Microarrays, deep sequencing and the true measure of the transcriptome

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

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays

(2010) Ashish Agarwal et al.   BMC GENOMICS

A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling

(2010) James R Bradford et al.   BMC GENOMICS

Statistical Design and Analysis of RNA Sequencing Data

(2010) P. L. Auer et al.   GENETICS

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

(2010)   NATURE BIOTECHNOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments

(2010) Hugues Richard et al.   NUCLEIC ACIDS RESEARCH

Biases in Illumina transcriptome sequencing caused by random hexamer priming

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

Consistency of predictive signature genes and classifiers generated using different microarray platforms

(2010) X Fan et al.   PHARMACOGENOMICS JOURNAL

A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data

(2010) J Luo et al.   PHARMACOGENOMICS JOURNAL

The missing graphical user interface for genomics

(2010) Michael C Schatz   GENOME BIOLOGY

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

(2010) Jun Li et al.   GENOME BIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays

(2009) Joshua S Bloom et al.   BMC GENOMICS

Estimating accuracy of RNA-Seq and microarrays with proteomics

(2009) Xing Fu et al.   BMC GENOMICS

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Next-Generation DNA Sequencing Methods

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

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

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

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

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