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Endre Bakken Stovner et al.
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Anchor: trans-cell type prediction of transcription factor binding sites
Hongyang Li et al.
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Accurate prediction of cell type-specific transcription factor binding
Jens Keilwagen et al.
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Advances of DNase-seq for mapping active gene regulatory elements across the genome in animals
Ailing Chen et al.
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Shinya Oki et al.
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DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter
Bryan Quach et al.
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An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites
Peter J. Skene et al.
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Genomic footprinting
Jeff Vierstra et al.
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BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data
Juhani Kahara et al.
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Francisco Charte et al.
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Anshul Kundaje et al.
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Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues
Jason Ernst et al.
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Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
Babak Alipanahi et al.
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Jian Zhou et al.
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Manu Setty et al.
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Anil Raj et al.
PLOS ONE (2015)
Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity
Matthew T. Weirauch et al.
CELL (2014)
Using Targeted Chromatin Regulators to Engineer Combinatorial and Spatial Transcriptional Regulation
Albert J. Keung et al.
CELL (2014)
Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments
Pouya Kheradpour et al.
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Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
Jason D. Buenrostro et al.
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On use of partial area under the ROC curve for evaluation of diagnostic performance
Hua Ma et al.
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Transcription factor co-localization patterns affect human cell type-specific gene expression
Dennis Wang et al.
BMC GENOMICS (2012)
An expansive human regulatory lexicon encoded in transcription factor footprints
Shane Neph et al.
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An integrated encyclopedia of DNA elements in the human genome
Ian Dunham et al.
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The accessible chromatin landscape of the human genome
Robert E. Thurman et al.
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The sequence read archive: explosive growth of sequencing data
Yuichi Kodama et al.
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FIMO: scanning for occurrences of a given motif
Charles E. Grant et al.
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Wenjie Shu et al.
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BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan et al.
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Cory Y. McLean et al.
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High-resolution mapping and characterization of open chromatin across the genome
Alan P. Boyle et al.
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Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang et al.
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The complex language of chromatin regulation during transcription
Shelley L. Berger
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The role of chromatin during transcription
Bing Li et al.
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The UCSC Genome Browser Database: update 2006
A. S. Hinrichs et al.
NUCLEIC ACIDS RESEARCH (2006)
Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails
Y Zhang et al.
GENES & DEVELOPMENT (2001)