bioRxiv Channel: Iowa State University https://biorxiv.org This feed contains articles for bioRxiv Channel "Iowa State University" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Natural variation in teosinte at the domestication locus teosinte branched1 (tb1) ]]> https://biorxiv.org/content/10.1101/005819v1?rss=1 Laura Vann Thomas Kono Tanja Pyha ̈j ̈arvi Matthew B Hufford Jeffrey Ross-Ibarra 2014-06-03 doi:10.1101/005819 Cold Spring Harbor Laboratory Press 2014-06-03 <![CDATA[ Gene regulatory network inference from perturbed time-series expression data via ordered dynamical expansion of non-steady state actors ]]> https://biorxiv.org/content/10.1101/007906v1?rss=1 Mahdi Zamanighomi Mostafa Zamanian Michael J Kimber Zhengdao Wang 2014-09-29 doi:10.1101/007906 Cold Spring Harbor Laboratory Press 2014-09-29 <![CDATA[ When Less is More: "Slicing" Sequencing Data Improves Read Decoding Accuracy and De Novo Assembly Quality ]]> https://biorxiv.org/content/10.1101/013425v1?rss=1 Stefano Lonardi Hamid Mirebrahim Steve Wanamaker Matthew Alpert Gianfranco Ciardo Denisa Duma Timothy J Close 2015-01-03 doi:10.1101/013425 Cold Spring Harbor Laboratory Press 2015-01-03 <![CDATA[ The origin and evolution of maize in the American Southwest ]]> https://biorxiv.org/content/10.1101/013540v1?rss=1 Rute R da Fonseca Bruce D Smith Nathan Wales Enrico Cappellini Pontus Skoglund Matteo Fumagalli José Alfredo Samaniego Christian Carøe María C Ávila-Arcos David E Hufnagel Thorfinn Sand Korneliussen Filipe Garrett Vieira Mattias Jakobsson Bernardo Arriaza Eske Willerslev Rasmus Nielsen Matthew B Hufford Anders Albrechtsen Jeffrey Ross-Ibarra M Thomas P Gilbert 2015-01-11 doi:10.1101/013540 Cold Spring Harbor Laboratory Press 2015-01-11 <![CDATA[ Independent molecular basis of convergent highland adaptation in maize ]]> https://biorxiv.org/content/10.1101/013607v1?rss=1 Shohei Takuno Peter Ralph Kelly Swarts Rob J Elshire Jeffrey C Glaubitz Edward S. Buckler Matthew B Hufford Jeffrey Ross-Ibarra 2015-01-09 doi:10.1101/013607 Cold Spring Harbor Laboratory Press 2015-01-09 <![CDATA[ RNA-seq: primary cells, cell lines and heat stress ]]> https://biorxiv.org/content/10.1101/013979v1?rss=1 Carl J Schmdt Elizabeth M Pritchett Liang Sun Richard V.N. Davis Allen Hubbard Kalmia E Kniel Sarah M Markland Qing Wang Chris Ashwell Michael Persia Max F. Rothschild Susan J. Lamont 2015-01-19 doi:10.1101/013979 Cold Spring Harbor Laboratory Press 2015-01-19 <![CDATA[ Sequencing of 15,622 gene-bearing BACs reveals new features of the barley genome ]]> https://biorxiv.org/content/10.1101/018978v1?rss=1 María Muñoz-Amatriaín Stefano Lonardi MingCheng Luo Kavitha Madishetty Jan Svensson Matthew Moscou Steve Wanamaker Tao Jiang Andris Kleinhofs Gary Muehlbauer Roger Wise Nils Stein Yaqin Ma Edmundo Rodriguez Dave Kudrna Prasanna R Bhat Shiaoman Chao Pascal Condamine Shane Heinen Josh Resnik Rod Wing Heather N Witt Matthew Alpert Marco Beccuti Serdar Bozdag Francesca Cordero Hamid Mirebrahim Rachid Ounit Yonghui Wu Frank You Jie Zheng Hana Šimková Jaroslav Doležel Jane Grimwood Jeremy Schmutz Denisa Duma Lothar Altschmied Tom Blake Phil Bregitzer Laurel Cooper Muharrem Dilbirligi Anders Falk Lei 2015-05-05 doi:10.1101/018978 Cold Spring Harbor Laboratory Press 2015-05-05 <![CDATA[ Pollen contaminated with field-relevant levels of cyhalothrin affects honey bee survival, nutritional physiology, and pollen consumption behavior ]]> https://biorxiv.org/content/10.1101/025189v1?rss=1 Adam G Dolezal Jimena Carrillo-Tripp Wyatt Allen Miller Bryony B Bonning Amy L Toth 2015-08-21 doi:10.1101/025189 Cold Spring Harbor Laboratory Press 2015-08-21 <![CDATA[ Crop diversity enhances disease suppressive potential in soils ]]> https://biorxiv.org/content/10.1101/030528v1?rss=1 Ariane L Peralta Yanmei Sun Marshall D McDaniel Jay T Lennon 2015-11-04 doi:10.1101/030528 Cold Spring Harbor Laboratory Press 2015-11-04 <![CDATA[ Recent demography drives changes in linked selection across the maize genome ]]> https://biorxiv.org/content/10.1101/031666v1?rss=1 Timothy Mathes Beissinger Li Wang Kate Crosby Arun Durvasula Matthew B Hufford Jeff Ross-Ibarra 2015-11-13 doi:10.1101/031666 Cold Spring Harbor Laboratory Press 2015-11-13 <![CDATA[ Strawberry: fast and accurate genome-guided transcript reconstruction and quantification from RNA-seq ]]> https://biorxiv.org/content/10.1101/043802v1?rss=1 Ruolin Liu Julie Dickerson 2016-03-16 doi:10.1101/043802 Cold Spring Harbor Laboratory Press 2016-03-16 <![CDATA[ Hierarchical Association Coefficient Algorithm ]]> https://biorxiv.org/content/10.1101/043844v1?rss=1 Bongsong Kim 2016-03-15 doi:10.1101/043844 Cold Spring Harbor Laboratory Press 2016-03-15 <![CDATA[ Evaluation of a Computational Diagnostic for Epistasis in Plant Breeding Populations ]]> https://biorxiv.org/content/10.1101/044453v1?rss=1 Reka Howard William D Beavis Alicia Carriquiry 2016-03-17 doi:10.1101/044453 Cold Spring Harbor Laboratory Press 2016-03-17 <![CDATA[ Inferring node dates from tip dates in fossil Canidae: the importance of tree priors ]]> https://biorxiv.org/content/10.1101/049643v1?rss=1 Nicholas Joseph Matzke April Wright 2016-04-21 doi:10.1101/049643 Cold Spring Harbor Laboratory Press 2016-04-21 <![CDATA[ The last common ancestor of most bilaterian animals possessed at least 9 opsins ]]> https://biorxiv.org/content/10.1101/052902v1?rss=1 M Desmond Ramirez Autum N Pairett M Sabrina Pankey Jeanne M Serb Daniel I Speiser Andrew J Swafford Todd H. Oakley 2016-05-13 doi:10.1101/052902 Cold Spring Harbor Laboratory Press 2016-05-13 <![CDATA[ RefSoil: A reference database of soil microbial genomes ]]> https://biorxiv.org/content/10.1101/053397v1?rss=1 Jinlyung Choi Fan Yang Ramunas Stepanauskas Erick Cardenas Aaron Garoutte Ryan Williams Jared Flater James M Tiedje Kirsten S. Hofmockel Brian Gelder Adina Howe 2016-05-14 doi:10.1101/053397 Cold Spring Harbor Laboratory Press 2016-05-14 <![CDATA[ Tissue-Driven Hypothesis of Transcriptome Evolution: An Update ]]> https://biorxiv.org/content/10.1101/054890v1?rss=1 Howard T. Hallmark Jeffrey A. Haltom Xun Gu 2016-05-24 doi:10.1101/054890 Cold Spring Harbor Laboratory Press 2016-05-24 <![CDATA[ Fungal Induced Protein Hyperacetylation Identified by Acetylome Profiling ]]> https://biorxiv.org/content/10.1101/057174v1?rss=1 Justin W Walley Zhouxin Shen Maxwell R McReynolds Steven P Briggs 2016-06-05 doi:10.1101/057174 Cold Spring Harbor Laboratory Press 2016-06-05 <![CDATA[ S2 from Equine infectious anemia virus is an infectivity factor which counteracts the retroviral inhibitors SERINC5 and SERINC3 ]]> https://biorxiv.org/content/10.1101/065078v1?rss=1 Ajit Chande Emilia Cuccurullo Annachiara Rosa Serena Ziglio Susan Carpenter Massimo Pizzato 2016-07-21 doi:10.1101/065078 Cold Spring Harbor Laboratory Press 2016-07-21 <![CDATA[ Numericware i: Identical in state matrix calculator ]]> https://biorxiv.org/content/10.1101/075267v1?rss=1 Bongsong Kim William D Beavis 2016-09-14 doi:10.1101/075267 Cold Spring Harbor Laboratory Press 2016-09-14 <![CDATA[ Case study: Paralog diverged features may help reduce off-target effects of drugs ]]> https://biorxiv.org/content/10.1101/078063v1?rss=1 Zhining Sa Jingqi Zou Yangyun Zou Xun Gu 2016-09-28 doi:10.1101/078063 Cold Spring Harbor Laboratory Press 2016-09-28 <![CDATA[ The accuracy and bias of single-step genomic prediction for populationsunder selection ]]> https://biorxiv.org/content/10.1101/090274v1?rss=1 Hsu, W.-L. Garrick, D. J. Fernando, R. L. 2016-11-28 doi:10.1101/090274 Cold Spring Harbor Laboratory Press 2016-11-28 <![CDATA[ Tunable Genotyping-By-Sequencing (tGBS(R)) Enables Reliable Genotyping of Heterozygous Loci ]]> https://biorxiv.org/content/10.1101/100461v1?rss=1 97-99%) even for heterozygous sites and less missing data per marker. tGBS genotyping is expected to be particularly useful for genomic selection, which requires the ability to genotype populations of individuals that are heterozygous at many loci. ]]> Ott, A. Liu, S. Schnable, J. C. Yeh, C.-T. Wang, C. Schnable, P. S. 2017-01-15 doi:10.1101/100461 Cold Spring Harbor Laboratory Press 2017-01-15 <![CDATA[ Transposons modulate transcriptomic and phenotypic variation via the formation of circular RNAs in maize ]]> https://biorxiv.org/content/10.1101/100578v1?rss=1 Chen, L. Zhang, P. Fan, Y. Huang, J. Lu, Q. Li, Q. Yan, J. Muehlbauer, G. J. Schnable, P. S. Dai, M. Li, L. 2017-01-15 doi:10.1101/100578 Cold Spring Harbor Laboratory Press 2017-01-15 <![CDATA[ Multiple-trait Bayesian Regression Methods with Mixture Priors for Genomic Prediction ]]> https://biorxiv.org/content/10.1101/102962v1?rss=1 CHENG, H. Kizilkaya, K. Zeng, J. Garrick, D. Fernando, R. 2017-01-25 doi:10.1101/102962 Cold Spring Harbor Laboratory Press 2017-01-25 <![CDATA[ The Potential Role of Genetic Assimilation during Maize Domestication ]]> https://biorxiv.org/content/10.1101/105940v1?rss=1 Lorant, A. Perdersen, S. Holst, I. Hufford, M. B. Winter, K. Piperno, D. Ross-Ibarra, J. 2017-02-03 doi:10.1101/105940 Cold Spring Harbor Laboratory Press 2017-02-03 <![CDATA[ The interplay of demography and selection during maize domestication and expansion ]]> https://biorxiv.org/content/10.1101/114579v1?rss=1 Wang, L. Beissinger, T. M. Lorant, A. Ross-Ibarra, C. Ross-Ibarra, J. Hufford, M. 2017-03-07 doi:10.1101/114579 Cold Spring Harbor Laboratory Press 2017-03-07 <![CDATA[ Colonization History Of The Western Corn Rootworm (Diabrotica virgifera virgifera) In North America: Insights From Random Forest ABC Using Microsatellite Data ]]> https://biorxiv.org/content/10.1101/117424v1?rss=1 Lombaert, E. Ciosi, M. Miller, N. J. Sappington, T. W. Blin, A. Guillemaud, T. 2017-03-16 doi:10.1101/117424 Cold Spring Harbor Laboratory Press 2017-03-16 <![CDATA[ Transcriptome sequencing and delimitation of cryptic Oscarella species (O. carmela and O. pearsei sp. nov) from California, USA. ]]> https://biorxiv.org/content/10.1101/126326v1?rss=1 Ereskovsky, A. Richter, D. J. Lavrov, D. V. Schippers, K. J. Nichols, S. A. 2017-04-11 doi:10.1101/126326 Cold Spring Harbor Laboratory Press 2017-04-11 <![CDATA[ Genotype-by-Environment Interactions Affecting Heterosis in Maize ]]> https://biorxiv.org/content/10.1101/131342v1?rss=1 Li, Z. Coffey, L. Garfin, J. Miller, N. D. White, M. R. Spalding, E. P. Leon, N. d. Kaeppler, S. M. Schnable, P. S. Springer, N. M. Hirsch, C. N. 2017-04-26 doi:10.1101/131342 Cold Spring Harbor Laboratory Press 2017-04-26 <![CDATA[ A Method To Assess Significance Of Differences In RNA Expression Levels Among Specific Groups Of Genes ]]> https://biorxiv.org/content/10.1101/136143v1?rss=1 He, M. Liu, P. Lawrence-Dill, C. J. 2017-05-09 doi:10.1101/136143 Cold Spring Harbor Laboratory Press 2017-05-09 <![CDATA[ Heart-Specific Activin Signaling Promotes Cardiomyopathy And Organismal Aging Through Autophagy Inhibition ]]> https://biorxiv.org/content/10.1101/139360v1?rss=1 Chang, K. Kang, P. Liu, Y. Huang, K. Taylor, E. Bodmer, R. Ocorr, K. Bai, H. 2017-05-31 doi:10.1101/139360 Cold Spring Harbor Laboratory Press 2017-05-31 <![CDATA[ Parallel Computing to Speed up Whole-Genome Bayesian Regression Analyses Using Orthogonal Data Augmentation ]]> https://biorxiv.org/content/10.1101/148965v1?rss=1 Cheng, H. Fernando, R. Garrick, D. 2017-06-12 doi:10.1101/148965 Cold Spring Harbor Laboratory Press 2017-06-12 <![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[ Toward A Scalable Exploratory Framework for Complex High-Dimensional Phenomics Data ]]> https://biorxiv.org/content/10.1101/159954v1?rss=1 Kamruzzaman, M. Kalyanaraman, A. Krishnamoorthy, B. Schnable, P. S. 2017-07-05 doi:10.1101/159954 Cold Spring Harbor Laboratory Press 2017-07-05 <![CDATA[ Drosophila Kruppel homolog 1 represses lipolysis through interaction with dFOXO ]]> https://biorxiv.org/content/10.1101/165456v1?rss=1 Kang, P. Chang, K. Liu, Y. Bousk, M. Karashchuk, G. Thakore, R. Zheng, W. Post, S. Brent, C. Li, S. Tatar, M. Bai, H. 2017-07-18 doi:10.1101/165456 Cold Spring Harbor Laboratory Press 2017-07-18 <![CDATA[ Mammalian Orthoreovirus Factories Modulate Stress Granule Protein Localization by Interaction with G3BP1 ]]> https://biorxiv.org/content/10.1101/169433v1?rss=1 Choudhury, P. Bussiere, L. Miller, C. L. 2017-07-28 doi:10.1101/169433 Cold Spring Harbor Laboratory Press 2017-07-28 <![CDATA[ Characterization of a replicating mammalian orthoreovirus with tetracysteine tagged μNS for live cell visualization of viral factories ]]> https://biorxiv.org/content/10.1101/174235v1?rss=1 Bussiere, L. Choudhury, P. Bellaire, B. Miller, C. L. 2017-08-09 doi:10.1101/174235 Cold Spring Harbor Laboratory Press 2017-08-09 <![CDATA[ A gut pathobiont synergizes with the microbiota to instigate inflammatory disease marked by immunoreactivity against other symbionts but not itself ]]> https://biorxiv.org/content/10.1101/178038v1?rss=1 Gomes-Neto, J. C. Kittana, H. Mantz, S. Segura Munoz, R. R. Schmaltz, R. J. Bindels, L. B. Clarke, J. Hostetter, J. M. Benson, A. K. Walter, J. Ramer-Tait, A. E. 2017-08-18 doi:10.1101/178038 Cold Spring Harbor Laboratory Press 2017-08-18 <![CDATA[ Impaired phloem loading in genome-edited triple knock-out mutants of SWEET13 sucrose transporters ]]> https://biorxiv.org/content/10.1101/197921v1?rss=1 Frommer, W. Bezrutczyk, M. Hartwig, T. Horschman, M. Char, S. N. Yang, J. Yang, B. Sosso, D. 2017-10-03 doi:10.1101/197921 Cold Spring Harbor Laboratory Press 2017-10-03 <![CDATA[ SWEET11 and 15 as key players in seed filling in rice ]]> https://biorxiv.org/content/10.1101/198325v1?rss=1 Yang, J. Luo, D. Yang, B. Frommer, W. Eom, J.-S. 2017-10-04 doi:10.1101/198325 Cold Spring Harbor Laboratory Press 2017-10-04 <![CDATA[ Continuous interdomain orientation distributions reveal components of binding thermodynamics ]]> https://biorxiv.org/content/10.1101/200238v1?rss=1 Qi, Y. Martin, J. W. Barb, A. W. Thelot, F. Yan, A. Donald, B. R. Oas, T. G. 2017-10-11 doi:10.1101/200238 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ Genetic characterization of Streptococcus equi subspecies zooepidemicus associated with high swine mortality in United States ]]> https://biorxiv.org/content/10.1101/2019.12.12.874644v1?rss=1 Chen, X. Resende-De-Macedo, N. Sitthicharoenchai, P. Sahin, O. Burrough, E. Clavijo, M. Derscheid, R. Schwartz, K. Lantz, K. Robbe-Austerman, S. Main, R. Li, G. 2019-12-12 doi:10.1101/2019.12.12.874644 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ Hierarchical Markov Random Field model captures spatial dependency in gene expression, demonstrating regulation via the 3D genome ]]> https://biorxiv.org/content/10.1101/2019.12.16.878371v1?rss=1 Zhou, N. Friedberg, I. Kaiser, M. S. 2019-12-17 doi:10.1101/2019.12.16.878371 Cold Spring Harbor Laboratory Press 2019-12-17 <![CDATA[ Homoeologous gene expression and co-expression network analyses and evolutionary inference in allopolyploids ]]> https://biorxiv.org/content/10.1101/2019.12.16.878900v1?rss=1 Hu, G. Grover, C. Arick, M. A. Liu, M. Peterson, D. Wendel, J. 2019-12-17 doi:10.1101/2019.12.16.878900 Cold Spring Harbor Laboratory Press 2019-12-17 <![CDATA[ Maximizing prediction of orphan genes in assembled genomes ]]> https://biorxiv.org/content/10.1101/2019.12.17.880294v1?rss=1 Seetharam, A. S. Singh, U. Li, J. Bhandary, P. Arendsee, Z. Wurtele, E. S. 2019-12-18 doi:10.1101/2019.12.17.880294 Cold Spring Harbor Laboratory Press 2019-12-18 <![CDATA[ One-Pot E. coli Cell-Free Extract for in vitro Expression of Disulfide Bonded Proteins ]]> https://biorxiv.org/content/10.1101/2019.12.19.883413v1?rss=1 Dopp, J. L. Reuel, N. F. 2019-12-20 doi:10.1101/2019.12.19.883413 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ rMSIcleanup: An open-source tool for matrix-related peak annotation in mass spectrometry imaging and its application to silver-assisted laser desorption/ionization ]]> https://biorxiv.org/content/10.1101/2019.12.20.884957v1?rss=1 Baquer, G. Semente, L. Garcia-Altares, M. Lee, Y. J. Chaurand, P. Correig, X. Rafols, P. 2019-12-23 doi:10.1101/2019.12.20.884957 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ Identifying Core Operons in Metagenomic Data ]]> https://biorxiv.org/content/10.1101/2019.12.20.885269v1?rss=1 Hu, X. Friedberg, I. 2019-12-21 doi:10.1101/2019.12.20.885269 Cold Spring Harbor Laboratory Press 2019-12-21 <![CDATA[ Small non-coding RNA CjNC110 influences motility, autoagglutination, AI-2 localization, and chicken colonization in Campylobacter jejuni ]]> https://biorxiv.org/content/10.1101/2020.01.02.893479v1?rss=1 Kreuder, A. J. Ruddell, B. Mou, K. Hassall, A. Zhang, Q. Plummer, P. J. 2020-01-03 doi:10.1101/2020.01.02.893479 Cold Spring Harbor Laboratory Press 2020-01-03 <![CDATA[ Dual-localized enzymatic components that constitute the mitochondrial and plastidial fatty acid synthase systems ]]> https://biorxiv.org/content/10.1101/2020.01.03.894386v1?rss=1 Guan, X. Okazaki, Y. Zhang, R. Saito, K. Nikolau, B. J. 2020-01-03 doi:10.1101/2020.01.03.894386 Cold Spring Harbor Laboratory Press 2020-01-03 <![CDATA[ siRNA-mediated de novo silencing of Ac/Ds transposons is initiated by alternative transposition in maize ]]> https://biorxiv.org/content/10.1101/2020.01.07.897926v1?rss=1 Wang, D. Zhang, J. Zuo, T. Lisch, D. Zhao, M. Peterson, T. 2020-01-08 doi:10.1101/2020.01.07.897926 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Multi-scalar Approaches to the stable isotope ecology of late Quaternary Proboscideans in the Midcontinent ]]> https://biorxiv.org/content/10.1101/2020.01.08.896647v1?rss=1 Widga, C. Hodgins, G. Kolis, K. Lengyel, S. N. Saunders, J. J. Walker, J. D. Wanamaker, A. D. 2020-01-09 doi:10.1101/2020.01.08.896647 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ The RNA of maize chlorotic mottle virus - the essential virus in maize lethal necrosis disease - is translated via a panicum mosaic virus-like cap-independent translation element ]]> https://biorxiv.org/content/10.1101/2020.01.08.898825v1?rss=1 Carino, E. J. Scheets, K. Miller, W. A. 2020-01-09 doi:10.1101/2020.01.08.898825 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ The Gossypium longicalyx genome as a resource for cotton breeding and evolution ]]> https://biorxiv.org/content/10.1101/2020.01.08.898908v1?rss=1 Grover, C. E. Pan, M. Yuan, D. Arick, M. A. Hu, G. Brase, L. Stelly, D. M. Lu, Z. Schmitz, R. J. Peterson, D. G. Wendel, J. F. Udall, J. A. 2020-01-09 doi:10.1101/2020.01.08.898908 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Phase Transition of RNA-protein Complexes into Ordered Hollow Condensates ]]> https://biorxiv.org/content/10.1101/2020.01.10.902353v1?rss=1 Alshareedah, I. Moosa, M. M. Raju, M. Potoyan, D. A. Banerjee, P. R. 2020-01-12 doi:10.1101/2020.01.10.902353 Cold Spring Harbor Laboratory Press 2020-01-12 <![CDATA[ A New Model of Genetic Variation and Evolution Evaluates Relative Impacts of Background Selections and Selective Sweeps ]]> https://biorxiv.org/content/10.1101/2020.01.11.901066v1?rss=1 Gu, X. 2020-01-14 doi:10.1101/2020.01.11.901066 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Ignoring fossil age uncertainty leads to inaccurate topology and divergence times in time calibrated tree inference ]]> https://biorxiv.org/content/10.1101/2020.01.14.906107v1?rss=1 Barido-Sottani, J. van Tiel, N. Hopkins, M. J. Wright, D. F. Stadler, T. Warnock, R. C. 2020-01-15 doi:10.1101/2020.01.14.906107 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Gapless assembly of maize chromosomes using long read technologies ]]> https://biorxiv.org/content/10.1101/2020.01.14.906230v1?rss=1 Dawe, K. Liu, J. Seetharam, A. S. Chougule, K. Ou, S. Swentowsky, K. W. Gent, J. I. Llaca, V. Woodhouse, M. Manchanda, N. Presting, G. G. Kudrna, D. Alabady, M. Hirsch, C. Fengler, K. Ware, D. Michael, T. Hufford, M. 2020-01-15 doi:10.1101/2020.01.14.906230 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ A metabolomics study of ascorbic acid-induced in situ freezing tolerance in spinach (Spinacia oleracea L.) ]]> https://biorxiv.org/content/10.1101/2020.01.23.916973v1?rss=1 Arora, R. Min, K. Chen, K. 2020-01-24 doi:10.1101/2020.01.23.916973 Cold Spring Harbor Laboratory Press 2020-01-24 <![CDATA[ Low ribosomal RNA genes copy number provoke genomic instability and chromosomal segment duplication events that modify global gene expression and plant-pathogen response ]]> https://biorxiv.org/content/10.1101/2020.01.24.917823v1?rss=1 Picart-Picolo, A. Grob, S. Picault, N. Franek, M. Halter, T. Maier, T. R. Llauro, C. Jobet, E. Zhang, P. Vijayapalani, P. Baum, T. J. Navarro, L. Dvorackova, M. Mirouze, M. Pontvianne, F. 2020-01-25 doi:10.1101/2020.01.24.917823 Cold Spring Harbor Laboratory Press 2020-01-25 <![CDATA[ Tandem tension sensor reveals substrate rigidity-dependence of integrin molecular tensions in live cells ]]> https://biorxiv.org/content/10.1101/2020.01.24.918946v1?rss=1 Sarkar, A. LeVine, D. Zhao, Y. Mollaeian, K. Ren, J. Wang, X. 2020-01-24 doi:10.1101/2020.01.24.918946 Cold Spring Harbor Laboratory Press 2020-01-24 <![CDATA[ Modulation of plant Acetyl CoA Synthetase activity by acetylation ]]> https://biorxiv.org/content/10.1101/2020.01.31.928937v1?rss=1 Sofeo, N. Leung, K. Nikolau, B. J. 2020-02-04 doi:10.1101/2020.01.31.928937 Cold Spring Harbor Laboratory Press 2020-02-04 <![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[ Tracing Evolutionary Ages of Cancer-Driving Sites by Cancer Somatic Mutations ]]> https://biorxiv.org/content/10.1101/2020.02.09.940528v1?rss=1 Gu, X. Zhou, Z. Yang, J. 2020-02-10 doi:10.1101/2020.02.09.940528 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ Factors affecting Response to Recurrent Genomic Selection in Soybeans ]]> https://biorxiv.org/content/10.1101/2020.02.14.949008v1?rss=1 Ramasubramanian, V. Beavis, W. D. 2020-02-14 doi:10.1101/2020.02.14.949008 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ Functional principal component based time-series genome-wide association in sorghum ]]> https://biorxiv.org/content/10.1101/2020.02.16.951467v1?rss=1 Miao, C. Xu, Y. Liu, S. Schnable, P. S. Schnable, J. C. 2020-02-17 doi:10.1101/2020.02.16.951467 Cold Spring Harbor Laboratory Press 2020-02-17 <![CDATA[ Structure and immune recognition of the porcine epidemic diarrhea virus spike protein ]]> https://biorxiv.org/content/10.1101/2020.02.18.955195v1?rss=1 Kirchdoerfer, R. Bhandari, M. Martini, O. Sewell, L. M. Bangaru, S. Yoon, K.-J. Ward, A. 2020-02-19 doi:10.1101/2020.02.18.955195 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Δ-dN/dS: New Criteria to Distinguish among Different Selection Modes in Gene Evolution ]]> https://biorxiv.org/content/10.1101/2020.02.21.960450v1?rss=1 1 statistically significantly. However, due to selective constraints imposed on amino acid sites, most encoding genes demonstrate dN/dS<1. As a result, dN/dS of a gene is less than 1, even some sites may have experienced positive selections. In this paper, we develop a new criterion, called{Delta} -dN/dS, for positive selection testing by introducing an index H, which is a relative measure of rate variation among sites. Under the context of strong purifying selection at some amino acid sites, our model predicts dN/dS=1-H for the neutral evolution, dN/dS<1-H for the nearly-neutral selection, and dN/dS>1-H for the adaptive evolution. The potential of this new method for resolving the neutral-adaptive debates has been illustrated by case studies. For over 4000 vertebrate genes, virtually all of them showed dN/dS<1-H, indicating the dominant role of the nearly-neutral selection in molecular evolution. Moreover, we calculated the dN/dS ratio for cancer somatic mutations of a human gene, specifically denoted by CN/CS. For over 4000 human genes in cancer genomics, about 55% of genes showed 1-H1 (strong positive selection) or 1-H gu, x. 2020-02-23 doi:10.1101/2020.02.21.960450 Cold Spring Harbor Laboratory Press 2020-02-23 <![CDATA[ A Sequence-Pair-Classification-Based Method For Detecting And Correcting Under-Clustered Gene Families ]]> https://biorxiv.org/content/10.1101/2020.02.22.942557v1?rss=1 Yadav, A. Fernandez-Baca, D. Cannon, S. B. 2020-02-23 doi:10.1101/2020.02.22.942557 Cold Spring Harbor Laboratory Press 2020-02-23 <![CDATA[ AmpliCI: A High-resolution Model-Based Approach for Denoising Illumina Amplicon Data ]]> https://biorxiv.org/content/10.1101/2020.02.23.961227v1?rss=1 Peng, X. Dorman, K. S. 2020-02-25 doi:10.1101/2020.02.23.961227 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Genomic Prediction with Genotype by Environment Interaction Analysis for Kernel Zinc Concentration in Tropical Maize Germplasm ]]> https://biorxiv.org/content/10.1101/2020.02.24.963090v1?rss=1 Lee, M. Mageto, E. K. Crossa, J. Perez-Rodriguez, P. Dhliwayo, T. Palacios, N. Guo, R. Zhang, X. San Vicente, F. Vemuri, H. 2020-02-26 doi:10.1101/2020.02.24.963090 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ Evaluation of the functional role of the maize Glossy2 and Glossy2-like genes in cuticular lipid deposition ]]> https://biorxiv.org/content/10.1101/2020.02.27.968321v1?rss=1 Alexander, L. E. Okazaki, Y. Schelling, M. A. Davis, A. Zheng, X. Rizhsky, L. Yandeau-Nelson, M. Saito, K. Nikolau, B. J. 2020-02-27 doi:10.1101/2020.02.27.968321 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ pyrpipe: a python package for RNA-Seq workflows ]]> https://biorxiv.org/content/10.1101/2020.03.04.925818v1?rss=1 Singh, U. Li, J. Seetharam, A. S. Wurtele, E. S. 2020-03-08 doi:10.1101/2020.03.04.925818 Cold Spring Harbor Laboratory Press 2020-03-08 <![CDATA[ Intraepithelial T cells diverge by intestinal location as pigs age ]]> https://biorxiv.org/content/10.1101/2020.03.05.973248v1?rss=1 78% of total IETs at all intestinal locations and ages examined. Greater percentages of {gamma}{delta} IETs were present in large intestine compared to small intestine in older pigs. Small intestinal tissues had greater percentages of CD2+CD8- {gamma}{delta} IETs, while CD2+CD8+ {gamma}{delta} IET percentages were greater in the large intestine. Percentages of CD4-CD8+ {beta} IETs increased over time across all intestinal sites. Moreover, percentages of CD27+ cells decreased in ileum and large intestine over time, indicating increased IET activation as pigs aged. Percentages of CD27+ cells were also higher in small intestine compared to large intestine at later timepoints. Results herein emphasize 4 to 8 weeks of age as a critical window of IET maturation and suggest strong associations between intestinal location and age with IET heterogeneity in pigs. ]]> Wiarda, J. E. Trachsel, J. M. Bond, Z. F. Byrne, K. A. Gabler, N. K. Loving, C. L. 2020-03-06 doi:10.1101/2020.03.05.973248 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ Evolutionary Distance of Gene-Gene Interactions: Estimation under Statistical Uncertainty ]]> https://biorxiv.org/content/10.1101/2020.03.08.982710v1?rss=1 Gu, X. 2020-03-09 doi:10.1101/2020.03.08.982710 Cold Spring Harbor Laboratory Press 2020-03-09 <![CDATA[ Dynamic Behaviors of Expression Compensation between Duplicate Genes ]]> https://biorxiv.org/content/10.1101/2020.03.10.986166v1?rss=1 Gu, X. 2020-03-11 doi:10.1101/2020.03.10.986166 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Distinguish between Duplication of Essential Genes and Duplication of Dispensable Genes ]]> https://biorxiv.org/content/10.1101/2020.03.10.986257v1?rss=1 Gu, X. 2020-03-11 doi:10.1101/2020.03.10.986257 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement ]]> https://biorxiv.org/content/10.1101/2020.03.21.001396v1?rss=1 Badaczewska-Dawid, A. Kmiecik, S. Kolinski, M. 2020-03-23 doi:10.1101/2020.03.21.001396 Cold Spring Harbor Laboratory Press 2020-03-23 <![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[ The effects of soil depth on the structure of microbial communities in agricultural soils in Iowa, USA ]]> https://biorxiv.org/content/10.1101/2020.03.31.018416v1?rss=1 Hao, J. Chai, Y. N. Ordonez, R. A. Wright, E. E. Archontoulis, S. Schachtman, D. 2020-03-31 doi:10.1101/2020.03.31.018416 Cold Spring Harbor Laboratory Press 2020-03-31 <![CDATA[ Widespread imprinting of transposable elements and young genes in the maize endosperm ]]> https://biorxiv.org/content/10.1101/2020.04.08.032573v1?rss=1 Anderson, S. N. Zhou, P. Higgins, K. Brandvain, Y. Springer, N. M. 2020-04-09 doi:10.1101/2020.04.08.032573 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ A Statistical Framework for Evolutionary Analysis of Recurrent Somatic Mutations in Cancers ]]> https://biorxiv.org/content/10.1101/2020.04.10.036095v1?rss=1 Gu, X. 2020-04-13 doi:10.1101/2020.04.10.036095 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ FOXO regulates neuromuscular junction homeostasis during Drosophila aging ]]> https://biorxiv.org/content/10.1101/2020.04.13.040121v1?rss=1 Birnbaum, A. Chang, K. Bai, H. 2020-04-14 doi:10.1101/2020.04.13.040121 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Maternally administered naltrexone and its major active metabolite 6β-naltrexol transport across the placental barrier in vitro ]]> https://biorxiv.org/content/10.1101/2020.04.16.045229v1?rss=1 Pemathilaka, R. L. Reynolds, D. E. Hashemi, N. N. 2020-04-18 doi:10.1101/2020.04.16.045229 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ An in silico map of the SARS-CoV-2 RNA Structurome ]]> https://biorxiv.org/content/10.1101/2020.04.17.045161v1?rss=1 Andrews, R. J. Peterson, J. M. Haniff, H. F. Chen, J. Williams, C. Greffe, M. Disney, M. D. Moss, W. N. 2020-04-18 doi:10.1101/2020.04.17.045161 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Genotypic characterization of the U.S. peanut core collection ]]> https://biorxiv.org/content/10.1101/2020.04.17.047019v1?rss=1 Otyama, P. I. Kulkarni, R. Chamberlin, K. Ozias-Akins, P. K. Chu, J. Lincoln, L. M. MacDonald, G. E. Anglin, N. L. Dash, S. Bertioli, D. Fernandez-Baca, D. F. Graham, M. A. Cannon, S. B. Cannon, E. K. 2020-04-18 doi:10.1101/2020.04.17.047019 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Transfer learning improves antibiotic resistance class prediction ]]> https://biorxiv.org/content/10.1101/2020.04.17.047316v1?rss=1 Hamid, M. N. Friedberg, I. 2020-04-18 doi:10.1101/2020.04.17.047316 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ The draft genome sequence of herbaceous diploid bamboo Raddia distichophylla ]]> https://biorxiv.org/content/10.1101/2020.04.27.064089v1?rss=1 Li, W. Shi, C. Li, K. Zhang, Q. Tong, Y. Zhang, Y. Wang, J. Clark, L. Gao, L.-z. 2020-04-29 doi:10.1101/2020.04.27.064089 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ Biochemically diverse CRISPR-Cas9 orthologs ]]> https://biorxiv.org/content/10.1101/2020.04.29.066654v1?rss=1 Gasiunas, G. Young, J. K. Karvelis, T. Kazlauskas, D. Urbaitis, T. Jasnauskaite, M. Grusyte, M. Paulraj, S. Wang, P.-H. Hou, Z. Dooley, S. K. Cigan, M. Alarcon, C. Chilcoat, N. D. Bigelyte, G. Curcuru, J. L. Mabuchi, M. Sun, Z. Fuchs, R. T. Schildkraut, E. Weigele, P. R. Jack, W. E. Robb, G. B. Venclovas, C. Siksnys, V. 2020-04-30 doi:10.1101/2020.04.29.066654 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Inside-out regulation of E-cadherin conformation and adhesion ]]> https://biorxiv.org/content/10.1101/2020.05.02.074187v1?rss=1 Koirala, R. Priest, A. V. Yen, C.-F. Cheah, J. S. Gloerich, M. Yamada, S. Sivasankar, S. 2020-05-03 doi:10.1101/2020.05.02.074187 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ The enemy of my enemy is my friend: Nematode infection of pollinating and non-pollinating fig wasps has net benefits for the fig-fig wasp pollination mutualism ]]> https://biorxiv.org/content/10.1101/2020.05.08.084400v1?rss=1 Van Goor, J. Piatscheck, F. Houston, D. D. Nason, J. D. 2020-05-10 doi:10.1101/2020.05.08.084400 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ High-throughput in vitro specificity profiling of natural and high-fidelity CRISPR-Cas9 variants ]]> https://biorxiv.org/content/10.1101/2020.05.12.091991v1?rss=1 Murugan, K. Seetharam, A. S. Severin, A. J. Sashital, D. G. 2020-05-12 doi:10.1101/2020.05.12.091991 Cold Spring Harbor Laboratory Press 2020-05-12 <![CDATA[ Robust scan synchronized force-fluorescence imaging. ]]> https://biorxiv.org/content/10.1101/2020.05.15.098970v1?rss=1 Schmidt, P. Lajoie, J. Sivasankar, S. 2020-05-16 doi:10.1101/2020.05.15.098970 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Evolutionary Transcriptome Analysis Based on Differentially Expressed (DE) Genes ]]> https://biorxiv.org/content/10.1101/2020.05.16.099804v1?rss=1 Gu, X. 2020-05-19 doi:10.1101/2020.05.16.099804 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ The transcriptome of Listeria monocytogenes during co-cultivation with cheese rind bacteria suggests adaptation by induction of ethanolamine and 1,2-propanediol catabolism pathway genes ]]> https://biorxiv.org/content/10.1101/2020.05.18.101832v1?rss=1 Anast, J. M. Schmitz-Esser, S. 2020-05-18 doi:10.1101/2020.05.18.101832 Cold Spring Harbor Laboratory Press 2020-05-18 <![CDATA[ Cis-regulatory elements within TEs can influence expression of nearby maize genes ]]> https://biorxiv.org/content/10.1101/2020.05.20.107169v1?rss=1 Noshay, J. Marand, A. P. Anderson, S. N. Zhou, P. Mejia Guerra, M. K. Lu, Z. O'Connor, C. Crisp, P. A. Hirsch, C. N. Schmitz, R. J. Springer, N. M. 2020-05-22 doi:10.1101/2020.05.20.107169 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Engineering 6-phosphogluconate dehydrogenase to improve heat tolerance in maize seed development ]]> https://biorxiv.org/content/10.1101/2020.05.21.108985v1?rss=1 Ribeiro, C. Hennen-Bierwagen, T. Myers, A. Cline, K. Settles, A. M. 2020-05-22 doi:10.1101/2020.05.21.108985 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Design and Validation of a Frugal, Automated, Solid-Phase Peptide Synthesizer ]]> https://biorxiv.org/content/10.1101/2020.05.21.109215v1?rss=1 Kallmyer, N. E. Rider, N. E. Reuel, N. F. 2020-05-25 doi:10.1101/2020.05.21.109215 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Influence of the artificial sodium saccharin sweetener Sucram(R) on the microbial community composition in the rumen content and attached to the rumen epithelium in dairy cattle: A pilot study ]]> https://biorxiv.org/content/10.1101/2020.05.22.110429v1?rss=1 Koester, L. R. Anderson, C. J. Cortes, B. W. Lyte, M. Schmitz-Esser, S. 2020-05-22 doi:10.1101/2020.05.22.110429 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Functional analysis of the teosinte branched 1 genes in the tetraploid switchgrass (Panicum virgatum L.) by CRISPR/Cas9-directed mutagenesis ]]> https://biorxiv.org/content/10.1101/2020.05.23.112961v1?rss=1 LIU, Y. Wang, W. Yang, B. Currey, C. Fei, S.-z. 2020-05-26 doi:10.1101/2020.05.23.112961 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Coordinated evolution between N2 neuraminidase and H1 and H3 hemagglutinin genes increased influenza A virus genetic diversity in swine ]]> https://biorxiv.org/content/10.1101/2020.05.29.123828v1?rss=1 Zeller, M. A. Chang, J. Vincent, A. L. Gauger, P. C. Anderson, T. K. 2020-05-31 doi:10.1101/2020.05.29.123828 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Fluorogenic DNase Sensor Reveals Ubiquitous DNase Activity in Podosomes and Invadopodia ]]> https://biorxiv.org/content/10.1101/2020.06.01.127902v1?rss=1 Pal, K. Zhao, Y. Wang, Y. Wang, X. 2020-06-02 doi:10.1101/2020.06.01.127902 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ Robotic Assay for Drought (RoAD): An Automated Phenotyping System for Brassinosteroid and Drought Response ]]> https://biorxiv.org/content/10.1101/2020.06.01.128199v1?rss=1 Xiang, L. Nolan, T. M. Bao, Y. Elmore, M. Tuel, T. Gai, J. Shah, D. Huser, N. M. Hurd, A. M. McLaughlin, S. A. Howell, S. H. Walley, J. W. Yin, Y. Tang, L. 2020-06-02 doi:10.1101/2020.06.01.128199 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ STREPTOCOCCUS PNEUMONIAE SEROTYPE 22F INFECTION IN RESPIRATORY SYNCYTIAL VIRUS INFECTED NEONATAL LAMBS ENHANCES MORBIDITY ]]> https://biorxiv.org/content/10.1101/2020.06.09.142034v1?rss=1 Alnajjar, S. Sitthicharoenchai, P. Gallup, J. Ackermann, M. Verhoeven, D. 2020-06-09 doi:10.1101/2020.06.09.142034 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Differential expression of COVID-19-related genes in European Americans and African Americans ]]> https://biorxiv.org/content/10.1101/2020.06.09.143271v1?rss=1 Singh, U. Wurtele, E. S. 2020-06-10 doi:10.1101/2020.06.09.143271 Cold Spring Harbor Laboratory Press 2020-06-10 <![CDATA[ The 20-hydroxyecdysone agonist, halofenozide, primes anti-Plasmodium immunity in Anopheles gambiae via the ecdysone receptor ]]> https://biorxiv.org/content/10.1101/2020.06.19.162081v1?rss=1 Reynolds, R. A. Smith, R. C. 2020-06-19 doi:10.1101/2020.06.19.162081 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Organic Dust Exposure Induces Stress Response and Mitochondrial Dysfunction in Monocytic Cells ]]> https://biorxiv.org/content/10.1101/2020.06.30.180323v1?rss=1 Mahadev-Bhat, S. Shrestha, D. Massey, N. Karriker, L. A. Kanthasamy, A. Charavaryamath, C. 2020-07-01 doi:10.1101/2020.06.30.180323 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Organic dust induced mitochondrial dysfunction could be targeted via cGAS-STING or mitochondrial NOX-2 inhibition ]]> https://biorxiv.org/content/10.1101/2020.07.01.182535v1?rss=1 Massey, N. Shrestha, D. Bhat, S. M. Kondru, N. Charli, A. Karriker, L. A. Kanthasamy, A. Charavaryamath, C. 2020-07-02 doi:10.1101/2020.07.01.182535 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ MetaFunPrimer: primer design for targeting genes observed in metagenomes ]]> https://biorxiv.org/content/10.1101/2020.07.01.183509v1?rss=1 Liu, J. Villanueva, P. Choi, J. Gunturu, S. Ouyang, Y. Tiemann, L. Cole, J. R. Lee, J. Howe, A. 2020-07-02 doi:10.1101/2020.07.01.183509 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ CYFIP2 containing WAVE complexes inhibit cell migration ]]> https://biorxiv.org/content/10.1101/2020.07.02.184655v1?rss=1 Polesskaya, A. Boutillon, A. Wang, Y. Lavielle, M. Vacher, S. Schnitzler, A. Molinie, N. Rocques, N. Fokin, A. Bieche, I. David, N. B. Gautreau, A. M. 2020-07-03 doi:10.1101/2020.07.02.184655 Cold Spring Harbor Laboratory Press 2020-07-03 <![CDATA[ Identification of Bovine Genotypes Conferring Diminished Susceptibility to Salmonellosis and Colonization by Salmonella and E. coli O157:H7 ]]> https://biorxiv.org/content/10.1101/2020.07.06.190751v1?rss=1 Anderson, K. L. Ramsey, D. K. Day, T. A. Carlson, S. A. 2020-07-07 doi:10.1101/2020.07.06.190751 Cold Spring Harbor Laboratory Press 2020-07-07 <![CDATA[ Whole genome survey of big cats (Genus: Panthera) identifies novel microsatellites of utility in conservation genetic study ]]> https://biorxiv.org/content/10.1101/2020.07.08.193318v1?rss=1 Jee Yun Hyun Puneet Pandey Kyung Seok Kim Alvin Chon Daecheol Jeong Jong Bhak Mi-Hyun Yoo Hey-Kyung Song Randeep Singh Mi-Sook Min Surendra Prakash Goyal Damdingiin Bayarkhagva Hang Lee 2020-07-08 doi:10.1101/2020.07.08.193318 Cold Spring Harbor Laboratory Press 2020-07-08 <![CDATA[ Constrained non-coding sequence provides insights into regulatory elements and loss of gene expression in maize ]]> https://biorxiv.org/content/10.1101/2020.07.11.192575v1?rss=1 Baoxing Song 2020-07-12 doi:10.1101/2020.07.11.192575 Cold Spring Harbor Laboratory Press 2020-07-12 <![CDATA[ Single-cell analysis of mosquito hemocytes identifies signatures of immune cell sub-types and cell differentiation ]]> https://biorxiv.org/content/10.1101/2020.07.11.197939v1?rss=1 Hyeogsun Kwon Oscar Franzen Mubasher Mohammed Johan Ankarklev Ryan C Smith 2020-07-11 doi:10.1101/2020.07.11.197939 Cold Spring Harbor Laboratory Press 2020-07-11 <![CDATA[ Liquid-liquid phase separation driven compartmentalization of reactive nucleoplasm. ]]> https://biorxiv.org/content/10.1101/2020.07.13.200980v1?rss=1 Laghmach, R. Potoyan, D. A. 2020-07-14 doi:10.1101/2020.07.13.200980 Cold Spring Harbor Laboratory Press 2020-07-14 <![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[ Aspirin inhibition of prostaglandin synthesis impairs egg development across mosquito taxa ]]> https://biorxiv.org/content/10.1101/2020.07.17.208389v1?rss=1 Al Baki, M. A. Ahmed, S. Kwon, H. Hall, D. Smith, R. Kim, Y. 2020-07-17 doi:10.1101/2020.07.17.208389 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Ivermectin inhibits extracellular vesicle secretion from parasitic nematodes ]]> https://biorxiv.org/content/10.1101/2020.07.20.212290v1?rss=1 Loghry, H. J. Yuan, W. Zamanian, M. Wheeler, N. J. Day, T. A. Kimber, M. J. 2020-07-21 doi:10.1101/2020.07.20.212290 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Endogenous zebrafish neural Cre drivers generated by CRISPR/Cas9 short homology directed targeted integration ]]> https://biorxiv.org/content/10.1101/2020.07.21.214452v1?rss=1 Almeida, M. P. Welker, J. M. Ekker, S. C. Clark, K. J. Essner, J. J. McGrail, M. 2020-07-22 doi:10.1101/2020.07.21.214452 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ Automated Classification of Bacterial Cell Sub-Populations with Convolutional Neural Networks. ]]> https://biorxiv.org/content/10.1101/2020.07.22.216028v1?rss=1 Tamiev, D. Furman, P. E. Reuel, N. F. 2020-07-22 doi:10.1101/2020.07.22.216028 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation ]]> https://biorxiv.org/content/10.1101/2020.07.23.217067v1?rss=1 Espin Palazon, R. Campbell, C. A. Fursova, O. Cheng, X. Snella, E. McCune, A. Li, L. Solchenberger, B. Schmid, B. Sahoo, D. Morton, M. Traver, D. 2020-07-23 doi:10.1101/2020.07.23.217067 Cold Spring Harbor Laboratory Press 2020-07-23 <![CDATA[ Long non-coding RNA regulation of spermatogenesis and endosomal processes via the spectrin cytoskeleton in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.07.24.220640v1?rss=1 Bouska, M. Bai, H. 2020-07-26 doi:10.1101/2020.07.24.220640 Cold Spring Harbor Laboratory Press 2020-07-26 <![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[ Identification of a prostaglandin E2 receptor that regulates mosquito oenocytoid immune cell function in limiting bacteria and parasite infection ]]> https://biorxiv.org/content/10.1101/2020.08.03.235432v1?rss=1 Kwon, H. Hall, D. R. Smith, R. C. 2020-08-04 doi:10.1101/2020.08.03.235432 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Machine learning prediction and experimental validation of antigenic drift in H3 influenza A viruses in swine ]]> https://biorxiv.org/content/10.1101/2020.08.07.238279v1?rss=1 Zeller, M. A. Gauger, P. C. Arendsee, Z. W. Souza, C. K. Vincent, A. L. Anderson, T. K. 2020-08-07 doi:10.1101/2020.08.07.238279 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization ]]> https://biorxiv.org/content/10.1101/2020.08.09.243188v1?rss=1 Goren, E. Wang, C. He, Z. Sheflin, A. M. Chiniquy, D. Prenni, J. E. Tringe, S. Schachtman, D. P. Liu, P. 2020-08-12 doi:10.1101/2020.08.09.243188 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Ectopic expression of a maize gene is induced by Composite Insertions generated by Alternative Transposition ]]> https://biorxiv.org/content/10.1101/2020.08.10.245175v1?rss=1 Peterson, T. Zuo, T. Su, W. 2020-08-10 doi:10.1101/2020.08.10.245175 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues ]]> https://biorxiv.org/content/10.1101/2020.08.13.249870v1?rss=1 Halstead, M. M. Kern, C. Saelao, P. Wang, Y. Chanthavixay, G. Medrano, J. F. Van Eenennaam, A. L. Korf, I. Tuggle, C. K. Ernst, C. W. Zhou, H. ROSS, P. J. 2020-08-14 doi:10.1101/2020.08.13.249870 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Inheritance of Rootstock Effects in Avocado ( Persea americana Mill.) cv. Hass ]]> https://biorxiv.org/content/10.1101/2020.08.21.261883v1?rss=1 Reyes-Herrera, P. H. Munoz-Baena, L. Velasquez-Zapata, V. Patino, L. Delgado-Paz, O. A. Diaz-Diez, C. A. Navas-Arboleda, A. A. Cortes, A. J. 2020-08-24 doi:10.1101/2020.08.21.261883 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Generation of thymidine auxotrophic Agrobacterium tumefaciens strains for plant transformation ]]> https://biorxiv.org/content/10.1101/2020.08.21.261941v1?rss=1 Aliu, E. Azanu, M. K. Wang, K. Lee, K. 2020-08-24 doi:10.1101/2020.08.21.261941 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Analysis of the oxidative stress regulon identifies soxS as a genetic target for resistance reversal in multi-drug resistant Klebsiella pneumoniae ]]> https://biorxiv.org/content/10.1101/2020.08.21.262022v1?rss=1 Anes, J. Dever, K. Eshwar, A. Nguyen, S. Cao, Y. Sivasankaran, S. K. Sakalauskaite, S. Lehner, A. Devineau, S. Daugelavicius, R. Fanning, S. Srikumar, S. 2020-08-21 doi:10.1101/2020.08.21.262022 Cold Spring Harbor Laboratory Press 2020-08-21 <![CDATA[ Genome-wide methylation prediction of biological age using reproducing kernel Hilbert spaces and Bayesian ridge regressions ]]> https://biorxiv.org/content/10.1101/2020.08.25.266924v1?rss=1 Amiri Roudbar, M. Momen, M. Mousavi, S. F. Salek Ardestani, S. Brito Lopes, F. Gianola, D. Khatib, H. 2020-08-25 doi:10.1101/2020.08.25.266924 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ Genetic and epigenetic contributions to variation in transposable element expression responses to abiotic stress in maize ]]> https://biorxiv.org/content/10.1101/2020.08.26.268102v1?rss=1 Liang, Z. Anderson, S. N. Noshay, J. M. Crisp, P. A. Enders, T. A. Springer, N. M. 2020-08-27 doi:10.1101/2020.08.26.268102 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ Sequence-encoded and Composition-dependent Protein-RNA Interactions Control Multiphasic Condensate Topologies ]]> https://biorxiv.org/content/10.1101/2020.08.30.273748v1?rss=1 Kaur, T. Raju, M. Alshareedah, I. Davis, R. B. Potoyan, D. A. Banerjee, P. R. 2020-08-31 doi:10.1101/2020.08.30.273748 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ A Look-ahead Monte Carlo Simulation Method for Improving Parental Selection in Trait Introgression ]]> https://biorxiv.org/content/10.1101/2020.09.01.278242v1?rss=1 Moeinizade, S. Han, Y. Pham, H. Hu, G. Wang, L. 2020-09-02 doi:10.1101/2020.09.01.278242 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ Inhibition of HIF-1α accumulation in prostate cancer cells is initiated during early stages of mammalian orthoreovirus infection ]]> https://biorxiv.org/content/10.1101/2020.09.02.279810v1?rss=1 Bussiere, L. D. Miller, C. L. 2020-09-02 doi:10.1101/2020.09.02.279810 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ Identification and evolution of Cas9 tracrRNAs ]]> https://biorxiv.org/content/10.1101/2020.09.02.279885v1?rss=1 Dooley, S. K. Baken, E. K. Moss, W. Howe, A. Young, J. K. 2020-09-03 doi:10.1101/2020.09.02.279885 Cold Spring Harbor Laboratory Press 2020-09-03 <![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[ Y2H-SCORES: A statistical framework to infer protein-protein interactions from next-generation yeast-two-hybrid sequence data ]]> https://biorxiv.org/content/10.1101/2020.09.08.288365v1?rss=1 Velasquez-Zapata, V. Elmore, J. M. Banerjee, S. Dorman, K. S. Wise, R. P. 2020-09-09 doi:10.1101/2020.09.08.288365 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Protocols for rational design of protein solubility and aggregation properties using Aggrescan3D standalone ]]> https://biorxiv.org/content/10.1101/2020.09.09.276915v1?rss=1 Kuriata, A. Badaczewska-Dawid, A. Pujols, J. Ventura, S. Kmiecik, S. 2020-09-09 doi:10.1101/2020.09.09.276915 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Chromosome-level Genome Assembly of a Regenerable Maize Inbred Line A188 ]]> https://biorxiv.org/content/10.1101/2020.09.09.289611v1?rss=1 Lin, G. He, C. Zheng, J. Koo, D.-H. Le, H. Zheng, H. Tamang, T. M. Lin, J. Liu, Y. Zhao, M. Hao, Y. McFarland, F. Wang, B. Qin, Y. Tang, H. McCarty, D. R. Wei, H. Cho, M.-J. Park, S. Kaeppler, H. Kaeppler, S. Liu, Y. Springer, N. M. Schnable, P. S. Wang, G. White, F. F. Liu, S. 2020-09-10 doi:10.1101/2020.09.09.289611 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Automatic Traits Extraction and Fitting for Field High-throughput Phenotyping Systems ]]> https://biorxiv.org/content/10.1101/2020.09.09.289769v1?rss=1 Guo, X. Qiu, Y. Nettleton, D. Yeh, C.-T. Zheng, Z. Hey, S. Schnable, P. S. 2020-09-10 doi:10.1101/2020.09.09.289769 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Susceptibility of domestic swine to experimental infection with SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.09.10.288548v1?rss=1 Pickering, B. Smith, G. Pinette, M. Embury-Hyatt, C. Moffat, E. Marszal, P. Lewis, C. E. 2020-09-10 doi:10.1101/2020.09.10.288548 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ NGPINT: A Next-generation protein-protein interaction software ]]> https://biorxiv.org/content/10.1101/2020.09.11.277483v1?rss=1 Banerjee, S. Velasquez-Zapata, V. Fuerst, G. Elmore, J. M. Wise, R. P. 2020-09-12 doi:10.1101/2020.09.11.277483 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ A long-range chromatin interaction regulates SATB homeobox 1 gene expression in trophoblast stem cells ]]> https://biorxiv.org/content/10.1101/2020.09.11.294181v1?rss=1 Yu, W. Chakravarthi, V. P. Borosha, S. Ratri, A. Dalal, K. Wolfe, M. W. Starks, R. R. Tuteja, G. Rumi, M. A. K. 2020-09-11 doi:10.1101/2020.09.11.294181 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.) ]]> https://biorxiv.org/content/10.1101/2020.09.15.298315v1?rss=1 McGrath, J. M. Funk, A. Galewski, P. Ou, S. Townsend, B. J. Davenport, K. Daligault, H. Johnson, S. Lee, J. Hastie, A. R. Darracq, A. Willems, G. Barnes, S. Liachko, I. Sullivan, S. Koren, S. Phillippy, A. Wang, J. Liu, T. Pulman, J. A. Childs, K. Yocum, A. Fermin, D. Mutasa-Gottgens, E. Stevanato, P. Taguchi, K. Dorn, K. 2020-09-16 doi:10.1101/2020.09.15.298315 Cold Spring Harbor Laboratory Press 2020-09-16 <![CDATA[ The narrow-spectrum anthelmintic oxantel is a potent agonist of a novel acetylcholine receptor subtype in whipworms ]]> https://biorxiv.org/content/10.1101/2020.09.17.301192v1?rss=1 Hansen, T. V. A. Cirera, S. Neveu, C. Calloe, K. Klaerke, D. Martin, R. 2020-09-17 doi:10.1101/2020.09.17.301192 Cold Spring Harbor Laboratory Press 2020-09-17 <![CDATA[ Applications of spatial models to ordinal data: Geospatial Statistics for Soybean Iron Deficiency Chlorosis ]]> https://biorxiv.org/content/10.1101/2020.09.21.306001v1?rss=1 Xu, Z. Cannon, S. B. Beavis, W. D. 2020-09-21 doi:10.1101/2020.09.21.306001 Cold Spring Harbor Laboratory Press 2020-09-21 <![CDATA[ Song type variations of Louisiana Waterthrush (Parkesia motacilla) and their geographic distributions ]]> https://biorxiv.org/content/10.1101/2020.09.24.312454v1?rss=1 90%) for Type A with slightly less agreement on Types B and C. User error rates (proportion of the Linear Discriminant Analysis classifications that were incorrect) were <10% for Types A and B, but 26% for Type C, while producer error rates (proportion of the song type for which the Linear Discriminant Analysis was incorrect) were >25% for Types A and C, but <5% for Type B. Our findings confirmed in a subset of 87 individuals that most between-individual variation was in the number of notes and note sequence duration while most within-individual variation resulted from the percent of downstrokes. The location of each singer was plotted on a map of the breeding range and results indicated the song types have large-scale discrete geographic distributions that co-occur in some regions but not range-wide. Evaluation of the distributions provided tentative support for a hypothesis that two of the song types may independently exhibit congruence with the geographic extent of Pleistocene glacial boundaries and the third song type may be distinguished by a lack of congruence, but further investigation is needed to elucidate whether the song variations represent subpopulations with three separate evolutionary histories. ]]> Silcock, R. Schwartz, S. L. Carlini, J. U. Dinsmore, S. J. 2020-09-25 doi:10.1101/2020.09.24.312454 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Population Level Variation of Transposable Elements in a Maize Diversity Panel ]]> https://biorxiv.org/content/10.1101/2020.09.25.314401v1?rss=1 O'Connor, C. Qiu, Y. Della Coletta, R. Monnahan, P. Noshay, J. M. Gilbert, A. Anderson, S. N. McGaugh, S. E. Springer, N. M. Hirsch, C. 2020-09-26 doi:10.1101/2020.09.25.314401 Cold Spring Harbor Laboratory Press 2020-09-26 <![CDATA[ A pseudomolecule assembly of the Rocky Mountain elk genome reveals putative immune system gene loss near chromosomal fissions ]]> https://biorxiv.org/content/10.1101/2020.09.30.320150v1?rss=1 Masonbrink, R. Alt, D. Bayles, D. O. Boggiatto, P. Edwards, W. Tatum, F. Williams, J. Wilson-Welder, J. Zimin, A. Severin, A. Olsen, S. 2020-09-30 doi:10.1101/2020.09.30.320150 Cold Spring Harbor Laboratory Press 2020-09-30 <![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[ Algorithmic and data modeling: will algorithmic modeling improve predictions of traits evaluated on ordinal scales? ]]> https://biorxiv.org/content/10.1101/2020.10.07.329466v1?rss=1 Xu, Z. Kurek, A. Cannon, S. Beavis, W. D. 2020-10-07 doi:10.1101/2020.10.07.329466 Cold Spring Harbor Laboratory Press 2020-10-07 <![CDATA[ Using Machine Learning To Develop A Fully Automated Soybean Nodule Acquisition Pipeline (SNAP) ]]> https://biorxiv.org/content/10.1101/2020.10.12.336156v1?rss=1 Jubery, T. Z. Carley, C. Sarkar, S. Singh, A. Ganapathysubramanian, B. Singh, A. K. 2020-10-12 doi:10.1101/2020.10.12.336156 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ How do neuroglial cells respond to ultrasound induced cavitation? ]]> https://biorxiv.org/content/10.1101/2020.10.14.339002v1?rss=1 Wrede, A. H. Luo, J. Montazami, R. Kanthasamy, A. Hashemi, N. N. 2020-10-14 doi:10.1101/2020.10.14.339002 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Meta-GWAS for quantitative trait loci identification in soybean ]]> https://biorxiv.org/content/10.1101/2020.10.17.343707v1?rss=1 Shook, J. M. Zhang, J. Jones, S. E. Singh, A. Diers, B. W. Singh, A. K. 2020-10-17 doi:10.1101/2020.10.17.343707 Cold Spring Harbor Laboratory Press 2020-10-17 <![CDATA[ PATRIOT: A pipeline for tracing identical-by-descent chromosome segments to improve genomic prediction in self-pollinating crop species ]]> https://biorxiv.org/content/10.1101/2020.10.17.343780v1?rss=1 Shook, J. M. Lourenco, D. Singh, A. K. 2020-10-17 doi:10.1101/2020.10.17.343780 Cold Spring Harbor Laboratory Press 2020-10-17 <![CDATA[ orfipy: a fast and flexible tool for extracting ORFs ]]> https://biorxiv.org/content/10.1101/2020.10.20.348052v1?rss=1 Singh, U. Wurtele, E. S. 2020-10-21 doi:10.1101/2020.10.20.348052 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Silver nanoparticles induce a triclosan like antibacterial action mechanism in multi-drug resistant Klebsiella pneumoniae ]]> https://biorxiv.org/content/10.1101/2020.10.24.337204v1?rss=1 Pareek, V. Devineau, S. Sivasankaran, S. K. Bhargava, A. Panwar, J. Srikumar, S. Fanning, S. 2020-10-25 doi:10.1101/2020.10.24.337204 Cold Spring Harbor Laboratory Press 2020-10-25 <![CDATA[ Meta-Analysis Identifies Pleiotropic Loci Controlling Phenotypic Trade-offs in Sorghum ]]> https://biorxiv.org/content/10.1101/2020.10.27.355495v1?rss=1 Mural, R. V. Grzybowski, M. Miao, C. Damke, A. Sapkota, S. Boyles, R. E. Salas Fernandez, M. G. Schnable, P. S. Sigmon, B. Kresovich, S. Schnable, J. C. 2020-10-27 doi:10.1101/2020.10.27.355495 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ A skyline birth-death process for inferring the population size from a reconstructed tree with occurrences ]]> https://biorxiv.org/content/10.1101/2020.10.27.356758v1?rss=1 Andreoletti, J. Zwaans, A. Warnock, R. C. Aguirre-Fernandez, G. Barido-Sottani, J. Gupta, A. Stadler, T. Manceau, M. 2020-10-27 doi:10.1101/2020.10.27.356758 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Paper-based Sensing of Fucosylated Biological Compounds ]]> https://biorxiv.org/content/10.1101/2020.10.30.362889v1?rss=1 Enam, F. Mansell, T. J. Kramer, E. Robinson, F. Alvarez-Acosta, A. Cademartiri, R. 2020-11-01 doi:10.1101/2020.10.30.362889 Cold Spring Harbor Laboratory Press 2020-11-01 <![CDATA[ Characterization of Nonmotor Symptoms in the MitoPark Mouse Model of Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2020.11.02.365874v1?rss=1 Langley, M. R. Ghaisas, S. Palanisamy, B. Ay, M. Jin, H. Anantharam, V. Kanthasamy, A. Kanthasamy, A. 2020-11-03 doi:10.1101/2020.11.02.365874 Cold Spring Harbor Laboratory Press 2020-11-03 <![CDATA[ High-Throughput Image-Based Plant Stand Count Estimation Using Convolutional Neural Networks ]]> https://biorxiv.org/content/10.1101/2020.11.05.370437v1?rss=1 Khaki, S. Pham, H. Han, Y. Kent, W. Wang, L. 2020-11-06 doi:10.1101/2020.11.05.370437 Cold Spring Harbor Laboratory Press 2020-11-06 <![CDATA[ Disproportionate CH4 sink strength from an endemic, sub-alpine Australian soil microbial community ]]> https://biorxiv.org/content/10.1101/2020.11.08.373464v1?rss=1 McDaniel, M. D. Hernandez, M. Dumont, M. G. Ingram, L. J. Adams, M. A. 2020-11-08 doi:10.1101/2020.11.08.373464 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ DeepCorn: A Semi-Supervised Deep Learning Method for High-Throughput Image-Based Corn Kernel Counting and Yield Estimation ]]> https://biorxiv.org/content/10.1101/2020.11.09.375535v1?rss=1 Khaki, S. Pham, H. Han, Y. Kuhl, A. Kent, W. Wang, L. 2020-11-10 doi:10.1101/2020.11.09.375535 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ Phenotypic and environmental predictors of reproductive success in painted turtles ]]> https://biorxiv.org/content/10.1101/2020.11.10.377028v1?rss=1 Judson, J. M. Hoekstra, L. Holden, K. Janzen, F. 2020-11-11 doi:10.1101/2020.11.10.377028 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ High Spatial-Resolution Imaging Of The Dynamics Of Cuticular Lipid Deposition During Arabidopsis Flower Development ]]> https://biorxiv.org/content/10.1101/2020.11.17.387241v1?rss=1 Alexander, L. E. Gilbertson, J. S. Xie, B. Song, Z. Nikolau, B. J. 2020-11-17 doi:10.1101/2020.11.17.387241 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ Peroxisome import stress impairs ribosome biogenesis and induces endoplasmic reticulum genes ]]> https://biorxiv.org/content/10.1101/2020.11.19.390609v1?rss=1 Bai, H. Huang, K. Kim, J. 2020-11-20 doi:10.1101/2020.11.19.390609 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ A novel high-accuracy genome assembly method utilizing a high-throughput workflow ]]> https://biorxiv.org/content/10.1101/2020.11.26.400507v1?rss=1 Zeng, Q. Cao, W. Xing, L. Qin, G. Wu, J. Nagle, M. F. Xiong, Q. Chen, J. Yang, L. Bajaj, P. Chitikineni, A. Zhou, Y. Yu, Y. Xu, J. Nie, X. Huang, L. Liu, S. Safar, J. Simkova, H. Song, W. Guo, B. Chen, S. Dolezel, J. Hao, Z. Cheng, Q. Liang, J. Tang, J. Cao, A. Wang, Q. Lu, X. Yang, S. Ma, H. Liu, J. Wang, X. Zhang, H. Wang, Z. Ji, W. Wang, C. Yuan, F. Shi, J. Varshney, R. K. Kang, Z. Han, D. Xu, H. 2020-11-27 doi:10.1101/2020.11.26.400507 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ Characterization of genetic diversity and population structure within Staphylococcus chromogenes by multilocus sequence Typing ]]> https://biorxiv.org/content/10.1101/2020.11.30.403683v1?rss=1 Huebner, R. Mugabi, R. Hetesy, G. Fox, L. De Vliegher, S. De Visscher, A. Barlow, J. W. Sensabaugh, G. 2020-11-30 doi:10.1101/2020.11.30.403683 Cold Spring Harbor Laboratory Press 2020-11-30 <![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[ YieldNet: A Convolutional Neural Network for Simultaneous Corn and Soybean Yield Prediction Based on Remote Sensing Data ]]> https://biorxiv.org/content/10.1101/2020.12.05.413203v1?rss=1 Khaki, S. Pham, H. Wang, L. 2020-12-07 doi:10.1101/2020.12.05.413203 Cold Spring Harbor Laboratory Press 2020-12-07 <![CDATA[ Genome-wide sequence data show no evidence of admixture and introgression among pollinator wasps associated with a community of Panamanian strangler figs ]]> https://biorxiv.org/content/10.1101/2020.12.09.418376v1?rss=1 Satler, J. D. Herre, E. A. Heath, T. A. Machado, C. A. Zuniga, A. G. Nason, J. D. 2020-12-09 doi:10.1101/2020.12.09.418376 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Plasmodesmata-dependent intercellular movement of bacterial effectors ]]> https://biorxiv.org/content/10.1101/2020.12.10.420240v1?rss=1 Li, Z. Variz, H. Chen, Y. Liu, S.-L. Aung, K. 2020-12-11 doi:10.1101/2020.12.10.420240 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Gastrointestinal ulceration in calves presented to a central Iowa veterinary referral facility: An underappreciated morbidity? ]]> https://biorxiv.org/content/10.1101/2020.12.17.423269v1?rss=1 Mosichuk, A. P. Smith, J. Tatarniuk, D. Kreuder, A. 2020-12-18 doi:10.1101/2020.12.17.423269 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ Dynamic evolution of the MutS family in animals: multiple losses of MSH paralogues and gain of a viral MutS homologue in octocorals ]]> https://biorxiv.org/content/10.1101/2020.12.22.424024v1?rss=1 Muthye, V. R. Lavrov, D. V. 2020-12-22 doi:10.1101/2020.12.22.424024 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Land-use and forest floor explain prokaryotic metacommunity structuring and spatial turnover in Amazonian forest-to-pasture conversion areas ]]> https://biorxiv.org/content/10.1101/2020.12.30.424814v1?rss=1 Rocha, F. I. Ribeiro, T. G. Fontes, M. A. Shwab, S. Coelho, M. R. R. Lumbreras, J. F. da Motta, P. E. F. Teixeira, W. G. Cole, J. R. Borsanelli, A. C. Dutra, I. d. S. Howe, A. de Oliveira, A. P. Jesus, E. d. C. 2020-12-30 doi:10.1101/2020.12.30.424814 Cold Spring Harbor Laboratory Press 2020-12-30 <![CDATA[ Quantitative proteomics reveals extensive lysine ubiquitination in the Arabidopsis root proteome and uncovers novel transcription factor stability states ]]> https://biorxiv.org/content/10.1101/2021.01.07.425780v1?rss=1 Song, G. Olatunji, D. Montes, C. Clark, N. M. Pu, Y. Kelley, D. R. Walley, J. W. 2021-01-07 doi:10.1101/2021.01.07.425780 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ MCPdb: The Bacterial Microcompartment Database ]]> https://biorxiv.org/content/10.1101/2021.01.09.426059v1?rss=1 Ochoa, J. M. Bair, K. Holton, T. Bobik, T. A. Yeates, T. O. 2021-01-10 doi:10.1101/2021.01.09.426059 Cold Spring Harbor Laboratory Press 2021-01-10 <![CDATA[ Native structure of the RhopH complex, a key determinant of malaria parasite nutrient acquisition ]]> https://biorxiv.org/content/10.1101/2021.01.10.425752v1?rss=1 Ho, C.-M. Jih, J. Lai, M. Li, X. Goldberg, D. Beck, J. R. Zhou, H. 2021-01-11 doi:10.1101/2021.01.10.425752 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Rapid screening of pest resistance genes in maize using a sugarcane mosaic virus vector ]]> https://biorxiv.org/content/10.1101/2021.01.13.425472v1?rss=1 Chung, S. H. Bigham, M. Lappe, R. R. Chan, B. Nagalakshmi, U. Whitham, S. A. Dinesh-Kumar, S. P. Jander, G. 2021-01-13 doi:10.1101/2021.01.13.425472 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes ]]> https://biorxiv.org/content/10.1101/2021.01.14.426684v1?rss=1 Hufford, M. B. Seetharam, A. S. Woodhouse, M. R. Chougule, K. M. Ou, S. LIU, J. Ricci, W. A. Guo, T. Olson, A. Qiu, Y. Della Coletta, R. Tittes, S. Hudson, A. I. Marand, A. P. Wei, S. Lu, Z. Wang, B. Tello-Ruiz, M. K. Piri, R. D. Wang, N. Kim, D. w. Zeng, Y. O'Connor, C. H. Li, X. Gilbert, A. M. Baggs, E. Krasileva, K. V. Portwood, J. L. Cannon, E. K. Andorf, C. M. MANCHANDA, N. Snodgrass, S. J. Hufnagel, D. E. Jiang, Q. Pedersen, S. Syring, M. L. Kudrna, D. A. Llaca, V. Fengler, K. Schmitz, R. J. Ross-Ibarra, J. Yu, J. Gent, J. I. Hirsch, C. N. Ware 2021-01-16 doi:10.1101/2021.01.14.426684 Cold Spring Harbor Laboratory Press 2021-01-16 <![CDATA[ Programmable Viscoelasticity in Protein-RNA Condensates with Disordered Sticker-Spacer Polypeptides ]]> https://biorxiv.org/content/10.1101/2021.01.24.427968v1?rss=1 Alshareedah, I. Moosa, M. M. Banerjee, P. R. 2021-01-26 doi:10.1101/2021.01.24.427968 Cold Spring Harbor Laboratory Press 2021-01-26 <![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[ DROSOPHILA MTOR COMPLEX 2 PRESERVES MITOCHONDRIAL AND CARDIAC FUNCTION UNDER HIGH FAT DIET TREATMENT ]]> https://biorxiv.org/content/10.1101/2021.01.27.428443v1?rss=1 Chang, K. Requejo Figueroa, G. A. Bai, H. 2021-01-28 doi:10.1101/2021.01.27.428443 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Bridging Between Material Properties Of Proteins And The Underlying Molecular Interactions ]]> https://biorxiv.org/content/10.1101/2021.02.03.429521v1?rss=1 Song, G. 2021-02-03 doi:10.1101/2021.02.03.429521 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ The Case for Retaining Natural Language Descriptions of Phenotypes in Plant Databases and a Web Application as Proof of Concept ]]> https://biorxiv.org/content/10.1101/2021.02.04.429796v1?rss=1 Braun, I. R. Bassham, D. C. Lawrence-Dill, C. J. 2021-02-06 doi:10.1101/2021.02.04.429796 Cold Spring Harbor Laboratory Press 2021-02-06 <![CDATA[ FINDER: An automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences ]]> https://biorxiv.org/content/10.1101/2021.02.04.429837v1?rss=1 Banerjee, S. Bhandary, P. Woodhouse, M. R. Sen, T. Z. Wise, R. P. Andorf, C. M. 2021-02-06 doi:10.1101/2021.02.04.429837 Cold Spring Harbor Laboratory Press 2021-02-06 <![CDATA[ An MILP Model for Corn Planting and Harvest Scheduling Considering Storage Capacity and Growing Degree Units ]]> https://biorxiv.org/content/10.1101/2021.02.06.430062v1?rss=1 Khalilzadeh, Z. Wang, L. 2021-02-08 doi:10.1101/2021.02.06.430062 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ Evidence for Multiple Teosinte Hybrid Zones in Central Mexico ]]> https://biorxiv.org/content/10.1101/2021.02.11.430632v1?rss=1 Hufnagel, D. E. Kananen, K. Glaubitz, J. C. Sanchez-Gonzalez, J. d. J. Doebley, J. F. Hufford, M. B. 2021-02-12 doi:10.1101/2021.02.11.430632 Cold Spring Harbor Laboratory Press 2021-02-12 <![CDATA[ BIAPSS - BioInformatic Analysis of liquid-liquid Phase-Separating protein Sequences ]]> https://biorxiv.org/content/10.1101/2021.02.11.430806v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@1d90ddorg.highwire.dtl.DTLVardef@111d084org.highwire.dtl.DTLVardef@90b3b0org.highwire.dtl.DTLVardef@51d71_HPS_FORMAT_FIGEXP M_FIG TOC - graphical abstract C_FIG Author summaryProteins, especially those with low complexity and intrinsically disordered regions, have recently come into the limelight because of mounting evidence showing that these regions can drive the formation of membraneless organelles (MLOs) in cells. The underlying physical mechanism for forming MLOs is liquid-liquid phase separation (LLPS); a thermodynamically driven process whereby a cellular milieu with a relatively well-mixed distribution of biomolecules gets decomposed into liquid droplets where the concentration of selected biomolecules is higher. Deciphering molecular sequence grammar of phase separation has turned out to be challenging because of the complexity of this process in cells and the vastness of sequence space of LLPS-driver proteins. While the field is still in its infancy the growth of experimental data has already spurred the creation of several major databases which collect and annotate bimolecular systems with confirmed LLPS behavior. What is currently missing is a framework that would leverage the existing databases by integrating them with deep biophysical and bioinformatic analysis for identifying statistically significant features of protein sequences implicated in LLPS. In this work, we have addressed this challenge by creating an open-source web platform named BIAPSS (BioInformatic Analysis of liquid-liquid Phase-Separating protein Sequences) which integrates a comprehensive repository of pre-processed bioinformatic data for LLPS-driver protein sequences with interactive analytic applications for on-the-fly analysis of biophysical features relevant for LLPS behavior. BIAPSS empowers users with novel and effective tools for exploring LLPS-related sequence signals for individual proteins (SingleSEQ tab) and globally by integrating common regularities across subgroups or the entire LLPS sequence superset (MultiSEQ). The long-term plan for BIAPSS is to serve as a unifying hub for the experimental and computational community with a comprehensive set of analytic tools, biophysically featured data, and standardized protocols facilitating the identification of sequence hot spots driving the LLPS, which all can support applications for designing new sequences of biomedical interest. ]]> Badaczewska-Dawid, A. Potoyan, D. A. 2021-02-12 doi:10.1101/2021.02.11.430806 Cold Spring Harbor Laboratory Press 2021-02-12 <![CDATA[ slim shady is a novel allele of PHYTOCHROMEB present in the T-DNA line SALK_015201 ]]> https://biorxiv.org/content/10.1101/2021.02.12.430994v1?rss=1 Dash, L. McEwan, R. E. Montes, C. Mejia, L. Walley, J. W. Dilkes, B. P. Kelley, D. R. 2021-02-13 doi:10.1101/2021.02.12.430994 Cold Spring Harbor Laboratory Press 2021-02-13 <![CDATA[ Interplay between brassinosteroids and TORC signaling in Arabidopsis revealed by integrated multi-dimensional analysis ]]> https://biorxiv.org/content/10.1101/2021.02.12.431003v1?rss=1 Montes, C. Liao, C.-Y. Nolan, T. M. Song, G. Clark, N. M. Guo, H. Bassham, D. C. Yin, Y. Walley, J. 2021-02-13 doi:10.1101/2021.02.12.431003 Cold Spring Harbor Laboratory Press 2021-02-13 <![CDATA[ scGAE: topology-preserving dimensionality reduction for single-cell RNA-seq data using graph autoencoder ]]> https://biorxiv.org/content/10.1101/2021.02.16.431357v1?rss=1 Luo, Z. Xu, C. Zhang, Z. Jin, W. 2021-02-17 doi:10.1101/2021.02.16.431357 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ pSONIC: Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity ]]> https://biorxiv.org/content/10.1101/2021.02.18.431864v1?rss=1 Conover, J. L. Sharbrough, J. Wendel, J. F. 2021-02-18 doi:10.1101/2021.02.18.431864 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Strategies to assure optimal trade-offs among competing objectives for genetic improvement of soybean ]]> https://biorxiv.org/content/10.1101/2021.02.19.431938v1?rss=1 Ramasubramanian, V. Beavis, W. D. 2021-02-19 doi:10.1101/2021.02.19.431938 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Collagen has a unique SEC24 preference for efficient export from the endoplasmic reticulum ]]> https://biorxiv.org/content/10.1101/2021.02.23.431880v1?rss=1 Lu, C.-L. Cain, J. Brudvig, J. Ortmeier, S. Boyadjiev, S. Weimer, J. M. Kim, J. 2021-02-23 doi:10.1101/2021.02.23.431880 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ The Gossypium stocksii genome as a novel resource for cotton improvement ]]> https://biorxiv.org/content/10.1101/2021.02.23.432605v1?rss=1 Grover, C. E. Yuan, D. Arick, M. A. Miller, E. R. Hu, G. Peterson, D. G. Wendel, J. F. Udall, J. A. 2021-02-24 doi:10.1101/2021.02.23.432605 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ Regulation of plasmodesmata at specific cell-cell interfaces ]]> https://biorxiv.org/content/10.1101/2021.02.25.432931v1?rss=1 Li, Z. Aung, K. 2021-02-25 doi:10.1101/2021.02.25.432931 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Lamp1 mediates lipid transport, but is dispensable for autophagy in Drosophila ]]> https://biorxiv.org/content/10.1101/2021.03.03.432938v1?rss=1 Chaudrhy, N. Sica, M. Surabhi, S. Sanchez Hernandez, D. Mesquita, A. Selimovic, A. Riaz, A. Bai, H. Macintosh, G. C. Jenny, A. 2021-03-03 doi:10.1101/2021.03.03.432938 Cold Spring Harbor Laboratory Press 2021-03-03 <![CDATA[ Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps ]]> https://biorxiv.org/content/10.1101/2021.03.08.434433v1?rss=1 Park, J. Foox, J. Hether, T. Danko, D. Warren, S. Kim, Y. Reeves, J. Butler, D. J. Mozsary, C. Rosiene, J. Shaiber, A. Afshinnekoo, E. MacKay, M. Bram, Y. Chandar, V. Geiger, H. Craney, A. Velu, P. Melnick, A. M. Hajirasouliha, I. Beheshti, A. Taylor, D. Saravia-Butler, A. Singh, U. Wurtele, E. S. Schisler, J. Fenessey, S. Corvelo, A. Zody, M. C. Germer, S. Salvatore, S. Levy, S. Wu, S. Tatonetti, N. Shapira, S. Salvatore, M. Loda, M. Westblade, L. F. Cushing, M. Rennert, H. Kriegel, A. J. Elemento, O. Imielinski, M. Borczuk, A. C. Meydan, C. Schwar 2021-03-09 doi:10.1101/2021.03.08.434433 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ Transposon-induced inversions activate gene expression in Maize pericarp ]]> https://biorxiv.org/content/10.1101/2021.03.08.434479v1?rss=1 Sharma, S. P. Zuo, T. Peterson, T. 2021-03-09 doi:10.1101/2021.03.08.434479 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ Multiple resource limitations explain biomass-precipitation relationships in grasslands ]]> https://biorxiv.org/content/10.1101/2021.03.09.434527v1?rss=1 Bharath, S. Adler, P. B. Fay, P. A. Seabloom, E. Hautier, Y. Biederman, L. Bugalho, M. N. Caldeira, M. Eskelinen, A. Knops, J. M. H. McCulley, R. Morgan, J. Power, S. A. Risch, A. C. Schuetz, M. Stevens, C. J. Timothy, O. Virtanen, R. Borer, E. T. 2021-03-10 doi:10.1101/2021.03.09.434527 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Crosstalk in oxygen homeostasis networks: SKN-1/NRF inhibits the HIF-1 hypoxia-inducible factor in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2021.03.12.435071v1?rss=1 Feng, D. Zhai, Z. Shao, Z. Zhang, Y. Powell-Coffman, J. A. 2021-03-12 doi:10.1101/2021.03.12.435071 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ The interplay of chromatin phase separation and lamina interactions in nuclear organisation ]]> https://biorxiv.org/content/10.1101/2021.03.16.435657v1?rss=1 Laghmach, R. Di Pierro, M. Potoyan, D. A. 2021-03-17 doi:10.1101/2021.03.16.435657 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ 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[ Co-targeting strategy for precise, scarless gene editing with CRISPR/Cas9 and donor ssODNs in Chlamydomonas ]]> https://biorxiv.org/content/10.1101/2021.03.26.437214v1?rss=1 Cerutti, H. D. Akella, S. Ma, X. Bacova, R. Harmer, Z. Kolackova, M. Wen, X. Wright, D. A. Spalding, M. H. Weeks, D. P. 2021-03-26 doi:10.1101/2021.03.26.437214 Cold Spring Harbor Laboratory Press 2021-03-26 <![CDATA[ Genetic Architecture of Kernel Compositional Variation in a Maize Diversity Panel ]]> https://biorxiv.org/content/10.1101/2021.03.29.436703v1?rss=1 Renk, J. Gilbert, A. Hattery, T. O'Connor, C. Monnahan, P. Anderson, N. Waters, A. Eickholt, D. Flint-Garcia, S. Yandeau-Nelson, M. Hirsch, C. 2021-03-30 doi:10.1101/2021.03.29.436703 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ Dynamic product-precursor relationships underlie cuticular lipid accumulation on maize silks ]]> https://biorxiv.org/content/10.1101/2021.03.31.437946v1?rss=1 Chen, K. Alexander, L. E. Mahgoub, U. Okazaki, Y. Higashi, Y. Takano, K. Loneman, D. Dennison, T. S. Lopez, M. Claussen, R. Peddicord, L. Saito, K. Lauter, N. Dorman, K. S. Nikolau, B. J. Yandeau-Nelson, M. D. 2021-04-01 doi:10.1101/2021.03.31.437946 Cold Spring Harbor Laboratory Press 2021-04-01 <![CDATA[ Reference transcriptomes of porcine peripheral immune cells created through bulk and single-cell RNA sequencing ]]> https://biorxiv.org/content/10.1101/2021.04.02.438107v1?rss=1 Herrera-Uribe, J. Wiarda, J. E. Sivasankaran, S. K. Daharsh, L. Liu, H. Byrne, K. A. Smith, T. Lunney, J. K. Loving, C. L. Tuggle, C. K. 2021-04-04 doi:10.1101/2021.04.02.438107 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ Behavior of Neural Cells Post Manufacturing and After Prolonged Encapsulation within Conductive Graphene-Laden Alginate Microfibers ]]> https://biorxiv.org/content/10.1101/2021.04.04.438421v1?rss=1 McNamara, M. C. Niaraki Asli, A. E. Pemathilaka, R. L. Wrede, A. H. Montazami, R. Hashemi, N. 2021-04-05 doi:10.1101/2021.04.04.438421 Cold Spring Harbor Laboratory Press 2021-04-05 <![CDATA[ Interpretable Artificial Neural Networks incorporating Bayesian Alphabet Models for Genome-wide Prediction and Association Studies ]]> https://biorxiv.org/content/10.1101/2021.04.07.438762v1?rss=1 Cheng, H. Zhao, T. Fernando, R. L. 2021-04-08 doi:10.1101/2021.04.07.438762 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ Portrait of a genus: the genetic diversity of Zea ]]> https://biorxiv.org/content/10.1101/2021.04.07.438828v1?rss=1 Chen, L. Luo, J. Jin, M. Yang, N. Liu, X. Peng, Y. Li, W. Qing, L. Yin, Y. Ye, X. Yan, J. Zhang, Q. Zhang, X. Gui, S. Wu, S. Wang, Y. Luo, Y. Jiang, C. Deng, M. Jin, M. Jian, L. Yu, Y. Zhang, M. Yang, X. Hufford, M. B. Fernie, A. R. Warburton, M. L. Ross-Ibarra, J. Yan, J. 2021-04-09 doi:10.1101/2021.04.07.438828 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ Estimating the age of poorly dated fossil specimens and deposits using a total-evidence approach and the fossilized birth-death process ]]> https://biorxiv.org/content/10.1101/2021.04.12.439507v1?rss=1 Barido-Sottani, J. Zyla, D. Heath, T. A. 2021-04-13 doi:10.1101/2021.04.12.439507 Cold Spring Harbor Laboratory Press 2021-04-13 <![CDATA[ Identification of beneficial and detrimental bacteria that impact sorghum responses to drought using multi-scale and multi-system microbiome comparisons ]]> https://biorxiv.org/content/10.1101/2021.04.13.437608v1?rss=1 Qi, M. Berry, J. C. Veley, K. O'Connor, L. Finkel, O. M. Salas-Gonzalez, I. Kuhs, M. Jupe, J. Holcomb, E. Glavina del Rio, T. Creech, C. Liu, P. Tringe, S. G. Dangl, J. L. Schachtman, D. Bart, R. 2021-04-14 doi:10.1101/2021.04.13.437608 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Clinical Efficacy of Prebiotics and Glycosaminoglycans versus Placebo In Dogs with Food Responsive Enteropathy Receiving a Hydrolyzed Diet: A Pilot Study ]]> https://biorxiv.org/content/10.1101/2021.04.13.439608v1?rss=1 Allenspach, K. Glanemann, B. Seo, Y.-J. Priestnall, S. L. Garden, O. A. Kilburn, L. Rossoni-Serao, M. Segarra, S. Mochel, J. P. 2021-04-13 doi:10.1101/2021.04.13.439608 Cold Spring Harbor Laboratory Press 2021-04-13 <![CDATA[ Males perceive honest information from female released sex pheromone in a moth ]]> https://biorxiv.org/content/10.1101/2021.04.14.439460v1?rss=1 Golov, Y. Gonzalez-Karlsson, A. Steinitz, H. Moncaz, A. Halon, E. Horowitz, R. Goldenberg, I. Gurka, R. Liberzon, A. Soroker, V. Jurenka, R. Harari, A. 2021-04-15 doi:10.1101/2021.04.14.439460 Cold Spring Harbor Laboratory Press 2021-04-15 <![CDATA[ The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine ]]> https://biorxiv.org/content/10.1101/2021.04.16.439882v1?rss=1 Anderson, T. K. Inderski, B. K. Diel, D. G. Hause, B. M. Porter, E. Clement, T. Nelson, E. A. Bai, J. Christopher-Hennings, J. Gauger, P. C. Zhang, J. Harmon, K. M. Main, R. Lager, K. M. Faaberg, K. S. 2021-04-19 doi:10.1101/2021.04.16.439882 Cold Spring Harbor Laboratory Press 2021-04-19 <![CDATA[ A bacterial "shield and sword": A previously uncharacterized two-component system protects uropathogenic Escherichia coli from host-derived oxidative insults and promotes hemolysin-mediated host cell pyroptosis ]]> https://biorxiv.org/content/10.1101/2021.04.19.440293v1?rss=1 Gu, H. Cai, X. Zhang, X. Luo, J. Zhang, X. Cai, W. Li, G. 2021-04-19 doi:10.1101/2021.04.19.440293 Cold Spring Harbor Laboratory Press 2021-04-19 <![CDATA[ Targeted next-generation sequencing of Candidate Regions Identified by GWAS Revealed SNPs Associated with IBD in GSDs ]]> https://biorxiv.org/content/10.1101/2021.04.20.440584v1?rss=1 Peiravan, A. Salavati, M. Psifidi, A. Sharman, M. Kent, A. Watson, P. Allenspach, K. Werling, D. 2021-04-21 doi:10.1101/2021.04.20.440584 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Genome-centric analyses of seasonal phyllosphere microbiome activities in perennial crops ]]> https://biorxiv.org/content/10.1101/2021.04.20.440608v1?rss=1 50% complete. Classes represented by these MAGs (Actinomycetia, Alpha- and Gamma-Proteobacteria, and Bacteroidota) were active and had seasonal dynamics in key functions, including enrichments in transcripts for of short chain dehydrogenase, molybdopterin oxioreductase, and polyketide cyclase in the late season. The majority of MAGs had activated stress-associated pathways, including trehalose metabolism, indole acetic acid degradation, betaine biosynthesis, and reactive oxygen species degradation, suggesting direct engagement with the host environment. We also detected seasonally activated biosynthetic pathways for terpenes (carotenoid and isoprenoids), and for various non-ribosomal peptide pathways that were poorly annotated. Overall, this study overcame laboratory and bioinformatic challenges associated with field-based leaf metatranscriptome analysis to inform potential key activities of these phyllosphere populations. These activities collectively support that leaf-associated bacterial populations are seasonally dynamic, responsive to host cues and interactively engage in feedbacks with the plant. ]]> Howe, A. C. Stopnisek, N. Dooley, S. K. Yang, F. M. Grady, K. L. Shade, A. 2021-04-20 doi:10.1101/2021.04.20.440608 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Leveraging probability concepts for genotype by environment recommendation ]]> https://biorxiv.org/content/10.1101/2021.04.21.440774v1?rss=1 Dias, K. O. d. G. dos Santos, J. P. R. Krause, M. D. Piepho, H.-P. Guimaraes, L. J. M. Pastina, M. M. Garcia, A. A. F. 2021-04-22 doi:10.1101/2021.04.21.440774 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Inclusion of environmentally themed search terms improved Elastic Net regression nowcasts of regional Lyme disease rates ]]> https://biorxiv.org/content/10.1101/2021.04.22.440883v1?rss=1 Kontowicz, E. Brown, G. Torner, J. Carrel, M. Baker, K. K. Petersen, C. A. 2021-04-22 doi:10.1101/2021.04.22.440883 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection ]]> https://biorxiv.org/content/10.1101/2021.04.23.441024v1?rss=1 McDonald, J. T. Enguita, F. J. Taylor, D. Bowen, R. A. Griffin, R. J. Priebe, W. Emmett, M. R. McGrath, M. Sajadi, M. Harris, A. D. Clement, J. Dybas, J. M. Aykin-Burns, N. Guarnieri, J. W. Singh, L. N. Grabham, P. Baylin, S. Yousey, A. Pearson, A. N. Corry, P. M. Saravia-Butler, A. Aunins, T. R. Nagpal, P. Meydan, C. Foox, J. Mozsary, C. Cerqueira, B. Zaksas, V. Singh, U. Wurtele, E. S. Costes, S. V. Galeano, D. Paccanaro, A. Meinig, S. L. Hagan, R. S. Bowman, N. M. UNC COVID-19 Pathobiology Consortium, Wolfgang, M. C. Altinok, S. Sapoval, N. Treangen 2021-04-23 doi:10.1101/2021.04.23.441024 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ The Brachypodium distachyon cold-acclimated plasma membrane proteome is primed for stress resistance ]]> https://biorxiv.org/content/10.1101/2021.04.23.441164v1?rss=1 Juurakko, C. L. Bredow, M. Nakayama, T. Imai, H. Kawamura, Y. diCenzo, G. C. Uemura, M. Walker, V. K. 2021-04-23 doi:10.1101/2021.04.23.441164 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ Standardized genome-wide function prediction enables comparative functional genomics in plants: a new application area for Gene Ontologies ]]> https://biorxiv.org/content/10.1101/2021.04.25.441366v1?rss=1 Fattel, L. Psaroudakis, D. Yanarella, C. Chiteri, K. Dostalik, H. A. Joshi, P. Starr, D. C. Vu, H. Wimalanathan, K. Lawrence-Dill, C. J. 2021-04-28 doi:10.1101/2021.04.25.441366 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Increased signal to noise ratios within experimental field trials by regressing spatially distributed soil properties as principal components. ]]> https://biorxiv.org/content/10.1101/2021.04.29.441834v1?rss=1 Berry, J. C. Qi, M. Sonawane, B. V. Sheflin, A. Cousins, A. Prenni, J. Schachtman, D. Liu, P. Bart, R. S. 2021-04-30 doi:10.1101/2021.04.29.441834 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ RF-Net 2: Fast Inference of Virus Reassortment and Hybridization Networks ]]> https://biorxiv.org/content/10.1101/2021.05.05.442676v1?rss=1 Markin, A. Wagle, S. Anderson, T. K. Eulenstein, O. 2021-05-06 doi:10.1101/2021.05.05.442676 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Independent dynamics of slow, intermediate, and fast intracranial EEG spectral activities during human memory formation ]]> https://biorxiv.org/content/10.1101/2021.05.06.442655v1?rss=1 Marks, V. S. Saboo, K. Topcu, C. Thayib, T. P. Nejedly, P. Kremen, V. Worrell, G. A. Kucewicz, M. T. 2021-05-07 doi:10.1101/2021.05.06.442655 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ RevGadgets: an R Package for visualizing Bayesian phylogenetic analyses from RevBayes ]]> https://biorxiv.org/content/10.1101/2021.05.10.443470v1?rss=1 Tribble, C. M. Freyman, W. A. Lim, J. Y. Landis, M. J. Barido-Sottani, J. Kopperud, B. T. Höhna, S. May, M. R. 2021-05-11 doi:10.1101/2021.05.10.443470 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ Micafungin-induced Cell Wall Damage Stimulates Microcycle Conidiation in Aspergillus nidulans ]]> https://biorxiv.org/content/10.1101/2021.05.19.444817v1?rss=1 Reese, S. Chelius, C. Riekhof, W. R. Marten, M. R. Harris, S. D. 2021-05-19 doi:10.1101/2021.05.19.444817 Cold Spring Harbor Laboratory Press 2021-05-19 <![CDATA[ Predicting Moisture Content During Maize Nixtamalization Using Machine Learning with NIR Spectroscopy ]]> https://biorxiv.org/content/10.1101/2021.05.19.444884v1?rss=1 Burns, M. Renk, J. Eickholt, D. Gilbert, A. Hattery, T. Holmes, M. Anderson, N. Waters, A. Kalambur, S. Flint-Garcia, S. Yandeau-Nelson, M. Annor, G. Hirsch, C. 2021-05-21 doi:10.1101/2021.05.19.444884 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ Extraordinarily precise nematode sex ratios: Adaptive responses to vanishingly rare mating options ]]> https://biorxiv.org/content/10.1101/2021.05.25.445688v1?rss=1 Van Goor, J. Herre, E. A. Gomez, A. Nason, J. D. 2021-05-26 doi:10.1101/2021.05.25.445688 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ Additive and epistatic effects influence spectral tuning in molluscan retinochrome opsin ]]> https://biorxiv.org/content/10.1101/2021.05.26.445805v1?rss=1 Smedley, G. D. McElroy, K. E. Serb, J. M. 2021-05-26 doi:10.1101/2021.05.26.445805 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in peanut (Arachis hypogaea L.). ]]> https://biorxiv.org/content/10.1101/2021.06.03.446924v1?rss=1 Otyama, P. I. Chamberlin, K. Ozias-Akins, P. Graham, M. A. Cannon, E. K. S. Cannon, S. B. MacDonald, G. E. Anglin, N. L. 2021-06-03 doi:10.1101/2021.06.03.446924 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ The Streptochaeta genome and the evolution of the grasses ]]> https://biorxiv.org/content/10.1101/2021.06.08.444730v1?rss=1 Seetharam, A. S. Yu, Y. Belanger, S. Clark, L. G. Meyers, B. C. Kellogg, E. A. Hufford, M. B. 2021-06-08 doi:10.1101/2021.06.08.444730 Cold Spring Harbor Laboratory Press 2021-06-08 <![CDATA[ Nuclear-cytoplasmic balance: whole genome duplications induce elevated organellar genome copy number ]]> https://biorxiv.org/content/10.1101/2021.06.08.447629v1?rss=1 Fernandes Gyorfy, M. Miller, E. R. Conover, J. L. Grover, C. E. Wendel, J. F. Sloan, D. B. Sharbrough, J. 2021-06-09 doi:10.1101/2021.06.08.447629 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ Does time matter in phylogeny? A perspective from the fossil record ]]> https://biorxiv.org/content/10.1101/2021.06.11.445746v1?rss=1 Guenser, P. Warnock, R. C. M. Donoghue, P. C. J. Jarochowska, E. 2021-06-11 doi:10.1101/2021.06.11.445746 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ The Gossypium anomalum genome as a resource for cotton improvement and evolutionary analysis of hybrid incompatibility ]]> https://biorxiv.org/content/10.1101/2021.06.16.448676v1?rss=1 Grover, C. E. Yuan, D. Arick, M. A. Miller, E. R. Hu, G. Peterson, D. G. Wendel, J. F. Udall, J. A. 2021-06-17 doi:10.1101/2021.06.16.448676 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Zebrafish Cre/lox regulated UFlip alleles generated by CRISPR/Cas targeted integration provide cell-type specific conditional gene inactivation ]]> https://biorxiv.org/content/10.1101/2021.06.18.448732v1?rss=1 99% reduction of gene expression in homozygotes and recapitulate known indel loss of function phenotypes. Passive, gene on orientation rbbp4-UFlip-On and rb1-UFlip-On integration alleles do not cause phenotypes in trans-heterozygous combination with an indel mutation. Cre recombinase injection leads to recombination at alternating pairs of loxP and lox2272 sites, inverting and locking the cassette into the active, gene off orientation, and the expected mutant phenotypes. In combination with our endogenous neural progenitor Cre drivers we demonstrate rbbp4-UFlip-On and rb1-UFlip-On gene inactivation phenotypes can be restricted to specific neural cell populations. Replacement of the UFlip mRFP primary reporter gene trap with a 2A-RFP in rbbp4-UFlip-Off, or 2A-KalTA4 in rb1-UFlip-Off, shows strong RFP expression in wild type or UAS:RFP injected embryos, respectively. Together these results validate a simplified approach for efficient isolation of highly mutagenic Cre/lox responsive conditional gene alleles to advance zebrafish Cre recombinase genetics. ]]> Almeida, M. P. Kambakam, S. Liu, F. Ming, Z. Welker, J. M. Wierson, W. A. Schultz-Rogers, L. E. Ekker, S. C. Clark, K. J. Essner, J. J. McGrail, M. 2021-06-18 doi:10.1101/2021.06.18.448732 Cold Spring Harbor Laboratory Press 2021-06-18 <![CDATA[ Large structural variations in the haplotype-resolved African cassava genome. ]]> https://biorxiv.org/content/10.1101/2021.06.25.450005v1?rss=1 Mansfeld, B. N. Boyher, A. Berry, J. C. Wilson, M. Ou, S. Polydore, S. Michael, T. P. Fahlgren, N. Bart, R. 2021-06-26 doi:10.1101/2021.06.25.450005 Cold Spring Harbor Laboratory Press 2021-06-26 <![CDATA[ Betacoronavirus-specific alternate splicing ]]> https://biorxiv.org/content/10.1101/2021.07.02.450920v1?rss=1 Karlebach, G. Aronow, B. J. Baylin, S. J. Butler, D. Foox, J. Levy, S. Meydan, C. Mozsary, C. Saravia-Butler, A. M. Taylor, D. M. Wurtele, E. Mason, C. Beheshti, A. Robinson, P. N. 2021-07-02 doi:10.1101/2021.07.02.450920 Cold Spring Harbor Laboratory Press 2021-07-02 <![CDATA[ Global patterns of subgenome evolution in organelle-targeted genes of sixallotetraploid angiosperms ]]> https://biorxiv.org/content/10.1101/2021.07.09.451712v1?rss=1 340,000 genes from 23 species to test whether whole genome duplications are associated with genetic mismatches between the nuclear, mitochondrial, and chloroplast genomes. We discovered tremendous differences between duplicated copies of nuclear genomes; however, mitochondria-nuclear and chloroplast-nuclear mismatches do not appear to be common following whole genome duplications. Together these genomic data represent the most extensive analysis yet performed on how polyploids maintain the delicate and finely tuned balance between the nuclear, mitochondrial, and chloroplast genomes. ]]> Sharbrough, J. Conover, J. Fernandes Gyorfy, M. Grover, C. Miller, E. R. Wendel, J. F. Sloan, D. B. 2021-07-09 doi:10.1101/2021.07.09.451712 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Plumage balances camouflage and thermoregulation in Horned Larks (Eremophila alpestris) ]]> https://biorxiv.org/content/10.1101/2021.07.15.452373v1?rss=1 Mason, N. A. Riddell, E. Romero, F. Cicero, C. Bowie, R. C. K. 2021-07-15 doi:10.1101/2021.07.15.452373 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ An active RNA transport mechanism into plant vacuoles ]]> https://biorxiv.org/content/10.1101/2021.07.28.454214v1?rss=1 Floyd, B. E. Kazibwe, Z. Morriss, S. C. Mugume, Y. Liu, A.-Y. Ridout, V. Luo, X. MacIntosh, G. C. Bassham, D. C. 2021-07-28 doi:10.1101/2021.07.28.454214 Cold Spring Harbor Laboratory Press 2021-07-28 <![CDATA[ Limited variation between SARS-CoV-2-infected individuals in domain specificity and relative potency of the antibody response against the spike glycoprotein ]]> https://biorxiv.org/content/10.1101/2021.08.04.455181v1?rss=1 Van Ert, H. A. Bohan, D. W. Rogers, K. J. Fili, M. Rojas Chavez, A. R. Qing, E. Han, C. Dempewolf, S. M. Hu, G. Schwery, N. Sevcik, K. M. Ruggio, N. Boyt, D. Pentella, M. Gallagher, T. Jackson, J. B. Merrill, A. E. Knudson, C. M. Brown, G. Maury, W. Haim, H. 2021-08-05 doi:10.1101/2021.08.04.455181 Cold Spring Harbor Laboratory Press 2021-08-05 <![CDATA[ Revealing how variations in antibody repertoires correlate with vaccine responses ]]> https://biorxiv.org/content/10.1101/2021.08.06.454618v1?rss=1 Safonova, Y. Shin, S. B. Kramer, L. Reecy, J. Watson, C. T. Smith, T. P. L. Pevzner, P. A. 2021-08-09 doi:10.1101/2021.08.06.454618 Cold Spring Harbor Laboratory Press 2021-08-09 <![CDATA[ Diversity of Antibiotic Resistance genes and Transfer Elements-Quantitative Monitoring (DARTE-QM): a method for detection of antimicrobial resistance in environmental samples ]]> https://biorxiv.org/content/10.1101/2021.08.06.455440v1?rss=1 Smith, S. D. Choi, J. Ricker, N. Yang, F. Hinsa-Leasure, S. Soupir, M. Allen, H. Howe, A. 2021-08-06 doi:10.1101/2021.08.06.455440 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Recombinant NAGLU-IGF2 prevents physical and neurological disease and improves survival in Sanfilippo B syndrome ]]> https://biorxiv.org/content/10.1101/2021.08.06.455469v1?rss=1 Le, S. Q. Kan, S.-h. Nunez, M. Dearborn, J. Wang, F. LI, S. Snella, L. Jens, J. K. Valentine, B. N. Nelvagal, H. R. Sorensen, A. Cooper, J. D. Chou, T.-F. Ellinwood, N. M. Smith, J. D. Sands, M. S. Dickson, P. 2021-08-08 doi:10.1101/2021.08.06.455469 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ CULTURE AND MAINTENANCE OF URINE-DERIVED, 3-DIMENSIONAL CANINE TRANSITIONAL CELL CARCINOMA ORGANOIDS ]]> https://biorxiv.org/content/10.1101/2021.08.24.457548v1?rss=1 Thenuwara, S. Schneider, B. Mosichuk, A. Gabriel, V. Zdyrski, C. Dao, K. Iennarella-Servantez, C. Colosimo, M. Sahoo, D. Bourgois-Mochel, A. Musser, M. Johannes, C. Palerme, J.-S. Allenspach, K. Mochel, J. P. 2021-08-24 doi:10.1101/2021.08.24.457548 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ Evidence for a selective link between cooperation and individual recognition ]]> https://biorxiv.org/content/10.1101/2021.09.07.459327v1?rss=1 Tumulty, J. P. Miller, S. E. Van Belleghem, S. M. Weller, H. I. Jernigan, C. M. Vincent, S. Staudenraus, R. J. Legan, A. W. Polnaszek, T. J. Uy, F. M. K. Walton, A. Sheehan, M. J. 2021-09-08 doi:10.1101/2021.09.07.459327 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ Large dataset of octocoral mitochondrial genomes provides new insights into mt-mutS evolution and function ]]> https://biorxiv.org/content/10.1101/2021.09.08.459357v1?rss=1 Muthye, V. R. Mackereth, C. Stewart, J. Lavrov, D. V. 2021-09-09 doi:10.1101/2021.09.08.459357 Cold Spring Harbor Laboratory Press 2021-09-09 <![CDATA[ SARS-CoV-2 expresses a microRNA-like small RNA able to selectively repress host genes ]]> https://biorxiv.org/content/10.1101/2021.09.08.459464v1?rss=1 Pawlica, P. Yario, T. White, S. Wang, J. Moss, W. Hui, P. Vinetz, J. M. Steitz, J. A. 2021-09-08 doi:10.1101/2021.09.08.459464 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[ 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[ Deleterious Mutations Accumulate Faster in Allopolyploid than Diploid Cotton (Gossypium) and Unequally Between Subgenomes ]]> https://biorxiv.org/content/10.1101/2021.09.22.461419v1?rss=1 Conover, J. L. Wendel, J. F. 2021-09-24 doi:10.1101/2021.09.22.461419 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ A model screening pipeline for bile acid converting anti-Clostridioides difficile bacteria reveals unique biotherapeutic potential of Peptacetobacter hiranonis ]]> https://biorxiv.org/content/10.1101/2021.09.29.462466v1?rss=1 A. Vinithakumari, A. Hernandez, B. G. Ghimire, S. Adams, S. Stokes, C. Jepsen, I. Brezina, C. Sahin, O. Li, G. Tangudu, C. Andreasen, C. Phillips, G. J. Wannemuehler, M. Jergens, A. E. Scaria, J. Sponseller, B. Mooyottu, S. 2021-09-30 doi:10.1101/2021.09.29.462466 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B. ]]> https://biorxiv.org/content/10.1101/2021.10.01.462558v1?rss=1 Siddique, S. Radakovic, Z. S. Hiltl, C. Pellegrin, C. Baum, T. J. Beasley, H. Chitambo, O. Chopra, D. Danchin, E. G. J. Grenier, E. Habash, S. S. Hasan, M. S. Helder, J. Hewezi, T. Holbein, J. Holterman, M. Janakowski, S. Koutsovoulos, G. D. Kranse, O. P. Lozano-Torres, J. L. Maier, T. R. Masonbrink, R. E. Mendy, B. Riemer, E. Sobczak, M. Sonawala, U. Sterken, M. G. Thorpe, P. van Steenbrugge, J. J. M. Zahid, N. Grundler, F. Eves-van den Akker, S. 2021-10-01 doi:10.1101/2021.10.01.462558 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ The maize gene maternal depression of r1 (mdr1) encodes a DNA glycosylase with maternal and paternal fertility functions ]]> https://biorxiv.org/content/10.1101/2021.10.04.463062v1?rss=1 Gent, J. I. Swentowsky, K. W. Higgins, K. M. Fu, F.-F. Zeng, Y. Kim, D. W. Dawe, R. K. Springer, N. M. Anderson, S. N. 2021-10-05 doi:10.1101/2021.10.04.463062 Cold Spring Harbor Laboratory Press 2021-10-05 <![CDATA[ Ligands with poly-fluorophenyl moieties promote a local structural rearrangement in the Spinach2 and Broccoli aptamers that increases ligand affinities ]]> https://biorxiv.org/content/10.1101/2021.10.05.463302v1?rss=1 Anisuzzaman, S. Geraskin, I. M. Ilgu, M. Bendickson, L. Kraus, G. A. Nilsen-Hamilton, M. 2021-10-07 doi:10.1101/2021.10.05.463302 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ Cholesterol dynamics are essential for the growth and development of Plasmodium falciparum within the erythrocyte ]]> https://biorxiv.org/content/10.1101/2021.10.06.463412v1?rss=1 Ahiya, A. I. Bhatnagar, S. Morrisey, J. M. Beck, J. R. Vaidya, A. B. 2021-10-06 doi:10.1101/2021.10.06.463412 Cold Spring Harbor Laboratory Press 2021-10-06 <![CDATA[ Frugivore gut passage increases seed germination: an updated meta-analysis ]]> https://biorxiv.org/content/10.1101/2021.10.12.462022v1?rss=1 Rogers, H. S. Cavazos, B. R. Gawel, A. M. Karnish, A. T. Ray, C. A. Rose, E. Thierry, H. Fricke, E. C. 2021-10-13 doi:10.1101/2021.10.12.462022 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Dual domestication, diversity, and differential introgression in Old World cotton diploids ]]> https://biorxiv.org/content/10.1101/2021.10.20.465142v1?rss=1 Grover, C. E. Arick, M. A. Thrash, A. Sharbrough, J. Hu, G. Yuan, D. Miller, E. R. Ramaraj, T. Peterson, D. G. Udall, J. A. Wendel, J. F. 2021-10-21 doi:10.1101/2021.10.20.465142 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ A tiger in the Upper Midwest: Surveillance and genetic data support the introduction and establishment of Aedes albopictus in Iowa, USA ]]> https://biorxiv.org/content/10.1101/2021.10.20.465182v1?rss=1 Hall, D. R. Tokarz, R. E. Field, E. N. Smith, R. C. 2021-10-21 doi:10.1101/2021.10.20.465182 Cold Spring Harbor Laboratory Press 2021-10-21 <![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[ A method for identifying environmental stimuli and genes responsible for genotype-by-environment interactions from a large-scale multi-environment data set ]]> https://biorxiv.org/content/10.1101/2021.10.25.465681v1?rss=1 Onogi, A. Sekine, D. Kaga, A. Nakano, S. Yamada, T. Yu, J. Ninomiya, S. 2021-10-26 doi:10.1101/2021.10.25.465681 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Response of total (DNA) and metabolically active (RNA) microbial communities in Miscanthus x giganteus cultivated soil to different nitrogen fertilization rates ]]> https://biorxiv.org/content/10.1101/2021.10.28.466385v1?rss=1 Yang, J. Lee, J. Choi, J. Ma, L. Heaton, E. Howe, A. C. 2021-10-29 doi:10.1101/2021.10.28.466385 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ Multiple spillovers and onward transmission of SARS-Cov-2 in free-living and captive White-tailed deer (Odocoileus virginianus) ]]> https://biorxiv.org/content/10.1101/2021.10.31.466677v1?rss=1 Kuchipudi, S. V. Surendran-Nair, M. Ruden, R. M. Yon, M. Nissly, R. H. Nelli, R. K. Li, L. Jayarao, B. M. Vandegrift, K. Maranas, C. D. Levine, N. Willgert, K. Conlan, A. J. K. Olsen, R. J. Davis, J. Musser, J. M. Hudson, P. J. Kapur, V. 2021-11-01 doi:10.1101/2021.10.31.466677 Cold Spring Harbor Laboratory Press 2021-11-01 <![CDATA[ An interolog-based barley interactome as an integration framework for immune signaling ]]> https://biorxiv.org/content/10.1101/2021.11.02.466982v1?rss=1 Velasquez-Zapata, V. Elmore, J. M. Fuerst, G. Wise, R. 2021-11-04 doi:10.1101/2021.11.02.466982 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Blueprint for Phasing and Assembling the Genomes of Heterozygous Polyploids: Application to the Octoploid Genome of Strawberry ]]> https://biorxiv.org/content/10.1101/2021.11.03.467115v1?rss=1 Hardigan, M. A. Feldmann, M. J. Pincot, D. D. Famula, R. A. Vachev, M. V. Madera, M. A. Zerbe, P. J. Mars, K. Peluso, P. Rank, D. Ou, S. Saski, C. A. Acharya, C. B. Cole, G. S. Yocca, A. E. Platts, A. E. Edger, P. P. Knapp, S. J. 2021-11-04 doi:10.1101/2021.11.03.467115 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ De novo assembly of 20 chickens reveals the undetectable phenomenon for thousands of core genes on sub-telomeric regions ]]> https://biorxiv.org/content/10.1101/2021.11.05.467060v1?rss=1 Li, M. Sun, C. Xu, N. Bian, P. Tian, X. Wang, X. Wang, Y. Jia, X. Heller, R. Wang, M. Wang, F. Dai, X. Luo, R. Guo, Y. Wang, X. Yang, P. Zhang, S. Li, X. Wen, C. Lan, F. SIDDIKI, A. Z. Suwannapoom, C. Zhao, X. Nie, Q. Hu, X. Jiang, Y. Yang, N. 2021-11-05 doi:10.1101/2021.11.05.467060 Cold Spring Harbor Laboratory Press 2021-11-05 <![CDATA[ A3D Database: Structure-based Protein Aggregation Predictions for the Human Proteome ]]> https://biorxiv.org/content/10.1101/2021.11.17.468872v1?rss=1 Badaczewska-Dawid, A. E. Garcia-Pardo, J. Kuriata, A. Pujols, J. Ventura, S. Kmiecik, S. 2021-11-19 doi:10.1101/2021.11.17.468872 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Genetic and antigenic characterization of an expanding H3 influenza A virus clade in US swine visualized by Nextstrain ]]> https://biorxiv.org/content/10.1101/2021.11.17.469008v1?rss=1 Neveau, M. N. Zeller, M. A. Kaplan, B. S. Souza, C. K. Gauger, P. C. Vincent, A. L. Anderson, T. K. 2021-11-19 doi:10.1101/2021.11.17.469008 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Analysis of RNA sequence and structure in key genes of Mycobacterium ulcerans reveals conserved structural motifs and regions with apparent pressure to remain unstructured ]]> https://biorxiv.org/content/10.1101/2021.11.23.469657v1?rss=1 Rouse, W. B. Gart, J. Peysakhova, L. Moss, W. 2021-11-23 doi:10.1101/2021.11.23.469657 Cold Spring Harbor Laboratory Press 2021-11-23 <![CDATA[ Deciphering the potential niche of novel black yeast fungal isolates in a biological soil crust based on genomes, phenotyping, and melanin regulation ]]> https://biorxiv.org/content/10.1101/2021.12.03.471027v1?rss=1 Carr, E. C. Barton, Q. Grambo, S. Renfro, C. Sullivan, M. T. Kuo, A. Pangilinan, J. Lipzen, A. Keymanesh, K. Savage, E. Barry, K. Grigoriev, I. V. Riekhof, W. R. Harris, S. D. 2021-12-04 doi:10.1101/2021.12.03.471027 Cold Spring Harbor Laboratory Press 2021-12-04 <![CDATA[ Does extracellular DNA mask microbial responses to a pulse disturbance? ]]> https://biorxiv.org/content/10.1101/2021.12.04.471228v1?rss=1 Kittredge, H. Dougherty, K. Glanville, K. Evans, S. E. 2021-12-04 doi:10.1101/2021.12.04.471228 Cold Spring Harbor Laboratory Press 2021-12-04 <![CDATA[ Phosphorylation dynamics in a flg22 induced, heterotrimeric G protein dependent signaling network in Arabidopsis thaliana reveals a candidate PP2A phosphatase involved in AtRGS1 trafficking ]]> https://biorxiv.org/content/10.1101/2021.12.06.471472v1?rss=1 Watkins, J. M. Jones, A. M. Walley, J. Clark, N. M. Urano, D. Mishra, B. Mukhtar, M. S. Oliveira, C. Song, G. Brachova, L. Seifert, C. Mitchell, M. Reis, P. 2021-12-07 doi:10.1101/2021.12.06.471472 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ Phosphorylation dynamics in a flg22-induced, G-protein dependent network in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2021.12.07.471565v1?rss=1 Watkins, J. M. Clark, N. M. Song, G. Oliveira, C. C. Mishra, B. Brachova, L. Siefert, C. M. Mitchell, M. S. dos Reis, P. B. Urano, D. Mukhtar, S. Walley, J. W. Jones, A. M. 2021-12-07 doi:10.1101/2021.12.07.471565 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ ABRIDGE: An ultra-compression software for SAM alignment files ]]> https://biorxiv.org/content/10.1101/2022.01.04.474935v1?rss=1 Banerjee, S. Andorf, C. 2022-01-05 doi:10.1101/2022.01.04.474935 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ Acetyl-CoA mediated autoacetylation of fatty acid synthase in de novo lipogenesis ]]> https://biorxiv.org/content/10.1101/2022.01.06.475252v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@db2042org.highwire.dtl.DTLVardef@22dde8org.highwire.dtl.DTLVardef@116b3a5org.highwire.dtl.DTLVardef@16c2dc9_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIAcetylation modification of FASN, but not protein expression, positively correlates with de novo lipogenesis during Drosophila larval development C_LIO_LISite-specific acetylation at K813 residue enhances FASN enzymatic activity C_LIO_LIK813 residue is autoacetylated by acetyl-CoA, independent of KATs C_LIO_LIA novel N-xx-G-x-A motif is required for autoacetylation of K813 C_LI ]]> Miao, T. Kim, J. Kang, P. Bai, H. 2022-01-06 doi:10.1101/2022.01.06.475252 Cold Spring Harbor Laboratory Press 2022-01-06 <![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[ Porcine intestinal innate lymphoid cells and lymphocyte spatial context revealed through single-cell RNA sequencing ]]> https://biorxiv.org/content/10.1101/2022.01.09.475571v1?rss=1 Wiarda, J. E. Trachsel, J. M. Sivasankaran, S. K. Tuggle, C. K. Loving, C. L. 2022-01-11 doi:10.1101/2022.01.09.475571 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ Semi-field evaluations of three botanically derived repellents against the blacklegged tick, Ixodes scapularis (Acari: Ixodidae) ]]> https://biorxiv.org/content/10.1101/2022.01.12.476114v1?rss=1 Lee, X. Wong, C. Coats, J. Paskewitz, S. M. 2022-01-13 doi:10.1101/2022.01.12.476114 Cold Spring Harbor Laboratory Press 2022-01-13 <![CDATA[ Cold Tolerance is Governed by Diverse Genetic Mechanisms Including Those Regulated by NB-LRR-type Receptor Proteins in Arabidopsis. ]]> https://biorxiv.org/content/10.1101/2022.01.18.476799v1?rss=1 Sahoo, D. K. Hegde, C. Bhattacharyya, M. K. 2022-01-21 doi:10.1101/2022.01.18.476799 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Tardigrade community microbiomes in North American orchards include putative endosymbionts and plant pathogens ]]> https://biorxiv.org/content/10.1101/2022.01.28.478239v1?rss=1 Tibbs-Cortes, L. E. Tibbs-Cortes, B. W. Schmitz-Esser, S. 2022-01-28 doi:10.1101/2022.01.28.478239 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ A New Classification Method Based on Dynamic Ensemble Selection and its Application to Predict Variance Patterns in HIV-1 Env ]]> https://biorxiv.org/content/10.1101/2022.01.31.478521v1?rss=1 Fili, M. Hu, G. Han, C. Kort, A. Trettin, J. Haim, H. 2022-02-02 doi:10.1101/2022.01.31.478521 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ Patterns of Volatility Across the Spike Protein Accurately Predict the Emergence of Mutations within SARS-CoV-2 Lineages ]]> https://biorxiv.org/content/10.1101/2022.02.01.478697v1?rss=1 Rojas Chavez, R. A. Fili, M. Han, C. Rahman, S. A. Bicar, I. G. L. Hu, G. Das, J. Brown, G. D. Haim, H. 2022-02-02 doi:10.1101/2022.02.01.478697 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ Temporal and spatial auxin responsive networks in maize primary roots ]]> https://biorxiv.org/content/10.1101/2022.02.01.478706v1?rss=1 McReynolds, M. R. Dash, L. Montes, C. Draves, M. A. Lang, M. G. Walley, J. W. Kelley, D. R. 2022-02-02 doi:10.1101/2022.02.01.478706 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ New Functions Identified for HIV gp120 with the New ProtSub Sequence Matching ]]> https://biorxiv.org/content/10.1101/2022.02.01.478707v1?rss=1 Litterer, B. Shome, S. Jia, K. Jernigan, R. L. 2022-02-04 doi:10.1101/2022.02.01.478707 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Expression and secretion of circular RNAs in the parasitic nematode, Ascaris suum ]]> https://biorxiv.org/content/10.1101/2022.02.08.479594v1?rss=1 Minkler, S. Loghry, H. J. Sondjaja, N. A. Kimber, M. J. 2022-02-08 doi:10.1101/2022.02.08.479594 Cold Spring Harbor Laboratory Press 2022-02-08 <![CDATA[ polishCLR: a Nextflow workflow for polishing PacBio CLR genome assemblies ]]> https://biorxiv.org/content/10.1101/2022.02.10.480011v1?rss=1 Chang, J. Stahlke, A. R. Chudalayandi, S. Rosen, B. D. Childers, A. K. Severin, A. 2022-02-11 doi:10.1101/2022.02.10.480011 Cold Spring Harbor Laboratory Press 2022-02-11 <![CDATA[ Cold-inducible promoter-driven knockdown of Brachypodium antifreeze proteins confers freeze sensitivity ]]> https://biorxiv.org/content/10.1101/2022.02.15.480542v1?rss=1 Juurakko, C. L. Bredow, M. diCenzo, G. C. Walker, V. K. 2022-02-18 doi:10.1101/2022.02.15.480542 Cold Spring Harbor Laboratory Press 2022-02-18 <![CDATA[ Targeted Down Regulation Of Core Mitochondrial Genes During SARS-CoV-2 Infection ]]> https://biorxiv.org/content/10.1101/2022.02.19.481089v1?rss=1 Guarnieri, J. W. Dybas, J. M. Fazelinia, H. Kim, M. S. Frere, J. Zhang, Y. Albrecht, Y. S. Murdock, D. G. Angelin, A. Singh, L. N. Weiss, S. L. Best, S. M. Lott, M. T. Cope, H. Zaksas, V. Saravia-Butler, A. Meydan, C. Foox, J. Mozsary, C. Kidane, Y. H. Priebe, W. Emmett, M. Meller, R. Singh, U. Bram, Y. tenOever, B. R. Heise, M. T. Moorman, N. J. Madden, E. A. Taft-Benz, S. A. Anderson, E. J. Sanders, W. A. Dickmander, R. J. Baxter, V. K. Baylin, S. Wurtele, E. Moraes-vieira, P. Taylor, D. Mason, C. Schisler, J. C. Schwartz, R. E. Beheshti, A. Wallace, 2022-02-22 doi:10.1101/2022.02.19.481089 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ Use of sugarcane mosaic virus for virus-induced gene silencing in maize ]]> https://biorxiv.org/content/10.1101/2022.02.20.481188v1?rss=1 Chung, S. H. Zhang, S. Song, H. Whitham, S. A. Jander, G. 2022-02-20 doi:10.1101/2022.02.20.481188 Cold Spring Harbor Laboratory Press 2022-02-20 <![CDATA[ Brassinosteroids modulate autophagy through phosphorylation of RAPTOR1B by the GSK3-like kinase BIN2 in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2022.02.21.481334v1?rss=1 Liao, C.-Y. Pu, Y. Nolan, T. M. Montes, C. Guo, H. Walley, J. Yin, Y. Bassham, D. C. 2022-02-22 doi:10.1101/2022.02.21.481334 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ Discovery of small molecule inhibitors of Plasmodium falciparum apicoplast DNA polymerase ]]> https://biorxiv.org/content/10.1101/2022.03.04.482688v1?rss=1 Kaur, S. Nieto, N. McDonald, P. Beck, J. R. Honzatko, R. B. Roy, A. Nelson, S. W. 2022-03-04 doi:10.1101/2022.03.04.482688 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Promising Antimalarials targeting Apicoplast DNA Polymerase from Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/2022.03.07.483284v1?rss=1 Cheda, P. Nieto, N. Kaur, S. Beck, J. M. Beck, J. R. Kerns, R. Honzatko, R. B. Nelson, S. W. 2022-03-07 doi:10.1101/2022.03.07.483284 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ A happy accident: a novel turfgrass reference genome ]]> https://biorxiv.org/content/10.1101/2022.03.08.483531v1?rss=1 Phillips, A. R. Seetharam, A. S. AuBuchon-Elder, T. Buckler, E. S. Gillespie, L. J. Hufford, M. Llaca, V. Romay, C. Soreng, R. J. Kellogg, E. Ross-Ibarra, J. 2022-03-09 doi:10.1101/2022.03.08.483531 Cold Spring Harbor Laboratory Press 2022-03-09 <![CDATA[ Fabrication of Conductive Hollow Microfibers for Encapsulation of Astrocyte Cells ]]> https://biorxiv.org/content/10.1101/2022.03.09.483669v1?rss=1 Alimoradi, N. Nasirian, V. Aykar, S. S. McNamara, M. C. Niaraki-Asli, A. E. Montazami, R. Makowski, A. Hashemi, N. N. 2022-03-11 doi:10.1101/2022.03.09.483669 Cold Spring Harbor Laboratory Press 2022-03-11 <![CDATA[ Comparison of sampling methods for small oxbow wetland fish communities ]]> https://biorxiv.org/content/10.1101/2022.03.10.483761v1?rss=1 Osterhaus, D. M. Leberg, S. S. Pierce, C. L. Stewart, T. W. McCombs, A. 2022-03-10 doi:10.1101/2022.03.10.483761 Cold Spring Harbor Laboratory Press 2022-03-10 <![CDATA[ Protein Language Model Performs Efficient Homology Detection ]]> https://biorxiv.org/content/10.1101/2022.03.10.483778v1?rss=1 Kilinc, M. Jia, K. Jernigan, R. L. 2022-03-13 doi:10.1101/2022.03.10.483778 Cold Spring Harbor Laboratory Press 2022-03-13 <![CDATA[ Variation in cytonuclear expression accommodation among allopolyploid plants ]]> https://biorxiv.org/content/10.1101/2022.03.10.483839v1?rss=1 Grover, C. E. Forsythe, E. S. Sharbrough, J. Miller, E. R. Conover, J. L. DeTar, R. A. Chavarro, C. Arick, M. A. Peterson, D. G. Leal-Bertioli, S. C. M. Sloan, D. B. Wendel, J. F. 2022-03-12 doi:10.1101/2022.03.10.483839 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ Integration of multi-omics data reveals interplay between brassinosteroid and TORC signaling in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2022.03.11.484017v1?rss=1 Montes, C. Wang, P. Liao, C.-Y. Nolan, T. M. Song, G. Clark, N. M. Elmore, J. M. Guo, H. Bassham, D. Yin, Y. Walley, J. 2022-03-13 doi:10.1101/2022.03.11.484017 Cold Spring Harbor Laboratory Press 2022-03-13 <![CDATA[ Organellar transcripts dominate the cellular mRNA pool across plants of varying ploidy levels ]]> https://biorxiv.org/content/10.1101/2022.03.12.484027v1?rss=1 Forsythe, E. S. Grover, C. E. Miller, E. R. Conover, J. L. Arick, M. A. Chavarro, M. C. F. Leal-Bertioli, S. C. M. Peterson, D. G. Sharbrough, J. Wendel, J. F. Sloan, D. B. 2022-03-14 doi:10.1101/2022.03.12.484027 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Near telomere-to-telomere nuclear phased chromosomes of the dikaryotic wheat fungus Rhizoctonia cerealis ]]> https://biorxiv.org/content/10.1101/2022.03.18.484966v1?rss=1 Zeng, Q. Cao, W. Li, W. Wu, J. Figueroa, M. Liu, H. Qin, G. Wang, Q. Yang, L. Zhou, Y. Yu, Y. Huang, L. Liu, S. Luo, Y. Mu, Z. Li, X. Liu, J. Wang, X. Wang, C. Yuan, F. Chen, H. Xu, H. Dodds, P. Han, D. Kang, Z. 2022-03-20 doi:10.1101/2022.03.18.484966 Cold Spring Harbor Laboratory Press 2022-03-20 <![CDATA[ The genomics and physiology of abiotic stressors associated with global elevation gradients in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2022.03.22.485410v1?rss=1 Gamba, D. Lorts, C. Haile, A. Sahay, S. Lopez, L. Xia, T. Kulesza, E. Elango, D. Kerby, J. Yifru, M. Bulafu, C. E. Wondimu, T. Glowacka, K. Lasky, J. 2022-03-25 doi:10.1101/2022.03.22.485410 Cold Spring Harbor Laboratory Press 2022-03-25 <![CDATA[ The interplay between lncRNAs, RNA-binding proteins and viral genome during SARS-CoV-2 infection reveals strong connections with regulatory events involved in RNA metabolism and immune response. ]]> https://biorxiv.org/content/10.1101/2022.03.26.485903v1?rss=1 View larger version (46K): org.highwire.dtl.DTLVardef@4368c9org.highwire.dtl.DTLVardef@1948201org.highwire.dtl.DTLVardef@e31fd9org.highwire.dtl.DTLVardef@1400805_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical abstractModel of interactions among lncRNA and cognate RNA-binding proteins in SARS-CoV-2 infection. According to our model, the viral genome can establish direct interactions with three core proteins (DDX3X, UPF1 and IGF2BP2) involved in mRNA metabolism and regulation of the interferon response, which are also components of a SARS-CoV-2 lncRNA-centered regulatory network. The competition between viral RNA and lncRNAs could act as a counteracting factor for the normal function of homeostatic lncRNA-centered regulatory networks, contributing to viral progression and replication. Black arrows depict physical interactions between network components; red arrows represent functional relationships. ]]> Enguita, F. J. Leitao, A. L. McDonald, J. T. Zaksas, V. Das, S. Galeano, D. Taylor, D. Syrkin Wurtele, E. Saravia-Butler, A. Baylin, S. B. Meller, R. Porterfield, D. M. Wallace, D. C. Schisler, J. C. Mason, C. E. Beheshti, A. 2022-03-28 doi:10.1101/2022.03.26.485903 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain ]]> https://biorxiv.org/content/10.1101/2022.04.01.486706v1?rss=1 Wu, D. Li, X. Tanaka, R. Wood, J. C. Tibbs-Cortes, L. E. Magallanes-Lundback, M. Bornowski, N. Hamilton, J. P. Vaillancourt, B. Diepenbrock, C. H. Li, X. Deason, N. T. Schoenbaum, G. R. Yu, J. Buell, C. R. DellaPenna, D. Gore, M. A. 2022-04-03 doi:10.1101/2022.04.01.486706 Cold Spring Harbor Laboratory Press 2022-04-03 <![CDATA[ Transmission of human influenza A virus in pigs selects for adaptive mutations on the HA gene ]]> https://biorxiv.org/content/10.1101/2022.04.04.487085v1?rss=1 Mo, J.-s. Abente, E. J. Sutton, T. C. Ferreri, L. M. Geiger, G. Gauger, P. C. Perez, D. R. Vincent, A. L. Rajao, D. S. 2022-04-05 doi:10.1101/2022.04.04.487085 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Energy demand and the context-dependent effects of genetic interactions ]]> https://biorxiv.org/content/10.1101/209510v1?rss=1 Hoekstra, L. A. Julick, C. R. Mika, K. M. Montooth, K. L. 2017-10-26 doi:10.1101/209510 Cold Spring Harbor Laboratory Press 2017-10-26 <![CDATA[ Quantitative proteomic analysis of auxin signaling during seedling development ]]> https://biorxiv.org/content/10.1101/211532v1?rss=1 Kelley, D. Shen, Z. Walley, J. W. Chapman, E. J. Briggs, S. P. Estelle, M. 2017-10-30 doi:10.1101/211532 Cold Spring Harbor Laboratory Press 2017-10-30 <![CDATA[ An analytical framework to understand regulatory novelty accompanying allopolyploidization ]]> https://biorxiv.org/content/10.1101/212092v1?rss=1 Hu, G. Wendel, J. 2017-11-07 doi:10.1101/212092 Cold Spring Harbor Laboratory Press 2017-11-07 <![CDATA[ Ancestral Reconstruction of Gene Blocks using an Event-Based Method ]]> https://biorxiv.org/content/10.1101/212886v1?rss=1 Nguyen, H. N. Jain, A. Eulenstein, O. Friedberg, I. 2017-11-01 doi:10.1101/212886 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Maize GO Annotation - Methods, Evaluation, and Review (maize-GAMER) ]]> https://biorxiv.org/content/10.1101/222836v1?rss=1 Wimalanathan, K. Friedberg, I. Andorf, C. M. Lawrence-Dill, C. J. 2017-11-21 doi:10.1101/222836 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides ]]> https://biorxiv.org/content/10.1101/227504v1?rss=1 Mohimani, H. Gurevich, A. Alexander, K. L. Naman, C. B. Leao, T. Glukhov, E. Moss, N. A. Luzzatto Knaan, T. Vargas, F. Nothias, L.-F. Singh, N. K. Sanders, J. G. Benitez, R. A. S. Thompson, L. R. Hamid, M. N. Morton, J. T. Mikheenko, A. Shlemov, A. Korobeynikov, A. Friedberg, I. Knight, R. Venkateswaran, K. Gerwick, W. Gerwick, L. Dorrestein, P. C. Pevzner, P. A. 2017-12-03 doi:10.1101/227504 Cold Spring Harbor Laboratory Press 2017-12-03 <![CDATA[ Broad spectrum proteomics analysis of the inferior Colliculus following acute hydrogen sulfide exposure ]]> https://biorxiv.org/content/10.1101/237370v1?rss=1 Kim, D.-S. Anantharam, P. Hoffman, A. Meade, M. L. Grobe, N. Gearhart, J. M. Whitley, E. M. Mahama, B. Rumbeiha, W. K. 2017-12-28 doi:10.1101/237370 Cold Spring Harbor Laboratory Press 2017-12-28 <![CDATA[ FarmCPUpp: Efficient Large-Scale GWAS ]]> https://biorxiv.org/content/10.1101/238832v1?rss=1 Schnable, P. S. Kusmec, A. 2017-12-24 doi:10.1101/238832 Cold Spring Harbor Laboratory Press 2017-12-24 <![CDATA[ Identifying Antimicrobial Peptides using Word Embedding with Deep Recurrent Neural Networks ]]> https://biorxiv.org/content/10.1101/255505v1?rss=1 Hamid, M. N. Friedberg, I. 2018-01-29 doi:10.1101/255505 Cold Spring Harbor Laboratory Press 2018-01-29 <![CDATA[ Crowdsourcing Image Analysis for Plant Phenomics to Generate Ground Truth Data for Machine Learning ]]> https://biorxiv.org/content/10.1101/265918v1?rss=1 Siegel, Z. D. Zhou, N. Zarecor, S. Lee, N. Campbell, D. A. Andorf, C. M. Nettleton, D. Lawrence-Dill, C. J. Ganapathysubramanian, B. Friedberg, I. Kelly, J. W. 2018-02-15 doi:10.1101/265918 Cold Spring Harbor Laboratory Press 2018-02-15 <![CDATA[ SeqStruct : A New Amino Acid Similarity Matrix Based on Sequence Correlations and Structural Contacts Yields Sequence-Structure Congruence ]]> https://biorxiv.org/content/10.1101/268904v1?rss=1 Jia, K. Jernigan, R. L. 2018-02-21 doi:10.1101/268904 Cold Spring Harbor Laboratory Press 2018-02-21 <![CDATA[ Ribo-tag translatomic profiling of Drosophila oenocyte reveals down-regulation of peroxisome and mitochondria biogenesis under aging and oxidative stress ]]> https://biorxiv.org/content/10.1101/272179v1?rss=1 Huang, K. Chen, W. Bai, H. 2018-02-26 doi:10.1101/272179 Cold Spring Harbor Laboratory Press 2018-02-26 <![CDATA[ Evidence for a unique DNA-dependent RNA polymerase in cereal crops ]]> https://biorxiv.org/content/10.1101/272708v1?rss=1 nView larger version (32K):norg.highwire.dtl.DTLVardef@13d3515org.highwire.dtl.DTLVardef@16831d5org.highwire.dtl.DTLVardef@19f99b8org.highwire.dtl.DTLVardef@1253e70_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG Significance statementThe grass family is critically important for humans, as this group contains cereal grains such as rice, wheat, and corn that form the bulk of the human diet. Here we provide evidence that grasses have evolved a unique polymerase complex of unknown function, suggesting a novel mechanism of gene regulation in the grass lineage. In addition to implications for the biology of grasses, this system offers an opportunity to understand how evolution shapes multi-subunit complexes through duplication of individual components. ]]> Trujillo, J. T. Seetharam, A. S. Hufford, M. B. Beilstein, M. A. Mosher, R. A. 2018-02-28 doi:10.1101/272708 Cold Spring Harbor Laboratory Press 2018-02-28 <![CDATA[ Assessment and refinement of sample preparation methods for deep and quantitative plant proteome profiling ]]> https://biorxiv.org/content/10.1101/273656v1?rss=1 Song, G. Hsu, P. Y. Walley, J. W. 2018-02-28 doi:10.1101/273656 Cold Spring Harbor Laboratory Press 2018-02-28 <![CDATA[ Toward Precision Molecular Surgery: Robust, Selective Induction of Microhomology-mediated End Joining in vivo ]]> https://biorxiv.org/content/10.1101/291187v1?rss=1 Ata, H. Ekstrom, T. L. Martinez-Galvez, G. Mann, C. M. Dvornikov, A. V. Schaefbauer, K. J. Ma, A. C. Dobbs, D. Clark, K. J. Ekker, S. C. 2018-03-28 doi:10.1101/291187 Cold Spring Harbor Laboratory Press 2018-03-28 <![CDATA[ Shared Data Science Infrastructure for Genomics Data ]]> https://biorxiv.org/content/10.1101/307777v1?rss=1 Bagheri, H. Muppirala, U. Severin, A. J. Rajan, H. 2018-04-25 doi:10.1101/307777 Cold Spring Harbor Laboratory Press 2018-04-25 <![CDATA[ Novel antimicrobial peptide discovery using machine learning and biophysical selection of minimal bacteriocin domains ]]> https://biorxiv.org/content/10.1101/314740v1?rss=1 Fields, F. R. Freed, S. D. Carothers, K. E. Hamid, M. N. Hammers, D. E. Ross, J. N. Kalwajtys, V. R. Gonzalez, A. J. Hildreth, A. D. Friedberg, I. Lee, S. W. 2018-05-04 doi:10.1101/314740 Cold Spring Harbor Laboratory Press 2018-05-04 <![CDATA[ Genetic Dissection of Haploid Male Fertility in Maize (Zea mays L.) ]]> https://biorxiv.org/content/10.1101/318386v1?rss=1 Yang, J. Li, H. Qu, Y. Chen, Q. Tang, J. lübberstedt, T. Liu, Z. 2018-05-09 doi:10.1101/318386 Cold Spring Harbor Laboratory Press 2018-05-09 <![CDATA[ Integrating genotype and weather variables for soybean yield prediction using deep learning ]]> https://biorxiv.org/content/10.1101/331561v1?rss=1 Shook, J. M. Wu, L. Gangopadhyay, T. Ganapathysubramanian, B. Sarkar, S. Singh, A. K. 2018-05-25 doi:10.1101/331561 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Identifying Mechanisms of Regulation to Model Carbon Flux During Heat Stress And Generate Testable Hypotheses ]]> https://biorxiv.org/content/10.1101/340950v1?rss=1 Hubbard, A. Zhang, X. Singh, A. Jastrebski, S. Lamont, S. Schmidt, C. J. 2018-06-07 doi:10.1101/340950 Cold Spring Harbor Laboratory Press 2018-06-07 <![CDATA[ The role of homology and orthology in the phylogenomic analysis of metazoan gene content ]]> https://biorxiv.org/content/10.1101/341115v1?rss=1 Pett, W. Adamski, M. Adamska, M. Francis, W. R. Eitel, M. Pisani, D. Woerheide, G. 2018-06-08 doi:10.1101/341115 Cold Spring Harbor Laboratory Press 2018-06-08 <![CDATA[ Development of reduced gluten wheat enabled by determination of the genetic basis of the lys3a low hordein barley mutant ]]> https://biorxiv.org/content/10.1101/354548v1?rss=1 Moehs, C. P. Austill, W. J. Holm, A. Large, T. A. G. Loeffler, D. Mullenberg, J. Schnable, P. S. Skinner, W. van Boxtel, J. Wu, L. McGuire, C. 2018-06-23 doi:10.1101/354548 Cold Spring Harbor Laboratory Press 2018-06-23 <![CDATA[ phylostratr: A framework for phylostratigraphy ]]> https://biorxiv.org/content/10.1101/360164v1?rss=1 Arendsee, Z. Li, J. Singh, U. Seetharam, A. Dorman, K. Wurtele, E. S. 2018-07-03 doi:10.1101/360164 Cold Spring Harbor Laboratory Press 2018-07-03 <![CDATA[ Plasmodium falciparum Niemann-Pick Type C1-Related Protein is a Druggable Target Required for Parasite Membrane Homeostasis ]]> https://biorxiv.org/content/10.1101/371484v1?rss=1 Istvan, E. S. Das, S. Bhatnagar, S. Beck, J. R. Owen, E. LLinas, M. Ganesan, S. M. Niles, J. C. Winzeler, E. A. Vaidya, A. B. Goldberg, D. E. 2018-07-18 doi:10.1101/371484 Cold Spring Harbor Laboratory Press 2018-07-18 <![CDATA[ Maize defective kernel5 is a bacterial tamB homolog required for chloroplast envelope biogenesis ]]> https://biorxiv.org/content/10.1101/372045v1?rss=1 Zhang, J. Wu, S. Boehlein, S. K. McCarty, D. R. Song, G. Walley, J. W. Myers, A. Settles, A. M. 2018-07-18 doi:10.1101/372045 Cold Spring Harbor Laboratory Press 2018-07-18 <![CDATA[ Convergent evolution of effector protease recognition by Arabidopsis and barley ]]> https://biorxiv.org/content/10.1101/374264v1?rss=1 Carter, M. E. Helm, M. Chapman, A. Wan, E. Restrepo Sierra, A. M. Innes, R. W. Bogdanove, A. J. Wise, R. P. 2018-07-23 doi:10.1101/374264 Cold Spring Harbor Laboratory Press 2018-07-23 <![CDATA[ High Genetic Potential for Proteolytic Decomposition in Northern Peatland Ecosystems ]]> https://biorxiv.org/content/10.1101/375428v1?rss=1 Graham, E. B. Yang, F. Bell, S. Hofmockel, K. 2018-07-24 doi:10.1101/375428 Cold Spring Harbor Laboratory Press 2018-07-24 <![CDATA[ A novel maize gene, glossy6 involved in epicuticular wax deposition and drought tolerance ]]> https://biorxiv.org/content/10.1101/378687v1?rss=1 Li, L. Du, Y. He, C. Dietrich, C. R. Li, J. Ma, X. Wang, R. Liu, Q. Liu, S. Wang, G. Schnable, P. S. Zheng, J. 2018-07-27 doi:10.1101/378687 Cold Spring Harbor Laboratory Press 2018-07-27 <![CDATA[ Measurements of maize root plasticity under water stress in hydroponic chamber ]]> https://biorxiv.org/content/10.1101/380592v1?rss=1 Jubery, T. Z. Liu, S. Lubberstedt, T. Ganapathysubramanian, B. Attinger, D. 2018-07-30 doi:10.1101/380592 Cold Spring Harbor Laboratory Press 2018-07-30 <![CDATA[ Genome-wide association study, replication, and mega-analysis using a dense marker panel in a multi-generational mouse advanced intercross line ]]> https://biorxiv.org/content/10.1101/387613v1?rss=1 Zhou, X. St. Pierre, C. L. Gonzales, N. M. Cheng, R. Chitre, A. S. Sokoloff, G. Palmer, A. A. 2018-08-08 doi:10.1101/387613 Cold Spring Harbor Laboratory Press 2018-08-08 <![CDATA[ Resistant potato starch fuels beneficial host-microbe interactions in the gut ]]> https://biorxiv.org/content/10.1101/389007v1?rss=1 Trachsel, J. Briggs, C. Gabler, N. K. Allen, H. K. Loving, C. L. 2018-08-13 doi:10.1101/389007 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes ]]> https://biorxiv.org/content/10.1101/391276v1?rss=1 Masonbrink, R. E. Maier, T. R. Muppirala, U. Seetharam, A. S. Lord, E. Juvale, P. Schmutz, J. Johnson, N. T. Korkin, D. Mitchum, M. G. Mimee, B. Eves-van den Akker, S. Hudson, M. Severin, A. J. Baum, T. J. 2018-08-13 doi:10.1101/391276 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ Maize YABBY drooping leaf genes regulate floret development and floral meristem determinacy ]]> https://biorxiv.org/content/10.1101/395186v1?rss=1 Strable, J. Vollbrecht, E. 2018-08-20 doi:10.1101/395186 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ Epigenetic factors coordinate intestinal development ]]> https://biorxiv.org/content/10.1101/399410v1?rss=1 Ganz, J. Melancon, E. Wilson, C. Amores, A. Batzel, P. Strader, M. Braasch, I. Diba, P. Kuhlman, J. A. Postlethwait, J. H. Eisen, J. S. 2018-08-23 doi:10.1101/399410 Cold Spring Harbor Laboratory Press 2018-08-23 <![CDATA[ Analysis of a structured intronic region of the LMP2 pre-mRNA from EBV reveals associations with human regulatory proteins. ]]> https://biorxiv.org/content/10.1101/405977v1?rss=1 Moss, W. N. Kumarasinghe, N. 2018-08-31 doi:10.1101/405977 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ New Drosophila long-term memory genes revealed by assessing computational function prediction methods. ]]> https://biorxiv.org/content/10.1101/414565v1?rss=1 Kacsoh, B. Z. Barton, S. Jiang, Y. Zhou, N. Mooney, S. D. Friedberg, I. Radivojac, P. Greene, C. S. Bosco, G. 2018-09-11 doi:10.1101/414565 Cold Spring Harbor Laboratory Press 2018-09-11 <![CDATA[ PolyA tracks and poly-lysine repeats are the Achilles heel of Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/420109v1?rss=1 Pavlovic Djuranovic, S. Erath, J. Andrews, R. J. Bayguinov, P. O. Chung, J. J. Chalker, D. L. Fitzpatrick, J. A. Moss, W. N. Szczesny, P. Djuranovic, S. 2018-09-18 doi:10.1101/420109 Cold Spring Harbor Laboratory Press 2018-09-18 <![CDATA[ Chemical depletion of phagocytic immune cells reveals dual roles of mosquito hemocytes in Anopheles gambiae anti-Plasmodium immunity ]]> https://biorxiv.org/content/10.1101/422543v1?rss=1 Kwon, H. S. Smith, R. C. 2018-09-27 doi:10.1101/422543 Cold Spring Harbor Laboratory Press 2018-09-27 <![CDATA[ Chemosensory structure and function in the filarial nematode, Brugia malayi. ]]> https://biorxiv.org/content/10.1101/427229v1?rss=1 Fraser, L. M. Madriz, I. Srinivasan, D. Zamanian, M. Bartholomay, L. Kimber, M. 2018-09-26 doi:10.1101/427229 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ Retinoblastoma binding protein 4 maintains cycling neural stem cells and prevents DNA damage and Tp53-dependent apoptosis in rb1 mutant neural progenitors ]]> https://biorxiv.org/content/10.1101/427344v1?rss=1 Schultz-Rogers, L. E. Almeida, M. P. Wierson, W. A. Kool, M. McGrail, M. 2018-09-25 doi:10.1101/427344 Cold Spring Harbor Laboratory Press 2018-09-25 <![CDATA[ GeneWeld: a method for efficient targeted integration directed by short homology ]]> https://biorxiv.org/content/10.1101/431627v1?rss=1 Wierson, W. A. Welker, J. M. Almeida, M. P. Mann, C. M. Webster, D. A. Weiss, T. J. Torrie, M. E. Vollbrecht, M. K. Lan, M. McKeighan, K. C. Ming, Z. Wehmeier, A. Mikelson, C. S. Haltom, J. A. Kwan, K. M. Chien, C.-B. Balciunas, D. Ekker, S. C. Clark, K. J. Webber, B. R. Moriarity, B. Solin, S. L. Carlson, D. F. Dobbs, D. L. McGrail, M. Essner, J. J. 2018-10-03 doi:10.1101/431627 Cold Spring Harbor Laboratory Press 2018-10-03 <![CDATA[ RefSoil+: A reference for antimicrobial resistance genes on soil plasmids ]]> https://biorxiv.org/content/10.1101/435107v1?rss=1 Dunivin, T. K. Choi, J. Howe, A. C. Shade, A. 2018-10-04 doi:10.1101/435107 Cold Spring Harbor Laboratory Press 2018-10-04 <![CDATA[ Sacubitril/valsartan (LCZ696) Significantly Reduces Aldosterone and Increases cGMP Circulating Levels in a Canine Model of RAAS Activation ]]> https://biorxiv.org/content/10.1101/435560v1?rss=1 Mochel, J. P. Tang, C. H. Peyrou, M. Giraudel, J. Danhof, M. Rigel, D. 2018-10-05 doi:10.1101/435560 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ Age-dependent changes in transcription factor FOXO targeting in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/456426v1?rss=1 Birnbaum, A. Tatar, M. Bai, H. 2018-10-30 doi:10.1101/456426 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ Adult Canine Intestinal Derived Organoids: A Novel In Vitro System for Translational Research in Comparative Gastroenterology ]]> https://biorxiv.org/content/10.1101/466409v1?rss=1 Chandra, L. Borcherding, D. C. Kingsbury, D. Atherly, T. Ambrosini, Y. M. Bourgois-Mochel, A. Yuan, W. Kimber, M. Qi, Y. Wang, Q. Wannemuehler, M. Ellinwood, N. M. Snella, E. Martin, M. Skala, M. Meyerholz, D. Estes, M. Fernandez-Zapico, M. E. Jergens, A. E. Mochel, J. P. Allenspach, K. 2018-11-09 doi:10.1101/466409 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ Long-term surveillance defines spatial and temporal patterns implicating Culex tarsalis as the primary vector of West Nile virus in Iowa, USA ]]> https://biorxiv.org/content/10.1101/476234v1?rss=1 Dunphy, B. M. Kovach, K. B. Gehrke, E. J. Field, E. N. Rowley, W. A. Bartholomay, L. C. Smith, R. C. 2018-11-28 doi:10.1101/476234 Cold Spring Harbor Laboratory Press 2018-11-28 <![CDATA[ Microfluidic On-demand Engineering of Exosomes towards Cancer Immunotherapy ]]> https://biorxiv.org/content/10.1101/478875v1?rss=1 10 h) isolation protocols. Exosome engineering approaches, such as the transfection of parent cells, also suffer from poor yield, low purity, and time-consuming operations. In this paper, we introduce a streamlined microfluidic cell culture platform for integration of harvesting, antigenic modification, and photo-release of surface engineered exosomes in one workflow, which enables the production of intact, MHC peptide surface engineered exosomes for cytolysis activation. The PDMS microfluidic cell culture chip is simply cast from a 3D-printed mold. The proof-of-concept study demonstrated the enhanced ability of harvested exosomes in antigen presentation and T cell activation, by decorating melanoma tumor peptides on the exosome surface (e.g., gp-100, MART-1, MAGE-A3). Such surface engineered antigenic exosomes were harvested in real-time from the on-chip culture of leukocytes isolated from human blood, leading to much faster cellular uptake. The activation of gp100-specific CD8 T cells which were purified from the spleen of 2 Pmel1 transgenic mice was evaluated using surface engineered exosomes prepared from muring antigen presenting cells. Antigen-specific CD8 T cell proliferation was significantly induced by the engineered exosomes compared to native, non-engineered exosomes. This microfluidic platform serves as an automated and highly integrated cell culture device for rapid, and real-time production of therapeutic exosomes that could advance cancer immunotherapy. ]]> Zhao, Z. McGill, J. He, M. 2018-11-27 doi:10.1101/478875 Cold Spring Harbor Laboratory Press 2018-11-27 <![CDATA[ Engineering a decoy substrate in soybean to enable recognition of the Soybean Mosaic Virus NIa protease ]]> https://biorxiv.org/content/10.1101/484626v1?rss=1 Helm, M. Qi, M. Sarkar, S. Yu, H. Whitham, S. A. Innes, R. W. 2018-12-04 doi:10.1101/484626 Cold Spring Harbor Laboratory Press 2018-12-04 <![CDATA[ Inferring Processes of Coevolutionary Diversification in a Community of Panamanian Strangler Figs and Associated Pollinating Wasps ]]> https://biorxiv.org/content/10.1101/490862v1?rss=1 Satler, J. D. Herre, A. Jander, C. Eaton, D. A. R. Machado, C. A. Heath, T. A. Nason, J. D. 2018-12-09 doi:10.1101/490862 Cold Spring Harbor Laboratory Press 2018-12-09 <![CDATA[ An integrated transcriptomics and metabolomics analysis of the Cucurbita pepo nectary implicates key modules of primary metabolism involved in nectar synthesis and secretion ]]> https://biorxiv.org/content/10.1101/491597v1?rss=1 Solhaug, E. M. Roy, R. Chatt, E. C. Klinkenberg, P. M. Mohd-Fadzil, N.-A. Hampton, M. Nikolau, B. J. Carter, C. J. 2018-12-10 doi:10.1101/491597 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ Sparse functional data analysis accounts for missing information in single-cell epigenomics ]]> https://biorxiv.org/content/10.1101/504365v1?rss=1 Madrigal, P. Dai, X. Hadjipantelis, P. Z. 2018-12-21 doi:10.1101/504365 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ Distinct characteristics of genes associated with phenome-wide variation in maize (Zea mays) ]]> https://biorxiv.org/content/10.1101/534503v1?rss=1 Liang, Z. Qiu, Y. Schnable, J. 2019-01-29 doi:10.1101/534503 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Translational landscape in tomato revealed by transcriptome assembly and ribosome profiling ]]> https://biorxiv.org/content/10.1101/534677v1?rss=1 Wu, H.-Y. L. Song, G. Walley, J. W. Hsu, P. Y. 2019-01-30 doi:10.1101/534677 Cold Spring Harbor Laboratory Press 2019-01-30 <![CDATA[ Optimal Scheduling of Bevacizumab and Pemetrexed/Cisplatin Dosing in Non-Small Cell Lung Cancer ]]> https://biorxiv.org/content/10.1101/540849v1?rss=1 Schneider, B. Boyer, A. Ciccolini, J. Barlesi, F. Wang, K. Benzekry, S. Mochel, J. P. 2019-02-05 doi:10.1101/540849 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ SwiftOrtho: a Fast, Memory-Efficient, Multiple Genome Orthology Classifier ]]> https://biorxiv.org/content/10.1101/543223v1?rss=1 Hu, X. Friedberg, I. 2019-02-08 doi:10.1101/543223 Cold Spring Harbor Laboratory Press 2019-02-08 <![CDATA[ Self-Attention based model for de-novo antibiotic resistant gene classification with enhanced reliability for out of distribution data detection ]]> https://biorxiv.org/content/10.1101/543272v1?rss=1 Hamid, M. N. Friedberg, I. 2019-02-08 doi:10.1101/543272 Cold Spring Harbor Laboratory Press 2019-02-08 <![CDATA[ synder: inferring genomic orthologs from synteny maps ]]> https://biorxiv.org/content/10.1101/554501v1?rss=1 Arendsee, Z. Wilkey, A. Singh, U. Li, J. Hur, M. Wurtele, E. 2019-02-19 doi:10.1101/554501 Cold Spring Harbor Laboratory Press 2019-02-19 <![CDATA[ A semi-parametric Bayesian approach, iSBA, for differential expression analysis of RNA-seq data ]]> https://biorxiv.org/content/10.1101/558270v1?rss=1 Bi, R. Liu, P. 2019-02-22 doi:10.1101/558270 Cold Spring Harbor Laboratory Press 2019-02-22 <![CDATA[ Tissue-specific mouse mRNA isoform networks ]]> https://biorxiv.org/content/10.1101/558361v1?rss=1 Kandoi, G. Dickerson, J. 2019-02-23 doi:10.1101/558361 Cold Spring Harbor Laboratory Press 2019-02-23 <![CDATA[ Scans of the MYC mRNA reveal multiple stable secondary structures—including a 3′ UTR motif, conserved across vertebrates, that can affect gene expression. ]]> https://biorxiv.org/content/10.1101/564864v1?rss=1 O'Leary, C. Andrews, R. Tompkins, V. Chen, J. Childs-Disney, J. Disney, M. Moss, W. N. 2019-03-02 doi:10.1101/564864 Cold Spring Harbor Laboratory Press 2019-03-02 <![CDATA[ Redundant SCARECROW genes pattern distinct cell layers in roots and leaves of maize ]]> https://biorxiv.org/content/10.1101/567156v1?rss=1 Hughes, T. E. Sedelnikova, O. V. Wu, H. Becraft, P. W. Langdale, J. A. 2019-03-04 doi:10.1101/567156 Cold Spring Harbor Laboratory Press 2019-03-04 <![CDATA[ The RNA encoding the microtubule-associated protein tau has extensive structure that affects its biology ]]> https://biorxiv.org/content/10.1101/580407v1?rss=1 Chen, J. L. Moss, W. N. Spencer, A. Zhang, P. Childs-Disney, J. L. Disney, M. D. 2019-03-17 doi:10.1101/580407 Cold Spring Harbor Laboratory Press 2019-03-17 <![CDATA[ Controlling Heterogeneity and Increasing Titer from Riboswitch-Regulated Bacillus subtilis Spores for Time-Delayed Protein Expression Applications ]]> https://biorxiv.org/content/10.1101/592659v1?rss=1 Tamiev, D. Lantz, A. Vezeau, G. Salis, H. Reuel, N. 2019-03-30 doi:10.1101/592659 Cold Spring Harbor Laboratory Press 2019-03-30 <![CDATA[ Integrating case studies into graduate teaching assistant training to improve instruction in biology laboratory courses ]]> https://biorxiv.org/content/10.1101/594853v1?rss=1 Kraft, J. Walck-Shannon, e. Reilly, C. Stapleton, A. 2019-03-31 doi:10.1101/594853 Cold Spring Harbor Laboratory Press 2019-03-31 <![CDATA[ De novo design of proteins with two isoenergetic but structurally divergent ground states ]]> https://biorxiv.org/content/10.1101/597161v1?rss=1 Wei, K. Y. Moschidi, D. Bick, M. J. Nerli, S. McShan, A. C. Carter, L. P. Huang, P.-S. Fletcher, D. A. Sgourakis, N. G. Boyken, S. E. Baker, D. 2019-04-04 doi:10.1101/597161 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ SequelQC: Analyzing PacBio Sequel Raw Sequence Quality ]]> https://biorxiv.org/content/10.1101/611814v1?rss=1 Hufnagel, D. E. Hufford, M. B. Seetharam, A. S. 2019-04-18 doi:10.1101/611814 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Meningeal Worm Infection in Central Iowa Goat Herds II: Individual Cases and Treatment Using a Camelid Therapeutic Protocol ]]> https://biorxiv.org/content/10.1101/613562v1?rss=1 Smith, J. Kreuder, A. Breuer, R. Still-Brooks, K. 2019-04-18 doi:10.1101/613562 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Novel engraftment and T cell differentiation of human hematopoietic cells in Art-/- IL2RG-/ SCID pigs ]]> https://biorxiv.org/content/10.1101/614404v1?rss=1 Boettcher, A. Li, Y. Ahrens, A. Kiupel, M. Byrne, K. Loving, C. Cino-Ozuna, A. G. Wiarda, J. Adur, M. Schultz, B. Swanson, J. Snella, E. Ho, C.-S. Charley, S. Kiefer, Z. Cunnick, J. Powell, E. Dell'Anna, G. Jens, J. Sathe, S. Goldman, F. Westin, E. Dekkers, J. Ross, J. Tuggle, C. 2019-05-02 doi:10.1101/614404 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Genetic analysis of the transition from wild to domesticated cotton (G. hirsutum) ]]> https://biorxiv.org/content/10.1101/616763v1?rss=1 Grover, C. E. Yoo, M.-J. Gore, M. A. Harker, D. B. Byers, R. L. Lipka, A. E. Hu, G. Yuan, D. Conover, J. Udall, J. A. Paterson, A. H. Wendel, J. 2019-04-23 doi:10.1101/616763 Cold Spring Harbor Laboratory Press 2019-04-23 <![CDATA[ JASPer controls interphase histone H3S10 phosphorylation by chromosomal kinase JIL-1 in Drosophila ]]> https://biorxiv.org/content/10.1101/624023v1?rss=1 Albig, C. Wang, C. Dann, G. P. Wojcik, F. Schauer, T. Krause, S. Maenner, S. Cai, W. Li, Y. Girton, J. Muir, T. W. Johansen, J. Johansen, K. M. Becker, P. B. Regnard, C. 2019-04-30 doi:10.1101/624023 Cold Spring Harbor Laboratory Press 2019-04-30 <![CDATA[ VARIANT ANALYSIS PIPELINE FOR ACCURATE DETECTION OF GENOMIC VARIANTS FROM TRANSCRIPTOME SEQUENCING DATA. ]]> https://biorxiv.org/content/10.1101/625020v1?rss=1 97% precision and >99% sensitivity when compared with the matching whole genome sequencing (WGS) data. Over 65% of WGS coding variants were identified from RNA-seq. Further, our results discovered SNPs resulting from post translational modifications, such as RNA editing, which may reveal potentially functional variation that would have otherwise been missed in genomic data. Even with the limitation in detecting variants in expressed regions only, our method proves to be a reliable alternative for SNP identification using RNA-seq data. ]]> Adetunji, M. Schmidt, C. J. Abasht, B. Lamont, S. J. 2019-05-01 doi:10.1101/625020 Cold Spring Harbor Laboratory Press 2019-05-01 <![CDATA[ Comparative analysis of the Accelerated Aged seed transcriptome profiles of maize CSSLs (I178 and X178) ]]> https://biorxiv.org/content/10.1101/627117v1?rss=1 Li, L. Wang, F. Li, X. Peng, Y. Zhang, H. Hey, S. Wang, G. Wang, J. Li, L. 2019-05-03 doi:10.1101/627117 Cold Spring Harbor Laboratory Press 2019-05-03 <![CDATA[ The Vertebrate Codex Gene Breaking Protein Trap Library For Genomic Discovery and Disease Modeling Applications ]]> https://biorxiv.org/content/10.1101/630236v1?rss=1 Ichino, N. Serres, M. Urban, R. Urban, M. Schaefbauer, K. Greif, L. Varshney, G. K. Skuster, K. J. McNulty, M. Daby, C. Wang, Y. Liao, H.-k. El-Rass, S. Ding, Y. Liu, W. Schimmenti, L. A. Sivasubbu, S. Balciunas, D. Hammerschmidt, M. Farber, S. A. Wen, X.-Y. Xu, X. McGrail, M. Essner, J. Burgess, S. M. Clark, K. J. Ekker, S. C. 2019-05-07 doi:10.1101/630236 Cold Spring Harbor Laboratory Press 2019-05-07 <![CDATA[ Strategies for building computing skills to support microbiome analysis: a five-year perspective from the EDAMAME workshop ]]> https://biorxiv.org/content/10.1101/631267v1?rss=1 Shade, A. Dunivin, T. K. Choi, J. Teal, T. Howe, A. C. 2019-05-09 doi:10.1101/631267 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Mesoscale liquid model of chromatin recapitulates large-scale organization of eukaryotic cell nuclei. ]]> https://biorxiv.org/content/10.1101/634980v1?rss=1 Laghmach, R. Pierro, M. D. Potoyan, D. A. 2019-05-10 doi:10.1101/634980 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Robinson-Foulds Reticulation Networks ]]> https://biorxiv.org/content/10.1101/642793v1?rss=1 Markin, A. Anderson, T. K. Vadali, V. S. Eulenstein, O. 2019-05-20 doi:10.1101/642793 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Expanding The CRISPR Toolbox With Mad7 In Zebrafish And Human Cells ]]> https://biorxiv.org/content/10.1101/650515v1?rss=1 Wierson, W. A. Simone, B. W. WareJoncas, Z. C. Mann, C. Welker, J. M. Gendron, W. A. C. Barry, M. A. Clark, K. J. Dobbs, D. McGrail, M. A. Ekker, S. C. Essner, J. C. 2019-05-25 doi:10.1101/650515 Cold Spring Harbor Laboratory Press 2019-05-25 <![CDATA[ The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens ]]> https://biorxiv.org/content/10.1101/653105v1?rss=1 Zhou, N. Jiang, Y. Bergquist, T. R. Lee, A. J. Kacsoh, B. Z. Crocker, A. W. Lewis, K. A. Georghiou, G. Nguyen, H. N. Hamid, M. N. Davis, L. The Critical Assessment of Function Annotation, Rost, B. Brenner, S. E. Orengo, C. A. Jeffery, C. J. Bosco, G. D. Hogan, D. A. Martin, M. J. O'Donovan, C. Mooney, S. D. Greene, C. S. Radivojac, P. Friedberg, I. 2019-05-29 doi:10.1101/653105 Cold Spring Harbor Laboratory Press 2019-05-29 <![CDATA[ Double triage to identify poorly annotated genes in Maize: The missing link in community curation ]]> https://biorxiv.org/content/10.1101/654848v1?rss=1 Tello-Ruiz, M. K. Marco, C. F. Hsu, F.-M. Khangura, R. S. Qiao, P. Sapkota, S. Stitzer, M. C. Wasikowski, R. Wu, H. Zhan, J. Chougule, K. Barone, L. C. Ghiban, C. Muna, D. Olson, A. C. Wang, L. C. Ware, D. Micklos, D. A. 2019-06-05 doi:10.1101/654848 Cold Spring Harbor Laboratory Press 2019-06-05 <![CDATA[ Pervasive off-target and double-stranded DNA nicking by CRISPR-Cas12a ]]> https://biorxiv.org/content/10.1101/657791v1?rss=1 Murugan, K. Seetharam, A. Severin, A. J. Sashital, D. G. 2019-06-02 doi:10.1101/657791 Cold Spring Harbor Laboratory Press 2019-06-02 <![CDATA[ Benchmarking Transposable Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline ]]> https://biorxiv.org/content/10.1101/657890v1?rss=1 Ou, S. Su, W. Liao, Y. Chougule, K. Ware, D. Peterson, T. Jiang, N. Hirsch, C. N. Hufford, M. B. 2019-06-03 doi:10.1101/657890 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Impaired peroxisomal import in Drosophila hepatocyte-like cells induces cardiac dysfunction through the pro-inflammatory cytokine Upd3 ]]> https://biorxiv.org/content/10.1101/659128v1?rss=1 Huang, K. Miao, T. Chang, K. Kang, P. Jiang, Q. Simmonds, A. J. Di Cara, F. Bai, H. 2019-06-03 doi:10.1101/659128 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Disorder mediated oligomerization of DISC1 proteins revealed by coarse-grained computer simulations. ]]> https://biorxiv.org/content/10.1101/660910v1?rss=1 Roche, J. Potoyan, D. A. 2019-06-05 doi:10.1101/660910 Cold Spring Harbor Laboratory Press 2019-06-05 <![CDATA[ An improved pig reference genome sequence to enable pig genetics and genomics research ]]> https://biorxiv.org/content/10.1101/668921v1?rss=1 90-fold) continuity and accuracy than Sscrofa10.2. These highly contiguous assemblies plus annotation of a further 11 short read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference genome for genomic research in pigs. ]]> Warr, A. Affara, N. Aken, B. Beiki, H. Bickhart, D. M. Billis, K. Chow, W. Eory, L. Finlayson, H. A. Flicek, P. Giron, C. G. Griffin, D. K. Hall, R. Hannum, G. Hourlier, T. Howe, K. Hume, D. A. Izuogu, O. Kim, K. Koren, S. Liu, H. Manchanda, N. Martin, F. J. Nonneman, D. J. O'Connor, R. E. Phillippy, A. M. Rohrer, G. A. Rosen, B. D. Rund, L. A. Sargent, C. A. Schook, L. B. Schroeder, S. G. Schwartz, A. S. Skinner, B. M. Talbot, R. Tseng, E. Tuggle, C. K. Watson, M. Smith, T. P. Archibald, A. L. 2019-06-13 doi:10.1101/668921 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ A reduced Gompertz model for predicting tumor age using a population approach ]]> https://biorxiv.org/content/10.1101/670869v1?rss=1 0.96 in all groups). Combining this structural correlation with rigorous population parameter estimation, we propose a novel reduced Gompertz function consisting of a single individual parameter. Leveraging the population approach using bayesian inference, we estimated the time of tumor initiation using three late measurement timepoints. The reduced Gompertz model was found to exhibit the best results, with drastic improvements when using bayesian inference as compared to likelihood maximization alone, for both accuracy and precision. Specifically, mean accuracy was 12.1% versus 74.1% and mean precision was 15.2 days versus 186 days, for the breast cancer cell line.nnThese results offer promising clinical perspectives for the personalized prediction of tumor age from limited data at diagnosis. In turn, such predictions could be helpful for assessing the extent of invisible metastasis at the time of diagnosis.nnAuthor summaryMathematical models for tumor growth kinetics have been widely used since several decades but mostly fitted to individual or average growth curves. Here we compared three classical models (Exponential, Logistic and Gompertz) using a population approach, which accounts for inter-animal variability. The Exponential and the Logistic models failed to fit the experimental data while the Gompertz model showed excellent descriptive power. Moreover, the strong correlation between the two parameters of the Gompertz equation motivated a simplification of the model, the reduced Gompertz model, with a single individual parameter and equal descriptive power. Combining the mixed-effects approach with Bayesian inference, we predicted the age of individual tumors with only few late measurements. Thanks to its simplicity, the reduced Gompertz model showed superior predictive power. Although our method remains to be extended to clinical data, these results are promising for the personalized estimation of the age of a tumor from limited measurements at diagnosis. Such predictions could contribute to the development of computational models for metastasis. ]]> Vaghi, C. Rodallec, A. Fanciullino, R. Ciccolini, J. Mochel, J. Mastri, M. Poignard, C. Ebos, J. M. Benzekry, S. 2019-06-13 doi:10.1101/670869 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ Recycling RNA-Seq Data to Identify Candidate Orphan Genes for experimental analysis ]]> https://biorxiv.org/content/10.1101/671263v1?rss=1 Li, J. Arendsee, Z. Singh, U. Wurtele, E. S. 2019-06-21 doi:10.1101/671263 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Switching between bacteriostatic and bactericidal antimicrobials for retreatment of bovine respiratory disease (BRD) relapses is associated with an increased frequency of resistant pathogen isolation from veterinary diagnostic laboratory submissions ]]> https://biorxiv.org/content/10.1101/675066v1?rss=1 Coetzee, J. Magstadt, D. R. Follett, L. Sidhu, P. K. Schuler, A. M. Krull, A. C. Cooper, V. L. Engelken, T. J. OConnor, A. M. 2019-06-18 doi:10.1101/675066 Cold Spring Harbor Laboratory Press 2019-06-18 <![CDATA[ Oncoprotein GT198 is a direct target of taxol ]]> https://biorxiv.org/content/10.1101/675579v1?rss=1 Yang, Z. Gurvich, V. J. Gupta, M. L. Mivechi, N. F. Ko, L. 2019-06-19 doi:10.1101/675579 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ Conformational dynamics of FERM-mediated autoinhibition in Pyk2 tyrosine kinase. ]]> https://biorxiv.org/content/10.1101/681932v1?rss=1 nView larger version (41K):norg.highwire.dtl.DTLVardef@36bf36org.highwire.dtl.DTLVardef@43afe2org.highwire.dtl.DTLVardef@1d0489forg.highwire.dtl.DTLVardef@14fecc9_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Loving, H. S. Underbakke, E. S. 2019-06-24 doi:10.1101/681932 Cold Spring Harbor Laboratory Press 2019-06-24 <![CDATA[ Yield, nutritional quality, and fatty acid content of organic winter rye (Secale cereale) and winter wheat (Triticum aestivum) forages under cattle (Bos taurus) grazing conditions ]]> https://biorxiv.org/content/10.1101/688952v1?rss=1 Phillips, H. Heins, B. J. Delate, K. Turnbull, R. 2019-07-01 doi:10.1101/688952 Cold Spring Harbor Laboratory Press 2019-07-01 <![CDATA[ Automated methods enable direct computation on phenotypic descriptions for novel candidate gene prediction ]]> https://biorxiv.org/content/10.1101/689976v1?rss=1 Braun, I. R. Lawrence-Dill, C. J. 2019-07-03 doi:10.1101/689976 Cold Spring Harbor Laboratory Press 2019-07-03 <![CDATA[ Genetic immunodeficiency and autoimmune disease reveal distinct roles of Hem1 in the WAVE2 and mTORC2 complexes ]]> https://biorxiv.org/content/10.1101/692004v1?rss=1 Comrie, W. A. Poli, M. C. Cook, S. A. Similuk, M. Oler, A. Faruqi, A. J. Kuhns, D. B. Yang, S. Carisey, A. F. Fournier, B. Anderson, D. E. Price, S. Chahla, W. A. Vargas-Hernandez, A. Forbes, L. R. Mace, E. M. Cao, T. N. Coban-Akdemir, Z. H. Jhangiani, S. N. Muzny, D. M. Gibbs, R. A. Lupski, J. R. Orange, J. S. Cuvelier, G. D. E. Al Hassani, M. AL Kaabi, N. Al Yafei, Z. Jyonouchi, S. Raje, N. Caldwell, J. W. Huang, Y. Burkhardt, J. K. Latour, S. Chen, B. ElGhazali, G. Rao, V. K. Chinn, I. K. Lenardo, M. J. 2019-07-04 doi:10.1101/692004 Cold Spring Harbor Laboratory Press 2019-07-04 <![CDATA[ MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets ]]> https://biorxiv.org/content/10.1101/698969v1?rss=1 Singh, U. Hur, M. Dorman, K. Wurtele, E. 2019-07-14 doi:10.1101/698969 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ Coupling Day Length Data and Genomic Prediction tools for Predicting Time-Related Traits under Complex Scenarios ]]> https://biorxiv.org/content/10.1101/703488v1?rss=1 Jarquin, D. Kajiya-Kanegae, H. Taishen, C. Yabe, S. Persa, R. Yu, J. Nakagawa, H. Yamazaki, M. Iwata, H. 2019-07-16 doi:10.1101/703488 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ A hierarchical Bayesian latent class mixture model with censorship for detection of linear temporal changes in antibiotic resistance ]]> https://biorxiv.org/content/10.1101/705897v1?rss=1 Zhang, M. Wang, C. O'Connor, A. 2019-07-17 doi:10.1101/705897 Cold Spring Harbor Laboratory Press 2019-07-17 <![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[ Endocytic Clathrin Coats Develop Curvature at Early Stages of Their Formation ]]> https://biorxiv.org/content/10.1101/715219v1?rss=1 Willy, N. Ferguson, J. Silahli, S. Cakez, C. Hasan, F. Chang, H. Travesset, A. Li, S. Zandi, R. Li, D. Betzig, E. Cocucci, E. Kural, C. 2019-07-26 doi:10.1101/715219 Cold Spring Harbor Laboratory Press 2019-07-26 <![CDATA[ Uncover the Mechanism of Nucleotide Import by HIV-1 Capsid ]]> https://biorxiv.org/content/10.1101/717173v1?rss=1 Song, G. 2019-07-28 doi:10.1101/717173 Cold Spring Harbor Laboratory Press 2019-07-28 <![CDATA[ Host-specific subtelomere: Genomic architecture of pathogen emergence in asexual filamentous fungi ]]> https://biorxiv.org/content/10.1101/721753v1?rss=1 Huang, X. 2019-08-01 doi:10.1101/721753 Cold Spring Harbor Laboratory Press 2019-08-01 <![CDATA[ A prospective role for the rumen in generating antibiotic resistance ]]> https://biorxiv.org/content/10.1101/729681v1?rss=1 Strachan, C. R. Mueller, A. J. Ghanbari, M. Neubauer, V. Zwirzitz, B. Thalguter, S. Dzieciol, M. Wetzels, S. U. Zanghellini, J. Wagner, M. Schmitz-Esser, S. Mann, E. 2019-08-12 doi:10.1101/729681 Cold Spring Harbor Laboratory Press 2019-08-12 <![CDATA[ Integrated Multi-omic Framework of the Plant Response to Jasmonic Acid ]]> https://biorxiv.org/content/10.1101/736363v1?rss=1 Zander, M. Lewsey, M. G. Clarke, N. M. Yin, L. Bartlett, A. Saldierna Guzman, J. P. Hann, E. Langford, A. Jow, B. Wise, A. Nery, J. R. Chen, H. Bar-Joseph, Z. Walley, J. Solano, R. Ecker, J. R. 2019-08-19 doi:10.1101/736363 Cold Spring Harbor Laboratory Press 2019-08-19 <![CDATA[ Characterizing allele-by-environment interactions using maize introgression lines ]]> https://biorxiv.org/content/10.1101/738070v1?rss=1 90% B73 genetic background and multiple Mo17 introgressions were grown in 16 different environments. These environments included five geographical locations with multiple planting dates and multiple planting densities. The phenotypic impact of the introgressions was evaluated for up to 26 traits that span different growth stages in each environment to assess allele-by-environment interactions. Results from this study showed that small portions of the genome can drive significant genotype-by-environment interaction across a wide range of vegetative and reproductive traits, and the magnitude of the allele-by-environment interaction varies across traits. Some introgressed segments were more prone to genotype-by-environment interaction than others when evaluating the interaction on a whole plant basis throughout developmental time, indicating variation in phenotypic plasticity throughout the genome. Understanding the profile of allele-by-environment interaction is useful in considerations of how small introgressions of QTL or transgene containing regions might be expected to impact traits in diverse environments.nnKey MessageSignificant allele-by-environment interactions are observed for traits throughout development from small introgressed segments of the genome. ]]> Li, Z. Tirado, S. B. Kadam, D. C. Coffey, L. Miller, N. D. Spalding, E. P. Lorenz, A. J. de Leon, N. Kaeppler, S. M. Schnable, P. S. Springer, N. M. Hirsch, C. N. 2019-08-16 doi:10.1101/738070 Cold Spring Harbor Laboratory Press 2019-08-16 <![CDATA[ The maize Hairy Sheath Frayed1 (Hsf1) mutant alters leaf patterning through increased cytokinin signaling ]]> https://biorxiv.org/content/10.1101/743898v1?rss=1 Muszynski, M. G. Moss-Taylor, L. Chudalayandi, S. Cahill, J. F. Del-Valle Echevarria, A. R. Alvarez-Castro, I. Petefish, A. Sakakibara, H. Krivosheev, D. M. Lomin, S. N. Romanov, G. A. Thamotharan, S. Dam, T. Li, B. Brugiere, N. 2019-08-22 doi:10.1101/743898 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[ Receptor-Like Kinase Phosphorylation of Arabidopsis Heterotrimeric G-Protein Gα - Subunit AtGPA1 ]]> https://biorxiv.org/content/10.1101/752337v1?rss=1 Jia, H. Song, G. Werth, E. G. Walley, J. W. Hicks, L. M. Jones, A. M. 2019-08-31 doi:10.1101/752337 Cold Spring Harbor Laboratory Press 2019-08-31 <![CDATA[ EXP1 is required for organization of the intraerythrocytic malaria parasite vacuole ]]> https://biorxiv.org/content/10.1101/752634v1?rss=1 Nessel, T. Beck, J. M. Rayatpisheh, S. Jami-Alahmadi, Y. Wohlschlegel, J. A. Goldberg, D. E. Beck, J. R. 2019-08-31 doi:10.1101/752634 Cold Spring Harbor Laboratory Press 2019-08-31 <![CDATA[ Cytokinin promotes jasmonic acid accumulation in the control of maize leaf growth. ]]> https://biorxiv.org/content/10.1101/760405v1?rss=1 Uyehara, A. N. Del Valle-Echevarria, A. R. Hunter, C. T. Nelissen, H. Demuynck, K. James, C. F. Jander, G. Muszynski, M. G. 2019-09-06 doi:10.1101/760405 Cold Spring Harbor Laboratory Press 2019-09-06 <![CDATA[ A method of back-calculating the log odds ratio and standard error of the log odds ratio from the reported group-level risk of disease ]]> https://biorxiv.org/content/10.1101/760942v1?rss=1 Hu, D. Wang, C. O'Connor, A. 2019-09-06 doi:10.1101/760942 Cold Spring Harbor Laboratory Press 2019-09-06 <![CDATA[ Establishing the phenotypic basis of adherent-invasive Escherichia coli (AIEC) pathogenicity in intestinal inflammation ]]> https://biorxiv.org/content/10.1101/772012v1?rss=1 Kittana, H. Gomes Neto, J. C. Heck, K. Sughroue, J. Xian, Y. Mantz, S. Segura Munoz, R. R. Cody, L. A. Schmaltz, R. J. Anderson, C. L. Moxley, R. A. Hostetter, J. M. Fernando, S. C. Clarke, J. Kachman, S. D. Cressler, C. E. Benson, A. K. Walter, J. Ramer-Tait, A. E. 2019-09-18 doi:10.1101/772012 Cold Spring Harbor Laboratory Press 2019-09-18 <![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[ Phylogenetic relationships of heteroscleromorph demosponges and the affinity of the genus Myceliospongia (Demospongiae incertae sedis) ]]> https://biorxiv.org/content/10.1101/793372v1?rss=1 Lavrov, D. V. Maldonado, M. Perez, T. Morrow, C. 2019-10-04 doi:10.1101/793372 Cold Spring Harbor Laboratory Press 2019-10-04 <![CDATA[ Exact Distribution of Linkage Disequilibrium in the Presence of Mutation, Selection or Minor Allele Frequency Filtering ]]> https://biorxiv.org/content/10.1101/794347v1?rss=1 Cheng, H. Qu, J. Fernando, R. L. Garrick, D. Kachman, S. 2019-10-07 doi:10.1101/794347 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ GenomeQC: A quality assessment tool for genome assemblies and gene structure annotations ]]> https://biorxiv.org/content/10.1101/795237v1?rss=1 Manchanda, N. Lawrence-Dill, C. J. Hufford, M. Andorf, C. M. Woodhouse, M. R. Seetharam, A. Portwood, J. L. 2019-10-07 doi:10.1101/795237 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Highly expressed maize pollen genes display coordinated expression with neighboring transposable elements and contribute to pollen fitness ]]> https://biorxiv.org/content/10.1101/796060v1?rss=1 Warman, C. Panda, K. Vejlupkova, Z. Hokin, S. Unger-Wallace, E. Cole, R. A. Chettoor, A. M. Jiang, D. Vollbrecht, E. Evans, M. M. Slotkin, R. K. Fowler, J. E. 2019-10-07 doi:10.1101/796060 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ TEsorter: lineage-level classification of transposable elements using conserved protein domains ]]> https://biorxiv.org/content/10.1101/800177v1?rss=1 Zhang, R.-G. Wang, Z.-X. Ou, S. Li, G.-Y. 2019-10-10 doi:10.1101/800177 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Malaria parasite immune evasion and adaptation to its mosquito host is influenced by the acquisition of multiple blood meals ]]> https://biorxiv.org/content/10.1101/801480v1?rss=1 Kwon, H. Reynolds, R. A. Simoes, M. L. Dimopoulos, G. Smith, R. C. 2019-10-15 doi:10.1101/801480 Cold Spring Harbor Laboratory Press 2019-10-15 <![CDATA[ Genetic regulators of mineral amount in Nelore cattle muscle predicted by a new co-expression and regulatory impact factor approach ]]> https://biorxiv.org/content/10.1101/804419v1?rss=1 Afonso, J. Fortes, M. R. S. Reverter-Gomez, A. Diniz, W. Cesar, A. de Lima, A. Petrini, J. de Souza, M. Coutinho, L. Mourao, G. Zerlotini, A. Gromboni, C. Nogueira, A. R. Regitano, L. 2019-10-15 doi:10.1101/804419 Cold Spring Harbor Laboratory Press 2019-10-15 <![CDATA[ Identification of a small molecule that stimulates human beta-cell proliferation and insulin secretion, and protects against cytotoxic stress in rat insulinoma cells ]]> https://biorxiv.org/content/10.1101/804807v1?rss=1 Hohmeier, H. E. Zhang, L. Taylor, B. Stephens, S. McNamara, P. Laffitte, B. Newgard, C. 2019-10-14 doi:10.1101/804807 Cold Spring Harbor Laboratory Press 2019-10-14 <![CDATA[ Mitochondrial Dysfunction Induces Epigenetic Dysregulation by H3K27 Hyperacetylation to Perturb Active Enhancers in Parkinson’s Disease Models ]]> https://biorxiv.org/content/10.1101/808246v1?rss=1 Huang, M. Lou, D. Charli, A. Kong, D. Jin, H. Anantharam, V. Kanthasamy, A. Wang, Z. Kanthasamy, A. 2019-10-17 doi:10.1101/808246 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Gene Ontology Meta Annotator for Plants ]]> https://biorxiv.org/content/10.1101/809988v1?rss=1 Wimalanathan, K. Lawrence-Dill, C. J. 2019-10-18 doi:10.1101/809988 Cold Spring Harbor Laboratory Press 2019-10-18 <![CDATA[ Replaying the evolutionary tape to investigate subgenome dominance in allopolyploidBrassica napus ]]> https://biorxiv.org/content/10.1101/814491v1?rss=1 Bird, K. A. Niederhuth, C. Ou, S. A. Gehan, M. A. Pires, J. C. Xiong, Z. VanBuren, R. Edger, P. P. 2019-10-22 doi:10.1101/814491 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Transcriptomic Profile Analysis of Brain Inferior Colliculus Following Acute Hydrogen Sulfide Exposure ]]> https://biorxiv.org/content/10.1101/816710v1?rss=1 1.5). Hydrogen sulfide exposure modulated multiple biological pathways including unfolded protein response, neurotransmitters, oxidative stress, hypoxia, calcium signaling, and inflammatory response in the IC. Hydrogen sulfide exposure activated PI3K/Akt and MAPK signaling pathways. Pro-inflammatory cytokines were shown to be potential initiators of the modulated signaling pathways following H2S exposure. Furthermore, microglia were shown to release IL-18 and astrocytes released both IL-1{beta} and IL-18 in response to H2S. This transcriptomic analysis data revealed complex signaling pathways involved in H2S-induced neurotoxicity and may provide important associated mechanistic insights. HighlightsO_LITranscriptomic profiling analyses following acute exposure to H2S were performed C_LIO_LIMultiple signaling pathways were dysregulated following H2S exposure C_LIO_LIPI3K/Akt and MAPK signaling pathways were activated after H2S exposure C_LIO_LIMRI scan analysis revealed lesions in the IC and TH following H2S exposure C_LIO_LIAcute H2S exposure induced a neuroinflammatory response C_LI ]]> Kim, D.-S. Anantharam, P. Padhi, P. Thedens, D. R. Li, G. Gilbreath, E. Rumbeiha, W. K. 2019-10-24 doi:10.1101/816710 Cold Spring Harbor Laboratory Press 2019-10-24 <![CDATA[ 20-hydroxyecdysone (20E) primes innate immune responses that limit bacteria and malaria parasite survival in Anopheles gambiae ]]> https://biorxiv.org/content/10.1101/818526v1?rss=1 Reynolds, R. A. Kwon, H. Smith, R. C. 2019-10-28 doi:10.1101/818526 Cold Spring Harbor Laboratory Press 2019-10-28 <![CDATA[ Causes and consequences of mitochondrial proteome size-variation in animals ]]> https://biorxiv.org/content/10.1101/829127v1?rss=1 Muthye, V. R. Lavrov, D. V. 2019-11-05 doi:10.1101/829127 Cold Spring Harbor Laboratory Press 2019-11-05 <![CDATA[ A multiple-trait Bayesian Lasso for genome-enabled analysis and prediction of complex traits ]]> https://biorxiv.org/content/10.1101/852749v1?rss=1 GIANOLA, D. FERNANDO, R. L. 2019-11-22 doi:10.1101/852749 Cold Spring Harbor Laboratory Press 2019-11-22 <![CDATA[ Systems analyses of key metabolic modules of floral and extrafloral nectaries of cotton ]]> https://biorxiv.org/content/10.1101/857771v1?rss=1 Chatt, E. C. Mahalim, S.-N. Mohd-Fadzil, N.-A. Roy, R. Klinkenberg, P. M. Horner, H. T. Hampton, M. Carter, C. J. Nikolau, B. J. 2019-11-27 doi:10.1101/857771 Cold Spring Harbor Laboratory Press 2019-11-27 <![CDATA[ Effect of Sequence Depth and Length in Long-read Assembly of the Maize Inbred NC358 ]]> https://biorxiv.org/content/10.1101/858365v1?rss=1 Ou, S. LIU, J. Chougule, K. M. Fungtammasan, A. Seetharam, A. Stein, J. Llaca, V. MANCHANDA, N. Gilbert, A. M. Wei, X. Chin, C.-S. Hufnagel, D. E. Pedersen, S. Snodgrass, S. Fengler, K. Woodhouse, M. Walenz, B. P. Koren, S. Phillippy, A. M. Hannigan, B. T. Dawe, R. K. Hirsch, C. Hufford, M. Ware, D. 2019-11-29 doi:10.1101/858365 Cold Spring Harbor Laboratory Press 2019-11-29 <![CDATA[ Contacting domains that segregate lipid from solute transporters in malaria parasites ]]> https://biorxiv.org/content/10.1101/863993v1?rss=1 Garten, M. Beck, J. R. Roth, R. Tenkova-Heuser, T. Heuser, J. Bleck, C. K. Goldberg, D. E. Zimmerberg, J. 2019-12-06 doi:10.1101/863993 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ The tuatara genome: insights into vertebrate evolutionfrom the sole survivor of an ancient reptilian order ]]> https://biorxiv.org/content/10.1101/867069v1?rss=1 Gemmell, N. Rutherford, K. Prost, S. Tollis, M. Winter, D. J. Macey, J. R. Adelson, D. L. Suh, A. Bertozzi, T. Grau, J. Organ, C. Gardner, P. Muffato, M. Patricio, M. Billis, K. Martin, F. J. Flicek, P. Petersen, B. Kang, L. Michalak, P. Buckley, T. Wilson, M. A. Cheng, Y. Miller, H. Schott, R. K. Jordan, M. Newcomb, R. Arroyo, J. I. Valenzuela, N. Hore, T. A. Renart, J. Peona, V. Peart, C. Warmuth, V. ZENG, L. Kortschak, D. Raison, J. M. Zapata, V. V. Wu, Z. Santesmasses, D. Mariotti, M. Guigo, R. Rupp, S. Twort, V. Dussex, N. Taylor, H. R. Abe, H 2019-12-08 doi:10.1101/867069 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ Unraveling a tangled skein: Evolutionary analysis of the bacterial gibberellin biosynthetic operon ]]> https://biorxiv.org/content/10.1101/868042v1?rss=1 Nett, R. S. Nguyen, N. N. Nagel, R. Marcassa, A. Charles, T. C. Friedberg, I. Peters, R. J. 2019-12-08 doi:10.1101/868042 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ Using large soybean historical data to study genotype by environment variation and identify mega-environments with the integration of genetic and non-genetic factors ]]> https://biorxiv.org/content/10.1101/2022.04.11.487885v1?rss=1 Dalsente Krause, M. Olimpio das Gracas Dias, K. Singh, A. K. Beavis, W. D. 2022-04-11 doi:10.1101/2022.04.11.487885 Cold Spring Harbor Laboratory Press 2022-04-11 <![CDATA[ Extracellular vesicles secreted by Brugia malayi microfilariae modulate the melanization pathway in the mosquito host ]]> https://biorxiv.org/content/10.1101/2022.04.11.487926v1?rss=1 Loghry, H. J. Kwon, H. Smith, R. C. Sondjaja, N. A. Minkler, S. Young, S. Wheeler, N. J. Zamanian, M. Bartholomay, L. Kimber, M. J. 2022-04-12 doi:10.1101/2022.04.11.487926 Cold Spring Harbor Laboratory Press 2022-04-12 <![CDATA[ A chromosome-scale genome assembly of a Bacillus thuringiensis Cry1Ac insecticidal protein resistant strain of Helicoverpa zea ]]> https://biorxiv.org/content/10.1101/2022.04.12.488070v1?rss=1 Stahlke, A. R. Chang, J. Tembrock, L. R. Sim, S. B. Chudalayandi, S. Geib, S. M. Scheffler, B. R. Perera, O. P. Gilligan, T. M. Childers, A. K. Hackett, K. J. Coates, B. S. 2022-04-12 doi:10.1101/2022.04.12.488070 Cold Spring Harbor Laboratory Press 2022-04-12 <![CDATA[ The field of protein function prediction as viewed by different domain scientists ]]> https://biorxiv.org/content/10.1101/2022.04.18.488641v1?rss=1 Ramola, R. Friedberg, I. Radivojac, P. 2022-04-18 doi:10.1101/2022.04.18.488641 Cold Spring Harbor Laboratory Press 2022-04-18 <![CDATA[ CAPG: Comprehensive Allopolyploid Genotyper ]]> https://biorxiv.org/content/10.1101/2022.04.21.488948v1?rss=1 Kulkarni, R. Zhang, Y. Cannon, S. B. Dorman, K. S. 2022-04-22 doi:10.1101/2022.04.21.488948 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Powdery mildew effectors AVRA1 and BEC1016 target the ER J-domain protein HvERdj3B required for immunity in barley ]]> https://biorxiv.org/content/10.1101/2022.04.27.489729v1?rss=1 Li, Z. Velasquez-Zapata, V. Elmore, J. M. Li, X. Xie, W. Banerjee, S. Jorgensen, H. J. L. Pedersen, C. Wise, R. P. Thordal-Christensen, H. 2022-04-29 doi:10.1101/2022.04.27.489729 Cold Spring Harbor Laboratory Press 2022-04-29 <![CDATA[ A QuantCrit investigation of society's educational debts due to racism, sexism, and classism in biology student learning ]]> https://biorxiv.org/content/10.1101/2022.05.05.490808v1?rss=1 Nissen, J. Van Dusen, B. Kukday, S. 2022-05-06 doi:10.1101/2022.05.05.490808 Cold Spring Harbor Laboratory Press 2022-05-06 <![CDATA[ Population genomics provide insights into the global genetic structure of Colletotrichum graminicola, the causal agent of maize anthracnose ]]> https://biorxiv.org/content/10.1101/2022.05.07.490914v1?rss=1 Rogerio, F. Baroncelli, R. Cuevas-Fernandez, F. B. Becerra, S. Crouch, J. A. Bettiol, W. Azcarate-Peril, M. A. Malapi-Wigh, M. Ortega, V. Betran, J. Tenuta, A. Dambolena, J. S. Esker, P. Revilla, P. Jackson-Ziems, T. Hiltbrunner, J. Munkvold, G. Buhinicek, I. Vicente-Villardon, J. L. Sukno, S. A. Thon, M. R. 2022-05-09 doi:10.1101/2022.05.07.490914 Cold Spring Harbor Laboratory Press 2022-05-09 <![CDATA[ Structures reveal a key mechanism of WAVE Regulatory Complex activation by Rac1 GTPase ]]> https://biorxiv.org/content/10.1101/2022.05.10.491380v1?rss=1 Ding, B. Yang, S. Schaks, M. Liu, Y. Brown, A. Rottner, K. Chowdhury, S. Chen, B. 2022-05-10 doi:10.1101/2022.05.10.491380 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Dendrite branching receptor HPO-30 uses two novel mechanisms to regulate actin cytoskeletal remodeling ]]> https://biorxiv.org/content/10.1101/2022.05.13.491788v1?rss=1 Kramer, D. A. Narvaez-Ortiz, H. Y. Roche, J. Nolen, B. J. Chen, B. 2022-05-13 doi:10.1101/2022.05.13.491788 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Arf GTPase activates the WAVE Regulatory Complex through a novel binding site ]]> https://biorxiv.org/content/10.1101/2022.05.13.491857v1?rss=1 Yang, S. Liu, Y. Brown, A. Schaks, M. Ding, B. Kramer, D. A. Ding, L. Alekhina, O. Billadeau, D. D. Chowdhury, S. Wang, J. Rottner, K. Chen, B. 2022-05-13 doi:10.1101/2022.05.13.491857 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Mammary Tissue-Derived Extracellular Matrix Hydrogels Reveal the Role of the Irradiated Microenvironment in Breast Cancer Recurrence ]]> https://biorxiv.org/content/10.1101/2022.05.16.492117v1?rss=1 Zhu, T. Alves, S. M. Adamo, A. Wen, X. Corn, K. C. Shostak, A. Shaub, N. D. Hacker, B. C. D'Amore, A. Bardhan, R. Rafat, M. 2022-05-16 doi:10.1101/2022.05.16.492117 Cold Spring Harbor Laboratory Press 2022-05-16 <![CDATA[ Identifying novel regulators of placental development using time series transcriptomic data and network analyses ]]> https://biorxiv.org/content/10.1101/2022.05.17.492330v1?rss=1 Vu, H. T. H. Kaur, H. Kies, K. R. Starks, R. R. Tuteja, G. 2022-05-17 doi:10.1101/2022.05.17.492330 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ Semi-field and surveillance data define the natural diapause timeline for Culex pipiens across the United States ]]> https://biorxiv.org/content/10.1101/2022.05.19.492729v1?rss=1 Field, E. N. Shepard, J. J. Clifton, M. E. Price, K. J. Witmier, B. J. Johnson, K. Boze, B. Abadam, C. Ebel, G. D. Armstrong, P. M. Barker, C. M. Smith, R. C. 2022-05-20 doi:10.1101/2022.05.19.492729 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Secreted filarial nematode galectins modulate host immune cells ]]> https://biorxiv.org/content/10.1101/2022.05.23.493127v1?rss=1 Loghry, H. J. Sondjaja, N. A. Minkler, S. Kimber, M. J. 2022-05-23 doi:10.1101/2022.05.23.493127 Cold Spring Harbor Laboratory Press 2022-05-23 <![CDATA[ FcRγ- NK cell induction by specific CMV and expansion by subclinical viral infections in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2022.05.26.493509v1?rss=1 Lee, J. Chang, W. Scott, J. M. Hong, S. Lee, T. Deere, J. D. Park, P. Sparger, E. E. Dandekar, S. Hartigan-O'Connor, D. Barry, P. A. Kim, S. 2022-05-27 doi:10.1101/2022.05.26.493509 Cold Spring Harbor Laboratory Press 2022-05-27 <![CDATA[ MATTE: anti-noise module alignment for phenotype-gene-related analysis ]]> https://biorxiv.org/content/10.1101/2022.05.29.493935v1?rss=1 Cai, G. Zhou, Z. Gu, X. 2022-05-30 doi:10.1101/2022.05.29.493935 Cold Spring Harbor Laboratory Press 2022-05-30 <![CDATA[ CRISPR-Cas effector specificity and target mismatches determine phage escape outcomes ]]> https://biorxiv.org/content/10.1101/2022.05.30.494023v1?rss=1 Schelling, M. A. Nguyen, G. T. Sashital, D. G. 2022-05-30 doi:10.1101/2022.05.30.494023 Cold Spring Harbor Laboratory Press 2022-05-30 <![CDATA[ PAM binding ensures orientational integration during Cas4-Cas1-Cas2 mediated CRISPR adaptation ]]> https://biorxiv.org/content/10.1101/2022.05.30.494039v1?rss=1 Dhingra, Y. Suresh, S. K. Juneja, P. Sashital, D. G. 2022-05-30 doi:10.1101/2022.05.30.494039 Cold Spring Harbor Laboratory Press 2022-05-30 <![CDATA[ Complex chromosomal rearrangements induced by transposons in maize ]]> https://biorxiv.org/content/10.1101/2022.06.01.494422v1?rss=1 Sharma, S. P. Peterson, T. 2022-06-03 doi:10.1101/2022.06.01.494422 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication ]]> https://biorxiv.org/content/10.1101/2022.06.07.494775v1?rss=1 Ramaraj, T. Grover, C. E. Mendoza, A. C. Arick, M. A. Jareczek, J. J. Leach, A. G. Peterson, D. G. Wendel, J. F. Udall, J. A. 2022-06-09 doi:10.1101/2022.06.07.494775 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Accurate Estimation of Molecular Counts from Amplicon Sequence Data with Unique Molecular Identifiers ]]> https://biorxiv.org/content/10.1101/2022.06.12.495839v1?rss=1 Peng, X. Dorman, K. 2022-06-16 doi:10.1101/2022.06.12.495839 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ Nemacol is a Small Molecule Inhibitor of C. elegans Vesicular Acetylcholine Transporter with Anthelmintic Potential ]]> https://biorxiv.org/content/10.1101/2022.06.14.496146v1?rss=1 Harrington, S. Pyche, J. Burns, A. R. Spalholz, T. Baker, R. J. Ching, J. Lautens, M. Kulke, D. Deuther-Conrad, W. Brust, P. Roy, P. J. 2022-06-17 doi:10.1101/2022.06.14.496146 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Conservation at the uterine-placental interface ]]> https://biorxiv.org/content/10.1101/2022.06.14.496152v1?rss=1 Scott, R. L. Vu, H. T. H. Jain, A. Iqbal, K. Tuteja, G. Soares, M. J. 2022-06-17 doi:10.1101/2022.06.14.496152 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Temperature Sensitive Contacts in Disordered Loops Tune Enzyme I Activity ]]> https://biorxiv.org/content/10.1101/2022.06.18.496683v1?rss=1 Burns, D. Singh, A. Venditti, V. Potoyan, D. A. 2022-06-19 doi:10.1101/2022.06.18.496683 Cold Spring Harbor Laboratory Press 2022-06-19 <![CDATA[ Non-catalyzable denitrification intermediates induce nitrous oxide reduction in two purple nonsulfur bacteria ]]> https://biorxiv.org/content/10.1101/2022.06.21.497020v1?rss=1 LaSarre, B. Morlen, R. Neumann, G. C. Harwood, C. S. McKinlay, J. B. 2022-06-21 doi:10.1101/2022.06.21.497020 Cold Spring Harbor Laboratory Press 2022-06-21 <![CDATA[ L-norepinephrine induces ROS formation but alters microbial community composition by altering cellular metabolism ]]> https://biorxiv.org/content/10.1101/2022.06.28.482069v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@1d80968org.highwire.dtl.DTLVardef@51cb63org.highwire.dtl.DTLVardef@b37org.highwire.dtl.DTLVardef@e07503_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOTOC FigureC_FLOATNO C_FIG ]]> Bains, A. Dahal, S. Manna, B. Lyte, M. Kolodziej, E. P. Chaplen, F. W. R. Yang, L. Singhal, N. 2022-06-28 doi:10.1101/2022.06.28.482069 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ Establishment and Characterization of Novel Canine Organoids with Organ-Specific Physiological Similarity ]]> https://biorxiv.org/content/10.1101/2022.07.15.500059v1?rss=1 Zdyrski, C. Gabriel, V. Ospina, O. E. Wickham, H. Sahoo, D. K. Dao, K. Aguilar Meza, L. S. Bedos, L. Honold, S. Pineyro, P. Mochel, J. P. Allenspach, K. 2022-07-16 doi:10.1101/2022.07.15.500059 Cold Spring Harbor Laboratory Press 2022-07-16 <![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[ Fine-mapping and comparative genomic analysis reveal the gene composition at the S and Z self-incompatibility loci in grasses ]]> https://biorxiv.org/content/10.1101/2022.07.18.499170v1?rss=1 Rohner, M. Manzanares, C. Yates, S. Thorogood, D. Copetti, D. Lübberstedt, T. Asp, T. Studer, B. 2022-07-18 doi:10.1101/2022.07.18.499170 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ Robust probabilistic modeling for single-cell multimodal mosaic integration and imputation ]]> https://biorxiv.org/content/10.1101/2022.07.25.501456v1?rss=1 Du, J.-H. Cai, Z. Roeder, K. 2022-07-25 doi:10.1101/2022.07.25.501456 Cold Spring Harbor Laboratory Press 2022-07-25 <![CDATA[ TSNAdb v2.0: the updated version of tumor-specific neoantigen database ]]> https://biorxiv.org/content/10.1101/2022.07.28.501872v1?rss=1 Wu, J. Chen, W. Zhou, Y. Chi, Y. Hua, X. Wu, J. Gu, X. Chen, S. Zhou, Z. 2022-08-01 doi:10.1101/2022.07.28.501872 Cold Spring Harbor Laboratory Press 2022-08-01 <![CDATA[ Adoption of modern pest control systems associated with declines in butterfly abundance across Midwestern monitoring network ]]> https://biorxiv.org/content/10.1101/2022.07.29.502042v1?rss=1 Van Deynze, B. Swinton, S. M. Hennessy, D. A. Ries, L. 2022-08-02 doi:10.1101/2022.07.29.502042 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Pollinator and host sharing lead to hybridization and introgression in Panamanian free-standing figs, but not in their pollinator wasps ]]> https://biorxiv.org/content/10.1101/2022.08.04.502839v1?rss=1 Satler, J. D. Herre, E. A. Heath, T. A. Machado, C. A. Zuniga, A. G. Jander, K. C. Eaton, D. A. R. Nason, J. D. 2022-08-05 doi:10.1101/2022.08.04.502839 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Sex-based de novo transcriptome assemblies of the parasitoid wasp Encarsia suzannae, a host of the manipulative heritable symbiont Cardinium hertigii ]]> https://biorxiv.org/content/10.1101/2022.08.05.502955v1?rss=1 Schultz, D. L. Selberherr, E. Stouthamer, C. M. Doremus, M. Kelly, S. E. Hunter, M. S. Schmitz-Esser, S. 2022-08-05 doi:10.1101/2022.08.05.502955 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Plasmodesmata-located proteins regulate plasmodesmal function at specific cell interfaces in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2022.08.05.502996v1?rss=1 Li, Z. Liu, S.-L. Montes-Serey, C. Walley, J. W. Aung, K. 2022-08-07 doi:10.1101/2022.08.05.502996 Cold Spring Harbor Laboratory Press 2022-08-07 <![CDATA[ Trypanosoma brucei Mitochondrial DNA Polymerase POLIB Contains a Novel Thumb Insertion That Confers Dominant Exonuclease Activity ]]> https://biorxiv.org/content/10.1101/2022.08.12.503786v1?rss=1 Klingbeil, M. M. Nelson, S. W. Frost, M. P. Delzell, S. B. 2022-08-12 doi:10.1101/2022.08.12.503786 Cold Spring Harbor Laboratory Press 2022-08-12 <![CDATA[ Protein Fold Classification using Graph Neural Network and Protein Topology Graph ]]> https://biorxiv.org/content/10.1101/2022.08.10.503436v1?rss=1 Sayeed, S. D. Wolf, J. N. Koch, I. Song, G. 2022-08-13 doi:10.1101/2022.08.10.503436 Cold Spring Harbor Laboratory Press 2022-08-13 <![CDATA[ Single-molecule sequencing of animal mitochondrial genomes reveals chloroplast-like architecture and repeat-mediated recombination ]]> https://biorxiv.org/content/10.1101/2022.08.11.503648v1?rss=1 Sharbrough, J. Bankers, L. Cook, E. Fields, P. D. Jalinsky, J. McElroy, K. E. Neiman, M. Logsdon, J. M. Boore, J. L. 2022-08-14 doi:10.1101/2022.08.11.503648 Cold Spring Harbor Laboratory Press 2022-08-14 <![CDATA[ Leveraging prior biological knowledge improves prediction of tocochromanols in maize grain ]]> https://biorxiv.org/content/10.1101/2022.08.16.502005v1?rss=1 Tanaka, R. Wu, D. Li, X. Tibbs-Cortes, L. E. Wood, J. C. Magallanes-Lundback, M. Bornowski, N. Hamilton, J. P. Vaillancourt, B. Li, X. Deason, N. T. Schoenbaum, G. R. Buell, C. R. DellaPenna, D. Yu, J. Gore, M. A. 2022-08-16 doi:10.1101/2022.08.16.502005 Cold Spring Harbor Laboratory Press 2022-08-16 <![CDATA[ Discovering genomic islands in unannotated bacterialgenomes using sequence embedding ]]> https://biorxiv.org/content/10.1101/2022.08.25.505341v1?rss=1 Banerjee, P. Eulenstein, O. Friedberg, I. 2022-08-26 doi:10.1101/2022.08.25.505341 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Environmentally robust cis-regulatory changes underlie rapid climatic adaptation ]]> https://biorxiv.org/content/10.1101/2022.08.29.505745v1?rss=1 Ballinger, M. A. Mack, K. L. Durkin, S. M. Riddell, E. A. Nachman, M. W. 2022-09-01 doi:10.1101/2022.08.29.505745 Cold Spring Harbor Laboratory Press 2022-09-01 <![CDATA[ Innovations in double digest restriction-site associated DNA sequencing (ddRAD-Seq) method for more efficient SNP identification ]]> https://biorxiv.org/content/10.1101/2022.09.06.506835v1?rss=1 Magbanua, Z. V. Hsu, C.-y. Pechanova, O. Arick, M. Grover, C. E. Peterson, D. G. 2022-09-07 doi:10.1101/2022.09.06.506835 Cold Spring Harbor Laboratory Press 2022-09-07 <![CDATA[ A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination ]]> https://biorxiv.org/content/10.1101/2022.09.08.507226v1?rss=1 Arick, M. A. Grover, C. E. Hsu, C.-Y. Magbanua, Z. V. Pechanova, O. Miller, E. R. Thrash, A. Youngblood, R. C. Ezzell, L. Alam, M. S. Benzie, J. A. H. Hamilton, M. G. Karsi, A. Lawrence, M. L. Peterson, D. G. 2022-09-12 doi:10.1101/2022.09.08.507226 Cold Spring Harbor Laboratory Press 2022-09-12 <![CDATA[ PARNAS: Objectively Selecting the Most Representative Taxa on a Phylogeny ]]> https://biorxiv.org/content/10.1101/2022.09.12.507613v1?rss=1 Markin, A. Wagle, S. Grover, S. Vincent Baker, A. L. Eulenstein, O. Anderson, T. K. 2022-09-14 doi:10.1101/2022.09.12.507613 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ Brassinosteroid gene regulatory networks at cellular resolution ]]> https://biorxiv.org/content/10.1101/2022.09.16.508001v1?rss=1 Nolan, T. M. Vukasinovic, N. Hsu, C.-W. Zhang, J. Vanhoutte, I. Shahan, R. Taylor, I. W. Greenstreet, L. Heitz, M. Wang, P. Szekely, P. Brosnan, A. Yin, Y. Schiebinger, G. Ohler, U. Russinova, E. Benfey, P. N. 2022-09-17 doi:10.1101/2022.09.16.508001 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Transpiration and water use efficiency of sorghum canopies have a large genetic variability and are positively related under naturally high evaporative demand. ]]> https://biorxiv.org/content/10.1101/2022.09.21.508841v1?rss=1 Pilloni, R. Kakkera, A. El Ghazzal, Z. Kar, S. Kumar, A. A. Hajjarpoor, A. Affortit, P. Ribiere, W. Kholova, J. Tardieu, F. Vadez, V. 2022-09-22 doi:10.1101/2022.09.21.508841 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Global diversification of the common moonwort ferns (Botrychium lunaria group, Ophioglossaceae) was mainly driven by Pleistocene climatic shifts ]]> https://biorxiv.org/content/10.1101/2022.09.28.509846v1?rss=1 Mossion, V. Koenen, E. Grant, J. Croll, D. Farrar, D. R. Kessler, M. 2022-09-28 doi:10.1101/2022.09.28.509846 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Using Machine Learning Enabled Phenotyping To Characterize Nodulation In Three Early Vegetative Stages In Soybean ]]> https://biorxiv.org/content/10.1101/2022.09.28.509969v1?rss=1 Carley, C. Zubrod, M. Dutta, S. Singh, A. K. 2022-09-30 doi:10.1101/2022.09.28.509969 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ The PTEX pore component EXP2 is important for intrahepatic development during the Plasmodium liver stage ]]> https://biorxiv.org/content/10.1101/2022.10.02.510306v1?rss=1 Hussain, T. Linera-Gonzalez, J. Beck, J. M. Fierro, M. A. Mair, G. R. Smith, R. C. Beck, J. R. 2022-10-03 doi:10.1101/2022.10.02.510306 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ A novel knock sideways approach for Plasmodium secreted proteins reveals a surprising insensitivity to vacuolar depletion of PTEX component HSP101 ]]> https://biorxiv.org/content/10.1101/2022.10.02.510311v1?rss=1 Fierro, M. A. Hussain, T. Campin, L. J. Beck, J. R. 2022-10-03 doi:10.1101/2022.10.02.510311 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ Validation of the linear regression method to evaluate population accuracy and bias of predictions for non-linear models ]]> https://biorxiv.org/content/10.1101/2022.10.02.510518v1?rss=1 Yu, H. Fernando, R. L. Dekkers, J. C. M. 2022-10-05 doi:10.1101/2022.10.02.510518 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Functional genomics of cattle through integration of multi-omics data ]]> https://biorxiv.org/content/10.1101/2022.10.05.510963v1?rss=1 Beiki, H. Murdoch, B. M. Park, C. A. Kern, C. Kontechy, D. Becker, G. Rincon, G. Jiang, H. Zhou, H. Thorne, J. Koltes, J. E. Michal, J. J. Davenport, K. Rijnkels, M. Ross, P. J. Hu, R. Corum, S. McKay, S. Smith, T. P. L. Liu, W. Ma, W. Zhang, X. Xu, X. Han, X. Jiang, Z. Hu, Z.-L. Reecy, J. M. 2022-10-06 doi:10.1101/2022.10.05.510963 Cold Spring Harbor Laboratory Press 2022-10-06 <![CDATA[ Disentangling positive vs. relaxed selection in animal mitochondrial genomes ]]> https://biorxiv.org/content/10.1101/2022.10.05.510972v1?rss=1 Zwonitzer, K. D. Iverson, E. N. K. Sterling, J. J. Weaver, R. J. Maclaine, B. A. Havird, J. C. 2022-10-06 doi:10.1101/2022.10.05.510972 Cold Spring Harbor Laboratory Press 2022-10-06 <![CDATA[ Chromosome-scale genome assembly of the pink bollworm, Pectinophora gossypiella, a global pest of cotton ]]> https://biorxiv.org/content/10.1101/2022.10.07.511331v1?rss=1 Stahlke, A. R. Chang, J. Chudalayandi, S. Heu, C. C. Geib, S. M. Scheffler, B. E. Childers, A. K. Fabrick, J. A. 2022-10-07 doi:10.1101/2022.10.07.511331 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Differences in activity and stability drive transposable element variation in tropical and temperate maize. ]]> https://biorxiv.org/content/10.1101/2022.10.09.511471v1?rss=1 Ou, S. Collins, T. Qiu, Y. Seetharam, A. S. Menard, C. C. Manchanda, N. Gent, J. I. Schatz, M. C. Anderson, S. N. Hufford, M. B. Hirsch, C. N. 2022-10-09 doi:10.1101/2022.10.09.511471 Cold Spring Harbor Laboratory Press 2022-10-09 <![CDATA[ A human DCC variant causing mirror movement disorder reveals an essential role for the Wave regulatory complex in Netrin/DCC signaling ]]> https://biorxiv.org/content/10.1101/2022.10.13.511954v1?rss=1 Chaudhari, K. Zhang, K. Yam, P. T. Zang, Y. Kramer, D. A. Schlienger, S. Calabretta, S. Collins, M. Srour, M. Chen, B. Charron, F. Bashaw, G. J. 2022-10-17 doi:10.1101/2022.10.13.511954 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Gene regulatory network inference in soybean upon infection by Phytophthora sojae ]]> https://biorxiv.org/content/10.1101/2022.10.19.512983v1?rss=1 Hale, B. Ratnayake, S. Flory, A. Wijeratne, R. Schmidt, C. Robertson, A. Wijeratne, A. 2022-10-21 doi:10.1101/2022.10.19.512983 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ SiPhyNetwork: An R package for Simulating Phylogenetic Networks ]]> https://biorxiv.org/content/10.1101/2022.10.26.513953v1?rss=1 Justison, J. Solis-Lemus, C. Heath, T. A. 2022-10-28 doi:10.1101/2022.10.26.513953 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Evasive spike variants elucidate the preservation of T cell immune response to the SARS-CoV-2 omicron variant ]]> https://biorxiv.org/content/10.1101/2022.11.04.515139v1?rss=1 Solanki, A. Cornette, J. Udell, J. Vasmatzis, G. Riedel, M. 2022-11-10 doi:10.1101/2022.11.04.515139 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ Rickettsia parkeri Hijacks Tick Hemocytes to Manipulate Cellular and Humoral Transcriptional Responses ]]> https://biorxiv.org/content/10.1101/2022.11.09.515877v1?rss=1 11,000 of which were immune genes. Silencing two differentially regulated phagocytic immune marker genes (nimrod B2 and eater) significantly reduced hemocyte phagocytosis. Together, these findings represent a significant step forward in understanding how hemocytes regulate microbial homeostasis and vector competence. ]]> Adegoke, A. Ribeiro, J. M. C. Brown, S. Smith, R. C. Karim, S. 2022-11-10 doi:10.1101/2022.11.09.515877 Cold Spring Harbor Laboratory Press 2022-11-10 <![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[ Exploring the distribution of phylogenetic networks generated under a birth-death-hybridization process ]]> https://biorxiv.org/content/10.1101/2022.11.10.516033v1?rss=1 Justison, J. Heath, T. A. 2022-11-14 doi:10.1101/2022.11.10.516033 Cold Spring Harbor Laboratory Press 2022-11-14 <![CDATA[ FASSO: An AlphaFold based method to assign functional annotations by combining sequence and structure orthology ]]> https://biorxiv.org/content/10.1101/2022.11.10.516002v1?rss=1 Andorf, C. M. Sen, S. Hayford, R. K. Portwwod, J. L. Cannon, E. K. Harper, L. C. Gardiner, J. M. Sen, T. Z. Woodhouse, M. R. 2022-11-15 doi:10.1101/2022.11.10.516002 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Breakthrough: A First-In-Class Virtual Simulator for Dose Optimization of ACE Inhibitors in Veterinary Cardiology ]]> https://biorxiv.org/content/10.1101/2022.11.14.516497v1?rss=1 0.25 mg/kg P.O, thereby providing a rationale for the European label dose of 0.25 mg/kg P.O q24h in dogs with cardiovascular diseases. However, most of these earlier studies on benazepril pharmacodynamics relied on measures of ACE activity - a sub-optimal endpoint to characterize the effect of benazepril on the RAAS. Nonlinear mixed-effects (NLME) modeling is an established framework for characterizing the effect of therapeutics on complex biological systems, such as the RAAS cascade. Importantly for therapeutic schedule optimization, one can use such a model to predict the outcomes of various hypothetical dosing schedules via simulation. The objectives of this study were (i) to expand on previous NLME modeling efforts of the dose-exposure-response relationship of benazepril on biomarkers of the RAAS which are relevant to CHF pathophysiology and disease prognosis {angiotensins I, II, III, IV, (1-7)} by using a quantitative systems pharmacology (QSP) modeling approach; and (ii) to develop a software implementation of the model capable of simulating clinical trials in benazepril in dogs bedside dose optimization. This study expands on previous modeling efforts to characterize the changes in RAAS pharmacodynamics in response to benazepril administration and showcase how QSP modeling can be used for efficient dose optimization of ACEis at the bedside. Our results suggest that 0.5 mg/kg PO q12h of benazepril produced the most robust reduction in AngII and upregulation of RAAS alternative pathway biomarkers. This model will eventually be expanded to include relevant clinical endpoints, which will be evaluated in an upcoming prospective trial in canine patients with CHF. AO_SCPLOWUTHORC_SCPLOW SO_SCPLOWUMMARYC_SCPLOWCongestive heart failure (CHF) is a disease of the heart, common to both dogs and humans, where the heart is not healthy enough to pump blood around the body efficiently. Because the blood isnt moving around the body as efficiently, it tends to get congested in various areas of the body and increases strain on the heart. Benazepril is a drug for CHF used in both dogs and humans to reduce congestion and improve the functioning of the cardiovascular system. Although benazepril is effective, theres evidence that suggests the dosing could be improved if the therapeutic was further studied. In this experiment, we tested benazepril at several safe dosages in well-cared for and healthy dogs to collect data on the relationship between dose size, dosing frequency, and effect on the cardiovascular system. Using this data, we built computer models of benazepril to simulate many clinical trials. By studying these simulations, we were able to make several predictions about the optimal dosing schedule of benazepril in dogs. Weve also built a web-app version of the computer model for veterinary researchers to use, modify, and study. This work also provides a platform and roadmap for optimizing benazepril dosages in human CHF. ]]> Schneider, B. K. Ward, J. Sotillo, S. Garelli-Paar, C. Guillot, E. Prikazsky, M. Mochel, J. P. 2022-11-16 doi:10.1101/2022.11.14.516497 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Nod1-dependent NF-kB activation initiates hematopoietic stem cell specification in response to small Rho GTPases ]]> https://biorxiv.org/content/10.1101/2022.11.19.517153v1?rss=1 Cheng, X. Barakat, R. Gorden, A. Snella, E. Zhang, Y. Dorman, K. Fidanza, A. Campbell, C. A. Espin Palazon, R. 2022-11-19 doi:10.1101/2022.11.19.517153 Cold Spring Harbor Laboratory Press 2022-11-19 <![CDATA[ Self-Supervised Maize Kernel Classification and Segmentation for Embryo Identification ]]> https://biorxiv.org/content/10.1101/2022.11.25.517990v1?rss=1 Dong, D. Nagasubramanian, K. Wang, R. Frei, U. K. Jubery, T. Z. Lübberstedt, T. Ganapathysubramanian, B. 2022-11-26 doi:10.1101/2022.11.25.517990 Cold Spring Harbor Laboratory Press 2022-11-26 <![CDATA[ Evolution along allometric lines of least resistance: Morphological differentiation in Pristurus geckos ]]> https://biorxiv.org/content/10.1101/2022.11.28.518148v1?rss=1 Tejero-Cicuendez, H. Menendez, I. Talavera, A. Riano, G. Burriel-Carranza, B. Simo-Riudalbas, M. Carranza, S. Adams, D. C. 2022-11-28 doi:10.1101/2022.11.28.518148 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ Rethinking bacterial relationships in light of their molecular abilities ]]> https://biorxiv.org/content/10.1101/2022.11.28.518265v1?rss=1 Mahlich, Y. Zhu, C. Chung, H. Velaga, P. K. de Paolis Kaluza, M. C. Radivojac, P. Friedberg, I. Bromberg, Y. 2022-11-29 doi:10.1101/2022.11.28.518265 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ GOThresher: a program to remove annotation biases from protein function annotation datasets ]]> https://biorxiv.org/content/10.1101/2022.11.30.506803v1?rss=1 Joshi, P. Banerjee, S. Hu, X. Khade, P. M. Friedberg, I. 2022-12-02 doi:10.1101/2022.11.30.506803 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ The Class VIII myosin ATM1 is required for root apical meristem function ]]> https://biorxiv.org/content/10.1101/2022.11.30.518567v1?rss=1 Olatunji, D. Clark, N. M. Kelley, D. R. 2022-12-02 doi:10.1101/2022.11.30.518567 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ Activation loop phosphorylation tunes conformational dynamics underlying Pyk2 tyrosine kinase activation ]]> https://biorxiv.org/content/10.1101/2022.12.03.518986v1?rss=1 View larger version (56K): org.highwire.dtl.DTLVardef@17c310org.highwire.dtl.DTLVardef@77884org.highwire.dtl.DTLVardef@79470dorg.highwire.dtl.DTLVardef@27d8fd_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Palhano Zanela, T. M. Woudenberg, A. Romero Bello, K. G. Underbakke, E. S. 2022-12-04 doi:10.1101/2022.12.03.518986 Cold Spring Harbor Laboratory Press 2022-12-04 <![CDATA[ Cuticle development and underlying transcriptome-metabolome associations during early seedling establishment ]]> https://biorxiv.org/content/10.1101/2022.12.09.519822v1?rss=1 Chen, K. Bhunia, R. McNinch, C. Campidilli, G. Hassan, A. Li, L. Nikolau, B. J. Yandeau-Nelson, M. D. 2022-12-12 doi:10.1101/2022.12.09.519822 Cold Spring Harbor Laboratory Press 2022-12-12 <![CDATA[ Genomic loci involved in sensing environmental cues and metabolism affect seasonal coat shedding in Bos taurus and Bos indicus cattle ]]> https://biorxiv.org/content/10.1101/2022.12.14.520472v1?rss=1 Durbin, H. J. Yampara, H. Rowan, T. N. Schnabel, R. D. Koltes, J. E. Powell, J. G. Decker, J. E. 2022-12-15 doi:10.1101/2022.12.14.520472 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Reverse-zoonoses of 2009 H1N1 pandemic influenza A viruses and evolution in United States swine results in viruses with zoonotic potential ]]> https://biorxiv.org/content/10.1101/2022.12.15.520479v1?rss=1 Markin, A. Ciacci Zanella, G. Arendsee, Z. W. Zhang, J. Krueger, K. M. Gauger, P. C. Vincent Baker, A. L. Anderson, T. K. 2022-12-15 doi:10.1101/2022.12.15.520479 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Dissecting Complexity: The Hidden Impact of Application Parameters on Bioinformatics Research ]]> https://biorxiv.org/content/10.1101/2022.12.20.521257v1?rss=1 Cashman, M. Cohen, M. B. Marsh, A. L. Cottingham, R. W. 2022-12-21 doi:10.1101/2022.12.20.521257 Cold Spring Harbor Laboratory Press 2022-12-21 <![CDATA[ Genetic characterization of the zoonotic parasite Ancylostoma caninum in the central and eastern USA ]]> https://biorxiv.org/content/10.1101/2022.12.22.521591v1?rss=1 Quintana, T. A. Johnson, W. L. Ritchie, D. Smith, V. Martin, K. A. McMahan, K. Brewer, M. T. Jesudoss Chelladurai, J. R. J. 2022-12-22 doi:10.1101/2022.12.22.521591 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Accuracy of functional gene community detection in Saccharomyces cerevisiae by maximizing Generalized Modularity Density ]]> https://biorxiv.org/content/10.1101/2022.12.28.522153v1?rss=1 Singh, P. Guo, J. Li, J. Singh, U. Wurtele, E. S. Bassler, K. E. 2022-12-30 doi:10.1101/2022.12.28.522153 Cold Spring Harbor Laboratory Press 2022-12-30 <![CDATA[ Temperature-Sensitive Contact Modes Allosterically Gate TRPV3 ]]> https://biorxiv.org/content/10.1101/2023.01.02.522497v1?rss=1 Burns, D. Venditti, V. Potoyan, D. A. 2023-01-03 doi:10.1101/2023.01.02.522497 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Unsupervised Contrastive Peak Caller for ATAC-seq ]]> https://biorxiv.org/content/10.1101/2023.01.07.523108v1?rss=1 Vu, H. T. H. Zhang, Y. Tuteja, G. Dorman, K. 2023-01-08 doi:10.1101/2023.01.07.523108 Cold Spring Harbor Laboratory Press 2023-01-08 <![CDATA[ Efficiency enhancement of microparticles seeding density on the inner surface of polymer hollow microfibers using microfluidics ]]> https://biorxiv.org/content/10.1101/2023.01.16.524327v1?rss=1 Aykar, S. S. Hashemi, N. N. 2023-01-19 doi:10.1101/2023.01.16.524327 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Characterizing the Interactions of Cell Membrane-Disrupting Peptides with Lipid-Functionalized Single-Walled Carbon Nanotube Systems for Antimicrobial Screening ]]> https://biorxiv.org/content/10.1101/2023.01.25.525557v1?rss=1 View larger version (53K): org.highwire.dtl.DTLVardef@4c5645org.highwire.dtl.DTLVardef@1b3cd30org.highwire.dtl.DTLVardef@1643c6corg.highwire.dtl.DTLVardef@1bb096e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yadav, A. Kelich, P. Kallmyer, N. E. Reuel, N. F. Vukovic, L. 2023-01-25 doi:10.1101/2023.01.25.525557 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogens ]]> https://biorxiv.org/content/10.1101/2023.02.05.527183v1?rss=1 Huang, X. 2023-02-05 doi:10.1101/2023.02.05.527183 Cold Spring Harbor Laboratory Press 2023-02-05 <![CDATA[ GAUT10 is required for Arabidopsis root cell differentiation and elongation ]]> https://biorxiv.org/content/10.1101/2023.02.07.527497v1?rss=1 Dash, L. Swaminathan, S. Simura, J. Montes, C. Solanki, N. Mejia, L. Ljung, K. Zabotina, O. Kelley, D. R. 2023-02-07 doi:10.1101/2023.02.07.527497 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ The E. coli pathobiont LF82 encodes a unique variant of σ70 that results in specific gene expression changes and altered phenotypes ]]> https://biorxiv.org/content/10.1101/2023.02.08.523653v1?rss=1 Arroyo-Mendoza, M. Proctor, A. Correa-Medina, A. Brand, M. W. Rosas, V. Wannemuehler, M. J. Phillips, G. J. Hinton, D. M. 2023-02-08 doi:10.1101/2023.02.08.523653 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ Spanve: an Effective Statistical Method to Detect Spatially Variable Genes in Large-scale Spatial Transcriptomics Data ]]> https://biorxiv.org/content/10.1101/2023.02.08.527623v1?rss=1 View larger version (52K): org.highwire.dtl.DTLVardef@1574cfcorg.highwire.dtl.DTLVardef@7f3f56org.highwire.dtl.DTLVardef@1732a3org.highwire.dtl.DTLVardef@fdaafa_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cai, G. Chen, Y. Gu, X. Zhou, Z. 2023-02-08 doi:10.1101/2023.02.08.527623 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ Root associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum ]]> https://biorxiv.org/content/10.1101/2023.02.08.527764v1?rss=1 Chai, Y. N. Qi, Y. Goren, E. Sheflin, A. M. Tringe, S. Prenni, J. E. Liu, P. Schachtman, D. P. 2023-02-09 doi:10.1101/2023.02.08.527764 Cold Spring Harbor Laboratory Press 2023-02-09 <![CDATA[ Streamline unsupervised machine learning to survey and graph indel-based haplotypes from pan-genomes ]]> https://biorxiv.org/content/10.1101/2023.02.11.527743v1?rss=1 Zhang, B. Huang, H. Tibbs-Cortes, L. E. Vanous, A. Zhang, Z. Sanguinet, K. Garland-Campbell, K. A. Yu, J. Li, X. 2023-02-13 doi:10.1101/2023.02.11.527743 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ DeepTAP: an RNN-based method of TAP-binding peptide prediction in the selection of tumor neoantigens ]]> https://biorxiv.org/content/10.1101/2023.02.13.528393v1?rss=1 Zhang, X. Wu, J. Baeza, J. Gu, K. Zhou, Z. 2023-02-15 doi:10.1101/2023.02.13.528393 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Characterization of the First Turtle Organoids: A Model for Investigating Unique Adaptations with Biomedical Potential ]]> https://biorxiv.org/content/10.1101/2023.02.20.527070v1?rss=1 Zdyrski, C. Gabriel, V. Gessler, T. B. Ralston, A. Sifuentes-Romero, I. Kundu, D. Honold, S. Wickham, H. Topping, N. E. Sahoo, D. K. Bista, B. Tamplin, J. Ospina, O. Pineyro, P. Meyerholz, D. K. Allenspach, K. Mochel, J. P. Valenzuela, N. 2023-02-21 doi:10.1101/2023.02.20.527070 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Assessment of long-term trends in genetic mean and variance after the introduction of genomic selection in layers: a simulation study ]]> https://biorxiv.org/content/10.1101/2023.02.20.529187v1?rss=1 Pocrnic, I. Obsteter, J. Gaynor, R. C. Wolc, A. Gorjanc, G. 2023-02-21 doi:10.1101/2023.02.20.529187 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Rapid genotyping of porcine reproductive and respiratory syndrome virus (PRRSV) using MinION nanopore sequencing ]]> https://biorxiv.org/content/10.1101/2023.02.23.529665v1?rss=1 Caserta, L. C. Zhang, J. Pineyro, P. Diel, D. G. 2023-02-23 doi:10.1101/2023.02.23.529665 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ Litter Matters: The Importance of Decomposition Products for Soil Bacterial Diversity and abundance of key groups of the N cycle in Tropical Areas ]]> https://biorxiv.org/content/10.1101/2023.03.03.530969v1?rss=1 Diniz, P. P. Borges, B. M. F. Oliveira, A. P. d. Coelho, M. R. Aragao, O. O. d. S. Ribeiro, T. G. Rocha, F. I. Coelho, M. R. R. Dias, E. S. Cole, J. R. R. Howe, A. C. Mui, T. S. Jesus, E. d. C. 2023-03-04 doi:10.1101/2023.03.03.530969 Cold Spring Harbor Laboratory Press 2023-03-04 <![CDATA[ Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways ]]> https://biorxiv.org/content/10.1101/2023.03.07.531630v1?rss=1 Yin, L. Zander, M. Huang, S.-s. C. Xie, M. Song, L. Saldierna Guzman, J. P. Hann, E. Shanbhag, B. K. Ng, S. Jain, S. Janssen, B. J. Clark, N. M. Walley, J. Beddoe, T. Bar-Joseph, Z. Lewsey, M. G. Ecker, J. R. 2023-03-09 doi:10.1101/2023.03.07.531630 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Pathology of natural infection with highly pathogenic avian influenza virus (H5N1) clade 2.3.4.4b in wild terrestrial mammals in the United States in 2022 ]]> https://biorxiv.org/content/10.1101/2023.03.10.532068v1?rss=1 Elsmo, E. J. Wunschmann, A. Beckmen, K. B. Broughton-Neiswanger, L. B. Buckles, E. L. Ellis, J. Fitzgerald, S. D. Gerlach, R. Hawkins, S. Ip, H. Lankton, J. Lemley, E. M. Lenoch, J. Killian, M. L. Lantz, K. Long, L. Maes, R. Mainenti, M. Melotti, J. Moriarty, M. E. Nakagun, S. Ruden, R. M. Shearn-Bochsler, V. Thompson, D. Torchetti, M. K. Van Wettere, A. J. Wise, A. G. Lim, A. 2023-03-12 doi:10.1101/2023.03.10.532068 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ In vitro comparison of SARS-CoV-2 variants ]]> https://biorxiv.org/content/10.1101/2023.03.11.532212v1?rss=1 Phadke, K. S. Higdon, N. B. A. Bellaire, B. H. 2023-03-13 doi:10.1101/2023.03.11.532212 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ Uncovering the Environmental Conditions Required for Phyllachora maydis Infection and Tar Spot Development on Corn in the United States for Use as Predictive Models for Future Epidemics ]]> https://biorxiv.org/content/10.1101/2023.03.18.533264v1?rss=1 Webster, R. W. Nicolli, C. Allen, T. W. Bish, M. D. Bissonette, K. Check, J. C. Chilvers, M. I. Kleczewski, N. Mueller, B. D. Price, P. P. Paul, P. Robertson, A. E. Ross, T. J. Schmidt, C. Schmidt, R. Schmidt, T. Shim, S. Telenko, D. E. P. Wise, K. Smith, D. L. 2023-03-21 doi:10.1101/2023.03.18.533264 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ CORE CONSERVED TRANSCRIPTIONAL REGULATORY NETWORKS DEFINE THE INVASIVE TROPHOBLAST CELL LINEAGE ]]> https://biorxiv.org/content/10.1101/2023.03.30.534962v1?rss=1 Vu, H. T. H. Scott, R. L. Iqbal, K. Soares, M. J. Tuteja, G. 2023-04-03 doi:10.1101/2023.03.30.534962 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ A soybean pattern recognition receptor conferring broad-spectrum pathogen and pest resistance regulates expression of several NLR receptor proteins ]]> https://biorxiv.org/content/10.1101/2023.04.04.535565v1?rss=1 Ngaki, M. N. Srivastava, S. K. Wang, F. Bhattacharyya, M. K. 2023-04-06 doi:10.1101/2023.04.04.535565 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ A single amino acid substitution in MdLAZY1A dominantly impairs shoot gravitropism in Malus ]]> https://biorxiv.org/content/10.1101/2023.04.05.535771v1?rss=1 C that leads to a leucine to proline (L195P) substitution within a predicted transmembrane domain that co-localizes with Region III, one of the five conserved regions in LAZY1-like proteins. Subcellular localization revealed that MdLAZY1A localizes to the plasma membrane and nucleus in plant cells. Over-expressing the weeping allele in apple cultivar Royal Gala (RG) with standard growth habit impaired its gravitropic response and altered the growth to weeping-like. Suppressing the standard allele (MdLAZY1A-S) by RNA interference (RNAi) in RG similarly changed the branch growth direction to downward. Overall, the L195P mutation in MdLAZY1A is genetically causal for weeping growth, underscoring not only the crucial roles of residue L195 and Region III in MdLAZY1A-mediated gravitropic response, but also a potential DNA base editing target for tree architecture improvement in Malus and other crops. ]]> Dougherty, L. Borejsza-Wysocka, E. Miaule, A. Wang, P. Zheng, D. Jansen, M. BROWN, S. K. Pineros, M. A. Dardick, C. D. Xu, K. 2023-04-06 doi:10.1101/2023.04.05.535771 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Clathrin Light Chains are essential in negative regulation of cell death and immunity in Arabidopsis through interacting with autophagy pathway ]]> https://biorxiv.org/content/10.1101/2023.04.09.535952v1?rss=1 Lan, H.-J. Ran, J. Zhang, L. Wu, N.-N. Wang, W.-X. Ni, M. Cheng, N. Nakata, P. A. Pan, J. Whitham, S. Liu, J. 2023-04-10 doi:10.1101/2023.04.09.535952 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ Diethylcarbamazine elicits Ca2+ signals through TRP-2 channels that are potentiated by emodepside in Brugia malayi muscles ]]> https://biorxiv.org/content/10.1101/2023.04.10.536248v1?rss=1 Williams, P. D. Kashyap, S. S. Robertson, A. Martin, R. J. 2023-04-11 doi:10.1101/2023.04.10.536248 Cold Spring Harbor Laboratory Press 2023-04-11 <![CDATA[ An accurate and interpretable model to predict antimicrobial resistance in One Health settings ]]> https://biorxiv.org/content/10.1101/2023.04.18.537400v1?rss=1 Chung, H. C. Foxx, C. L. Hicks, J. A. Stuber, T. P. Friedberg, I. Dorman, K. S. Harris, B. N. 2023-04-18 doi:10.1101/2023.04.18.537400 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ How Do Deer Respiratory Epithelial Cells Weather The Initial Storm of SARS-CoV-2? ]]> https://biorxiv.org/content/10.1101/2023.04.24.538130v1?rss=1 Davila, K. M. S. Nelli, R. K. Phadke, K. S. Ruden, R. M. Sang, Y. Bellaire, B. H. Gimenez-Lirola, L. G. Miller, L. C. 2023-04-25 doi:10.1101/2023.04.24.538130 Cold Spring Harbor Laboratory Press 2023-04-25 <![CDATA[ Mammalian orthoreovirus infection in human epidermal growth factor receptor 2 positive (HER2+) breast cancer cells ]]> https://biorxiv.org/content/10.1101/2023.05.10.540250v1?rss=1 Jandick, N. A. Kirner, N. Miller, C. L. 2023-05-10 doi:10.1101/2023.05.10.540250 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ Conformational landscape of the transcription factor ATF4 is dominated by disordered-mediated inter-domain coupling ]]> https://biorxiv.org/content/10.1101/2023.05.12.540518v1?rss=1 Patel, U. Siang, S. Potoyan, D. Roche, J. 2023-05-13 doi:10.1101/2023.05.12.540518 Cold Spring Harbor Laboratory Press 2023-05-13 <![CDATA[ Models to Estimate Genetic Gain of Soybean Seed Yield from Annual Multi-Environment Field Trials ]]> https://biorxiv.org/content/10.1101/2023.05.13.540664v1?rss=1 Dalsente Krause, M. Piepho, H.-P. Dias Olimpio das Gracas, K. Singh, A. K. Beavis, W. D. 2023-05-14 doi:10.1101/2023.05.13.540664 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs ]]> https://biorxiv.org/content/10.1101/2023.05.17.540811v1?rss=1 Murray, G. G. R. Hossain, A. S. M. M. Miller, E. Bruchmann, S. Balmer, A. J. Matuszewska, M. Herbert, J. Hadjirin, N. F. Mugabi, R. Li, G. Ferrando, M. L. Fernades de Oliveira, I. M. Nguyen, T. Yen, P. L. K. Moe, A. Z. Wai, T. S. Gottschalk, M. Aragon, V. Valentin-Weigand, P. Heegaard, P. M. H. Vrieling, M. Maw, M. T. Myint, H. T. Win, Y. T. Hoa, N. T. Bentley, S. D. Clavijo, M. J. Wells, J. M. Tucker, A. D. Weinert, L. A. 2023-05-19 doi:10.1101/2023.05.17.540811 Cold Spring Harbor Laboratory Press 2023-05-19 <![CDATA[ Sequences at gene segment termini inclusive of untranslated regions and partial open reading frames play a critical role in mammalianorthoreovirus S gene packaging ]]> https://biorxiv.org/content/10.1101/2023.05.25.542362v1?rss=1 Dhar, D. Mehanovic, S. Moss, W. Miller, C. L. 2023-05-26 doi:10.1101/2023.05.25.542362 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ Conformational heterogeneity of the BTK PHTH domain drives multiple regulatory states ]]> https://biorxiv.org/content/10.1101/2023.06.02.543453v1?rss=1 Lin, D. Y.-w. Kueffer, L. E. Juneja, P. Wales, T. E. Engen, J. R. Andreotti, A. H. 2023-06-03 doi:10.1101/2023.06.02.543453 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ Cas4/1 dual nuclease activities enable prespacer maturation and directional integration in a type I-G CRISPR-Cas system ]]> https://biorxiv.org/content/10.1101/2023.06.05.543779v1?rss=1 Dhingra, Y. Sashital, D. G. 2023-06-05 doi:10.1101/2023.06.05.543779 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Phylomitogenomics bolsters the high-level classification of Demospongiae (phylum Porifera) ]]> https://biorxiv.org/content/10.1101/2023.06.04.543631v1?rss=1 Lavrov, D. V. Diaz, C. Maldonado, M. Morrow, C. Perez, T. Pomponi, S. A. Thucker, R. W. 2023-06-06 doi:10.1101/2023.06.04.543631 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ Structural Organization of the Retriever-CCC Endosomal Recycling Complex ]]> https://biorxiv.org/content/10.1101/2023.06.06.543888v1?rss=1 Boesch, D. J. Singla, A. Han, Y. Kramer, D. A. Liu, Q. Suzuki, K. Juneja, P. Zhao, X. Long, X. Medlyn, M. J. Billadeau, D. D. Chen, Z. Chen, B. Burstein, E. 2023-06-07 doi:10.1101/2023.06.06.543888 Cold Spring Harbor Laboratory Press 2023-06-07 <![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[ CREATION AND CHARACTERIZATION OF A RECOMBINANT MAMMALIAN ORTHOREOVIRUS EXPRESSING HUMAN EPIDERMAL GROWTH FACTOR RECEPTOR 2 PEPTIDES ]]> https://biorxiv.org/content/10.1101/2023.06.12.544655v1?rss=1 Jandick, N. A. Miller, C. L. 2023-06-13 doi:10.1101/2023.06.12.544655 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ Evidence of Disrupted-in Schizophrenia 1 (DISC1) as an arsenic binding protein and implications regarding its role as a translational activator ]]> https://biorxiv.org/content/10.1101/2023.06.14.544995v1?rss=1 Watanabe, M. Khu, T. M. Warren, G. Shin, J. Stewart, C. E. Roche, J. 2023-06-14 doi:10.1101/2023.06.14.544995 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ The ChickenGTEx pilot analysis: a reference of regulatory variants across 28 chicken tissues ]]> https://biorxiv.org/content/10.1101/2023.06.27.546670v1?rss=1 Guan, D. Bai, Z. Zhu, X. Zhong, C. Hou, Y. Lan, F. Diao, S. Yao, Y. Zhao, B. Zhu, D. Li, X. Pan, Z. Gao, Y. Wang, Y. Zou, D. Wang, R. Xu, T. Sun, C. Yin, H. Teng, J. Xu, Z. Lin, Q. Shi, S. Shao, D. Degalez, F. Lagarrigue, S. Wang, Y. Wang, M. Peng, M. Rocha, D. Charles, M. Smith, J. Watson, K. Buitenhuis, A. J. Sahana, G. Lund, M. S. Warren, W. Frantz, L. Larson, G. Lamont, S. J. Si, W. Zhao, X. Li, B. Zhang, H. Luo, C. Shu, D. Qu, H. Luo, W. Li, Z. Nie, Q. Zhang, X. Zhang, Z. Zhang, Z. Liu, G. E. Cheng, H. Yang, N. Hu, X. Zhou, H. Fang 2023-06-29 doi:10.1101/2023.06.27.546670 Cold Spring Harbor Laboratory Press 2023-06-29 <![CDATA[ A Molecular Communication model for cellular metabolism ]]> https://biorxiv.org/content/10.1101/2023.06.28.546976v1?rss=1 Sakkaff, Z. Freiburger, A. Catlett, J. L. Cashman, M. Immaneni, A. Buan, N. R. Cohen, M. Henry, C. Pierobon, M. 2023-06-30 doi:10.1101/2023.06.28.546976 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Concise functional enrichment of ranked gene lists ]]> https://biorxiv.org/content/10.1101/2023.06.30.547164v1?rss=1 Jia, X. Phan, A. Kadelka, C. 2023-07-02 doi:10.1101/2023.06.30.547164 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Transcriptome brings variations of gene expression, alternative splicing, and structural variations into gene-scale trait dissection in soybean ]]> https://biorxiv.org/content/10.1101/2023.07.03.545230v1?rss=1 Li, D. Wang, Q. Tian, Y. Lyu, X. Zhang, H. Sun, Y. Hong, H. Gao, H. Li, Y.-F. Zhao, C. Wang, J. Wang, R. Yang, J. Liu, B. Schnable, P. S. Schnable, J. C. Li, Y. Qiu, L. 2023-07-04 doi:10.1101/2023.07.03.545230 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ Multi-organ Metabolic Model of Zea mays Connects Temperature Stress with Thermodynamics-Reducing Power-Energy Generation Axis ]]> https://biorxiv.org/content/10.1101/2023.07.09.548275v1?rss=1 Chowdhury, N. B. Decouard, B. Quillere, I. Rigault, M. Sajeevan, K. A. Acharya, B. Chowdhury, R. Hirel, B. Dellagi, A. Maranas, C. D. Saha, R. 2023-07-10 doi:10.1101/2023.07.09.548275 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ PEXEL is a proteolytic maturation site for both exported and non-exported Plasmodium proteins ]]> https://biorxiv.org/content/10.1101/2023.07.12.548774v1?rss=1 Fierro, M. A. Muheljic, A. Sha, J. Wohlschlegel, J. A. Beck, J. R. 2023-07-12 doi:10.1101/2023.07.12.548774 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ Reinforcement learning-guided control strategies for CAR T-cell activation and expansion: Simulation study with a virtual cell culture environment ]]> https://biorxiv.org/content/10.1101/2023.07.14.548968v1?rss=1 Ferdous, M. S. Shihab, I. F. Chowdhury, R. Reuel, N. F. 2023-07-15 doi:10.1101/2023.07.14.548968 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ GIS-FA: An approach to integrate thematic maps, factor-analytic and envirotyping for cultivar targeting ]]> https://biorxiv.org/content/10.1101/2023.07.15.549137v1?rss=1 Araujo, M. S. Chaves, S. F. S. Dias, L. A. S. Ferreira, F. M. Pereira, G. R. Bezerra, A. R. G. Alves, R. S. Heinemann, A. B. Breseghello, F. Carneiro, P. C. S. Krause, M. D. Costa-Neto, G. Dias, K. O. G. 2023-07-15 doi:10.1101/2023.07.15.549137 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ ZmPILS6 is an auxin efflux carrier required for maize root morphogenesis ]]> https://biorxiv.org/content/10.1101/2023.08.01.551510v1?rss=1 Cowling, C. L. Homayouni, A. Callwood, J. B. McReynolds, M. R. Khor, J. Ke, H. Draves, M. A. Dehesh, K. Walley, J. W. Strader, L. C. Kelley, D. R. 2023-08-02 doi:10.1101/2023.08.01.551510 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ CONDITIONALLY MUTANT ANIMAL MODEL FOR INVESTIGATING THE INVASIVE TROPHOBLAST CELL LINEAGE ]]> https://biorxiv.org/content/10.1101/2023.08.02.551740v1?rss=1 Iqbal, K. Nixon, B. Crnkovich, B. Dominguez, E. M. Moreno Irusta, A. Scott, R. L. vu, h. Tuteja, G. Vivian, J. L. Soares, M. 2023-08-05 doi:10.1101/2023.08.02.551740 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ Molecularly imprinted nanoparticles reveal new insights into Pyk2 tyrosine kinase regulatory features ]]> https://biorxiv.org/content/10.1101/2023.08.05.552112v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@148d26borg.highwire.dtl.DTLVardef@1eea6daorg.highwire.dtl.DTLVardef@10c571borg.highwire.dtl.DTLVardef@12ab033_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Palhano Zanela, T. M. Zangiabadi, M. Zhao, Y. Underbakke, E. S. 2023-08-05 doi:10.1101/2023.08.05.552112 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ Phenotypic variation in maize can be largely explained by genetic variation at transcription factor binding sites ]]> https://biorxiv.org/content/10.1101/2023.08.08.551183v1?rss=1 Engelhorn, J. Snodgrass, S. J. Kok, A. Seetharam, A. S. Schneider, M. Kiwit, T. Singh, A. Banf, M. Khaipho-Burch, M. Runcie, D. E. Camargo, V. S. Torres-Rodriguez, J. V. Sun, G. Stam, M. Fiorani, F. Schnable, J. C. Bass, H. W. Hufford, M. B. Stich, B. Frommer, W. B. Ross-Ibarra, J. Hartwig, T. 2023-08-09 doi:10.1101/2023.08.08.551183 Cold Spring Harbor Laboratory Press 2023-08-09 <![CDATA[ The Auxin Response Factor ARF27 is required for maize root morphogenesis ]]> https://biorxiv.org/content/10.1101/2023.08.15.553439v1?rss=1 Dash, L. McReynolds, M. R. Draves, M. A. Khangura, R. S. Muench, R. L. Khor, J. Cowling, C. L. Callwood, J. B. Mejia, L. Lang, M. Dilkes, B. P. Walley, J. W. Kelley, D. R. 2023-08-16 doi:10.1101/2023.08.15.553439 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ Thermodynamic Coupling of the tandem RRM domains of hnRNP A1 underlie its Pleiotropic RNA Binding Functions ]]> https://biorxiv.org/content/10.1101/2023.08.17.553700v1?rss=1 Levengood, J. D. Potoyan, D. Penumutchu, S. Kumar, A. Wang, Y. Hansen, A. L. Kutluay, S. Roche, J. Tolbert, B. S. 2023-08-17 doi:10.1101/2023.08.17.553700 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ A future food boom rescues the negative effects of cumulative early-life adversity on lifespan in a small mammal ]]> https://biorxiv.org/content/10.1101/2023.08.16.553597v1?rss=1 Petrullo, L. Delaney, D. Boutin, S. Lane, J. E. McAdam, A. G. Dantzer, B. 2023-08-18 doi:10.1101/2023.08.16.553597 Cold Spring Harbor Laboratory Press 2023-08-18 <![CDATA[ <Ehrlichia chaffeensis/> co-opts phagocytic hemocytes for systemic dissemination in the Lone Star tick, <Amblyomma americanum/>. ]]> https://biorxiv.org/content/10.1101/2023.08.17.553720v1?rss=1 Adegoke, A. Hanson, J. Smith, R. C. Karim, S. 2023-08-19 doi:10.1101/2023.08.17.553720 co-opts phagocytic hemocytes for systemic dissemination in the Lone Star tick, .]]> Cold Spring Harbor Laboratory Press 2023-08-19 <![CDATA[ Insights into Phakopsora pachyrhizi effector-effector interactions ]]> https://biorxiv.org/content/10.1101/2023.08.30.555440v1?rss=1 Qi, M. Yu, H. Bredow, M. Chicowski, A. S. Fields, L. D. Whitham, S. A. 2023-09-01 doi:10.1101/2023.08.30.555440 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Geographically Biased Composition of NetMHCpan Training Datasets and Evaluation of MHC-Peptide Binding Prediction Accuracy on Novel Alleles ]]> https://biorxiv.org/content/10.1101/2023.09.03.556092v1?rss=1 Atkins, T. K. Solanki, A. Cornette, J. Vasmatzis, G. Riedel, M. 2023-09-06 doi:10.1101/2023.09.03.556092 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ A soybean rust effector protease suppresses host immunity and cleaves a 3-deoxy-7-phosphoheptulonate synthase ]]> https://biorxiv.org/content/10.1101/2023.09.07.556260v1?rss=1 Chicowski, A. S. Qi, M. Variz, H. Bredow, M. Montes-Serey, C. Caiazza, F. Dong, H. Margets, A. C. Mejias, J. Walley, J. Craik, C. Pedley, K. F. Aung, K. Innes, R. W. Whitham, S. 2023-09-08 doi:10.1101/2023.09.07.556260 Cold Spring Harbor Laboratory Press 2023-09-08 <![CDATA[ Improved Super-Resolution Ribosome Profiling Revealed Prevalent Translation of Upstream ORFs and Small ORFs in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2023.09.08.556947v1?rss=1 Wu, L. Ai, Q. Teixeira, R. T. Song, G. Montes-Serey, C. Elmore, J. M. Walley, J. Hsu, P. Y. 2023-09-11 doi:10.1101/2023.09.08.556947 Cold Spring Harbor Laboratory Press 2023-09-11 <![CDATA[ Dissecting Metabolic Landscape of Alveolar Macrophage ]]> https://biorxiv.org/content/10.1101/2023.09.08.556783v1?rss=1 Malla, S. Sajeevan, K. A. Acharya, B. Chowdhury, R. Saha, R. 2023-09-12 doi:10.1101/2023.09.08.556783 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Modularity of biological systems: a link between structure and function ]]> https://biorxiv.org/content/10.1101/2023.09.11.557227v1?rss=1 Kadelka, C. Wheeler, M. Veliz-Cuba, A. Murrugarra, D. Laubenbacher, R. 2023-09-12 doi:10.1101/2023.09.11.557227 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Endocannabinoid and psychological responses to acute resistance exercise in trained and untrained adults ]]> https://biorxiv.org/content/10.1101/2023.09.08.556874v1?rss=1 Sirotiak, Z. Gallagher, B. T. Smith-Hernandez, C. A. Showman, L. J. Hillard, C. J. Brellenthin, A. G. 2023-09-14 doi:10.1101/2023.09.08.556874 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ Fishing for a reelGene: evaluating gene models with evolution and machine learning ]]> https://biorxiv.org/content/10.1101/2023.09.19.558246v1?rss=1 Schulz, A. J. Zhai, J. AuBuchon-Elder, T. El-Walid, M. Ferebee, T. H. Gilmore, E. H. Hufford, M. B. Johnson, L. C. Kellogg, E. La, T. Long, E. Miller, Z. R. Romay, C. Seetharam, A. S. Stitzer, M. C. Wrightsman, T. Buckler, E. S. Monier, B. Hsu, S.-K. 2023-09-21 doi:10.1101/2023.09.19.558246 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Transcriptome-based host epistasis and pathogen co-expression in barley-powdery mildew interactions ]]> https://biorxiv.org/content/10.1101/2023.09.18.558274v1?rss=1 Velasquez-Zapata, V. Smith, S. D. Surana, P. Chapman, A. V. E. Wise, R. P. 2023-09-23 doi:10.1101/2023.09.18.558274 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ 4D Mesoscale liquid model of nucleus resolves chromatin's radial organization ]]> https://biorxiv.org/content/10.1101/2023.09.21.558819v1?rss=1 Laghmach, R. Di Pierro, M. Potoyan, D. 2023-09-23 doi:10.1101/2023.09.21.558819 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ Synthetic control of actin polymerization and symmetry breaking in activeprotocells ]]> https://biorxiv.org/content/10.1101/2023.09.22.559060v1?rss=1 Razavi, S. Wong, F. Abubaker-Sharif, B. Matsubayashi, H. T. Nakamura, H. Sandoval, E. Robinson, D. N. Chen, B. Liu, J. Iglesias, P. A. Inoue, T. 2023-09-23 doi:10.1101/2023.09.22.559060 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ PanEffect: A pan-genome visualization tool for variant effects in maize ]]> https://biorxiv.org/content/10.1101/2023.09.25.559155v1?rss=1 Andorf, C. M. Haley, O. C. Hayford, R. K. Portwood, J. L. Sen, S. Cannon, E. K. Gardiner, J. M. Woodhouse, M. R. 2023-09-26 doi:10.1101/2023.09.25.559155 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Rhythmic lipid and gene expression responses to chilling in panicoid grasses ]]> https://biorxiv.org/content/10.1101/2023.09.29.560160v1?rss=1 Kenchanmane Raju, S. K. Zhang, Y. Mahboub, S. Ngu, D. Qiu, Y. Harmon, F. Schnable, J. C. Roston, R. L. 2023-10-02 doi:10.1101/2023.09.29.560160 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Ptth regulates lifespan through innate immunity pathway in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.09.30.560323v1?rss=1 Kang, P. Liu, P. Kim, J. Bolton, M. Kumar, A. Miao, T. Shimell, M. O'Connor, M. B. Powell-Coffman, J. Bai, H. 2023-10-02 doi:10.1101/2023.09.30.560323 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Tick Innate Immune Responses to Hematophagy and Ehrlichia Infection at Single-Cell Resolution ]]> https://biorxiv.org/content/10.1101/2023.10.02.560565v1?rss=1 Adegoke, A. Ribeiro, J. M. Smith, R. C. Karim, S. 2023-10-03 doi:10.1101/2023.10.02.560565 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ LETHAL COVID-19 ASSOCIATES WITH RAAS-INDUCED INFLAMMATION FOR MULTIPLE ORGAN DAMAGE INCLUDING MEDIASTINAL LYMPH NODES ]]> https://biorxiv.org/content/10.1101/2023.10.08.561395v1?rss=1 Guarnieri, J. W. Topper, M. Beigel, K. Haltoom, J. A. Chadburn, A. Frere, J. An, J. Cope, H. Borczuk, A. Sinha, S. Lim, C. Kim, J. Park, J. Meydan, C. Foox, J. Mozsary, C. Bram, Y. Richard, S. Epsi, N. Agan, B. Chenoweth, J. Simons, M. Tribble, D. Burgess, T. Dalgard, C. L. Heise, M. T. Moorman, N. Baxter, V. Madden, E. A. Taft-Benz, S. Anderson, E. Sanders, W. A. Dickmander, R. J. Widjaja, G. A. Janssen, K. Lie, T. Murdock, D. G. Angelin, A. Albrecht, Y. E. S. Olali, A. Dybas, J. M. Priebe, W. Emmett, M. R. Best, S. Johnson, M. K. Trovao, N. S. Cl 2023-10-09 doi:10.1101/2023.10.08.561395 Cold Spring Harbor Laboratory Press 2023-10-09 <![CDATA[ Mapping energy landscapes of homopolymeric RNAs via simulated tempering and deep unsupervised learning ]]> https://biorxiv.org/content/10.1101/2023.10.10.561750v1?rss=1 Ramachandran, V. Potoyan, D. A. 2023-10-10 doi:10.1101/2023.10.10.561750 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Using encrypted genotypes and phenotypes for collaborative genomic analyses to maintain data confidentiality ]]> https://biorxiv.org/content/10.1101/2023.10.10.561761v1?rss=1 Zhao, T. Wang, F. Mott, R. Dekkers, J. C. M. Cheng, H. 2023-10-10 doi:10.1101/2023.10.10.561761 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ SydR, a redox-sensing MarR-type regulator of Sinorhizobium meliloti, is crucial for symbiotic infection of Medicago truncatula roots ]]> https://biorxiv.org/content/10.1101/2023.10.17.562213v1?rss=1 NAZARET, F. Farajzadeh, D. MEJIAS, J. PACOUD, M. COSI, A. Frendo, P. ALLOING, G. MANDON, K. 2023-10-17 doi:10.1101/2023.10.17.562213 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ A purine salvage bottleneck leads to bacterial adenine cross-feeding ]]> https://biorxiv.org/content/10.1101/2023.10.17.562681v1?rss=1 Chuang, Y.-C. Haas, N. W. Pepin, R. Behringer, M. Oda, Y. LaSarre, B. Harwood, C. S. McKinlay, J. B. 2023-10-17 doi:10.1101/2023.10.17.562681 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Viral protease NIa-Pro increases MEDIATOR SUBUNIT16 cleavage and plant susceptibility to turnip mosaic virus and its aphid vector Myzus persicae. ]]> https://biorxiv.org/content/10.1101/2023.10.24.563845v1?rss=1 Ray, S. Murad, T. Arena, G. D. Arshad, K. Arendsee, Z. Herath, V. Whitham, S. A. Casteel, C. L. 2023-10-27 doi:10.1101/2023.10.24.563845 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Nucleoprotein reassortment enhanced transmissibility of H3 1990.4.a clade influenza A virus in swine ]]> https://biorxiv.org/content/10.1101/2023.10.30.564250v1?rss=1 Thomas, M. N. Ciacci Zanella, G. Cowan, B. Caceres, C. J. Rajao, D. Perez, D. R. Gauger, P. C. Baker, A. L. Anderson, T. K. 2023-10-30 doi:10.1101/2023.10.30.564250 Cold Spring Harbor Laboratory Press 2023-10-30 <![CDATA[ Small but significant genetic differentiation among populations of Phyllachora maydis in the midwestern United States revealed by microsatellite (SSR) markers. ]]> https://biorxiv.org/content/10.1101/2023.10.31.563566v1?rss=1 0.001). Structure analysis showed the samples were not geographically structured but rather grouped into two genetic clusters (k =2) of severe genetic admixture suggesting possible long-distance dispersal of aerial spores or infected corn materials among the five Midwest states. Both principal coordinate analysis (PCoA) and discriminate analysis of principal component (DAPC) supported the STRUCTURE analysis of the two clusters. These 13 highly polymorphic molecular markers could be used for future investigations of this pathogens population dynamics within the U.S., and possibly populations outside. ]]> Ross, T. J. Jumbam, B. Bonkowski, J. Chaky, J. Chilvers, M. Goodwin, S. B. Kleczewski, N. M. Mueller, D. S. Robertson, A. E. Smith, D. L. Telenko, D. E. P. 2023-11-02 doi:10.1101/2023.10.31.563566 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Genome evolution and introgression in the New Zealand mud snails Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa ]]> https://biorxiv.org/content/10.1101/2023.10.31.565016v1?rss=1 Fields, P. Jalinsky, J. Bankers, L. McElroy, K. Sharbrough, J. Higgins, C. Morgan-Richards, M. Boore, J. Neiman, M. Logsdon, J. M. 2023-11-02 doi:10.1101/2023.10.31.565016 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Little Evidence for Homoeologous Gene Conversion and Homoeologous Exchange Events in Gossypium Allopolyploids ]]> https://biorxiv.org/content/10.1101/2023.11.08.566278v1?rss=1 Conover, J. L. Grover, C. E. Sharbrough, J. Sloan, D. Peterson, D. G. Wendel, J. 2023-11-12 doi:10.1101/2023.11.08.566278 Cold Spring Harbor Laboratory Press 2023-11-12 <![CDATA[ Whole genome profiling of short-term hypoxia induced genes and identification of HIF-1 binding sites provide insights into HIF-1 function in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2023.11.15.567310v1?rss=1 Feng, D. Qu, L. 2023-11-17 doi:10.1101/2023.11.15.567310 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Transcriptome analyses describe the consequences of persistent HIF-1 over-activation in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2023.11.15.567311v1?rss=1 Feng, D. Qu, L. 2023-11-17 doi:10.1101/2023.11.15.567311 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ The nematode (Ascaris suum) intestine is a location of synergistic anthelmintic effects of Cry5B and levamisole ]]> https://biorxiv.org/content/10.1101/2023.11.20.567786v1?rss=1 Williams, P. D. E. Brewer, M. Aroian, R. Robertson, A. P. Martin, R. J. 2023-11-20 doi:10.1101/2023.11.20.567786 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ Inbreeding depression leads to reduced fitness in declining populations of wild maize ]]> https://biorxiv.org/content/10.1101/2023.11.20.567972v1?rss=1 Schulz, A. J. Hufnagel, D. E. Gepts, P. Hufford, M. B. 2023-11-21 doi:10.1101/2023.11.20.567972 Cold Spring Harbor Laboratory Press 2023-11-21 <![CDATA[ CRISPR-Cas12a exhibits metal-dependent specificity switching ]]> https://biorxiv.org/content/10.1101/2023.11.29.569287v1?rss=1 Nguyen, G. T. Schelling, M. A. Buscher, K. A. Sritharan, A. Sashital, D. G. 2023-11-29 doi:10.1101/2023.11.29.569287 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ GWAS From Spoken Phenotypic Descriptions: A Proof of Concept From Maize Field Studies ]]> https://biorxiv.org/content/10.1101/2023.12.11.570820v1?rss=1 Yanarella, C. F. Fattel, L. Lawrence-Dill, C. J. 2023-12-12 doi:10.1101/2023.12.11.570820 Cold Spring Harbor Laboratory Press 2023-12-12 <![CDATA[ Data driven discovery and quantification of hyperspectral leaf reflectance phenotypes across a maize diversity panel ]]> https://biorxiv.org/content/10.1101/2023.12.15.571950v1?rss=1 Tross, M. C. Grzybowski, M. W. Jubery, T. Z. Grove, R. J. Nishimwe, A. V. Torres-Rodriguez, J. V. Sun, G. Ganapathysubramanian, B. Schnable, J. C. 2023-12-16 doi:10.1101/2023.12.15.571950 Cold Spring Harbor Laboratory Press 2023-12-16 <![CDATA[ The SUbventral-Gland master Regulator (SUGR) of nematode virulence ]]> https://biorxiv.org/content/10.1101/2024.01.22.576598v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@cebedaorg.highwire.dtl.DTLVardef@153fe87org.highwire.dtl.DTLVardef@16b6957org.highwire.dtl.DTLVardef@d0e920_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pellegrin, C. Damm, A. Sperling, A. L. Molloy, B. Shin, D. S. Long, J. Brett, P. Bravo, A. D.-T. Lynch, S. J. Senatori, B. Vieira, P. Mejias, J. Kumar, A. Masonbrink, R. E. Maier, T. R. Baum, T. J. Eves-van den Akker, S. 2024-01-24 doi:10.1101/2024.01.22.576598 Cold Spring Harbor Laboratory Press 2024-01-24 <![CDATA[ Epitranscriptomic Reader YTHDF2 Regulates SEK1(MAP2K4)-JNK-cJUN Inflammatory Signaling in Astrocytes during Neurotoxic Stress ]]> https://biorxiv.org/content/10.1101/2024.01.26.577106v1?rss=1 Malovic, E. Ealy, A. Hsu, P. J. Sarkar, S. Miller, C. Rokad, D. Goeser, C. Hartman, A. K. Zhu, A. Palanisamy, B. Zenitsky, G. Jin, H. Anantharam, V. Kanthasamy, A. He, C. Kanthasamy, A. 2024-01-26 doi:10.1101/2024.01.26.577106 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ A common set of structurally distinct endogenous retroviruses predict survival in multiple human tumor types ]]> https://biorxiv.org/content/10.1101/2024.02.07.579350v1?rss=1 Massa, A. L. Chintalapudi, H. Coppenbarger, E. C. Peterson, J. M. Moss, W. N. Frost, H. R. Leach, S. D. 2024-02-10 doi:10.1101/2024.02.07.579350 Cold Spring Harbor Laboratory Press 2024-02-10 <![CDATA[ Nuclear pore complexes undergo Nup221 exchange during blood stage asexual replication of Plasmodium parasites. ]]> https://biorxiv.org/content/10.1101/2024.02.16.580747v1?rss=1 Blauwkamp, J. A. Ambekar, S. V. Hussain, T. Mair, G. R. Beck, J. R. Absalon, S. 2024-02-17 doi:10.1101/2024.02.16.580747 Cold Spring Harbor Laboratory Press 2024-02-17 <![CDATA[ A pan-tissue, pan-disease compendium of human orphan genes ]]> https://biorxiv.org/content/10.1101/2024.02.21.581488v1?rss=1 Singh, U. Haltom, J. Guarnieri, J. Li, J. Seetharam, A. Beheshti, A. Aronow, B. Wurtele, E. S. 2024-02-23 doi:10.1101/2024.02.21.581488 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication. ]]> https://biorxiv.org/content/10.1101/2024.02.22.581585v1?rss=1 Cahn, J. Regulski, M. Lynn, J. Ernst, E. de Santis Alves, C. Ramakrishnan, S. Chougule, K. Wei, S. Lu, Z. Xu, X. Drenkow, J. Kramer, M. Seetharam, A. Hufford, M. B. McCombie, W. R. Ware, D. Jackson, D. Schatz, M. C. Gingeras, T. R. Martienssen, R. A. 2024-02-23 doi:10.1101/2024.02.22.581585 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ EpicTope: narrating protein sequence features to identify non-disruptive epitope tagging sites ]]> https://biorxiv.org/content/10.1101/2024.03.03.583232v1?rss=1 Zinski, J. Chung, H. Joshi, P. Warrick, F. Berg, B. D. Glova, G. McGrail, M. A. Balciunas, D. Friedberg, I. Mullins, M. C. 2024-03-06 doi:10.1101/2024.03.03.583232 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ A zebrafish system for identifying genetic dependencies in melanocytes and melanoma ]]> https://biorxiv.org/content/10.1101/2024.03.22.586101v1?rss=1 Perlee, S. Ma, Y. Hunter, M. V. Swanson, J. B. Ming, Z. Xia, J. Lionnet, T. McGrail, M. White, R. 2024-03-23 doi:10.1101/2024.03.22.586101 Cold Spring Harbor Laboratory Press 2024-03-23 <![CDATA[ Assembling bacterial puzzles: piecing together functions into microbial pathways ]]> https://biorxiv.org/content/10.1101/2024.03.27.587058v1?rss=1 Chung, H. Friedberg, I. Bromberg, Y. 2024-03-27 doi:10.1101/2024.03.27.587058 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Design and Assembly of a Cargo-agnostic Hollow Two-lidded DNA Box for Drug Delivery ]]> https://biorxiv.org/content/10.1101/2024.03.27.586853v1?rss=1 View larger version (19K): org.highwire.dtl.DTLVardef@97179corg.highwire.dtl.DTLVardef@18f0b46org.highwire.dtl.DTLVardef@2d390eorg.highwire.dtl.DTLVardef@fcf35c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Koep, A. Masud, N. Van't Hul, J. Stanley, C. Nilsen-Hamilton, M. Sarkar, A. Schneider, I. C. 2024-03-30 doi:10.1101/2024.03.27.586853 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ Conservation and diversification of genes regulating brassinosteroid biosynthesis and signaling ]]> https://biorxiv.org/content/10.1101/2024.03.26.586792v1?rss=1 Zebosi, B. Vollbrecht, E. B. Best, N. B. 2024-04-02 doi:10.1101/2024.03.26.586792 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ An effective and safe maize seed chipping protocol using clipping pliers with applications in small-scale genotyping and marker-assisted breeding ]]> https://biorxiv.org/content/10.1101/2024.04.01.587552v1?rss=1 Zebosi, B. Ssengo, J. Geadelmann, L. Unger-Wallace, E. Vollbrecht, E. 2024-04-02 doi:10.1101/2024.04.01.587552 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Single-cell proteomics differentiates Arabidopsis root cell types ]]> https://biorxiv.org/content/10.1101/2024.04.09.588771v1?rss=1 Montes, C. Zhang, J. Nolan, T. M. Walley, J. W. 2024-04-10 doi:10.1101/2024.04.09.588771 Cold Spring Harbor Laboratory Press 2024-04-10 <![CDATA[ Highly Pathogenic Avian Influenza A (H5N1) clade 2.3.4.4b Virus detected in dairy cattle ]]> https://biorxiv.org/content/10.1101/2024.04.16.588916v1?rss=1 Hu, X. Saxena, A. Magstadt, D. R. Gauger, P. C. Burrough, E. Zhang, J. Siepker, C. Mainenti, M. Gorden, P. Plummer, P. Li, G. 2024-04-16 doi:10.1101/2024.04.16.588916 Cold Spring Harbor Laboratory Press 2024-04-16 <![CDATA[ Successful Cardiac Resynchronization Therapy Reduces Negative Septal Work in Patient-Specific Models of Dyssynchronous Heart Failure ]]> https://biorxiv.org/content/10.1101/2024.05.13.593804v1?rss=1 Craine, A. Krishnamurthy, A. Villongco, C. T. Vincent, K. Krummen, D. E. Narayan, S. M. Kerckhoffs, R. C. P. Omens, J. H. Contijoch, F. McCulloch, A. D. 2024-05-14 doi:10.1101/2024.05.13.593804 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Nuclear phylogenomics of grasses (Poaceae) supports current classification and reveals repeated reticulation ]]> https://biorxiv.org/content/10.1101/2024.05.28.596153v1?rss=1 Grass Phylogeny Working Group 3, Arthan, W. Baker, W. J. Barrett, M. D. Barrett, R. L. Bennetzen, J. Besnard, G. Bianconi, M. E. Birch, J. L. Catalan, P. Chen, W. Christenhusz, M. Christin, P.-A. Clark, L. G. Couch, C. A. Columbus, J. T. Crayn, D. M. Davidse, G. Dunning, L. T. Duvall, M. R. Dransfield, S. Ficinski, S. Z. Fisher, A. E. Fjellheim, S. Forest, F. Gillespie, L. J. Hackel, J. Haevermans, T. Hodkinson, T. R. Huang, C.-H. Huang, W. Humphreys, A. M. Jobson, R. W. Kayombo, C. J. Kellogg, E. A. Kimeu, J. M. Larridon, I. Letsara, R. Li, D.-Z. Liu, 2024-06-02 doi:10.1101/2024.05.28.596153 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ Transcription factor binding site divergence across maize inbred lines drives transcriptional and phenotypic variation ]]> https://biorxiv.org/content/10.1101/2024.05.31.596834v1?rss=1 Galli, M. Chen, Z. Ghandour, T. Chaudhry, A. Gregory, J. Li, M. Zhang, X. Dong, Y. Song, G. Walley, J. Chuck, G. Whipple, C. J. Kaeppler, H. F. Huang, S.-s. C. Gallavotti, A. 2024-06-03 doi:10.1101/2024.05.31.596834 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Amplified DNA Heterogeneity Assessment with Oxford Nanopore Sequencing Applied to Cell Free Expression Templates ]]> https://biorxiv.org/content/10.1101/2024.06.02.597048v1?rss=1 Hejazi, S. S. Hejazi, S. S. Kashani, M. Reuel, N. F. 2024-06-03 doi:10.1101/2024.06.02.597048 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Elevated CO2 alters soybean physiology and defense responses, and has disparate effects on susceptibility to diverse microbial pathogens ]]> https://biorxiv.org/content/10.1101/2024.06.04.595564v1?rss=1 Bredow, M. Khwanbua, E. Sartor Chicowski, A. Breitzman, M. W. Qi, Y. Holan, K. L. Liu, P. Graham, M. A. Whitham, S. 2024-06-06 doi:10.1101/2024.06.04.595564 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ Genotypic and Phenotypic Analyses Show Ralstonia solanacearum Cool Virulence is a Quantitative Trait Not Restricted to 'Race 3 biovar 2' ]]> https://biorxiv.org/content/10.1101/2024.06.13.598915v1?rss=1 Dewberry, R. J. Sharma, P. Prom, J. L. Kinscherf, N. A. Lowe-Power, T. Mazloom, R. Zhang, X. Arif, M. Stulberg, M. Heath, L. S. Eversole, K. Beattie, G. A. Vinatzer, B. Allen, C. 2024-06-13 doi:10.1101/2024.06.13.598915 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Single-nucleus RNA sequencing of striatal microglia reveals distinct transcriptomic signatures of acute stress and chronic exercise ]]> https://biorxiv.org/content/10.1101/2024.06.24.600469v1?rss=1 Connolly, M. G. Johnson, Z. V. Chu, L. Johnson, N. D. Buhr, T. J. McNeill, E. M. Clark, P. J. Rhodes, J. S. 2024-06-26 doi:10.1101/2024.06.24.600469 Cold Spring Harbor Laboratory Press 2024-06-26 <![CDATA[ Leveraging Crosslinker Diffusion to Template Stiffness Gradients in Alginate Hydrogels ]]> https://biorxiv.org/content/10.1101/2024.06.26.599742v1?rss=1 View larger version (14K): org.highwire.dtl.DTLVardef@1182404org.highwire.dtl.DTLVardef@1e4bfb1org.highwire.dtl.DTLVardef@e52778org.highwire.dtl.DTLVardef@8237bd_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ostrowski, Z. Price, T. Zhang, J. Kaufmann, T. Judka, N. Gardner, T. Thatcher, M. Miller, E. Mesyk, L. Koep, A. Melvin, A. T. Ren, J. Schneider, I. C. 2024-06-29 doi:10.1101/2024.06.26.599742 Cold Spring Harbor Laboratory Press 2024-06-29 <![CDATA[ Active surveillance for influenza A virus in swine reveals within-farm reassortment and cocirculation of distinct subtypes and genetic clades ]]> https://biorxiv.org/content/10.1101/2024.06.28.601245v1?rss=1 Thomas, M. N. Janzen, G. M. Markin, A. K. Sharma, A. Hewitt, K. S. Li, G. Baker, A. L. Gauger, P. C. Anderson, T. K. 2024-07-02 doi:10.1101/2024.06.28.601245 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ The Soybean Cyst Nematode Effector Cysteine Protease 1 (CPR1) Targets a Mitochondrial Soybean Branched-Chain Amino Acid Aminotransferase (GmBCAT1) for Degradation ]]> https://biorxiv.org/content/10.1101/2024.07.01.601533v1?rss=1 Margets, A. Foster, J. Kumar, A. Maier, T. Masonbrink, R. E. Mejias, J. Baum, T. J. Innes, R. W. 2024-07-03 doi:10.1101/2024.07.01.601533 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ Limitations of Current Machine-Learning Models in Predicting Enzymatic Functions for Uncharacterized Proteins ]]> https://biorxiv.org/content/10.1101/2024.07.01.601547v1?rss=1 de Crecy-Lagard, V. Dias, R. Friedberg, I. Yuan, Y. Swairjo, M. 2024-07-03 doi:10.1101/2024.07.01.601547 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ Stat3 mediates Fyn kinase driven dopaminergic neurodegeneration and microglia activation ]]> https://biorxiv.org/content/10.1101/2024.07.05.602238v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@1d783a4org.highwire.dtl.DTLVardef@3b838org.highwire.dtl.DTLVardef@33790eorg.highwire.dtl.DTLVardef@1508c64_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO - Neural Fyn signaling drives dopaminergic neurodegeneration, mitochondria accumulation, and microglia activation - Fyn driven neurodegeneration and cytokine expression are dependent on Stat3 - Stat3 and NF-kB pathways synergize in dopaminergic neuron degeneration C_FIG ]]> Siddiqui, S. Liu, F. Kanthasamy, A. G. McGrail, M. 2024-07-09 doi:10.1101/2024.07.05.602238 Cold Spring Harbor Laboratory Press 2024-07-09 <![CDATA[ Nemacounter: A user-friendly software to accurately phenotype SCN cysts ]]> https://biorxiv.org/content/10.1101/2024.07.07.602381v1?rss=1 Mejias, J. Kozlowski, D. K. L. Goshon, J. Maier, T. R. Baum, T. J. 2024-07-10 doi:10.1101/2024.07.07.602381 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Complex Reticulation in Backbone Subfamily Relationships in Leguminosae ]]> https://biorxiv.org/content/10.1101/2024.07.12.603319v1?rss=1 Stai, J. Cardinal-McTeague, W. Bruneau, A. Cannon, S. B. 2024-07-16 doi:10.1101/2024.07.12.603319 Cold Spring Harbor Laboratory Press 2024-07-16 <![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[ Impaired experience-dependent inter-areal network connectivity across the visual cortex in Fmr1 KO mice ]]> https://biorxiv.org/content/10.1101/2024.07.23.601989v1?rss=1 Cheng, X. Nareddula, S. Gao, H.-C. Chen, Y. Xiao, T. Nadew, Y. Y. Xu, F. Edens, P. A. Quinn, C. J. Huang, F. Kimbrough, A. Chubykin, A. A. 2024-07-24 doi:10.1101/2024.07.23.601989 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ AraRoot - A Comprehensive Genome-Scale Metabolic Model for the Arabidopsis Root System. ]]> https://biorxiv.org/content/10.1101/2024.07.28.605515v1?rss=1 Esterhuizen, L. Ampimah, N. Yandeau-Nelson, M. Nikolau, B. J. Sparks, E. E. Saha, R. 2024-07-29 doi:10.1101/2024.07.28.605515 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ Using flux theory in dynamic omics data sets to identify differentially changing signals using DPoP ]]> https://biorxiv.org/content/10.1101/2024.07.29.605590v1?rss=1 Edwards, H. Zavorskas, J. Huso, W. Doan, A. G. Silbiger, C. Harris, S. Srivastava, R. Marten, M. R. 2024-07-30 doi:10.1101/2024.07.29.605590 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ MDR1 DNA glycosylase regulates the expression of genomically imprinted genes and helitrons ]]> https://biorxiv.org/content/10.1101/2024.07.31.606038v1?rss=1 Higgins, K. M. Gent, J. I. Anderson, S. N. 2024-08-01 doi:10.1101/2024.07.31.606038 Cold Spring Harbor Laboratory Press 2024-08-01 <![CDATA[ Isolation and molecular characterization of an enteric isolate of the Genotype-I Bovine coronavirus with notable mutations in the receptor binding domain of the spike glycoprotein and deletion downstream the RNA binding domain of the nucleocapsid protein. ]]> https://biorxiv.org/content/10.1101/2024.08.03.606496v1?rss=1 Shah, A. U. Gauger, P. C. Hemida, M. H. 2024-08-04 doi:10.1101/2024.08.03.606496 Cold Spring Harbor Laboratory Press 2024-08-04 <![CDATA[ Dynamics of duplicated gene regulatory networks governing cotton fiber development following polyploidy ]]> https://biorxiv.org/content/10.1101/2024.08.12.607624v1?rss=1 Xiong, X. Zhu, D. Grover, C. E. Wendel, J. F. Ma, X. Hu, G. 2024-08-13 doi:10.1101/2024.08.12.607624 Cold Spring Harbor Laboratory Press 2024-08-13 <![CDATA[ Conservation of imprinted expression across genotypes is correlated with consistency of imprinting across endosperm development in maize ]]> https://biorxiv.org/content/10.1101/2024.08.16.608346v1?rss=1 Higgins, K. M. Nyabashi, V. I. Anderson, S. N. 2024-08-19 doi:10.1101/2024.08.16.608346 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Developmental variability in cotton fiber cell wall properties linked to important agronomic traits ]]> https://biorxiv.org/content/10.1101/2024.08.19.607249v1?rss=1 Wilson, M. C. Howell, A. H. Sood, A. Lee, Y. Yang, P. Rani, H. Yu, E. Mallery, E. L. Swaminathan, S. Grover, C. E. Wendel, J. F. Zabotina, O. A. Xie, J. Davis, C. S. Szymanski, D. 2024-08-19 doi:10.1101/2024.08.19.607249 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Identification of phenotypic and transcriptomic signatures underpinning maize crown root systems ]]> https://biorxiv.org/content/10.1101/2024.08.20.608626v1?rss=1 Callwood, J. B. Townsend, E. G. Malik, S. Draves, M. A. Khor, J. Marshall, J. P. Sweers, H. Cowling, C. L. Walley, J. W. Kelley, D. R. 2024-08-21 doi:10.1101/2024.08.20.608626 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ Exploring the uncharted: Novel potential filariasis vectors unveiled in Sri Lanka ]]> https://biorxiv.org/content/10.1101/2024.08.23.609308v1?rss=1 Nimalrathna, S. U. Amarasiri, C. Aluthge, K. Mallawarachchi, C. Chandrasena, N. de Silva, N. de Silva, N. Kimber, M. Harischandra, H. 2024-08-23 doi:10.1101/2024.08.23.609308 Cold Spring Harbor Laboratory Press 2024-08-23 <![CDATA[ RESPIRATORY SYNCYTIAL VIRUS NON-STRUCTURAL PROTEIN EXPRESSION ARE LIMITED IN NEUTROPHILS ]]> https://biorxiv.org/content/10.1101/2024.08.25.609617v1?rss=1 Thornhill, E. M. Verhoeven, D. 2024-08-26 doi:10.1101/2024.08.25.609617 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Regulatory architecture of disease resistance in maize revealed by multi-omic systems genetics ]]> https://biorxiv.org/content/10.1101/2024.08.29.610401v1?rss=1 Clark, N. M. Song, G. Kabahuma, M. K. Kolkman, J. M. Christensen, S. A. Montes-Serey, C. Malik, S. Nelson, R. J. Walley, J. W. 2024-08-30 doi:10.1101/2024.08.29.610401 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Use of equine H3N8 hemagglutinin as a broadly protective influenza vaccine immunogen ]]> https://biorxiv.org/content/10.1101/2024.08.30.610504v1?rss=1 Verhoeven, D. Sponseller, B. Crowe, J. E. Bangaru, S. Webby, R. J. Lee, B. M. 2024-09-02 doi:10.1101/2024.08.30.610504 Cold Spring Harbor Laboratory Press 2024-09-02 <![CDATA[ CRISPR-Cas9 target-strand nicking provides phage resistance by inhibiting replication ]]> https://biorxiv.org/content/10.1101/2024.09.05.611540v1?rss=1 Nguyen, G. T. Schelling, M. A. Sashital, D. G. 2024-09-05 doi:10.1101/2024.09.05.611540 Cold Spring Harbor Laboratory Press 2024-09-05 <![CDATA[ Effect of Genotype and Age on a Defined Microbiota in Gnotobiotic SCID Piglets ]]> https://biorxiv.org/content/10.1101/2024.09.03.611011v1?rss=1 Widmer, K. M. Rahic-Seggerman, F. Forster, A. Ahrens-Kress, A. Sauer, M. Mooyottu, S. Vinithakumari, A. Dunkerson-Kurzhumov, A. Sponseller, B. Kiupel, M. Schmitz-Esser, S. Tuggle, C. K. 2024-09-07 doi:10.1101/2024.09.03.611011 Cold Spring Harbor Laboratory Press 2024-09-07 <![CDATA[ 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[ Dietary specialization drives adaptation, convergence, and integration across the cranial and appendicular skeleton in Waterfowl (Anseriformes). ]]> https://biorxiv.org/content/10.1101/2024.09.21.614171v1?rss=1 Chatterji, R. M. Heath, T. A. James, H. F. Hofman, C. Sorenson, M. D. Buckner, J. C. 2024-09-24 doi:10.1101/2024.09.21.614171 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Developmental regulation of endothelial-to-hematopoietic transition from induced pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2024.09.24.612755v1?rss=1 Wellington, R. Cheng, X. Campbell, C. A. Trapnell, C. Espin-Palazon, R. Hadland, B. Doulatov, S. 2024-09-24 doi:10.1101/2024.09.24.612755 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ A genome-wide CRISPR screen in Anopheles mosquito cells identifies essential genes and required components of clodronate liposome function ]]> https://biorxiv.org/content/10.1101/2024.09.24.614595v1?rss=1 Mameli, E. Samantsidis, G.-R. Viswanatha, R. Kwon, H. Hall, D. R. Butnaru, M. Hu, Y. Mohr, S. E. Perrimon, N. Smith, R. C. 2024-09-24 doi:10.1101/2024.09.24.614595 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Nucleoprotein phase-separation affinities revealed via atomistic simulations of short peptide and RNA fragments ]]> https://biorxiv.org/content/10.1101/2024.09.24.614800v1?rss=1 Ramachandran, V. Brown, W. Potoyan, D. A. 2024-09-26 doi:10.1101/2024.09.24.614800 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Aspergillus nidulans cell wall integrity kinase, MpkA, impacts cellular phenotypes that alter mycelial-material mechanical properties ]]> https://biorxiv.org/content/10.1101/2024.09.28.615565v1?rss=1 Gray, K. Edwards, H. Doan, A. G. Huso, W. Lee, J. Pan, W. Bolima, N. Morse, M. E. Yoda, S. Gautam, I. Harris, S. Zupan, M. Wang, T. deCarvalho, T. Marten, M. R. 2024-09-30 doi:10.1101/2024.09.28.615565 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Diterpenoid phytoalexins shape rice root microbiomes and their associations with root parasitic nematodes ]]> https://biorxiv.org/content/10.1101/2024.09.30.615782v1?rss=1 Kudjordjie, E. N. Desmedt, W. Kyndt, T. Nicolaisen, M. Peters, R. J. Vestergard, M. 2024-09-30 doi:10.1101/2024.09.30.615782 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Thermal Adaptation of Cytosolic Malate Dehydrogenase Revealed by Deep Learning and Coevolutionary Analysis ]]> https://biorxiv.org/content/10.1101/2024.10.08.617074v1?rss=1 Shukla, D. Martin, J. Morcos, F. Potoyan, D. A. 2024-10-11 doi:10.1101/2024.10.08.617074 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Maximum vertical height during wing flapping of laying hens captured with a depth camera ]]> https://biorxiv.org/content/10.1101/2024.10.12.617995v1?rss=1 0.05). Hens in this study were from a single strain, were old enough to have keel damage, and were cage-reared and housed, preventing us from generalizing the results too far. However, depth cameras provide a useful approach to measure how much space laying hens of varying strains, ages, and rearing/housing methods need to perform dynamic behaviors. ]]> Grebey, T. Bongiorno, V. Han, J. Steibel, J. Siegford, J. M. 2024-10-14 doi:10.1101/2024.10.12.617995 Cold Spring Harbor Laboratory Press 2024-10-14 <![CDATA[ A novel toolbox of GATEWAY-compatible vectors for rapid functional gene analysis in soybean composite plants ]]> https://biorxiv.org/content/10.1101/2024.10.12.617978v1?rss=1 Mejias, J. Margets, A. Bredow, M. Foster, J. Khwanbua, E. Goshon, J. Maier, T. A. Whitham, S. A. Innes, R. W. Baum, T. J. 2024-10-15 doi:10.1101/2024.10.12.617978 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ Light-guided actin polymerization drives directed motility in protocells ]]> https://biorxiv.org/content/10.1101/2024.10.14.617543v1?rss=1 Matsubayashi, H. T. Razavi, S. Rock, T. W. Nakajima, D. Nakamura, H. Kramer, D. A. Matsuura, T. Chen, B. Murata, S. Nomura, S.-i. M. Inoue, T. 2024-10-15 doi:10.1101/2024.10.14.617543 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ A Longitudinal Analysis of Function Annotations of the Human Proteome Reveals Consistently High Biases ]]> https://biorxiv.org/content/10.1101/2024.10.18.619148v1?rss=1 Phan, A. Joshi, P. Kadelka, C. Friedberg, I. 2024-10-22 doi:10.1101/2024.10.18.619148 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Exploring new dimensions of immune cell biology in Anopheles gambiae through genetic immunophenotyping ]]> https://biorxiv.org/content/10.1101/2024.10.22.619690v1?rss=1 Samantsidis, G.-R. Smith, R. C. 2024-10-25 doi:10.1101/2024.10.22.619690 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[ Genomic and Phenomic Prediction for Soybean Seed Yield, Protein, and Oil ]]> https://biorxiv.org/content/10.1101/2024.11.01.621550v1?rss=1 Van der Laan, L. Parmley, K. Saadati, M. Torres Pacin, H. Panthulugiri, S. Sarkar, S. Ganapathysubramanian, B. Lorenz, A. J. Singh, A. K. 2024-11-02 doi:10.1101/2024.11.01.621550 Cold Spring Harbor Laboratory Press 2024-11-02 <![CDATA[ High Temperature and Microbiome Conditions Affect Gene Expression in Soybean ]]> https://biorxiv.org/content/10.1101/2024.11.04.620947v1?rss=1 Van der Laan, L. Elango, D. Ferela, A. O'Rourke, J. Singh, A. K. 2024-11-05 doi:10.1101/2024.11.04.620947 Cold Spring Harbor Laboratory Press 2024-11-05 <![CDATA[ Effects of live yeasts and their metabolic products on bumble bee microcolony development ]]> https://biorxiv.org/content/10.1101/2024.11.06.622134v1?rss=1 Rutkowski, D. Weston, M. Vannette, R. 2024-11-08 doi:10.1101/2024.11.06.622134 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Interplay between autophagy, the unfolded protein response and the cytoplasmic heat stress response during heat stress in maize ]]> https://biorxiv.org/content/10.1101/2024.11.06.622333v1?rss=1 Tang, J. Li, Z. Bassham, D. C. 2024-11-08 doi:10.1101/2024.11.06.622333 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Assessment of the Genetic Diversity of Atlantic Bottlenose Dolphin (Tursiops truncatus) Strandings in the Mississippi Sound (USA) ]]> https://biorxiv.org/content/10.1101/2024.11.09.622766v1?rss=1 Arick, M. Landrau-Giovannetti, N. Hsu, C.-Y. Grover, C. E. Reichley, S. Magbanua, Z. V. Pechanova, O. Moore, D. Kayal, E. Linhoss, A. Madrigal, T. Peterman, M. Ozdemir, O. Peterson, D. G. Solangi, M. Lawrence, M. Karsi, A. 2024-11-11 doi:10.1101/2024.11.09.622766 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Measuring Growth, Resistance and Recovery after Artemisinin Treatment of Plasmodium falciparum in a semi-high-throughput Assay ]]> https://biorxiv.org/content/10.1101/2024.11.11.623064v1?rss=1 Sievert, M. A. Singh, P. P. Shoue, D. A. Needham, L. A. C. Brenneman, K. M. Qahash, T. Cassady, Z. Kumar, S. Li, X. Nosten, F. H. Anderson, T. J. Vaughan, A. M. Romero-Severson, J. Ferdig, M. T. 2024-11-11 doi:10.1101/2024.11.11.623064 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ The conserved aphid saliva chemosensory protein effector Mp10 targets plant AMSH deubiquitinases at cellular membranes to suppress pattern-triggered immunity ]]> https://biorxiv.org/content/10.1101/2024.11.15.622802v1?rss=1 Gravino, M. Mugford, S. T. Kreuter, N. Joyce, J. Wilson, C. Kliot, A. Canham, J. Mathers, T. C. Drurey, C. Maqbool, A. Saalbach, G. Martins, C. Hogenhout, S. A. 2024-11-17 doi:10.1101/2024.11.15.622802 Cold Spring Harbor Laboratory Press 2024-11-17 <![CDATA[ Aspergillus nidulans Transcription Factor BrlA is Utilized in a Conidiation-Independent Response to Cell-Wall Stress ]]> https://biorxiv.org/content/10.1101/2024.11.21.624663v1?rss=1 Edwards, H. Zavorskas, J. Huso, W. Doan, A. G. Lee, J. Morse, M. E. Wilkinson, H. H. Ebbole, D. Shaw, B. Harris, S. Srivastava, R. Marten, M. R. 2024-11-21 doi:10.1101/2024.11.21.624663 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Molecular evolution of a reproductive barrier in maize and related species ]]> https://biorxiv.org/content/10.1101/2024.12.02.626474v1?rss=1 Cryan, E. Phinney, G. Seetharam, A. S. Evans, M. M. S. Kellogg, E. A. Zhan, J. Meyers, B. C. Kliebenstein, D. Ross-Ibarra, J. 2024-12-03 doi:10.1101/2024.12.02.626474 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Lineage labeling with zebrafish hand2 Cre and CreERT2 recombinase CRISPR knock-ins ]]> https://biorxiv.org/content/10.1101/2024.12.04.626907v1?rss=1 View larger version (20K): org.highwire.dtl.DTLVardef@12f58cborg.highwire.dtl.DTLVardef@16e95c8org.highwire.dtl.DTLVardef@12b8e9dorg.highwire.dtl.DTLVardef@a01848_HPS_FORMAT_FIGEXP M_FIG C_FIG Zebrafish hand2 Cre and CreERT2 drivers generated with GeneWeld CRISPR/Cas9 precision targeted integration label numerous lineages from the mesoderm and ectoderm. Temporal CreERT2 Tamoxifen regulated switching re{-} veals late emerging hand2 progenitors contribute to the embryonic venous vasculature and larval organs. ]]> Ming, Z. Liu, F. Moran, H. R. Lalonde, R. L. Adams, M. Restrepo, N. K. Joshi, P. Ekker, S. C. Clark, K. J. Friedberg, I. Yin, C. Sumanas, S. Mosimann, C. Essner, J. J. McGrail, M. 2024-12-05 doi:10.1101/2024.12.04.626907 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Enhanced identification of small molecules binding to hnRNPA1 via cryptic pockets mapping coupled with X-Ray fragment screening ]]> https://biorxiv.org/content/10.1101/2024.12.17.628909v1?rss=1 Dunnett, L. Das, S. Venditti, V. Prischi, F. 2024-12-18 doi:10.1101/2024.12.17.628909 Cold Spring Harbor Laboratory Press 2024-12-18 <![CDATA[ Transcriptional responses to in vitro macrocyclic lactone exposure in Toxocara canis larvae using RNA-seq ]]> https://biorxiv.org/content/10.1101/2024.12.20.629602v1?rss=1 Quintana, T. A. Brewer, M. T. Jesudoss Chelladurai, J. R. J. 2024-12-20 doi:10.1101/2024.12.20.629602 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Maize and wild relatives show distinct patterns of genome downsizing following polyploidy ]]> https://biorxiv.org/content/10.1101/2024.12.24.630189v1?rss=1 Snodgrass, S. J. Woodhouse, M. R. Seetharam, A. S. Stitzer, M. C. Hufford, M. 2024-12-25 doi:10.1101/2024.12.24.630189 Cold Spring Harbor Laboratory Press 2024-12-25 <![CDATA[ Branched and Linear F-actin Networks Control Directional Migration Switching Behavior on Aligned Collagen Fibrils ]]> https://biorxiv.org/content/10.1101/2025.01.03.631234v1?rss=1 Foroozandehfar, A. Tohidi, S. Siddiqui, S. A. Namanda, F. R. Schneider, I. 2025-01-04 doi:10.1101/2025.01.03.631234 Cold Spring Harbor Laboratory Press 2025-01-04 <![CDATA[ Dipeptidase 1 is a functional receptor for coronavirus PHEV ]]> https://biorxiv.org/content/10.1101/2025.01.09.632101v1?rss=1 Dufloo, J. Fernandez, I. Arbabian, A. Haouz, A. Gimenez-Lirola, L. G. Rey, F. A. Sanjuan, R. 2025-01-10 doi:10.1101/2025.01.09.632101 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ Molecular Drivers of RNA Phase Separation ]]> https://biorxiv.org/content/10.1101/2025.01.20.633842v1?rss=1 Poly(A) > Poly(C) > Poly(U) order shaped by the interplay of base-stacking and hydrogen bonding interactions. Furthermore, our simulations show that ionic conditions and post-translational modifications can fine-tune RNA self-assembly and modulate condensate physical properties. Author SummaryRNA molecules are essential for organizing membraneless compartments that play critical roles in cellular processes. While many of these condensates form through interactions between RNA and proteins, recent studies have shown that certain RNA sequences can self-assemble into condensates without protein assistance. This ability is influenced by the sequence composition of RNA and the presence of ions like magnesium. Using detailed molecular simulations we carried out systematic study to reveal how temperature and ionic conditions affect RNA condensation. We discovered that magnesium ions play a key role in driving RNA molecules to condense at lower temperatures by promoting structural changes within the RNA. Our findings also revealed that the stability of RNA condensates varies depending on the RNA sequence, with guanine-rich sequences being the most stable. Additionally, we demonstrated how chemical modifications and ionic conditions can fine-tune the properties of RNA condensates. This study provides new insights into how RNA forms condensates and highlights potential strategies to control their behavior, which could have implications for understanding cellular organization and developing new therapies. ]]> Ramachandran, V. Potoyan, D. A. 2025-01-22 doi:10.1101/2025.01.20.633842 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Assessing the impact of yield plasticity on hybrid performance in maize ]]> https://biorxiv.org/content/10.1101/2025.01.21.634104v1?rss=1 Davis, J. M. Coffey, L. M. Turkus, J. Lopez-Corona, L. Linders, K. Ullagaddi, C. Santra, D. K. Schnable, P. S. Schnable, J. C. 2025-01-24 doi:10.1101/2025.01.21.634104 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Extensive genome evolution distinguishes maize within a stable tribe of grasses ]]> https://biorxiv.org/content/10.1101/2025.01.22.633974v1?rss=1 Stitzer, M. C. Seetharam, A. S. Scheben, A. Hsu, S.-K. Schulz, A. J. AuBuchon-Elder, T. El-Walid, M. Ferebee, T. H. Hale, C. O. La, T. Liu, Z.-Y. McMorrow, S. J. Minx, P. Phillips, A. Syring, M. Wrightsman, T. Zhai, J. Pasquet, R. McAllister, C. Malcomber, S. Traiperm, P. Layton, D. Zhong, J. Costich, D. E. Dawe, R. K. Fengler, K. Harris, C. Irelan, Z. Llaca, V. Parakkal, P. Zastrow-Hayes, G. Woodhouse, M. R. Cannon, E. K. Portwood, J. Andorf, C. M. Albert, P. S. Birchler, J. A. Siepel, A. Ross-Ibarra, J. Romay, M. C. Kellogg, E. Buckler, E. S. Hufford 2025-01-24 doi:10.1101/2025.01.22.633974 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ GO Big or Go Home: A New Gene Ontology Subset that Improves Plant Gene Function Prediction ]]> https://biorxiv.org/content/10.1101/2025.01.26.634938v1?rss=1 Fattel, L. Lawrence-Dill, C. J. 2025-01-27 doi:10.1101/2025.01.26.634938 Cold Spring Harbor Laboratory Press 2025-01-27 <![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[ Revealing the hidden social structure of pigs with AI assisted automated monitoring data and social network analysis ]]> https://biorxiv.org/content/10.1101/2025.01.30.635669v1?rss=1 Agha, S. Psota, E. Turner, S. P. Lewis, C. R. G. Steibel, J. P. Doeschl-Wilson, A. 2025-01-30 doi:10.1101/2025.01.30.635669 Cold Spring Harbor Laboratory Press 2025-01-30 <![CDATA[ Estimation of total mediation effect for a binary trait in a case-control study for high-dimensional omics mediators ]]> https://biorxiv.org/content/10.1101/2025.01.28.635396v1?rss=1 Kang, Z. Chen, L. Wei, P. Xu, Z. Li, C. Yang, T. 2025-02-02 doi:10.1101/2025.01.28.635396 Cold Spring Harbor Laboratory Press 2025-02-02 <![CDATA[ Positive allosteric modulation of emodepside sensitive Brugia malayi SLO-1F and Onchocerca volvulus SLO-1A potassium channels by GoSlo-SR-5-69 ]]> https://biorxiv.org/content/10.1101/2025.01.31.635861v1?rss=1 McHugh, M. Njeshi, C. N. Smith, N. Kashyap, S. S. Datta, R. Sun, H. Robertson, A. P. Martin, R. J. 2025-02-05 doi:10.1101/2025.01.31.635861 Cold Spring Harbor Laboratory Press 2025-02-05 <![CDATA[ Proteomics-based models of gene expression and cellular control of cotton fiber development ]]> https://biorxiv.org/content/10.1101/2025.02.05.636703v1?rss=1 Lee, Y. Yang, P. Rani, H. Miller, G. Grover, C. E. Swaminathan, S. Zabotina, O. A. Wendel, J. F. Xie, J. Szymanski, D. B. 2025-02-06 doi:10.1101/2025.02.05.636703 Cold Spring Harbor Laboratory Press 2025-02-06 <![CDATA[ A Multi-Model Ensemble Reveals Soil Carbon Gains from Regenerative Practices in the U.S. Midwest Cropland ]]> https://biorxiv.org/content/10.1101/2025.02.04.636509v1?rss=1 Basso, B. Tadiello, T. Millar, N. Maureira, F. Albarenque, S. Baer, B. Price, L. Sharma, P. Villalobos, C. Paustian, K. Fowler, A. Delandmeter, M. Acutis, M. Archontoulis, S. Covey, K. Doro, L. Dumont, B. Grace, P. Hoogenboom, G. Jones, J. W. Perego, A. Robertson, G. P. Ruane, A. Stockle, C. Zhang, Y. 2025-02-08 doi:10.1101/2025.02.04.636509 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Crusty-Pinky: A Novel Polyextremotolerant Fungus and its Methylobacterium Symbionts Could be an Essential Symbiosis for the Biological Soil Crust Consortium ]]> https://biorxiv.org/content/10.1101/2025.02.11.633654v1?rss=1 Carr, E. C. Saha, R. Harris, S. D. Riekhof, W. R. 2025-02-12 doi:10.1101/2025.02.11.633654 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Robust Prediction of Enzyme Variant Kinetics with RealKcat ]]> https://biorxiv.org/content/10.1101/2025.02.10.637555v1?rss=1 Sajeevan, K. A. Osinuga, A. B, A. Ferdous, S. Shahreen, N. Noor, M. Koneru, S. Santa-Correa, L. M. Salehi, R. Chowdhury, N. B. Calderon-Lopez, B. Mali, A. Saha, R. Chowdhury, R. 2025-02-15 doi:10.1101/2025.02.10.637555 Cold Spring Harbor Laboratory Press 2025-02-15 <![CDATA[ Rationally Designed PKD1 Activator Protects Against Neurodegeneration in Pre-clinical Models of Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2025.02.13.637661v1?rss=1 Asaithambi, A. Jang, A. Ghosh, A. Ay, M. Jin, H. Anantharam, V. Kanthasamy, A. Kanthasamy, A. G. 2025-02-21 doi:10.1101/2025.02.13.637661 Cold Spring Harbor Laboratory Press 2025-02-21 <![CDATA[ ESMStabP: A Regression Model for Protein Thermostability Prediction ]]> https://biorxiv.org/content/10.1101/2025.02.18.638450v1?rss=1 Ramos, M. A. Jernigan, R. L. Kilinc, M. 2025-02-23 doi:10.1101/2025.02.18.638450 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ Synthetic Generation of Dynamic Omics Data Demonstrates Aspergillus nidulans BrlA Paradoxical Wall Stress Response ]]> https://biorxiv.org/content/10.1101/2025.03.02.638868v1?rss=1 Zavorskas, J. Edwards, H. Huso, W. Doan, A. G. Marten, M. R. Harris, S. Srivastava, R. 2025-03-03 doi:10.1101/2025.03.02.638868 Cold Spring Harbor Laboratory Press 2025-03-03 <![CDATA[ Thermal Adaptation of Extremozymes: Temperature-Sensitive Contact Analysis of Serine Proteases ]]> https://biorxiv.org/content/10.1101/2025.03.03.641325v1?rss=1 Kulathunga, D. P. Potoyan, D. 2025-03-06 doi:10.1101/2025.03.03.641325 Cold Spring Harbor Laboratory Press 2025-03-06 <![CDATA[ Phylo-rs: an extensible phylogenetic analysis library in Rust ]]> https://biorxiv.org/content/10.1101/2025.03.10.642340v1?rss=1 Vijendran, S. Anderson, T. Markin, A. Eulenstein, O. 2025-03-13 doi:10.1101/2025.03.10.642340 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Development and Characterization of Chicken Lung Organoids for Future In Vitro Modeling of Avian Influenza Virus-Host Cell Interaction ]]> https://biorxiv.org/content/10.1101/2025.03.12.640685v1?rss=1 Nicholson, H. Zdyrski, C. Corbett, M. P. Lowen, A. C. Catucci, M. Melvin, B. J. Stabler, L. J. Douglass, E. Mochel, J. P. Allenspach, K. Carnaccini, S. 2025-03-14 doi:10.1101/2025.03.12.640685 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Whole-genome sequence of Potamopyrgus antipodarum: a model system for the maintenance of sexual reproduction reveals a recent whole-genome duplication ]]> https://biorxiv.org/content/10.1101/2025.03.16.643514v1?rss=1 Jalinsky, J. R. McElroy, K. E. Sharbrough, J. Bankers, L. Fields, P. Higgins, C. Toll, C. Boore, J. Logsdon, J. M. Neiman, M. 2025-03-17 doi:10.1101/2025.03.16.643514 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ Genetic analysis of pigment production in the fungus Exophiala dermatitidis ]]> https://biorxiv.org/content/10.1101/2025.03.19.644242v1?rss=1 Harris, S. D. Chhoker, K. Hausner, G. 2025-03-20 doi:10.1101/2025.03.19.644242 Cold Spring Harbor Laboratory Press 2025-03-20 <![CDATA[ Impacts of competition and phenotypic plasticity on the viability of adaptive therapy ]]> https://biorxiv.org/content/10.1101/2025.03.20.644475v1?rss=1 Vibishan, B. Jain, P. Sharma, V. Hari, K. Kadelka, C. George, J. T. Jolly, M. K. 2025-03-25 doi:10.1101/2025.03.20.644475 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ Genome reannotation and effector candidate identification in Meloidogyne chitwoodi through gland-specific transcriptome analysis ]]> https://biorxiv.org/content/10.1101/2025.03.27.645669v1?rss=1 Teixeira, M. Ko, I. Bali, S. Vieira, P. Maier, T. R. Baum, T. J. Gleason, C. 2025-03-29 doi:10.1101/2025.03.27.645669 Cold Spring Harbor Laboratory Press 2025-03-29 <![CDATA[ The impact of fungal developmental structures on mechanical properties of mycelial materials. ]]> https://biorxiv.org/content/10.1101/2025.04.01.644731v1?rss=1 Gray, K. J. Edwards, H. Doan, A. G. Huso, W. Lee, J. Pan, W. Bolima, N. Gautam, I. Wang, T. Srivastava, R. Zupan, M. Harris, S. Marten, M. R. 2025-04-01 doi:10.1101/2025.04.01.644731 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Tubulin isotypes contribute opposing properties to balance anaphase spindle morphogenesis ]]> https://biorxiv.org/content/10.1101/2025.04.04.647290v1?rss=1 Nsamba, E. T. Bera, A. Todi, V. Savoy, L. Gupta, R. M. Gupta, M. L. 2025-04-05 doi:10.1101/2025.04.04.647290 Cold Spring Harbor Laboratory Press 2025-04-05 <![CDATA[ Histone H3 tail charge patterns govern nucleosome condensate formation and dynamics ]]> https://biorxiv.org/content/10.1101/2025.04.09.647968v1?rss=1 Hammonds, E. F. Singh, A. Suresh, K. K. Yang, S. Meidl Zahorodny, S. S. Gupta, R. Potoyan, D. A. Banerjee, P. R. Morrison, E. A. 2025-04-10 doi:10.1101/2025.04.09.647968 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ Two Spore Types in a Marine Parasite of Dinoflagellates ]]> https://biorxiv.org/content/10.1101/2025.04.10.648098v1?rss=1 Szymczak, J. Pinaud, S. Romero Rodriguez, I. Walde, M. Kayal, E. Alves-de-Souza, C. Bigeard, E. Gallet, B. Gachenot, M. Le Panse, S. Jauzein, C. Le Gac, M. Decelle, J. Pohnert, G. Vallet, M. Talman, A. M. Guillou, L. 2025-04-10 doi:10.1101/2025.04.10.648098 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ Exploring influenza A virus receptor distribution in the lactating mammary gland of domesticated livestock and in human breast tissue. ]]> https://biorxiv.org/content/10.1101/2025.04.16.649193v1?rss=1 Harm, T. A. Arruda, B. Siepker, C. Fasina, O. Groeltz, J. Baker, A. Phillips, R. Jones, B. Espina, V. Seger, H. Plummer, P. Bell, T. Nelli, R. K. 2025-04-21 doi:10.1101/2025.04.16.649193 Cold Spring Harbor Laboratory Press 2025-04-21 <![CDATA[ Comparative multi-omics profiling of Gossypium hirsutum and Gossypium barbadense fibers at high temporal resolution reveals key differences in polysaccharide composition and associated glycosyltransferases ]]> https://biorxiv.org/content/10.1101/2025.04.26.650795v1?rss=1 Swaminathan, S. Lee, Y. Grover, C. E. DeTemple, M. F. Mugisha, A. S. Sichterman, L. E. Yang, P. Xie, J. Wendel, J. F. Szymanski, D. B. Zabotina, O. A. 2025-04-30 doi:10.1101/2025.04.26.650795 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ Sewing the future of cotton: a multi-omics study combining nanomechanics, transcriptomics, and phenotypic traits ]]> https://biorxiv.org/content/10.1101/2025.05.12.653486v1?rss=1 Hasib, M. H. H. Masud, N. Biswas, A. Jubery, T. Z. Stanley, C. Swaminathan, S. Grover, C. E. Wendel, J. F. Sarkar, S. Zabotina, O. A. Sarkar, A. 2025-05-15 doi:10.1101/2025.05.12.653486 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Application of post glycosylation modifying enzymes for mass spectrometry imaging of modified N-glycans in situ. ]]> https://biorxiv.org/content/10.1101/2025.05.14.654078v1?rss=1 Dreifus, J. E. Chuzel, L. Escobar, E. E. Grimsley, G. Bai, H. Hanneman, A. J. Fossa, S. L. Gregory, V. Martin, R. J. Drake, R. R. Foster, J. Taron, C. H. 2025-05-15 doi:10.1101/2025.05.14.654078 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Comparative population genomics of relictual Caribbean island Gossypium hirsutum ]]> https://biorxiv.org/content/10.1101/2025.06.02.657498v1?rss=1 Ning, W. Hu, G. Yuan, D. Arick, M. A. Hsu, C.-Y. Magbanua, Z. V. Pechanova, O. Peterson, D. G. Dong, Y. Udall, J. Grover, C. Wendel, J. 2025-06-06 doi:10.1101/2025.06.02.657498 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Postnatal Pulmonary Artery Development from Transcript to Tissue ]]> https://biorxiv.org/content/10.1101/2025.06.03.657639v1?rss=1 Schwarz, E. L. Ramachandra, A. B. Yeung, N. Manning, E. P. Weiss, D. Humphrey, J. D. 2025-06-06 doi:10.1101/2025.06.03.657639 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Proximal Pulmonary Artery Stiffening as a Biomarker of Cardiopulmonary Aging ]]> https://biorxiv.org/content/10.1101/2025.06.10.658632v1?rss=1 De Man, R. Cai, Z. Doddaballapur, P. Guerrera, N. Lin, L. Justet, A. Abu Hussein, N. S. Cavinato, C. Raredon, M. S. B. Heerdt, P. Singh, I. Yan, X. Kang, M.-J. Bruns, D. R. Lee, P. J. Tellides, G. Humphrey, J. Kaminski, N. Ramachandra, A. B. Manning, E. P. 2025-06-15 doi:10.1101/2025.06.10.658632 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Backbone Rigidity Encodes Universal Viscoelastic Signatures in Biomolecular Condensates ]]> https://biorxiv.org/content/10.1101/2025.06.10.658939v1?rss=1 Yang, S. Biswas, S. Potoyan, D. A. 2025-06-15 doi:10.1101/2025.06.10.658939 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Flexible docking of cyclic peptides to proteins using CABS-dock ]]> https://biorxiv.org/content/10.1101/2025.06.18.660300v1?rss=1 Zalewski, M. Badaczewska-Dawid, A. E. Kmiecik, S. 2025-06-21 doi:10.1101/2025.06.18.660300 Cold Spring Harbor Laboratory Press 2025-06-21 <![CDATA[ Toxoplasma effector TgWIP hijacks dendritic cell actin and motility via Nck1/Grb2 and the WAVE complex ]]> https://biorxiv.org/content/10.1101/2025.06.22.660983v1?rss=1 Morales, P. Kramer, D. A. de Moraes de Siqueira, C. Brown, A. J. Sangare, L. Chen, B. Saeij, J. P. J. 2025-06-23 doi:10.1101/2025.06.22.660983 Cold Spring Harbor Laboratory Press 2025-06-23 <![CDATA[ Rapid Cell-Free Combinatorial Mutagenesis Workflow Using Small Oligos Suitable for High-Iteration, Active Learning-Guided Protein Engineering ]]> https://biorxiv.org/content/10.1101/2025.06.18.660386v1?rss=1 80% size reduction from current fragment-based shu2ling strategies also helps avoid including multiple mutations on the same fragment, reducing the number one must order to cover the design space. By screening 3-10 fragment assemblies for two di2erent proteins, we show our approach is a general, scalable, and cost-e2ective platform for high-iteration protein engineering. ]]> Godin, R. Hejazi, S. S. Lange, B. Aldamak, B. Reuel, N. F. 2025-06-24 doi:10.1101/2025.06.18.660386 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ Peroxisomal import is circadian in glia and regulates sleep and lipid metabolism ]]> https://biorxiv.org/content/10.1101/2025.06.23.661129v1?rss=1 Das, A. Serna, I. M. R. Kumar, A. Kalita, H. Sherpa, L. Vaughen, J. P. Bai, H. 2025-06-25 doi:10.1101/2025.06.23.661129 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Recessive antimorph alleles reveal novel functions of the OPAQUE1 myosin XI in maize ]]> https://biorxiv.org/content/10.1101/2025.06.26.661838v1?rss=1 Zebosi, B. Martinez, S. E. Wimalanathan, K. Ssengo, J. Brown, G. Best, N. B. Facette, M. Rasmussen, C. G. Vollbrecht, E. 2025-06-30 doi:10.1101/2025.06.26.661838 Cold Spring Harbor Laboratory Press 2025-06-30 <![CDATA[ Variability in cadmium accumulation in quinoa grain: potential role of crop domestication and other factors mediating differences in resilience and uptake ]]> https://biorxiv.org/content/10.1101/2025.06.30.662325v1?rss=1 Rodriguez-Sanchez, A. Jimenez-Castaneda, M. Filley, T. Brenner, D. Macedo, D. Casa, V. H. Hoagland, L. 2025-07-01 doi:10.1101/2025.06.30.662325 Cold Spring Harbor Laboratory Press 2025-07-01 <![CDATA[ Allelic Variation in CYP3A4 and PLB1 Drives Feed Efficiency and Immunometabolic Resilience in Beef Cattle ]]> https://biorxiv.org/content/10.1101/2025.07.02.662800v1?rss=1 Morenikeji, O. B. Taiwo, G. Idowu, M. Gratz, L. M. Olabosoye, B. King, R. E. Andrews, N. D. Saccoh, F. Grytsay, A. Ogunade, I. 2025-07-08 doi:10.1101/2025.07.02.662800 Cold Spring Harbor Laboratory Press 2025-07-08 <![CDATA[ Heat Stress and Soil Microbial Disturbance Influence Soybean Root Metabolite, Microbiome Profiles, and Nodulation ]]> https://biorxiv.org/content/10.1101/2025.07.13.664636v1?rss=1 Elango, D. Van der Laan, L. Gholizadeh, S. Premarathne, M. D. G. P. Dutter, C. R. DePew, C. McDaniel, M. Singh, A. K. 2025-07-14 doi:10.1101/2025.07.13.664636 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ Population Genomics Informs Conservation Strategies for Critically Endangered Kokia Species in Hawaii ]]> https://biorxiv.org/content/10.1101/2025.07.17.665168v1?rss=1 Ning, W. Kayal, E. Wendel, J. F. Hsu, C.-y. Magbanua, Z. V. Pechanova, O. Yorkston, M. Morden, C. W. Keir, M. J. VanDeMark, J. R. Peterson, D. G. Arick, M. A. Grover, C. E. 2025-07-21 doi:10.1101/2025.07.17.665168 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Genome analysis of Lactobacillus plantarum and Lactobacillus brevis isolated from traditionally fermented Ethiopian kocho and their probiotic properties ]]> https://biorxiv.org/content/10.1101/2025.09.04.674358v1?rss=1 Goulart, D. Mulaw, G. Tesfay, T. Sisay, T. Muleta, D. Musa, A. Narayanan, N. 2025-09-07 doi:10.1101/2025.09.04.674358 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ Human shields alter antipredator behavior in Guenther's dik-dik (Madoqua guentheri) ]]> https://biorxiv.org/content/10.1101/2025.09.07.674752v1?rss=1 Owino, R. O. Hawkins, I. Noordermeer, I. Rodriguez, M. M. Stanton, L. A. Goheen, J. R. Alston, J. M. 2025-09-10 doi:10.1101/2025.09.07.674752 Cold Spring Harbor Laboratory Press 2025-09-10 <![CDATA[ Prokineticin-2 Upregulates GDNF in Astrocytes and Pharmacological Modulation of PK2 Receptors offers Neuroprotection in Experimental Models of Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2025.09.08.674934v1?rss=1 Luo, J. Clabaugh, G. R. Neal, M. Huang, M. Sarkar, S. Zenitsky, G. Jin, H. Anantharam, V. Nebigil, C. Desaubry, L. Kanthasamy, A. Kanthasamy, A. G. 2025-09-14 doi:10.1101/2025.09.08.674934 Cold Spring Harbor Laboratory Press 2025-09-14 <![CDATA[ Genetic and environmental factors regulating soybean reproductive stages and their transitions ]]> https://biorxiv.org/content/10.1101/2025.09.10.675456v1?rss=1 Chakrabarty, S. Shook, J. M. Singh, A. K. 2025-09-16 doi:10.1101/2025.09.10.675456 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ A single-cell immune atlas of primary and secondary lymphoid organs in pigs ]]> https://biorxiv.org/content/10.1101/2025.09.11.675613v1?rss=1 Wiarda, J. E. Kapoor, M. Sivasankaran, S. K. Byrne, K. A. Loving, C. L. Tuggle, C. K. 2025-09-16 doi:10.1101/2025.09.11.675613 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ A Structure-Aware Generative Framework for Exploring Protein Sequence and Function Space ]]> https://biorxiv.org/content/10.1101/2025.09.18.676787v1?rss=1 Shukla, D. Martin, J. Morcos, F. Potoyan, D. A. 2025-09-19 doi:10.1101/2025.09.18.676787 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Soybean aphids exploit abscisic acid signaling to suppress jasmonate defense responses ]]> https://biorxiv.org/content/10.1101/2025.09.21.677601v1?rss=1 Hohenstein, J. D. Kanobe, C. Natukunda, M. I. Gallardo, P. Zhang, D. Kovinich, N. Helms, A. M. Tooker, J. F. MacIntosh, G. C. 2025-09-21 doi:10.1101/2025.09.21.677601 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Structurally Informed Fitness Landscapes for Surveillance of Emerging PRRSV Variants ]]> https://biorxiv.org/content/10.1101/2025.10.06.680729v1?rss=1 Chowdhury, R. Srinivasan Raghunath, V. Dey, S. Ferdous, S. Danurdoro, R. A Zeller, M. 2025-10-06 doi:10.1101/2025.10.06.680729 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ PPARG directs trophoblast cell fate and establishment of the uterine-placental interface ]]> https://biorxiv.org/content/10.1101/2025.10.08.681177v1?rss=1 Dominguez, E. M. Irusta, A. M. IQBAL, K. Chen, K. Finlinson, A. Parrish, M. Okae, H. Arima, T. Tuteja, G. Soares, M. J. 2025-10-08 doi:10.1101/2025.10.08.681177 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Adaptive evolution of Candida maltosa improves the bioconversion of depolymerized plastic feedstock by targeting biosurfactant production ]]> https://biorxiv.org/content/10.1101/2025.10.11.681799v1?rss=1 100% increase in specific growth rate when using TOD_HDPE as a carbon source. The evolved strain was compared to the parent strain to identify the cellular and biochemical changes associated with the improved phenotype and the uptake mechanisms involved in the bioconversion of TOD_HDPE. This comparison found that C. maltosa secretes biosurfactants capable of solubilizing hydrocarbons. The adaptive evolution resulted in changes in biosurfactant production that translated to improved emulsification of alkanes and increased solubilization of fatty alcohols and alkanes. In addition to the changes in metabolites, the study identified increases in membrane permeability associated with a reduction in ergosterol that may also play a role in the improved phenotype. These findings support the development of C. maltosa and other potential microbial cell factories for plastic biorefineries and may inform future design strategies. ]]> Rodriguez-Ocasio, E. Noroozi, K. Khalid, A. Brown, J. Brown, R. C. Blenner, M. Jarboe, L. R. 2025-10-12 doi:10.1101/2025.10.11.681799 Cold Spring Harbor Laboratory Press 2025-10-12 <![CDATA[ SmartHisto: Bayesian Active Learning for Histology Images ]]> https://biorxiv.org/content/10.1101/2025.10.13.681994v1?rss=1 Vijendran, S. Arruda, B. Anderson, T. K. Eulenstein, O. 2025-10-14 doi:10.1101/2025.10.13.681994 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Large Numbers of New Human Paralogs Discovered ]]> https://biorxiv.org/content/10.1101/2025.10.15.680306v1?rss=1 Bk, P. Deng, W. Hemmat, M. A. Daniels, I. L. Jernigan, R. L. 2025-10-15 doi:10.1101/2025.10.15.680306 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Trends in stomatal density and size in maize hybrids representing 100 years of long-term breeding for yield ]]> https://biorxiv.org/content/10.1101/2025.10.21.683719v1?rss=1 Bilgici, M. Ebrahimi, E. Miranda, L. P. d. Lira, S. Borras, L. Young, T. Yavuz, R. Moore, K. J. Dixon, P. Lubberstedt, T. 2025-10-22 doi:10.1101/2025.10.21.683719 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Modulating inter-mitochondrial contacts to increase membrane potential for mitigating blue light damage ]]> https://biorxiv.org/content/10.1101/2025.10.24.684455v1?rss=1 Wang, Y. Qiu, K. Zou, W. Amom, P. Ganjawala, T. Lee, E. Tian, Z. Xu, X. Huang, T. Tsai, N.-P. Shi, D. Kang, P. Bai, H. Zacharias, A. L. Zhang, K. Diao, J. 2025-10-25 doi:10.1101/2025.10.24.684455 Cold Spring Harbor Laboratory Press 2025-10-25 <![CDATA[ Viral lineage and mode of exposure modulate within host spatial dynamics of influenza A viruses ]]> https://biorxiv.org/content/10.1101/2025.11.03.686270v1?rss=1 Leyson, C. Vargas-Maldonado, N. Gaddy, M. Raghunathan, V. Matias-Ferreri, L. Sethi, M. Patatanian, K. Carnaccini, S. Ganti, K. VanInsberghe, D. Lowen, A. C. 2025-11-03 doi:10.1101/2025.11.03.686270 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ The dominance of gene expression controlled by trans-eQTL hotspots contributes to phenotypic heterosis in maize ]]> https://biorxiv.org/content/10.1101/2025.11.03.686376v1?rss=1 Xu, G. Yang, X. Zhang, M. Kang, C. Tian, Z. Qi, Y. Luo, M. Liu, P. Ross-Ibarra, J. Yang, J. Liu, H. 2025-11-05 doi:10.1101/2025.11.03.686376 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Automated Seizure Detection in Animal EEG Signals ]]> https://biorxiv.org/content/10.1101/2025.11.04.686618v1?rss=1 Ganguly, S. Jiang, Z. Massey, N. Rao, N. S. Thippeswamy, T. Sarkar, S. 2025-11-06 doi:10.1101/2025.11.04.686618 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ Dairy manure analysis reveals significant risk of Antibiotic resistance from Extracellular DNA in Manure storage Pit ]]> https://biorxiv.org/content/10.1101/2025.11.07.687174v1?rss=1 Sakib, N. Andersen, D. S. Jarboe, L. R. Howe, A. 2025-11-07 doi:10.1101/2025.11.07.687174 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ AI-assisted Image-Based Phenotyping Reveals Genetic Architecture of Pod Traits in Mungbean (Vigna radiata L.) ]]> https://biorxiv.org/content/10.1101/2025.11.06.687031v1?rss=1 0.96 for pod length and seed per pod). Four complementary GWAS models identified 45 significant SNPs associated with pod curvature, length, width, and seed per pod traits. Notably, a significant SNP (5_35265704) on chromosome 1 was linked to pod dimensional traits, length, width, and curvature. A candidate gene, Vradi01g00001116, was located within the linkage disequilibrium (LD) region of this SNP, is part of the GH3 gene family, and has an Arabidopsis ortholog (AT4G27260) known for influencing organ elongation, pod, and seed development. Another SNP, 5_210437 on chromosome 2, has been found to be significantly associated with both pod length and seed per pod. A candidate gene, Vradi02g00003971, located in the LD region of this SNP, belongs to the potassium transporter family and shares homology with the HAK5 gene family (AT4G13420) in Arabidopsis, which influences pod and seed growth. Image-based measurements achieved genomic prediction accuracies ranging from 0.61 to 0.85 across various traits, exhibiting an improvement of 12-22% over manual methods. These results demonstrate the potential of AI-assisted phenomics integrated with genomic tools to accelerate selection for improved pod architecture in mungbean breeding programs across the Midwestern United States and globally. ]]> Boddepalli, V. N. Jubery, T. Z. Dutta, S. Ganapathysubramanian, B. Singh, A. 2025-11-08 doi:10.1101/2025.11.06.687031 Cold Spring Harbor Laboratory Press 2025-11-08 <![CDATA[ Attractors are less stable than their basins: Canalization creates a coherence gap in gene regulatory networks ]]> https://biorxiv.org/content/10.1101/2025.11.06.687062v1?rss=1 Bavisetty, V. S. N. Wheeler, M. Kadelka, C. 2025-11-08 doi:10.1101/2025.11.06.687062 Cold Spring Harbor Laboratory Press 2025-11-08 <![CDATA[ Defining the Growth Stages of Mungbean (Vigna radiata L.) using the BBCH Scale ]]> https://biorxiv.org/content/10.1101/2025.11.09.687504v1?rss=1 Singh, A. Boddepalli, V. N. 2025-11-11 doi:10.1101/2025.11.09.687504 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ Molecular Evolutionary Analysis for Estimating the Strength of Fluctuating Selection among Individuals (FSI) ]]> https://biorxiv.org/content/10.1101/2025.11.10.687654v1?rss=1 Gu, X. 2025-11-11 doi:10.1101/2025.11.10.687654 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ SNaQ.jl: Improved Scalability for Phylogenetic Network Inference ]]> https://biorxiv.org/content/10.1101/2025.11.17.688917v1?rss=1 Kolbow, N. Kong, S. Chafin, T. Justison, J. Ane, C. Solis-Lemus, C. 2025-11-18 doi:10.1101/2025.11.17.688917 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ Impact of Maternal Antibodies and Weaning Stress on the Replication and Transmission of Human H3N2 Influenza A in Piglets ]]> https://biorxiv.org/content/10.1101/2025.11.18.689042v1?rss=1 Ciacci Zanella, G. Cardenas Perez, M. Hutter, C. R. Snyder, C. A. Wymore Brand, M. (Wilberts) Arruda, B. Perez, D. R. Anderson, T. Rajao, D. S. Baker, A. L. 2025-11-19 doi:10.1101/2025.11.18.689042 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ Molecular Evolution under Macro-Perturbation Barrier and the Fixation Process of Polyploidization ]]> https://biorxiv.org/content/10.1101/2025.11.19.689354v1?rss=1 v if s>0 (positive selection), {lambda}=v if s=0 (neutrality) or {lambda} Gu, X. 2025-11-20 doi:10.1101/2025.11.19.689354 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ The Pleiotropy Hypothesis of Molecular Evolution ]]> https://biorxiv.org/content/10.1101/2025.11.19.689358v1?rss=1 Gu, X. 2025-11-21 doi:10.1101/2025.11.19.689358 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Gene-transcription factor regulatory networks implicate primary cilia in the evolution of vertebrate sex determination and expand models of epigenetic regulation ]]> https://biorxiv.org/content/10.1101/2025.11.21.689810v1?rss=1 Gessler, T. B. Adams, D. C. Valenzuela, N. 2025-11-24 doi:10.1101/2025.11.21.689810 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Initial identification of genomic islands in Taylorella equigenitalis and Taylorella asinigenitalis and their distribution in isolates from around the world ]]> https://biorxiv.org/content/10.1101/2025.11.26.686905v1?rss=1 Hicks, J. A. Li, G. Petry, S. Duquesne, F. Choi, J. G. Overesh, G. Lantz, K. Robbe Austerman, S. Huang, X. 2025-11-27 doi:10.1101/2025.11.26.686905 Cold Spring Harbor Laboratory Press 2025-11-27 <![CDATA[ Widespread sex-biased gene expression reflects female-biased longevity in a species with environmental sex determination ]]> https://biorxiv.org/content/10.1101/2025.11.26.690843v1?rss=1 Bock, S. Hoekstra, L. A. Hagerty, K. Schmidt, R. E. Judson, J. Adorsoo, M. Singh, R. Janzen, F. J. Bronikowski, A. M. 2025-12-01 doi:10.1101/2025.11.26.690843 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Developmental conditions shape lifetime reproductive strategies in a wild mammal ]]> https://biorxiv.org/content/10.64898/2025.12.05.692614v1?rss=1 1,000 reproductive attempts across the lifetimes of 405 wild female red squirrels, we show that developmental adversity prompts adaptive reorganization of reproductive investment across the lifespan. Hardships reduced lifetime reproductive opportunities, but triggered opposing strategies. Extrinsic mortality risk predicted frontloading of reproduction at debut, while poor maternal investment predicted terminal reproductive effort at a cost to future generations. Both strategies preserved lifetime fitness, revealing how context-dependent reproductive plasticity over the life course can rescue the fitness consequences of developmental hardship. ]]> Petrullo, L. Delaney, D. M. Boutin, S. Lane, J. E. McAdam, A. G. Dantzer, B. 2025-12-06 doi:10.64898/2025.12.05.692614 Cold Spring Harbor Laboratory Press 2025-12-06 <![CDATA[ Finite-State Likelihood: an Approximation for Genome Phylogeny Inference based on Generalized Gene Contents ]]> https://biorxiv.org/content/10.64898/2025.12.08.693040v1?rss=1 Gu, X. 2025-12-10 doi:10.64898/2025.12.08.693040 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ Population Genetics of Fluctuating Selection among Individuals (FSI): a New Paradigm of Molecular Evolution ]]> https://biorxiv.org/content/10.64898/2025.12.08.693052v1?rss=1 0, could lead to two interpretations: when the observed is below a threshold, the selection-duality is favored; otherwise an adaptive evolution is favored. We calculated the threshold for several mammals (human, macaque, lemur and vole), and found that all those observed values (from 3.5% to 29%) were below the threshold and so they be interpreted by the selection duality rather than adaptive evolution. ]]> Gu, X. 2025-12-10 doi:10.64898/2025.12.08.693052 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ Detection of Mid-parent Heterosis Genes in Large-Scale Unreplicated RNA-Seq Experiments ]]> https://biorxiv.org/content/10.64898/2025.12.11.693571v1?rss=1 Qi, Y. Liu, P. 2025-12-14 doi:10.64898/2025.12.11.693571 Cold Spring Harbor Laboratory Press 2025-12-14 <![CDATA[ Four Decades of Breeding and Increasing Plant Density Management Reshaped Maize Root System Architecture ]]> https://biorxiv.org/content/10.64898/2025.12.10.693575v1?rss=1 Thies, A. Sciarresi, C. Trifunovic, S. Eudy, D. Vyn, T. J. Archontoulis, S. Topp, C. N. 2025-12-16 doi:10.64898/2025.12.10.693575 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Nano-Sieve Enabled On Chip Concentration and Multiplexed Detection of Raman-Dye Labeled Nanocubes ]]> https://biorxiv.org/content/10.64898/2025.12.17.695009v1?rss=1 Ng, T. Yang, Z. Chen, X. Yoon, K.-J. Guo, H. Bok, E.-Y. Lao, K. Do, Y. J. Yan, R. Du, K. 2025-12-19 doi:10.64898/2025.12.17.695009 Cold Spring Harbor Laboratory Press 2025-12-19 <![CDATA[ Dynamic ASK1 proximity networks uncover SCF-dependent and noncanonical roles in ABA and drought adaptation ]]> https://biorxiv.org/content/10.64898/2025.12.22.696057v1?rss=1 Rodriguez-Zaccaro, F. D. Moe-Lange, J. Malik, S. Montes-Serey, C. Hamada, N. Groover, A. Walley, J. Shabek, N. 2025-12-25 doi:10.64898/2025.12.22.696057 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ The interaction of the Arabidopsis Xyloglucan Xylosyltransferases XXTs with the COPII member SAR1 via their di-Arginine motifs is critical for delivery to the Golgi. ]]> https://biorxiv.org/content/10.64898/2025.12.30.697048v1?rss=1 Zhang, N. Julian, J. D. Zabotina, O. A. 2025-12-31 doi:10.64898/2025.12.30.697048 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ MATERNAL AUTOPHAGY CONTRIBUTES TO GRAIN YIELD IN MAIZE ]]> https://biorxiv.org/content/10.64898/2025.12.30.697098v1?rss=1 Tang, J. Avin-Wittenberg, T. Vollbrecht, E. Bassham, D. 2025-12-31 doi:10.64898/2025.12.30.697098 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Effects of atmospheric CO2 levels on the susceptibility of maize to diverse pathogens ]]> https://biorxiv.org/content/10.64898/2025.12.31.697224v1?rss=1 Khwanbua, E. Qi, Y. Ssengo, J. Liu, P. Graham, M. A. Whitham, S. 2026-01-02 doi:10.64898/2025.12.31.697224 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ DNA methylation reveals evolved buffering responses to climate-driven sex ratio skew in sea turtles ]]> https://biorxiv.org/content/10.64898/2026.01.06.697884v1?rss=1 Yen, E. C. Carvajal, G. A. Bazely, J. O. Gilbert, J. D. Taxonera, A. Fairweather, K. Lopes, A. Afonso, I. O. Newlands, D. Bentley, B. P. Correia, S. M. Allen, C. D. Staman, M. K. Sifuentes-Romero, I. Martin-Duran, J. M. Komoroske, L. M. Wyneken, J. Eizaguirre, C. 2026-01-06 doi:10.64898/2026.01.06.697884 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ 3D genome architecture regulates the traffic of transcription factors throughout human chromosomes ]]> https://biorxiv.org/content/10.64898/2026.01.06.698019v1?rss=1 Das, A. Cheng, R. R. Potoyan, D. A. Di Pierro, M. 2026-01-06 doi:10.64898/2026.01.06.698019 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ Characterization of the clade 4 non-toxigenic C. difficile isolate L-NTCD03 carrying the cfr(B) gene ]]> https://biorxiv.org/content/10.64898/2026.01.12.695941v1?rss=1 Nibbering, B. Nooij, S. Harmanus, C. Sanders, I. M. J. G. Miedema, I. M. Vossen, R. H. A. M. Kloet, S. Ardis, C. K. Britton, R. A. Yousefi, F. Bayne, J. Charavaryamath, C. Law, A. Murphy, M. L. Sponseller, B. Burrough, E. R. Mooyottu, S. Opriessnig, T. Kuijper, E. J. Smits, W. K. 2026-01-12 doi:10.64898/2026.01.12.695941 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ Novel Protoporphyrinogen oxidase 1 mutations endow resistance to PPO-inhibiting herbicides in Bassia scoparia ]]> https://biorxiv.org/content/10.64898/2026.01.15.699694v1?rss=1 Porri, A. Geddes, C. Law, Q. Ikley, J. Willingham, S. Johnen, P. Meiners, I. Al-Sammarraie, S. Crommar, K. Ouwerkerk, P. B. F. Betz, M. Jenks, B. M. Heiser, H. Baumann, F. Braendle, F. Lerchl, J. 2026-01-15 doi:10.64898/2026.01.15.699694 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ Foliar fungal symbionts in sympatric yellow monkeyflowers along elevation gradients in the Sierra Nevada ]]> https://biorxiv.org/content/10.64898/2026.01.18.700187v1?rss=1 Rolon, B. A. Ferris, K. G. Van Bael, S. 2026-01-21 doi:10.64898/2026.01.18.700187 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ PDLP5 regulates aquaporin-mediated hydrogen peroxide transport in Arabidopsis ]]> https://biorxiv.org/content/10.64898/2026.01.21.700913v1?rss=1 Li, Z. Liu, S.-L. Islam, S. Clements, M. Chen, Y. Aung, K. 2026-01-23 doi:10.64898/2026.01.21.700913 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ FSI (Fluctuating Selection among Individuals) Reduces the Mean Fixation Time (Generations) of a Mutation ]]> https://biorxiv.org/content/10.64898/2026.01.21.700920v1?rss=1 Gu, X. 2026-01-23 doi:10.64898/2026.01.21.700920 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Quantification of Aspergillus nidulans Actin Dynamics during Early Growth and Septum Formation ]]> https://biorxiv.org/content/10.64898/2026.01.27.701996v1?rss=1 Huso, W. Hill, G. Tarimala, G. Lee, J. Doan, A. G. Lee, J. Gray, K. J. Edwards, H. Harris, S. Marten, M. R. 2026-01-28 doi:10.64898/2026.01.27.701996 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ Targeted mutagenesis in Ehrlichia canis deleting the phage head-to-tail connector protein gene and its assessment as a vaccine candidate preventing canine ehrlichiosis ]]> https://biorxiv.org/content/10.64898/2026.01.29.702648v1?rss=1 Ferm, D. Nair, A. Ferm, J. D. Liu, H. Wang, Y. Crosby, L. F. McGill, J. F. Latre de Late, P. Stoll, I. Chauhan, D. Choudhury, D. Madesh, S. Ganta, S. Burne, A. Ozubek, S. Ganta, R. R. 2026-01-30 doi:10.64898/2026.01.29.702648 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Comparison of environmental DNA and bulk DNA metabarcoding for assessing terrestrial arthropod diversity across three habitat types on Guam ]]> https://biorxiv.org/content/10.64898/2026.02.02.703366v1?rss=1 Banerjee, P. Al-Bayer, S. Calaor, J. Weber, S. Graham, N. C. Andersen, J. P. Economo, E. Kennedy, S. Krehenwinkel, H. Gillespie, R. Roderick, G. Rogers, H. P. Puliafico, K. 2026-02-04 doi:10.64898/2026.02.02.703366 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ Hierarchical organization in sparse gene regulatory networks shapes structural coherence and emergent regulatory coordination ]]> https://biorxiv.org/content/10.64898/2026.02.04.703680v1?rss=1 Harlapur, P. Jagadeesan, R. Ribeiro, A. S. Kadelka, C. Jolly, M. K. 2026-02-05 doi:10.64898/2026.02.04.703680 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ Viromics in flat mites from Hawaii shows abundant arrays of viruses, expands the evolutionary origin of plant viruses, and provides a surveillance tool for Brevipalpus-transmitted viruses ]]> https://biorxiv.org/content/10.64898/2026.02.11.705406v1?rss=1 Olmedo-Velarde, A. Nakasato, K. Larrea-Sarmiento, A. E. Melzer, M. 2026-02-12 doi:10.64898/2026.02.11.705406 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ FHOD3 and DIAPH3 control cell migration and differentially shift the balance of parallel and perpendicular stress fibers ]]> https://biorxiv.org/content/10.64898/2026.02.13.703290v1?rss=1 Namanda, F. R. Foroozandehfar, A. Schneider, I. C. 2026-02-16 doi:10.64898/2026.02.13.703290 Cold Spring Harbor Laboratory Press 2026-02-16 <![CDATA[ FiCOPS: Hardware/Software Co-Design of FPGA Computational Framework for Mass Spectrometry-Based Peptide Database Search ]]> https://biorxiv.org/content/10.64898/2026.02.15.706012v1?rss=1 Kumar, S. Zambreno, J. Khokhar, A. Akram, S. Saeed, F. 2026-02-17 doi:10.64898/2026.02.15.706012 Cold Spring Harbor Laboratory Press 2026-02-17 <![CDATA[ Validation of TRIzol-Based Inactivation Protocol with Failure Scenario Testing for Bacterial Select Agent Surrogates ]]> https://biorxiv.org/content/10.64898/2026.02.22.707045v1?rss=1 Shahid, U. R. Lueth, P. A. Bellaire, B. H. 2026-02-22 doi:10.64898/2026.02.22.707045 Cold Spring Harbor Laboratory Press 2026-02-22 <![CDATA[ The sugar-beet cyst nematode effector Hs2B11 targets the Arabidopsis serine protease inhibitor AtPR-6 to favor parasitism ]]> https://biorxiv.org/content/10.64898/2026.02.21.707195v1?rss=1 Mejias, J. Bredow, M. Kumar, A. Juvale, P. S. Maier, T. A. Khwanbua, E. Whitham, S. A. Eves-van den Akker, S. Baum, T. J. 2026-02-23 doi:10.64898/2026.02.21.707195 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ A PLUM Job: Peptide modeLs for Understanding and engineering antiMicrobial therapeutics ]]> https://biorxiv.org/content/10.64898/2026.02.21.707214v1?rss=1 Banerjee, P. Friedberg, I. Rued, B. E. Eulenstein, O. 2026-02-23 doi:10.64898/2026.02.21.707214 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ How Not to be Seen: Predicting Unseen Enzyme Functions using Contrastive Learning ]]> https://biorxiv.org/content/10.64898/2026.02.23.707489v1?rss=1 Ma, X. Joshi, P. Friedberg, I. Li, Q. 2026-02-24 doi:10.64898/2026.02.23.707489 Cold Spring Harbor Laboratory Press 2026-02-24 <![CDATA[ Structural and Metabolic Characterization of Ni(I)-inhibitors Provide a Robust Anti-Methanogenicity Scoring System ]]> https://biorxiv.org/content/10.64898/2026.02.25.708075v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@1d38d21org.highwire.dtl.DTLVardef@1d681d9org.highwire.dtl.DTLVardef@1e70c0corg.highwire.dtl.DTLVardef@1c8223f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Aryee, R. Zargar, M. R. SR, V. B, A. Dey, S. Mohammed, N. S. Sanjeevan, K. A. Frazier, N. A. Koziel, J. A. Beck, M. Mansell, T. J. Chowdhury, R. 2026-02-27 doi:10.64898/2026.02.25.708075 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ PREMISE: A Quality-Aware Probabilistic Framework for Pathogen Resolution and Source Assignment in Viral mNGS ]]> https://biorxiv.org/content/10.64898/2026.03.15.711921v1?rss=1 Vijendran, S. Dorman, K. Anderson, T. K. Eulenstein, O. 2026-03-18 doi:10.64898/2026.03.15.711921 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Polypharmacology of an Optimal Kinase Library ]]> https://biorxiv.org/content/10.64898/2026.03.17.711623v1?rss=1 Mills, C. E. Hug, C. Sajeevan, K. A. Clark, N. Victor, C. Chung, M. Rawat, S. Aldridge, B. Albers, M. W. Chowdhury, R. Gyori, B. M. Sorger, P. K. 2026-03-19 doi:10.64898/2026.03.17.711623 Cold Spring Harbor Laboratory Press 2026-03-19 <![CDATA[ Dispersal, adaptation and persistence of H5N1 in the sub-Antarctic and Antarctica ]]> https://biorxiv.org/content/10.64898/2026.03.20.713283v1?rss=1 Clessin, A. Brusselmans, M. Hong, S. L. Tornos, J. Lejeune, M. Shao, Y. Briand, F.-X. Abolnik, C. Kaza, B. Suchard, M. A. Aguado, B. Alcami, A. Barbraud, C. Beer, M. Bennison, A. Bonadonna, F. Bonnet, T. Bost, C.-A. Boucheron, S. Bralet, T. Catry, P. Cleeland, J. Connan, M. Coombes, H. A. Delord, K. C. de Pasquale, C. Dewar, M. L. Dong, X. C. Emerit, J. Fischer, R. Fountain-Jones, N. Galimberti, F. Gonzalez-Solis, J. Guinet, C. Gunn, C. Gunther, A. Iervolino, M. James, J. Ji, X. Jonsen, I. Jones, C. Kuepfer, A. Kuiken, T. Lebohec, C. Lisovski, S. Zu 2026-03-21 doi:10.64898/2026.03.20.713283 Cold Spring Harbor Laboratory Press 2026-03-21 <![CDATA[ Denatured Albumin Gains a Function of Regulating Platelet Activity ]]> https://biorxiv.org/content/10.64898/2026.03.30.715112v1?rss=1 Pandey, V. Kundu, S. Wang, S. Pyne, A. Que, L. Wang, X. 2026-03-31 doi:10.64898/2026.03.30.715112 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ The emergence and molecular evolution of H5N1 influenza viruses in United States dairy cattle ]]> https://biorxiv.org/content/10.64898/2026.03.30.713641v1?rss=1 Pekar, J. E. Gangavarapu, K. Crespo-Bellido, A. Peacock, T. P. Wertheim, J. O. Dudas, G. Joy, J. B. Chand, M. Debarre, F. Gangavarapu, P. Goldhill, D. H. Groves, N. Ji, X. Malpica Serrano, L. Moncla, L. Rasmussen, A. L. Ruis, C. Venkatesh, D. Kraemer, M. U. G. Pybus, O. G. Andersen, K. G. Suchard, M. A. Nelson, M. I. Lemey, P. Worobey, M. Rambaut, A. 2026-04-01 doi:10.64898/2026.03.30.713641 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ CLEAR: Concise List Enrichment Analysis Reducing Redundancy ]]> https://biorxiv.org/content/10.64898/2026.03.30.715378v1?rss=1 Jia, X. Phan, A. Dorman, K. Kadelka, C. 2026-04-01 doi:10.64898/2026.03.30.715378 Cold Spring Harbor Laboratory Press 2026-04-01