Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges by Keira A. Cohen, Abigail L. Manson, Christopher A. Desjardins, Thomas Abeel, Ashlee M. Earl

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Establishing the role of the gut microbiota in susceptibility to recurrent urinary tract infections by Colin J. Worby, Benjamin S. Olson, Karen W. Dodson, Ashlee M. Earl, Scott J. Hultgren

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The Role of Mobile Genetic Elements in Virulence Factor Carriage from Symptomatic and Asymptomatic Cases of Escherichia coli Bacteriuria by Grace Morales, Benjamin Abelson, Seth Reasoner, Jordan Miller, Ashlee M. Earl, Maria Hadjifrangiskou, Jonathan Schmitz

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Genes Contributing to the Unique Biology and Intrinsic Antibiotic Resistance of <named-content content-type="genus-species">Enterococcus faecalis</named-content> by Michael S. Gilmore, Rauf Salamzade, Elizabeth Selleck, Noelle Bryan, Suelen S. Mello, Abigail L. Manson, Ashlee M. Earl

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ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database. by João L Reis-Cunha, Daniella C Bartholomeu, Abigail L Manson, Ashlee M Earl, Gustavo C Cerqueira

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Genomic epidemiology and antibiotic susceptibility profiling of uropathogenic Escherichia coli among children in the United States by Rauf Salamzade, Christi L. McElheny, Abigail L. Manson, Ashlee M. Earl, Nader Shaikh, Yohei Doi

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Evidence of Extensive DNA Transfer between <italic toggle="yes">Bacteroidales</italic> Species within the Human Gut by Michael J. Coyne, Naamah Levy Zitomersky, Abigail Manson McGuire, Ashlee M. Earl, Laurie E. Comstock

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QuantTB – a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data by Christine Anyansi, Arlin Keo, Bruce J. Walker, Timothy J. Straub, Abigail L. Manson, Ashlee M. Earl, Thomas Abeel

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Preserving genome integrity: the DdrA protein of Deinococcus radiodurans R1. by Dennis R Harris, Masashi Tanaka, Sergei V Saveliev, Edmond Jolivet, Ashlee M Earl, Michael M Cox, John R Battista

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Correction: Preserving Genome Integrity: The DdrA Protein of Deinococcus radiodurans R1. by Dennis R Harris, Masashi Tanaka, Sergei V Saveliev, Edmond Jolivet, Ashlee M Earl, Michael M Cox, John R Battista

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Computational Methods for Strain-Level Microbial Detection in Colony and Metagenome Sequencing Data by Christine Anyansi, Christine Anyansi, Timothy J. Straub, Timothy J. Straub, Abigail L. Manson, Ashlee M. Earl, Thomas Abeel, Thomas Abeel

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Modulating the evolutionary trajectory of tolerance using antibiotics with different metabolic dependencies by Erica J. Zheng, Ian W. Andrews, Alexandra T. Grote, Abigail L. Manson, Miguel A. Alcantar, Ashlee M. Earl, James J. Collins

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Benchmarking AlphaFold‐enabled molecular docking predictions for antibiotic discovery by Felix Wong, Aarti Krishnan, Erica J Zheng, Hannes Stärk, Abigail L Manson, Ashlee M Earl, Tommi Jaakkola, James J Collins

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Populations of latent Mycobacterium tuberculosis lack a cell wall: Isolation, visualization, and whole-genome characterization by Ali Akbar Velayati, Thomas Abeel, Terrance Shea, Gennady Konstantinovich Zhavnerko, Bruce Birren, Gail H Cassell, Ashlee M Earl, Sven Hoffner, Parissa Farnia

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Whole genome characterization of the mechanisms of daptomycin resistance in clinical and laboratory derived isolates of Staphylococcus aureus. by Anton Y Peleg, Spiros Miyakis, Doyle V Ward, Ashlee M Earl, Aileen Rubio, David R Cameron, Satish Pillai, Robert C Moellering, George M Eliopoulos

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Key Transitions in the Evolution of Rapid and Slow Growing Mycobacteria Identified by Comparative Genomics by Nathan L. Bachmann, Nathan L. Bachmann, Rauf Salamzade, Abigail L. Manson, Richard Whittington, Richard Whittington, Vitali Sintchenko, Vitali Sintchenko, Ashlee M. Earl, Ben J. Marais

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Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics by Peijun Ma, Lorrie L He, Alejandro Pironti, Hannah H Laibinis, Christoph M Ernst, Abigail L Manson, Roby P Bhattacharyya, Ashlee M Earl, Jonathan Livny, Deborah T Hung

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Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. by Bruce J Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K Young, Ashlee M Earl

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The "most wanted" taxa from the human microbiome for whole genome sequencing. by Anthony A Fodor, Todd Z DeSantis, Kristine M Wylie, Jonathan H Badger, Yuzhen Ye, Theresa Hepburn, Ping Hu, Erica Sodergren, Konstantinos Liolios, Heather Huot-Creasy, Bruce W Birren, Ashlee M Earl

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Emergence of Epidemic Multidrug-Resistant <named-content content-type="genus-species">Enterococcus faecium</named-content> from Animal and Commensal Strains by François Lebreton, Willem van Schaik, Abigail Manson McGuire, Paul Godfrey, Allison Griggs, Varun Mazumdar, Jukka Corander, Lu Cheng, Sakina Saif, Sarah Young, Qiandong Zeng, Jennifer Wortman, Bruce Birren, Rob J. L. Willems, Ashlee M. Earl, Michael S. Gilmore

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