ArticleGenome biology2016
A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- PySimi: a unified framework for similarity measure evaluation in spectral clustering with applications to omics data.Frontiers in genetics · 2026Article
- Examining the dynamics of three-dimensional genome organization with multitask matrix factorization.Genome research · 2025Article
- Esearch3D: propagating gene expression in chromatin networks to illuminate active enhancers.Nucleic acids research · 2023Article
- GILoop: Robust chromatin loop calling across multiple sequencing depths on Hi-C data.iScience · 2022Article
- GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization.Genome biology · 2021Article
- A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies.Nucleic acids research · 2021Article
- Advances in Chromatin and Chromosome Research: Perspectives from Multiple Fields.Molecular cell · 2020Review
- SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering.BMC bioinformatics · 2020Article
- BHi-Cect: a top-down algorithm for identifying the multi-scale hierarchical structure of chromosomes.Nucleic acids research · 2020Article
- Identification of FMR1-regulated molecular networks in human neurodevelopment.Genome research · 2020Article
- Topological structure analysis of chromatin interaction networks.BMC bioinformatics · 2019Article
- Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis.BMC bioinformatics · 2019Article
- MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions.PLoS computational biology · 2017Article
- Inference of cell type specific regulatory networks on mammalian lineages.Current opinion in systems biology · 2017Article
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Authors and funding
3 authors.
Funding
Abstract
Chromosome conformation capture methods are being increasingly used to study three-dimensional genome architecture in multiple cell types and species. An important challenge is to examine changes in three-dimensional architecture across cell types and species. We present Arboretum-Hi-C, a multi-task spectral clustering method, to identify common and context-specific aspects of genome architecture. Compared to standard clustering, Arboretum-Hi-C produced more biologically consistent patterns of conservation. Most clusters are conserved and enriched for either high- or low-activity genomic signals. Most genomic regions diverge between clusters with similar chromatin state except for a few that are associated with lamina-associated domains and open chromatin.
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