Elucidation of Sigma Factor-Associated Networks in Pseudomonas aeruginosa Reveals a Modular Architecture with Limited and Function-Specific Crosstalk

Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states

(2014) Byung-Kwan Cho et al.   BMC BIOLOGY

Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks

(2013) Yu Qiu et al.   Nature Communications

Single-tube linear DNA amplification for genome-wide studies using a few thousand cells

(2012) Pattabhiraman Shankaranarayanan et al.   Nature Protocols

The Pseudomonas aeruginosa Transcriptome in Planktonic Cultures and Static Biofilms Using RNA Sequencing

(2012) Andreas Dötsch et al.   PLoS One

Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

(2012) P. Nicolas et al.   SCIENCE

The Single-Nucleotide Resolution Transcriptome of Pseudomonas aeruginosa Grown in Body Temperature

(2012) Omri Wurtzel et al.   PLoS Pathogens

Roles of Two Shewanella oneidensis MR-1 Extracellular Endonucleases

(2011) Julia Gödeke et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

The E. coli Anti-Sigma Factor Rsd: Studies on the Specificity and Regulation of Its Expression

(2011) Nina Hofmann et al.   PLoS One

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Antagonistic regulation of motility and transcriptome expression by RpoN and RpoS in Escherichia coli

(2010) Tao Dong et al.   MOLECULAR MICROBIOLOGY

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Independent filtering increases detection power for high-throughput experiments

(2010) R. Bourgon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Evaluation of a microarray-hybridization based method applicable for discovery of single nucleotide polymorphisms (SNPs) in the Pseudomonas aeruginosa genome

(2009) Andreas Dötsch et al.   BMC GENOMICS

Dissecting Regulatory Networks in Host-Pathogen Interaction Using ChIP-on-chip Technology

(2009) Claudia Sala et al.   Cell Host & Microbe

Direct methods for studying transcription regulatory proteins and RNA polymerase in bacteria

(2009) David C Grainger et al.   CURRENT OPINION IN MICROBIOLOGY

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) σ factor protein family

(2009) Anna Staroń et al.   MOLECULAR MICROBIOLOGY

Promoter and regulon analysis of nitrogen assimilation factor, σ54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis

(2009) Kai Zhao et al.   NUCLEIC ACIDS RESEARCH

MEME SUITE: tools for motif discovery and searching

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

Physiological and transcriptomic characterization of a fliA mutant of Pseudomonas putida KT2440

(2009) José Juan Rodríguez-Herva et al.   Environmental Microbiology Reports

A Novel Extracytoplasmic Function (ECF) Sigma Factor Regulates Virulence in Pseudomonas aeruginosa

(2009) María A. Llamas et al.   PLoS Pathogens

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

The relative value of operon predictions

(2008) R. W. W. Brouwer et al.   BRIEFINGS IN BIOINFORMATICS

Swarming of Pseudomonas aeruginosa Is a Complex Adaptation Leading to Increased Production of Virulence Factors and Antibiotic Resistance

(2008) J. Overhage et al.   JOURNAL OF BACTERIOLOGY

DOOR: a database for prokaryotic operons

(2008) Fenglou Mao et al.   NUCLEIC ACIDS RESEARCH

Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes

(2008) G. L. Winsor et al.   NUCLEIC ACIDS RESEARCH

Dynamics of Pseudomonas aeruginosa genome evolution

(2008) K. Mathee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY