RTFBSDB: an integrated framework for transcription factor binding site analysis

Identification of active transcriptional regulatory elements from GRO-seq data

(2015) Charles G Danko et al.   NATURE METHODS

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium

(2012) J. Wang et al.   NUCLEIC ACIDS RESEARCH

APCluster: an R package for affinity propagation clustering

(2011) U. Bodenhofer et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE