Chromatin-state discovery and genome annotation with ChromHMM

Nature Protocols
Jason Ernst, Manolis Kellis


Noncoding DNA regions have central roles in human biology, evolution, and disease. ChromHMM helps to annotate the noncoding genome using epigenomic information across one or multiple cell types. It combines multiple genome-wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer a complete annotation for each cell type. ChromHMM learns chromatin-state signatures using a multivariate hidden Markov model (HMM) that explicitly models the combinatorial presence or absence of each mark. ChromHMM uses these signatures to generate a genome-wide annotation for each cell type by calculating the most probable state for each genomic segment. ChromHMM provides an automated enrichment analysis of the resulting annotations to facilitate the functional interpretations of each chromatin state. ChromHMM is distinguished by its modeling emphasis on combinations of marks, its tight integration with downstream functional enrichment analyses, its speed, and its ease of use. Chromatin states are learned, annotations are produced, and enrichments are computed within 1 d.


May 26, 2018·Circulation Research·Manuel Rosa-GarridoThomas M Vondriska
Aug 24, 2018·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Ryan A HladyKeith D Robertson
May 1, 2019·The Journal of Clinical Endocrinology and Metabolism·Matthew DapasM Geoffrey Hayes
Jun 27, 2019·Toxicological Sciences : an Official Journal of the Society of Toxicology·Andy RampersaudDavid J Waxman
Aug 30, 2019·Epigenetics : Official Journal of the DNA Methylation Society·Elizabeth KennedyCarmen J Marsit
Nov 16, 2019·Nature Reviews. Genetics·Noa Gil, Igor Ulitsky
Aug 3, 2019·Annals of the Rheumatic Diseases·Javier Rodríguez-UbrevaEsteban Ballestar
Jan 1, 2020·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Philipp Benner, Martin Vingron
Jul 3, 2019·Alzheimer's & Dementia : the Journal of the Alzheimer's Association·Michael W LutzOrnit Chiba-Falek
Nov 13, 2019·Nucleic Acids Research·Yunhai LuoJ Michael Cherry
May 16, 2020·International Journal of Molecular Sciences·Iván Fernández-FríasJavier Díaz-Nido
Jun 3, 2020·Environmental Health Perspectives·Arce Domingo-RellosoMaria Tellez-Plaza
May 31, 2020·Proceedings of the National Academy of Sciences of the United States of America·Theodore P BraunJulia E Maxson
Mar 21, 2020·Annual Review of Biochemistry·Andrew Field, Karen Adelman
Jul 16, 2020·The Journal of Experimental Medicine·Agata CieslakVahid Asnafi
Sep 2, 2020·Epigenomics·Brian Z HuangZuo-Feng Zhang
Aug 8, 2018·Nucleic Acids Research·Joyce J ThompsonKeith D Robertson
Nov 24, 2018·Nature Communications·Xiaoguang XuMaciej Tomaszewski
Jun 28, 2019·Nature Communications·Laura GodfreyThomas A Milne
Mar 19, 2020·BMC Bioinformatics·Joshua J LevyBrock C Christensen
May 1, 2020·NPJ Breast Cancer·Hanan S ElsarrajFariba Behbod
Jul 22, 2020·Proceedings of the National Academy of Sciences of the United States of America·Mariam OkhovatLucia Carbone
Aug 19, 2020·Nature Neuroscience·Lee L MarshallViviane Labrie
Sep 19, 2020·Nature Communications·Kushal K DeyAlkes L Price
Aug 9, 2020·Applications in Plant Sciences·Elizabeth H MahoodGaurav D Moghe
Mar 7, 2019·Frontiers in Pharmacology·Emma CazalyJing Tang
Feb 12, 2020·Nature Plants·Zoé Joly-LopezMichael D Purugganan
Dec 29, 2019·BMC Bioinformatics·Juris ViksnaPeteris Rucevskis
Apr 21, 2020·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Edwin K SilvermanJan Baumbach


Jun 5, 2002·Genome Research·W James KentDavid Haussler
Mar 27, 2007·Bioinformatics·Nathan DayWilliam Stafford Noble
Jun 15, 2007·Genome Research·Robert E ThurmanJohn A Stamatoyannopoulos
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Dec 24, 2010·Science·modENCODE ConsortiumManolis Kellis
Dec 24, 2010·Nature·Peter V KharchenkoPeter J Park
Mar 29, 2011·Nature·Jason ErnstBradley E Bernstein
Apr 14, 2011·The EMBO Journal·François RoudierVincent Colot
Mar 1, 2012·Nature Methods·Jason Ernst, Manolis Kellis
Mar 20, 2012·Nature Methods·Michael M HoffmanWilliam Stafford Noble
Sep 8, 2012·Nature·ENCODE Project Consortium
Sep 8, 2012·Nature·Robert E ThurmanJohn A Stamatoyannopoulos
Sep 8, 2012·Nature·Shane NephJohn A Stamatoyannopoulos
Sep 8, 2012·Science·Matthew T MauranoJohn A Stamatoyannopoulos
Sep 8, 2012·Genome Research·Alan P BoyleMichael Snyder
Sep 8, 2012·Genome Research·Stephen G LandtMichael Snyder
Nov 30, 2012·Nucleic Acids Research·Kate R RosenbloomW James Kent
Dec 12, 2012·Nucleic Acids Research·Michael M HoffmanWilliam Stafford Noble
Mar 14, 2013·Nucleic Acids Research·Kyoung-Jae WonWei Wang
Apr 11, 2013·Genomics·Jessica L LarsonGuo-Cheng Yuan
Jun 14, 2013·BMC Bioinformatics·Jacob BiesingerXiaohui Xie
Jul 13, 2013·Genome Biology·Xin ZengSündüz Keleş
Oct 16, 2013·Proceedings of the National Academy of Sciences of the United States of America·Stephen C J ParkerNISC Comparative Sequencing Program Authors
Oct 19, 2013·Science·Maya KasowskiMichael Snyder
Oct 22, 2013·Genome Biology·Steve Horvath
Jan 28, 2014·Nature Neuroscience·Bess FrostMel B Feany
Feb 12, 2014·Genome Research·Fides D LayPeter A Jones
May 21, 2014·Genome Research·Emily J Brown, Doris Bachtrog
Aug 19, 2014·Nature Neuroscience·Philip L De JagerDavid A Bennett
Oct 30, 2014·Nucleic Acids Research·Fiona CunninghamPaul Flicek
Nov 21, 2014·Nature·Feng YueMouse ENCODE Consortium

Related Concepts

Medical Research Activity
Genome Mapping
Computer Programs and Programming
Software Design
Chromatin Remodeling
Gene Annotation
Cell Type

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Sexual Dimorphism in Neurodegeneration

There exist sex differences in neurodevelopmental and neurodegenerative disorders. For instance, multiple sclerosis is more common in women, whereas Parkinson’s disease is more common in men. Here is the latest research on sexual dimorphism in neurodegeneration

HLA Genetic Variation

HLA genetic variation has been found to confer risk for a wide variety of diseases. Identifying these associations and understanding their molecular mechanisms is ongoing and holds promise for the development of therapeutics. Find the latest research on HLA genetic variation here.

Super-resolution Microscopy

Super-resolution microscopy is the term commonly given to fluorescence microscopy techniques with resolutions that are not limited by the diffraction of light. Here are the latest discoveries pertaining to super-resolution microscopy.

Genetic Screens in iPSC-derived Brain Cells

Genetic screening is a critical tool that can be employed to define and understand gene function and interaction. This feed focuses on genetic screens conducted using induced pluripotent stem cell (iPSC)-derived brain cells.

Brain Lower Grade Glioma

Low grade gliomas in the brain form from oligodendrocytes and astrocytes and are the slowest-growing glioma in adults. Discover the latest research on these brain tumors here.

CD4/CD8 Signaling

Cluster of differentiation 4 and 8 (CD8 and CD8) are glycoproteins founds on the surface of immune cells. Here is the latest research on their role in cell signaling pathways.

Alignment-free Sequence Analysis Tools

Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. Here is the latest research.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.