SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps
出版年份 2015 全文链接
标题
SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps
作者
关键词
Sequence motif analysis, Cell binding, Genomic signal processing, Deoxyribonucleases, Transcription factors, Kernel methods, Cell binding assay, Chromatin
出版物
PLoS Computational Biology
Volume 11, Issue 5, Pages e1004271
出版商
Public Library of Science (PLoS)
发表日期
2015-05-28
DOI
10.1371/journal.pcbi.1004271
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- Regularization Paths for Generalized Linear Models via Coordinate Descent
- (2015) Jerome Friedman et al. Journal of Statistical Software
- Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape
- (2014) Richard I Sherwood et al. NATURE BIOTECHNOLOGY
- Predicting the human epigenome from DNA motifs
- (2014) John W Whitaker et al. NATURE METHODS
- Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features
- (2014) Mahmoud Ghandi et al. PLoS Computational Biology
- Evaluation of methods for modeling transcription factor sequence specificity
- (2013) Matthew T Weirauch et al. NATURE BIOTECHNOLOGY
- Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
- (2013) Jason D Buenrostro et al. NATURE METHODS
- JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles
- (2013) Anthony Mathelier et al. NUCLEIC ACIDS RESEARCH
- Software for Computing and Annotating Genomic Ranges
- (2013) Michael Lawrence et al. PLoS Computational Biology
- Distinct Lineage Specification Roles for NANOG, OCT4, and SOX2 in Human Embryonic Stem Cells
- (2012) Zheng Wang et al. Cell Stem Cell
- Sequence and chromatin determinants of cell-type-specific transcription factor binding
- (2012) A. Arvey 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
- An expansive human regulatory lexicon encoded in transcription factor footprints
- (2012) Shane Neph et al. NATURE
- Topological domains in mammalian genomes identified by analysis of chromatin interactions
- (2012) Jesse R. Dixon et al. NATURE
- ChromHMM: automating chromatin-state discovery and characterization
- (2012) Jason Ernst et al. NATURE METHODS
- DREME: motif discovery in transcription factor ChIP-seq data
- (2011) Timothy L. Bailey BIOINFORMATICS
- MEME-ChIP: motif analysis of large DNA datasets
- (2011) Philip Machanick et al. BIOINFORMATICS
- Discriminative prediction of mammalian enhancers from DNA sequence
- (2011) D. Lee et al. GENOME RESEARCH
- Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
- (2010) R. Pique-Regi et al. GENOME RESEARCH
- 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
- High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions
- (2010) Phaedra Agius et al. PLoS Computational Biology
- Evidence-ranked motif identification
- (2010) Stoyan Georgiev et al. GENOME BIOLOGY
- Differential expression analysis for sequence count data
- (2010) Simon Anders et al. GENOME BIOLOGY
- Enhancers: The abundance and function of regulatory sequences beyond promoters
- (2009) Michael Bulger et al. DEVELOPMENTAL BIOLOGY
- POIMs: positional oligomer importance matrices—understanding support vector machine-based signal detectors
- (2008) Sören Sonnenburg et al. BIOINFORMATICS
- UniPROBE: an online database of protein binding microarray data on protein-DNA interactions
- (2008) D. E. Newburger et al. NUCLEIC ACIDS RESEARCH
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAsk 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