ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments

GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments

(2016) Ivan Yevshin et al.   NUCLEIC ACIDS RESEARCH

Genenames.org: the HGNC and VGNC resources in 2017

(2016) Bethan Yates et al.   NUCLEIC ACIDS RESEARCH

ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data

(2016) Ke-Ren Zhou et al.   NUCLEIC ACIDS RESEARCH

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

(2016) Shenglin Mei et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2017

(2016) Bronwen L. Aken et al.   NUCLEIC ACIDS RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape

(2014) Aurélien Griffon et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

(2013) B. J. Raney et al.   BIOINFORMATICS

Large-Scale Quality Analysis of Published ChIP-seq Data

(2013) Georgi K. Marinov et al.   G3-Genes Genomes Genetics

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources

(2010) M. Gremse et al.   NUCLEIC ACIDS RESEARCH

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

(2008) B. Paten et al.   GENOME RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY