RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study

Two regulatory RNA elements affect TisB-dependent depolarization and persister formation

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Identifying stably expressed genes from multiple RNA-Seq data sets

(2016) Bin Zhuo et al.   PeerJ

Analysis of the TGFβ-induced program in primary airway epithelial cells shows essential role of NF-κB/RelA signaling network in type II epithelial mesenchymal transition

(2015) Bing Tian et al.   BMC GENOMICS

limma powers differential expression analyses for RNA-sequencing and microarray studies

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RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella Typhimurium

(2015) Shabarinath Srikumar et al.   PLoS Pathogens

Akt-Dependent Metabolic Reprogramming Regulates Tumor Cell Histone Acetylation

(2014) Joyce V. Lee et al.   Cell Metabolism

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts

(2014) Marc P. Hoeppner et al.   PLoS One

An Infection-Relevant Transcriptomic Compendium for Salmonella enterica Serovar Typhimurium

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Global changes in gene expression by the opportunistic pathogen Burkholderia cenocepacia in response to internalization by murine macrophages

(2012) Jennifer S Tolman et al.   BMC GENOMICS

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

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Revisiting Global Gene Expression Analysis

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Transcriptional Amplification in Tumor Cells with Elevated c-Myc

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Persister-promoting bacterial toxin TisB produces anion-selective pores in planar lipid bilayers

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RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more

(2012) Heladia Salgado et al.   NUCLEIC ACIDS RESEARCH

Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR

(2011) Kang Zhou et al.   BMC MOLECULAR BIOLOGY

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Genome-wide synteny through highly sensitive sequence alignment: Satsuma

(2010) M. G. Grabherr et al.   BIOINFORMATICS

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

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Ciprofloxacin Causes Persister Formation by Inducing the TisB toxin in Escherichia coli

(2010) Tobias Dörr et al.   PLOS BIOLOGY

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

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

Data-driven normalization strategies for high-throughput quantitative RT-PCR

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Construction of a functional network for common DNA damage responses in Escherichia coli

(2009) Jungeui Hong et al.   GENOMICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

SOS Response Induces Persistence to Fluoroquinolones in Escherichia coli

(2009) Tobias Dörr et al.   PLoS Genetics

A small SOS-induced toxin is targeted against the inner membrane in Escherichia coli

(2008) Cecilia Unoson et al.   MOLECULAR MICROBIOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS