Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans

The EbpA-RpoN Regulatory Pathway of the Pathogen Leptospira interrogans Is Essential for Survival in the Environment

(2016) Wei-Lin Hu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

In vivoexpression technology and 5′ end mapping of theBorrelia burgdorferitranscriptome identify novel RNAs expressed during mammalian infection

(2016) Philip P. Adams et al.   NUCLEIC ACIDS RESEARCH

What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira

(2016) Derrick E. Fouts et al.   PLoS Neglected Tropical Diseases

Transcriptome Sequencing Reveals Wide Expression Reprogramming of Basal and Unknown Genes in Leptospira biflexa Biofilms

(2016) Gregorio Iraola et al.   mSphere

RNA-Seq of Borrelia burgdorferi in Multiple Phases of Growth Reveals Insights into the Dynamics of Gene Expression, Transcriptome Architecture, and Noncoding RNAs

(2016) William K. Arnold et al.   PLoS One

Control of Gene Expression in Leptospira spp. by Transcription Activator-Like Effectors Demonstrates a Potential Role for LigA and LigB in Leptospira interrogans Virulence

(2015) Christopher J. Pappas et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The global transcriptional landscape of Bacillus amyloliquefaciens XH7 and high-throughput screening of strong promoters based on RNA-seq data

(2015) Yuling Liao et al.   GENE

Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori

(2015) Thorsten Bischler et al.   METHODS

Global Morbidity and Mortality of Leptospirosis: A Systematic Review

(2015) Federico Costa et al.   PLoS Neglected Tropical Diseases

Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function

(2014) Quan Zeng et al.   BMC GENOMICS

RNA Sequencing and Proteogenomics Reveal the Importance of Leaderless mRNAs in the Radiation-Tolerant Bacterium Deinococcus deserti

(2014) Arjan de Groot et al.   Genome Biology and Evolution

Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity

(2014) Karsten Voigt et al.   ISME Journal

HemR is an OmpR/PhoB-like response regulator fromLeptospira, which simultaneously effects transcriptional activation and repression of key haem metabolism genes

(2014) Natalia R. Morero et al.   MOLECULAR MICROBIOLOGY

Rfam 12.0: updates to the RNA families database

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

A Model System for Studying the Transcriptomic and Physiological Changes Associated with Mammalian Host-Adaptation by Leptospira interrogans Serovar Copenhageni

(2014) Melissa J. Caimano et al.   PLoS Pathogens

Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021

(2013) Jan-Philip Schlüter et al.   BMC GENOMICS

AlienTrimmer: A tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads

(2013) Alexis Criscuolo et al.   GENOMICS

Role for cis-Acting RNA Sequences in the Temperature-Dependent Expression of the Multiadhesive Lig Proteins in Leptospira interrogans

(2013) J. Matsunaga et al.   JOURNAL OF BACTERIOLOGY

CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria

(2013) Sefa Kılıç et al.   NUCLEIC ACIDS RESEARCH

Computational analysis of bacterial RNA-Seq data

(2013) Ryan McClure et al.   NUCLEIC ACIDS RESEARCH

Genome-wide Mapping of Transcriptional Start Sites Defines an Extensive Leaderless Transcriptome in Mycobacterium tuberculosis

(2013) Teresa Cortes et al.   Cell Reports

High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates

(2013) Gaurav Dugar et al.   PLoS Genetics

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates

(2012) Mikhail Pachkov et al.   NUCLEIC ACIDS RESEARCH

MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

(2012) David Vallenet 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

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

(2012) Tobias Sahr et al.   RNA Biology

Whole Genome Analysis of Leptospira licerasiae Provides Insight into Leptospiral Evolution and Pathogenicity

(2012) Jessica N. Ricaldi et al.   PLoS Neglected Tropical Diseases

The Single-Nucleotide Resolution Transcriptome of Pseudomonas aeruginosa Grown in Body Temperature

(2012) Omri Wurtzel et al.   PLoS Pathogens

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Global discovery of small RNAs in Yersinia pseudotuberculosis identifies Yersinia-specific small, noncoding RNAs required for virulence

(2011) J. T. Koo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ARNold: A web tool for the prediction of Rho-independent transcription terminators

(2011) Magali Naville et al.   RNA Biology

Pathogenesis of leptospirosis: The influence of genomics

(2011) Ben Adler et al.   VETERINARY MICROBIOLOGY

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Global transcriptomic response of Leptospira interrogans serovar Copenhageni upon exposure to serum

(2010) Kanitha Patarakul et al.   BMC MICROBIOLOGY

Transcriptional Response of Leptospira interrogans to Iron Limitation and Characterization of a PerR Homolog

(2010) M. Lo et al.   INFECTION AND IMMUNITY

Transcriptional Responses of Leptospira interrogans to Host Innate Immunity: Significant Changes in Metabolism, Oxygen Tolerance, and Outer Membrane

(2010) Feng Xue et al.   PLoS Neglected Tropical Diseases

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A single-base resolution map of an archaeal transcriptome

(2009) O. Wurtzel et al.   GENOME RESEARCH

Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans

(2009) Johan Malmström et al.   NATURE

Leptospira: the dawn of the molecular genetics era for an emerging zoonotic pathogen

(2009) Albert I. Ko et al.   NATURE REVIEWS MICROBIOLOGY

MEME SUITE: tools for motif discovery and searching

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

MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes

(2008) H. Noguchi et al.   DNA RESEARCH