Review Application of RNA-seq to reveal the transcript profile in bacteria

A pipeline for RNA-seq data processing and quality assessment

(2011) Angela Goncalves et al.   BIOINFORMATICS

Identification, variation and transcription of pneumococcal repeat sequences

(2011) Nicholas J Croucher et al.   BMC GENOMICS

Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae

(2011) Vincent M Isabella et al.   BMC GENOMICS

Orientation and expression of methicillin-resistant Staphylococcus aureus small RNAs by direct multiplexed measurements using the nCounter of NanoString technology

(2011) Marie Beaume et al.   JOURNAL OF MICROBIOLOGICAL METHODS

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Bacillus anthracis genome organization in light of whole transcriptome sequencing

(2010) Jeffrey Martin et al.   BMC BIOINFORMATICS

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

(2010) James H Bullard 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 primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays

(2010) Roland J. Siezen et al.   Microbial Biotechnology

Molecular Mechanisms of Ethanol-Induced Pathogenesis Revealed by RNA-Sequencing

(2010) Laura Camarena et al.   PLoS Pathogens

Cloud-scale RNA-sequencing differential expression analysis with Myrna

(2010) Ben Langmead et al.   GENOME BIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing

(2009) Nathan L. Clement et al.   BIOINFORMATICS

PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds

(2009) Yangho Chen et al.   BIOINFORMATICS

CloudBurst: highly sensitive read mapping with MapReduce

(2009) M. C. Schatz   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing

(2009) Shrinivasrao P Mane et al.   BMC GENOMICS

Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs

(2009) Haley F Oliver et al.   BMC GENOMICS

Next generation sequencing of microbial transcriptomes: challenges and opportunities

(2009) Arnoud H.M. van Vliet   FEMS MICROBIOLOGY LETTERS

RazerS--fast read mapping with sensitivity control

(2009) D. Weese et al.   GENOME RESEARCH

Structure and Complexity of a Bacterial Transcriptome

(2009) K. D. Passalacqua et al.   JOURNAL OF BACTERIOLOGY

Network-assisted protein identification and data interpretation in shotgun proteomics

(2009) Jing Li et al.   Molecular Systems Biology

The Listeria transcriptional landscape from saprophytism to virulence

(2009) Alejandro Toledo-Arana et al.   NATURE

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

(2009) Rotem Sorek et al.   NATURE REVIEWS GENETICS

Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity

(2009) Nicolas Philippe et al.   NUCLEIC ACIDS RESEARCH

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome

(2009) Marco Albrecht et al.   NUCLEIC ACIDS RESEARCH

BFAST: An Alignment Tool for Large Scale Genome Resequencing

(2009) Nils Homer et al.   PLoS One

Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing

(2009) D. R. Yoder-Himes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome Complexity in a Genome-Reduced Bacterium

(2009) M. Guell et al.   SCIENCE

Perspectives of DNA microarray and next-generation DNA sequencing technologies

(2009) XiaoKun Teng et al.   Science in China. Series C, Life sciences / Chinese Academy of Sciences

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

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

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

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

Gene expression changes linked to antimicrobial resistance, oxidative stress, iron depletion and retained motility are observed when Burkholderia cenocepaciagrows in cystic fibrosis sputum

(2008) Pavel Drevinek et al.   BMC INFECTIOUS DISEASES

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Applications of next-generation sequencing technologies in functional genomics

(2008) Olena Morozova et al.   GENOMICS

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE