Genomic analysis reveals epistatic silencing of “expensive” genes in Escherichia coli K-12

Gene silencing and large-scale domain structure of the E. coli genome

(2013) Mina Zarei et al.   Molecular BioSystems

DNA thermodynamic stability and supercoil dynamics determine the gene expression program during the bacterial growth cycle

(2013) Patrick Sobetzko et al.   Molecular BioSystems

NuST: analysis of the interplay between nucleoid organization and gene expression

(2012) V. F. Scolari et al.   BIOINFORMATICS

Rho and NusG suppress pervasive antisense transcription in Escherichia coli

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

High Expression Hampers Horizontal Gene Transfer

(2012) Chungoo Park et al.   Genome Biology and Evolution

Involvement of the Global Regulator H-NS in the Survival of Escherichia coli in Stationary Phase

(2012) S. Chib et al.   JOURNAL OF BACTERIOLOGY

The nucleoid-associated proteins H-NS and FIS modulate the DNA supercoiling response of the pel genes, the major virulence factors in the plant pathogen bacterium Dickeya dadantii

(2012) Zghidi-Abouzid Ouafa et al.   NUCLEIC ACIDS RESEARCH

Context-dependent conservation of DNA methyltransferases in bacteria

(2012) Aswin Sai Narain Seshasayee et al.   NUCLEIC ACIDS RESEARCH

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

A selective force favoring increased G+C content in bacterial genes

(2012) R. Raghavan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modulation of Rho-Dependent Transcription Termination in Escherichia coli by the H-NS Family of Proteins

(2011) S. Saxena et al.   JOURNAL OF BACTERIOLOGY

Gene silencing H-NS paralogue StpA forms a rigid protein filament along DNA that blocks DNA accessibility

(2011) Ci Ji Lim et al.   NUCLEIC ACIDS RESEARCH

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

Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins

(2011) B. R. G. Gordon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle

(2011) P. Sobetzko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria

(2011) W. Wang et al.   SCIENCE

A divalent switch drives H-NS/DNA-binding conformations between stiffening and bridging modes

(2010) Y. Liu et al.   GENES & DEVELOPMENT

Gene clusters reflecting macrodomain structure respond to nucleoid perturbations

(2010) Vittore F. Scolari et al.   Molecular BioSystems

Cost of Unneeded Proteins in E. coli Is Reduced after Several Generations in Exponential Growth

(2010) Irit Shachrai et al.   MOLECULAR CELL

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

Mycobacterium tuberculosis nucleoid-associated DNA-binding protein H-NS binds with high-affinity to the Holliday junction and inhibits strand exchange promoted by RecA protein

(2010) N. Sharadamma et al.   NUCLEIC ACIDS RESEARCH

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

Cryptic prophages help bacteria cope with adverse environments

(2010) Xiaoxue Wang et al.   Nature Communications

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

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

A Systematic In Vitro Study of Nucleoprotein Complexes Formed by Bacterial Nucleoid-Associated Proteins Revealing Novel Types of DNA Organization

(2009) Sebastian Maurer et al.   JOURNAL OF MOLECULAR BIOLOGY

Protein Occupancy Landscape of a Bacterial Genome

(2009) Tiffany Vora et al.   MOLECULAR CELL

Investigation of the self-association and hetero-association interactions of H-NS and StpA fromEnterobacteria

(2009) Paul G. Leonard et al.   MOLECULAR MICROBIOLOGY

The H-NS-like protein StpA represses the RpoS (σ38) regulon during exponential growth ofSalmonellaTyphimurium

(2009) Sacha Lucchini et al.   MOLECULAR MICROBIOLOGY

Backup in gene regulatory networks explains differences between binding and knockout results

(2009) Anthony Gitter et al.   Molecular Systems Biology

Differential Regulation of Horizontally Acquired and Core Genome Genes by the Bacterial Modulator H-NS

(2009) Rosa C. Baños et al.   PLoS Genetics

The impact of horizontal gene transfer in shaping operons and protein interaction networks – direct evidence of preferential attachment

(2008) Wagied Davids et al.   BMC EVOLUTIONARY BIOLOGY

A global modulatory role for the Yersinia enterocolitica H-NS protein

(2008) R. C. Banos et al.   MICROBIOLOGY-SGM

Anti-silencing: overcoming H-NS-mediated repression of transcription in Gram-negative enteric bacteria

(2008) D. M. Stoebel et al.   MICROBIOLOGY-SGM

The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli

(2008) Matthew F. Traxler et al.   MOLECULAR MICROBIOLOGY

Termination Factor Rho and Its Cofactors NusA and NusG Silence Foreign DNA in E. coli

(2008) C. J. Cardinale et al.   SCIENCE

Integration of Horizontally Transferred Genes into Regulatory Interaction Networks Takes Many Million Years

(2007) M. J. Lercher et al.   MOLECULAR BIOLOGY AND EVOLUTION