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

Co-operative roles for DNA supercoiling and nucleoid-associated proteins in the regulation of bacterial transcription

(2013) Charles J. Dorman   BIOCHEMICAL SOCIETY TRANSACTIONS

Host-Derived Nitrate Boosts Growth of E. coli in the Inflamed Gut

(2013) S. E. Winter et al.   SCIENCE

Activating Transcription in Bacteria

(2012) David J. Lee et al.   Annual Review of Microbiology

Architectural organization in E. coli nucleoid

(2012) Mirjana Macvanin et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Normalization of ChIP-seq data with control

(2012) Kun Liang et al.   BMC BIOINFORMATICS

Rho and NusG suppress pervasive antisense transcription in Escherichia coli

(2012) J. M. Peters et al.   GENES & DEVELOPMENT

Novel regulation targets of the metal-response BasS-BasR two-component system of Escherichia coli

(2012) H. Ogasawara et al.   MICROBIOLOGY-SGM

LeuO is a global regulator of gene expression inSalmonella entericaserovar Typhimurium

(2012) Shane C. Dillon et al.   MOLECULAR MICROBIOLOGY

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Promiscuous restriction is a cellular defense strategy that confers fitness advantage to bacteria

(2012) K. Vasu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A Fundamental Regulatory Mechanism Operating through OmpR and DNA Topology Controls Expression of Salmonella Pathogenicity Islands SPI-1 and SPI-2

(2012) Andrew D. S. Cameron et al.   PLoS Genetics

Iron-containing transcription factors and their roles as sensors

(2011) Angela S Fleischhacker et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Pervasive regulation of nucleoid structure and function by nucleoid-associated proteins

(2011) Sylvie Rimsky et al.   CURRENT OPINION IN MICROBIOLOGY

Genotype and Phenotypes of an Intestine-Adapted Escherichia coli K-12 Mutant Selected by Animal Passage for Superior Colonization

(2011) Andrew J. Fabich et al.   INFECTION AND IMMUNITY

The Identification of a Novel Protein Involved in Molybdenum Cofactor Biosynthesis inEscherichia coli

(2011) Jan-Ulrik Dahl et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Statistical Framework for the Analysis of ChIP-Seq Data

(2011) Pei Fen Kuan et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1, hilA

(2011) M. H. Queiroz et al.   MICROBIOLOGY-SGM

Integrated Approaches Reveal Determinants of Genome-wide Binding and Function of the Transcription Factor Pho4

(2011) Xu Zhou et al.   MOLECULAR CELL

Novel roles of LeuO in transcription regulation of E. coli genome: antagonistic interplay with the universal silencer H-NS

(2011) Tomohiro Shimada et al.   MOLECULAR MICROBIOLOGY

TFG-1 function in protein secretion and oncogenesis

(2011) Kristen Witte et al.   NATURE CELL BIOLOGY

Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12

(2011) Ana I. Prieto et al.   NUCLEIC ACIDS RESEARCH

Novel Roles of cAMP Receptor Protein (CRP) in Regulation of Transport and Metabolism of Carbon Sources

(2011) Tomohiro Shimada et al.   PLoS One

baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

MochiView: versatile software for genome browsing and DNA motif analysis

(2010) Oliver R Homann et al.   BMC BIOLOGY

Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression

(2010) Douglas F Browning et al.   CURRENT OPINION IN MICROBIOLOGY

Overlapping Repressor Binding Sites Result in Additive Regulation of Escherichia coli FadH by FadR and ArcA

(2010) Y. Feng et al.   JOURNAL OF BACTERIOLOGY

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

Reprogramming of anaerobic metabolism by the FnrS small RNA

(2010) Sylvain Durand et al.   MOLECULAR MICROBIOLOGY

Genome-wide analysis of the H-NS and Sfh regulatory networks in Salmonella Typhimurium identifies a plasmid-encoded transcription silencing mechanism

(2010) Shane C. Dillon et al.   MOLECULAR MICROBIOLOGY

Modulation of Shigella virulence in response to available oxygen in vivo

(2010) Benoit Marteyn et al.   NATURE

Bacterial nucleoid-associated proteins, nucleoid structure and gene expression

(2010) Shane C. Dillon et al.   NATURE REVIEWS MICROBIOLOGY

Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli

(2010) Christina Kahramanoglou et al.   NUCLEIC ACIDS RESEARCH

A novel nucleoid protein of Escherichia coli induced under anaerobiotic growth conditions

(2010) Jun Teramoto et al.   NUCLEIC ACIDS RESEARCH

EcoCyc: a comprehensive database of Escherichia coli biology

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

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

Bacterial sensors of oxygen

(2009) Jeffrey Green et al.   CURRENT OPINION IN MICROBIOLOGY

Differential Binding Profiles of StpA in Wild-Type and hns Mutant Cells: a Comparative Analysis of Cooperative Partners by Chromatin Immunoprecipitation-Microarray Analysis

(2009) E. Uyar et al.   JOURNAL OF BACTERIOLOGY

ChIPing away at the genome: the new frontier travel guide

(2009) Jelena Aleksic et al.   Molecular BioSystems

The transcription unit architecture of the Escherichia coli genome

(2009) Byung-Kwan Cho et al.   NATURE BIOTECHNOLOGY

Insights from genomic profiling of transcription factors

(2009) Peggy J. Farnham   NATURE REVIEWS GENETICS

Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli

(2009) Alfredo Mendoza-Vargas et al.   PLoS One

Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts

(2008) B.-K. Cho et al.   GENOME RESEARCH

Catabolite Repression Control ofnapF(Periplasmic Nitrate Reductase) Operon Expression inEscherichia coliK-12

(2008) Valley Stewart et al.   JOURNAL OF BACTERIOLOGY

Functional organisation of Escherichia coli transcriptional regulatory network

(2008) Agustino Martínez-Antonio 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

Characterization of the Escherichia coli K-12 ydhYVWXUT operon: regulation by FNR, NarL and NarP

(2008) J. D. Partridge et al.   MICROBIOLOGY-SGM

An integrated software system for analyzing ChIP-chip and ChIP-seq data

(2008) Hongkai Ji et al.   NATURE BIOTECHNOLOGY

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

(2008) Anton Valouev et al.   NATURE METHODS

Determination of tag density required for digital transcriptome analysis: Application to an androgen-sensitive prostate cancer model

(2008) H. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predictive Behavior Within Microbial Genetic Networks

(2008) I. Tagkopoulos et al.   SCIENCE