Chromatin-state discovery and genome annotation with ChromHMM

Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes

(2017) Sushmita Roy et al.   GENOME RESEARCH

Multi-scale chromatin state annotation using a hierarchical hidden Markov model

(2017) Eugenio Marco et al.   Nature Communications

Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression

(2017) Petko Fiziev et al.   Cell Reports

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

(2017) Benedikt Zacher et al.   PLoS One

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

(2016) Biola M. Javierre et al.   CELL

Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions

(2016) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Jointly characterizing epigenetic dynamics across multiple human cell types

(2016) Yu Zhang et al.   NUCLEIC ACIDS RESEARCH

Nucleosome Density ChIP-Seq Identifies Distinct Chromatin Modification Signatures Associated with MNase Accessibility

(2016) Alireza Lorzadeh et al.   Cell Reports

Learning chromatin states with factorized information criteria

(2015) Michiaki Hamada et al.   BIOINFORMATICS

hiHMM: Bayesian non-parametric joint inference of chromatin state maps

(2015) Kyung-Ah Sohn et al.   BIOINFORMATICS

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression

(2015) Maxwell W. Libbrecht et al.   GENOME RESEARCH

Human Promoters Are Intrinsically Directional

(2015) Sascha H.C. Duttke et al.   MOLECULAR CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Common genetic variants influence human subcortical brain structures

(2015) Derrek P. Hibar et al.   NATURE

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease

(2015) Elizabeta Gjoneska et al.   NATURE

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

(2015) Jason Ernst et al.   NATURE BIOTECHNOLOGY

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

(2015) Melina Claussnitzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

A new GWAS and meta-analysis with 1000Genomes imputation identifies novel risk variants for colorectal cancer

(2015) Nada A. Al-Tassan et al.   Scientific Reports

Spectacle: fast chromatin state annotation using spectral learning

(2015) Jimin Song 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

Reprogramming of the human intestinal epigenome by surgical tissue transposition

(2014) F. D. Lay et al.   GENOME RESEARCH

The chromatin landscape of Drosophila: comparisons between species, sexes, and chromosomes

(2014) E. J. Brown et al.   GENOME RESEARCH

Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer

(2014) Phillippa C. Taberlay 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

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

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

(2014) Leighton J Core et al.   NATURE GENETICS

Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci

(2014) Philip L De Jager et al.   NATURE NEUROSCIENCE

Tau promotes neurodegeneration through global chromatin relaxation

(2014) Bess Frost et al.   NATURE NEUROSCIENCE

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Sparsely correlated hidden Markov models with application to genome-wide location studies

(2013) Hyungwon Choi et al.   BIOINFORMATICS

Hierarchical Mechanisms for Direct Reprogramming of Fibroblasts to Neurons

(2013) Orly L. Wapinski et al.   CELL

Long-Range Chromatin Contacts in Embryonic Stem Cells Reveal a Role for Pluripotency Factors and Polycomb Proteins in Genome Organization

(2013) Matthew Denholtz et al.   Cell Stem Cell

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

(2013) P. Kheradpour et al.   GENOME RESEARCH

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

(2013) A. Mortazavi 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

A tiered hidden Markov model characterizes multi-scale chromatin states

(2013) Jessica L. Larson et al.   GENOMICS

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

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

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive Variation in Chromatin States Across Humans

(2013) M. Kasowski et al.   SCIENCE

Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape

(2013) Kenneth Day et al.   GENOME BIOLOGY

jMOSAiCS: joint analysis of multiple ChIP-seq datasets

(2013) Xin Zeng et al.   GENOME BIOLOGY

DNA methylation age of human tissues and cell types

(2013) Steve Horvath   GENOME BIOLOGY

Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation

(2012) P. Yu et al.   GENOME RESEARCH

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Annotation of functional variation in personal genomes using RegulomeDB

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

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

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

Integrative annotation of chromatin elements from ENCODE data

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

ENCODE Data in the UCSC Genome Browser: year 5 update

(2012) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

(2011) François Roudier et al.   EMBO JOURNAL

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

(2011) Jason Ernst et al.   NATURE

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

(2011) L. D. Ward et al.   NUCLEIC ACIDS RESEARCH

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

(2010) A. P. Boyle et al.   GENOME RESEARCH

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

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

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome

(2008) Gary Hon et al.   PLoS Computational Biology

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY