Advances and Challenges in Metatranscriptomic Analysis by Migun Shakya, Chien-Chi Lo, Patrick S. G. Chain

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Recruiting human microbiome shotgun data to site-specific reference genomes. by Gary Xie, Chien-Chi Lo, Matthew Scholz, Patrick S G Chain

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Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-Producing <i>Escherichia coli</i> O145:H28 by Michelle Qiu Carter, Nicole Laniohan, Chien-Chi Lo, Patrick S. G. Chain

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CRP-Mediated Carbon Catabolite Regulation of Yersinia pestis Biofilm Formation Is Enhanced by the Carbon Storage Regulator Protein, CsrA. by Stephan P Willias, Sadhana Chauhan, Chien-Chi Lo, Patrick S G Chain, Vladimir L Motin

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Under-detection of endospore-forming Firmicutes in metagenomic data by Sevasti Filippidou, Thomas Junier, Tina Wunderlin, Chien-Chi Lo, Po-E Li, Patrick S. Chain, Pilar Junier

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The Gut Microbiome and Alcoholic Liver Disease: Ethanol Consumption Drives Consistent and Reproducible Alteration in Gut Microbiota in Mice by Erick S. LeBrun, Meghali Nighot, Viszwapriya Dharmaprakash, Anand Kumar, Chien-Chi Lo, Patrick S. G. Chain, Thomas Y. Ma

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Bioinformatic and Mechanistic Analysis of the Palmerolide PKS-NRPS Biosynthetic Pathway From the Microbiome of an Antarctic Ascidian by Nicole E. Avalon, Alison E. Murray, Hajnalka E. Daligault, Chien-Chi Lo, Karen W. Davenport, Armand E. K. Dichosa, Patrick S. G. Chain, Bill J. Baker

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Brief Protocol for EDGE Bioinformatics: Analyzing Microbial and Metagenomic NGS Data by Casandra Philipson, Karen Davenport, Logan Voegtly, Chien-Chi Lo, Po-E Li, Yan Xu, Migun Shakya, Regina Cer, Kimberly Bishop-Lilly, Theron Hamilton, Patrick Chain

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Genomic and Phenotypic Characterization of Shiga Toxin-Producing <i>Escherichia albertii</i> Strains Isolated from Wild Birds in a Major Agricultural Region in California by Michelle Qiu Carter, Beatriz Quiñones, Xiaohua He, Antares Pham, Diana Carychao, Michael B. Cooley, Chien-Chi Lo, Patrick S. G. Chain, Rebecca L. Lindsey, James L. Bono

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Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach. by Erin A Gontang, Frank O Aylward, Camila Carlos, Tijana Glavina Del Rio, Mansi Chovatia, Alison Fern, Chien-Chi Lo, Stephanie A Malfatti, Susannah G Tringe, Cameron R Currie, Roberto Kolter

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Discovery of an Antarctic Ascidian-Associated Uncultivated Verrucomicrobia with Antimelanoma Palmerolide Biosynthetic Potential by Alison E. Murray, Chien-Chi Lo, Hajnalka E. Daligault, Nicole E. Avalon, Robert W. Read, Karen W. Davenport, Mary L. Higham, Yuliya Kunde, Armand E. K. Dichosa, Bill J. Baker, Patrick S. G. Chain

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Artificial polyploidy improves bacterial single cell genome recovery. by Armand E K Dichosa, Michael S Fitzsimons, Chien-Chi Lo, Lea L Weston, Lara G Preteska, Jeremy P Snook, Xiaojing Zhang, Wei Gu, Kim McMurry, Lance D Green, Patrick S Chain, J Chris Detter, Cliff S Han

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Uncovering the Core Microbiome and Distribution of Palmerolide in <i>Synoicum adareanum</i> Across the Anvers Island Archipelago, Antarctica by Alison E. Murray, Nicole E. Avalon, Lucas Bishop, Karen W. Davenport, Erwan Delage, Armand E.K. Dichosa, Damien Eveillard, Mary L. Higham, Sofia Kokkaliari, Chien-Chi Lo, Christian S. Riesenfeld, Ryan M. Young, Patrick S.G. Chain, Bill J. Baker

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Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo. by Athe M N Tsibris, Bette Korber, Ramy Arnaout, Carsten Russ, Chien-Chi Lo, Thomas Leitner, Brian Gaschen, James Theiler, Roger Paredes, Zhaohui Su, Michael D Hughes, Roy M Gulick, Wayne Greaves, Eoin Coakley, Charles Flexner, Chad Nusbaum, Daniel R Kuritzkes

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Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia. by Manuel Martinez-Garcia, David M Brazel, Brandon K Swan, Carol Arnosti, Patrick S G Chain, Krista G Reitenga, Gary Xie, Nicole J Poulton, Monica Lluesma Gomez, Dashiell E D Masland, Brian Thompson, Wendy K Bellows, Kai Ziervogel, Chien-Chi Lo, Sanaa Ahmed, Cheryl D Gleasner, Chris J Detter, Ramunas Stepanauskas

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Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing. by Will Fischer, Vitaly V Ganusov, Elena E Giorgi, Peter T Hraber, Brandon F Keele, Thomas Leitner, Cliff S Han, Cheryl D Gleasner, Lance Green, Chien-Chi Lo, Ambarish Nag, Timothy C Wallstrom, Shuyi Wang, Andrew J McMichael, Barton F Haynes, Beatrice H Hahn, Alan S Perelson, Persephone Borrow, George M Shaw, Tanmoy Bhattacharya, Bette T Korber

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Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows by Ryan Connor, Migun Shakya, David A. Yarmosh, Wolfgang Maier, Ross Martin, Rebecca Bradford, J. Rodney Brister, Patrick S. G. Chain, Courtney A. Copeland, Julia di Iulio, Bin Hu, Philip Ebert, Jonathan Gunti, Yumi Jin, Kenneth S. Katz, Andrey Kochergin, Tré LaRosa, Jiani Li, Po-E Li, Chien-Chi Lo, Sujatha Rashid, Evguenia S. Maiorova, Chunlin Xiao, Vadim Zalunin, Lisa Purcell, Kim D. Pruitt

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Benchmark datasets for SARS-CoV-2 surveillance bioinformatics by Lingzi Xiaoli, Jill V. Hagey, Daniel J. Park, Christopher A. Gulvik, Erin L. Young, Nabil-Fareed Alikhan, Adrian Lawsin, Norman Hassell, Kristen Knipe, Kelly F. Oakeson, Adam C. Retchless, Migun Shakya, Chien-Chi Lo, Patrick Chain, Andrew J. Page, Benjamin J. Metcalf, Michelle Su, Jessica Rowell, Eshaw Vidyaprakash, Clinton R. Paden, Andrew D. Huang, Dawn Roellig, Ketan Patel, Kathryn Winglee, Michael R. Weigand, Lee S. Katz

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Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale by Bin Hu, Shane Canon, Emiley A. Eloe-Fadrosh, Anubhav, Michal Babinski, Yuri Corilo, Karen Davenport, William D. Duncan, Kjiersten Fagnan, Mark Flynn, Brian Foster, David Hays, Marcel Huntemann, Elais K. Player Jackson, Julia Kelliher, Po-E. Li, Chien-Chi Lo, Douglas Mans, Lee Ann McCue, Nigel Mouncey, Christopher J. Mungall, Paul D. Piehowski, Samuel O. Purvine, Montana Smith, Neha Jacob Varghese, Donald Winston, Yan Xu, Patrick S. G. Chain

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Genomic comparison of Escherichia coli O104:H4 isolates from 2009 and 2011 reveals plasmid, and prophage heterogeneity, including shiga toxin encoding phage stx2. by Sanaa A Ahmed, Joy Awosika, Carson Baldwin, Kimberly A Bishop-Lilly, Biswajit Biswas, Stacey Broomall, Patrick S G Chain, Olga Chertkov, Otar Chokoshvili, Susan Coyne, Karen Davenport, J Chris Detter, William Dorman, Tracy H Erkkila, Jason P Folster, Kenneth G Frey, Matroner George, Cheryl Gleasner, Matthew Henry, Karen K Hill, Kyle Hubbard, Joseph Insalaco, Shannon Johnson, Aaron Kitzmiller, Michael Krepps, Chien-Chi Lo, Truong Luu, Lauren A McNew, Timothy Minogue, Christine A Munk, Brian Osborne, Mohit Patel, Krista G Reitenga, C Nicole Rosenzweig, April Shea, Xiaohong Shen, Nancy Strockbine, Cheryl Tarr, Hazuki Teshima, Eric van Gieson, Kathleen Verratti, Mark Wolcott, Gary Xie, Shanmuga Sozhamannan, Henry S Gibbons, Threat Characterization Consortium

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