Revealing 29 sets of independently modulated genes inStaphylococcus aureus, their regulators, and role in key physiological response

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types

(2019) Yara Seif et al.   PLoS Computational Biology

Stress-induced inactivation of the Staphylococcus aureus purine biosynthesis repressor leads to hypervirulence

(2019) Mariya I. Goncheva et al.   Nature Communications

Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media

(2019) Saugat Poudel et al.   Scientific Data

The purine biosynthesis regulator PurR moonlights as a virulence regulator in Staphylococcus aureus

(2019) William E. Sause et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration

(2019) Amitesh Anand et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Escherichia coli transcriptome mostly consists of independently regulated modules

(2019) Anand V. Sastry et al.   Nature Communications

Guanine Limitation Results in CodY-Dependent and -Independent Alteration of Staphylococcus aureus Physiology and Gene Expression

(2018) Alyssa N. King et al.   JOURNAL OF BACTERIOLOGY

A comprehensive evaluation of module detection methods for gene expression data

(2018) Wouter Saelens et al.   Nature Communications

Genome-scale analysis of Methicillin-resistant Staphylococcus aureus USA300 reveals a tradeoff between pathogenesis and drug resistance

(2018) Donghui Choe et al.   Scientific Reports

Thermal and Nutritional Regulation of Ribosome Hibernation in Staphylococcus aureus

(2018) Arnab Basu et al.   JOURNAL OF BACTERIOLOGY

RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12

(2018) Alberto Santos-Zavaleta et al.   NUCLEIC ACIDS RESEARCH

The commensal lifestyle of Staphylococcus aureus and its interactions with the nasal microbiota

(2017) Bernhard Krismer et al.   NATURE REVIEWS MICROBIOLOGY

PRODORIC2: the bacterial gene regulation database in 2018

(2017) Denitsa Eckweiler et al.   NUCLEIC ACIDS RESEARCH

IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets

(2017) Claire Bertelli et al.   NUCLEIC ACIDS RESEARCH

Amino Acid Catabolism in Staphylococcus aureus and the Function of Carbon Catabolite Repression

(2017) Cortney R. Halsey et al.   mBio

De NovoGuanine Biosynthesis but Not the Riboswitch-Regulated Purine Salvage Pathway Is Required for Staphylococcus aureus InfectionIn Vivo

(2016) Eric M. Kofoed et al.   JOURNAL OF BACTERIOLOGY

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

CtaM Is Required for Menaquinol Oxidase aa 3 Function in Staphylococcus aureus

(2016) Neal D. Hammer et al.   mBio

Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions

(2016) Ulrike Mäder et al.   PLoS Genetics

The SaeRS Two‐Component System of Staphylococcus aureus

(2016) Qian Liu et al.   Genes

Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution

(2016) Jose Utrilla et al.   Cell Systems

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Staphylococcus aureus Infections: Epidemiology, Pathophysiology, Clinical Manifestations, and Management

(2015) Steven Y. C. Tong et al.   CLINICAL MICROBIOLOGY REVIEWS

Staphylococcal adaptation to diverse physiologic niches: an overview of transcriptomic and phenotypic changes in different biological environments

(2015) Sana S Dastgheyb et al.   Future Microbiology

Many Means to a Common End: the Intricacies of (p)ppGpp Metabolism and Its Control of Bacterial Homeostasis

(2015) Anthony O. Gaca et al.   JOURNAL OF BACTERIOLOGY

The DNA-binding network of Mycobacterium tuberculosis

(2015) Kyle J. Minch et al.   Nature Communications

Sigma Factor SigB Is Crucial to Mediate Staphylococcus aureus Adaptation during Chronic Infections

(2015) Lorena Tuchscherr et al.   PLoS Pathogens

Genomic and transcriptomic differences in community acquired methicillin resistant Staphylococcus aureus USA300 and USA400 strains

(2015) Marcus B Jones et al.   BMC GENOMICS

Insights into the Staphylococcus aureus-Host Interface: Global Changes in Host and Pathogen Gene Expression in a Rabbit Skin Infection Model

(2015) Natalia Malachowa et al.   PLoS One

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

(2014) S. Anders et al.   BIOINFORMATICS

Investigating the genetic regulation of the ECF sigma factor σS in Staphylococcus aureus

(2014) Whittney N Burda et al.   BMC MICROBIOLOGY

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

Metabolic sensor governing bacterial virulence inStaphylococcus aureus

(2014) Yue Ding et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global analysis of transcriptional regulators in Staphylococcus aureus

(2013) Jose Antonio Ibarra et al.   BMC GENOMICS

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria

(2013) Sefa Kılıç et al.   NUCLEIC ACIDS RESEARCH

Nox2 Modification of LDL Is Essential for Optimal Apolipoprotein B-mediated Control of agr Type III Staphylococcus aureus Quorum-sensing

(2013) Pamela R. Hall et al.   PLoS Pathogens

VraT/YvqF Is Required for Methicillin Resistance and Activation of the VraSR Regulon in Staphylococcus aureus

(2012) Susan Boyle-Vavra et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The WalKR System Controls Major Staphylococcal Virulence Genes and Is Involved in Triggering the Host Inflammatory Response

(2012) Aurélia Delauné et al.   INFECTION AND IMMUNITY

The Extracytoplasmic Function Sigma Factor  S Protects against both Intracellular and Extracytoplasmic Stresses in Staphylococcus aureus

(2012) H. K. Miller et al.   JOURNAL OF BACTERIOLOGY

A Novel Mode of Regulation of theStaphylococcus aureusCatabolite Control Protein A (CcpA) Mediated by Stk1 Protein Phosphorylation

(2012) Jade Leiba et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Analysis of omics data with genome-scale models of metabolism

(2012) Daniel R. Hyduke et al.   Molecular BioSystems

Direct Regulation of GTP Homeostasis by (p)ppGpp: A Critical Component of Viability and Stress Resistance

(2012) Allison Kriel et al.   MOLECULAR CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Expression of a Cryptic Secondary Sigma Factor Gene Unveils Natural Competence for DNA Transformation in Staphylococcus aureus

(2012) Kazuya Morikawa et al.   PLoS Pathogens

CcpA Regulates Arginine Biosynthesis in Staphylococcus aureus through Repression of Proline Catabolism

(2012) Austin S. Nuxoll et al.   PLoS Pathogens

Role of the Accessory Gene Regulatoragrin Community-Associated Methicillin-Resistant Staphylococcus aureus Pathogenesis

(2011) Gordon Y. C. Cheung et al.   INFECTION AND IMMUNITY

Inference of the Transcriptional Regulatory Network in Staphylococcus aureus by Integration of Experimental and Genomics-Based Evidence

(2011) D. A. Ravcheev et al.   JOURNAL OF BACTERIOLOGY

CcpA coordinates central metabolism and biofilm formation in Staphylococcus epidermidis

(2011) M. R. Sadykov et al.   MICROBIOLOGY-SGM

Global Changes in Staphylococcus aureus Gene Expression in Human Blood

(2011) Natalia Malachowa et al.   PLoS One

Investigation of the Staphylococcus aureus GraSR Regulon Reveals Novel Links to Virulence, Stress Response and Cell Wall Signal Transduction Pathways

(2011) Mélanie Falord et al.   PLoS One

Subinhibitory Concentrations of Protein Synthesis-Inhibiting Antibiotics Promote Increased Expression of the agr Virulence Regulator and Production of Phenol-Soluble Modulin Cytolysins in Community-Associated Methicillin-Resistant Staphylococcus aureus

(2010) H.-S. Joo et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Immune evasion cluster-positive bacteriophages are highly prevalent among human Staphylococcus aureus strains, but they are not essential in the first stages of nasal colonization

(2010) N.J. Verkaik et al.   CLINICAL MICROBIOLOGY AND INFECTION

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

(2010) M. Valiev et al.   COMPUTER PHYSICS COMMUNICATIONS

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

Role of PknB Kinase in Antibiotic Resistance and Virulence in Community-Acquired Methicillin-Resistant Staphylococcus aureus Strain USA300

(2010) S. Tamber et al.   INFECTION AND IMMUNITY

Adaptation of Staphylococcus aureus to the cystic fibrosis lung

(2010) Christiane Goerke et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Regulatory Adaptation of Staphylococcus aureus during Nasal Colonization of Humans

(2010) Marc Burian et al.   PLoS One

Effect of a glucose impulse on the CcpA regulon in Staphylococcus aureus

(2009) Kati Seidl et al.   BMC MICROBIOLOGY

CodY in Staphylococcus aureus: a Regulatory Link between Metabolism and Virulence Gene Expression

(2009) K. Pohl et al.   JOURNAL OF BACTERIOLOGY

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Quorum Sensing in Staphylococci

(2008) Richard P. Novick et al.   Annual Review of Genetics

Apolipoprotein B Is an Innate Barrier against Invasive Staphylococcus aureus Infection

(2008) M. Michal Peterson et al.   Cell Host & Microbe

Control of bacterial transcription, translation and replication by (p)ppGpp

(2008) Anjana Srivatsan et al.   CURRENT OPINION IN MICROBIOLOGY

OperonDB: a comprehensive database of predicted operons in microbial genomes

(2008) M. Pertea et al.   NUCLEIC ACIDS RESEARCH

Context-Specific Metabolic Networks Are Consistent with Experiments

(2008) Scott A. Becker et al.   PLoS Computational Biology

The alternative sigma factor sigma B of Staphylococcus aureus modulates virulence in experimental central venous catheter-related infections

(2007) Udo Lorenz et al.   MICROBES AND INFECTION