H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes

Endosymbiotic origin and differential loss of eukaryotic genes

(2015) Chuan Ku et al.   NATURE

Gene Regulation by H-NS as a Function of Growth Conditions Depends on Chromosomal Position in Escherichia coli

(2015) Elisa Brambilla et al.   G3-Genes Genomes Genetics

Bridged filaments of histone-like nucleoid structuring protein pause RNA polymerase and aid termination in bacteria

(2015) Matthew V Kotlajich et al.   eLife

Widespread suppression of intragenic transcription initiation by H-NS

(2014) S. S. Singh et al.   GENES & DEVELOPMENT

Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli

(2014) Maureen K. Thomason et al.   JOURNAL OF BACTERIOLOGY

Origins of major archaeal clades correspond to gene acquisitions from bacteria

(2014) Shijulal Nelson-Sathi et al.   NATURE

Pervasive transcription: illuminating the dark matter of bacterial transcriptomes

(2014) Joseph T. Wade et al.   NATURE REVIEWS MICROBIOLOGY

The genome-scale interplay amongst xenogene silencing, stress response and chromosome architecture in Escherichia coli

(2014) Rajalakshmi Srinivasan et al.   NUCLEIC ACIDS RESEARCH

MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data

(2014) Ikuo Uchiyama et al.   NUCLEIC ACIDS RESEARCH

A pause sequence enriched at translation start sites drives transcription dynamics in vivo

(2014) M. H. Larson et al.   SCIENCE

Interactions between RNA polymerase and the "core recognition element" counteract pausing

(2014) I. O. Vvedenskaya et al.   SCIENCE

Silencing by H-NS Potentiated the Evolution of Salmonella

(2014) Sabrina S. Ali et al.   PLoS Pathogens

Functions of the Hha and YdgT Proteins in Transcriptional Silencing by the Nucleoid Proteins, H-NS and StpA, in Escherichia coli

(2013) T. Ueda et al.   DNA RESEARCH

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

(2013) Rajalakshmi Srinivasan et al.   Molecular BioSystems

Phylogenetic group-associated differences in regulation of the common colonization factor Mat fimbria inEscherichia coli

(2013) Timo A. Lehti et al.   MOLECULAR MICROBIOLOGY

Unipro UGENE: a unified bioinformatics toolkit

(2012) Konstantin Okonechnikov et al.   BIOINFORMATICS

Rho and NusG suppress pervasive antisense transcription in Escherichia coli

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Nucleoid-Associated Proteins Affect Mutation Dynamics in E. coli in a Growth Phase-Specific Manner

(2012) Tobias Warnecke et al.   PLoS Computational Biology

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

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

Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)

(2011) G. E. Sims et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution in Regulatory Regions Rapidly Compensates the Cost of Nonoptimal Codon Usage

(2010) D. Amoros-Moya et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

(2010) S. Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Gene doctoring: a method for recombineering in laboratory and pathogenic Escherichia coli strains

(2009) David J Lee et al.   BMC MICROBIOLOGY

Complete Genome Sequence of the Wild-Type Commensal Escherichia coli Strain SE15, Belonging to Phylogenetic Group B2

(2009) H. Toh et al.   JOURNAL OF BACTERIOLOGY

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

MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity

(2009) Ikuo Uchiyama et al.   NUCLEIC ACIDS RESEARCH

ACLAME: A CLAssification of Mobile genetic Elements, update 2010

(2009) Raphaël Leplae et al.   NUCLEIC ACIDS RESEARCH

Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli

(2009) Y. Ogura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon 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

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

New insights into transcriptional regulation by H-NS

(2008) Ferric C Fang et al.   CURRENT OPINION IN MICROBIOLOGY

Complete Genome Sequence and Comparative Analysis of the Wild-type Commensal Escherichia coli Strain SE11 Isolated from a Healthy Adult

(2008) K. Oshima et al.   DNA RESEARCH

NCBI Reference Sequences: current status, policy and new initiatives

(2008) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Uncertainty in homology inferences: Assessing and improving genomic sequence alignment

(2007) G. Lunter et al.   GENOME RESEARCH

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

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