Stem cell transcriptome profiling via massive-scale mRNA sequencing

Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments

2004 • 11,620 citations

<tt>BLAT</tt>—The <tt>BLAST</tt>-Like Alignment Tool

2002 • 8,153 citations

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

2007 • 5,117 citations

Serial Analysis of Gene Expression

1995 • 3,659 citations

The Transcriptional Landscape of the Mammalian Genome

2005 • 3,444 citations

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

2008 • 2,448 citations

RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription

2007 • 2,414 citations

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

2008 • 2,354 citations

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

2002 • 1,612 citations

Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome

2005 • 1,373 citations

Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs

2004 • 1,079 citations

Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage

2003 • 721 citations

Functional annotation of a full-length mouse cDNA collection

2001 • 663 citations

AceView: a comprehensive cDNA-supported gene and transcripts annotation

2006 • 621 citations

The UCSC Genome Browser Database: 2008 update

2007 • 537 citations

Genomewide Analysis of mRNA Processing in Yeast Using Splicing-Specific Microarrays

2002 • 406 citations

ESTablishing a human transcript map

1995 • 391 citations

Amplification of cDNA ends based on template-switching effect and step- out PCR

1999 • 376 citations

Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array

2006 • 347 citations

Complex Loci in Human and Mouse Genomes

2006 • 300 citations

A gene regulatory network in mouse embryonic stem cells

2007 • 280 citations

Extending assembly of short DNA sequences to handle error

2007 • 271 citations

The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes

2004 • 225 citations

Polony Multiplex Analysis of Gene Expression (PMAGE) in Mouse Hypertrophic Cardiomyopathy

2007 • 200 citations

Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms

2002 • 155 citations

Disclosing hidden transcripts: Mouse natural sense–antisense transcripts tend to be poly(A) negative and nuclear localized

2005 • 144 citations

In vitro differentiation of murine embryonic stem cells toward a renal lineage

2007 • 119 citations

CapSelect: a highly sensitive method for 5' CAP-dependent enrichment of full-length cDNA in PCR-mediated analysis of mRNAs

1999 • 101 citations

CapSelect: A highly sensitive method for 5' CAP-dependent enrichment of full-length cDNA in PCR-mediated analysis of mRNAs

1999 • 99 citations

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

2008 • 99 citations

Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeBMP4 culture

2007 • 69 citations

Transcriptional profiling of mouse and human ES cells identifies SLAIN1, a novel stem cell gene

2006 • 59 citations

Determination of the Capped Site Sequence of mRNA Based on the Detection of Cap-Dependent Nucleotide Addition Using an Anchor Ligation Method

2004 • 27 citations