» Articles » PMID: 22373907

ChromHMM: Automating Chromatin-state Discovery and Characterization

Overview
Journal Nat Methods
Date 2012 Mar 1
PMID 22373907
Citations 1342
Authors
Affiliations
Soon will be listed here.
Citing Articles

Atlas of imprinted and allele-specific DNA methylation in the human body.

Rosenski J, Peretz A, Magenheim J, Loyfer N, Shemer R, Glaser B Nat Commun. 2025; 16(1):2141.

PMID: 40069157 PMC: 11897249. DOI: 10.1038/s41467-025-57433-1.


A chromosome-scale genome assembly and epigenomic profiling reveal temperature-dependent histone methylation in iridoid biosynthesis regulation in .

Xu Q, Liu C, Li B, Tian K, You L, Xie L Hortic Res. 2025; 12(3):uhae328.

PMID: 40046319 PMC: 11879554. DOI: 10.1093/hr/uhae328.


iModEst: disentangling -omic impacts on gene expression variation across genes and tissues.

Sokolowski D, Mai M, Verma A, Morgenshtern G, Subasri V, Naveed H NAR Genom Bioinform. 2025; 7(1):lqaf011.

PMID: 40041206 PMC: 11879402. DOI: 10.1093/nargab/lqaf011.


Evaluation of genomic selection models using whole genome sequence data and functional annotation in Belgian Blue cattle.

Yuan C, Gillon A, Gualdron Duarte J, Takeda H, Coppieters W, Georges M Genet Sel Evol. 2025; 57(1):10.

PMID: 40038647 PMC: 11881496. DOI: 10.1186/s12711-025-00955-5.


Circulating cell-free DNA methylation profiles as noninvasive multiple sclerosis biomarkers: A proof-of-concept study.

Fu H, Huang K, Zhu W, Zhang L, Bandaru R, Wang L medRxiv. 2025; .

PMID: 40034794 PMC: 11875267. DOI: 10.1101/2025.02.14.25322180.


References
1.
Day N, Hemmaplardh A, Thurman R, Stamatoyannopoulos J, Noble W . Unsupervised segmentation of continuous genomic data. Bioinformatics. 2007; 23(11):1424-6. DOI: 10.1093/bioinformatics/btm096. View

2.
Roy S, Ernst J, Kharchenko P, Kheradpour P, Negre N, Eaton M . Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010; 330(6012):1787-97. PMC: 3192495. DOI: 10.1126/science.1198374. View

3.
Ernst J, Kellis M . Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol. 2010; 28(8):817-25. PMC: 2919626. DOI: 10.1038/nbt.1662. View

4.
Kent W, Sugnet C, Furey T, Roskin K, Pringle T, Zahler A . The human genome browser at UCSC. Genome Res. 2002; 12(6):996-1006. PMC: 186604. DOI: 10.1101/gr.229102. View

5.
Ernst J, Kheradpour P, Mikkelsen T, Shoresh N, Ward L, Epstein C . Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011; 473(7345):43-9. PMC: 3088773. DOI: 10.1038/nature09906. View