The Transcriptional landscape of Streptococcus pneumoniae TIGR4 reveals a complex operon architecture and abundant riboregulation critical for growth and virulence

Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics

(2017) Katherine James et al.   METHODS

Structure and mapping of spontaneous mutational sites of PyrR from Mycobacterium tuberculosis

(2016) Pramila Ghode et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Natural antisense RNAs as mRNA regulatory elements in bacteria: a review on function and applications

(2016) Fatemeh Saberi et al.   CELLULAR & MOLECULAR BIOLOGY LETTERS

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

A 3′ UTR-Derived Small RNA Provides the Regulatory Noncoding Arm of the Inner Membrane Stress Response

(2016) Yanjie Chao et al.   MOLECULAR CELL

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

RNA- and protein-mediated control of Listeria monocytogenes virulence gene expression

(2016) Alice Lebreton et al.   RNA Biology

Revisiting operons: an analysis of the landscape of transcriptional units in E. coli

(2015) Xizeng Mao et al.   BMC BIOINFORMATICS

Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae

(2015) Isabelle Rosinski-Chupin et al.   BMC GENOMICS

Selective small-molecule inhibition of an RNA structural element

(2015) John A. Howe et al.   NATURE

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Simultaneous generation of many RNA-seq libraries in a single reaction

(2015) Alexander A Shishkin et al.   NATURE METHODS

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

De novo assembly of bacterial transcriptomes from RNA-seq data

(2015) Brian Tjaden   GENOME BIOLOGY

A small RNA controls a protein regulator involved in antibiotic resistance in Staphylococcus aureus

(2014) Alex Eyraud et al.   NUCLEIC ACIDS RESEARCH

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

The Streptococcus suis transcriptional landscape reveals adaptation mechanisms in pig blood and cerebrospinal fluid

(2014) Z. Wu et al.   RNA

A riboswitch-containing sRNA controls gene expression by sequestration of a response regulator

(2014) S. DebRoy et al.   SCIENCE

Sequestration of a two-component response regulator by a riboswitch-regulated noncoding RNA

(2014) J. R. Mellin et al.   SCIENCE

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

(2014) T. Conway et al.   mBio

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria

(2013) Pavel S Novichkov et al.   BMC GENOMICS

The promise of riboswitches as potential antibacterial drug targets

(2013) Christina E. Lünse et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Most RNAs regulating ribosomal protein biosynthesis in Escherichia coli are narrowly distributed to Gammaproteobacteria

(2013) Yang Fu 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

Novel Regulatory Small RNAs in Streptococcus pyogenes

(2013) Rafael A. Tesorero et al.   PLoS One

RNA-Mediated Regulation in Pathogenic Bacteria

(2013) I. Caldelari et al.   Cold Spring Harbor Perspectives in Medicine

The Pneumococcus: Epidemiology, Microbiology, and Pathogenesis

(2013) B. Henriques-Normark et al.   Cold Spring Harbor Perspectives in Medicine

Base Pairing Interaction between 5′- and 3′-UTRs Controls icaR mRNA Translation in Staphylococcus aureus

(2013) Igor Ruiz de los Mozos et al.   PLoS Genetics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

A fine scale phenotype-genotype virulence map of a bacterial pathogen

(2012) T. van Opijnen et al.   GENOME RESEARCH

Comparative transcriptomics of pathogenic and non-pathogenic Listeria species

(2012) Omri Wurtzel et al.   Molecular Systems Biology

Identification of 88 regulatory small RNAs in the TIGR4 strain of the human pathogen Streptococcus pneumoniae

(2012) P. Acebo et al.   RNA

Control of Virulence by Small RNAs in Streptococcus pneumoniae

(2012) Beth Mann et al.   PLoS Pathogens

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Dual-function RNA regulators in bacteria

(2011) Carin K. Vanderpool et al.   BIOCHIMIE

Prospects for Riboswitch Discovery and Analysis

(2011) Ronald R. Breaker   MOLECULAR CELL

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III

(2011) Elitza Deltcheva et al.   NATURE

An in silico model for identification of small RNAs in whole bacterial genomes: characterization of antisense RNAs in pathogenic Escherichia coli and Streptococcus agalactiae strains

(2011) Christophe Pichon et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Identification of novel non-coding small RNAs from Streptococcus pneumoniae TIGR4 using high-resolution genome tiling arrays

(2010) Ranjit Kumar et al.   BMC GENOMICS

Regulatory RNA in Bacterial Pathogens

(2010) Kai Papenfort et al.   Cell Host & Microbe

Therapeutic applications of ribozymes and riboswitches

(2010) Jérôme Mulhbacher et al.   CURRENT OPINION IN PHARMACOLOGY

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Regulatory RNAs in Bacteria

(2009) Lauren S. Waters et al.   CELL

MEME SUITE: tools for motif discovery and searching

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

Transcriptome Complexity in a Genome-Reduced Bacterium

(2009) M. Guell et al.   SCIENCE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

DOOR: a database for prokaryotic operons

(2008) Fenglou Mao et al.   NUCLEIC ACIDS RESEARCH