Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data

Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment

(2014) Rebecca Worsley Hunt et al.   BMC GENOMICS

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

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

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Nencki Genomics Database—Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs

(2013) Izabella Krystkowiak et al.   Database-The Journal of Biological Databases and Curation

Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions

(2012) Yue Zhao et al.   GENETICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models

(2012) Ivan V. Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates

(2012) Mikhail Pachkov et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Quantitative analysis demonstrates most transcription factors require only simple models of specificity

(2011) Yue Zhao et al.   NATURE BIOTECHNOLOGY

Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development

(2011) Tommy Kaplan et al.   PLoS Genetics

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

bioDBnet: the biological database network

(2009) Uma Mudunuri et al.   BIOINFORMATICS

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

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

Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs

(2009) Bartek Wilczynski et al.   BMC BIOINFORMATICS

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

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

(2008) Michael F. Berger et al.   CELL

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules

(2008) Jean-Valery Turatsinze et al.   Nature Protocols