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bwtool: a tool for bigWig files
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Leighton J. Core et al.
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Daria Shlyueva et al.
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Chromatin state dynamics during blood formation
David Lara-Astiaso et al.
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Robin Andersson et al.
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Xuebing Wu et al.
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Joseph D. Fleming et al.
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Eliezer Calo et al.
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Minna U. Kaikkonen et al.
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Len A. Pennacchio et al.
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NCBI GEO: archive for functional genomics data sets-update
Tanya Barrett et al.
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Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq
Cosmas D. Arnold et al.
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Eli Eisenberg et al.
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The Genomic and Transcriptomic Landscape of a HeLa Cell Line
Jonathan J. M. Landry et al.
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RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State
Nisha Rajagopal et al.
PLOS COMPUTATIONAL BIOLOGY (2013)
Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization
Iouri Chepelev et al.
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Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
Jie Wang et al.
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The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
Thomas Derrien et al.
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An integrated encyclopedia of DNA elements in the human genome
Ian Dunham et al.
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Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development
Stefan Bonn et al.
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Unsupervised pattern discovery in human chromatin structure through genomic segmentation
Michael M. Hoffman et al.
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ChromHMM: automating chromatin-state discovery and characterization
Jason Ernst et al.
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Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
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clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
Guangchuang Yu et al.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY (2012)
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Qunhua Li et al.
ANNALS OF APPLIED STATISTICS (2011)
H3K4 tri-methylation provides an epigenetic signature of active enhancers
Aleksandra Pekowska 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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Discover regulatory DNA elements using chromatin signatures and artificial neural network
Hiram A. Firpi et al.
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Brad G. Hoffman et al.
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Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
Sven Heinz et al.
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Differential expression analysis for sequence count data
Simon Anders et al.
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Evidence for human microRNA-offset RNAs in small RNA sequencing data
David Langenberger et al.
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Nathaniel D. Heintzman et al.
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Da Wei Huang et al.
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Shadow enhancers as a source of evolutionary novelty
Joung-Woo Hong et al.
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Leighton J. Core et al.
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Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang et al.
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Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
Nathaniel D. Heintzman et al.
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Hoxb1 enhancer and control of rhombomere 4 expression:: Complex interplay between PREP1-PBX1-HOXB1 binding sites
E Ferretti et al.
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M García-Cosío et al.
MODERN PATHOLOGY (2004)
The RNA polymerase II core promoter: a key component in the regulation of gene expression
JEF Butler et al.
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