ArticleNature methods2020
FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation.
Article in Nature methods, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Epigenetic biomarkers in inflammatory bowel diseases-computational challenges and opportunities.Journal of Crohn's & colitis · 2026Review
- scDIAGRAM: detecting chromatin compartments from individual single-cell Hi-C matrix without imputation or reference features.Briefings in bioinformatics · 2026Article
- Charm is a flexible pipeline to simulate chromosomal rearrangements on Hi-C-like data.NAR genomics and bioinformatics · 2025Article
- Hidden origami inmBio · 2025Article
- Tracing cancer evolution and heterogeneity using Hi-C.Nature communications · 2023Article
- scHi-CSim: a flexible simulator that generates high-fidelity single-cell Hi-C data for benchmarking.Journal of molecular cell biology · 2023Article
- HiSV: A control-free method for structural variation detection from Hi-C data.PLoS computational biology · 2023Article
- Reconstruct high-resolution 3D genome structures for diverse cell-types using FLAMINGO.Nature communications · 2022Article
- Clipper: p-value-free FDR control on high-throughput data from two conditions.Genome biology · 2021Article
- FreeHi-C spike-in simulations for benchmarking differential chromatin interaction detection.Methods (San Diego, Calif.) · 2021Article
- Sündüz Keleş.Nature methods · 2020Article
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2 authors.
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Abstract
The ability to simulate high-throughput chromatin conformation (Hi-C) data is foundational for benchmarking Hi-C data analysis methods. Here we present a nonparametric strategy named FreeHi-C to simulate Hi-C data from the interacting genome fragments. Data from FreeHi-C exhibit high fidelity to biological Hi-C data. FreeHi-C boosts the precision and power of differential chromatin interaction detection through data augmentation under preserved false discovery rate control.
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