Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection
出版年份 2014 全文链接
标题
Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection
作者
关键词
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出版物
NUCLEIC ACIDS RESEARCH
Volume 42, Issue 19, Pages 11865-11878
出版商
Oxford University Press (OUP)
发表日期
2014-10-08
DOI
10.1093/nar/gku810
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes
- (2014) Petra C Schwalie et al. GENOME BIOLOGY
- Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions
- (2013) N. C. Sheffield et al. GENOME RESEARCH
- Transcriptome and genome sequencing uncovers functional variation in humans
- (2013) Tuuli Lappalainen et al. NATURE
- DNase I–hypersensitive exons colocalize with promoters and distal regulatory elements
- (2013) Tim R Mercer et al. NATURE GENETICS
- Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification
- (2013) Housheng Hansen He et al. NATURE METHODS
- Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data
- (2013) Jason Piper et al. NUCLEIC ACIDS RESEARCH
- Chromatin Accessibility Data Sets Show Bias Due to Sequence Specificity of the DNase I Enzyme
- (2013) Hashem Koohy et al. PLoS One
- Widespread Misinterpretable ChIP-seq Bias in Yeast
- (2013) Daechan Park et al. PLoS One
- Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins
- (2013) L. Teytelman et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Probing DNA shape and methylation state on a genomic scale with DNase I
- (2013) A. Lazarovici et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Extensive Variation in Chromatin States Across Humans
- (2013) M. Kasowski et al. SCIENCE
- Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
- (2012) Dominic Schmidt et al. CELL
- Predicting cell-type-specific gene expression from regions of open chromatin
- (2012) A. Natarajan et al. GENOME RESEARCH
- ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- (2012) S. G. Landt et al. GENOME RESEARCH
- B-lineage transcription factors and cooperating gene lesions required for leukemia development
- (2012) E Tijchon et al. LEUKEMIA
- An expansive human regulatory lexicon encoded in transcription factor footprints
- (2012) Shane Neph et al. NATURE
- The accessible chromatin landscape of the human genome
- (2012) Robert E. Thurman et al. NATURE
- Unsupervised pattern discovery in human chromatin structure through genomic segmentation
- (2012) Michael M Hoffman et al. NATURE METHODS
- Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
- (2012) M. T. Maurano et al. SCIENCE
- Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity
- (2012) Alok K Tewari et al. GENOME BIOLOGY
- Modeling gene expression using chromatin features in various cellular contexts
- (2012) Xianjun Dong et al. GENOME BIOLOGY
- Epigenetic priors for identifying active transcription factor binding sites
- (2011) Gabriel Cuellar-Partida et al. BIOINFORMATICS
- Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
- (2011) L. Song et al. GENOME RESEARCH
- Mapping and analysis of chromatin state dynamics in nine human cell types
- (2011) Jason Ernst et al. NATURE
- Cooperative transcription factor associations discovered using regulatory variation
- (2011) Konrad J. Karczewski et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights
- (2011) Raluca Gordân et al. GENOME BIOLOGY
- High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells
- (2010) A. P. Boyle 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
- A transcription factor affinity-based code for mammalian transcription initiation
- (2009) M. Megraw et al. GENOME RESEARCH
- Distinguishing direct versus indirect transcription factor-DNA interactions
- (2009) R. Gordan et al. GENOME RESEARCH
- Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
- (2009) Jay R Hesselberth et al. NATURE METHODS
- Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
- (2009) L. A. Hindorff et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Diversity and Complexity in DNA Recognition by Transcription Factors
- (2009) G. Badis et al. SCIENCE
- F-Seq: a feature density estimator for high-throughput sequence tags
- (2008) A. P. Boyle et al. BIOINFORMATICS
- High-Resolution Mapping and Characterization of Open Chromatin across the Genome
- (2008) Alan P. Boyle et al. CELL
- Design and analysis of ChIP-seq experiments for DNA-binding proteins
- (2008) Peter V Kharchenko et al. NATURE BIOTECHNOLOGY
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