A semi-parametric statistical model for integrating gene expression profiles across different platforms

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets

(2013) Xiao Xu et al.   BMC BIOINFORMATICS

Towards the integration, annotation and association of historical microarray experiments with RNA-seq

(2013) Shweta S Chavan et al.   BMC BIOINFORMATICS

A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data

(2012) Vanessa M. Kvam et al.   AMERICAN JOURNAL OF BOTANY

Removing technical variability in RNA-seq data using conditional quantile normalization

(2012) K. D. Hansen et al.   BIOSTATISTICS

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

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

(2012) Intawat Nookaew et al.   NUCLEIC ACIDS RESEARCH

A Powerful Method for Transcriptional Profiling of Specific Cell Types in Eukaryotes: Laser-Assisted Microdissection and RNA Sequencing

(2012) Marc W. Schmid et al.   PLoS One

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

AnyExpress: Integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm

(2011) Jihoon Kim et al.   BMC BIOINFORMATICS

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Detection and Removal of Biases in the Analysis of Next-Generation Sequencing Reads

(2011) Schraga Schwartz et al.   PLoS One

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

MicroRNA profiling: separating signal from noise

(2010) Monya Baker   NATURE METHODS

A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species

(2010) Song Liu et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

A-MADMAN: Annotation-based microarray data meta-analysis tool

(2009) Andrea Bisognin et al.   BMC BIOINFORMATICS

Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers

(2009) Jonathan M Dreyfuss et al.   Molecular Cancer

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

(2009) H. Willenbrock et al.   RNA

TiGER: a database for tissue-specific gene expression and regulation

(2008) Xiong Liu et al.   BMC BIOINFORMATICS

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

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

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS