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

BayesPeak—an R package for analysing ChIP-seq data

(2011) Jonathan Cairns et al.   BIOINFORMATICS

Nucleoid-associated protein HU controls three regulons that coordinate virulence, response to stress and general physiology in Salmonella enterica serovar Typhimurium

(2011) M. W. Mangan et al.   MICROBIOLOGY-SGM

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

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

BayesPeak: Bayesian analysis of ChIP-seq data

(2009) Christiana Spyrou et al.   BMC BIOINFORMATICS

Coordination of genomic structure and transcription by the main bacterial nucleoid-associated protein HU

(2009) Michael Berger et al.   EMBO REPORTS

DNA relaxation-dependent phase biasing of thefimgenetic switch inEscherichia colidepends on the interplay of H-NS, IHF and LRP

(2009) Colin P. Corcoran et al.   MOLECULAR MICROBIOLOGY

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

MEME SUITE: tools for motif discovery and searching

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

The HU Regulon Is Composed of Genes Responding to Anaerobiosis, Acid Stress, High Osmolarity and SOS Induction

(2009) Jacques Oberto et al.   PLoS One

Mechanisms of Specific and Nonspecific Binding of Architectural Proteins in Prokaryotic Gene Regulation†

(2008) James M. Benevides et al.   BIOCHEMISTRY

Genome-wide Analysis Reveals MOF as a Key Regulator of Dosage Compensation and Gene Expression in Drosophila

(2008) Jop Kind et al.   CELL

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

Regulation by Nucleoid-Associated Proteins at the Escherichia coli nir Operon Promoter

(2008) D. F. Browning et al.   JOURNAL OF BACTERIOLOGY

EcoCyc: A comprehensive view of Escherichia coli biology

(2008) I. M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals

(2008) Yair Field et al.   PLoS Computational Biology