Computation for ChIP-seq and RNA-seq studies

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

2009 • 20,860 citations

Model-based Analysis of ChIP-Seq (MACS)

2008 • 15,719 citations

Mapping and quantifying mammalian transcriptomes by RNA-Seq

2008 • 12,817 citations

TopHat: discovering splice junctions with RNA-Seq

2009 • 11,483 citations

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

2008 • 9,415 citations

High-Resolution Profiling of Histone Methylations in the Human Genome

2007 • 6,479 citations

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

2007 • 5,117 citations

Alternative isoform regulation in human tissue transcriptomes

2008 • 4,870 citations

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

2007 • 3,994 citations

SOAP: short oligonucleotide alignment program

2008 • 3,006 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

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

2008 • 2,354 citations

Variance stabilization applied to microarray data calibration and to the quantification of differential expression

2002 • 2,340 citations

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

2007 • 1,389 citations

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

2008 • 1,270 citations

Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

2006 • 1,176 citations

Stem cell transcriptome profiling via massive-scale mRNA sequencing

2008 • 1,026 citations

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

2009 • 1,004 citations

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

2008 • 956 citations

Design and analysis of ChIP-seq experiments for DNA-binding proteins

2008 • 909 citations

An integrated software system for analyzing ChIP-chip and ChIP-seq data

2008 • 718 citations

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

2008 • 690 citations

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

2009 • 552 citations

Genome-wide identification ofin vivoprotein-DNA binding sites from ChIP-Seq data

2008 • 530 citations

Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing

2009 • 516 citations

Transcript length bias in RNA-seq data confounds systems biology

2009 • 502 citations

Statistical inferences for isoform expression in RNA-Seq

2009 • 469 citations

De novo transcriptome assembly with ABySS

2009 • 394 citations

F-Seq: a feature density estimator for high-throughput sequence tags

2008 • 371 citations

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses

2009 • 363 citations

How to map billions of short reads onto genomes

2009 • 302 citations

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

2008 • 266 citations

Sequence census methods for functional genomics

2007 • 265 citations

Annotating genomes with massive-scale RNA sequencing

2008 • 238 citations

Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks

2008 • 223 citations

Comparative analysis of processed pseudogenes in the mouse and human genomes

2003 • 217 citations

Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq

2009 • 177 citations

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis

2009 • 166 citations

RNA Pol II Accumulates at Promoters of Growth Genes During Developmental Arrest

2009 • 164 citations

ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome

2008 • 151 citations

An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data

2008 • 148 citations

Optimal spliced alignments of short sequence reads

2008 • 117 citations

Extracting transcription factor targets from ChIP-Seq data

2009 • 113 citations

Optimal spliced alignments of short sequence reads

2008 • 87 citations

A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level

2009 • 55 citations

RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data

2009 • 47 citations