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

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Improved yield of high molecular weight DNA coincides with increased microbial diversity access from iron oxide cemented sub-surface clay environments. by Richard A Hurt, Michael S Robeson, Migun Shakya, James G Moberly, Tatiana A Vishnivetskaya, Baohua Gu, Dwayne A Elias

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Intrahost SARS-CoV-2 k-mer Identification Method (iSKIM) for Rapid Detection of Mutations of Concern Reveals Emergence of Global Mutation Patterns by Ashley Thommana, Migun Shakya, Jaykumar Gandhi, Christian K. Fung, Patrick S. G. Chain, Irina Maljkovic Berry, Matthew A. Conte

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A Gene Cluster That Encodes Histone Deacetylase Inhibitors Contributes to Bacterial Persistence and Antibiotic Tolerance in Burkholderia thailandensis by Sofiya N. Micheva-Viteva, Migun Shakya, Samantha H. Adikari, Cheryl D. Gleasner, Nileena Velappan, Judith R. Mourant, Patrick S. G. Chain, Elizabeth Hong-Geller

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A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees. by Migun Shakya, Neil Gottel, Hector Castro, Zamin K Yang, Lee Gunter, Jessy Labbé, Wellington Muchero, Gregory Bonito, Rytas Vilgalys, Gerald Tuskan, Mircea Podar, Christopher W Schadt

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Comparative genomic and phenotypic characterization of invasive non-typhoidal Salmonella isolates from Siaya, Kenya. by Jessica Z Kubicek-Sutherland, Gary Xie, Migun Shakya, Priya K Dighe, Lindsey L Jacobs, Hajnalka Daligault, Karen Davenport, Loreen R Stromberg, Zachary R Stromberg, Qiuying Cheng, Prakasha Kempaiah, John Michael Ong'echa, Vincent Otieno, Evans Raballah, Samuel Anyona, Collins Ouma, Patrick S G Chain, Douglas J Perkins, Harshini Mukundan, Benjamin H McMahon, Norman A Doggett

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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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NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index by Joan Martí-Carreras, Alejandro Rafael Gener, Sierra D. Miller, Anderson F. Brito, Christiam E. Camacho, Ryan Connor, Ward Deboutte, Cody Glickman, David M. Kristensen, Wynn K. Meyer, Sejal Modha, Alexis L. Norris, Surya Saha, Anna K. Belford, Evan Biederstedt, James Rodney Brister, Jan P. Buchmann, Nicholas P. Cooley, Robert A. Edwards, Kiran Javkar, Michael Muchow, Harihara Subrahmaniam Muralidharan, Charles Pepe-Ranney, Nidhi Shah, Migun Shakya, Michael J. Tisza, Benjamin J. Tully, Bert Vanmechelen, Valerie C. Virta, JL Weissman, Vadim Zalunin, Alexandre Efremov, Ben Busby

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