A. Magness, S. T. Burclaff, J. 2023-10-10 doi:10.1101/2023.10.09.561410 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Early root architectural traits and their relationship with yield in Ipomoea batatas L. ]]> https://biorxiv.org/content/10.1101/2023.10.20.563294v1?rss=1 Duque, L. O. Hoffmann, G. Pecota, K. V. Yencho, C. 2023-10-21 doi:10.1101/2023.10.20.563294 Cold Spring Harbor Laboratory Press 2023-10-21 <![CDATA[ Simple Design for Membrane-Free Microphysiological Systems to Model the Blood-Tissue Barriers ]]> https://biorxiv.org/content/10.1101/2023.10.20.563328v1?rss=1 Young, A. Deal, H. Rusch, G. Pozdin, V. Brown, A. C. Daniele, M. 2023-10-23 doi:10.1101/2023.10.20.563328 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Bacterial diversity and composition on the rinds of specific melon cultivars and hybrids from across different growing regions in the United States ]]> https://biorxiv.org/content/10.1101/2023.10.23.563553v1?rss=1 Goforth, M. Obergh, V. Park, R. Porchas, M. Crosby, K. M. Jifon, J. L. Ravishankar, S. Brierley, P. Leskovar, D. L. Turini, T. A. Schultheis, J. Coolong, T. Miller, R. Koiwa, H. Patil, B. S. Cooper, M. A. Huynh, S. Parker, C. T. Guan, W. Cooper, K. 2023-10-24 doi:10.1101/2023.10.23.563553 Cold Spring Harbor Laboratory Press 2023-10-24 <![CDATA[ Characteristics of antimicrobial resistance in Escherichia coli isolated from retail meat products in North Carolina ]]> https://biorxiv.org/content/10.1101/2023.10.26.564154v1?rss=1 Aworh, M. Thakur, S. Gensler, C. Harrell, E. Harden, L. Fedorka-Cray, P. Jacob, M. 2023-10-27 doi:10.1101/2023.10.26.564154 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ A normalization method that controls for total RNA abundance affects the identification of differentially expressed genes, revealing bias toward morning-expressed responses ]]> https://biorxiv.org/content/10.1101/2023.10.28.564442v1?rss=1 Laosuntisuk, K. Vennapusa, A. R. Somayanda, I. M. Leman, A. R. Jagadish, S. K. Doherty, C. J. 2023-10-29 doi:10.1101/2023.10.28.564442 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ No trade-off between ovary activation and immune protein expression in female bumble bees (Bombus impatiens) ]]> https://biorxiv.org/content/10.1101/2023.10.27.564231v1?rss=1 McAfee, A. Chapman, A. Bao, G. Tarpy, D. R. Foster, L. J. 2023-11-01 doi:10.1101/2023.10.27.564231 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Lewy Body Radius Growth: The Hypothesis of the Cube Root of Time Dependency ]]> https://biorxiv.org/content/10.1101/2023.10.30.564787v1?rss=1 Kuznetsov, A. V. 2023-11-02 doi:10.1101/2023.10.30.564787 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ TaxaNorm: a novel taxa-specific normalization approach for microbiome data ]]> https://biorxiv.org/content/10.1101/2023.10.31.563648v1?rss=1 Wang, Z. Lloyd, D. Zhao, S. Motsinger-Reif, A. 2023-11-02 doi:10.1101/2023.10.31.563648 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Examination of the quantitative relationship between proteome- and transcriptome-level responses in larval guts of Frankliniella occidentalis infected with an orthotospovirus. ]]> https://biorxiv.org/content/10.1101/2023.10.31.564998v1?rss=1 Han, J. Rotenberg, D. 2023-11-02 doi:10.1101/2023.10.31.564998 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Histone H1x in mouse ventral hippocampus correlates with, but does not cause behavioral adaptations to stress ]]> https://biorxiv.org/content/10.1101/2023.11.06.565881v1?rss=1 Kim, R. K. Truby, N. L. Silva, G. M. Picone, J. A. Miller, C. S. Neve, R. L. Cui, X. Hamilton, P. J. 2023-11-07 doi:10.1101/2023.11.06.565881 Cold Spring Harbor Laboratory Press 2023-11-07 <![CDATA[ Model-based inference of a plant-specific dual role for HOPS in regulating guard cell vacuole fusion ]]> https://biorxiv.org/content/10.1101/2023.11.07.565947v1?rss=1 Hodgens, C. Flaherty, D. Pullen, A.-M. Khan, I. English, N. J. Gillan, L. Rojas-Pierce, M. Akpa, B. 2023-11-09 doi:10.1101/2023.11.07.565947 Cold Spring Harbor Laboratory Press 2023-11-09 <![CDATA[ Design of parallel ????-sheet nanofibrils using Monte-Carlo search, coarse-grained simulations, and experimental testing ]]> https://biorxiv.org/content/10.1101/2023.11.09.565678v1?rss=1 Sarma, S. Sudarshan, T. R. Nguyen, V. Robang, A. S. Xiao, X. Le, J. V. Helmicki, M. E. Paravastu, A. K. Hall, C. K. 2023-11-13 doi:10.1101/2023.11.09.565678 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment ]]> https://biorxiv.org/content/10.1101/2023.11.09.566470v1?rss=1 Daugird, T. A. Shi, Y. Holland, K. L. Rostamian, H. Liu, Z. Lavis, L. D. Rodriguez, J. Strahl, B. D. Legant, W. R. 2023-11-13 doi:10.1101/2023.11.09.566470 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Quantitative Cross-Species Comparison of Serum Albumin Binding of Per- and Polyfluoroalkyl Substances from Five Structural Classes ]]> https://biorxiv.org/content/10.1101/2023.11.10.566613v1?rss=1 Starnes, H. M. Jackson, T. W. Rock, K. D. Belcher, S. M. 2023-11-14 doi:10.1101/2023.11.10.566613 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ Rapid Adeno-Associated Virus Genome Quantification with Amplification-Free CRISPR-Cas12a ]]> https://biorxiv.org/content/10.1101/2023.11.14.567134v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@1bfce18org.highwire.dtl.DTLVardef@17393c9org.highwire.dtl.DTLVardef@eb7c1forg.highwire.dtl.DTLVardef@2203cd_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hetzler, Z. Marinakos, S. M. Lott, N. Mohammad, N. Lass-Napiorkowska, A. Kolbe, J. Turrentine, L. Fields, D. Overton, L. Marie, H. Hucknall, A. Rammo, O. George, H. Wei, Q. 2023-11-15 doi:10.1101/2023.11.14.567134 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Programming Probiotics: Diet-responsive gene expression and colonization control in engineered S. boulardii ]]> https://biorxiv.org/content/10.1101/2023.11.17.567539v1?rss=1 Durmusoglu, D. Haller, D. J. Al'Abri, I. S. Day, K. Sands, C. Clark, A. S. San Miguel, A. Vazquez-Uribe, R. Sommer, M. O. Crook, N. C. 2023-11-17 doi:10.1101/2023.11.17.567539 Cold Spring Harbor Laboratory Press 2023-11-17 <![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[ Mechanism of high energy efficiency of carbon fixation by sulfur-oxidizing symbionts revealed by single-cell analyses and metabolic modeling ]]> https://biorxiv.org/content/10.1101/2023.11.25.568684v1?rss=1 Kleiner, M. Polerecky, L. Lott, C. Bergin, C. Haeusler, S. Liebeke, M. Wentrup, C. Musat, N. Kuypers, M. M. M. Dubilier, N. 2023-11-26 doi:10.1101/2023.11.25.568684 Cold Spring Harbor Laboratory Press 2023-11-26 <![CDATA[ Reduced Achilles tendon stiffness in aging persists at matched activations and associates with higher metabolic cost of walking ]]> https://biorxiv.org/content/10.1101/2023.11.27.568808v1?rss=1 Franz, J. R. Krupenevich, R. Gray, A. Batsis, J. A. Sawicki, G. S. 2023-11-27 doi:10.1101/2023.11.27.568808 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ Visualizing tomato spotted wilt virus protein localization: Cross-kingdom comparisons of protein-protein interactions. ]]> https://biorxiv.org/content/10.1101/2023.11.27.568851v1?rss=1 Martin, K. M. Chen, Y. Mayfield, M. A. Montero-Astua, M. Whitfield, A. E. 2023-11-27 doi:10.1101/2023.11.27.568851 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ Drivers of population dynamics of at-risk populations change with pathogen arrival ]]> https://biorxiv.org/content/10.1101/2023.11.27.568870v1?rss=1 Grimaudo, A. T. Hoyt, J. R. King, R. A. Toomey, R. S. Simpson, C. Holliday, C. Silvis, A. Doyle, R. T. Kath, J. A. Armstrong, M. P. Brack, V. Reynolds, R. J. Williamson, R. H. Turner, G. G. Kuczynska, V. Meyer, J. J. Jansky, K. Herzog, C. J. Hopkins, S. R. Langwig, K. E. 2023-11-27 doi:10.1101/2023.11.27.568870 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ Simulating growth of TDP-43 cytosolic inclusion bodies in neuron soma ]]> https://biorxiv.org/content/10.1101/2023.11.28.569118v1?rss=1 Kuznetsov, A. V. 2023-11-30 doi:10.1101/2023.11.28.569118 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ Enhancing Light-Sheet Fluorescence Microscopy Illumination Beams through Deep Design Optimization ]]> https://biorxiv.org/content/10.1101/2023.11.29.569329v1?rss=1 Li, C. Rai, M. R. Cai, Y. Ghashghaei, H. T. Greenbaum, A. 2023-12-01 doi:10.1101/2023.11.29.569329 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ CRISPR/Cas9-mediated genome editing of Frankliniella occidentalis, the western flower thrips, via embryonic microinjection ]]> https://biorxiv.org/content/10.1101/2023.11.30.569456v1?rss=1 Han, J. Klobasa, W. de Oliveira, L. Rotenberg, D. Whitfield, A. E. Lorenzen, M. D. 2023-12-01 doi:10.1101/2023.11.30.569456 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ A Ratiometric Nonfluorescent CRISPR Assay Utilizing Cas12a-Induced Plasmid Supercoil Relaxation ]]> https://biorxiv.org/content/10.1101/2023.12.04.570032v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@2c81b3org.highwire.dtl.DTLVardef@1f7453aorg.highwire.dtl.DTLVardef@e1eb06org.highwire.dtl.DTLVardef@cf103_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Mohammad, N. Talton, L. Dalgan, S. Wei, Q. 2023-12-05 doi:10.1101/2023.12.04.570032 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Quantitative Modeling of the Short-Term Response to Nitrogen Availability that Coordinates Early Events in Lateral Root Initiation ]]> https://biorxiv.org/content/10.1101/2023.12.05.570292v1?rss=1 Gaudinier, A. Van den Broeck, L. Moreno-Risueno, M. Rodriguez-Mendina, J. Sozzani, R. Brady, S. 2023-12-06 doi:10.1101/2023.12.05.570292 Cold Spring Harbor Laboratory Press 2023-12-06 <![CDATA[ DisDock: A Deep Learning Method for Metal Ion-Protein Redocking ]]> https://biorxiv.org/content/10.1101/2023.12.07.570531v1?rss=1 Lin, M. Li, K. Zhang, Y. Pan, F. Wu, W. Zhang, J. 2023-12-08 doi:10.1101/2023.12.07.570531 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Effective seed sterilization methods require optimization across maize genotypes ]]> https://biorxiv.org/content/10.1101/2023.12.14.571779v1?rss=1 Parnell, J. J. Pal, G. Awan, A. Vintila, S. Houdinet, G. Hawkes, C. V. Balint-Kurti, P. Wagner, M. R. Kleiner, M. 2023-12-15 doi:10.1101/2023.12.14.571779 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ Quantifying the strength of viral fitness tradeoffs between hosts: A meta-analysis of pleiotropic fitness effects ]]> https://biorxiv.org/content/10.1101/2023.12.16.571995v1?rss=1 Wang, X. M. Muller, J. McDowell, M. Rasmussen, D. A. 2023-12-16 doi:10.1101/2023.12.16.571995 Cold Spring Harbor Laboratory Press 2023-12-16 <![CDATA[ Temporal Transcriptome Analysis Uncovers Regulatory Modules Programming Embryo Development from Embryonic Morphogenesis to Post-Germination ]]> https://biorxiv.org/content/10.1101/2023.12.26.573376v1?rss=1 Wang, Y.-C. Hsieh, W.-H. Huang, C.-J. Jhan, Y.-T. Zhan, J. Chang, C.-C. Hsieh, T.-F. Lin, J.-Y. 2023-12-27 doi:10.1101/2023.12.26.573376 Cold Spring Harbor Laboratory Press 2023-12-27 <![CDATA[ Chewing Through Challenges: Exploring the Evolutionary Pathways to Wood-Feeding in Insects ]]> https://biorxiv.org/content/10.1101/2023.12.27.573094v1?rss=1 Beza-Beza, C. F. Wiegmann, B. M. Ware, J. A. Petersen, M. Gunter, N. Cole, M. E. Schwarz, M. Bertone, M. A. Young, D. Mikaelyan, A. 2023-12-28 doi:10.1101/2023.12.27.573094 Cold Spring Harbor Laboratory Press 2023-12-28 <![CDATA[ Inferring neural dynamics of memory during naturalistic social communication ]]> https://biorxiv.org/content/10.1101/2024.01.26.577404v1?rss=1 Pang, R. Baker, C. A. Murthy, M. Pillow, J. W. 2024-01-27 doi:10.1101/2024.01.26.577404 Cold Spring Harbor Laboratory Press 2024-01-27 <![CDATA[ Loss of UBE3A impacts both neuronal and non-neuronal cells in human cerebral organoids ]]> https://biorxiv.org/content/10.1101/2024.02.09.579672v1?rss=1 Estridge, R. C. Yagci, Z. B. Sen, D. Ptacek, T. S. Simon, J. M. Keung, A. J. 2024-02-10 doi:10.1101/2024.02.09.579672 Cold Spring Harbor Laboratory Press 2024-02-10 <![CDATA[ Enable, Empower, Succeed: Harnessing Open Science for Antimicrobial Resistance Containment ]]> https://biorxiv.org/content/10.1101/2024.02.20.580892v1?rss=1 Founou, L. L. Lawal, O. U. Djiyou, A. Odih, E. E. Amoako, D. G. Fadanka, S. Aworh, M. K. Lukhele, S. Nikolic, D. Matimba, A. Founou, R. C. 2024-02-23 doi:10.1101/2024.02.20.580892 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ A synergistic culture dependent and independent approach reveals a conserved wheat seed mycobiome ]]> https://biorxiv.org/content/10.1101/2024.02.22.581674v1?rss=1 Becker, L. E. Marshall, D. Cubeta, M. A. 2024-02-23 doi:10.1101/2024.02.22.581674 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Stability of the Wheat Seed Mycobiome Across North Carolina's Longitudinal Gradient ]]> https://biorxiv.org/content/10.1101/2024.02.22.581680v1?rss=1 Becker, L. Hawkes, C. V. Heiniger, R. W. Cubeta, M. A. 2024-02-23 doi:10.1101/2024.02.22.581680 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Development of MHC Class I Blocking Peptides to Target Metabolic Dysfunction-Associated Steatohepatitis CD8+ T Cell Activation ]]> https://biorxiv.org/content/10.1101/2024.03.12.584666v1?rss=1 Adams, V. Sarma, S. Hall, C. K. Kennedy, A. 2024-03-14 doi:10.1101/2024.03.12.584666 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Modeling the impact of optimized airflow and sick pen management on the spread of infectious diseases in swine barns ]]> https://biorxiv.org/content/10.1101/2024.03.13.584486v1?rss=1 Safari, M. Fleming, C. Galvis, J. A. Deka, A. Sanchez, F. Machado, G. Yeh, C.-A. 2024-03-15 doi:10.1101/2024.03.13.584486 Cold Spring Harbor Laboratory Press 2024-03-15 <![CDATA[ The Sociodemographic and Lifestyle Correlates of Epigenetic Aging in a Nationally Representative U.S. Study of Younger Adults ]]> https://biorxiv.org/content/10.1101/2024.03.21.585983v1?rss=1 Harris, K. M. Levitt, B. E. Gaydosh, L. Martin, C. Meyer, J. M. Mishra, A. A. Kelly, A. L. Aiello, A. E. 2024-03-27 doi:10.1101/2024.03.21.585983 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Intercontinental dissemination and diversification of Xanthomonas perforans in tomato production ]]> https://biorxiv.org/content/10.1101/2024.03.22.585974v1?rss=1 Timilsina, S. Iruegas-Bocardo, F. Jibrin, M. O. Sharma, A. Subedi, A. Minsavage, G. V. Huguet-Tapia, J. Klein-Gordon, J. Adhikari, P. Adhikari, T. B. Cirvilleri, G. Belen Tapia de la Barrera, L. Bernal, E. Creswell, T. C. Doan, T. T. K. Coutinho, T. A. Egel, D. S. Felix-Gastelum, R. Francis, D. M. Kebede, M. Lewis Ivey, M. Louws, F. J. Luo, L. Maynard, E. T. Miller, S. A. Nguyen, N. T. T. Osdaghi, E. Quezado-Duval, A. M. Roach, R. Rotondo, F. Ruhl, G. E. Shutt, V. M. Thummabenjapone, P. Trueman, C. Roberts, P. D. Jones, J. B. Vallad, G. E. Goss, E. M. 2024-03-22 doi:10.1101/2024.03.22.585974 Cold Spring Harbor Laboratory Press 2024-03-22 <![CDATA[ Human long noncoding RNA, VILMIR, is induced by major respiratory viral infections and modulates the host interferon response ]]> https://biorxiv.org/content/10.1101/2024.03.25.586578v1?rss=1 John, K. Huntress, I. Smith, E. Chou, H. Tollison, T. S. Covarrubias, S. Crisci, E. Carpenter, S. Peng, X. 2024-03-29 doi:10.1101/2024.03.25.586578 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Pseudo-pac site sequences used by phage P22 in generalized transduction of Salmonella ]]> https://biorxiv.org/content/10.1101/2024.03.25.586692v1?rss=1 Maier, J. Gin, C. Callahan, B. Sheriff, E. K. Duerkop, B. A. Kleiner, M. 2024-03-25 doi:10.1101/2024.03.25.586692 Cold Spring Harbor Laboratory Press 2024-03-25 <![CDATA[ Microbial ecology and site characteristics underlie differences in salinity-methane relationships in coastal wetlands ]]> https://biorxiv.org/content/10.1101/2024.04.02.587477v1?rss=1 Bueno de Mesquita, C. P. Hartman, W. H. Ardon, M. Bernhardt, E. S. Neubauer, S. C. Weston, N. B. Tringe, S. G. 2024-04-02 doi:10.1101/2024.04.02.587477 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Dietary protein source strongly alters gut microbiota composition and function ]]> https://biorxiv.org/content/10.1101/2024.04.04.588169v1?rss=1 Blakeley-Ruiz, J. A. Bartlett, A. McMillan, A. S. Awan, A. Vanhoy Walsh, M. Meyerhoffer, A. K. Vintila, S. Maier, J. Richie, T. Theriot, C. M. Kleiner, M. 2024-04-05 doi:10.1101/2024.04.04.588169 Cold Spring Harbor Laboratory Press 2024-04-05 <![CDATA[ Metabolically-versatile Ca. Thiodiazotropha symbionts of the deep-sea lucinid clam Lucinoma kazani have the genetic potential to fix nitrogen ]]> https://biorxiv.org/content/10.1101/2024.04.05.588213v1?rss=1 Ratinskaia, L. Malavin, S. Zvi-Kedem, T. Vintila, S. Kleiner, M. Rubin-Blum, M. 2024-04-05 doi:10.1101/2024.04.05.588213 Cold Spring Harbor Laboratory Press 2024-04-05 <![CDATA[ The growth rate of senile plaques is determined by the competition between the rate of deposition of free Aβ aggregates into plaques and the autocatalytic production of free Aβ aggregates ]]> https://biorxiv.org/content/10.1101/2024.04.06.588435v1?rss=1 Kuznetsov, A. V. 2024-04-10 doi:10.1101/2024.04.06.588435 Cold Spring Harbor Laboratory Press 2024-04-10 <![CDATA[ Metaproteomics and DNA metabarcoding as tools to assess dietary intake in humans ]]> https://biorxiv.org/content/10.1101/2024.04.09.588275v1?rss=1 Petrone, B. L. Bartlett, A. Jiang, S. Korenek, A. Vintila, S. Tenekjian, C. B. Yancy, W. S. David, L. A. Kleiner, M. 2024-04-10 doi:10.1101/2024.04.09.588275 Cold Spring Harbor Laboratory Press 2024-04-10 <![CDATA[ Trends and drivers of hypoxic thickness and volume in Northern Gulf of Mexico: 1985-2018 ]]> https://biorxiv.org/content/10.1101/2024.04.12.589301v1?rss=1 Matli, V. R. R. Obenour, D. 2024-04-15 doi:10.1101/2024.04.12.589301 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ A framework for quality control in quantitative proteomics ]]> https://biorxiv.org/content/10.1101/2024.04.12.589318v1?rss=1 Tsantilas, K. A. Merrihew, G. E. Robbins, J. E. Johnson, R. S. Park, J. Plubell, D. L. Huang, E. Riffle, M. Sharma, V. MacLean, B. X. Eckels, J. Bereman, M. B. Spencer, S. E. Hoofnagle, A. N. MacCoss, M. J. 2024-04-13 doi:10.1101/2024.04.12.589318 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ Common viral infections inhibit egg laying in honey bee queens and are linked to premature supersedure ]]> https://biorxiv.org/content/10.1101/2024.04.16.589807v1?rss=1 Chapman, A. A. McAfee, A. Tarpy, D. R. Fine, J. Rempel, Z. Peters, K. Currie, R. Foster, L. 2024-04-20 doi:10.1101/2024.04.16.589807 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Ruvbl1 is required for the reproduction of the corn planthopper, Peregrinus maidis ]]> https://biorxiv.org/content/10.1101/2024.04.17.589929v1?rss=1 Xavier, C. A. D. Tyson, C. Whitfield, A. E. 2024-04-17 doi:10.1101/2024.04.17.589929 Cold Spring Harbor Laboratory Press 2024-04-17 <![CDATA[ Comparative Analysis of Machine Learning Algorithms for Breast Cancer Classification: SVM Outperforms XGBoost, CNN, RNN, and Others ]]> https://biorxiv.org/content/10.1101/2024.04.22.590658v1?rss=1 Chatterjee, D. Ghosh, P. 2024-04-26 doi:10.1101/2024.04.22.590658 Cold Spring Harbor Laboratory Press 2024-04-26 <![CDATA[ Deep learning-driven imaging of cell division and cell growth across an entire eukaryotic life cycle ]]> https://biorxiv.org/content/10.1101/2024.04.25.591211v1?rss=1 Ramakanth, S. Kennedy, T. Yalcinkaya, B. Neupane, S. Tadic, N. Buchler, N. E. Arguello-Miranda, O. 2024-04-27 doi:10.1101/2024.04.25.591211 Cold Spring Harbor Laboratory Press 2024-04-27 <![CDATA[ Derivation of human trophoblast stem cells from placentas at birth ]]> https://biorxiv.org/content/10.1101/2024.05.01.592064v1?rss=1 Karakis, V. Britt, J. W. Jabeen, M. San Miguel, A. Rao, B. M. 2024-05-02 doi:10.1101/2024.05.01.592064 Cold Spring Harbor Laboratory Press 2024-05-02 <![CDATA[ DNA replication errors are a major source of adaptive gene amplification ]]> https://biorxiv.org/content/10.1101/2024.05.03.589936v1?rss=1 Chuong, J. Ben Nun, N. Suresh, I. Matthews, J. De, T. Avecilla, G. Abdul-Rahman, F. Brandt, N. Ram, Y. Gresham, D. 2024-05-06 doi:10.1101/2024.05.03.589936 Cold Spring Harbor Laboratory Press 2024-05-06 <![CDATA[ Transit amplifying cells balance growth and differentiation in above-ground meristems ]]> https://biorxiv.org/content/10.1101/2024.05.04.592499v1?rss=1 Joossens, J. Herwegh, D. Laureyns, R. Pevernagie, J. Van Hautegem, T. Polaris, L. bhattacharya, S. Korfhage, C. Depuydt, T. Demuynck, K. Vandepoele, K. Saeys, Y. Whipple, C. Strable, J. Nelissen, H. 2024-05-05 doi:10.1101/2024.05.04.592499 Cold Spring Harbor Laboratory Press 2024-05-05 <![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[ Proteomic and Lipidomic Plasma Evaluations Reveal Biomarkers for Domoic Acid Toxicosis in California Sea Lions ]]> https://biorxiv.org/content/10.1101/2024.05.06.592757v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@b61289org.highwire.dtl.DTLVardef@17ae9f7org.highwire.dtl.DTLVardef@96904eorg.highwire.dtl.DTLVardef@dc299a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Solosky, A. M. Claudio, I. M. Chappel, J. R. Kirkwood-Donelson, K. I. Janech, M. G. Bland, A. M. Gulland, F. Neely, B. A. Baker, E. 2024-05-09 doi:10.1101/2024.05.06.592757 Cold Spring Harbor Laboratory Press 2024-05-09 <![CDATA[ Into the Void: Cavities and Tunnels are Essential for Functional Protein Design ]]> https://biorxiv.org/content/10.1101/2024.05.06.592825v1?rss=1 Zhang, J. Peng, Z. 2024-05-10 doi:10.1101/2024.05.06.592825 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Amyloid β Induces Hormetic-Like Effects Through Major Stress Pathways in a C. elegans Model of Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2024.05.07.593003v1?rss=1 Lichty, J. D. San Miguel, A. 2024-05-10 doi:10.1101/2024.05.07.593003 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Investigating spatial dynamics in spatial omics data with StarTrail ]]> https://biorxiv.org/content/10.1101/2024.05.08.593025v1?rss=1 Chen, J. Xiong, C. Sun, Q. Wang, G. W. Gupta, G. P. Halder, A. Li, Y. Li, D. 2024-05-10 doi:10.1101/2024.05.08.593025 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Fight, Retreat, Repeat: Field observation of male-male agonistic behavior in the wood-feeding cockroach, Panesthia angustipennis spadica (Dictyoptera: Blattodea: Blaberidae) ]]> https://biorxiv.org/content/10.1101/2024.05.09.593021v1?rss=1 Osaki, H. Nakazono, T. Yabe, K. Takata, M. Mikaelyan, A. 2024-05-09 doi:10.1101/2024.05.09.593021 Cold Spring Harbor Laboratory Press 2024-05-09 <![CDATA[ Utility of thromboelastography with platelet mapping (TEG-PM) for monitoring platelet transfusion in qualitative platelet disorders ]]> https://biorxiv.org/content/10.1101/2024.05.09.593198v1?rss=1 Lee, R. H. Rudran, T. Bergmeier, W. 2024-05-14 doi:10.1101/2024.05.09.593198 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy. ]]> https://biorxiv.org/content/10.1101/2024.05.09.593304v1?rss=1 Bobay, L.-M. Diop, A. 2024-05-09 doi:10.1101/2024.05.09.593304 Cold Spring Harbor Laboratory Press 2024-05-09 <![CDATA[ Wheat Enhanced Disease Resistance EMS-Mutants Include Lesion-mimics With Adult Plant Resistance to Stripe Rust ]]> https://biorxiv.org/content/10.1101/2024.05.10.593581v1?rss=1 Lunde, C. Seong, K. Kumar, R. Deatker, A. Chhabra, B. Wang, M. Kaur, S. Song, S. Palayur, A. Davies, C. Cumberlich, W. Gill, U. Rawat, N. Chen, X. Aoun, M. Mundt, C. Krasileva, K. V. 2024-05-13 doi:10.1101/2024.05.10.593581 Cold Spring Harbor Laboratory Press 2024-05-13 <![CDATA[ Enterococcal quorum-controlled protease alters phage infection ]]> https://biorxiv.org/content/10.1101/2024.05.10.593607v1?rss=1 Sheriff, E. K. Salvato, F. Andersen, S. E. Chatterjee, A. Kleiner, M. Duerkop, B. A. 2024-05-11 doi:10.1101/2024.05.10.593607 Cold Spring Harbor Laboratory Press 2024-05-11 <![CDATA[ Population origin, body mass, and viral infections influence drone honey bee (Apis mellifera) heat tolerance ]]> https://biorxiv.org/content/10.1101/2024.05.12.593456v1?rss=1 McAfee, A. Metz, B. N. Connor, P. Du, K. Allen, C. W. Frausto, L. A. Swensen, M. P. Phillips, K. S. Julien, M. Baer, B. Tarpy, D. R. Foster, L. J. 2024-05-14 doi:10.1101/2024.05.12.593456 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Frequencies of house fly proto-Y chromosomes across populations are predicted by temperature heterogeneity within populations ]]> https://biorxiv.org/content/10.1101/2024.05.15.594357v1?rss=1 Foy, P. D. Loetzerich, S. R. Boxler, D. Burgess, E. R. Trout Fryxell, R. T. Gerry, A. C. Hinkle, N. C. Machtinger, E. T. Olds, C. Tarone, A. M. Watson, W. Scott, J. G. Meisel, R. P. 2024-05-18 doi:10.1101/2024.05.15.594357 Cold Spring Harbor Laboratory Press 2024-05-18 <![CDATA[ Two germ granule eIF4E isoforms reside in different mRNPs to hand off C elegans mRNAs from translational repression to activation ]]> https://biorxiv.org/content/10.1101/2024.05.24.595216v1?rss=1 Gajjar, G. Huggins, H. P. Kim, E. S. Huang, W. Bonnet, F. X. Updike, D. L. Keiper, B. D. 2024-05-26 doi:10.1101/2024.05.24.595216 Cold Spring Harbor Laboratory Press 2024-05-26 <![CDATA[ Exploring the Effects of Glutathione Supplementation on Liver Enzymes and Serum Electrolyte Levels in Mice Exposed to 850-1900 MHz Mobile Phone Radiation: An Investigation into Radiative Stress and Potential Protective Measures ]]> https://biorxiv.org/content/10.1101/2024.05.24.595675v1?rss=1 Binhambali, A. Ahmed, A. T. Umar, A. H. Abdoulie, A. T. Mukhtar, A. I. Pate, A. A. Nuhu, A. Ipinlaiye, T. Ismail, U. Kolo, H. M. Magaji, R. A. 2024-05-29 doi:10.1101/2024.05.24.595675 Cold Spring Harbor Laboratory Press 2024-05-29 <![CDATA[ Homologous Recombination Shapes the Architecture and Evolution of Bacterial Genomes ]]> https://biorxiv.org/content/10.1101/2024.05.31.596828v1?rss=1 Torrance, E. L. Diop, A. Bobay, L.-M. 2024-06-03 doi:10.1101/2024.05.31.596828 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Mosquito population dynamics is shaped by the interaction among larval density, season, and land use ]]> https://biorxiv.org/content/10.1101/2024.06.08.598043v1?rss=1 Solano, N. Herring, E. C. Hintz, C. W. Newberry, P. M. Schatz, A. M. Walker, J. W. Osenberg, C. W. Murdock, C. C. 2024-06-10 doi:10.1101/2024.06.08.598043 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Quantifying the genomic determinants of fitness in E. coli ST131 using phylodynamics ]]> https://biorxiv.org/content/10.1101/2024.06.10.598183v1?rss=1 Kepler, L. M. Jara, M. Mahmud, B. Dantas, G. Dubberke, E. Lanzas, C. Rasmussen, D. A. 2024-06-10 doi:10.1101/2024.06.10.598183 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ SEGS-1 episomes generated during cassava mosaic disease influence disease severity ]]> https://biorxiv.org/content/10.1101/2024.06.12.598742v1?rss=1 Chiunga, E. Aimone, C. D. Rajabu, C. A. Dallas, M. M. Ndunguru, J. Ascencio-Ibanez, J. T. Ateka, E. M. Hanley-Bowdoin, L. 2024-06-12 doi:10.1101/2024.06.12.598742 Cold Spring Harbor Laboratory Press 2024-06-12 <![CDATA[ LMNA-Related Dilated Cardiomyopathy: Single-Cell Transcriptomics during Patient-derived iPSC Differentiation Support Cell type and Lineage-specific Dysregulation of Gene Expression and Development for Cardiomyocytes and Epicardium-Derived Cells with Lamin A/C Haploinsufficiency ]]> https://biorxiv.org/content/10.1101/2024.06.12.598335v1?rss=1 G splice-site mutation. We differentiated one LMNA mutant iPSC line derived from an affected female (Patient) and two non-mutant iPSC lines derived from her unaffected sister (Control) and conducted single-cell RNA sequencing for 12 samples (4 Patient and 8 Control) across seven time points: Day 0, 2, 4, 9, 16, 19, and 30. Our bioinformatics workflow identified 125,554 cells in raw data and 110,521 (88%) high-quality cells in sequentially processed data. Unsupervised clustering, cell annotation, and trajectory inference found complex heterogeneity: ten main cell types; many possible subtypes; and lineage bifurcation for Cardiac Progenitors to Cardiomyocytes (CM) and Epicardium-Derived Cells (EPDC). Data integration and comparative analyses of Patient and Control cells found cell type and lineage differentially expressed genes (DEG) with enrichment to support pathway dysregulation. Top DEG and enriched pathways included: 10 ZNF genes and RNA polymerase II transcription in Pluripotent cells (PP); BMP4 and TGF Beta/BMP signaling, sarcomere gene subsets and cardiogenesis, CDH2 and EMT in CM; LMNA and epigenetic regulation and DDIT4 and mTORC1 signaling in EPDC. Top DEG also included: XIST and other X-linked genes, six imprinted genes: SNRPN, PWAR6, NDN, PEG10, MEG3, MEG8, and enriched gene sets in metabolism, proliferation, and homeostasis. We confirmed Lamin A/C haploinsufficiency by allelic expression and Western blot. Our complex Patient-derived iPSC model for Lamin A/C haploinsufficiency in PP, CM, and EPDC provided support for dysregulation of genes and pathways, many previously associated with Lamin A/C defects, such as epigenetic gene expression, signaling, and differentiation. Our findings support disruption of epigenomic developmental programs as proposed in other LMNA disease models. We recognized other factors influencing epigenetics and differentiation; thus, our approach needs improvement to further investigate this mechanism in an iPSC-derived model. ]]> Zaragoza, M. V. Bui, T.-A. Widyastuti, L. Mehrabi, M. Cang, Z. Sha, Y. Grosberg, A. Nie, Q. 2024-06-14 doi:10.1101/2024.06.12.598335 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ UNVEILING STEM CELL INDUCTION MECHANISMS FROM SPATIOTEMPORAL CELL-TYPE-SPECIFIC GENE REGULATORY NETWORKS IN POSTEMBRYONIC ROOT ORGANOGENSIS ]]> https://biorxiv.org/content/10.1101/2024.06.13.598926v1?rss=1 Cabrera, J. Sanchez-Corrionero, A. de Luis Balaguer, A. Serrano-Ron, L. del Barrio, C. Cubas, P. Perez-Garcia, P. Sozzani, R. Moreno-Risueno, M. 2024-06-14 doi:10.1101/2024.06.13.598926 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ Dietary protein from different sources escapes host digestion and is differentially modified by the microbiota ]]> https://biorxiv.org/content/10.1101/2024.06.26.600830v1?rss=1 Awan, A. Bartlett, A. Blakeley-Ruiz, J. Richie, T. G. Theriot, C. M. Kleiner, M. 2024-06-27 doi:10.1101/2024.06.26.600830 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ Lethal Disruption of the Symbiotic Gut Community in Eastern Subterranean Termite Caused by Boric Acid ]]> https://biorxiv.org/content/10.1101/2024.06.26.600876v1?rss=1 Ashbrook, A. R. Schwarz, M. Schal, C. Mikaelyan, A. 2024-06-30 doi:10.1101/2024.06.26.600876 Cold Spring Harbor Laboratory Press 2024-06-30 <![CDATA[ Single-cell analysis of human diversity in circulating immune cells ]]> https://biorxiv.org/content/10.1101/2024.06.30.601119v1?rss=1 Kock, K. H. Tan, L. M. Han, K. Y. Ando, Y. Jevapatarakul, D. Chatterjee, A. Lin, Q. X. X. Buyamin, E. V. Sonthalia, R. Rajagopalan, D. Tomofuji, Y. Sankaran, S. Park, M.-S. Abe, M. Chantaraamporn, J. Furukawa, S. Ghosh, S. Inoue, G. Kojima, M. Kouno, T. Lim, J. Myouzen, K. Nguantad, S. Oh, J.-M. Rayan, N. A. Sarkar, S. Suzuki, A. Thungsatianpun, N. Venkatesh, P. N. Moody, J. Nakano, M. Chen, Z. Tian, C. Zhang, Y. Tong, Y. Tan, C. T. Y. Tizazu, A. M. SG10K_Health Consortium, Loh, M. Hwang, Y. Y. Ho, R. C. Larbi, A. Ng, T. P. Won, H.-H. Wright, F. A. 2024-07-01 doi:10.1101/2024.06.30.601119 Cold Spring Harbor Laboratory Press 2024-07-01 <![CDATA[ An Autonomous Implantable Device for the Prevention of Death from Opioid Overdose ]]> https://biorxiv.org/content/10.1101/2024.06.27.600919v1?rss=1 Ciatti, J. L. Vazquez-Guardado, A. Brings, V. E. Park, J. Ruyle, B. Ober, R. A. McLuckie, A. J. Talcott, M. R. Carter, E. A. Burrell, A. R. Sponenburg, R. A. Trueb, J. Gupta, P. Kim, J. Avila, R. Seong, M. Slivicki, R. A. Kaplan, M. A. Villalpando, B. Massaly, N. Montana, M. C. Pet, M. Huang, Y. Moron, J. A. Gereau, R. W. Rogers, J. A. 2024-07-02 doi:10.1101/2024.06.27.600919 Cold Spring Harbor Laboratory Press 2024-07-02 <![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[ Divide and conquer: Using RhizoVision Explorer to aggregate data from multiple root scans using image concatenation and statistical methods ]]> https://biorxiv.org/content/10.1101/2024.07.05.602287v1?rss=1 Seethepalli, A. Ottley, C. Fine, A. Cope, K. Lagergren, J. Iversen, C. Kalluri, U. York, L. M. 2024-07-10 doi:10.1101/2024.07.05.602287 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Meta-omics reveals role of photosynthesis in Microbially Induced Carbonate Precipitation at a CO2-rich Geyser ]]> https://biorxiv.org/content/10.1101/2024.07.20.604422v1?rss=1 Violette, M. Hyland, E. Burgener, L. Ghosh, A. Montoya, B. Kleiner, M. 2024-07-20 doi:10.1101/2024.07.20.604422 Cold Spring Harbor Laboratory Press 2024-07-20 <![CDATA[ A high-resolution model of gene expression during Gossypium hirsutum (cotton) fiber development ]]> https://biorxiv.org/content/10.1101/2024.07.20.604417v1?rss=1 Grover, C. E. Jareczek, J. J. Swaminathan, S. Lee, Y. Howell, A. H. Rani, H. Arick, M. A. Leach, A. G. Miller, E. R. Yang, P. Hu, G. Xiong, X. Mallery, E. L. Peterson, D. G. Xie, J. Haigler, C. H. Zabotina, O. A. Szymanski, D. B. Wendel, J. F. 2024-07-22 doi:10.1101/2024.07.20.604417 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ The LYCOPENE EPSILON CYCLASE untranslated mRNA leader modulates carotenoid feedback and post-transcriptional regulation ]]> https://biorxiv.org/content/10.1101/2024.07.19.604344v1?rss=1 Alagoz, Y. Nayak, J. Aryal, R. Watkins, J. Holland, S. Tissue, D. Pogson, B. J. Cazzonelli, C. I. 2024-07-23 doi:10.1101/2024.07.19.604344 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ The Biochemical Effects of Carotenoids in Orange Carrots on the Colonic Proteome in a Mouse Model of Diet-induced Obesity ]]> https://biorxiv.org/content/10.1101/2024.07.23.604335v1?rss=1 Balbuena, E. Milhem, F. Kiremitci, Z. Williams, T. I. Collins, L. Shu, Q. Eroglu, A. 2024-07-24 doi:10.1101/2024.07.23.604335 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Mapping the nuclear landscape with multiplexed super-resolution fluorescence microscopy ]]> https://biorxiv.org/content/10.1101/2024.07.27.605159v1?rss=1 Rahman, F. Augoustides, V. Tyler, E. Daugird, T. A. Arthur, C. Legant, W. R. 2024-07-29 doi:10.1101/2024.07.27.605159 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ ALPHA: A High Throughput System for Quantifying Growth In Aquatic Plants ]]> https://biorxiv.org/content/10.1101/2024.07.30.605820v1?rss=1 Robinson, K. A. Augoustides, V. Madenyika, T. Sartor, R. C. 2024-07-31 doi:10.1101/2024.07.30.605820 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ CoMPHI: A Novel Composite Machine Learning Approach Utilizing Multiple FeatureRepresentation to Predict Hosts of Bacteriophages ]]> https://biorxiv.org/content/10.1101/2024.07.29.604684v1?rss=1 Bodaka, S. Malgonde, O. 2024-08-02 doi:10.1101/2024.07.29.604684 Cold Spring Harbor Laboratory Press 2024-08-02 <![CDATA[ Modeling the transmission dynamics of African swine fever virus within commercial swine barns: Quantifying the contribution of multiple transmission pathways ]]> https://biorxiv.org/content/10.1101/2024.08.02.604486v1?rss=1 Deka, A. Galvis, J. A. Fleming, C. Safari, M. Yeh, C.