mRNA enrichment protocols determine the quantification characteristics of external RNA spike-in controls in RNA-Seq studies

Sources of variation in false discovery rate estimation include sample size, correlation, and inherent differences between groups

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Characterization of in vitro transcription amplification linearity and variability in the low copy number regime using External RNA Control Consortium (ERCC) spike-ins

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Next-generation sequencing in the clinic: Promises and challenges

(2012) Jiekun Xuan et al.   CANCER LETTERS

Revisiting Global Gene Expression Analysis

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Scale integration: the structure and dynamics of macromolecular assemblies, cells and tissues

(2012) Jason Swedlow et al.   CURRENT OPINION IN CELL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing

(2012) Justin M. Zook et al.   PLoS One

Bias detection and correction in RNA-Sequencing data

(2011) Wei Zheng et al.   BMC BIOINFORMATICS

Evaluation of external RNA controls for the standardisation of gene expression biomarker measurements

(2011) Alison S Devonshire et al.   BMC GENOMICS

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Synthetic spike-in standards for RNA-seq experiments

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

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BEDTools: a flexible suite of utilities for comparing genomic features

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The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

(2010)   NATURE BIOTECHNOLOGY

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

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

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