RNA-Seq gene expression estimation with read mapping uncertainty

Maximum Likelihood from Incomplete Data Via the EM Algorithm

1977 • 46,601 citations

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

2009 • 20,860 citations

Mapping and quantifying mammalian transcriptomes by RNA-Seq

2008 • 12,817 citations

RNA-Seq: a revolutionary tool for transcriptomics

2008 • 11,957 citations

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

2008 • 2,741 citations

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

2008 • 2,448 citations

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

2008 • 2,354 citations

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

2008 • 1,081 citations

Stem cell transcriptome profiling via massive-scale mRNA sequencing

2008 • 1,026 citations

The UCSC Known Genes

2006 • 495 citations

Statistical inferences for isoform expression in RNA-Seq

2009 • 469 citations

Profiling the HeLa S3 Transcriptome using Randomly Primed cDNA and Massively Parallel Short-Read Sequencing

2008 • 411 citations

A strategy of DNA sequencing employing computer programs

1979 • 391 citations

Statistical modeling of sequencing errors in SAGE libraries

2004 • 107 citations

A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE

2008 • 99 citations

Exact Transcriptome Reconstruction from Short Sequence Reads

2008 • 56 citations

Cross-hybridization modeling on Affymetrix exon arrays

2008 • 39 citations