Comprehensive transcriptome and improved genome annotation ofBacillus licheniformisWX-02

Deletion of meso-2,3-butanediol dehydrogenase gene budC for enhanced D-2,3-butanediol production in Bacillus licheniformis

(2014) Gaofu Qi et al.   Biotechnology for Biofuels

RNA-Seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentation

(2013) Sandra Wiegand et al.   BMC GENOMICS

Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling

(2013) Shan Li et al.   BMC GENOMICS

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data

(2013) S. Li et al.   GENOME RESEARCH

Stress Responses of the Industrial Workhorse Bacillus licheniformis to Osmotic Challenges

(2013) Rebecca Schroeter et al.   PLoS One

Genome Sequence of Bacillus licheniformis WX-02

(2012) W. Yangtse et al.   JOURNAL OF BACTERIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

RNA-Seq Based Transcriptional Map of Bovine Respiratory Disease Pathogen “Histophilus somni 2336”

(2012) Ranjit Kumar et al.   PLoS One

Strand-Specific RNA-Seq Reveals Ordered Patterns of Sense and Antisense Transcription in Bacillus anthracis

(2012) Karla D. Passalacqua et al.   PLoS One

Local and global factors affecting RNA sequencing analysis

(2011) Edward Sendler et al.   ANALYTICAL BIOCHEMISTRY

A tissue-specific landscape of sense/antisense transcription in the mouse intestine

(2011) Ulrich C Klostermeier et al.   BMC GENOMICS

Proline Utilization by Bacillus subtilis: Uptake and Catabolism

(2011) S. Moses et al.   JOURNAL OF BACTERIOLOGY

Systematic bias in high-throughput sequencing data and its correction by BEADS

(2011) Ming-Sin Cheung et al.   NUCLEIC ACIDS RESEARCH

Genome-wide antisense transcription drives mRNA processing in bacteria

(2011) I. Lasa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq

(2010) Zhengpeng Wu et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Transcriptome Analysis of Pseudomonas syringae Identifies New Genes, Noncoding RNAs, and Antisense Activity

(2010) M. J. Filiatrault et al.   JOURNAL OF BACTERIOLOGY

The Prevalence and Regulation of Antisense Transcripts in Schizosaccharomyces pombe

(2010) Ting Ni et al.   PLoS One

Efficient production of acetoin by the newly isolated Bacillus licheniformis strain MEL09

(2010) Yongfeng Liu et al.   PROCESS BIOCHEMISTRY

Modeling non-uniformity in short-read rates in RNA-Seq data

(2010) Jun Li et al.   GENOME BIOLOGY

Isolation of Halotolerant Bacillus licheniformis WX-02 and Regulatory Effects of Sodium Chloride on Yield and Molecular Sizes of Poly-γ-Glutamic Acid

(2009) Xuetuan Wei et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

A Comprehensive Proteomics and Transcriptomics Analysis of Bacillus subtilis Salt Stress Adaptation

(2009) H. Hahne et al.   JOURNAL OF BACTERIOLOGY

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

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi

(2009) Timothy T. Perkins et al.   PLoS Genetics

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

DOOR: a database for prokaryotic operons

(2008) Fenglou Mao et al.   NUCLEIC ACIDS RESEARCH

OperonDB: a comprehensive database of predicted operons in microbial genomes

(2008) M. Pertea et al.   NUCLEIC ACIDS RESEARCH