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

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

TFBSshape: a motif database for DNA shape features of transcription factor binding sites

(2013) Lin Yang et al.   NUCLEIC ACIDS RESEARCH

The Next Generation of Transcription Factor Binding Site Prediction

(2013) Anthony Mathelier et al.   PLoS Computational Biology

A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

(2012) Guillaume Junion et al.   CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Inferring direct DNA binding from ChIP-seq

(2012) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

The Transcription Factor Encyclopedia

(2012) Dimas Yusuf et al.   GENOME BIOLOGY

Cross species comparison of C/EBPα and PPARγ profiles in mouse and human adipocytes reveals interdependent retention of binding sites

(2011) Søren F Schmidt et al.   BMC GENOMICS

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

(2010) Elizabeth G. Wilbanks et al.   PLoS One

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

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

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

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences

(2008) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH