Impact of Library Preparation on Downstream Analysis and Interpretation of RNA-Seq Data: Comparison between Illumina PolyA and NuGEN Ovation Protocol

Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues

(2012) Levi Waldron et al.   BMC CANCER

Characterizing the Impact of Smoking and Lung Cancer on the Airway Transcriptome Using RNA-Seq

(2011) J. Beane et al.   Cancer Prevention Research

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Whole-transcriptome RNAseq analysis from minute amount of total RNA

(2011) Muhammad A. Tariq et al.   NUCLEIC ACIDS RESEARCH

A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines

(2011) Yan W. Asmann et al.   NUCLEIC ACIDS RESEARCH

Integrated Analysis of Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells by Deep Sequencing

(2011) Zhifu Sun et al.   PLoS One

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors

(2010) Rodrigo Goya et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Optimization of whole-transcriptome amplification from low cell density deep-sea microbial samples for metatranscriptomic analysis

(2010) Jieying Wu et al.   JOURNAL OF MICROBIOLOGICAL METHODS

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

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

Methods comparison for high-resolution transcriptional analysis of archival material on Affymetrix Plus 2.0 and Exon 1.0 microarrays

(2009) Kim M. Linton et al.   BIOTECHNIQUES

Identification of methods for use of formalin-fixed, paraffin-embedded tissue samples in RNA expression profiling

(2009) Lisa Roberts et al.   GENOMICS

Mammary Involution and Breast Cancer Risk: Transgenic Models and Clinical Studies

(2009) Derek C. Radisky et al.   JOURNAL OF MAMMARY GLAND BIOLOGY AND NEOPLASIA

Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution

(2009) Sohrab P. Shah et al.   NATURE

Mutation ofFOXL2in Granulosa-Cell Tumors of the Ovary

(2009) Sohrab P. Shah et al.   NEW ENGLAND JOURNAL OF MEDICINE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS