RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections
Published 2017 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections
Authors
Keywords
-
Journal
NUCLEIC ACIDS RESEARCH
Volume 45, Issue 13, Pages e119-e119
Publisher
Oxford University Press (OUP)
Online
2017-06-04
DOI
10.1093/nar/gkx314
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- 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
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started