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

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

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

A roadmap of constitutive NF-κB activity in Hodgkin lymphoma: Dominant roles of p50 and p52 revealed by genome-wide analyses

(2016) Kivia A. P. de Oliveira et al.   Genome Medicine

Alignment-free clustering of transcription factor binding motifs using a genetic-k-medoids approach

(2015) Pilib Ó Broin et al.   BMC BIOINFORMATICS

Selective influence of Sox2 on POU transcription factor binding in embryonic and neural stem cells

(2015) T. K. Mistri et al.   EMBO REPORTS

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

C2H2 zinc finger proteins greatly expand the human regulatory lexicon

(2015) Hamed S Najafabadi et al.   NATURE BIOTECHNOLOGY

Varying levels of complexity in transcription factor binding motifs

(2015) Jens Keilwagen et al.   NUCLEIC ACIDS RESEARCH

HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

(2015) Ivan V. Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

RSAT 2015: Regulatory Sequence Analysis Tools

(2015) Alejandra Medina-Rivera et al.   NUCLEIC ACIDS RESEARCH

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

A promoter-level mammalian expression atlas

(2014)   NATURE

DMINDA: an integrated web server for DNA motif identification and analyses

(2014) Qin Ma et al.   NUCLEIC ACIDS RESEARCH

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions

(2014) Maxwell A. Hume et al.   NUCLEIC ACIDS RESEARCH

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

Jaccard index based similarity measure to compare transcription factor binding site models

(2013) Ilya E Vorontsov et al.   Algorithms for Molecular Biology

footprintDB: a database of transcription factors with annotated cis elements and binding interfaces

(2013) Alvaro Sebastian et al.   BIOINFORMATICS

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Evaluation of methods for modeling transcription factor sequence specificity

(2013) Matthew T Weirauch et al.   NATURE BIOTECHNOLOGY

OnTheFly: a database ofDrosophila melanogastertranscription factors and their binding sites

(2013) Shula Shazman 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

A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs

(2013) Philip Stegmaier et al.   PLoS Computational Biology

The Next Generation of Transcription Factor Binding Site Prediction

(2013) Anthony Mathelier et al.   PLoS Computational Biology

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs

(2012) Morgane Thomas-Chollier et al.   Nature Protocols

TFClass: an expandable hierarchical classification of human transcription factors

(2012) Edgar Wingender et al.   NUCLEIC ACIDS RESEARCH

The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences

(2012) S. Luehr et al.   NUCLEIC ACIDS RESEARCH

Improved similarity scores for comparing motifs

(2011) Emi Tanaka et al.   BIOINFORMATICS

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

D³ Data-Driven Documents

(2011) M. Bostock et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Theoretical and empirical quality assessment of transcription factor-binding motifs

(2011) Alejandra Medina-Rivera et al.   NUCLEIC ACIDS RESEARCH

RSAT 2011: regulatory sequence analysis tools

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

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

(2011) Morgane Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

Identification of Context-Dependent Motifs by Contrasting ChIP Binding Data

(2010) Mike J. Mason et al.   BIOINFORMATICS

Deep and wide digging for binding motifs in ChIP-Seq data

(2010) I. V. Kulakovskiy 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

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

(2010) Lihua Julie Zhu et al.   NUCLEIC ACIDS RESEARCH

A Novel Alignment-Free Method for Comparing Transcription Factor Binding Site Motifs

(2010) Minli Xu et al.   PLoS One

hPDI: a database of experimental human protein-DNA interactions

(2009) Z. Xie et al.   BIOINFORMATICS

Natural similarity measures between position frequency matrices with an application to clustering

(2008) Utz J. Pape et al.   BIOINFORMATICS

Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites

(2008) Marcus B. Noyes et al.   CELL

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes

(2008) D. Tantin et al.   GENOME RESEARCH

AthaMap, integrating transcriptional and post-transcriptional data

(2008) L. Bulow et al.   NUCLEIC ACIDS RESEARCH

A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval

(2008) Naomi Habib et al.   PLoS Computational Biology