-A. Machado, G. 2024-08-04 doi:10.1101/2024.08.02.604486 Cold Spring Harbor Laboratory Press 2024-08-04 <![CDATA[ Commensal-derived short-chain fatty acids disrupt lipid membrane homeostasis in Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/2024.08.12.607382v1?rss=1 Fletcher, J. R. Hansen, L. A. Martinez, R. Freeman, C. D. Thorns, N. Villareal, A. R. Penningroth, M. R. Vogt, G. A. Tyler, M. Hines, K. M. Hunter, R. C. 2024-08-12 doi:10.1101/2024.08.12.607382 Cold Spring Harbor Laboratory Press 2024-08-12 <![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[ A criterion characterizing accumulated toxicity of Aβ oligomers in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2024.08.19.608707v1?rss=1 Kuznetsov, A. V. 2024-08-20 doi:10.1101/2024.08.19.608707 Cold Spring Harbor Laboratory Press 2024-08-20 <![CDATA[ Large scale comparative wheat phosphoproteome profiling pinpoints temperature-associated molecular signatures ]]> https://biorxiv.org/content/10.1101/2024.08.20.608123v1?rss=1 Fonseca de Lima, C. F. Zhu, T. Van den Broeck, L. Van De Cotte, B. Locke, A. M. Sozzani, R. De Smet, I. 2024-08-21 doi:10.1101/2024.08.20.608123 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plate ]]> https://biorxiv.org/content/10.1101/2024.08.25.609458v1?rss=1 Brooks, E. R. Moorman, A. R. Bhattacharya, B. Prudhomme, I. Land, M. Alcorn, H. L. Sharma, R. Pe'er, D. Zallen, J. A. 2024-08-26 doi:10.1101/2024.08.25.609458 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Phylodynamics beyond neutrality: The impact ofincomplete purifying selection on viral phylogeniesand inference ]]> https://biorxiv.org/content/10.1101/2024.08.28.610037v1?rss=1 Koelle, K. Rasmussen, D. 2024-08-28 doi:10.1101/2024.08.28.610037 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ Temperature affects recombination rate plasticity and meiotic success between thermotolerant and cold tolerant yeast species ]]> https://biorxiv.org/content/10.1101/2024.08.28.610152v1?rss=1 McNeill, J. Brandt, N. Schwarzkopf, E. J. Jimenez Gallardo, M. Smukowski Heil, C. 2024-08-29 doi:10.1101/2024.08.28.610152 Cold Spring Harbor Laboratory Press 2024-08-29 <![CDATA[ A Systematic Analysis of Read-Across Adaptations in Testing Proposal Evaluations by the European Chemicals Agency ]]> https://biorxiv.org/content/10.1101/2024.08.29.610278v1?rss=1 Roe, H. Tsai, H.-H. D. Ball, N. Wright, F. A. Chiu, W. Rusyn, I. 2024-08-30 doi:10.1101/2024.08.29.610278 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Highly dynamic mechanical transitions in embryonic cell populations during Drosophila gastrulation ]]> https://biorxiv.org/content/10.1101/2024.08.29.610383v1?rss=1 Gomez, J. M. Bevilacqua, C. Thayambath, A. Leptin, M. Belmonte, J. Prevedel, R. 2024-08-30 doi:10.1101/2024.08.29.610383 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Fluralaner treatment of chickens kills the southern house mosquito, Culex quinquefasciatus ]]> https://biorxiv.org/content/10.1101/2024.08.30.610151v1?rss=1 Knape, K. Tian, Y. Durden, C. Adams, D. R. Garza, M. Carey, J. B. Hamer, S. A. Hamer, G. L. 2024-08-30 doi:10.1101/2024.08.30.610151 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ The interaction between abiotic and biotic soil factors drive heterosis expression in maize ]]> https://biorxiv.org/content/10.1101/2024.08.30.610574v1?rss=1 Clouse, K. M. Ellis, M. L. Ford, N. E. Hostetler, R. L. Balint-Kurti, P. Kleiner, M. Wagner, M. R. 2024-09-02 doi:10.1101/2024.08.30.610574 Cold Spring Harbor Laboratory Press 2024-09-02 <![CDATA[ Methods for high throughput discovery of fluoroprobes that recognize tau fibril polymorphs ]]> https://biorxiv.org/content/10.1101/2024.09.02.610853v1?rss=1 Carroll, E. C. Yang, H. E. Jones, J. G. Oehler, A. Charvat, A. F. Montgomery, K. M. Yung, A. Millbern, Z. Vinueza, N. R. Degrado, W. F. Mordes, D. A. Condello, C. Gestwicki, J. E. 2024-09-02 doi:10.1101/2024.09.02.610853 Cold Spring Harbor Laboratory Press 2024-09-02 <![CDATA[ Adaptation to climate in the native and introduced ranges of a cosmopolitan plant ]]> https://biorxiv.org/content/10.1101/2024.09.16.613311v1?rss=1 Albano, L. J. Bastias, C. C. Estarague, A. Hendrickson, B. T. Innes, S. G. King, N. Patterson, C. M. Tudoran, A. Vasseur, F. Puentes, A. Violle, C. Kooyers, N. J. Johnson, M. T. 2024-09-19 doi:10.1101/2024.09.16.613311 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[ Patterned wireless transcranial optogenetics generates artificial perception ]]> https://biorxiv.org/content/10.1101/2024.09.20.613966v1?rss=1 Wu, M. Yang, Y. Zhang, J. Efimov, A. I. Vazquez-Guardado, A. Li, X. Zhang, K. Wang, Y. Gu, J. Zeng, L. Liu, J. Riahi, M. Yoon, H. Kim, M. Zhang, H. Lee, M. Kang, J. Ting, K. Cheng, S. Zhang, W. Banks, A. Good, C. H. Cox, J. M. Pinto, L. Huang, Y. Kozorovitskiy, Y. Rogers, J. A. 2024-09-20 doi:10.1101/2024.09.20.613966 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Histone deacetylase 5 in prelimbic prefrontal cortex limits context-associated cocaine seeking ]]> https://biorxiv.org/content/10.1101/2024.09.21.614125v1?rss=1 Barry, S. M. Huebschman, J. DeVries, D. M. McCue, L. M. Tsvetkov, E. Anderson, E. M. Siemsen, B. M. Scofield, M. D. Taniguchi, M. Penrod, R. D. Cowan, C. W. 2024-09-21 doi:10.1101/2024.09.21.614125 Cold Spring Harbor Laboratory Press 2024-09-21 <![CDATA[ Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome ]]> https://biorxiv.org/content/10.1101/2024.09.18.613707v1?rss=1 Rajczewski, A. T. Blakeley-Ruiz, J. Meyer, A. Vintila, S. Mcilvin, M. R. Van Den Bossche, T. Searle, B. C. Griffin, T. Saito, M. Kleiner, M. Jagtap, P. 2024-09-22 doi:10.1101/2024.09.18.613707 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ The utility of environmental data from traditionalvarieties for climate-adaptive maize breeding ]]> https://biorxiv.org/content/10.1101/2024.09.19.613351v1?rss=1 Li, F. Gates, D. J. Buckler, E. S. Hufford, M. B. Janzen, G. M. Rellan-Alvarez, R. Rodriguez-Zapata, F. Navarro, J. A. R. Sawers, R. J. Snodgrass, S. J. Sonder, K. Willcox, M. C. Hearne, S. Ross-Ibarra, J. Runcie, D. E. 2024-09-23 doi:10.1101/2024.09.19.613351 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ GRAS Family Transcription Factor Binding Behaviors in Sorghum bicolor, Oyrza, and Maize ]]> https://biorxiv.org/content/10.1101/2024.09.23.614502v1?rss=1 Gladman, N. P. Kumari, S. Fahey, A. Regulski, M. Ware, D. 2024-09-25 doi:10.1101/2024.09.23.614502 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ Criterion for assessing accumulated neurotoxicity of alpha-synuclein oligomers in Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2024.09.23.614584v1?rss=1 Kuznetsov, A. V. 2024-09-25 doi:10.1101/2024.09.23.614584 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ Estimating sampling and laboratory capacity for a simulated African swine fever outbreak in the United States ]]> https://biorxiv.org/content/10.1101/2024.09.26.615206v1?rss=1 Galvis, J. A. Satici, M. Y. Sykes, A. L. OHara, K. C. Rochette, L. Roberts, D. Machado, G. 2024-09-29 doi:10.1101/2024.09.26.615206 Cold Spring Harbor Laboratory Press 2024-09-29 <![CDATA[ Directed evolution of a plant immune receptor for broad spectrum recognition of pathogen effectors ]]> https://biorxiv.org/content/10.1101/2024.09.30.614878v1?rss=1 Rim, E. Y. Garrett, O. D. Howard, A. J. Shim, Y. Li, Y. Van Dyke, J. E. Packer, R. C. Ho, N. Jain, R. S. Stewart, V. J. Dinesh-Kumar, S. P. Notwell, J. H. Ronald, P. C. 2024-10-01 doi:10.1101/2024.09.30.614878 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Scaling laws of plasmids across the microbial tree of life ]]> https://biorxiv.org/content/10.1101/2024.10.04.616653v1?rss=1 Maddamsetti, R. Wilson, M. L. Son, H.-I. Zhou, Z. Lu, J. You, L. 2024-10-05 doi:10.1101/2024.10.04.616653 Cold Spring Harbor Laboratory Press 2024-10-05 <![CDATA[ Prevalence and Dynamics of Genome Rearrangements in Bacteria and Archaea ]]> https://biorxiv.org/content/10.1101/2024.10.04.616710v1?rss=1 Martinez-Gutierrez, C. A. Bobay, L.-M. 2024-10-05 doi:10.1101/2024.10.04.616710 Cold Spring Harbor Laboratory Press 2024-10-05 <![CDATA[ Connected Chromatin Amplifies Acetylation-modulated Nucleosome Interactions ]]> https://biorxiv.org/content/10.1101/2024.10.11.617935v1?rss=1 Li, R. Lin, X. 2024-10-13 doi:10.1101/2024.10.11.617935 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ Caging of membrane-to-cortex attachment proteins can trigger cellular symmetry breaking ]]> https://biorxiv.org/content/10.1101/2024.10.14.618153v1?rss=1 Dar, S. Moreno, R. T. Palaia, I. Gopalan, A. B. Sun, Z. G. Strauss, L. Springer, R. Belmonte, J. M. Foster, S. K. Murrell, M. Ejsing, C. S. Saric, A. Leptin, M. Diz-Munoz, A. 2024-10-14 doi:10.1101/2024.10.14.618153 Cold Spring Harbor Laboratory Press 2024-10-14 <![CDATA[ A novel dataset of 2,362 equine fecal microbiomes from eight veterinary teaching hospital on three continents reveals dominant effects of geography, breed, and disease ]]> https://biorxiv.org/content/10.1101/2024.10.21.619412v1?rss=1 McAdams, Z. L. Campbell, E. J. Dorfmeyer, R. A. Turner, G. Shaffer, S. Ford, T. Lawson, J. Terry, J. Raju, M. Coghill, L. Cresci, L. Lascola, K. Pridgen, T. L. Blikslager, A. Barrell, E. Banse, H. Paul, L. Gillen, A. Nott, S. VandeCandelaere, M. van Galen, G. Townsend, K. S. Martin, L. M. Johnson, P. J. Ericsson, A. C. 2024-10-22 doi:10.1101/2024.10.21.619412 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Defining Cellular Diversity at the Swine Maternal-Fetal Interface Using Spatial Transcriptomics and Organoids ]]> https://biorxiv.org/content/10.1101/2024.10.21.619461v1?rss=1 McCutcheon, C. Caldwell, A. Yang, L. Crisci, E. Pasternak, J. A. Coyne, C. 2024-10-22 doi:10.1101/2024.10.21.619461 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Evolutionary rescue during extreme drought ]]> https://biorxiv.org/content/10.1101/2024.10.24.619808v1?rss=1 Anstett, D. N. Anstett, J. Sheth, S. N. Moxley, D. Jahani, M. Huang, K. Todesco, M. Jordan, R. Lazaro-Guevara, J. M. Rieseberg, L. H. Angert, A. L. 2024-10-24 doi:10.1101/2024.10.24.619808 Cold Spring Harbor Laboratory Press 2024-10-24 <![CDATA[ CRISPR knockout of winter-biased SUT4 alters phenology, biomass accrual, and fertility of field-grown hybrid poplar ]]> https://biorxiv.org/content/10.1101/2024.10.22.619524v1?rss=1 Tuma, T. T. McInnes, H. A. Pham, H. Bewg, W. P. Deguchi, M. Zhou, R. Surber, S. M. Lipzen, A. Barry, K. W. Lieb, B. Weber Wyneken, D. L. Harman-Ware, A. E. Dahlen, J. Harding, S. Tsai, C.-J. 2024-10-25 doi:10.1101/2024.10.22.619524 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ A mathematical model informs optimal fungicide use against Sclerotinia stem rot to maximize profits in soybean production ]]> https://biorxiv.org/content/10.1101/2024.10.30.621166v1?rss=1 Byer, T. Hatfield, T. Kadelka, C. 2024-11-02 doi:10.1101/2024.10.30.621166 Cold Spring Harbor Laboratory Press 2024-11-02 <![CDATA[ Genomes of Poaceae sisters reveal key metabolic innovations preceding the emergence of grasses ]]> https://biorxiv.org/content/10.1101/2024.11.06.622220v1?rss=1 View larger version (108K): org.highwire.dtl.DTLVardef@117dd71org.highwire.dtl.DTLVardef@1cb5daborg.highwire.dtl.DTLVardef@72a331org.highwire.dtl.DTLVardef@38124e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Takeda-Kimura, Y. Moore, B. Holden, S. Deb, S. K. Barrett, M. Lorence, D. de Oliveira, M. V. V. Grimwood, J. Williams, M. Boston, L. B. Jenkins, J. W. Plott, C. Shu, S. Barry, K. W. Goodstein, D. M. Schmutz, J. Moscou, M. J. McKain, M. R. Leebens-Mack, J. H. Maeda, H. A. 2024-11-07 doi:10.1101/2024.11.06.622220 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ Fishnet mesh of centrin-Sfi1 drives ultrafast calcium-activated contraction of the giant cell Spirostomum ambiguum ]]> https://biorxiv.org/content/10.1101/2024.11.07.622534v1?rss=1 Lannan, J. Floyd, C. Xu, L. X. Yan, C. Marshall, W. F. Vaikuntanathan, S. Dinner, A. R. Honts, J. E. Bhamla, S. Elting, M. W. 2024-11-08 doi:10.1101/2024.11.07.622534 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ How population control of pests is modulated by density dependence: The perspective of genetic biocontrol ]]> https://biorxiv.org/content/10.1101/2024.11.08.622719v1?rss=1 Butler, C. D. Lloyd, A. L. 2024-11-11 doi:10.1101/2024.11.08.622719 Cold Spring Harbor Laboratory Press 2024-11-11 <![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[ Identification and characterization of substrate- and product-selective nylon hydrolases ]]> https://biorxiv.org/content/10.1101/2024.11.14.623603v1?rss=1 Drufva, E. Cahill, J. F. Saint-Vincent, P. Williams, A. Bocharova, V. Capra, N. Meilleur, F. Carper, D. Bourgery, C. Miyazaki, K. Yonemura, M. Shiraishi, Y. Parks, J. Zhou, M. Dishner, I. Foster, J. Koehler, S. Valentino, H. Sedova, A. Kertesz, V. Vasileva, D. Hochanadel, L. Figg, A. Negoro, S. Kato, D.-i. Chen, S. H. Michener, J. K. 2024-11-14 doi:10.1101/2024.11.14.623603 Cold Spring Harbor Laboratory Press 2024-11-14 <![CDATA[ Minus the Error: Estimating dN/dS and Testing for Natural Selection in the Presence of Residual Alignment Errors ]]> https://biorxiv.org/content/10.1101/2024.11.13.620707v1?rss=1 Selberg, A. Chikina, M. Sackton, T. B. Muse, S. Lucaci, A. Weaver, S. Nekrutenko, A. Clark, N. Pond, S. L. K. 2024-11-15 doi:10.1101/2024.11.13.620707 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes ]]> https://biorxiv.org/content/10.1101/2024.11.17.623984v1?rss=1 Patinios, C. Gupta, D. Bassett, H. V. Collins, S. P. Kamm, C. Kibe, A. Wang, Y. Zhao, C. Vollen, K. Toussaint, C. Polkoff, K. M. Nguyen, T. Calvin, I. Migur, A. Al'Abri, I. Achmedov, T. del Re, A. Saliba, A.-E. Crook, N. Stepanova, A. N. Alonso, J. M. Beisel, C. L. 2024-11-17 doi:10.1101/2024.11.17.623984 Cold Spring Harbor Laboratory Press 2024-11-17 <![CDATA[ Adaptations in gut Bacteroidales facilitate stable co-existence with their lytic bacteriophages ]]> https://biorxiv.org/content/10.1101/2024.11.17.624012v1?rss=1 Cortes-Martin, A. Buttimer, C. Maier, J. Tobin, C. A. Draper, L. Ross, R. P. Kleiner, M. Hill, C. Shkoporov, A. N. 2024-11-17 doi:10.1101/2024.11.17.624012 Cold Spring Harbor Laboratory Press 2024-11-17 <![CDATA[ Measuring regulatory network inheritance in dividing yeast cells using ordinary differential equations ]]> https://biorxiv.org/content/10.1101/2024.11.23.624995v1?rss=1 Wu, W. Kennedy, T. Arguello-Miranda, O. Lin, K. Z. 2024-11-24 doi:10.1101/2024.11.23.624995 Cold Spring Harbor Laboratory Press 2024-11-24 <![CDATA[ CNV-Profile Regression: A New Approach for Copy Number Variant Association Analysis in Whole Genome Sequencing Data ]]> https://biorxiv.org/content/10.1101/2024.11.23.624994v1?rss=1 50 base pairs. Assessing CNV effects on disease risk requires consideration of several factors. First, there are no natural definitions for CNV loci. Second, CNV effects can depend on dosage and length. Third, CNV effects can be more accurately estimated when all CNV events in a genomic region are analyzed together to assess their joint effects. We propose a new framework for association analysis that directly models an individuals entire CNV profile within a genomic region. This framework represents an individuals CNVs using a CNV profile curve to capture variations in CNV length and dosage and to bypass the need to predefine CNV loci. CNV effects are estimated at each genome position, making the results comparable across different studies. To jointly estimate the effects of all CNVs, we use a Lasso penalty to select CNVs associated with the trait and integrate a weighted L2-fusion penalty to encourage similar effects of adjacent CNVs when supported by the data. Simulations show that the proposed model can more effectively identify causal CNVs while maintaining false positive rates comparable to baseline methods and yield more precise effect-size estimates across different settings. When applied to CNV derived from whole genome sequencing data of the Alzheimers Disease Sequencing Project, the proposed methods identify additional CNVs associated with Alzheimers Disease (AD). These identified CNVs overlap with several known AD-risk genes and are significantly enriched by biological processes related to neuron structures and functions crucial in AD development. ]]> Si, Y. Lu, W. Holloway, S. T. Wang, H. Tucci, A. A. Brucker, A. Cheng, Y. Wang, L.-S. Schellenberg, G. D. Lee, W.-P. Tzeng, J.-Y. 2024-11-25 doi:10.1101/2024.11.23.624994 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Cervicovaginal microbial features predicts Chlamydia trachomatis spread to the upper genital tract of infected women ]]> https://biorxiv.org/content/10.1101/2024.11.26.625070v1?rss=1 Jeong, S. Tollison, T. S. Brochu, H. Huntress, I. Yount, K. S. Zheng, X. Darville, T. O'Connell, C. M. Peng, X. 2024-11-28 doi:10.1101/2024.11.26.625070 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Establishing reliable blood biomarkers for trimethylamine N-oxide status in rodents: effects of oral choline challenge, dietary choline and fasting conditions ]]> https://biorxiv.org/content/10.1101/2024.12.06.627229v1?rss=1 Din, A. U. Sweet, M. G. McAmis, A. M. Ratliff, J. G. Pon Velayutham, A. B. Neilson, A. P. 2024-12-07 doi:10.1101/2024.12.06.627229 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ Trophic level associated gut length divergence evolved under sexual conflict in Lake Malawi cichlids ]]> https://biorxiv.org/content/10.1101/2024.12.09.627601v1?rss=1 Carmona Baez, A. Ciccotto, P. J. Moore, E. C. Peterson, E. N. Lamm, M. S. Roberts, N. B. Coyle, K. P. Barker, M. K. Dickson, E. Cass, A. N. da Silva Pereira, G. S. Zeng, Z.-B. Guerrero, R. F. Roberts, R. B. 2024-12-11 doi:10.1101/2024.12.09.627601 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ The evolution of heteromorphic sex chromosomes in plants ]]> https://biorxiv.org/content/10.1101/2024.12.09.627636v1?rss=1 36 MYA. Due to the inheritance patterns of the XYs, the male-specific region of the Y is highly-degenerated, with substantial gene loss, while the X shows faster rates of molecular evolution. Consistent with the theory that these species lack an active-Y system, no clear sex-determining genes reside on the Y. Instead, an X-linked homolog of aminocyclopropane-1-carboxylate synthase (ACS), that is involved in the ethylene biosynthesis pathway, determines the fate of the female inflorescence. Beyond sex determination, the sex chromosomes contribute to the sexual dimorphism in ecology and physiology and have played a role in the domestication and breeding of these species. ]]> Carey, S. B. Bentz, P. C. Lovell, J. T. Akozbek, L. M. Havill, J. S. Padgitt-Cobb, L. Lynch, R. C. Allsing, N. Osmanski, A. Easterling, K. A. Orozco, L. R. Hale, H. McCoy, H. Meharg, Z. McKay, J. Grimwood, J. B. Vergara, D. Guerrero, R. F. Kane, N. Michael, T. P. Muehlbauer, G. Harkess, A. 2024-12-11 doi:10.1101/2024.12.09.627636 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ Stable isotope fingerprinting can directly link intestinal microorganisms with their carbon source and captures diet-induced substrate switching in vivo ]]> https://biorxiv.org/content/10.1101/2024.12.10.627769v1?rss=1 Mordant, A. Blakeley-Ruiz, J. A. Kleiner, M. 2024-12-11 doi:10.1101/2024.12.10.627769 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ A Dual-Functional Needle-Based VOC Sensing Platform for Rapid Vegetable Quality Examination ]]> https://biorxiv.org/content/10.1101/2024.12.12.628229v1?rss=1 View larger version (44K): org.highwire.dtl.DTLVardef@12bf541org.highwire.dtl.DTLVardef@f2a809org.highwire.dtl.DTLVardef@f5f5b7org.highwire.dtl.DTLVardef@1d7027f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hossain, O. Wang, Y. Li, M. Jamalzadegan, S. Mohammad, N. Alireza, A. Poonam, A. D. Wei, Q. 2024-12-13 doi:10.1101/2024.12.12.628229 Cold Spring Harbor Laboratory Press 2024-12-13 <![CDATA[ Maize inbreds show allelic variation for diel transcription patterns ]]> https://biorxiv.org/content/10.1101/2024.12.16.628400v1?rss=1 Gage, J. L. Romay, M. C. Buckler, E. S. 2024-12-17 doi:10.1101/2024.12.16.628400 Cold Spring Harbor Laboratory Press 2024-12-17 <![CDATA[ Wnt pathway modulation is required to correctly execute multiple independent cellular dynamic programs during cranial neural tube closure ]]> https://biorxiv.org/content/10.1101/2024.12.19.629501v1?rss=1 Bogart, A. H. Brooks, E. R. 2024-12-20 doi:10.1101/2024.12.19.629501 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ An injectable chitosan hydrogel localizes and tunably releases immunotherapeutics intratumorally eliminating both treated and abscopal murine triple negative breast tumors ]]> https://biorxiv.org/content/10.1101/2024.12.19.629422v1?rss=1 Mantooth, S. M. Green, J. M. Green, W. D. Nguyen, K. G. Mantooth, K. A. Meritet, D. M. Milner, J. J. Zaharoff, D. A. 2024-12-22 doi:10.1101/2024.12.19.629422 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Genetic analyses suggest that larval and adult stages of Lucilia cuprina employ different sensory systems ]]> https://biorxiv.org/content/10.1101/2024.12.20.629795v1?rss=1 Wulff, J. P. Laminack, R. K. Scott, M. J. 2024-12-22 doi:10.1101/2024.12.20.629795 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Acoustic tumor paint for real-time imaging, surgical guidance and recurrence monitoring of brain tumors with ultrasound ]]> https://biorxiv.org/content/10.1101/2024.12.22.629782v1?rss=1 Rabut, C. Daghlian, G. H. Barturen-Larrea, P. Li, H. R. Vorder Bruegge, R. Jones, R. M. Malounda, D. Pinton, G. F. Shapiro, M. G. 2024-12-22 doi:10.1101/2024.12.22.629782 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Mixed DAMP/MAMP oligosaccharides promote both growth and defense against fungal pathogens of cucumber ]]> https://biorxiv.org/content/10.1101/2024.12.27.630494v1?rss=1 Pring, S. Kato, H. Taniuchi, K. Camagna, M. Saito, M. Tanaka, A. Merritt, B. A. Arguello-Miranda, O. Sato, I. Chiba, S. Takemoto, D. 2024-12-28 doi:10.1101/2024.12.27.630494 Cold Spring Harbor Laboratory Press 2024-12-28 <![CDATA[ CD44 and Ezrin restrict EGF receptor mobility to generate a novel spatial arrangement of cytoskeletal signaling modules driving bleb-based migration ]]> https://biorxiv.org/content/10.1101/2024.12.31.630838v1?rss=1 Jha, A. Chandra, A. Farahani, P. Toettcher, J. E. Haugh, J. M. Waterman, C. M. 2025-01-01 doi:10.1101/2024.12.31.630838 Cold Spring Harbor Laboratory Press 2025-01-01 <![CDATA[ Identifying control strategies to eliminate African swine fever from the United States swine industry in under 12 months ]]> https://biorxiv.org/content/10.1101/2024.12.17.628884v1?rss=1 Sykes, A. L. Galvis, J. A. O'Hara, K. C. Holmstrom, L. Corzo, C. Machado, G. 2025-01-04 doi:10.1101/2024.12.17.628884 Cold Spring Harbor Laboratory Press 2025-01-04 <![CDATA[ A High Sensitivity Assay of UBE3A Ubiquitin Ligase Activity ]]> https://biorxiv.org/content/10.1101/2025.01.05.631408v1?rss=1 Han, L. Yagci, Z. B. Keung, A. J. 2025-01-06 doi:10.1101/2025.01.05.631408 Cold Spring Harbor Laboratory Press 2025-01-06 <![CDATA[ Nondestructive Detection and Quantification of Dysprosium in Plant Tissues ]]> https://biorxiv.org/content/10.1101/2025.01.07.631589v1?rss=1 Hernandez-Pagan, E. Laosuntisuk, K. Harris, A. T. Haynes, A. N. Buitrago, D. Rajabu, C. Kudenov, M. W. Doherty, C. J. 2025-01-08 doi:10.1101/2025.01.07.631589 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ Influence of Sequencing Technology on Pangenome-level Analysis and Detection of Antimicrobial Resistance Genes in ESKAPE Pathogens ]]> https://biorxiv.org/content/10.1101/2025.01.08.631980v1?rss=1 Frias-De-Diego, A. Jara, M. Lanzas, C. 2025-01-11 doi:10.1101/2025.01.08.631980 Cold Spring Harbor Laboratory Press 2025-01-11 <![CDATA[ Modeling of ATP Transport in an Axon: Effects of Spontaneous Neuron Firing and Mitochondrial Transfer via Tunneling Nanotubes ]]> https://biorxiv.org/content/10.1101/2025.01.14.633089v1?rss=1 Kuznetsov, A. V. 2025-01-19 doi:10.1101/2025.01.14.633089 Cold Spring Harbor Laboratory Press 2025-01-19 <![CDATA[ Mammal niches are not conserved over continental scales ]]> https://biorxiv.org/content/10.1101/2025.01.17.633640v1?rss=1 Goldstein, B. R. Pacifici, K. Jensen, A. J. Reich, B. J. Cove, M. V. McShea, W. J. Rooney, B. Kierepka, E. M. Roberts, R. A. Kays, R. 2025-01-22 doi:10.1101/2025.01.17.633640 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Warming disrupts plant-fungal endophyte symbiosis more strongly in leaves than roots ]]> https://biorxiv.org/content/10.1101/2025.01.22.634355v1?rss=1 Edwards, J. Kazenel, M. R. Luo, Y. Lynn, J. S. McCulley, R. L. Souza, L. Young, C. Rudgers, J. A. Kivlin, S. N. 2025-01-25 doi:10.1101/2025.01.22.634355 Cold Spring Harbor Laboratory Press 2025-01-25 <![CDATA[ Evaluation of porcine epidemic diarrhea virus RNA contamination on swine industry transportation vehicles ]]> https://biorxiv.org/content/10.1101/2025.01.24.634714v1?rss=1 Parker, T. B. Meiklejohn, K. A. Machado, G. Rahe, M. Darrow, B. S. Ferreira, J. B. 2025-01-25 doi:10.1101/2025.01.24.634714 Cold Spring Harbor Laboratory Press 2025-01-25 <![CDATA[ Western red cedar (Thuja plicata) beehives have no impact on honey bee (Apis mellifera) overwintering colony survival or detoxification enzyme expression ]]> https://biorxiv.org/content/10.1101/2025.01.23.634475v1?rss=1 McAfee, A. Tarpy, D. R. Foster, L. J. 2025-01-26 doi:10.1101/2025.01.23.634475 Cold Spring Harbor Laboratory Press 2025-01-26 <![CDATA[ Ancient origin of an urban underground mosquito ]]> https://biorxiv.org/content/10.1101/2025.01.26.634793v1?rss=1 1000 years, likely in concert with the rise of agricultural civilizations. Our results highlight the role of early human society in priming taxa for contemporary urban evolution and have important implications for understanding arbovirus transmission. ]]> Haba, Y. Aardema, M. L. Afonso, M. O. Agramonte, N. M. Albright, J. Alho, A. M. Almeida, A. P. G. Alout, H. Alten, B. Altinli, M. Amara Korba, R. Andreadis, S. S. Anghel, V. Arich, S. Arsenault-Benoit, A. Atyame, C. Aubry, F. Avila, F. W. Ayala, D. Azrag, R. S. Babayan, L. Bear, A. Becker, N. Bega, A. G. Bejarano, S. Ben-Avi, I. Benoit, J. B. Boubidi, S. C. Bradshaw, W. E. Bravo-Barriga, D. Bueno-Mari, R. Busic, N. Cabanova, V. Cabeje, B. Caputo, B. Cardo, M. V. Carpenter, S. Carreton, E. Chouaibou, M. S. Christian, M. Coetzee, M. Conner, W. R. Cornel, 2025-01-28 doi:10.1101/2025.01.26.634793 Cold Spring Harbor Laboratory Press 2025-01-28 <![CDATA[ Three-dimensional cellularization in chytrid fungi uses distinct mechanisms from those driving one- and two-dimensional cytokinesis in animals and yeast ]]> https://biorxiv.org/content/10.1101/2025.01.30.635136v1?rss=1 Medina, E. M. Elting, M. W. Fritz-Laylin, L. K. 2025-01-30 doi:10.1101/2025.01.30.635136 Cold Spring Harbor Laboratory Press 2025-01-30 <![CDATA[ A maize near-isogenic line population designed for gene discovery and characterization of allelic effects ]]> https://biorxiv.org/content/10.1101/2025.01.29.635337v1?rss=1 Zhong, T. Mullens, A. Morales, L. Swarts, K. Stafstrom, W. He, Y. Sermons, S. Yang, Q. Lopez-Zuniga, L. O. Rucker, E. Thomason, W. Nelson, R. Jamann, T. M. Balint-Kurti, P. Holland, J. B. 2025-02-02 doi:10.1101/2025.01.29.635337 Cold Spring Harbor Laboratory Press 2025-02-02 <![CDATA[ TaWUS2D regulates the number of grains per spikelet by enhancing the number of fertile ovaries in Multi-Ovary Wheat ]]> https://biorxiv.org/content/10.1101/2025.02.05.636547v1?rss=1 Schoen, A. W. Sharma, P. K. Mahlandt, A. Chen, A. Sheng, H. Kochian, L. Gao, P. Xiang, D. Quilichini, T. Venglat, P. Wang, S. Yadav, I. S. Gu, Y. Rodriguez-Leal, D. Luo, W. Qi, Y. Meier, N. Kajla, A. Willman, M. Brown-Guedira, G. Youngblood, C. Hulse-Kemp, A. Murphy, A. Gill, B. Uauy, C. Datla, R. Rawat, N. Tiwari, V. 2025-02-08 doi:10.1101/2025.02.05.636547 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Development of ferret immune repertoire reference resources and single-cell-based high-throughput profiling assays ]]> https://biorxiv.org/content/10.1101/2025.02.05.636682v1?rss=1 Walsh, E. S. Yang, K. Tollison, T. S. Seenu, S. Adams, N. Zeitoun, G. Sideri, I. Folch, G. Brochu, H. Chou, H. Kossida, S. York, I. A. Peng, X. 2025-02-10 doi:10.1101/2025.02.05.636682 Cold Spring Harbor Laboratory Press 2025-02-10 <![CDATA[ Which plant traits increase soil carbon sequestration? Empirical evidence from a long-term poplar genetic diversity trial ]]> https://biorxiv.org/content/10.1101/2025.02.17.638464v1?rss=1 Field, J. L. Sloan, B. P. Craig, M. E. Calloway, P. Ottinger, S. L. Mead, T. Abramoff, R. Z. Venegas, M. P. Chhetri, H. B. Haiby, K. Kalluri, U. C. Muchero, W. Schadt, C. W. Mayes, M. A. 2025-02-22 doi:10.1101/2025.02.17.638464 Cold Spring Harbor Laboratory Press 2025-02-22 <![CDATA[ Dirt floors and domestic animals are associated with soilborne exposure to antimicrobial resistant E. coli in rural Bangladeshi households ]]> https://biorxiv.org/content/10.1101/2025.02.21.639507v1?rss=1 Ercumen, A. Hossain, M. S. Tabassum, T. Haque, A. Rahman, A. Rahman, M. H. Anderson, C. Tazin, S. Hanif, S. Barratt Heitmann, G. Miah, R. Yeamin, A. Jahan, F. Shoab, A. K. Mahmud, Z. H. Rahman, M. Benjamin-Chung, J. 2025-02-23 doi:10.1101/2025.02.21.639507 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ Predicting Biological Age Using an Accumulated Neurotoxicity Biomarker for Amyloid Beta Oligomers ]]> https://biorxiv.org/content/10.1101/2025.02.28.640920v1?rss=1 Kuznetsov, A. V. 2025-03-06 doi:10.1101/2025.02.28.640920 Cold Spring Harbor Laboratory Press 2025-03-06 <![CDATA[ DASH: A versatile and high-capacity gene stacking system for plant synthetic biology ]]> https://biorxiv.org/content/10.1101/2025.03.04.641457v1?rss=1 Zhao, C. Stepanova, A. N. Alonso, J. M. 2025-03-06 doi:10.1101/2025.03.04.641457 Cold Spring Harbor Laboratory Press 2025-03-06 <![CDATA[ A preclinical pig model of Angelman syndrome mirrors the early developmental trajectory of the human condition ]]> https://biorxiv.org/content/10.1101/2025.03.04.641215v1?rss=1 Myers, L. S. Christian, S. G. Simpson, S. Sper, R. Taylor, C. Montes, L. Jepp, T. B. C. Ramos, D. Schuller, L. Konganti, K. Friedeck, W. Habib, O. Hodge, M. Taylor, A. J. Coffell, A. Schlafer, A. Matt, M. Revell, B. Knight, C. Barrena, C. C. FAST Integrative Research Environment (FIRE) Initiative, Murphy, W. J. Piedrahita, J. Dindot, S. V. 2025-03-11 doi:10.1101/2025.03.04.641215 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Clostridioides difficile Toxins Alter Host Metabolic Pathway and Bile Acid Homeostasis Gene Expression In Colonic Epithelium ]]> https://biorxiv.org/content/10.1101/2025.03.21.644594v1?rss=1 Thomas, S. A. Pike, C. M. Perkins, C. E. Brown, S. T. Espinoza Jaen, X. M. McMillan, A. S. Theriot, C. M. 2025-03-21 doi:10.1101/2025.03.21.644594 Cold Spring Harbor Laboratory Press 2025-03-21 <![CDATA[ Contextual Science and Genome Analysis for Air-Gapped AI Research ]]> https://biorxiv.org/content/10.1101/2025.03.21.644606v1?rss=1 Lazo, G. R. Ayyappan, D. Sharma, P. K. Tiwari, V. K. 2025-03-24 doi:10.1101/2025.03.21.644606 Cold Spring Harbor Laboratory Press 2025-03-24 <![CDATA[ Adaptive pangenomic remodeling in the Azolla cyanobiont amid a transient microbiome ]]> https://biorxiv.org/content/10.1101/2025.03.24.644982v1?rss=1 Armitage, D. W. Alonso-Sanchez, A. G. Coy, S. R. Cheng, Z. Hagenbeek, A. Lopez-Martinez, K. P. Phua, Y. H. Sears, A. R. 2025-03-24 doi:10.1101/2025.03.24.644982 Cold Spring Harbor Laboratory Press 2025-03-24 <![CDATA[ Novel PFAS in Alligator Blood Discovered with Non-Targeted Ion Mobility-Mass Spectrometry ]]> https://biorxiv.org/content/10.1101/2025.03.20.644452v1?rss=1 Boatman, A. K. Kudzin, G. P. Rock, K. D. Guillette, M. P. Robb, F. Belcher, S. M. Baker, E. 2025-03-25 doi:10.1101/2025.03.20.644452 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ Generative frame interpolation enhances tracking of biological objects in time-lapse microscopy ]]> https://biorxiv.org/content/10.1101/2025.03.23.644838v1?rss=1 Kaondal, S. Taassob, A. Jeon, S. Lee, S. H. Nunez, H. L. Akindipe, B. A. Lee, H. Joo, S. Y. Oliveira, S. M. D. Arguello-Miranda, O. 2025-03-26 doi:10.1101/2025.03.23.644838 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ Co-occurrence drives horizontal gene transfer among marine prokaryotes ]]> https://biorxiv.org/content/10.1101/2025.03.25.645238v1?rss=1 Douglas, G. M. Tromas, N. Gaudin, M. Lypaczewski, P. Bobay, L.-M. Shapiro, B. J. Chaffron, S. 2025-03-28 doi:10.1101/2025.03.25.645238 Cold Spring Harbor Laboratory Press 2025-03-28 <![CDATA[ Designed Peptides as Affinity Ligands for Extracellular-Vesicle-based Cancer Biomarker Detection ]]> https://biorxiv.org/content/10.1101/2025.03.27.645572v1?rss=1 Sarma, S. Cho, Y. Tapdiya, A. Park, J. Lee, H. Hall, C. K. 2025-04-01 doi:10.1101/2025.03.27.645572 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Integrating affinity chromatography in the platform process for Adenovirus purification ]]> https://biorxiv.org/content/10.1101/2025.03.31.646491v1?rss=1 5{middle dot}1010 vp per mL of resin) and yield under mild elution conditions ([~]50% at pH 8.0). Peptide-functionalized adsorbents prepared using different matrices (polymethylmethacrylate vs. agarose) were initially tested to compare the purification performance. AEFFIWNA-SulfoLink resin was selected for its yield of cell- transducing AdVs ([~]50%) and removal of HCPs and hcDNA (144-fold and 56-fold). Similarly, TNDGPDYSSPLTGSG-Toyopearl(R) resin afforded [~]50% yield and >50-fold reduction of con- taminants. Additional gains in product purity were achieved by optimizing the washing step, which removed free hexon proteins and additional HCPs. All peptide-functionalized resins maintained their purification performance for ten cycles upon regeneration at pH [~]2.0. The purification process was assembled to include clarification, affinity capture in bind-and-elute mode using AEFFIWNA-SulfoLink resin, and polishing in flow-through mode using mixed- mode resins. The optimized process provided a yield [~]50% of cell-infecting units (IFU) and a product titer [~]107 IFU/mL, along with residual HCP and hcDNA levels ([~]10 ng/mL and 44 ng per dose, respectively) that meet clinical requirements. ]]> Wu, Y. Barbieri, E. Smith, W. Minzoni, A. Kilgore, R. Chu, W. Daniele, M. Menegatti, S. 2025-04-05 doi:10.1101/2025.03.31.646491 Cold Spring Harbor Laboratory Press 2025-04-05 <![CDATA[ Real-Time Quantitative PCR Method for Assessing Wheat Cultivars for Resistance to Zymoseptoria tritici ]]> https://biorxiv.org/content/10.1101/2025.04.02.646880v1?rss=1 Adhikari, T. B. Balaji, B. Goodwin, S. B. 2025-04-06 doi:10.1101/2025.04.02.646880 Cold Spring Harbor Laboratory Press 2025-04-06 <![CDATA[ Trophic Transfer of Perfluoroalkyl Acids in a Periphyton-Mayfly-Zebrafish Food Chain ]]> https://biorxiv.org/content/10.1101/2025.04.09.647996v1?rss=1 70%) for all compounds. Bioaccumulation of PFAS in periphyton and mayflies was positively correlated with log KOW and number of carbons. ]]> Farrell, M. R. Buchwalter, D. B. Weed, R. A. Enders, J. R. Planchart, A. 2025-04-15 doi:10.1101/2025.04.09.647996 Cold Spring Harbor Laboratory Press 2025-04-15 <![CDATA[ American black bear (Ursus americanus) as a potential host for Campylobacter jejuni ]]> https://biorxiv.org/content/10.1101/2025.04.14.648838v1?rss=1 Parker, C. T. Kathariou, S. Miller, W. G. Huynh, S. Pascoe, B. Cooper, K. 2025-04-15 doi:10.1101/2025.04.14.648838 Cold Spring Harbor Laboratory Press 2025-04-15 <![CDATA[ Feedforward Extraction of Behaviorally Significant Information by Neocortical Columns ]]> https://biorxiv.org/content/10.1101/2025.04.20.649709v1?rss=1 Favorov, O. V. Kursun, O. 2025-04-22 doi:10.1101/2025.04.20.649709 Cold Spring Harbor Laboratory Press 2025-04-22 <![CDATA[ Early-Life Environmental Exposures Reprogram Epigenomic Aging to Alter Gene Expression Trajectories ]]> https://biorxiv.org/content/10.1101/2025.04.21.649824v1?rss=1 Grimm, S. L. Jangid, R. Bartolomei, M. S. Dolinoy, D. C. Aylor, D. L. Mutlu, G. M. Biswal, S. Zhang, B. Wang, T. TaRGET II Consortium, Coarfa, C. Walker, C. L. 2025-04-22 doi:10.1101/2025.04.21.649824 Cold Spring Harbor Laboratory Press 2025-04-22 <![CDATA[ SARS-CoV-2 causes chronic lung inflammation and impaired respiratory capacity in aged Roborovski dwarf hamsters ]]> https://biorxiv.org/content/10.1101/2025.04.23.650177v1?rss=1 Karimi, A. Lieber, C. M. Sakamoto, K. Plemper, R. K. 2025-04-23 doi:10.1101/2025.04.23.650177 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ Identifiability of Phylogenetic Level-2 Networks under the Jukes-Cantor Model ]]> https://biorxiv.org/content/10.1101/2025.04.18.649493v1?rss=1 Englander, A. K. Frohn, M. Gross, E. Holtgrefe, N. van Iersel, L. Jones, M. Sullivant, S. 2025-04-24 doi:10.1101/2025.04.18.649493 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ TARRAGON: Therapeutic Target Applicability Ranking and Retrieval-Augmented Generation Over Networks ]]> https://biorxiv.org/content/10.1101/2025.04.19.649662v1?rss=1 Beasley, J.-M. Schatz, K. Ding, E. DeLuca, M. Abu Zaid, N. Tucker, N. Chirkova, R. Crona, D. Tropsha, A. Muratov, E. 2025-04-24 doi:10.1101/2025.04.19.649662 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Wild raccoons are more innovative but not bolder than another ecological generalist, the Virginia opossum, on a pull-string task ]]> https://biorxiv.org/content/10.1101/2025.04.21.649439v1?rss=1 Adaway, K. A. Snider, M. H. Vinciguerra, C. Kupferman, C. A. Beasley, J. C. Morton, B. 2025-04-24 doi:10.1101/2025.04.21.649439 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Single cell omics extends metabolic regulon via orthologous transcription factors from a pair of medicinal plant species ]]> https://biorxiv.org/content/10.1101/2025.04.22.650021v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@81dcf0org.highwire.dtl.DTLVardef@1d03ae1org.highwire.dtl.DTLVardef@1c9b0a9org.highwire.dtl.DTLVardef@6d5238_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1.C_FLOATNO Single cell multi-ome of Camptotheca acuminata leaf. (A) The proposed biosynthetic pathway for camptotheci . Solid arrows indicate previously characterized enzymatic steps. Dashed arrows indicate proposed enzymatic steps (see Table S7 for gene name abbreviations). (B) Uniform Manifold Approximation and Projection (UMAP) of nuclei of the single nuclei RNA-seq dataset (n = 4,012), color coded by cell clusters. (C) Gene expression heatmap of MIA biosynthetic genes across cell clusters. Rows are expressed biosynthetic genes, which are ordered from upstream to downstream. Color scale shows the average scaled expression of each gene at each cell cluster. Cell clusters are sorted by cell types. Dot size indicates the percentage of cells where a given gene is detected. The predicted cell type for each cell cluster is annotated by the color strip below the x-axis. Box highlights expression of STR genes. (D) Heat map showing accessibility of cell type marker peaks across cell clusters. Each row is an ATAC-seq peak. Each column is a cell cluster. Color scale is maxed out at 90th percentile of normalized ATAC-seq signal. The predicted cell type for each cell cluster is annotated by the color strip below the x-axis, with the same color palette as (B). (E) Heatmap showing gene expression across cell clusters. Each row is a gene within 2-kb of a STR+ marker peak. Each column is a cell cluster. The predicted cell type for each cell cluster is annotated by the color strip below the x-axis, with the same color palette as (B). (F) DNA motif enriched in STR+ marker peaks, as well as a reference MYB motif. C_FIG ]]> Bui, V.-H. Wood, J. C. Vaillancourt, B. Hamilton, J. P. Jones, S. L. Carlton, L. H. Vu, A. H. Buell, C. R. Caputi, L. Dang, T.-T. T. Li, C. 2025-04-24 doi:10.1101/2025.04.22.650021 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Optimizing canine T cell activation, expansion, and transduction ]]> https://biorxiv.org/content/10.1101/2025.04.26.650803v1?rss=1 Davis, T. W. Holmes, J. C. He, A. Hess, P. R. Mariani, C. L. Brudno, Y. 2025-04-30 doi:10.1101/2025.04.26.650803 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ Passive muscle forces in Drosophila are large but insufficient to support a flys weight ]]> https://biorxiv.org/content/10.1101/2025.04.29.651225v1?rss=1 Wang, N. Babski, H. Perdomo, J. E. McMahan, S. B. Ramakrishnan, A. Biswas, T. Bhandawat, V. 2025-04-30 doi:10.1101/2025.04.29.651225 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ Range-wide responses to an extreme heat event in Mimulus cardinalis ]]> https://biorxiv.org/content/10.1101/2025.05.01.651703v1?rss=1 Albano, L. J. Bingham, R. A. Correa, S. Laufenberg, C. G. Payst, C. Muir, C. D. Sheth, S. N. 2025-05-07 doi:10.1101/2025.05.01.651703 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Unraveling Cross-Cellular Communication in Cannabis sativa Sex Determination: A Network Ontology Transcript Annotation (Nota) Analysis. ]]> https://biorxiv.org/content/10.1101/2025.05.05.650505v1?rss=1 Orozco, L. R. Weaver, A. E. Pauli, C. C. Grassa, C. J. Vergara, D. Baptista, A. White, K. Emery, B. F. Castro, N. R. M. Guerrero, R. F. Keegan, B. C. Kane, N. C. 2025-05-07 doi:10.1101/2025.05.05.650505 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Associations between floor material and E. coli contamination in rural Bangladeshi households ]]> https://biorxiv.org/content/10.1101/2025.05.07.652756v1?rss=1 Tazin, S. Islam, M. Pickering, A. J. Kwong, L. H. Mertens, A. Niven, C. Arnold, B. F. Hubbard, A. E. Alam, M. Sen, D. Islam, S. Rahman, M. Unicomb, L. Luby, S. P. Benjamin-Chung, J. Ercumen, A. 2025-05-08 doi:10.1101/2025.05.07.652756 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ Rhs-toxin Abundance, Diversity, and Function in Four Genera of Plant Pathogenic Bacteria: Xanthomonas, Ralstonia, Pectobacterium, and Dickeya. ]]> https://biorxiv.org/content/10.1101/2025.05.08.652813v1?rss=1 Gomez Cabrera, A. Ameen, Y. O. DAmico-Willman, K. Joglekar, P. Huguet-Tapia, J. Carbone, I. Huerta Vazquez, A. I. 2025-05-13 doi:10.1101/2025.05.08.652813 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Customized and rapid observational delimiting surveys for plant pests based on transect data and scouting ]]> https://biorxiv.org/content/10.1101/2025.05.08.652837v1?rss=1 Caton, B. Pallipparambil, G. Fang, H. 2025-05-13 doi:10.1101/2025.05.08.652837 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Seasonal assembly of the phyllosphere fungal microbiome of a perennial grass is robust to nutrient addition ]]> https://biorxiv.org/content/10.1101/2025.05.08.652919v1?rss=1 Green, E. Mitchell, C. Carbone, I. 2025-05-14 doi:10.1101/2025.05.08.652919 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Spring ephemeral Erythronium umbilicatum may not be vulnerable to phenological mismatch with overstory trees ]]> https://biorxiv.org/content/10.1101/2025.05.14.652260v1?rss=1 Schopler, M. Simha, A. Dalton, R. M. Wilson, E. M. Redick, E. Youngsteadt, E. Petry, W. K. 2025-05-16 doi:10.1101/2025.05.14.652260 Cold Spring Harbor Laboratory Press 2025-05-16 <![CDATA[ Arabidopsis lines with modified ascorbate concentrations reveal a link between ascorbate and auxin biosynthesis ]]> https://biorxiv.org/content/10.1101/2025.05.15.654287v1?rss=1 Fenech, M. Zulian, V. Moya-Cuevas, J. Arnaud, D. Morilla, I. Smirnoff, N. Botella, M. A. Stepanova, A. N. Alonso, J. M. Martin-Pizarro, C. Amorim-Silva, V. 2025-05-16 doi:10.1101/2025.05.15.654287 Cold Spring Harbor Laboratory Press 2025-05-16 <![CDATA[ Benchmarking Spectral Library and Database Search Approaches for Metaproteomics Using a Ground-Truth Microbiome Dataset ]]> https://biorxiv.org/content/10.1101/2025.05.15.654320v1?rss=1 Rajczewski, A. T. Mehta, S. Wagner, R. Gabriel, W. Johnson, J. Do, K. Vintila, S. Wilhelm, M. Kleiner, M. Searle, B. C. Griffin, T. Jagtap, P. 2025-05-20 doi:10.1101/2025.05.15.654320 Cold Spring Harbor Laboratory Press 2025-05-20 <![CDATA[ Brachial Plexus Birth Injury Causes Location-Dependent Detriments in Glenohumeral Trabecular Bone Microstructure ]]> https://biorxiv.org/content/10.1101/2025.05.22.655580v1?rss=1 Fawcett, E. B. Dixit, N. N. Saul, K. R. Cole, J. H. 2025-05-27 doi:10.1101/2025.05.22.655580 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Bone Mineralization and Metabolism are Altered in a Rat Model of Brachial Plexus Birth Injury ]]> https://biorxiv.org/content/10.1101/2025.05.22.655603v1?rss=1 Fawcett, E. B. Potts, J. R. Dixit, N. N. Saul, K. R. Cole, J. H. 2025-05-27 doi:10.1101/2025.05.22.655603 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ EBSn, a robust synthetic reporter for monitoring ethylene responses in plants ]]> https://biorxiv.org/content/10.1101/2025.05.23.655144v1?rss=1 Fernandez-Moreno, J.-P. Fenech, M. Yaschenko, A. E. Zhao, C. Neubauer, M. Davis, H. N. Marchi, A. J. Concannon, R. Keren-Keiserman, A. Reuveni, M. Levitsky, V. G. Oshchepkov, D. Dolgikh, V. Goldshmidt, A. Ascencio-Ibanez, J. T. Zemlyanskaya, E. Alonso, J. M. Stepanova, A. N. 2025-05-28 doi:10.1101/2025.05.23.655144 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Start Small: A Model for Tissue-wide Planar Cell Polarity without Morphogens ]]> https://biorxiv.org/content/10.1101/2025.05.26.655839v1?rss=1 Thayambath, A. Belmonte, J. M. 2025-05-30 doi:10.1101/2025.05.26.655839 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ Differential metaproteomics of bacteria grown in vitro and in planta reveals functions used during growth on maize roots ]]> https://biorxiv.org/content/10.1101/2025.06.02.657423v1?rss=1 Garrell, A.-K. Cheadle, J. Crook, N. Pal, G. Septer, A. N. Wagner, M. R. Beck, A. E. Kleiner, M. 2025-06-02 doi:10.1101/2025.06.02.657423 Cold Spring Harbor Laboratory Press 2025-06-02 <![CDATA[ The Neuromuscular system of Chironomus vitellinus (Diptera: Chironomidae) ]]> https://biorxiv.org/content/10.1101/2025.06.01.657287v1?rss=1 Reyes-Maldonado, R. Ramirez, A. Marie, B. 2025-06-03 doi:10.1101/2025.06.01.657287 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Microneedle-based precision payload delivery in plants ]]> https://biorxiv.org/content/10.1101/2025.06.04.657704v1?rss=1 90% less). This MN system facilitates the delivery of diverse small molecules, ranging from fluorescent dyes, growth promoters, to antiviral hormones, into plant tissues, on the other hand showing limited wounding stress to the plant. By applying fluorescent dye-loaded MNs onto tomato stems, we demonstrated effective molecular diffusion through vascular tissues. Additionally, MNs loaded with gibberellic acid (GA3) enhanced stem and branch growth in tomatoes and restored the lateral flowering phenotype in Arabidopsis ft-10 mutants, with significant upregulation of GA receptor gene expression. Lastly, salicylic acid (SA) injections with MNs induced resistance to tomato spotted wilt virus (TSWV) in Nicotiana benthamiana, comparable to conventional spray and infiltration-based approaches. This easily fabricated and cost-effective MN system offers a promising tool for precision agriculture, enhancing plant health and productivity while significantly reducing the use of agrochemicals. ]]> Li, M. Poonam, A. D. Singh, D. Whitfield, A. E. Wei, Q. 2025-06-06 doi:10.1101/2025.06.04.657704 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ In vivo investigation of STN1 downregulation in melanoma formation in adult mice following UV irradiation ]]> https://biorxiv.org/content/10.1101/2025.06.04.657974v1?rss=1 Knowles, S. Wang, F. Bosland, M. C. Gaddameedhi, S. Chai, W. 2025-06-07 doi:10.1101/2025.06.04.657974 Cold Spring Harbor Laboratory Press 2025-06-07 <![CDATA[ Effects of Ambient Temperature During Pregnancy on Newborn Birthweight ]]> https://biorxiv.org/content/10.1101/2025.06.10.658978v1?rss=1 Nargund, R. Marchesoni, J. Bareja, A. W. Sosnowski, D. Peng, G. Hoyo, C. Pan, W. K. Murphy, S. 2025-06-15 doi:10.1101/2025.06.10.658978 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Topologically-based parameter inference for agent-based model selection from spatiotemporal cellular data ]]> https://biorxiv.org/content/10.1101/2025.06.13.659586v1?rss=1 Wenzel, A. R. Haughey, P. M. Nguyen, K. C. Nardini, J. T. Haugh, J. M. Flores, K. B. 2025-06-15 doi:10.1101/2025.06.13.659586 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Connectivity and Contraction in Cytoskeletal Networks ]]> https://biorxiv.org/content/10.1101/2025.06.12.659219v1?rss=1 Norman, M. J. Leske, A. Belmonte, J. M. 2025-06-16 doi:10.1101/2025.06.12.659219 Cold Spring Harbor Laboratory Press 2025-06-16 <![CDATA[ Non-Thermal Plasma Activated Water is an Effective Nitrogen Fertilizer Alternative for Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2025.06.12.659237v1?rss=1 Kizer, J. J. Robinson, C. D. Lucas, T. Shannon, S. Hernandez, R. Stapelmann, K. Rojas-Pierce, M. 2025-06-17 doi:10.1101/2025.06.12.659237 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Attomolar Detection of HIV-1 with Label-Free RCA-rCRISPR on Smartphone ]]> https://biorxiv.org/content/10.1101/2025.06.15.659809v1?rss=1 Mohammad, N. Steksova, A. Tang, Y. Huang, L. Velayati, A. Zhang, S. Dey Poonam, A. Jamalzadegan, S. Breen, M. Jiang, G. Wei, Q. 2025-06-17 doi:10.1101/2025.06.15.659809 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Study of changes in brain dynamics during sleep cycles in dogs under effect of trazodone ]]> https://biorxiv.org/content/10.1101/2025.06.16.659841v1?rss=1 Catanzariti, M. Mondino, A. Torterolo, P. Aimar, H. Olby, N. Mateos, D. M. 2025-06-17 doi:10.1101/2025.06.16.659841 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Cross-feeding interactions between Fusobacterium nucleatum and the glycan forager Segatella oris ]]> https://biorxiv.org/content/10.1101/2025.06.18.660387v1?rss=1 Fletcher, J. R. Hunter, R. C. 2025-06-19 doi:10.1101/2025.06.18.660387 Cold Spring Harbor Laboratory Press 2025-06-19 <![CDATA[ Impacts of sea level rise on an endemic butterfly and its freshwater wetland habitat in the Florida Keys ]]> https://biorxiv.org/content/10.1101/2025.06.16.659612v1?rss=1 Cabrera, S. R. S. Sarabia, R. Henry, E. H. Anderson, C. T. Daniels, J. C. 2025-06-21 doi:10.1101/2025.06.16.659612 Cold Spring Harbor Laboratory Press 2025-06-21 <![CDATA[ An atlas of cell type specific regulatory effects in cattle ]]> https://biorxiv.org/content/10.1101/2025.06.23.661035v1?rss=1 Li, H. Zhang, H. Zhao, P. Zhang, Q. Zhu, S. Shi, T. Wang, Y.-N. Lu, J.-S. Yang, L. O'Grady, J. F. MacHugh, D. E. Wang, Y. Wei, Z. Lv, X. Wang, M.-S. Han, B. Zheng, W. Chen, A. Akter, S. Bhowmik, N. Ma, Y. Baldwin VI, R. L. Li, C. Jiang, J. Ma, L. Maltecca, C. Wang, J. Gong, M. Zhu, X. Lin, Q. Xi, Y. Zhu, D. Teng, J. GUAN, D. An, B. Ren, J. Hou, Y. Wang, F. Li, B. Frantz, L. Larson, G. Cai, Z. Sahana, G. Jiang, Y. Sun, H. Sun, D. Liu, G. E. Fang, L. 2025-06-24 doi:10.1101/2025.06.23.661035 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ Optimizing genomic sampling for demographic and epidemiological inference with Markov decision processes ]]> https://biorxiv.org/content/10.1101/2025.06.30.662264v1?rss=1 Rasmussen, D. A. Bursell, M. G. Burkhart, F. 2025-07-04 doi:10.1101/2025.06.30.662264 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Rapid spread of knockdown resistance allele frequencies in a suburban population of Aedes albopictus ]]> https://biorxiv.org/content/10.1101/2025.06.30.662396v1?rss=1 Baltzegar, J. F. Butler, C. Beeson, C. Reed, E. M. Ding, J. Y. Reiskind, M. H. Reiskind, M. O. B. 2025-07-04 doi:10.1101/2025.06.30.662396 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Socioeconomic predictors of knockdown resistance in Aedes albopictus (Diptera: Culicidae) ]]> https://biorxiv.org/content/10.1101/2025.07.01.662680v1?rss=1 Butler, C. D. Ding, J. Y. Baltzegar, J. F. Brown, Z. S. Burford Reiskind, M. O. Reiskind, M. H. 2025-07-05 doi:10.1101/2025.07.01.662680 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ A Human Angelman Syndrome Class II Pluripotent Stem Cell line with Fluorescent Paternal UBE3A Reporter ]]> https://biorxiv.org/content/10.1101/2025.07.12.664539v1?rss=1 Kelkar, G. R. Stuppy, S. R. Sen, D. Yagci, Z. B. Han, L. Land, L. Hartman, J. K. Keung, A. J. 2025-07-14 doi:10.1101/2025.07.12.664539 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ A network perspective on the evolution of hybrid incompatibilities ]]> https://biorxiv.org/content/10.1101/2025.07.09.663985v1?rss=1 Brud, E. Guerrero, R. 2025-07-15 doi:10.1101/2025.07.09.663985 Cold Spring Harbor Laboratory Press 2025-07-15 <![CDATA[ Single-cell transcriptomics reveal alveolar macrophages-specific responses in single-hit ozone exposure model in mice ]]> https://biorxiv.org/content/10.1101/2025.07.11.664370v1?rss=1 Vo, T. Choudhary, I. Patial, S. Saini, Y. 2025-07-17 doi:10.1101/2025.07.11.664370 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Replication Timing Uncovers a Two-Compartment Nuclear Architecture of Interphase Euchromatin in Maize ]]> https://biorxiv.org/content/10.1101/2025.07.11.664491v1?rss=1 Akram, H. S. Wear, E. E. Mickelson-Young, L. Turpin, Z. M. Hanley-Bowdoin, L. Thompson, W. F. Lorenzo, C. Bass, H. W. 2025-07-17 doi:10.1101/2025.07.11.664491 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ A Way Through the Trees: Molecular Phylogenies Consistently Recover Two Clades of Aedes Mosquitoes ]]> https://biorxiv.org/content/10.1101/2025.07.16.665186v1?rss=1 Yeo, H. Chan, C. Morinaga, G. Wiegmann, B. M. Soghigian, J. 2025-07-18 doi:10.1101/2025.07.16.665186 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Self-medicating behavior in bumble bees has cascading consequences for pollination and plant reproduction ]]> https://biorxiv.org/content/10.1101/2025.07.21.665926v1?rss=1 Fitch, G. Donzelli, B. Irwin, R. E. Keefover-Ring, K. Adler, L. S. 2025-07-24 doi:10.1101/2025.07.21.665926 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ A Precision Ultrasound-Localized Sonoporation-Equipment (PULSE) Enabling Intratumoral Delivery for Cancer Immunotherapy ]]> https://biorxiv.org/content/10.1101/2025.07.22.665995v1?rss=1 Chen, M. Zhang, B. Kim, H. Kreager, B. C. Yang, W. Zhao, K. Moon, S. Wu, H. Crosby, E. J. Osada, T. Hu, J. Lyerly, H. K. Jiang, X. 2025-07-26 doi:10.1101/2025.07.22.665995 Cold Spring Harbor Laboratory Press 2025-07-26 <![CDATA[ Inertial sensing of water content in tumor spheroids ]]> https://biorxiv.org/content/10.1101/2025.07.24.665638v1?rss=1 Katsikis, G. Yoon, J. C. Usherwood, T. R. Malinowski, S. Yu, J. Chen, C. Son, S. Sutton, J. L. Ligon, K. L. Lee, J. Miettinen, T. P. Manalis, S. P. 2025-07-26 doi:10.1101/2025.07.24.665638 Cold Spring Harbor Laboratory Press 2025-07-26 <![CDATA[ Multi-omic analyses identify molecular targets of Chd7 that mediate CHARGE syndrome model phenotypes ]]> https://biorxiv.org/content/10.1101/2025.07.28.666396v1?rss=1 Hancock, M. B. Ruby, D. R. Bieler, R. A. Cole, D. C. Marsden, K. C. 2025-07-29 doi:10.1101/2025.07.28.666396 Cold Spring Harbor Laboratory Press 2025-07-29 <![CDATA[ Two decades of resurrection studies: What have we learned about contemporary evolution of plant species? ]]> https://biorxiv.org/content/10.1101/2025.07.27.667050v1?rss=1 Pennington, L. Sheth, S. N. Franks, S. J. Anderson, J. T. Hamann, E. 2025-07-31 doi:10.1101/2025.07.27.667050 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Does Human Transthyretin Aggregate in Blood Plasma or in Cardiac Tissue? A Mathematical Modeling Study ]]> https://biorxiv.org/content/10.1101/2025.07.29.667417v1?rss=1 Kuznetsov, A. V. 2025-08-01 doi:10.1101/2025.07.29.667417 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Comprehensive Transcriptomic and Epigenomic Insights into Environmental Toxicant Exposures: The TaRGET II Resource ]]> https://biorxiv.org/content/10.1101/2025.07.28.667191v1?rss=1 Zhang, B. A. Miao, B. Fu, S. Coarfa, C. Kumar, R. Kuntala, P. K. Park, B. Colacino, J. A. Svobada, L. K. Shao, W. Xing, X. Li, D. Liu, S. Hamanaka, R. B. Lalancette, C. Sartor, M. A. Krapp, C. Crawford, G. E. Patisaul, H. B. Wiltshire, T. Aylor, D. L. Biswal, S. Mutlu, G. M. Rajagopalan, S. Tang, W.-Y. Dolinoy, D. C. Wang, T. Bartolomei, M. S. Walker, C. L. Grimm, S. L. Ruiz-Echartea, E. Katz, T. Jangid, R. 2025-08-02 doi:10.1101/2025.07.28.667191 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Genomics of sable (Martes zibellina) x pine marten (Martes martes) hybridization ]]> https://biorxiv.org/content/10.1101/2025.08.01.668050v1?rss=1 Tomarovsky, A. A. Totikov, A. A. Bulyonkova, T. M. Perelman, P. L. Abramov, A. V. Serdyukova, N. A. Yakupova, A. R. Prokopov, D. Beklemisheva, V. R. Sinding, M.-H. S. Davletshina, G. Pobedintseva, M. Krasheninnikova, K. Foerster, D. W. Mukhacheva, A. S. Mironova, A. Sidorov, M. Nie, W. Wang, J. Romanenko, S. A. Proskuryakova, A. A. Ferguson-Smith, M. Yang, F. Cherkasov, N. Balanovskaya, E. Gilbert, M. T. P. Okhlopkov, I. M. Zhuk, A. Graphodatsky, A. S. Powell, R. Koepfli, K.-P. Kliver, S. 2025-08-02 doi:10.1101/2025.08.01.668050 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Early-Life Poultry-Derived Lactobacilli Drive Microbial Succession and Gut Immune Modulation in Broiler Chickens ]]> https://biorxiv.org/content/10.1101/2025.08.01.668251v1?rss=1 Abdelaziz, K. Sharma, S. Seekatz, A. Alizadeh, M. Hassan, H. Yitbarek, A. Pratt, S. 2025-08-02 doi:10.1101/2025.08.01.668251 Cold Spring Harbor Laboratory Press 2025-08-02 <![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[ Two mutations in the same MYC-bHLH transcription factor cause segregation of purple coloration of stolons and seed heads in Zoysia japonica x Zoysia matrella F2 and F1 populations ]]> https://biorxiv.org/content/10.1101/2025.08.04.668483v1?rss=1 Pradhan, S. Zhao, J. Spiekerman, J. J. Bennetzen, E. Khanal, S. Yu, X. Milla-Lewis, S. Conner, J. Schwartz, B. Devos, K. M. 2025-08-05 doi:10.1101/2025.08.04.668483 Cold Spring Harbor Laboratory Press 2025-08-05 <![CDATA[ Mapping of genotype-by-environment interaction loci for Metabolic Syndrome-like traits using the multi-parent Drosophila Synthetic Population Resource determines that main genetic effects are distinct from environment dependent plastic loci ]]> https://biorxiv.org/content/10.1101/2025.08.04.668530v1?rss=1 Dew-Budd, K. J. Mathur, R. Roy, S. Jarnigan, J. Moss, A. Bombin, A. Oza, V. Rele, C. Adams, A. Mendez, S. Bray, K. Davis, D. Kieffer, M. Leonard, L. Hubickey, J. Paiva, C. Izor, N. Nadella, D. Perkins, L. R. Zeng, X. Johnson, J. M. Motsinger-Reif, A. Reed, L. K. 2025-08-06 doi:10.1101/2025.08.04.668530 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ KeySDL: Sparse Dictionary Learning for Keystone Microbe Identification ]]> https://biorxiv.org/content/10.1101/2025.08.07.669165v1?rss=1 Gordon, M. Akyol, T. Y. Amos, B. K. Andersen, S. U. Williams, C. 2025-08-11 doi:10.1101/2025.08.07.669165 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ Evaluation of Parallel Accumulation-Serial Fragmentation methods for metaproteomics using a model microbiome ]]> https://biorxiv.org/content/10.1101/2025.08.13.670166v1?rss=1 Shrestha, R. Rajczewski, A. T. Do, K. Willetts, M. Kleiner, M. Griffin, T. Jagtap, P. D. 2025-08-15 doi:10.1101/2025.08.13.670166 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ VILMIR is a trans-acting long noncoding RNA that enhances the host interferon response in human epithelial cells ]]> https://biorxiv.org/content/10.1101/2025.08.18.670784v1?rss=1 John, K. Smith, E. Istishin, A. Mahmood, N. Diveley, K. Tollison, T. S. Carpenter, S. Peng, X. 2025-08-22 doi:10.1101/2025.08.18.670784 Cold Spring Harbor Laboratory Press 2025-08-22 <![CDATA[ Integrated Genomic and Methylome Profiling Reveals Promoter Repression and Age-Linked CpGs in the California Mussel ]]> https://biorxiv.org/content/10.1101/2025.08.27.672726v1?rss=1 Hiebert, L. S. Soesbe, A. Cui, Q. Hsieh, T.-F. Yi, S. V. 2025-09-01 doi:10.1101/2025.08.27.672726 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ Ambient temperature, clutch size, and daylight are the main drivers of incubation behavior in two neotropical swallows breeding 8,000 km apart ]]> https://biorxiv.org/content/10.1101/2025.08.27.672727v1?rss=1 Diez-Mendez, D. Liljeström, M. Cooper, C. B. Ardia, D. R. Winkler, D. 2025-09-01 doi:10.1101/2025.08.27.672727 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ Circular RNAs in Lotus japonicus Responses to Nutrient Supply and Symbiotic Interactions ]]> https://biorxiv.org/content/10.1101/2025.08.28.672498v1?rss=1 Utley, D. Budnick, A. Radutoiu, S. Sederoff, H. 2025-09-01 doi:10.1101/2025.08.28.672498 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ Coaxially Electrospun Myocardial dECM-based Nanofibrous Scaffolds Demonstrate Enhanced Cardiomyocyte Adhesion and Function ]]> https://biorxiv.org/content/10.1101/2025.09.02.673432v1?rss=1 View larger version (51K): org.highwire.dtl.DTLVardef@31a497org.highwire.dtl.DTLVardef@12cee05org.highwire.dtl.DTLVardef@beca77org.highwire.dtl.DTLVardef@1de5337_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Rajapakse, D. N. Ali, K. M. Khodadadi, M. Proctor, B. T. Upadhyay, T. Zha, D. Cook, S. H. Gluck, J. M. 2025-09-07 doi:10.1101/2025.09.02.673432 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ Lipid Nanoparticles with Aptamers Enable Targeted mRNA Delivery to CD4⁺ T Cells ]]> https://biorxiv.org/content/10.1101/2025.09.10.675359v1?rss=1 Shah, S. Ranasinghe, M. Decker, J. Fraser, K. Friedman, A. Wang, Y. Kinlaw, S. Barker, M. Patel, S. Yao, S. 2025-09-12 doi:10.1101/2025.09.10.675359 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ IRIS Integrates Sparse Sequence, Experimental, and AI-Predicted Structures for Protein-RNA Affinity Prediction and Motif Discovery ]]> https://biorxiv.org/content/10.1101/2025.09.10.675247v1?rss=1 Cisneros de la Rosa, E. Zhang, Y. Lin, X. 2025-09-16 doi:10.1101/2025.09.10.675247 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Natural history museums are missing an opportunity to present research and collections on YouTube ]]> https://biorxiv.org/content/10.1101/2025.09.16.676522v1?rss=1 Ruzi, S. A. Smith, A. A. Lee, N. M. Galvez, N. J. Dinh, T. A. 2025-09-19 doi:10.1101/2025.09.16.676522 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Nicotinamide opposes ET-1's adverse effect on uterine decidualization via EDNRB ]]> https://biorxiv.org/content/10.1101/2025.09.18.677237v1?rss=1 Wang, Y. Ma, Q. Chen, M. Kayashima, Y. Zhou, J. Rao, B. Bowser, J. L. Yi, X. Maeda-Smithies, N. Li, F. 2025-09-19 doi:10.1101/2025.09.18.677237 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ RNAi Gene knockdown of R-opsin and F-actin in the marineannelid Streblospio benedicti by delivering dsRNA ]]> https://biorxiv.org/content/10.1101/2025.09.22.677873v1?rss=1 Aguilar-Camacho, J. M. Zakas, C. 2025-09-22 doi:10.1101/2025.09.22.677873 Cold Spring Harbor Laboratory Press 2025-09-22 <![CDATA[ Novel chromosome-length genome assemblies of three distinct subspecies of pine marten, sable, and yellow-throated marten (genus Martes, family Mustelidae) ]]> https://biorxiv.org/content/10.1101/2025.09.22.677678v1?rss=1 90% were assigned functional names. Repeats encompass 36.9-40.4% of the assemblies, with a prevalence of LINEs and SINEs, and is conservative across the genus. Synteny analysis of our generated and available marten genome assemblies revealed assembly artifacts in previously published assemblies, which we confirmed through investigation of Hi-C contact maps. Among other rearrangements, we verified a sable-specific inversion on chromosome 11 using the published cytogenetic data. Our assemblies broaden the genomic resources available for Martes, extending coverage to geographically distant and taxonomically significant subspecies. Together, they provide a robust framework for assessing intraspecific genetic diversity, identifying signatures of hybridization, and refining the complex taxonomy of the genus. Beyond conservation and evolutionary applications, these references will facilitate comparative genomics across Mustelidae and other carnivorans. ]]> Tomarovsky, A. A. Khan, R. Dudchenko, O. Beklemisheva, V. R. Perelman, P. L. Totikov, A. A. Serdyukova, N. A. Bulyonkova, T. M. Pobedintseva, M. Abramov, A. V. Weisz, D. Yakupova, A. Zhuk, A. Graphodatsky, A. S. Powell, R. Aiden, E. L. Koepfli, K.-P. Kliver, S. 2025-09-23 doi:10.1101/2025.09.22.677678 Cold Spring Harbor Laboratory Press 2025-09-23 <![CDATA[ Assessing contamination in DNA extraction kits commonly used for microbiome research ]]> https://biorxiv.org/content/10.1101/2025.09.23.677068v1?rss=1 Rabasco, J. T. Kisthardt, S. C. Theriot, C. M. Callahan, B. J. 2025-09-23 doi:10.1101/2025.09.23.677068 Cold Spring Harbor Laboratory Press 2025-09-23 <![CDATA[ Neurodegeneration Associated with Repeated High-Frequency Transcranial Focused Ultrasound ]]> https://biorxiv.org/content/10.1101/2025.09.23.674044v1?rss=1 Brna, A. P. Favorov, O. V. Challener, T. Biliroglu, A. O. Yamaner, F. Y. Kemal, R. E. Annayev, M. Oralkan, O. Eidum, D. Simons, S. B. Weisend, M. P. Connolly, P. M. 2025-09-25 doi:10.1101/2025.09.23.674044 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Birds that don't exist: niche pre-emption as a constraint on morphological evolution in the Passeroidea ]]> https://biorxiv.org/content/10.1101/2025.09.24.678290v1?rss=1 Chia, S. Y. Swain, A. Josephs, N. Lin, L. Fagan, W. F. 2025-09-26 doi:10.1101/2025.09.24.678290 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ Exploring the genetic basis of cluster architecture-related traits in grapevine through a Genome-wide Association Study ]]> https://biorxiv.org/content/10.1101/2025.09.24.678328v1?rss=1 de Oliveira, G. L. Francisco, F. R. de Moura, Y. A. Niederauer, G. F. Fritsche-Neto, R. de Souza, A. P. Furlan, M. F. M. 2025-09-26 doi:10.1101/2025.09.24.678328 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ A co-evolved peptide-GPCR system senses host entry to drive fungal infection ]]> https://biorxiv.org/content/10.1101/2025.09.26.678928v1?rss=1 Mendoza-Rojas, G. Nakonz, P. Lu, M. Postma, J. Shtakser, N. Heinen, M. Patel, M. Arguello-Miranda, O. Billerbeck, S. Altegoer, F. 2025-09-27 doi:10.1101/2025.09.26.678928 Cold Spring Harbor Laboratory Press 2025-09-27 <![CDATA[ Antibacterial wound dressing enables reliable detection of uric acid in exudates. ]]> https://biorxiv.org/content/10.1101/2025.09.29.679342v1?rss=1 lv, m. Li, b. 2025-10-01 doi:10.1101/2025.09.29.679342 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Regulation of Vacuole Fusion in Stomata by Dephosphorylation of the HOPS subunit VPS39 ]]> https://biorxiv.org/content/10.1101/2025.10.02.680005v1?rss=1 Pullen, A.