Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN

High-throughput mapping of regulatory DNA

(2016) Nisha Rajagopal et al.   NATURE BIOTECHNOLOGY

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

Scl binds to primed enhancers in mesoderm to regulate hematopoietic and cardiac fate divergence

(2015) T. Org et al.   EMBO JOURNAL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues

(2015) Jason Ernst et al.   NATURE BIOTECHNOLOGY

The selection and function of cell type-specific enhancers

(2015) Sven Heinz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease

(2015) Lucas D. Ward et al.   NUCLEIC ACIDS RESEARCH

Functional annotation of HOT regions in the human genome: implications for human disease and cancer

(2015) Hao Li et al.   Scientific Reports

The Ensembl Regulatory Build

(2015) Daniel R Zerbino et al.   GENOME BIOLOGY

Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome

(2015) Alessandro Mammana et al.   GENOME BIOLOGY

Promoter or enhancer, what's the difference? Deconstruction of established distinctions and presentation of a unifying model

(2014) Robin Andersson   BIOESSAYS

High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies

(2014) Michal Rabani et al.   CELL

High-throughput functional testing of ENCODE segmentation predictions

(2014) Jamie C. Kwasnieski et al.   GENOME RESEARCH

Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle

(2014) B. Zacher et al.   Molecular Systems Biology

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

Genome-wide analysis of noncoding regulatory mutations in cancer

(2014) Nils Weinhold et al.   NATURE GENETICS

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

DEEP: a general computational framework for predicting enhancers

(2014) Dimitrios Kleftogiannis et al.   NUCLEIC ACIDS RESEARCH

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

(2013) P. Kheradpour et al.   GENOME RESEARCH

Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types

(2013) J. Ernst et al.   GENOME RESEARCH

Comparative annotation of functional regions in the human genome using epigenomic data

(2013) Kyoung-Jae Won et al.   NUCLEIC ACIDS RESEARCH

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State

(2013) Nisha Rajagopal et al.   PLoS Computational Biology

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Normalization of ChIP-seq data with control

(2012) Kun Liang et al.   BMC BIOINFORMATICS

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature

(2012) E. Z. Kvon et al.   GENES & DEVELOPMENT

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Chromatin marks identify critical cell types for fine mapping complex trait variants

(2012) Gosia Trynka et al.   NATURE GENETICS

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

(2012) Kevin Y Yip et al.   GENOME BIOLOGY

Discriminative prediction of mammalian enhancers from DNA sequence

(2011) D. Lee et al.   GENOME RESEARCH

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

(2011) Gabriel E. Zentner et al.   GENOME RESEARCH

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

(2011) C. Miller et al.   Molecular Systems Biology

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Large-scale discovery of enhancers from human heart tissue

(2011) Dalit May et al.   NATURE GENETICS

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology