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

Antibiotic-Induced Replication Stress Triggers Bacterial Competence by Increasing Gene Dosage near the Origin

(2014) Jelle Slager et al.   CELL

Widespread suppression of intragenic transcription initiation by H-NS

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

Inhibition of factor-dependent transcription termination in Escherichia coli might relieve xenogene silencing by abrogating H-NS-DNA interactions in vivo

(2014) Deepti Chandraprakash et al.   JOURNAL OF BIOSCIENCES

A case of adaptation through a mutation in a tandem duplication during experimental evolution in Escherichia coli

(2013) Ram P Maharjan et al.   BMC GENOMICS

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

(2013) Mina Zarei et al.   Molecular BioSystems

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

(2013) Rajalakshmi Srinivasan et al.   Molecular BioSystems

Genome architecture and global gene regulation in bacteria: making progress towards a unified model?

(2013) Charles J. Dorman   NATURE REVIEWS MICROBIOLOGY

High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

(2013) T. B. K. Le et al.   SCIENCE

The Dynamics of Diverse Segmental Amplifications in Populations of Saccharomyces cerevisiae Adapting to Strong Selection

(2013) Celia Payen et al.   G3-Genes Genomes Genetics

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

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

H-NS Can Facilitate Specific DNA-binding by RNA Polymerase in AT-rich Gene Regulatory Regions

(2013) Shivani S. Singh et al.   PLoS Genetics

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

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

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

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

H-NS Regulation of IraD and IraM Antiadaptors for Control of RpoS Degradation

(2012) A. Battesti et al.   JOURNAL OF BACTERIOLOGY

FREQ-Seq: A Rapid, Cost-Effective, Sequencing-Based Method to Determine Allele Frequencies Directly from Mixed Populations

(2012) Lon M. Chubiz et al.   PLoS One

Chromosomal duplication is a transient evolutionary solution to stress

(2012) A. H. Yona et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation

(2011) Mark A. Umbarger et al.   MOLECULAR CELL

Replication and segregation of an Escherichia coli chromosome with two replication origins

(2011) X. Wang 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

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Massive Gene Duplication Event among Clinical Isolates of the Mycobacterium tuberculosis W/Beijing Family

(2010) P. Domenech et al.   JOURNAL OF BACTERIOLOGY

Gene clusters reflecting macrodomain structure respond to nucleoid perturbations

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

Chromosomal periodicity and positional networks of genes in Escherichia coli

(2010) Anthony Mathelier et al.   Molecular Systems Biology

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

Controlling biofilm formation, prophage excision and cell death by rewiring global regulator H-NS ofEscherichia coli

(2010) Seok Hoon Hong et al.   Microbial Biotechnology

Gene Amplification and Adaptive Evolution in Bacteria

(2009) Dan I. Andersson et al.   Annual Review of Genetics

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(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

Inverse Symmetry in Complete Genomes and Whole-Genome Inverse Duplication

(2009) Sing-Guan Kong et al.   PLoS One

Invariant Distribution of Promoter Activities in Escherichia coli

(2009) Alon Zaslaver et al.   PLoS Computational Biology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Dissecting the logical types of network control in gene expression profiles

(2008) Carsten Marr et al.   BMC Systems Biology

A prominent role for segmental duplications in modeling Eukaryotic genomes

(2008) Romain Koszul et al.   COMPTES RENDUS BIOLOGIES

Selective repression by Fis and H-NS at theEscherichia coli dpspromoter

(2008) David C. Grainger et al.   MOLECULAR MICROBIOLOGY

EcoCyc: A comprehensive view of Escherichia coli biology

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