Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis

FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions

(2014) Alberto Gatto et al.   NUCLEIC ACIDS RESEARCH

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Benchmarking short sequence mapping tools

(2013) Ayat Hatem et al.   BMC BIOINFORMATICS

Comparison of software packages for detecting differential expression in RNA-seq studies

(2013) F. Seyednasrollah et al.   BRIEFINGS IN BIOINFORMATICS

Paul Bertone

(2013) Vivien Marx   NATURE METHODS

Genomics: the state of the art in RNA-seq analysis

(2013) Ian Korf   NATURE METHODS

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

SeqEntropy: Genome-Wide Assessment of Repeats for Short Read Sequencing

(2013) Hsueh-Ting Chu et al.   PLoS One

RNA-Seq: revelation of the messengers

(2013) Marcel C. Van Verk et al.   TRENDS IN PLANT SCIENCE

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

(2013) Franck Rapaport et al.   GENOME BIOLOGY

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 new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data

(2012) H. Wu et al.   BIOSTATISTICS

Technical and biological variance structure in mRNA-Seq data: life in the real world

(2012) Ann L Oberg et al.   BMC GENOMICS

Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing

(2012) José A Robles et al.   BMC GENOMICS

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

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

Revisiting Global Gene Expression Analysis

(2012) Jakob Lovén et al.   CELL

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

(2012) Zhiyu Peng et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Modelling and simulating generic RNA-Seq experiments with the flux simulator

(2012) Thasso Griebel et al.   NUCLEIC ACIDS RESEARCH

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Estimation of alternative splicing isoform frequencies from RNA-Seq data

(2011) Marius Nicolae et al.   Algorithms for Molecular Biology

Comparative studies of de novo assembly tools for next-generation sequencing technologies

(2011) Yong Lin et al.   BIOINFORMATICS

Length bias correction for RNA-seq data in gene set analyses

(2011) Liyan Gao et al.   BIOINFORMATICS

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)

(2011) Gregory R. Grant et al.   BIOINFORMATICS

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

BM-Map: Bayesian Mapping of Multireads for Next-Generation Sequencing Data

(2011) Yuan Ji et al.   BIOMETRICS

Normalization, testing, and false discovery rate estimation for RNA-sequencing data

(2011) J. Li et al.   BIOSTATISTICS

Bias detection and correction in RNA-Sequencing data

(2011) Wei Zheng et al.   BMC BIOINFORMATICS

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data

(2011) F. Finotello et al.   BRIEFINGS IN BIOINFORMATICS

A comparison of analog and Next-Generation transcriptomic tools for mammalian studies

(2011) N. C. Roy et al.   Briefings in Functional Genomics

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing

(2011) J. H. Bahn et al.   GENOME RESEARCH

Sequencing technology does not eliminate biological variability

(2011) Kasper D Hansen et al.   NATURE BIOTECHNOLOGY

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data

(2011) Jun Li et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads

(2011) Ernest Turro et al.   GENOME BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

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

(2010) James H Bullard et al.   BMC BIOINFORMATICS

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

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

De Novo Transcriptome Sequencing in Anopheles funestus Using Illumina RNA-Seq Technology

(2010) Jacob E. Crawford et al.   PLoS One

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

Statistical inferences for isoform expression in RNA-Seq

(2009) Hui Jiang et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

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

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

Cancer genome sequencing: a review

(2009) E. R. Mardis et al.   HUMAN MOLECULAR GENETICS

Sense from sequence reads: methods for alignment and assembly

(2009) Paul Flicek et al.   NATURE METHODS

Compressed indexing and local alignment of DNA

(2008) T. W. Lam et al.   BIOINFORMATICS

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

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

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing

(2008) J. CRISTOBAL VERA et al.   MOLECULAR ECOLOGY

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

The beginning of the end for microarrays?

(2008) Jay Shendure   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

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE