Epigenome overlap measure (EPOM) for comparing tissue/cell types based on chromatin states

GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach

(2015) Ellen M. Schmidt et al.   BIOINFORMATICS

The Disease Ontology: fostering interoperability between biological and clinical human disease-related data

(2015) Lynn M. Schriml et al.   MAMMALIAN GENOME

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

Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data

(2014) J. J. Li et al.   GENOME RESEARCH

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

3D genome reconstruction from chromosomal contacts

(2014) Annick Lesne et al.   NATURE METHODS

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data

(2014) Warren A. Kibbe et al.   NUCLEIC ACIDS RESEARCH

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

Global view of enhancer-promoter interactome in human cells

(2014) B. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identifying Cell Types from Spatially Referenced Single-Cell Expression Datasets

(2014) Jean-Baptiste Pettit et al.   PLoS Computational Biology

Epigenetic Landscapes Explain Partially Reprogrammed Cells and Identify Key Reprogramming Genes

(2014) Alex H. Lang et al.   PLoS Computational Biology

Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies

(2013) Young-suk Lee et al.   BIOINFORMATICS

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb

(2012) Justin Cotney et al.   GENOME RESEARCH

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency

(2011) R David Hawkins et al.   CELL RESEARCH

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

GWASdb: a database for human genetic variants identified by genome-wide association studies

(2011) Mulin Jun Li et al.   NUCLEIC ACIDS RESEARCH

Concise Review: Induced Pluripotent Stem Cells Versus Embryonic Stem Cells: Close Enough or Yet Too Far Apart?

(2011) Josipa Bilic et al.   STEM CELLS

Epigenetic Mechanisms that Regulate Cell Identity

(2010) María J. Barrero et al.   Cell Stem Cell

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

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predictive chromatin signatures in the mammalian genome

(2009) G. C. Hon et al.   HUMAN MOLECULAR GENETICS

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE