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

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

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Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes by 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 by Abraham G. Moller, Robert A. Petit, Michelle H. Davis, Timothy D. Read

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

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Fine-scale differentiation between Bacillus anthracis and Bacillus cereus group signatures in metagenome shotgun data by 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 by Sandeep J. Joseph, Ben Li, Robert A. Petit III, Zhaohui S. Qin, Lyndsey Darrow, Timothy D. Read

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USA300 Staphylococcus aureus persists on multiple body sites following an infection by Timothy D. Read, Robert A. Petit, Zachary Yin, Tuyaa Montgomery, Moira C. McNulty, Michael Z. David

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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... by Eryn E. Bernardy, Robert A. Petit, Vishnu Raghuram, Ashley M. Alexander, Timothy D. Read, Joanna B. Goldberg

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Shiftwork, functional bowel symptoms, and the microbiome by 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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Transmission and Microevolution of USA300 MRSA in U.S. Households: Evidence from Whole-Genome Sequencing by Md Tauqeer Alam, Timothy D. Read, Robert A. Petit, Susan Boyle-Vavra, Loren G. Miller, Samantha J. Eells, Robert S. Daum, Michael Z. David

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Genomic analysis of variability in Delta-toxin levels between Staphylococcus aureus strains by 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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Clinical and Genomic Epidemiology of mcr-9-Carrying Carbapenem-Resistant Enterobacterales Isolates in Metropolitan Atlanta, 2012 to 2017 by Ahmed Babiker, Chris Bower, Joseph D. Lutgring, Robert A. Petit, Jessica Howard-Anderson, Uzma Ansari, Gillian McAllister, Michelle Adamczyk, Erin Breaker, Sarah W. Satola, Jesse T. Jacob, Michael H. Woodworth

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Erratum to: draft sequencing and assembly of the genome of the world’s largest fish, the whale shark: Rhincodon typus smith 1828 by Timothy D. Read, Robert A. Petit, Sandeep J. Joseph, Tauqeer Alam, M. Ryan Weil, Maida Ahmad, Ravila Bhimani, Jocelyn S. Vuong, Chad P. Haase, D. Harry Webb, Milton Tan, Alistair D.M. Dove

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Draft sequencing and assembly of the genome of the world’s largest fish, the whale shark: Rhincodon typus Smith 1828 by Timothy D. Read, Robert A. Petit, Sandeep J. Joseph, Md. Tauqeer Alam, M. Ryan Weil, Maida Ahmad, Ravila Bhimani, Jocelyn S. Vuong, Chad P. Haase, D. Harry Webb, Milton Tan, Alistair D. M. Dove

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Mycobacterium tuberculosis epidemiology in Oman: whole-genome sequencing uncovers transmission pathways by Hamza A Babiker, Amina Al-Jardani, Saleh Al-Azri, Robert A. Petit, Eltaib Saad, Sarah Al-Mahrouqi, Reham A.H. Mohamed, Salama Al-Hamidhi, Abdullah A. Balkhair, Najma Al Kharusi, Laila Al Balushi, Samiya Al Zadjali, Lucía Pérez-Pardal, Albano Beja-Pereira, Ahmed Babiker

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