Related references
Note: Only part of the references are listed.Identification of regulatory elements from nascent transcription using dREG
Zhong Wang et al.
GENOME RESEARCH (2019)
A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples
Han Chen et al.
CELL (2018)
Widespread transcriptional pausing and elongation control at enhancers
Telmo Henriques et al.
GENES & DEVELOPMENT (2018)
SRC-3 Coactivator Governs Dynamic Estrogen-Induced Chromatin Looping Interactions during Transcription
Anil K. Panigrahi et al.
MOLECULAR CELL (2018)
A global transcriptional network connecting noncoding mutations to changes in tumor gene expression
Wei Zhang et al.
NATURE GENETICS (2018)
Comprehensive comparative analysis of 5'-end RNA-sequencing methods
Xian Adiconis et al.
NATURE METHODS (2018)
RNA velocity of single cells
Gioele La Manno et al.
NATURE (2018)
De novo mutations in regulatory elements in neurodevelopmental disorders
Patrick J. Short et al.
NATURE (2018)
Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers
Jacob M. Tome et al.
NATURE GENETICS (2018)
Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme
Tinyi Chu et al.
NATURE GENETICS (2018)
TT-seq captures enhancer landscapes immediately after T-cell stimulation
Margaux Michel et al.
MOLECULAR SYSTEMS BIOLOGY (2017)
An atlas of human long non-coding RNAs with accurate 5′ ends
Chung-Chau Hon et al.
NATURE (2017)
Complex multi-enhancer contacts captured by genome architecture mapping
Robert A. Beagrie et al.
NATURE (2017)
High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing
Julien Lagarde et al.
NATURE GENETICS (2017)
Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines
Qin Cao et al.
NATURE GENETICS (2017)
The Ground State and Evolution of Promoter Region Directionality
Yi Jin et al.
CELL (2017)
dbSUPER: a database of super-enhancers in mouse and human genome
Aziz Khan et al.
NUCLEIC ACIDS RESEARCH (2016)
A predictive computational framework for direct reprogramming between human cell types
Owen J. L. Rackham et al.
NATURE GENETICS (2016)
Genome-wide profiling of RNA polymerase transcription at nucleotide resolution in human cells with native elongating transcript sequencing
Andreas Mayer et al.
NATURE PROTOCOLS (2016)
The regulation and functions of the nuclear RNA exosome complex
Cornelia Kilchert et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2016)
TT-seq maps the human transient transcriptome
Bjorn Schwalb et al.
SCIENCE (2016)
Enhancec Identification of Transcriptional Enhancers Provides Vechanistic Insights into Diseases
Yasuhiro Murakawa et al.
TRENDS IN GENETICS (2016)
Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution
Andreas Mayer et al.
CELL (2015)
Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing
Takayuki Nojima et al.
CELL (2015)
CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription
Zhonghui Tang et al.
CELL (2015)
Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin
Elizabeth Ing-Simmons et al.
GENOME RESEARCH (2015)
Creating reference gene annotation for the mouse C57BL6/J genome assembly
Jonathan M. Mudge et al.
MAMMALIAN GENOME (2015)
Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin
Benjamin S. Scruggs et al.
MOLECULAR CELL (2015)
Integrative analysis of 111 reference human epigenomes
Anshul Kundaje et al.
NATURE (2015)
Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes
Kaifu Chen et al.
NATURE GENETICS (2015)
Partitioning heritability by functional annotation using genome-wide association summary statistics
Hilary K. Finucane et al.
NATURE GENETICS (2015)
Identification of active transcriptional regulatory elements from GRO-seq data
Charles G. Danko et al.
NATURE METHODS (2015)
Inflammation-sensitive super enhancers form domains of coordinately regulated enhancer RNAs
Nasun Hah et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells
Erik Arner et al.
SCIENCE (2015)
Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells
Marco Mina et al.
SCIENTIFIC REPORTS (2015)
Genetic and epigenetic fine mapping of causal autoimmune disease variants
Kyle Kai-How Farh et al.
NATURE (2015)
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony M. Bolger et al.
BIOINFORMATICS (2014)
MOIRAI: a compact workflow system for CAGE analysis
Akira Hasegawa et al.
BMC BIOINFORMATICS (2014)
An atlas of active enhancers across human cell types and tissues
Robin Andersson et al.
NATURE (2014)
A promoter-level mammalian expression atlas
Alistair R. R. Forrest et al.
NATURE (2014)
Genome-wide analysis of noncoding regulatory mutations in cancer
Nils Weinhold et al.
NATURE GENETICS (2014)
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers
Leighton J. Core et al.
NATURE GENETICS (2014)
deepTools: a flexible platform for exploring deep-sequencing data
Fidel Ramirez et al.
NUCLEIC ACIDS RESEARCH (2014)
Enhancer RNAs and regulated transcriptional programs
Michael T. Y. Lam et al.
TRENDS IN BIOCHEMICAL SCIENCES (2014)
Differential protein occupancy profiling of the mRNA transcriptome
Markus Schueler et al.
GENOME BIOLOGY (2014)
STAR: ultrafast universal RNA-seq aligner
Alexander Dobin et al.
BIOINFORMATICS (2013)
Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes
Warren A. Whyte et al.
CELL (2013)
Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations
Yubo Zhang et al.
NATURE (2013)
Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants
Stephen C. J. Parker et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing
Hojoong Kwak et al.
SCIENCE (2013)
RSeQC: quality control of RNA-seq experiments
Liguo Wang et al.
BIOINFORMATICS (2012)
Transcript Dynamics of Proinflammatory Genes Revealed by Sequence Analysis of Subcellular RNA Fractions
Dev M. Bhatt et al.
CELL (2012)
Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation
Guoliang Li et al.
CELL (2012)
GENCODE: The reference human genome annotation for The ENCODE Project
Jennifer Harrow et al.
GENOME RESEARCH (2012)
The long-range interaction landscape of gene promoters
Amartya Sanyal et al.
NATURE (2012)
Landscape of transcription in human cells
Sarah Djebali et al.
NATURE (2012)
An integrated encyclopedia of DNA elements in the human genome
Ian Dunham et al.
NATURE (2012)
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
Davis J. McCarthy et al.
NUCLEIC ACIDS RESEARCH (2012)
H3K4 tri-methylation provides an epigenetic signature of active enhancers
Aleksandra Pekowska et al.
EMBO JOURNAL (2011)
Unamplified cap analysis of gene expression on a single-molecule sequencer
Mutsumi Kanamori-Katayama et al.
GENOME RESEARCH (2011)
Nascent transcript sequencing visualizes transcription at nucleotide resolution
L. Stirling Churchman et al.
NATURE (2011)
Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells
Michal Rabani et al.
NATURE BIOTECHNOLOGY (2011)
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
Mark D. Robinson et al.
BIOINFORMATICS (2010)
BigWig and BigBed: enabling browsing of large distributed datasets
W. J. Kent et al.
BIOINFORMATICS (2010)
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan et al.
BIOINFORMATICS (2010)
Widespread transcription at neuronal activity-regulated enhancers
Tae-Kyung Kim et al.
NATURE (2010)
Histone H3K27ac separates active from poised enhancers and predicts developmental state
Menno P. Creyghton et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
The Sequence Alignment/Map format and SAMtools
Heng Li et al.
BIOINFORMATICS (2009)
Divergent Transcription from Active Promoters
Amy C. Seila et al.
SCIENCE (2008)
Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters
Leighton J. Core et al.
SCIENCE (2008)
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
Nathaniel D. Heintzman et al.
NATURE GENETICS (2007)
The transcriptional landscape of the mammalian genome
P Carninci et al.
SCIENCE (2005)
Stimulus-specific induction of a novel nuclear factor-κB regulator, IκB-ζ, via toll/interleukin-1 receptor is mediated by mRNA stabilization
S Yamazaki et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2005)
The UCSC Table Browser data retrieval tool
D Karolchik et al.
NUCLEIC ACIDS RESEARCH (2004)
The human genome browser at UCSC
WJ Kent et al.
GENOME RESEARCH (2002)