-M. Billings, G. Hodgens, C. White, G. Akpa, B. Rojas-Pierce, M. 2025-10-02 doi:10.1101/2025.10.02.680005 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Glucose levels impact the morphology and cell-type composition of human cerebral organoids ]]> https://biorxiv.org/content/10.1101/2025.10.02.680109v1?rss=1 Kelkar, G. R. Rao, B. M. Keung, A. J. 2025-10-03 doi:10.1101/2025.10.02.680109 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Best practices and challenges for urban tree detection, classification, and geolocation with street-level images across North American cities ]]> https://biorxiv.org/content/10.1101/2025.10.09.681424v1?rss=1 Lake, T. A. Laginhas, B. B. Farrell, B. T. Meentemeyer, R. K. Jones, C. M. 2025-10-10 doi:10.1101/2025.10.09.681424 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ Optogenetic control of PLC-γ1 activity polarizes cell motility ]]> https://biorxiv.org/content/10.1101/2025.10.09.681531v1?rss=1 Appalabhotla, R. Siesser, P. F. Truscott, H. Hajicek, N. Sondek, J. Bear, J. E. Haugh, J. M. 2025-10-11 doi:10.1101/2025.10.09.681531 Cold Spring Harbor Laboratory Press 2025-10-11 <![CDATA[ TGA family of transcription factors are nitric oxide sensors in the root stem cell niche ]]> https://biorxiv.org/content/10.1101/2025.10.14.682262v1?rss=1 Fernandez-Espinosa, M. G. Gomez-Jimenez, S. Mata-Perez, C. Sanchez-Corrionero, A. Song, J. de Luis Balaguer, M. A. Sozzani, R. Gutsche, N. Zachgo, S. Leene, J. V. De Jaeger, G. Spoel, S. H. Lorenzo, O. 2025-10-15 doi:10.1101/2025.10.14.682262 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ The microbial landscape: soil microbiome properties predict plant species distributions ]]> https://biorxiv.org/content/10.1101/2025.10.14.682295v1?rss=1 70% of the predicted distribution for one species. We identified four microbiome attributes of landscape-scale importance for predicting plant species distributions including prokaryotic richness, fungal richness, the abundance of fungal pathogens, and the abundance of prokaryotic phosphate transport genes in soil. Our findings reveal a previously underappreciated role of the soil microbiome in shaping plant species distributions at a landscape scale, with implications for plant community structure in the context of both ecosystem restoration and future global change. ]]> Revillini, D. Mothes, C. C. Almeida, B. K. Charton, K. T. Koontz, S. David, A. S. Afkhami, M. E. Searcy, C. A. 2025-10-15 doi:10.1101/2025.10.14.682295 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ The Effect of Plasma Activated Water on the Rhizosphere Composition of Arabidopsis and Solanum lycopersicum ]]> https://biorxiv.org/content/10.1101/2025.10.15.682576v1?rss=1 Kizer, J. J. Allen, X. Robinson, C. D. Grunden, A. Stapelmann, K. Rojas-Pierce, M. 2025-10-15 doi:10.1101/2025.10.15.682576 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Guard Cell-Enriched Phosphoproteome Reveals Phosphorylation of Endomembrane Proteins in Closed Stomata ]]> https://biorxiv.org/content/10.1101/2025.10.15.682613v1?rss=1 Pullen, A.-M. Lyons, S. Mordant, A. Herring, L. E. Akpa, B. Rojas-Pierce, M. 2025-10-15 doi:10.1101/2025.10.15.682613 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Nectar yeast scent additions fail to impact overall bouquet composition and bumble bee visitation in a montane herb ]]> https://biorxiv.org/content/10.1101/2025.10.17.683152v1?rss=1 Dabagia, N. J. Martin, V. N. Souto-Vilaros, D. Schaeffer, R. Irwin, R. E. 2025-10-17 doi:10.1101/2025.10.17.683152 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ The influence of captivity on cardiac structure and function across age, in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2025.10.20.683517v1?rss=1 Dawkins, T. G. Curry, B. A. Drane, A. L. Rivas, V. N. Ueda, Y. Stern, J. A. Phillips, D. Negron-Del Valle, J. Cayo Biobank Research Unit, Higham, J. P. Snyder-Mackler, N. Brent, L. Shave, R. 2025-10-21 doi:10.1101/2025.10.20.683517 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Gonadal Transcriptome Differences Between the Sexes in Wild Caught Southern Flounder (Paralichthys lethostigma) During a Critical Development Period ]]> https://biorxiv.org/content/10.1101/2025.10.21.683694v1?rss=1 Harned, S. Mankiewicz, J. L. Smith, E. Borski, R. J. Guerrero, R. F. Burford Reiskind, M. O. Godwin, J. 2025-10-22 doi:10.1101/2025.10.21.683694 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Cover crop microbiomes affect legume cash crop growth but not consistently through enriching nitrogen-fixing rhizobia ]]> https://biorxiv.org/content/10.1101/2025.10.23.684197v1?rss=1 Clouse, K. Paillan, E. Depew, C. Harris, J. Jason, A. Mercurio, K. Swartley, A. Bingham, E. Burghardt, L. 2025-10-24 doi:10.1101/2025.10.23.684197 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ Temperature modulates PFAS accumulation and energy allocation in sheepshead minnows ]]> https://biorxiv.org/content/10.1101/2025.10.23.684267v1?rss=1 Grimmelpont, M. Rodgers, M. L. Levin, M. De Guise, S. Agrawal, A. Baron, J. Bolnick, D. I. Milligan-McClellan, K. Provotas, A. A. Brandt, J. E. 2025-10-24 doi:10.1101/2025.10.23.684267 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ Direct and diffuse cross-kingdom interactions in plant microbiome assembly ]]> https://biorxiv.org/content/10.1101/2025.10.24.684285v1?rss=1 Hammer, R. A. Lee, M. R. Kimbrel, J. Stuart, R. Hawkes, C. V. 2025-10-24 doi:10.1101/2025.10.24.684285 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ Nodule branching, size, and symbiosis outcomes are shaped by natural genetic variation in rhizobial bacteria and alfalfa hosts ]]> https://biorxiv.org/content/10.1101/2025.10.27.684485v1?rss=1 Paillan, E. L. Gil-Polo, A. Guha, S. Swartley, A. Burghardt, L. T. 2025-10-27 doi:10.1101/2025.10.27.684485 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Hi-C informed kernel association test: integrating 3-dimensional genome structure into variant-set association for whole-genome sequencing data ]]> https://biorxiv.org/content/10.1101/2025.10.28.684891v1?rss=1 Basu, R. Huang, Y. Tzeng, J. Y. Lu, W. Holloway, S. Li, Y. 2025-10-30 doi:10.1101/2025.10.28.684891 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Meta-analyses reveal no clear demographic consequences of phenological change across taxa ]]> https://biorxiv.org/content/10.1101/2025.10.29.685396v1?rss=1 Godtfredsen, E. B. CaraDonna, P. Foxx, A. J. Bain, J. A. Connolly, B. J. Dawdy, K. M. Doucet, A. M. Fitzgerald, J. L. Kirschke, G. E. Ogilvie, J. E. Rigby, C. C. Scholl, J. P. Sandacz, D. J. Rosa, S. Zink, A. C. Iler, A. M. 2025-10-31 doi:10.1101/2025.10.29.685396 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Mathematical modeling of light chain aggregation and cardiac damage in AL amyloidosis ]]> https://biorxiv.org/content/10.1101/2025.10.30.685705v1?rss=1 Kuznetsov, A. V. 2025-11-01 doi:10.1101/2025.10.30.685705 Cold Spring Harbor Laboratory Press 2025-11-01 <![CDATA[ First study of an aye-aye (Daubentonia madagascariensis) mother's anxiety behaviors peripartum ]]> https://biorxiv.org/content/10.1101/2025.11.08.686247v1?rss=1 Olson, R. V. Watts, D. Paciulli, L. M. 2025-11-10 doi:10.1101/2025.11.08.686247 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Postoperative Automated Platelet Count and Its Predictive Factors in Dogs Undergoing Mitral Valve Repair ]]> https://biorxiv.org/content/10.1101/2025.11.10.687737v1?rss=1 Kurogochi, K. Furusato, S. Nii, Y. Chen, A. Ueda, Y. Mizuno, M. Uechi, M. 2025-11-12 doi:10.1101/2025.11.10.687737 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Topological data analysis identifies PURPL as a prognostic gene in breast cancer Luminal A patients ]]> https://biorxiv.org/content/10.1101/2025.11.11.687413v1?rss=1 Ochoa Zavalza, S. J. Pouokam, M. Kruse, M. Gonzalez-Isunza, G. Sazdanovic, R. Arsuaga, J. 2025-11-13 doi:10.1101/2025.11.11.687413 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ mIDEA: An Interpretable Structure-Sequence Model for Methylation-Dependent Protein-DNA Binding Sensitivity ]]> https://biorxiv.org/content/10.1101/2025.11.14.688575v1?rss=1 Zhang, Y. Li, R. Zhong, J. Lin, X. 2025-11-16 doi:10.1101/2025.11.14.688575 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ PlantCV v4: Image analysis software for high-throughput plant phenotyping ]]> https://biorxiv.org/content/10.1101/2025.11.19.689271v1?rss=1 Schuhl, H. Brown, K. E. Sheng, H. Bhatt, P. K. Gutierrez, J. Schneider, D. Casto, A. L. Acosta-Gamboa, L. Ballenger, J. G. Barbero, F. Braley, J. Brown, A. M. Chavez, L. Cunningham, S. Dilhara, M. Dimech, A. M. Duenwald, J. G. Fischer, A. Gordon, J. M. Hendrikse, C. Hernandez, G. L. Hodge, J. G. Huber, M. Hurr, B. M. Jarolmasjed, S. Medina Jimenez, K. Kenney, S. Konkel, G. Kutschera, A. Lama, S. Lohbihler, M. Lorence, A. Luebbert, C. Ly, N. Manching, H. K. Marrano, A. Meerdink, S. Miklave, N. M. Mudrageda, P. Murphy, K. M. Peery, J. D. Pierik, R. Polyd 2025-11-20 doi:10.1101/2025.11.19.689271 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ Comparative genomics and interactions of vector thysanopterans and transmitted viruses ]]> https://biorxiv.org/content/10.1101/2025.11.21.689785v1?rss=1 Catto, M. A. Labadie, P. E. Kennedy, G. G. Jacobson, A. L. Hunt, B. G. Srinivasan, R. 2025-11-22 doi:10.1101/2025.11.21.689785 Cold Spring Harbor Laboratory Press 2025-11-22 <![CDATA[ Effects of environmental setting and diet on the gut microbial ecology of eastern hellbenders (Cryptobranchus alleganiensis alleganiensis) ]]> https://biorxiv.org/content/10.1101/2025.11.24.690264v1?rss=1 Cummins, C. Sutton, W. McLeod, T. Dallas, J. W. Ghotbi, M. Vargas-Gastelum, L. Alexander, N. R. Rurik, A. J. McGinnity, D. Reinsch, S. D. Sandonato, P. Arbour, J. Freake, M. Ashley, A. Ternes, W. Culp, E. Spatafora, J. McPhail, K. Stajich, J. E. Hardman, R. Walker, D. M. 2025-11-25 doi:10.1101/2025.11.24.690264 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Four Decades of Genomic Stability and Adaptive Divergence in Xanthomonas arboricola pv. pruni-Infecting Phages: Defining Duraznoxanthovirus arenicola and Its Evolutionary Framework ]]> https://biorxiv.org/content/10.1101/2025.11.25.690537v1?rss=1 95% nucleotide identity and 63 conserved core genes, forming a new genus and species, Duraznoxanthovirus arenicola. These findings challenge assumptions of pervasive genomic mosaicism, highlighting remarkable genomic stability alongside localized variability in accessory loci. Beyond genus-level characterization, our analyses support a broader taxonomic restructuring within the family Anamaviridae, introducing a new subfamily (Terravirinae) and two new genera (Duraznoxanthovirus and Ralstopathovirus). This work provides the first family-level framework for phages exclusively infecting plant-associated bacteria, offering evolutionary insights and a foundation for ecological studies and management strategies. ]]> D'Amico-Willman, K. M. Joglekar, P. Turner, D. Flaherty, M. Ritchie, D. F. Huerta, A. I. 2025-11-25 doi:10.1101/2025.11.25.690537 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Multi-Omics analyses reveal dynamic interactions between DNA methylation and transcriptional regulation during black raspberry ripening ]]> https://biorxiv.org/content/10.1101/2025.11.24.690302v1?rss=1 Hsieh, W.-H. Hung, Y.-H. Zhang, J.-H. Chen, H.-Y. Lin, L.-P. He, M.-H. Wang, Y.-C. Ho, Y.-Y. Fernandez, G. Perkins-Veazie, P. Le, B. Li, X. Hsieh, T.-F. Lin, J.-Y. 2025-11-27 doi:10.1101/2025.11.24.690302 Cold Spring Harbor Laboratory Press 2025-11-27 <![CDATA[ MosaicSim: A Novel Mosaic Variant Simulator Reveals Diminishing Returns of Ultra-High Coverage for Mosaic Variant Detection ]]> https://biorxiv.org/content/10.64898/2025.12.03.692191v1?rss=1 Stricker, E. Jaryani, F. Izydorczyk, M. Poon, C.-L. Sanio, P. Alexander, A. Deb, S. Sedlazeck, F. Rogers, J. Atkinson, E. G. 2025-12-07 doi:10.64898/2025.12.03.692191 Cold Spring Harbor Laboratory Press 2025-12-07 <![CDATA[ An integrated workflow for structural virology with a 100 keV electron microscope ]]> https://biorxiv.org/content/10.64898/2025.12.08.693081v1?rss=1 Pathirage, R. Dutta, M. Parsons, R. J. Lella, M. Atwood, E. Zhang, Q. E. May, A. Johnson, A. Huang, X. Flemming, J. Kumar, U. Marayati, B. F. Spurrier, M. A. Liu, C. Zhuo, J. Song, K. Devkota Adhikari, R. Sammour, S. Ilevbare, V. Abram, C. Diaz, M. Guzman, A. Rai, J. Skelly, A. N. Hogarty, M. P. Anasti, K. Purro, M. Lindsay, M. Alam, S. M. Weissman, D. Herschhorn, A. Hahn, B. H. Shaw, G. M. Sharma, A. Heaton, N. S. Edwards, R. J. Henderson, R. Denny, T. Saunders, K. O. Siliciano, J. D. Siliciano, R. F. Haynes, B. F. Janowska, K. Acharya, P. 2025-12-10 doi:10.64898/2025.12.08.693081 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ Immune-cancer analyses across mammals reveal a potential trophic level and platelet-linked tradeoff between cancer and trauma mortality ]]> https://biorxiv.org/content/10.64898/2025.12.09.693265v1?rss=1 Kapsetaki, S. E. Seyedi, S. Compton, Z. T. Rupp, S. M. Duke, E. G. Schiffman, J. D. Troan, B. V. Harrison, T. M. Maley, C. C. Abegglen, L. M. Boddy, A. M. 2025-12-11 doi:10.64898/2025.12.09.693265 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Efficient RNA Folding Simulation via a Structure-Based Single-Site-Per-Nucleotide Model ]]> https://biorxiv.org/content/10.64898/2025.12.13.694107v1?rss=1 Thornton, T. Lin, X. 2025-12-14 doi:10.64898/2025.12.13.694107 Cold Spring Harbor Laboratory Press 2025-12-14 <![CDATA[ Assessing PDMS Biocompatibility in Microfluidic Applications: Toxicity and Survival Outcomes in C. elegans ]]> https://biorxiv.org/content/10.64898/2025.12.11.693574v1?rss=1 Gomez, K. Efimenko, K. Genzer, J. San Miguel, A. 2025-12-15 doi:10.64898/2025.12.11.693574 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ Male songbirds show higher coccidia oocyst burdens than femalesfollowing anthelmintic treatment ]]> https://biorxiv.org/content/10.64898/2025.12.12.694047v1?rss=1 Talbott, K. Tysver, A. Wanamaker, S. Ketterson, E. 2025-12-15 doi:10.64898/2025.12.12.694047 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ Does more data solve the problem of deep support? A phylogenomic approach to clarifying evolutionary relationships in the Lecanoraceae ]]> https://biorxiv.org/content/10.64898/2025.12.18.694902v1?rss=1 Li, L. J. Ivanovich-Hichins, C. LaGreca, S. Muggia, L. Myllys, L. Perez-Ortega, S. Thor, G. Weber, L. Vakkari, E. Printzen, C. Gerasimova, J. 2025-12-20 doi:10.64898/2025.12.18.694902 Cold Spring Harbor Laboratory Press 2025-12-20 <![CDATA[ A Practical Roadmap For Sampling Floral Nectar From Communities of Many Plant Species ]]> https://biorxiv.org/content/10.64898/2025.12.19.695174v1?rss=1 Kirschke, G. E. Bain, J. A. Ogilvie, J. E. CaraDonna, P. J. 2025-12-20 doi:10.64898/2025.12.19.695174 Cold Spring Harbor Laboratory Press 2025-12-20 <![CDATA[ Cyfip2 mediates sensorimotor integration of visual input through Rac1-dependent actin remodeling ]]> https://biorxiv.org/content/10.64898/2025.12.21.695802v1?rss=1 Charron, K. M. Cole, D. C. Hancock, M. B. Sumathipala, S. H. Johnson, A. L. B. Frazier, K. J. Marsden, K. C. 2025-12-23 doi:10.64898/2025.12.21.695802 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ The control of prickle formation in Rubus ]]> https://biorxiv.org/content/10.64898/2025.12.22.695586v1?rss=1 St. Aubin, B. Poorten, T. Fister, A. Ochsenfeld, C. Reiner, J. Castillo, A. S. Aryal, R. Bruna, T. Dudchenko, O. Sargent, D. Mead, D. Buti, M. Silva, A. Pham, M. Weisz, D. Bassil, N. Ashrafi, H. Aiden, E. L. Graham, N. Chauhan, D. Dean, E. Lowry, W. Redpath, L. Marri, P. Lawit, S. Pham, G. Worthington, M. Crawford, B. C. W. 2025-12-23 doi:10.64898/2025.12.22.695586 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Does Fermentation Enhance Beverage Safety? Kombucha's Resistance to Microbial Invasion Suggests a Protective Role ]]> https://biorxiv.org/content/10.64898/2025.12.23.696228v1?rss=1 Marquez Alcaraz, G. Narayanan, S. Alcock, J. Ayers, J. D. Baciu, C. Berman, H. L. Dunn, R. R. Fortunato, A. May, A. Maley, C. C. Siegal, J. Yavari, B. 2025-12-24 doi:10.64898/2025.12.23.696228 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ Genetically engineered ESC-derived embryos reveal Vinculin-dependent force responses required for mammalian neural tube closure ]]> https://biorxiv.org/content/10.64898/2025.12.22.696028v1?rss=1 Prudhomme, I. S. Brooks, E. R. Taneja, N. Bhattacharya, B. LaFleche, B. J. Furuta, Y. Zallen, J. A. 2025-12-25 doi:10.64898/2025.12.22.696028 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ Neuropeptide F regulates adult female response to diet, larval locomotion and several larval physiological processes in Lucilia cuprina cuprina ]]> https://biorxiv.org/content/10.64898/2025.12.22.696103v1?rss=1 Wulff, J. P. Belikoff, E. J. Cunha, V. A. S. Mariano-Martins, P. Scott, M. J. 2025-12-25 doi:10.64898/2025.12.22.696103 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ Time-dependent Glucocorticoid-Induced Transcriptomic Changes in Human Trabecular Meshwork and Schlemm's Canal ]]> https://biorxiv.org/content/10.64898/2025.12.31.696882v1?rss=1 Mehrotra, S. Jeanneret, H. Perkumas, K. Liu, R. Lama, J. Huynh, K. Mukundan, A. Scott, H. Apivatthakakul, A. Wiggs, J. Stamer, D. Segre, A. Sobrin, L. 2026-01-01 doi:10.64898/2025.12.31.696882 Cold Spring Harbor Laboratory Press 2026-01-01 <![CDATA[ Selective Age-Related Changes in Brain Network Connectivity During Young Adulthood: Sensory Networks Decrease While Hub Networks Remain Stable ]]> https://biorxiv.org/content/10.64898/2026.01.08.698428v1?rss=1 0.15). Network coupling analysis revealed a mechanistic explanation: sensory networks decouple from hub networks with age (DMN-AUD: change = -0.77; DMN-VIS: change = -0.56), while sensory networks show increased coupling with each other (VIS-AUD: +0.18). This decoupling explains why only sensory networks show age-related changes, as they become independent from hub networks during young adulthood. Importantly, total IQ showed no significant association with network connectivity (all |r| < 0.10, all p > 0.43), strengthening the developmental interpretation. Machine learning revealed the somatomotor network was most predictive of age. All effects remained consistent after controlling for head motion and across sexes. These results demonstrate selective, network-specific developmental trajectories during young adulthood, with sensory networks becoming independent from hub networks and showing age-related decreases, while hub networks maintain stability. ]]> Zhou, Y.-H. Sun, G. 2026-01-09 doi:10.64898/2026.01.08.698428 Cold Spring Harbor Laboratory Press 2026-01-09 <![CDATA[ Inferring toxicant susceptibility in global populations from gene-environment interactions involving the Aryl Hydrocarbon Receptor ]]> https://biorxiv.org/content/10.64898/2026.01.10.698796v1?rss=1 Chimeh, U. S. Rogers, M. C. Aylor, D. L. 2026-01-10 doi:10.64898/2026.01.10.698796 Cold Spring Harbor Laboratory Press 2026-01-10 <![CDATA[ Genetic variation in a plant-parasitic nematode is associated with gene expression changes conserved across evolutionarily distant host plants ]]> https://biorxiv.org/content/10.64898/2026.01.07.698247v1?rss=1 Nielsen, D. M. 2026-01-12 doi:10.64898/2026.01.07.698247 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ Genomic and phenotypic diversification of Pseudomonas aeruginosa during sustained exposure to a ciliate predator ]]> https://biorxiv.org/content/10.64898/2026.01.13.699197v1?rss=1 Romo Bechara, N. Bardeskar, N. Hopkins, H. A. Raymann, K. 2026-01-13 doi:10.64898/2026.01.13.699197 Cold Spring Harbor Laboratory Press 2026-01-13 <![CDATA[ Behavior evolves as a correlated response to selection on cuticle color in Drosophila melanogaster and D. simulans ]]> https://biorxiv.org/content/10.64898/2026.01.13.699118v1?rss=1 Ruckman, S. N. Duffy, A. G. Mendez, P. M. McCaffery, K. D. Miller, S. Crews, A. Tan, N. Campbell, L. A. March, A. Brown, E. B. Houle, D. 2026-01-14 doi:10.64898/2026.01.13.699118 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Spindle biochemistry responds to compressive force from thenuclear envelope to tune spindle dynamics during closed mitosis ]]> https://biorxiv.org/content/10.64898/2026.01.15.699759v1?rss=1 Mahoney, T. Needham, C. Hakeem, R. Begley, M. Medina, C. P. Elting, M. W. 2026-01-15 doi:10.64898/2026.01.15.699759 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ Hydrodynamic dispersion drives viral-cellular contact for gene delivery in porous media ]]> https://biorxiv.org/content/10.64898/2026.01.15.699726v1?rss=1 Srikanth, V. Mallory, M. Ulmer, A. J. Legant, W. R. Kuznetsov, A. V. Brudno, Y. 2026-01-16 doi:10.64898/2026.01.15.699726 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ Multiscale temporal tuning of force generation complex machinery governs cortical microtubule interactions during the first mitotic division in C. elegans ]]> https://biorxiv.org/content/10.64898/2026.01.16.699965v1?rss=1 Edwards, G. A. Linehan, J. B. Maddox, P. S. Maddox, A. S. 2026-01-19 doi:10.64898/2026.01.16.699965 Cold Spring Harbor Laboratory Press 2026-01-19 <![CDATA[ The MexMAGIC population reveals the genetic architecture of clinal trait variation in Mexican native maize ]]> https://biorxiv.org/content/10.64898/2026.01.17.700095v1?rss=1 Perez-Limon, S. Alonso-Nieves, A. L. Ramirez-Flores, M. R. Cintora-Martinez, C. Salazar-Vidal, M. N. Carcano-Macias, J. Perryman, M. G. Paulson, O. H. Sidhu, J. S. Yu, P. Llaca, V. Fengler, K. A. Li, F. Runcie, D. E. Ross-Ibarra, J. Gillmor, C. S. Rellan-Alvarez, R. Sawers, R. J. H. 2026-01-21 doi:10.64898/2026.01.17.700095 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Pharmacokinetics and Physiologically Based Pharmacokinetic Modeling of Mycobacteriophages: Insights into Pulmonary Distribution and Clearance ]]> https://biorxiv.org/content/10.64898/2026.01.27.702067v1?rss=1 Sharma, R. Mahadevan, R. Divyash, S. Yeshwante, S. Matcha, S. Cheng, C. Talley, H. S. Schmalstig, A. A. Neupane, P. Maloney Norcross, S. E. Hickey, A. J. Hatfull, G. F. Braunstein, M. Rao, G. G. 2026-01-28 doi:10.64898/2026.01.27.702067 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ A biophysical framework for accurately identifying antigen single-amino acid escape variants and corresponding variant-specific compensatory TCR sequences ]]> https://biorxiv.org/content/10.64898/2026.02.02.703411v1?rss=1 Ghoreyshi, Z. S. Levine, H. Lin, X. Onuchic, J. N. George, J. T. 2026-02-05 doi:10.64898/2026.02.02.703411 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ A deep-learning-based score to evaluate multiple sequence alignments ]]> https://biorxiv.org/content/10.64898/2026.02.02.703429v1?rss=1 Serok, N. Polonsky, K. Ashkenazy, H. Mayrose, I. Thorne, J. L. Pupko, T. 2026-02-05 doi:10.64898/2026.02.02.703429 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ Springtail-inspired compliant hinge enables terrain-adaptable takeoff in insect-scale robots ]]> https://biorxiv.org/content/10.64898/2026.02.04.703923v1?rss=1 Harrison, J. Kim, B. Ko, H. Smith, A. Truong, T. Koh, J.-s. Bhamla, S. 2026-02-07 doi:10.64898/2026.02.04.703923 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ Changing pollination rates affect plant life history strategies ]]> https://biorxiv.org/content/10.64898/2026.02.11.705202v1?rss=1 Simpson, D. T. Petry, W. K. CaraDonna, P. J. Iler, A. M. 2026-02-14 doi:10.64898/2026.02.11.705202 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ Temporal stability and niche partitioning of bacterial communities in paired residential sink P-traps ]]> https://biorxiv.org/content/10.64898/2026.02.17.706431v1?rss=1 Hill, M. S. Stiffler, W. Rabasco, J. Blakley, I. C. SUN, S. Fodor, A. A. Gunsch, C. 2026-02-18 doi:10.64898/2026.02.17.706431 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Spatial confinement of gene drives: Assessing risk of failure using global sensitivity analysis ]]> https://biorxiv.org/content/10.64898/2026.02.18.706608v1?rss=1 Butler, C. D. Lloyd, A. L. 2026-02-19 doi:10.64898/2026.02.18.706608 Cold Spring Harbor Laboratory Press 2026-02-19 <![CDATA[ Unlocking the Bile Acid Universe: Advanced Workflows and a Multidimensional Library of 280 Unique Species ]]> https://biorxiv.org/content/10.64898/2026.02.18.706700v1?rss=1 Zhang, G. Vincent, E. C. Disselkoen, S. M. Dodds, J. N. DuVal-Smith, Q. Patan, A. Mohanty, I. Deleray, V. Zhang, J. Thiessen, P. A. Bolton, E. E. Schymanski, E. L. Dorrestein, P. C. Theriot, C. M. Baker, E. S. 2026-02-19 doi:10.64898/2026.02.18.706700 Cold Spring Harbor Laboratory Press 2026-02-19 <![CDATA[ Mathematical Modeling of AA Amyloidosis: Coupling SAA-HDL Binding Dynamics with Path-Dependent Renal Aging ]]> https://biorxiv.org/content/10.64898/2026.02.19.706923v1?rss=1 Kuznetsov, A. V. 2026-02-20 doi:10.64898/2026.02.19.706923 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ PFOA induced metabolic and immune perturbations in a SARS-2 infection model ]]> https://biorxiv.org/content/10.64898/2026.02.21.707085v1?rss=1 Lanier, D. N. Rowe Haas, D. Uchimiya, M. Jones, C. Johnson, S. Sakamoto, K. Chappel, J. R. Fry, A. N. Leach, F. E. DeWitt, J. Woodlief, T. Gaul, D. A. Baker, E. S. Fernandez, F. M. Tompkins, S. M. Edison, A. S. 2026-02-23 doi:10.64898/2026.02.21.707085 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ Hierarchical Multi-Omics Trajectory Prediction forFecal Microbiota Transplantation: A Novel MachineLearning Framework for Small-Sample LongitudinalMulti-Omics Integration ]]> https://biorxiv.org/content/10.64898/2026.02.21.707174v1?rss=1 0.7) involving top-predictive biomarkers, demonstrating its utility for both prediction and biological discovery in FMT applications. HMOTP provides a generalizable framework applicable to other small-sample multi-omics problems, offering a powerful tool for personalized medicine applications. Biographical NoteProf. Zhou is an interdisciplinary statistician and machine learning expert whose work develops innovative computational methods for multi-omics integration, biomedical prediction, and precision medicine applications. Key PointsOur novel framework, HMOTP, addresses this challenge through three key innovations: O_LIHierarchical feature construction using domain knowledge - Reduces dimensionality while preserving biological interpretability, unlike PCA-based methods C_LIO_LIMulti-level attention mechanisms - Learns feature importance at multiple biological scales (individual features [->] classes [->] cross-omics interactions) C_LIO_LIPatient-specific trajectory prediction with transfer learning - Enables personalized predictions despite limited sample sizes (parameter-sharing within the cohort, not external pre-training) C_LI ]]> Zhou, Y.-H. Sun, G. 2026-02-23 doi:10.64898/2026.02.21.707174 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ Smoothing over "rough" mismanagement: establishing protective harvest limits for native nongame fishes ]]> https://biorxiv.org/content/10.64898/2026.02.24.707793v1?rss=1 Ginez, A. N. David, S. R. Lackman, A. R. Myers, B. J. Winter, T. J. Lusardi, R. A. Rypel, A. L. 2026-02-26 doi:10.64898/2026.02.24.707793 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ Novel connections between B-vitamins and microbial communities along biogeochemical gradients in a large temperate estuary ]]> https://biorxiv.org/content/10.64898/2026.02.26.707256v1?rss=1 Bittner, M. J. Bannon, C. C. Rowland, E. Luetzenburg, G. Bertrand, E. M. Riemann, L. Paerl, R. W. 2026-02-27 doi:10.64898/2026.02.26.707256 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ Inter-variety competition dynamics in US inbred and hybrid maize ]]> https://biorxiv.org/content/10.64898/2026.02.26.708322v1?rss=1 Schulz, A. J. Bohn, M. O. Bradbury, P. Lima, D. C. De Leon, N. Flint-Garcia, S. Holland, J. B. Lepak, N. Lorenz, A. J. Romay, M. C. Hirsch, C. N. Buckler, E. S. Robbins, K. R. 2026-02-28 doi:10.64898/2026.02.26.708322 Cold Spring Harbor Laboratory Press 2026-02-28 <![CDATA[ Estrogen Receptor Expression Changes After Puberty in the Porcine Anterior Cruciate Ligament ]]> https://biorxiv.org/content/10.64898/2026.03.09.710593v1?rss=1 8 months) female Yorkshire cross-breed pigs (n=6/group) and analyzed using gene expression profiling, western blotting, and immunofluorescence. Pre-pubescent ACLs exhibited greater expression of primary matrix genes (COL1A1, COL1A2, ELN, TNMD), suggesting active matrix synthesis, while post-pubescent ACLs showed elevated secondary matrix genes (COL3A1, LUM, COMP), indicating a homeostatic state. Notably, estrogen receptor alpha (ER) gene and protein expression were significantly greater in post-pubescent ACLs, particularly in AM bundles, whereas G-protein coupled estrogen receptor (GPR30) expression was elevated pre-puberty. Both receptors were distributed homogeneously throughout the tissue. Progesterone receptor protein expression was not detected in any samples. Histologically, post-pubescent ACLs demonstrated decreased cellularity and thicker fascicles compared to pre-pubescent tissues. These findings indicate that ACL sensitivity to estrogen varies across development, with increased ER expression post-puberty potentially rendering the ligament more responsive to circulating estrogen. This work provides foundational evidence for age-dependent hormonal responsiveness in the ACL and motivates further investigation into how sex hormones influence ACL injury risk in adolescent females. ]]> Thompson, J. D. Fisher, M. B. 2026-03-11 doi:10.64898/2026.03.09.710593 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ DEX: a consensus-based amino acid exchangeability measure for improved codon substitution modelling ]]> https://biorxiv.org/content/10.64898/2026.03.09.710665v1?rss=1 Douglas, G. M. Bobay, L.-M. 2026-03-12 doi:10.64898/2026.03.09.710665 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ Digital twins of upright stance reveal mechanistic bifurcations underlying Parkinsonian sway phenotypes ]]> https://biorxiv.org/content/10.64898/2026.03.09.710685v1?rss=1 Matsui, K. Suzuki, Y. Smith, C. E. Nakamura, T. Endo, T. Sakoda, S. Morasso, P. Nomura, T. 2026-03-12 doi:10.64898/2026.03.09.710685 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ Structural and Oligomeric Characterization of Substrate- and Product-selective Nylon Hydrolases ]]> https://biorxiv.org/content/10.64898/2026.03.11.711162v1?rss=1 Capra, N. Bourgery, C. Parks, J. M. Carper, D. L. Cahill, J. F. Michener, J. K. Meilleur, F. 2026-03-12 doi:10.64898/2026.03.11.711162 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ A phase field model with stochastic input simulates cellular gradient sensing, morphodynamics, and fidelity of haptotaxis ]]> https://biorxiv.org/content/10.64898/2026.03.10.710962v1?rss=1 Koelbl, J. M. Haugh, J. M. 2026-03-13 doi:10.64898/2026.03.10.710962 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Route of Adenovirus Type 5-Vectored Influenza Vaccination Shapes Systemic and Mucosal Immunity in a Maternal-Neonatal Pig Model ]]> https://biorxiv.org/content/10.64898/2026.03.12.711389v1?rss=1 Langel, S. N. Byrne, J. J. Leal, D. Williams, A. Sirisereewan, C. Meritet, D. Rahe, M. C. Watanabe, T. T. N. Compton, S. Rajao, D. Ferreira, J. B. Tucker, S. Crisci, E. 2026-03-13 doi:10.64898/2026.03.12.711389 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ The enhanced multi-tissue atlas of regulatory effects in cattle ]]> https://biorxiv.org/content/10.64898/2026.03.18.712441v1?rss=1 Li, H. Zhang, H. Zhu, D. Zhao, P. Wei, Z. Lu, J. Gong, M. Zhang, Q. Zheng, W. Liu, X. GUAN, D. Teng, J. Lin, Q. Tang, Y. Gao, Y. Zhao, S. Zhang, Z. Du, J. Fang, C. An, B. Lin, B. Zhang, H. Tian, M. Tian, J. Chen, S. Liu, W. Wang, Y. Wang, M.-S. Ibeagha-Awemu, E. M. Crooijmans, R. Derks, M. Godia, M. Madsen, O. Pausch, H. Leonard, A. S. Frantz, L. MacHugh, D. E. Grady, J. F. O. Ionita-Laza, I. Zhao, X. Guan, L. Zhou, H. Marmol-Sanchez, E. van der Wijst, M. Lu, X. Jiang, H. Yang, Z. Yang, Q. Liu, Q. Xu, C. Li, M. Hou, Y. Pan, Z. Chen, Y. Xian 2026-03-20 doi:10.64898/2026.03.18.712441 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ DNA Traces on the Shroud of Turin: Metagenomics of the 1978 Official Sample Collection ]]> https://biorxiv.org/content/10.64898/2026.03.19.712852v1?rss=1 Barcaccia, G. Rambaldi Migliore, N. Gabelli, G. Agostini, V. Palumbo, F. Moroni, E. Nicolini, V. Gao, L. Mattutino, G. Porter, A. Palmowski, P. Procopio, N. Perego, U. A. Iorizzo, M. Sharbel, T. F. Baima Bollone, P. Torroni, A. Squartini, A. Achilli, A. 2026-03-22 doi:10.64898/2026.03.19.712852 Cold Spring Harbor Laboratory Press 2026-03-22 <![CDATA[ PhagePickr: A bacteria-centric computational tool for designing evolution-proof phage cocktails ]]> https://biorxiv.org/content/10.64898/2026.03.23.713575v1?rss=1 Oneto, A. Okamoto, K. W. 2026-03-23 doi:10.64898/2026.03.23.713575 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ ZeaMiC: a Publicly Available Culture Collection of Maize Root-Associated Bacteria ]]> https://biorxiv.org/content/10.64898/2026.03.23.713778v1?rss=1 Garrell, A.-K. Ginnan, N. Swift, J. F. Pal, G. Zervas, A. Pestalozzi, C. Tang, C. Tso, F. Ford, N. E. Niu, B. Castrillo, G. Schlaeppi, K. Hahnke, R. L. Wagner, M. R. Kleiner, M. 2026-03-24 doi:10.64898/2026.03.23.713778 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Structured Pooling Improves Detection of Rare Regulatory Mutations in Population-Scale Reporter Assays ]]> https://biorxiv.org/content/10.64898/2026.03.27.714794v1?rss=1 Dura, K. Siklenka, K. Strouse, K. P. Morrow, S. Zhang, C. Barrera, A. Allen, A. S. Reddy, T. E. Majoros, W. H. 2026-03-31 doi:10.64898/2026.03.27.714794 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ The geometry of dominance shows broad potential for stable polymorphism under antagonistic pleiotropy ]]> https://biorxiv.org/content/10.64898/2026.03.27.714876v1?rss=1 Brud, E. Guerrero, R. F. 2026-03-31 doi:10.64898/2026.03.27.714876 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Discovering Plastic-Binding Peptides with Favorable Affinity, Water Solubility, and Binding Specificity Through Deep Learning and Biophysical Modeling ]]> https://biorxiv.org/content/10.64898/2026.03.30.715295v1?rss=1 Tan, T. Bergman, M. Hall, C. K. You, F. 2026-04-01 doi:10.64898/2026.03.30.715295 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ TrIdent - An R package to automate transductomics analysis of virus-like particle mediated DNA mobilization ]]> https://biorxiv.org/content/10.64898/2026.03.31.715651v1?rss=1 Maier, J. Gin, C. Rabasco, J. Spencer, W. Bass, A. Duerkop, B. A. 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