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

The Sequence Alignment/Map format and SAMtools

2009 • 54,537 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

TopHat: discovering splice junctions with RNA-Seq

2009 • 11,483 citations

Alternative isoform regulation in human tissue transcriptomes

2008 • 4,870 citations

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

2009 • 3,955 citations

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

2007 • 2,764 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

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

2003 • 1,841 citations

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

2010 • 1,656 citations

miR-145 and miR-143 regulate smooth muscle cell fate and plasticity

2009 • 1,519 citations

RNA-Seq gene expression estimation with read mapping uncertainty

2009 • 1,135 citations

A Decomposition Theorem for Partially Ordered Sets

2009 • 1,039 citations

Stem cell transcriptome profiling via massive-scale mRNA sequencing

2008 • 1,026 citations

A Decomposition Theorem for Partially Ordered Sets

1950 • 948 citations

Transcriptome sequencing to detect gene fusions in cancer

2009 • 888 citations

The circuitry of a master switch: Myod and the regulation of skeletal muscle gene transcription

2005 • 722 citations

Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements

2007 • 636 citations

Computation for ChIP-seq and RNA-seq studies

2009 • 556 citations

Jensen-Shannon divergence and Hilbert space embedding

2004 • 520 citations

Statistical inferences for isoform expression in RNA-Seq

2009 • 469 citations

Skeletal muscle determination and differentiation: story of a core regulatory network and its context

1996 • 372 citations

A Myogenic Cell Line with Altered Serum Requirements for Differentiation

1977 • 305 citations

Modelling and simulating generic RNA-Seq experiments with the flux simulator

2012 • 285 citations

Annotating genomes with massive-scale RNA sequencing

2008 • 238 citations

Viral Population Estimation Using Pyrosequencing

2008 • 225 citations

Transcriptional and posttranscriptional control of c-myc during myogenesis: its mRNA remains inducible in differentiated cells and does not suppress the differentiated phenotype.

1986 • 157 citations

Identifiability of isoform deconvolution from junction arrays and RNA-Seq

2009 • 64 citations

FHL3 binds MyoD and negatively regulates myotube formation

2007 • 51 citations

Transcriptional and Posttranscriptional Control of c-myc During Myogenesis: Its mRNA Remains Inducible in Differentiated Cells and Does Not Suppress the Differentiated Phenotype

1986 • 41 citations