i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

EWS-FLI1 Utilizes Divergent Chromatin Remodeling Mechanisms to Directly Activate or Repress Enhancer Elements in Ewing Sarcoma

(2014) Nicolò Riggi et al.   CANCER CELL

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections

(2014) Rekin's Janky et al.   PLoS Computational Biology

Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool

(2013) Raymond K. Auerbach et al.   BIOINFORMATICS

Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites

(2013) Jian Yan et al.   CELL

oPOSSUM-3: Advanced Analysis of Regulatory Motif Over-Representation Across Genes or ChIP-Seq Datasets

(2013) Andrew T. Kwon et al.   G3-Genes Genomes Genetics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

UCNEbase—a database of ultraconserved non-coding elements and genomic regulatory blocks

(2012) Slavica Dimitrieva et al.   NUCLEIC ACIDS RESEARCH

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

(2012) Carl Herrmann et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

(2011) Morgane Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

(2010) V. Gotea et al.   GENOME RESEARCH

Integrating multiple evidence sources to predict transcription factor binding in the human genome

(2010) J. Ernst et al.   GENOME RESEARCH

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

DiRE: identifying distant regulatory elements of co-expressed genes

(2008) V. Gotea et al.   NUCLEIC ACIDS RESEARCH