Genome-Wide Analyses in Bacteria Show Small-RNA Enrichment for Long and Conserved Intergenic Regions

An intergenic regulatory region mediates Drosophila Myc-induced apoptosis and blocks tissue hyperplasia

(2014) C Zhang et al.   ONCOGENE

Conservation and Functional Element Discovery in 20 Angiosperm Plant Genomes

(2013) D. Hupalo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identification of Novel sRNAs in Mycobacterial Species

(2013) Chen-Hsun Tsai et al.   PLoS One

Computational identification of functional RNA homologs in metagenomic data

(2013) Eric P. Nawrocki et al.   RNA Biology

Regulation of small RNA stability: methylation and beyond

(2012) Lijuan Ji et al.   CELL RESEARCH

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

Noncoding RNAs Binding to the Nucleoid Protein HU in Escherichia coli

(2012) M. Macvanin et al.   JOURNAL OF BACTERIOLOGY

Comparison of Next-Generation Sequencing Systems

(2012) Lin Liu et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Rfam 11.0: 10 years of RNA families

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

BSRD: a repository for bacterial small regulatory RNA

(2012) Lei Li et al.   NUCLEIC ACIDS RESEARCH

A Genome-Wide Identification Analysis of Small Regulatory RNAs in Mycobacterium tuberculosis by RNA-Seq and Conservation Analysis

(2012) Danilo Pellin et al.   PLoS One

Comparative Profiling of Pseudomonas aeruginosa Strains Reveals Differential Expression of Novel Unique and Conserved Small RNAs

(2012) Silvia Ferrara et al.   PLoS One

Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens

(2012) Ina Wilms et al.   RNA 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

Accessibility and Evolutionary Conservation Mark Bacterial Small-RNA Target-Binding Regions

(2011) A. Peer et al.   JOURNAL OF BACTERIOLOGY

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Regulation by Small RNAs in Bacteria: Expanding Frontiers

(2011) Gisela Storz et al.   MOLECULAR CELL

Engineering Biological Systems with Synthetic RNA Molecules

(2011) Joe C. Liang et al.   MOLECULAR CELL

The intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages

(2011) Mobarak A. Mraheil et al.   NUCLEIC ACIDS RESEARCH

A simple and efficient method to search for selected primary transcripts: non-coding and antisense RNAs in the human pathogen Enterococcus faecalis

(2011) Aymeric Fouquier d’Hérouel et al.   NUCLEIC ACIDS RESEARCH

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

Genome-Wide Identification of Small RNAs in the Opportunistic Pathogen Enterococcus faecalis V583

(2011) Kouki Shioya et al.   PLoS One

Assessing computational tools for the discovery of small RNA genes in bacteria

(2011) X. Lu et al.   RNA

Sequence Conservation and Functional Constraint on Intergenic Spacers in Reduced Genomes of the Obligate Symbiont Buchnera

(2011) Patrick H. Degnan et al.   PLoS Genetics

A Genome-Wide Approach to Discovery of Small RNAs Involved in Regulation of Virulence in Vibrio cholerae

(2011) Evan S. Bradley et al.   PLoS Pathogens

Finding sRNA generative locales from high-throughput sequencing data with NiBLS

(2010) Daniel MacLean et al.   BMC 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

Translational Regulation of Gene Expression by an Anaerobically Induced Small Non-coding RNA in Escherichia coli

(2010) Anders Boysen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification of differentially expressed small non-protein-coding RNAs in Staphylococcus aureus displaying both the normal and the small-colony variant phenotype

(2010) Luay F. Abu-Qatouseh et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism

(2010) Chantal Bohn et al.   NUCLEIC ACIDS RESEARCH

Experimental identification and characterization of 97 novel npcRNA candidates in Salmonella enterica serovar Typhi

(2010) Suresh V. Chinni et al.   NUCLEIC ACIDS RESEARCH

Multiple small RNAs identified in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis

(2010) J. M. DiChiara et al.   NUCLEIC ACIDS RESEARCH

Identification of regulatory RNAs in Bacillus subtilis

(2010) Irnov Irnov et al.   NUCLEIC ACIDS RESEARCH

Cartography of Methicillin-Resistant S. aureus Transcripts: Detection, Orientation and Temporal Expression during Growth Phase and Stress Conditions

(2010) Marie Beaume et al.   PLoS One

Computational prediction of sRNAs and their targets in bacteria

(2010) Rolf Backofen et al.   RNA Biology

Bacterial Small RNA Regulators: Versatile Roles and Rapidly Evolving Variations

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

Biocomputational prediction of non-coding RNAs in model cyanobacteria

(2009) Björn Voß et al.   BMC GENOMICS

Regulatory RNAs in Bacteria

(2009) Lauren S. Waters et al.   CELL

Identification of Small Noncoding RNAs in Helicobacter pylori by a Bioinformatics-Based Approach

(2009) Bin Xiao et al.   CURRENT MICROBIOLOGY

Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles

(2009) A. Marchais et al.   GENOME RESEARCH

Whole-Genome Tiling Array Analysis of Mycobacterium leprae RNA Reveals High Expression of Pseudogenes and Noncoding Regions

(2009) T. Akama et al.   JOURNAL OF BACTERIOLOGY

The transcriptionally active regions in the genome ofBacillus subtilis

(2009) Simon Rasmussen et al.   MOLECULAR MICROBIOLOGY

The Listeria transcriptional landscape from saprophytism to virulence

(2009) Alejandro Toledo-Arana et al.   NATURE

The comprehensive microbial resource

(2009) Tanja Davidsen et al.   NUCLEIC ACIDS RESEARCH

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome

(2009) Marco Albrecht et al.   NUCLEIC ACIDS RESEARCH

A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation

(2009) Thomas Geissmann et al.   NUCLEIC ACIDS RESEARCH

Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing

(2009) Jane M. Liu et al.   NUCLEIC ACIDS RESEARCH

A Genome-Wide Analysis of Small Regulatory RNAs in the Human Pathogen Group A Streptococcus

(2009) Nataly Perez et al.   PLoS One

Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level

(2009) Kai Papenfort et al.   RESEARCH IN MICROBIOLOGY

Novel small RNA-encoding genes in the intergenic regions of Bacillus subtilis

(2008) Shinichi Saito et al.   GENE

Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools

(2008) E. Sonnleitner et al.   MICROBIOLOGY-SGM

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

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

(2008) Alexandra Sittka et al.   PLoS Genetics