Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes Bằng Robert A. Petit, Timothy D. Read

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Staphylococcus aureus viewed from the perspective of 40,000+ genomes Bằng Robert A. Petit III, Timothy D. Read

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The role of hypermutation and collateral sensitivity in antimicrobial resistance diversity of Pseudomonas aeruginosa populations in cystic fibrosis lung infection Bằng Jelly Vanderwoude, Sheyda Azimi, Timothy D. Read, Stephen P. Diggle

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Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes Bằng Rohan S Mehta, Robert A Petit, Timothy D Read, Daniel B Weissman

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Development of an Amplicon Nanopore Sequencing Strategy for Detection of Mutations Conferring Intermediate Resistance to Vancomycin in Staphylococcus aureus Strains Bằng Abraham G. Moller, Robert A. Petit, Michelle H. Davis, Timothy D. Read

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Chlamydia suis undergoes interclade recombination promoting Tet-island exchange Bằng Helena Seth-Smith, Sankhya Bommana, Deborah Dean, Timothy D. Read, Hanna Marti

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Average nucleotide identity-based Staphylococcus aureus strain grouping allows identification of strain-specific genes in the pangenome Bằng Vishnu Raghuram, Robert A. Petit, Zach Karol, Rohan Mehta, Daniel B. Weissman, Timothy D. Read

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Metagenomic Shotgun Sequencing of Endocervical, Vaginal, and Rectal Samples among Fijian Women with and without Chlamydia trachomatis Reveals Disparate Microbial Populations and Fu... Bằng Sankhya Bommana, Gracie Richards, Mike Kama, Reshma Kodimerla, Kenan Jijakli, Timothy D. Read, Deborah Dean

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Effect of genetic background on the evolution of Vancomycin-Intermediate Staphylococcus aureus (VISA) Bằng Michelle Su, Michelle H. Davis, Jessica Peterson, Claudia Solis-Lemus, Sarah W. Satola, Timothy D. Read

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Fine-scale differentiation between Bacillus anthracis and Bacillus cereus group signatures in metagenome shotgun data Bằng Robert A. Petit III, James M. Hogan, Matthew N. Ezewudo, Sandeep J. Joseph, Timothy D. Read

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The single-species metagenome: subtyping Staphylococcus aureus core genome sequences from shotgun metagenomic data Bằng Sandeep J. Joseph, Ben Li, Robert A. Petit III, Zhaohui S. Qin, Lyndsey Darrow, Timothy D. Read

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Genotypic and Phenotypic Diversity of <named-content content-type="genus-species">Staphylococcus aureus</named-content> Isolates from Cystic Fibrosis Patient Lung Infections and Th... Bằng Eryn E. Bernardy, Robert A. Petit, Vishnu Raghuram, Ashley M. Alexander, Timothy D. Read, Joanna B. Goldberg

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Unique microbial diversity, community composition, and networks among Pacific Islander endocervical and vaginal microbiomes with and without Chlamydia trachomatis infection in Fiji Bằng Sankhya Bommana, Yi-Juan Hu, Mike Kama, Ruohong Wang, Reshma Kodimerla, Kenan Jijakli, Timothy D. Read, Deborah Dean

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Strand-specific RNA-seq reveals ordered patterns of sense and antisense transcription in Bacillus anthracis. Bằng Karla D Passalacqua, Anjana Varadarajan, Charlotte Weist, Brian D Ondov, Benjamin Byrd, Timothy D Read, Nicholas H Bergman

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Factors associated with foreign body infection in methicillin-resistant Staphylococcus aureus bacteremia Bằng Kevin Bouiller, Kevin Bouiller, Natasia F. Jacko, Margot J. Shumaker, Brooke M. Talbot, Timothy D. Read, Michael Z. David

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Transcriptional activation of ompA in Neisseria gonorrhoeae mediated by the XRE family member protein NceR Bằng Concerta L. Holley, Vijaya Dhulipala, Stavaros A. Maurakis, Ashley Nicole Greenawalt, Timothy D. Read, Cynthia N. Cornelissen, William M. Shafer

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Shiftwork, functional bowel symptoms, and the microbiome Bằng Ann E. Rogers, Yi-Juan Hu, Ye Yue, Emily F. Wissel, Robert A. Petit III, Simone Jarrett, Jennifer Christie, Timothy D. Read

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Hypervirulent <named-content content-type="genus-species">Chlamydia trachomatis</named-content> Clinical Strain Is a Recombinant between Lymphogranuloma Venereum (L₂) an... Bằng Naraporn Somboonna, Raymond Wan, David M. Ojcius, Matthew A. Pettengill, Sandeep J. Joseph, Alexander Chang, Ray Hsu, Timothy D. Read, Deborah Dean

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Genomic analysis of variability in Delta-toxin levels between Staphylococcus aureus strains Bằng Michelle Su, James T. Lyles, Robert A. Petit III, Jessica Peterson, Michelle Hargita, Huaqiao Tang, Claudia Solis-Lemus, Cassandra L. Quave, Timothy D. Read

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Genomic insights into the evolution of secondary metabolism of Escovopsis and its allies, specialized fungal symbionts of fungus-farming ants Bằng Aileen Berasategui, Hassan Salem, Abraham G. Moller, Yuliana Christopher, Quimi Vidaurre Montoya, Caitlin Conn, Timothy D. Read, Andre Rodrigues, Nadine Ziemert, Nicole Gerardo

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