ArticleGenome medicine2020
Modeling and analysis of Hi-C data by HiSIF identifies characteristic promoter-distal loops.
Article in Genome medicine, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Integrated analysis of differential intra-chromosomal community interactions: A study of breast cancer.Artificial intelligence in medicine · 2025Article
- Integration of scHi-C and scRNA-seq data defines distinct 3D-regulated and biological-context dependent cell subpopulations.Nature communications · 2024Article
- From enhancers to genome conformation: complex transcriptional control underlies expression of a single herpesviral gene.bioRxiv : the preprint server for biology · 2024Article
- 3D Chromatin Alteration by Disrupting β-Catenin/CBP Interaction Is Enriched with Insulin Signaling in Pancreatic Cancer.Cancers · 2024Article
- Mapping nucleosome and chromatin architectures: A survey of computational methods.Computational and structural biotechnology journal · 2022Review
- Integrating whole genome sequencing, methylation, gene expression, topological associated domain information in regulatory mutation prediction: A study of follicular lymphoma.Computational and structural biotechnology journal · 2022Article
- Lattice simulation-based diffusion modelling of 3D chromatin structure.Computational and structural biotechnology journal · 2022Article
- Hi-C profiling of cancer spheroids identifies 3D-growth-specific chromatin interactions in breast cancer endocrine resistance.Clinical epigenetics · 2021Article
- Modeling and analysis of Hi-C data by HiSIF identifies characteristic promoter-distal loops.Genome medicine · 2020Article
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Authors and funding
9 authors.
Funding
Abstract
Current computational methods on Hi-C analysis focused on identifying Mb-size domains often failed to unveil the underlying functional and mechanistic relationship of chromatin structure and gene regulation. We developed a novel computational method HiSIF to identify genome-wide interacting loci. We illustrated HiSIF outperformed other tools for identifying chromatin loops. We applied it to Hi-C data in breast cancer cells and identified 21 genes with gained loops showing worse relapse-free survival in endocrine-treated patients, suggesting the genes with enhanced loops can be used for prognostic signatures for measuring the outcome of the endocrine treatment. HiSIF is available at https://github.com/yufanzhouonline/HiSIF .
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Registered trials
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