The Sequence Alignment/Map format and SAMtools

Heng Li, Alec Wysoker, Tim Fennell, +5

Bioinformatics

Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, Richard Durbin

Bioinformatics

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

Ben Langmead, Cole Trapnell, Mihai Pop, +1

Genome biology

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang, Tao Liu, Clifford A. Meyer, +8

Genome biology

The Human Genome Browser at UCSC

W. James Kent, Charles W. Sugnet, Terrence S. Furey, +4

Genome Research

High-Resolution Profiling of Histone Methylations in the Human Genome

Artem Barski, Suresh Cuddapah, Kairong Cui, +6

Cell

Histone ModificationsChromatinHistone MethylationsEpigenetic ChangeGenetics +5

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

Pamela J. Thomas

Nature

Functional GenomicsGene Sequence AnnotationGenome StudyGeneticsComputational Genomics +11

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

Tarjei S. Mikkelsen, Manching Ku, David B. Jaffe, +19

Nature

ChromatinChromatin StructureChromatin StateChromatin RemodelingNatural Sciences +10

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

David S. Johnson, A Mortazavi, R Myers, +1

Science

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

Gordon Robertson, Martin Hirst, Matthew N. Bainbridge, +13

Nature Methods

Genome-wide Association StudyChromatinNext-generation SequencingGeneticsGenome-wide Profiles +8