Comparative studies of differential gene calling using RNA-Seq data

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

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

Identifying differentially expressed transcripts from RNA-seq data with biological variation

(2012) Peter Glaus et al.   BIOINFORMATICS

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

(2012) Cole Trapnell et al.   Nature Protocols

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

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

RNA-seq: technical variability and sampling

(2011) Lauren M McIntyre et al.   BMC GENOMICS

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Empirical bayes analysis of sequencing-based transcriptional profiling without replicates

(2010) Zhijin Wu et al.   BMC 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

Statistical Design and Analysis of RNA Sequencing Data

(2010) P. L. Auer et al.   GENETICS

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

Modeling non-uniformity in short-read rates in RNA-Seq data

(2010) Jun Li et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li 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

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

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

(2008) M. Sultan et al.   SCIENCE

Posterior Error Probabilities and False Discovery Rates: Two Sides of the Same Coin

(2007) Lukas Käll et al.   JOURNAL OF PROTEOME RESEARCH