The Bacterial Response Regulator ArcA Uses a Diverse Binding Site Architecture to Regulate Carbon Oxidation Globally

Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding

(2013) Kevin S. Myers et al.   PLoS Genetics

Manipulation of the Anoxic Metabolism in Escherichia coli by ArcB Deletion Variants in the ArcBA Two-Component System

(2012) Gonzalo N. Bidart et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Complex Physiology and Compound Stress Responses during Fermentation of Alkali-Pretreated Corn Stover Hydrolysate by an Escherichia coli Ethanologen

(2012) Michael S. Schwalbach et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Redox balance is key to explaining full vs. partial switching to low-yield metabolism

(2012) Milan JA van Hoek et al.   BMC Systems Biology

ArcA and AppY Antagonize IscR Repression of Hydrogenase-1 Expression under Anaerobic Conditions, Revealing a Novel Mode of O2 Regulation of Gene Expression in Escherichia coli

(2012) A. D. Nesbit et al.   JOURNAL OF BACTERIOLOGY

ChIP-seq and transcriptome analysis of the OmpR regulon ofSalmonella entericaserovars Typhi and Typhimurium reveals accessory genes implicated in host colonization

(2012) Timothy T. Perkins et al.   MOLECULAR MICROBIOLOGY

Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli

(2012) Chi Yang et al.   PLoS One

Crystal Structure of the O 2 -Tolerant Membrane-Bound Hydrogenase 1 from Escherichia coli in Complex with Its Cognate Cytochrome b

(2012) Anne Volbeda et al.   STRUCTURE

Systems analysis of transcription factor activities in environments with stable and dynamic oxygen concentrations

(2012) M. D. Rolfe et al.   Open Biology

Comparative Analysis of Regulatory Elements between Escherichia coli and Klebsiella pneumoniae by Genome-Wide Transcription Start Site Profiling

(2012) Donghyuk Kim et al.   PLoS Genetics

Analysis of the ArcA regulon in anaerobically grown Salmonella enterica sv. Typhimurium

(2011) Matthew R Evans et al.   BMC MICROBIOLOGY

Transcript Profiling and Inference ofEscherichia coliK-12 ArcA Activity across the Range of Physiologically Relevant Oxygen Concentrations

(2011) Matthew D. Rolfe et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MochiView: versatile software for genome browsing and DNA motif analysis

(2010) Oliver R Homann et al.   BMC BIOLOGY

Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA

(2010) Pierre Mandin et al.   EMBO JOURNAL

Translational Regulation of Gene Expression by an Anaerobically Induced Small Non-coding RNA in Escherichia coli

(2010) Anders Boysen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metabolic and Transcriptional Response to Cofactor Perturbations in Escherichia coli

(2010) Anders K. Holm et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Lipoic acid: energy metabolism and redox regulation of transcription and cell signaling

(2010) Lester Packer et al.   JOURNAL OF CLINICAL BIOCHEMISTRY AND NUTRITION

Reprogramming of anaerobic metabolism by the FnrS small RNA

(2010) Sylvain Durand et al.   MOLECULAR MICROBIOLOGY

EcoCyc: a comprehensive database of Escherichia coli biology

(2010) I. M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Biological Insights from Structures of Two-Component Proteins

(2009) Rong Gao et al.   Annual Review of Microbiology

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Visualizing post genomics data-sets on customized pathway maps by ProMeTra – aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example

(2009) Heiko Neuweger et al.   BMC Systems Biology

The ArcBA Two-Component System of Escherichia coli Is Regulated by the Redox State of both the Ubiquinone and the Menaquinone Pool

(2009) M. Bekker et al.   JOURNAL OF BACTERIOLOGY

Sequence-Specific Binding to a Subset of IscR-Regulated Promoters Does Not Require IscR Fe–S Cluster Ligation

(2009) A.D. Nesbit et al.   JOURNAL OF MOLECULAR BIOLOGY

Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA

(2009) Kai Papenfort et al.   MOLECULAR MICROBIOLOGY

A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data

(2009) Desmond S Lun et al.   GENOME BIOLOGY

Redox Regulation of Cell Survival

(2008) Dunyaporn Trachootham et al.   ANTIOXIDANTS & REDOX SIGNALING

A Degenerate Tripartite DNA-Binding Site Required for Activation of ComA-Dependent Quorum Response Gene Expression in Bacillus subtilis

(2008) Kevin L. Griffith et al.   JOURNAL OF MOLECULAR BIOLOGY

Organization and Evolution of the Biological Response to Singlet Oxygen Stress

(2008) Yann S. Dufour et al.   JOURNAL OF MOLECULAR BIOLOGY

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

(2008) Anton Valouev et al.   NATURE METHODS

A high-throughput percentage-of-binding strategy to measure binding energies in DNA–protein interactions: application to genome-scale site discovery

(2008) Xiaohu Wang et al.   NUCLEIC ACIDS RESEARCH