Genome Plasticity of agr-Defective Staphylococcus aureus during Clinical Infection

Genetic Basis of Emerging Vancomycin, Linezolid, and Daptomycin Heteroresistance in a Case of Persistent Enterococcus faecium Bacteremia

(2018) Kieran I. Chacko et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

After the deluge: mining Staphylococcus aureus genomic data for clinical associations and host–pathogen interactions

(2018) Richard Copin et al.   CURRENT OPINION IN MICROBIOLOGY

Mutation of Agr Is Associated with the Adaptation of Staphylococcus aureus to the Host during Chronic Osteomyelitis

(2018) Carlos M. Suligoy et al.   Frontiers in Cellular and Infection Microbiology

Phenotypic changes of methicillin-resistant Staphylococcus aureus during vancomycin therapy for persistent bacteraemia and related clinical outcome

(2017) T. Kim et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Inactivation of Transcriptional Regulators during Within-Household Evolution of Escherichia coli

(2017) Dagmara I. Kisiela et al.   JOURNAL OF BACTERIOLOGY

Using Quantitative Spectrometry to Understand the Influence of Genetics and Nutritional Perturbations On the Virulence Potential ofStaphylococcus aureus

(2017) Jessica R. Chapman et al.   MOLECULAR & CELLULAR PROTEOMICS

Tuning of the Lethal Response to Multiple Stressors with a Single-Site Mutation during Clinical Infection by Staphylococcus aureus

(2017) Krishan Kumar et al.   mBio

Severe infections emerge from commensal bacteria by adaptive evolution

(2017) Bernadette C Young et al.   eLife

EssE Promotes Staphylococcus aureus ESS-Dependent Protein Secretion To Modify Host Immune Responses during Infection

(2016) Mark Anderson et al.   JOURNAL OF BACTERIOLOGY

Intrahost Evolution of Methicillin-ResistantStaphylococcus aureusUSA300 Among Individuals With Reoccurring Skin and Soft-Tissue Infections

(2016) Taj Azarian et al.   JOURNAL OF INFECTIOUS DISEASES

Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements

(2016) Supratim Mukherjee et al.   NUCLEIC ACIDS RESEARCH

Natural mutations in aStaphylococcus aureusvirulence regulator attenuate cytotoxicity but permit bacteremia and abscess formation

(2016) Sudip Das et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Staphylococcus aureus Coordinates Leukocidin Expression and Pathogenesis by Sensing Metabolic Fluxes via RpiRc

(2016) Divya Balasubramanian et al.   mBio

PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels

(2015) Yongwook Choi et al.   BIOINFORMATICS

Staphylococcus aureus Adapts to Oxidative Stress by Producing H2O2-Resistant Small-Colony Variants via the SOS Response

(2015) Kimberley L. Painter et al.   INFECTION AND IMMUNITY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

(2015) N. A. Rizvi et al.   SCIENCE

Convergent Adaptation in the Dominant Global Hospital Clone ST239 of Methicillin-Resistant Staphylococcus aureus

(2015) Sarah L. Baines et al.   mBio

Evolutionary Trade-Offs Underlie the Multi-faceted Virulence of Staphylococcus aureus

(2015) Maisem Laabei et al.   PLOS BIOLOGY

Transmission of Methicillin-ResistantStaphylococcus aureusvia Deceased Donor Liver Transplantation Confirmed by Whole Genome Sequencing

(2014) D. R. Altman et al.   AMERICAN JOURNAL OF TRANSPLANTATION

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

(2014) J. Chun et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Population Dynamics of an Acinetobacter baumannii Clonal Complex during Colonization of Patients

(2014) Hanchun Wen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Staphylococcus aureus β-toxin Production is Common in Strains With the β-toxin Gene Inactivated by Bacteriophage

(2014) Wilmara Salgado-Pabón et al.   JOURNAL OF INFECTIOUS DISEASES

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

What role does the quorum-sensing accessory gene regulator system play during Staphylococcus aureus bacteremia?

(2014) Kimberley L. Painter et al.   TRENDS IN MICROBIOLOGY

Absence of Patient-to-Patient Intrahospital Transmission of Staphylococcus aureus as Determined by Whole-Genome Sequencing

(2014) S. W. Long et al.   mBio

Mutations in Global Regulators Lead to Metabolic Selection during Adaptation to Complex Environments

(2014) Gerda Saxer et al.   PLoS Genetics

Production of an Attenuated Phenol-Soluble Modulin Variant Unique to the MRSA Clonal Complex 30 Increases Severity of Bloodstream Infection

(2014) Gordon Y. C. Cheung et al.   PLoS Pathogens

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Global Gene Expression of Methicillin-resistant Staphylococcus aureus USA300 During Human and Mouse Infection

(2013) Shailesh V. Date et al.   JOURNAL OF INFECTIOUS DISEASES

Persistent Staphylococcus aureus Bacteremia

(2013) Yong Pil Chong et al.   MEDICINE

Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures

(2013) Tami D Lieberman et al.   NATURE GENETICS

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of Recurrent Glioma

(2013) B. E. Johnson et al.   SCIENCE

RcsB Contributes to the Distinct Stress Fitness among Escherichia coli O157:H7 Curli Variants of the 1993 Hamburger-Associated Outbreak Strains

(2012) Michelle Q. Carter et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

ChromoZoom: a flexible, fluid, web-based genome browser

(2012) Theodore R. Pak et al.   BIOINFORMATICS

agr dysfunction and persistent methicillin-resistant Staphylococcus aureus bacteremia in patients with removed eradicable foci

(2012) S.-Y. Park et al.   INFECTION

Allele-Dependent Differences in Quorum-Sensing Dynamics Result in Variant Expression of Virulence Genes in Staphylococcus aureus

(2012) E. Geisinger et al.   JOURNAL OF BACTERIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Nasal Carriage as a Source of agr-Defective Staphylococcus aureus Bacteremia

(2012) Davida S. Smyth et al.   JOURNAL OF INFECTIOUS DISEASES

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease

(2012) B. C. Young et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive Evolution of the Lactose Utilization Network in Experimentally Evolved Populations of Escherichia coli

(2012) Selwyn Quan et al.   PLoS Genetics

EsaD, a Secretion Factor for the Ess Pathway in Staphylococcus aureus

(2011) M. Anderson et al.   JOURNAL OF BACTERIOLOGY

Evolutionary dynamics of bacteria in a human host environment

(2011) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular differentiation of historic phage-type 80/81 and contemporary epidemic Staphylococcus aureus

(2011) F. R. DeLeo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Increased Mortality with Accessory Gene Regulator (agr) Dysfunction inStaphylococcus aureusamong Bacteremic Patients

(2010) Marin L. Schweizer et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Mugsy: fast multiple alignment of closely related whole genomes

(2010) Samuel V. Angiuoli et al.   BIOINFORMATICS

Mutations inagrDo Not Persist in Natural Populations of Methicillin‐ResistantStaphylococcus aureus

(2010) Bo Shopsin et al.   JOURNAL OF INFECTIOUS DISEASES

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

Geographic Distribution of Staphylococcus aureus Causing Invasive Infections in Europe: A Molecular-Epidemiological Analysis

(2010) Hajo Grundmann et al.   PLOS MEDICINE

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

(2009) J. W. Nicol et al.   BIOINFORMATICS

Molecular Epidemiology of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Isolates from Global Clinical Trials

(2008) R. V. Goering et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Prevalence ofagrDysfunction among ColonizingStaphylococcus aureusStrains

(2008) Bo Shopsin et al.   JOURNAL OF INFECTIOUS DISEASES

agr function in clinical Staphylococcus aureus isolates

(2008) K. E. Traber et al.   MICROBIOLOGY-SGM

RNAIII-Independent Target Gene Control by the agr Quorum-Sensing System: Insight into the Evolution of Virulence Regulation in Staphylococcus aureus

(2008) Shu Y. Queck et al.   MOLECULAR CELL

EsaC substrate for the ESAT-6 secretion pathway and its role in persistent infections ofStaphylococcus aureus

(2008) Monica L. Burts et al.   MOLECULAR MICROBIOLOGY

Controlled degradation by ClpXP protease tunes the levels of the excision repair protein UvrA to the extent of DNA damage

(2008) Mihaela Pruteanu et al.   MOLECULAR MICROBIOLOGY

The Population Genetics of dN/dS

(2008) Sergey Kryazhimskiy et al.   PLoS Genetics