UniBind: maps of high-confidence direct TF-DNA interactions across nine species
Published 2021 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
UniBind: maps of high-confidence direct TF-DNA interactions across nine species
Authors
Keywords
-
Journal
BMC GENOMICS
Volume 22, Issue 1, Pages -
Publisher
Springer Science and Business Media LLC
Online
2021-06-27
DOI
10.1186/s12864-021-07760-6
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Enhancer Domains Predict Gene Pathogenicity and Inform Gene Discovery in Complex Disease
- (2020) Xinchen Wang et al. AMERICAN JOURNAL OF HUMAN GENETICS
- Global expression and CpG methylation analysis of primary endothelial cells before and after TNFa stimulation reveals gene modules enriched in inflammatory and infectious diseases and associated DMRs
- (2020) Brooke Rhead et al. PLoS One
- Determinants of transcription factor regulatory range
- (2020) Chen-Hao Chen et al. Nature Communications
- Global reference mapping of human transcription factor footprints
- (2020) Jeff Vierstra et al. NATURE
- Expanded encyclopaedias of DNA elements in the human and mouse genomes
- (2020) Jill E. Moore et al. NATURE
- Targeted sequencing of genes associated with the mismatch repair pathway in patients with endometrial cancer
- (2020) Ashish Kumar Singh et al. PLoS One
- Transcription Factors and DNA Play Hide and Seek
- (2020) David M. Suter TRENDS IN CELL BIOLOGY
- ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation
- (2020) Mette Bentsen et al. Nature Communications
- High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity
- (2019) Kaia Mattioli et al. GENOME RESEARCH
- Explore, edit and leverage genomic annotations using Python GTF toolkit
- (2019) F Lopez et al. BIOINFORMATICS
- TFEA.ChIP: A tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets
- (2019) Laura Puente-Santamaria et al. BIOINFORMATICS
- Identifying clusters of cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks
- (2019) Seyed Ali Madani Tonekaboni et al. GENOME RESEARCH
- OLOGRAM: Determining significance of total overlap length between genomic regions sets
- (2019) Q Ferré et al. BIOINFORMATICS
- Determinants of enhancer and promoter activities of regulatory elements
- (2019) Robin Andersson et al. NATURE REVIEWS GENETICS
- ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments
- (2019) Jeanne Chèneby et al. NUCLEIC ACIDS RESEARCH
- ChIPSummitDB: a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them
- (2019) Erik Czipa et al. Database-The Journal of Biological Databases and Curation
- BART: a transcription factor prediction tool with query gene sets or epigenomic profiles
- (2018) Zhenjia Wang et al. BIOINFORMATICS
- Comparison of discriminative motif optimization using matrix and DNA shape-based models
- (2018) Shuxiang Ruan et al. BMC BIOINFORMATICS
- Characterizing protein–DNA binding event subtypes in ChIP-exo data
- (2018) Naomi Yamada et al. BIOINFORMATICS
- MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations
- (2018) Oriol Fornes et al. Scientific Data
- BRENDA in 2019: a European ELIXIR core data resource
- (2018) Lisa Jeske et al. NUCLEIC ACIDS RESEARCH
- GTRD: a database on gene transcription regulation—2019 update
- (2018) Ivan Yevshin et al. NUCLEIC ACIDS RESEARCH
- A map of direct TF–DNA interactions in the human genome
- (2018) Marius Gheorghe et al. NUCLEIC ACIDS RESEARCH
- ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments
- (2017) Jeanne Chèneby et al. NUCLEIC ACIDS RESEARCH
- DNA methylation at enhancers identifies distinct breast cancer lineages
- (2017) Thomas Fleischer et al. Nature Communications
- ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data
- (2016) Ke-Ren Zhou et al. NUCLEIC ACIDS RESEARCH
- Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse
- (2016) Shenglin Mei et al. NUCLEIC ACIDS RESEARCH
- UniProt: the universal protein knowledgebase
- (2016) NUCLEIC ACIDS RESEARCH
- The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability
- (2016) Alexander D. Diehl et al. Journal of Biomedical Semantics
- DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo
- (2016) Anthony Mathelier et al. Cell Systems
- LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor
- (2015) Nathan C. Sheffield et al. BIOINFORMATICS
- ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization
- (2015) Guangchuang Yu et al. BIOINFORMATICS
- bwtool: a tool for bigWig files
- (2014) Andy Pohl et al. BIOINFORMATICS
- Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment
- (2014) Rebecca Worsley Hunt et al. BMC GENOMICS
- An atlas of active enhancers across human cell types and tissues
- (2014) Robin Andersson et al. NATURE
- iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections
- (2014) Rekin's Janky et al. PLoS Computational Biology
- CLO: The cell line ontology
- (2014) Sirarat Sarntivijai et al. Journal of Biomedical Semantics
- Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser
- (2013) B. J. Raney et al. BIOINFORMATICS
- Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model
- (2013) Robin P Smith et al. NATURE GENETICS
- 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
- Software for Computing and Annotating Genomic Ranges
- (2013) Michael Lawrence et al. PLoS Computational Biology
- The UCSC genome browser and associated tools
- (2012) R. M. Kuhn et al. BRIEFINGS IN BIOINFORMATICS
- GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility
- (2012) V. Theodorou et al. GENOME RESEARCH
- Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
- (2012) J. Wang et al. GENOME RESEARCH
- ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions
- (2012) Terrence S. Furey NATURE REVIEWS GENETICS
- Inferring direct DNA binding from ChIP-seq
- (2012) Timothy L. Bailey et al. NUCLEIC ACIDS RESEARCH
- Exploring Massive, Genome Scale Datasets with the GenometriCorr Package
- (2012) Alexander Favorov et al. PLoS Computational Biology
- Uberon, an integrative multi-species anatomy ontology
- (2012) Christopher J Mungall et al. GENOME BIOLOGY
- ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments
- (2010) Alexander Lachmann et al. BIOINFORMATICS
- Modeling sample variables with an Experimental Factor Ontology
- (2010) James Malone et al. BIOINFORMATICS
- BEDTools: a flexible suite of utilities for comparing genomic features
- (2010) Aaron R. Quinlan et al. BIOINFORMATICS
- AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana
- (2010) L. Bulow et al. Database-The Journal of Biological Databases and Curation
- GeneCards Version 3: the human gene integrator
- (2010) M. Safran et al. Database-The Journal of Biological Databases and Curation
- Detection of nonneutral substitution rates on mammalian phylogenies
- (2009) K. S. Pollard et al. GENOME RESEARCH
- Inferring Binding Energies from Selected Binding Sites
- (2009) Yue Zhao et al. PLoS Computational Biology
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreAsk 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