STREME: accurate and versatile sequence motif discovery

ProSampler: an ultra-fast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery

(2019) Yang Li et al.   BIOINFORMATICS

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

STEME: efficient EM to find motifs in large data sets

(2011) John E. Reid et al.   NUCLEIC ACIDS RESEARCH

RSAT 2011: regulatory sequence analysis tools

(2011) M. Thomas-Chollier et al.   NUCLEIC ACIDS 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