ChromHMM protocols

View ChromHMM computational protocol

ChromHMM statistics

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ChromHMM specifications


Unique identifier OMICS_03490
Name ChromHMM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes



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Publication for ChromHMM

ChromHMM in pipelines

PMCID: 5819162
PMID: 29458327
DOI: 10.1186/s12864-018-4533-0

[…] line, the alignment bed files of two replicates were pooled. the reads were extended to 200 bp from 5′ to 3′ or 3′ to 5′ direction for positive and negative strands alignments respectively. we used chromhmm v1.1.12 [] to binarize the chip-seq signals with default parameters and build the chromatin state model at 200 bp resolution (−b 200), on all cell line samples for 5 major histone marks: […]

PMCID: 5215532
PMID: 28052101
DOI: 10.1371/journal.pone.0169237

[…] without appreciable primary let-7 transcripts. these regions were frequently annotated as active tss, flanking active tss, bivalent/poised tss, enhancer, genic enhancer, and bivalent enhancer in the chromhmm chromatin state prediction algorithm performed on roadmap datasets., these hypothesized regulatory regions were then queried for transcription factor binding sites, based on known […]

PMCID: 5429095
PMID: 28395144
DOI: 10.7554/eLife.22194.055

[…] but overlapped with regions designated as being in an enhancer chromatin state (‘txenha’ or ‘enhwk’ or ‘enhp’ state in adult; ‘txenha1’ or ‘txenha2’ or ‘enhwk’ or ‘enhp’ state in larva) based on the chromhmm analysis. the activated enhancer elements were predicted intersecting enhancer elements with h3k27ac significant peaks, requiring a 50% minimal overlap fraction. bedtools v2.23.0 […]

PMCID: 5446398
PMID: 28550296
DOI: 10.1038/s41598-017-02547-w

[…] totaling 106,926 2 kb intervals centered on the tss, and intersected with atac-seq peaks using bedtools intersect with the -u option. epigenome roadmap 15-state chromhmm coordinates were obtained from coordinates […]

PMCID: 5529029
PMID: 28700586
DOI: 10.1371/journal.pgen.1006883

[…] release) and repbase update (1.1.3 release) in repbase ( dhs datasets were obtained from encode (). genome segmentations in six cell types (combined between chromhmm and segway) [–] were obtained from encode (). datasets of cold spring harbor laboratory (cshl) longpolya rna-seq were obtained from encode in the gtf format (). ontology file (go-basic.obo, […]

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ChromHMM in publications

PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] (h3k4me1, h3k27ac, h3k4me3, h3k27me3, and h3k9me3), dna methylation, and rna-seq on 24 human pdac samples grown as pdtxs (supplementary table ). using a multivariate hidden markov model, as built by chromhmm, our analysis assigned fifteen chromatin states along with the average genome coverage by each state (fig. ). in agreement with the encode roadmap project, we defined that h3k4me3 containing […]

PMCID: 5953939
PMID: 29765031
DOI: 10.1038/s41467-018-04310-9

[…] technologies could provide a unique opportunity to define the global epigenomic landscape of ra, they also pose a great challenge to analyze in one integrative model. segmentation methods, such as chromhmm and segway can identify functional elements but focus on histone modifications and have not incorporated other data such as dna methylation. furthermore, the epigenomic signals in ra and oa […]

PMCID: 5954283
PMID: 29764360
DOI: 10.1186/s12864-018-4459-6

[…] can be downloaded from, the majority of our datasets were adapted from targetfinder. promoter and enhancer regions were identified using encode segway [] and chromhmm [] annotations for k562, gm12878, hela-s3, and huvec cell lines, and using roadmap [] epigenomics chromhmm annotations for nhek and imr90 cell lines. since epis could only happen […]

PMCID: 5965702
PMID: 29719267
DOI: 10.1016/j.celrep.2018.03.129

[…] samples’ signals correlated well with their primary signals and clustered generally by mark and biological function (, ). using the imputed craniofacial data, we then segmented the genome using chromhmm for each embryonic sample based on previously generated models of 15, 18, and 25 states of chromatin activity (). we identified similar numbers and proportions of segments in each state […]

PMCID: 5928241
PMID: 29712937
DOI: 10.1038/s41598-018-24755-8

[…] chip-seq data for histone modifications, rna polymerase occupancy, and other chromatin features, ernst, et al. used a hidden markov model to partition the genome into functional domains, termed chromhmm. we analyzed the chromhmm states and existing genome-wide datasets to evaluate the chromatin structure surrounding the irradiation-sensitive cpg sites. this analysis revealed that the 56fe […]

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ChromHMM institution(s)
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA

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