JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

SMiLE-seq identifies binding motifs of single and dimeric transcription factors

(2017) Alina Isakova et al.   NATURE METHODS

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

(2017) Jaime Abraham Castro-Mondragon et al.   NUCLEIC ACIDS RESEARCH

Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors

(2017) Saeed Omidi et al.   PLoS Computational Biology

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs

(2016) David J. Arenillas et al.   BIOINFORMATICS

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

(2016) Ronan C. O’Malley et al.   CELL

REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis

(2016) Xia Cui et al.   NATURE GENETICS

Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences

(2016) Matthias Siebert et al.   NUCLEIC ACIDS RESEARCH

Induced Genome-Wide Binding of Three Arabidopsis WRKY Transcription Factors during Early MAMP-Triggered Immunity

(2016) Rainer P. Birkenbihl et al.   PLANT CELL

DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo

(2016) Anthony Mathelier et al.   Cell Systems

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

Genome-Wide Characterization ofcis-Acting DNA Targets Reveals the Transcriptional Regulatory Framework ofOpaque2in Maize

(2015) Chaobin Li et al.   PLANT CELL

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

A promoter-level mammalian expression atlas

(2014)   NATURE

TFClass: a classification of human transcription factors and their rodent orthologs

(2014) Edgar Wingender et al.   NUCLEIC ACIDS RESEARCH

A Generic Tool for Transcription Factor Target Gene Discovery in Arabidopsis Cell Suspension Cultures Based on Tandem Chromatin Affinity Purification

(2014) A. Verkest et al.   PLANT PHYSIOLOGY

DNA-binding specificities of plant transcription factors and their potential to define target genes

(2014) José M. Franco-Zorrilla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Regulatory modules controlling maize inflorescence architecture

(2013) A. L. Eveland et al.   GENOME RESEARCH

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

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

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

The Next Generation of Transcription Factor Binding Site Prediction

(2013) Anthony Mathelier et al.   PLoS Computational Biology

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Systematic characterization of protein-DNA interactions

(2011) Zhi Xie et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   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

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

DNA Motif Representation with Nucleotide Dependency

(2008) F. Chin et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics