ArticleNature genetics2020
CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction.
Article in Nature genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Spatiotemporal 3D chromatin organization across multiple brain regions during human fetal development.Cell discovery · 2025Article
- A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs.BMC genomics · 2025Article
- Examining the dynamics of three-dimensional genome organization with multitask matrix factorization.Genome research · 2025Article
- Topologically associating domains and the evolution of three-dimensional genome architecture in rice.The Plant journal : for cell and molecular biology · 2025Article
- Comparing chromatin contact maps at scale: methods and insights.Nature methods · 2025Article
- A comprehensive review and benchmark of differential analysis tools for Hi-C data.Briefings in bioinformatics · 2025Review
- The jet-like chromatin structure defines active secondary metabolism in fungi.Nucleic acids research · 2024Article
- Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci.Genome biology · 2024Article
- KDM3B inhibitors disrupt the oncogenic activity of PAX3-FOXO1 in fusion-positive rhabdomyosarcoma.Nature communications · 2024Article
- DiffDomain enables identification of structurally reorganized topologically associating domains.Nature communications · 2024Article
- Revisiting the use of structural similarity index in Hi-C.Nature genetics · 2023Article
- Transcription induces context-dependent remodeling of chromatin architecture during differentiation.PLoS biology · 2023Article
- The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data.Briefings in bioinformatics · 2023Review
- A deep learning method for replicate-based analysis of chromosome conformation contacts using Siamese neural networks.Nature communications · 2023Article
- Assessing chromatin relocalization in 3D using the patient rule induction method.Biostatistics (Oxford, England) · 2023Article
- Eighty million years of rapid evolution of the primate Y chromosome.Nature ecology & evolution · 2023Article
- Comparing chromatin contact maps at scale: methods and insights.Research square · 2023Article
- High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon.BMC plant biology · 2023Article
- Comparing chromatin contact maps at scale: methods and insights.bioRxiv : the preprint server for biology · 2023Article
- HiConfidence: a novel approach uncovering the biological signal in Hi-C data affected by technical biases.Briefings in bioinformatics · 2023Article
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6 authors.
Funding
Abstract
Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data.
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