Comparative Analysis of Lactobacillus plantarum WCFS1 Transcriptomes by Using DNA Microarray and Next-Generation Sequencing Technologies

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Transcript amplification from single bacterium for transcriptome analysis

(2011) Y. Kang et al.   GENOME RESEARCH

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays

(2010) Ashish Agarwal et al.   BMC GENOMICS

Identification of Genetic Loci in Lactobacillus plantarum That Modulate the Immune Response of Dendritic Cells Using Comparative Genome Hybridization

(2010) Marjolein Meijerink et al.   PLoS One

Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays

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

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Applications of New Sequencing Technologies for Transcriptome Analysis

(2009) Olena Morozova et al.   Annual Review of Genomics and Human Genetics

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays

(2009) Joshua S Bloom et al.   BMC GENOMICS

Next generation sequencing of microbial transcriptomes: challenges and opportunities

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

A single-base resolution map of an archaeal transcriptome

(2009) O. Wurtzel et al.   GENOME RESEARCH

Structure and Complexity of a Bacterial Transcriptome

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

A perspective: Metatranscriptomics as a tool for the discovery of novel biocatalysts

(2009) Falk Warnecke et al.   JOURNAL OF BIOTECHNOLOGY

RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing

(2009) Brian T. Wilhelm et al.   METHODS

 54-mediated control of the mannose phosphotransferase sytem in Lactobacillus plantarum impacts on carbohydrate metabolism

(2009) M. J. A. Stevens et al.   MICROBIOLOGY-SGM

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

(2009) Rotem Sorek et al.   NATURE REVIEWS GENETICS

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

Quantitative miRNA expression analysis: Comparing microarrays with next-generation sequencing

(2009) H. Willenbrock et al.   RNA

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

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

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

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

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

(2008) Peter A. C. 't Hoen et al.   NUCLEIC ACIDS RESEARCH

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

(2008) M. Sultan et al.   SCIENCE