{"id":"https://openalex.org/W4413445911","doi":"https://doi.org/10.1093/bioinformatics/btaf464","title":"CDACHIE: chromatin domain annotation by integrating chromatin interaction and epigenomic data with contrastive learning","display_name":"CDACHIE: chromatin domain annotation by integrating chromatin interaction and epigenomic data with contrastive learning","publication_year":2025,"publication_date":"2025-08-22","ids":{"openalex":"https://openalex.org/W4413445911","doi":"https://doi.org/10.1093/bioinformatics/btaf464","pmid":"https://pubmed.ncbi.nlm.nih.gov/40845158"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf464","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf464","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf464/64112015/btaf464.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf464/64112015/btaf464.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113423493","display_name":"Asato Yoshinaga","orcid":null},"institutions":[{"id":"https://openalex.org/I135598925","display_name":"Kyushu University","ror":"https://ror.org/00p4k0j84","country_code":"JP","type":"education","lineage":["https://openalex.org/I135598925"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Asato Yoshinaga","raw_affiliation_strings":["Graduate School of Design, Kyushu University , Fukuoka, 815-8540,","Graduate School of Design, Kyushu University, Fukuoka, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Design, Kyushu University , Fukuoka, 815-8540,","institution_ids":["https://openalex.org/I135598925"]},{"raw_affiliation_string":"Graduate School of Design, Kyushu University, Fukuoka, Japan","institution_ids":["https://openalex.org/I135598925"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035228232","display_name":"Osamu Maruyama","orcid":"https://orcid.org/0000-0002-5760-1507"},"institutions":[{"id":"https://openalex.org/I135598925","display_name":"Kyushu University","ror":"https://ror.org/00p4k0j84","country_code":"JP","type":"education","lineage":["https://openalex.org/I135598925"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Osamu Maruyama","raw_affiliation_strings":["Faculty of Design, Kyushu University , Fukuoka, 815-8540,","Faculty of Design, Kyushu University, Fukuoka, Japan"],"raw_orcid":"https://orcid.org/0000-0002-5760-1507","affiliations":[{"raw_affiliation_string":"Faculty of Design, Kyushu University , Fukuoka, 815-8540,","institution_ids":["https://openalex.org/I135598925"]},{"raw_affiliation_string":"Faculty of Design, Kyushu University, Fukuoka, Japan","institution_ids":["https://openalex.org/I135598925"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I135598925"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.4868,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.65940047,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"41","issue":"9","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.8245999813079834,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.8245999813079834,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.08110000193119049,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.048500001430511475,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/epigenomics","display_name":"Epigenomics","score":0.8006632328033447},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.7626374959945679},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.7486321926116943},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.6823315024375916},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6748802661895752},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43330293893814087},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3456113338470459},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33911705017089844},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2187187671661377},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1442786455154419},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.1095384955406189},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.09937211871147156},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08036336302757263}],"concepts":[{"id":"https://openalex.org/C121912465","wikidata":"https://www.wikidata.org/wiki/Q3589153","display_name":"Epigenomics","level":5,"score":0.8006632328033447},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.7626374959945679},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7486321926116943},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.6823315024375916},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6748802661895752},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43330293893814087},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3456113338470459},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33911705017089844},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2187187671661377},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1442786455154419},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.1095384955406189},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.09937211871147156},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08036336302757263},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf464","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf464","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf464/64112015/btaf464.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40845158","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40845158","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12422559","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12422559/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf464","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf464","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf464/64112015/btaf464.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4990465320","display_name":null,"funder_award_id":"JP23K21718","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413445911.pdf","grobid_xml":"https://content.openalex.org/works/W4413445911.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1973062929","https://openalex.org/W2018363492","https://openalex.org/W2070021921","https://openalex.org/W2090037139","https://openalex.org/W2146339031","https://openalex.org/W3010360466","https://openalex.org/W3125762071","https://openalex.org/W3207124649","https://openalex.org/W4230875896","https://openalex.org/W4312018781"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2795212387","https://openalex.org/W2988805143","https://openalex.org/W2625833328","https://openalex.org/W3160486573"],"abstract_inverted_index":{"MOTIVATION:":[0],"Chromatin":[1,56],"domain":[2,109],"annotation":[3],"identifies":[4],"functional":[5],"genomic":[6,95],"regions,":[7],"such":[8],"as":[9],"active":[10],"and":[11,23,37,64,76,124,138],"inactive":[12],"zones,":[13],"based":[14],"on":[15,168],"epigenomic":[16,38,77,139],"features":[17,140],"like":[18],"histone":[19],"modifications,":[20],"DNA":[21],"methylation,":[22],"chromatin":[24,32,72,108],"accessibility.":[25],"While":[26],"recent":[27],"methods":[28],"have":[29],"utilized":[30],"both":[31,90],"interaction":[33],"data":[34,48,91],"(e.g.":[35],"Hi-C)":[36],"data,":[39],"they":[40],"often":[41],"overlook":[42],"the":[43,142,160],"direct":[44],"relationship":[45],"between":[46,136],"these":[47],"types.":[49,110],"RESULTS:":[50],"In":[51],"this":[52,164],"study,":[53],"we":[54],"introduce":[55],"Domain":[57],"Annotation":[58],"using":[59,103],"Contrastive":[60],"Learning":[61],"for":[62,70,89],"Hi-C":[63,75,137],"Epigenomic":[65],"Data":[66],"(CDACHIE),":[67],"a":[68],"method":[69],"identifying":[71],"domains":[73],"from":[74],"data.":[78,126],"Our":[79],"approach":[80],"leverages":[81],"contrastive":[82],"learning":[83],"to":[84,105,132],"generate":[85],"aligned":[86],"representative":[87],"vectors":[88,99],"types":[92],"at":[93,153],"each":[94],"bin.":[96],"The":[97,148],"concatenated":[98],"are":[100],"then":[101],"clustered":[102],"K-means":[104],"classify":[106],"distinct":[107],"CDACHIE":[111],"achieves":[112],"superior":[113],"performance":[114],"in":[115,163],"Variance":[116],"Explained,":[117],"evaluated":[118],"across":[119],"gene":[120],"expression,":[121],"replication":[122],"timing,":[123],"ChIA-PET":[125],"This":[127],"highlights":[128],"its":[129],"robust":[130],"ability":[131],"integrate":[133],"semantic":[134],"associations":[135],"within":[141],"embedding":[143],"space.":[144],"AVAILABILITY":[145],"AND":[146],"IMPLEMENTATION:":[147],"source":[149],"code":[150,161],"is":[151,166],"available":[152,167],"GitHub:":[154],"https://github.com/maruyama-lab-design/CDACHIE.":[155],"An":[156],"archival":[157],"snapshot":[158],"of":[159],"used":[162],"study":[165],"Zenodo:":[169],"https://doi.org/10.5281/zenodo.15751780.":[170]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}