ArticleGenome biology2015
Spectacle: fast chromatin state annotation using spectral learning.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 58 citations in OpenAlex.
- Pan-cell type continuous chromatin state annotation of 1,698 epigenomes from the International Human Epigenome Consortium.Genome biology · 2026Article
- Chromatin Landscape Is Associated With Sex-Biased Expression and Drosophila-Like Dosage Compensation of the Z Chromosome in Artemia franciscana.Molecular biology and evolution · 2025Article
- Computational methods to explore chromatin state dynamics.Briefings in bioinformatics · 2022Review
- Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns.PLoS computational biology · 2021Review
- NucHMM: a method for quantitative modeling of nucleosome organization identifying functional nucleosome states distinctly associated with splicing potentiality.Genome biology · 2021Article
- Fast detection of differential chromatin domains with SCIDDO.Bioinformatics (Oxford, England) · 2021Article
- Self-organizing maps with variable neighborhoods facilitate learning of chromatin accessibility signal shapes associated with regulatory elements.BMC bioinformatics · 2021Article
- Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data.BMC genomics · 2021Article
- An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis.Genome research · 2020Article
- Athena: Automated Tuning of k-mer based Genomic Error Correction Algorithms using Language Models.Scientific reports · 2019Article
- EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences.Nucleic acids research · 2019Article
- Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model.BMC genomics · 2018Article
- HebbPlot: an intelligent tool for learning and visualizing chromatin mark signatures.BMC bioinformatics · 2018Article
- chromswitch: a flexible method to detect chromatin state switches.Bioinformatics (Oxford, England) · 2018Article
- Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements.Bioinformatics (Oxford, England) · 2018Article
- FUN-LDA: A Latent Dirichlet Allocation Model for Predicting Tissue-Specific Functional Effects of Noncoding Variation: Methods and Applications.American journal of human genetics · 2018Article
- Chromatin-state discovery and genome annotation with ChromHMM.Nature protocols · 2017Review
- EpiCompare: an online tool to define and explore genomic regions with tissue or cell type-specific epigenomic features.Bioinformatics (Oxford, England) · 2017Article
- Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data.Scientific reports · 2017Article
- A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets.Journal of computational biology : a journal of computational molecular cell biology · 2017Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Epigenomic data from ENCODE can be used to associate specific combinations of chromatin marks with regulatory elements in the human genome. Hidden Markov models and the expectation-maximization (EM) algorithm are often used to analyze epigenomic data. However, the EM algorithm can have overfitting problems in data sets where the chromatin states show high class-imbalance and it is often slow to converge. Here we use spectral learning instead of EM and find that our software Spectacle overcame these problems. Furthermore, Spectacle is able to find enhancer subtypes not found by ChromHMM but strongly enriched in GWAS SNPs. Spectacle is available at https://github.com/jiminsong/Spectacle.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.