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

Statistical Design and Analysis of RNA Sequencing Data

(2010) P. L. Auer et al.   GENETICS

Strand-specific deep sequencing of the transcriptome

(2010) A. P. Vivancos et al.   GENOME RESEARCH

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

(2010) P. Hammer et al.   GENOME RESEARCH

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Amplification-free digital gene expression profiling from minute cell quantities

(2010) Fatih Ozsolak et al.   NATURE METHODS

Next-generation sequencing: adjusting to data overload

(2010) Monya Baker   NATURE METHODS

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

(2010) Brian B. Tuch et al.   PLoS One

Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression

(2010) A. Git et al.   RNA

Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq

(2010) Augix Guohua Xu et al.   PLoS Computational Biology

The case for cloud computing in genome informatics

(2010) Lincoln D Stein   GENOME BIOLOGY

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

The History of the Cluster Heat Map

(2009) Leland Wilkinson et al.   AMERICAN STATISTICIAN

Applications of New Sequencing Technologies for Transcriptome Analysis

(2009) Olena Morozova et al.   Annual Review of Genomics and Human Genetics

Statistical methods of background correction for Illumina BeadArray data

(2009) Yang Xie 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

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer

(2009) Yan W Asmann et al.   BMC GENOMICS

The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments

(2009) S. A. Bustin et al.   CLINICAL CHEMISTRY

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Terminal differentiation of goat mammary tissue during pregnancy requires the expression of genes involved in immune functions

(2009) F. Faucon et al.   PHYSIOLOGICAL GENOMICS

A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds

(2009) James W. Kijas et al.   PLoS One

Development and Characterization of a High Density SNP Genotyping Assay for Cattle

(2009) Lakshmi K. Matukumalli et al.   PLoS One

Quantitative miRNA expression analysis: Comparing microarrays with next-generation sequencing

(2009) H. Willenbrock et al.   RNA

Assessment of the immune capacity of mammary epithelial cells: comparison with mammary tissue after challenge withEscherichia coli

(2009) Juliane Günther et al.   VETERINARY RESEARCH

Evaluation of next generation sequencing platforms for population targeted sequencing studies

(2009) Olivier Harismendy et al.   GENOME BIOLOGY

Cross-hybridization modeling on Affymetrix exon arrays

(2008) Karen Kapur et al.   BIOINFORMATICS

arrayQualityMetrics—a bioconductor package for quality assessment of microarray data

(2008) Audrey Kauffmann et al.   BIOINFORMATICS

lumi: a pipeline for processing Illumina microarray

(2008) P. Du et al.   BIOINFORMATICS

Probe signal correction for differential methylation hybridization experiments

(2008) Dustin P Potter et al.   BMC BIOINFORMATICS

Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays

(2008) Katerina Kechris et al.   BMC GENOMICS

PPARalpha-mediated effects of dietary lipids on intestinal barrier gene expression

(2008) Heleen M de Vogel-van den Bosch et al.   BMC GENOMICS

NuGO contributions to GenePattern

(2008) P. J. De Groot et al.   Genes and Nutrition

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

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

Extent of Linkage Disequilibrium in Holstein Cattle in North America

(2008) M. Sargolzaei et al.   JOURNAL OF DAIRY SCIENCE

Genome-Wide Analysis of Dietary Eicosapentaenoic Acid- and Oleic Acid-Induced Modulation of Colon Inflammation in Interleukin-10 Gene-Deficient Mice

(2008) Bianca Knoch et al.   Journal of Nutrigenetics and Nutrigenomics

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Digging deep with RNA-Seq

(2008) Louisa Flintoft   NATURE REVIEWS GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Effect of Synthetic Dietary Triglycerides: A Novel Research Paradigm for Nutrigenomics

(2008) Linda M. Sanderson et al.   PLoS One

In vivo gene expression in granulosa cells during pig terminal follicular development

(2008) A Bonnet et al.   REPRODUCTION

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

The impact of next-generation sequencing technology on genetics

(2008) Elaine R. Mardis   TRENDS IN GENETICS