Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

READemption--a tool for the computational analysis of deep-sequencing-based transcriptome data

(2014) K. U. Forstner et al.   BIOINFORMATICS

TSSAR: TSS annotation regime for dRNA-seq data

(2014) Fabian Amman et al.   BMC BIOINFORMATICS

Differential RNA-seq: the approach behind and the biological insight gained

(2014) Cynthia M Sharma et al.   CURRENT OPINION IN MICROBIOLOGY

The BCESM genomic region contains a regulator involved in quorum sensing and persistence in Burkholderia cenocepacia J2315

(2014) Heleen Van Acker et al.   Future Microbiology

A comparison of key aspects of gene regulation inStreptomyces coelicolorandEscherichia coliusing nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing

(2014) David A. Romero et al.   MOLECULAR MICROBIOLOGY

Pervasive transcription: illuminating the dark matter of bacterial transcriptomes

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

DMINDA: an integrated web server for DNA motif identification and analyses

(2014) Qin Ma et al.   NUCLEIC ACIDS RESEARCH

A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease

(2013) Yu-fei Lin et al.   BMC GENOMICS

The unexpected discovery of a novel low-oxygen-activated locus for the anoxic persistence of Burkholderia cenocepacia

(2013) Andrea M Sass et al.   ISME Journal

Biofilm-Grown Burkholderia cepacia Complex Cells Survive Antibiotic Treatment by Avoiding Production of Reactive Oxygen Species

(2013) Heleen Van Acker et al.   PLoS One

Burkholderia pseudomultivorans sp. nov., a novel Burkholderia cepacia complex species from human respiratory samples and the rhizosphere

(2013) Charlotte Peeters et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

The KdpD/KdpE Two-Component System: Integrating K+ Homeostasis and Virulence

(2013) Zoë N. Freeman et al.   PLoS Pathogens

Kinetic control of translation initiation in bacteria

(2012) Pohl Milón et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

A vast collection of microbial genes that are toxic to bacteria

(2012) A. Kimelman et al.   GENOME RESEARCH

Experimental identification of small non-coding regulatory RNAs in the opportunistic human pathogen Burkholderia cenocepacia J2315

(2012) Christian G. Ramos et al.   GENOMICS

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

High-Density Transcriptional Initiation Signals Underline Genomic Islands in Bacteria

(2012) Qianli Huang et al.   PLoS One

High Confidence Prediction of Essential Genes in Burkholderia Cenocepacia

(2012) Mario Juhas et al.   PLoS One

The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium

(2012) C. Kroger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Mechanisms of Chlorhexidine Tolerance in Burkholderia cenocepacia Biofilms

(2011) Tom Coenye et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Global Gene Expression Profile for Swarming Bacillus cereus Bacteria

(2011) Sara Salvetti et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Consistency of gene starts among Burkholderia genomes

(2011) John Dunbar et al.   BMC GENOMICS

Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes

(2011) Xiaobin Zheng et al.   BMC GENOMICS

Spontaneous and evolutionary changes in the antibiotic resistance of Burkholderia cenocepacia observed by global gene expression analysis

(2011) Andrea Sass et al.   BMC GENOMICS

Regulation by Small RNAs in Bacteria: Expanding Frontiers

(2011) Gisela Storz et al.   MOLECULAR CELL

NanoRNAs Prime Transcription Initiation In Vivo

(2011) Seth R. Goldman et al.   MOLECULAR CELL

Bacterial transcriptomics: what is beyond the RNA horiz-ome?

(2011) Marc Güell et al.   NATURE REVIEWS MICROBIOLOGY

Hfq and its constellation of RNA

(2011) Jörg Vogel et al.   NATURE REVIEWS MICROBIOLOGY

Deep sequencing-based identification of small non-coding RNAs inStreptomyces coelicolor

(2011) Michael-Paul Vockenhuber et al.   RNA Biology

Bacterial Antisense RNAs: How Many Are There, and What Are They Doing?

(2010) Maureen Kiley Thomason et al.   Annual Review of Genetics

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Transcriptional response of Burkholderia cenocepacia J2315 sessile cells to treatments with high doses of hydrogen peroxide and sodium hypochlorite

(2010) Elke Peeters et al.   BMC GENOMICS

Social interactions in theBurkholderia cepaciacomplex: biofilms and quorum sensing

(2010) Tom Coenye   Future Microbiology

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Riboswitches and the RNA World

(2010) R. R. Breaker   Cold Spring Harbor Perspectives in Biology

Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes

(2010) Zasha Weinberg et al.   GENOME BIOLOGY

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

(2009) J. W. Nicol et al.   BIOINFORMATICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing

(2009) D. R. Yoder-Himes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

(2009) Steve Hoffmann et al.   PLoS Computational Biology

The Burkholderia Genome Database: facilitating flexible queries and comparative analyses

(2008) G. L. Winsor et al.   BIOINFORMATICS

Gene expression changes linked to antimicrobial resistance, oxidative stress, iron depletion and retained motility are observed when Burkholderia cenocepaciagrows in cystic fibrosis sputum

(2008) Pavel Drevinek et al.   BMC INFECTIOUS DISEASES

The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients

(2008) M. T. G. Holden et al.   JOURNAL OF BACTERIOLOGY