Genome-Wide Identification of Regulatory RNAs in the Human Pathogen Clostridium difficile

Acting antisense: plasmid- and chromosome-encoded sRNAs from Gram-positive bacteria

(2012) Sabine Brantl   Future Microbiology

CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome

(2012) A. Stern et al.   GENOME RESEARCH

A metagenomic insight into our gut's microbiome

(2012) Patricia Lepage et al.   GUT

Cyclic Diguanylate Inversely Regulates Motility and Aggregation in Clostridium difficile

(2012) E. B. Purcell et al.   JOURNAL OF BACTERIOLOGY

Multiple Factors Modulate Biofilm Formation by the Anaerobic Pathogen Clostridium difficile

(2012) T. Thapa et al.   JOURNAL OF BACTERIOLOGY

Essential Features and Rational Design of CRISPR RNAs that Function with the Cas RAMP Module Complex to Cleave RNAs

(2012) Caryn R. Hale et al.   MOLECULAR CELL

Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis

(2012) Hagen Richter et al.   NUCLEIC ACIDS RESEARCH

SR1—a small RNA with two remarkably conserved functions

(2012) Matthias Gimpel et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Ina Wilms et al.   RNA Biology

Deep sequencing defines the transcriptional map ofL. pneumophilaand identifies growth phase-dependent regulated ncRNAs implicated in virulence

(2012) Tobias Sahr 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

Memory of viral infections by CRISPR-Cas adaptive immune systems: Acquisition of new information

(2012) Peter C. Fineran et al.   VIROLOGY

CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation

(2011) Devaki Bhaya et al.   Annual Review of Genetics

Genetic evidence for involvement of the alternative sigma factor SigI in controlling expression of the cell wall hydrolase gene lytE and contribution of LytE to heat survival of Bacillus subtilis

(2011) Chi-Ling Tseng et al.   ARCHIVES OF MICROBIOLOGY

An expanding universe of small proteins

(2011) Errett C Hobbs et al.   CURRENT OPINION IN MICROBIOLOGY

Cyclic di-GMP, an established secondary messenger still speeding up

(2011) Ute Römling   ENVIRONMENTAL MICROBIOLOGY

The Key Sigma Factor of Transition Phase, SigH, Controls Sporulation, Metabolism, and Virulence Factor Expression in Clostridium difficile

(2011) L. Saujet et al.   JOURNAL OF BACTERIOLOGY

Clostridium difficileHas Two Parallel and Essential Sec Secretion Systems

(2011) Robert P. Fagan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Reannotation of the genome sequence of Clostridium difficile strain 630

(2011) M. Monot et al.   JOURNAL OF MEDICAL MICROBIOLOGY

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

(2011) Elitza Deltcheva et al.   NATURE

Hfq and its constellation of RNA

(2011) Jörg Vogel et al.   NATURE REVIEWS MICROBIOLOGY

Evolution and classification of the CRISPR–Cas systems

(2011) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

RNApredator: fast accessibility-based prediction of sRNA targets

(2011) Florian Eggenhofer 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

Deep sequencing-based identification of small non-coding RNAs inStreptomyces coelicolor

(2011) Michael-Paul Vockenhuber et al.   RNA Biology

Mechanism for gene control by a natural allosteric group I ribozyme

(2011) A. G. Y. Chen et al.   RNA

Small RNAs in the Genus Clostridium

(2011) Y. Chen et al.   mBio

c-di-GMP Turn-Over in Clostridium difficile Is Controlled by a Plethora of Diguanylate Cyclases and Phosphodiesterases

(2011) Eric Bordeleau et al.   PLoS Genetics

Evaluation of candidate reference genes in Clostridium difficile for gene expression normalization

(2010) Devon Metcalf et al.   ANAEROBE

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

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

Regulatory RNA in Bacterial Pathogens

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

Studying bacterial transcriptomes using RNA-seq

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

Virulence factor p60 ofListeria monocytogenesmodulates innate immunity by inducing tumor necrosis factor α

(2010) Hiroshi Sashinami et al.   FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY

Integration of Metabolism and Virulence by Clostridium difficile CodY

(2010) S. S. Dineen et al.   JOURNAL OF BACTERIOLOGY

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

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

Stabilization of Clostridium perfringens collagenase mRNA by VR-RNA-dependent cleavage in 5′ leader sequence

(2010) Nozomu Obana et al.   MOLECULAR MICROBIOLOGY

Transcription, processing and function of CRISPR cassettes in Escherichia coli

(2010) Ksenia Pougach et al.   MOLECULAR MICROBIOLOGY

RNAs: regulators of bacterial virulence

(2010) Jonas Gripenland et al.   NATURE REVIEWS MICROBIOLOGY

Freiburg RNA Tools: a web server integrating INTARNA, EXPARNA and LOCARNA

(2010) C. Smith et al.   NUCLEIC ACIDS RESEARCH

An Allosteric Self-Splicing Ribozyme Triggered by a Bacterial Second Messenger

(2010) E. R. Lee et al.   SCIENCE

Cyclic-di-GMP Reaches Out into the Bacterial RNA World

(2010) R. Hengge   Science Signaling

Comparative genome-wide analysis of small RNAs of major Gram-positive pathogens: from identification to application

(2010) Mobarak A. Mraheil et al.   Microbial Biotechnology

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Regulatory RNAs in Bacteria

(2009) Lauren S. Waters et al.   CELL

An overview of RNAs with regulatory functions in gram-positive bacteria

(2009) Pascale Romby et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Activation of gene expression by small RNA

(2009) Kathrin S. Fröhlich et al.   CURRENT OPINION IN MICROBIOLOGY

RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis

(2009) Karen Shahbabian et al.   EMBO JOURNAL

The T box mechanism: tRNA as a regulatory molecule

(2009) Nicholas J. Green et al.   FEBS LETTERS

A single-base resolution map of an archaeal transcriptome

(2009) O. Wurtzel et al.   GENOME RESEARCH

New trends in Clostridium difficile virulence and pathogenesis

(2009) C. Denève et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Characterization of the Sporulation Initiation Pathway of Clostridium difficile and Its Role in Toxin Production

(2009) S. Underwood et al.   JOURNAL OF BACTERIOLOGY

Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity

(2009) Rotem Sorek et al.   NATURE REVIEWS GENETICS

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

(2009) Thomas Geissmann et al.   NUCLEIC ACIDS RESEARCH

Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium

(2009) Richard A Stabler et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Clostridium difficile toxin synthesis is negatively regulated by TcdC

(2008) B. Dupuy et al.   JOURNAL OF MEDICAL MICROBIOLOGY

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

Rfam: updates to the RNA families database

(2008) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

High-Throughput, Kingdom-Wide Prediction and Annotation of Bacterial Non-Coding RNAs

(2008) Jonathan Livny et al.   PLoS One

Comparative genomic analysis of T-box regulatory systems in bacteria

(2008) A. G. Vitreschak et al.   RNA

Riboswitches in Eubacteria Sense the Second Messenger Cyclic Di-GMP

(2008) N. Sudarsan et al.   SCIENCE

CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea

(2007) Rotem Sorek et al.   NATURE REVIEWS MICROBIOLOGY