Genome Rearrangements Can Make and Break Small RNA Genes

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

Evolutionary patterns of Escherichia coli small RNAs and their regulatory interactions

(2014) A. Peer et al.   RNA

An Infection-Relevant Transcriptomic Compendium for Salmonella enterica Serovar Typhimurium

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

Salmonella enterica Serovar Typhimurium Skills To Succeed in the Host: Virulence and Regulation

(2013) A. Fabrega et al.   CLINICAL MICROBIOLOGY REVIEWS

The Evolution of Genomic Instability in the Obligate Endosymbionts of Whiteflies

(2013) Daniel B. Sloan et al.   Genome Biology and Evolution

Bacterial Small RNA-based Negative Regulation: Hfq and Its Accomplices

(2013) Nicholas De Lay et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Characterisation of the stbD/E toxin–antitoxin system of pEP36, a plasmid of the plant pathogen Erwinia pyrifoliae

(2013) Simon J. Unterholzner et al.   PLASMID

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

(2012) Yanjie Chao et al.   EMBO JOURNAL

Evolutionary Dynamics of Small RNAs in 27 Escherichia coli and Shigella Genomes

(2012) Elizabeth Skippington et al.   Genome Biology and Evolution

The Adaptation of Temperate Bacteriophages to Their Host Genomes

(2012) Louis-Marie Bobay et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic analysis of a key innovation in an experimental Escherichia coli population

(2012) Zachary D. Blount et al.   NATURE

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

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

Real-Time Evolution of New Genes by Innovation, Amplification, and Divergence

(2012) J. Nasvall et al.   SCIENCE

Antisense Transcription Is Pervasive but Rarely Conserved in Enteric Bacteria

(2012) R. Raghavan et al.   mBio

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

(2011) R. Raghavan et al.   GENOME RESEARCH

Genome-Wide Identification of Transcription Start Sites Yields a Novel Thermosensing RNA and New Cyclic AMP Receptor Protein-Regulated Genes in Escherichia coli

(2011) R. Raghavan et al.   JOURNAL OF BACTERIOLOGY

The Base-Pairing RNA Spot 42 Participates in a Multioutput Feedforward Loop to Help Enact Catabolite Repression in Escherichia coli

(2011) Chase L. Beisel et al.   MOLECULAR CELL

Regulation by Small RNAs in Bacteria: Expanding Frontiers

(2011) Gisela Storz et al.   MOLECULAR CELL

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

(2011) Todd J. Treangen et al.   PLoS Genetics

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

Reprogramming of anaerobic metabolism by the FnrS small RNA

(2010) Sylvain Durand et al.   MOLECULAR MICROBIOLOGY

An antisense RNA that governs the expression kinetics of a multifunctional virulence gene

(2010) Eun-Jin Lee et al.   MOLECULAR MICROBIOLOGY

Widespread Antisense Transcription in Escherichia coli

(2010) J. E. Dornenburg et al.   mBio

Bacterial Small RNA Regulators: Versatile Roles and Rapidly Evolving Variations

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

Conditions for the Evolution of Gene Clusters in Bacterial Genomes

(2010) Sara Ballouz et al.   PLoS Computational Biology

The Extinction Dynamics of Bacterial Pseudogenes

(2010) Chih-Horng Kuo et al.   PLoS Genetics

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Citrobacter rodentium Genome Sequence Reveals Convergent Evolution with Human Pathogenic Escherichia coli

(2009) N. K. Petty et al.   JOURNAL OF BACTERIOLOGY

Signals, Regulatory Networks, and Materials That Build and Break Bacterial Biofilms

(2009) E. Karatan et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

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

(2009) Da Wei Huang et al.   Nature Protocols

Homologs of the small RNA SgrS are broadly distributed in enteric bacteria but have diverged in size and sequence

(2009) Richard S. P. Horler et al.   NUCLEIC ACIDS RESEARCH

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

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

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Cellulose modulates biofilm formation by counteracting curli-mediated colonization of solid surfaces in Escherichia coli

(2008) L. Gualdi et al.   MICROBIOLOGY-SGM

Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global Post-Transcriptional Regulator, Hfq

(2008) Alexandra Sittka et al.   PLoS Genetics