Differential expression of small RNAs under chemical stress and fed-batch fermentation in E. coli

Regulatory small RNAs from the 3′ regions of bacterial mRNAs

(2015) Masatoshi Miyakoshi et al.   CURRENT OPINION IN MICROBIOLOGY

Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA

(2015) M. Miyakoshi et al.   EMBO JOURNAL

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

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

Small RNAs in the control of RpoS, CsgD, and biofilm architecture ofEscherichia coli

(2014) Franziska Mika et al.   RNA Biology

Ménage à trois

(2014) Yvonne Göpel et al.   RNA Biology

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

(2014) T. Conway et al.   mBio

The damaging effects of short chain fatty acids on Escherichia coli membranes

(2013) Liam A. Royce et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Dual function of the McaS small RNA in controlling biofilm formation

(2013) M. G. Jorgensen et al.   GENES & DEVELOPMENT

Bacterial sRNAs: Regulation in stress

(2013) Chee-Hock Hoe et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Small Regulatory RNAs in the Control of Motility and Biofilm Formation in E. coli and Salmonella

(2013) Franziska Mika et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Synthetic tolerance: three noncoding small RNAs, DsrA, ArcZ and RprA, acting supra-additively against acid stress

(2013) S. M. Gaida et al.   NUCLEIC ACIDS RESEARCH

An RpoS-dependent sRNA regulates the expression of a chaperone involved in protein folding

(2013) I. J. Silva et al.   RNA

Roles ofrpoS-activating small RNAs in pathways leading to acid resistance ofEscherichia coli

(2013) Geunu Bak et al.   MicrobiologyOpen

An atlas of Hfq-bound transcripts reveals 3′ UTRs as a genomic reservoir of regulatory small RNAs

(2012) Yanjie Chao et al.   EMBO JOURNAL

Genome-wide identification of novel small RNAs in Pseudomonas aeruginosa

(2012) María Gómez-Lozano et al.   ENVIRONMENTAL MICROBIOLOGY

Post-transcriptional regulation on a global scale: form and function of Csr/Rsm systems

(2012) Tony Romeo et al.   ENVIRONMENTAL MICROBIOLOGY

Targeting of csgD by the small regulatory RNA RprA links stationary phase, biofilm formation and cell envelope stress in Escherichia coli

(2012) Franziska Mika et al.   MOLECULAR MICROBIOLOGY

A mixed double negative feedback loop between the sRNA MicF and the global regulator Lrp

(2012) Erik Holmqvist et al.   MOLECULAR MICROBIOLOGY

Small regulatory RNAs control the multi-cellular adhesive lifestyle of Escherichia coli

(2012) Mikkel Girke Jørgensen et al.   MOLECULAR MICROBIOLOGY

A complex network of small non-coding RNAs regulate motility inEscherichia coli

(2012) Nicholas De Lay et al.   MOLECULAR MICROBIOLOGY

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Heladia Salgado et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Atsuko Shinhara et al.   BMC GENOMICS

Genome-wide detection of novel regulatory RNAs in E. coli

(2011) R. Raghavan et al.   GENOME RESEARCH

Regulation by Small RNAs in Bacteria: Expanding Frontiers

(2011) Gisela Storz et al.   MOLECULAR CELL

Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA

(2011) Cynthia M. Sharma et al.   MOLECULAR MICROBIOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon

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

Regulating iron storage and metabolism with RNA: an overview of posttranscriptional controls of intracellular iron homeostasis

(2011) Hubert Salvail et al.   Wiley Interdisciplinary Reviews-RNA

Functional Genomic Study of Exogenous n-Butanol Stress in Escherichia coli

(2010) B. J. Rutherford et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Two antisense RNAs target the transcriptional regulator CsgD to inhibit curli synthesis

(2010) Erik Holmqvist et al.   EMBO JOURNAL

Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA

(2010) Pierre Mandin et al.   EMBO JOURNAL

Recognition of heptameric seed sequence underlies multi-target regulation by RybB small RNA in Salmonella enterica

(2010) Roberto Balbontín et al.   MOLECULAR MICROBIOLOGY

Evidence for an autonomous 5' target recognition domain in an Hfq-associated small RNA

(2010) K. Papenfort et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Positive regulation by small RNAs and the role of Hfq

(2010) T. Soper et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial Small RNA Regulators: Versatile Roles and Rapidly Evolving Variations

(2010) S. Gottesman et al.   Cold Spring Harbor Perspectives in Biology

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

De novo computational prediction of non-coding RNA genes in prokaryotic genomes

(2009) Thao T. Tran 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

Regulatory RNAs in Bacteria

(2009) Lauren S. Waters et al.   CELL

Experimental approaches for the discovery and characterization of regulatory small RNA

(2009) Cynthia Mira Sharma et al.   CURRENT OPINION IN MICROBIOLOGY

Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA

(2009) Kai Papenfort et al.   MOLECULAR MICROBIOLOGY

The transcription unit architecture of the Escherichia coli genome

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

The Crp-Activated Small Noncoding Regulatory RNA CyaR (RyeE) Links Nutritional Status to Group Behavior

(2008) N. De Lay et al.   JOURNAL OF BACTERIOLOGY

Identification of furfural as a key toxin in lignocellulosic hydrolysates and evolution of a tolerant yeast strain

(2008) Dominik Heer et al.   Microbial Biotechnology