ArticleGenome biology2021
GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 32 citations in OpenAlex.
- TADShop: systematic benchmarking and identification of topologically associating domains.Nature methods · 2026Article
- A comparative analysis of topological domain callers over RNA-associated interactome.BMC bioinformatics · 2026Article
- Dissecting regulatory non-coding GWAS loci reveals fibroblast causal genes with pathophysiological relevance to heart failure.Nature communications · 2025Article
- Deciphering chromatin domain, domain community and chromunity for 3D genome maps with Mactop.Communications biology · 2025Article
- RobusTAD: reference panel based annotation of nested topologically associating domains.Genome biology · 2025Article
- Examining the dynamics of three-dimensional genome organization with multitask matrix factorization.Genome research · 2025Article
- Uncovering topologically associating domains from three-dimensional genome maps with TADGATE.Nucleic acids research · 2025Article
- ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization.PLoS computational biology · 2025Article
- Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes.Genome research · 2024Article
- A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains.Nature communications · 2024Article
- Identifying TAD-like domains on single-cell Hi-C data by graph embedding and changepoint detection.Bioinformatics (Oxford, England) · 2024Article
- ChromaFactor: deconvolution of single-molecule chromatin organization with non-negative matrix factorization.bioRxiv : the preprint server for biology · 2023Article
- The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data.Briefings in bioinformatics · 2023Review
- DeDoc2 Identifies and Characterizes the Hierarchy and Dynamics of Chromatin TAD-Like Domains in the Single Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Reference panel-guided super-resolution inference of Hi-C data.Bioinformatics (Oxford, England) · 2023Article
- Integrative chromatin domain annotation through graph embedding of Hi-C data.Bioinformatics (Oxford, England) · 2023Article
- HPTAD: A computational method to identify topologically associating domains from HiChIP and PLAC-seq datasets.Computational and structural biotechnology journal · 2023Article
- GILoop: Robust chromatin loop calling across multiple sequencing depths on Hi-C data.iScience · 2022Article
- Reference panel guided topological structure annotation of Hi-C data.Nature communications · 2022Article
- A comparison of topologically associating domain callers over mammals at high resolution.BMC bioinformatics · 2022Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
High-throughput chromosome conformation capture assays, such as Hi-C, have shown that the genome is organized into organizational units such as topologically associating domains (TADs), which can impact gene regulatory processes. The sparsity of Hi-C matrices poses a challenge for reliable detection of these units. We present GRiNCH, a constrained matrix-factorization-based approach for simultaneous smoothing and discovery of TADs from sparse contact count matrices. GRiNCH shows superior performance against seven TAD-calling methods and three smoothing methods. GRiNCH is applicable to multiple platforms including SPRITE and HiChIP and can predict novel boundary factors with potential roles in genome organization.
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Registered trials
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.