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(2011) Manuel Garber et al.   NATURE METHODS

Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarrays

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From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples

(2010) Zhining Wen 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

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mRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain

(2010) P. Hammer et al.   GENOME RESEARCH

Conservation of an RNA regulatory map between Drosophila and mammals

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Alternative expression analysis by RNA sequencing

(2010) Malachi Griffith et al.   NATURE METHODS

Tumor Transcriptome Sequencing Reveals Allelic Expression Imbalances Associated with Copy Number Alterations

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How to Understand the Cell by Breaking It: Network Analysis of Gene Perturbation Screens

(2010) Florian Markowetz   PLoS Computational Biology

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

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Differential expression analysis for sequence count data

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DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

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

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(2009) Shirley Pepke et al.   NATURE METHODS

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(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

Cross-platform comparison of SYBR Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC) study

(2008) Emi Arikawa et al.   BMC GENOMICS

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

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

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