ChromHMM: automating chromatin state discovery and characterization
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Summary
ChromHMM is developed, an automated computational system for learning chromatin states, characterizing their biological functions and correlations with large-scale functional datasets, and visualizing the resulting genome-wide maps of chromatin state annotations.
- Type
- article
- Published
- 2012-02-01
- Cited by
- 2,434
- References
- 14
- Access
- Open access
- OpenAlex
- https://openalex.org/W1598350571
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:650176
Keywords
Chromatin, Computational biology, ChIA-PET, Annotation, Computer science
References
- Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
- Discovery and characterization of chromatin states for systematic annotation of the human genome
- The human genome browser at UCSC.
- Unsupervised segmentation of continuous genomic data
- UvA-DARE ( Digital Academic Repository ) Reading the maps : Organization and function of chromatin types in Drosophila Braunschweig
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- Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type
- Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals
- A glutamatergic network mediates lithium response in bipolar disorder as defined by epigenome pathway analysis.
- Integrative genomic analysis reveals functional diversification of APOBEC gene family in breast cancer
- Incorporating Functional Annotations for Fine-Mapping Causal Variants in a Bayesian Framework Using Summary Statistics
- Confident gene activity prediction based on single histone modification H2BK5ac in human cell lines
- ORIO (Online Resource for Integrative Omics): a web-based platform for rapid integration of next generation sequencing data
- ChromBiSim: Interactive chromatin biclustering using a simple approach.
- UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq
- The effect of genetic variation on promoter usage and enhancer activity
- Genome-wide prediction of cis-regulatory regions using supervised deep learning methods
- A comprehensive analysis of 195 DNA methylomes reveals shared and cell-specific features of partially methylated domains
- Informative combination of CLU rs11136000, serum HDL levels, diabetes, and age as a new piece of puzzle-picture of predictive medicine for cognitive disorders
- A Short Report on the Markov Property of DNA Sequences on 200-bp Genomic Units of Roadmap Genomics ChromHMM Annotations: A Computational Perspective
- Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency
- Fast detection of differential chromatin domains with SCIDDO
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