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

Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective

(2014) Andrey Feklístov et al.   Annual Review of Microbiology

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

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

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

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

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

MicL, a new  E-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein

(2014) M. S. Guo et al.   GENES & DEVELOPMENT

The double-stranded transcriptome of Escherichia coli

(2014) M. Lybecker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unprecedented High-Resolution View of Bacterial Operon Architecture Revealed by RNA Sequencing

(2014) T. Conway et al.   mBio

Conservation of Transcription Start Sites within Genes across a Bacterial Genus

(2014) W. Shao et al.   mBio

RNA-Seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentation

(2013) Sandra Wiegand et al.   BMC GENOMICS

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

Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling

(2013) Shan Li et al.   BMC GENOMICS

An Infection-Relevant Transcriptomic Compendium for Salmonella enterica Serovar Typhimurium

(2013) Carsten Kröger et al.   Cell Host & Microbe

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

(2013) Peter A C 't Hoen et al.   NATURE BIOTECHNOLOGY

Biases in small RNA deep sequencing data

(2013) Carsten A. Raabe et al.   NUCLEIC ACIDS RESEARCH

DOOR 2.0: presenting operons and their functions through dynamic and integrated views

(2013) Xizeng Mao et al.   NUCLEIC ACIDS RESEARCH

Computational analysis of bacterial RNA-Seq data

(2013) Ryan McClure et al.   NUCLEIC ACIDS RESEARCH

A riboswitch-regulated antisense RNA in Listeria monocytogenes

(2013) J. R. Mellin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates

(2013) Gaurav Dugar et al.   PLoS Genetics

How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?

(2012) Brian J Haas et al.   BMC GENOMICS

Rho and NusG suppress pervasive antisense transcription in Escherichia coli

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

A small RNA that regulates motility and biofilm formation in response to changes in nutrient availability in Escherichia coli

(2012) Maureen K. Thomason et al.   MOLECULAR MICROBIOLOGY

Comparative transcriptomics of pathogenic and non-pathogenic Listeria species

(2012) Omri Wurtzel et al.   Molecular Systems Biology

The excludon: a new concept in bacterial antisense RNA-mediated gene regulation

(2012) Nina Sesto et al.   NATURE REVIEWS MICROBIOLOGY

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more

(2012) Heladia Salgado et al.   NUCLEIC ACIDS RESEARCH

Strand-Specific RNA-Seq Reveals Ordered Patterns of Sense and Antisense Transcription in Bacillus anthracis

(2012) Karla D. Passalacqua 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

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

(2012) P. Nicolas et al.   SCIENCE

Antisense Transcription Is Pervasive but Rarely Conserved in Enteric Bacteria

(2012) R. Raghavan et al.   mBio

Comparative Analysis of Regulatory Elements between Escherichia coli and Klebsiella pneumoniae by Genome-Wide Transcription Start Site Profiling

(2012) Donghyuk Kim et al.   PLoS Genetics

Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli

(2011) Atsuko Shinhara et al.   BMC GENOMICS

cis-Antisense RNA, Another Level of Gene Regulation in Bacteria

(2011) J. Georg et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Direct and indirect effects in the regulation of overlapping promoters

(2011) Kristian Moss Bendtsen et al.   NUCLEIC ACIDS RESEARCH

Genome-wide antisense transcription drives mRNA processing in bacteria

(2011) I. Lasa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An experimentally anchored map of transcriptional start sites in the model cyanobacteriumSynechocystissp. PCC6803

(2011) Jan Mitschke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

The RpoS-Mediated General Stress Response inEscherichia coli

(2010) Aurelia Battesti et al.   Annual Review of Microbiology

Studying bacterial transcriptomes using RNA-seq

(2010) Nicholas J Croucher et al.   CURRENT OPINION IN MICROBIOLOGY

RNase III Participates in GadY-Dependent Cleavage of the gadX-gadW mRNA

(2010) Jason A. Opdyke et al.   JOURNAL OF MOLECULAR BIOLOGY

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Widespread Antisense Transcription in Escherichia coli

(2010) J. E. Dornenburg et al.   mBio

Next generation sequencing of microbial transcriptomes: challenges and opportunities

(2009) Arnoud H.M. van Vliet   FEMS MICROBIOLOGY LETTERS

The transcription unit architecture of the Escherichia coli genome

(2009) Byung-Kwan Cho et al.   NATURE BIOTECHNOLOGY

Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli

(2009) Alfredo Mendoza-Vargas et al.   PLoS One

Rho directs widespread termination of intragenic and stable RNA transcription

(2009) J. M. Peters 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

Small Toxic Proteins and the Antisense RNAs That Repress Them

(2008) E. M. Fozo et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal

(2008) Atilio Deana et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum

(2008) Gaëlle André et al.   NUCLEIC ACIDS RESEARCH