{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,11]],"date-time":"2025-09-11T22:47:55Z","timestamp":1757630875512,"version":"3.44.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2025,8,22]],"date-time":"2025-08-22T00:00:00Z","timestamp":1755820800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"KAKENHI","doi-asserted-by":"publisher","award":["JP23K21718"],"award-info":[{"award-number":["JP23K21718"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,9,1]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n Chromatin domain annotation identifies functional genomic regions, such as active and inactive zones, based on epigenomic features like histone modifications, DNA methylation, and chromatin accessibility. While recent methods have utilized both chromatin interaction data (e.g. Hi-C) and epigenomic data, they often overlook the direct relationship between these data types.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n In this study, we introduce Chromatin Domain Annotation using Contrastive Learning for Hi-C and Epigenomic Data (CDACHIE), a method for identifying chromatin domains from Hi-C and epigenomic data. Our approach leverages contrastive learning to generate aligned representative vectors for both data types at each genomic bin. The concatenated vectors are then clustered using K-means to classify distinct chromatin domain types. CDACHIE achieves superior performance in Variance Explained, evaluated across gene expression, replication timing, and ChIA-PET data. This highlights its robust ability to integrate semantic associations between Hi-C and epigenomic features within the embedding space.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n The source code is available at GitHub: https:\/\/github.com\/maruyama-lab-design\/CDACHIE. An archival snapshot of the code used in this study is available on Zenodo: https:\/\/doi.org\/10.5281\/zenodo.15751780.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf464","type":"journal-article","created":{"date-parts":[[2025,8,22]],"date-time":"2025-08-22T18:07:59Z","timestamp":1755886079000},"source":"Crossref","is-referenced-by-count":0,"title":["CDACHIE: chromatin domain annotation by integrating chromatin interaction and epigenomic data with contrastive learning"],"prefix":"10.1093","volume":"41","author":[{"given":"Asato","family":"Yoshinaga","sequence":"first","affiliation":[{"name":"Graduate School of Design, Kyushu University , Fukuoka, 815-8540,","place":["Japan"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5760-1507","authenticated-orcid":false,"given":"Osamu","family":"Maruyama","sequence":"additional","affiliation":[{"name":"Faculty of Design, Kyushu University , Fukuoka, 815-8540,","place":["Japan"]}]}],"member":"286","published-online":{"date-parts":[[2025,8,22]]},"reference":[{"key":"2025091016114567500_btaf464-B1","doi-asserted-by":"crossref","first-page":"1173","DOI":"10.1038\/s41467-020-14974-x","article-title":"Graph embedding and unsupervised learning predict genomic sub-compartments from HiC chromatin interaction data","volume":"11","author":"Ashoor","year":"2020","journal-title":"Nat Commun"},{"key":"2025091016114567500_btaf464-B2","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature11082","article-title":"Topological domains in mammalian genomes identified by analysis of chromatin interactions","volume":"485","author":"Dixon","year":"2012","journal-title":"Nature"},{"key":"2025091016114567500_btaf464-B3","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/nmeth.1906","article-title":"ChromHMM: automating chromatin-state discovery and characterization","volume":"9","author":"Ernst","year":"2012","journal-title":"Nat Methods"},{"key":"2025091016114567500_btaf464-B4","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1038\/nmeth.1937","article-title":"Unsupervised pattern discovery in human chromatin structure through genomic segmentation","volume":"9","author":"Hoffman","year":"2012","journal-title":"Nat Methods"},{"key":"2025091016114567500_btaf464-B5","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1101\/gr.184341.114","article-title":"Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression","volume":"25","author":"Libbrecht","year":"2015","journal-title":"Genome Res"},{"key":"2025091016114567500_btaf464-B6","doi-asserted-by":"crossref","first-page":"e1009423","DOI":"10.1371\/journal.pcbi.1009423","article-title":"Segmentation and genome annotation algorithms for identifying chromatin state and 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graph embedding of Hi-C data","volume":"39","author":"Shokraneh","year":"2023","journal-title":"Bioinformatics"},{"key":"2025091016114567500_btaf464-B11","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1186\/s13059-020-02253-3","article-title":"SPIN reveals genome-wide landscape of nuclear compartmentalization","volume":"22","author":"Wang","year":"2021","journal-title":"Genome 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