{"id":"https://openalex.org/W4400140616","doi":"https://doi.org/10.1093/bioinformatics/btae211","title":"Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model","display_name":"Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model","publication_year":2024,"publication_date":"2024-06-28","ids":{"openalex":"https://openalex.org/W4400140616","doi":"https://doi.org/10.1093/bioinformatics/btae211","pmid":"https://pubmed.ncbi.nlm.nih.gov/38940142"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae211","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae211","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/Supplement_1/i471/58354834/btae211.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/article-pdf/40/Supplement_1/i471/58354834/btae211.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111242956","display_name":"Tangqi Fang","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tangqi Fang","raw_affiliation_strings":["Paul G. Allen School of Computer Science and Engineering, University of Washington , Seattle, WA 98195, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Paul G. Allen School of Computer Science and Engineering, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100782689","display_name":"Yifeng Liu","orcid":"https://orcid.org/0009-0003-9435-1441"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yifeng Liu","raw_affiliation_strings":["Paul G. Allen School of Computer Science and Engineering, University of Washington , Seattle, WA 98195, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Paul G. Allen School of Computer Science and Engineering, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021334101","display_name":"Addie Woicik","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Addie Woicik","raw_affiliation_strings":["Paul G. Allen School of Computer Science and Engineering, University of Washington , Seattle, WA 98195, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Paul G. Allen School of Computer Science and Engineering, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101262029","display_name":"Minsi Lu","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Minsi Lu","raw_affiliation_strings":["Paul G. Allen School of Computer Science and Engineering, University of Washington , Seattle, WA 98195, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Paul G. Allen School of Computer Science and Engineering, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047581665","display_name":"Anupama Jha","orcid":"https://orcid.org/0000-0003-3029-2086"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anupama Jha","raw_affiliation_strings":["Department of Genome Sciences, University of Washington , Seattle, WA 98195, United States"],"raw_orcid":"https://orcid.org/0000-0003-3029-2086","affiliations":[{"raw_affiliation_string":"Department of Genome Sciences, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100753201","display_name":"Xiao Wang","orcid":"https://orcid.org/0000-0003-4206-9199"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiao Wang","raw_affiliation_strings":["Department of Computer Science, Purdue University , West Lafayette, IN 47907, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Purdue University , West Lafayette, IN 47907, United States","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100438758","display_name":"Gang Li","orcid":"https://orcid.org/0000-0003-0759-9063"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gang Li","raw_affiliation_strings":["Department of Genome Sciences, University of Washington , Seattle, WA 98195, United States","eScience Institute, University of Washington , Seattle, WA 98195, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genome Sciences, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"eScience Institute, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051558318","display_name":"Borislav H. Hristov","orcid":"https://orcid.org/0000-0002-1414-8378"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Borislav Hristov","raw_affiliation_strings":["Department of Genome Sciences, University of Washington , Seattle, WA 98195, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genome Sciences, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104181709","display_name":"Zixuan Liu","orcid":"https://orcid.org/0009-0000-8503-1508"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zixuan Liu","raw_affiliation_strings":["Paul G. Allen School of Computer Science and Engineering, University of Washington , Seattle, WA 98195, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Paul G. Allen School of Computer Science and Engineering, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069634574","display_name":"Hanwen Xu","orcid":"https://orcid.org/0000-0003-4865-7071"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hanwen Xu","raw_affiliation_strings":["Paul G. Allen School of Computer Science and Engineering, University of Washington , Seattle, WA 98195, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Paul G. Allen School of Computer Science and Engineering, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057375933","display_name":"William Stafford Noble","orcid":"https://orcid.org/0000-0001-7283-4715"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"William S Noble","raw_affiliation_strings":["Department of Genome Sciences, University of Washington , Seattle, WA 98195, United States","Paul G. Allen School of Computer Science and Engineering, University of Washington , Seattle, WA 98195, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genome Sciences, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Paul G. Allen School of Computer Science and Engineering, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100371324","display_name":"Sheng Wang","orcid":"https://orcid.org/0000-0003-4210-1670"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sheng Wang","raw_affiliation_strings":["Paul G. Allen School of Computer Science and Engineering, University of Washington , Seattle, WA 98195, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Paul G. Allen School of Computer Science and Engineering, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":12,"corresponding_author_ids":["https://openalex.org/A5057375933","https://openalex.org/A5100371324"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.1984,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.78005751,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"40","issue":"Supplement_1","first_page":"i471","last_page":"i480"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9836000204086304,"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":0.9836000204086304,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.006000000052154064,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0013000000035390258,"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/chromosome-conformation-capture","display_name":"Chromosome conformation capture","score":0.7673208713531494},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.7237962484359741},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7062703371047974},{"id":"https://openalex.org/keywords/ctcf","display_name":"CTCF","score":0.5805965662002563},{"id":"https://openalex.org/keywords/chromosome","display_name":"Chromosome","score":0.5223389863967896},{"id":"https://openalex.org/keywords/matrix","display_name":"Matrix (chemical analysis)","score":0.4653063416481018},{"id":"https://openalex.org/keywords/loop","display_name":"Loop (graph theory)","score":0.4318307936191559},{"id":"https://openalex.org/keywords/line","display_name":"Line (geometry)","score":0.4192464351654053},{"id":"https://openalex.org/keywords/high-resolution","display_name":"High resolution","score":0.4111822247505188},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4110637903213501},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3231585621833801},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.17892253398895264},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14652284979820251},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11671820282936096}],"concepts":[{"id":"https://openalex.org/C93946551","wikidata":"https://www.wikidata.org/wiki/Q5113914","display_name":"Chromosome conformation capture","level":5,"score":0.7673208713531494},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.7237962484359741},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7062703371047974},{"id":"https://openalex.org/C2778760011","wikidata":"https://www.wikidata.org/wiki/Q21163346","display_name":"CTCF","level":5,"score":0.5805965662002563},{"id":"https://openalex.org/C30481170","wikidata":"https://www.wikidata.org/wiki/Q37748","display_name":"Chromosome","level":3,"score":0.5223389863967896},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.4653063416481018},{"id":"https://openalex.org/C184670325","wikidata":"https://www.wikidata.org/wiki/Q512604","display_name":"Loop (graph theory)","level":2,"score":0.4318307936191559},{"id":"https://openalex.org/C198352243","wikidata":"https://www.wikidata.org/wiki/Q37105","display_name":"Line (geometry)","level":2,"score":0.4192464351654053},{"id":"https://openalex.org/C3020199158","wikidata":"https://www.wikidata.org/wiki/Q210521","display_name":"High resolution","level":2,"score":0.4111822247505188},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4110637903213501},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3231585621833801},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.17892253398895264},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14652284979820251},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11671820282936096},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"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/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.0},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C62649853","wikidata":"https://www.wikidata.org/wiki/Q199687","display_name":"Remote sensing","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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":"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":"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":"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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae211","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae211","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/Supplement_1/i471/58354834/btae211.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:38940142","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38940142","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:11211821","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11211821","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11211821/pdf/btae211.pdf","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/btae211","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae211","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/Supplement_1/i471/58354834/btae211.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/G399756631","display_name":null,"funder_award_id":"R01HG011466","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8813706751","display_name":null,"funder_award_id":"UM1HG011531","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G927148200","display_name":null,"funder_award_id":"UM1 HG011531","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4400140616.pdf"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1660678623","https://openalex.org/W1973062929","https://openalex.org/W1981276685","https://openalex.org/W2057267524","https://openalex.org/W2070021921","https://openalex.org/W2090037139","https://openalex.org/W2109949710","https://openalex.org/W2125397535","https://openalex.org/W2140952049","https://openalex.org/W2159479483","https://openalex.org/W2163412235","https://openalex.org/W2507209892","https://openalex.org/W2523285811","https://openalex.org/W2530292798","https://openalex.org/W2592955530","https://openalex.org/W2594764564","https://openalex.org/W2803256172","https://openalex.org/W2806123558","https://openalex.org/W2936970738","https://openalex.org/W2949514938","https://openalex.org/W2953462601","https://openalex.org/W2982661386","https://openalex.org/W3001791723","https://openalex.org/W3007609047","https://openalex.org/W3013167866","https://openalex.org/W3015754908","https://openalex.org/W3091034669","https://openalex.org/W3106437999","https://openalex.org/W3155072588","https://openalex.org/W3156421803","https://openalex.org/W4220661565","https://openalex.org/W4226014430","https://openalex.org/W4309076319","https://openalex.org/W4382631698","https://openalex.org/W6794269193"],"related_works":["https://openalex.org/W2582488421","https://openalex.org/W4394834518","https://openalex.org/W4220758050","https://openalex.org/W3195254751","https://openalex.org/W2001502812","https://openalex.org/W3116849561","https://openalex.org/W2136004413","https://openalex.org/W2521860411","https://openalex.org/W1968273299","https://openalex.org/W2111997778"],"abstract_inverted_index":{"MOTIVATION:":[0],"High-resolution":[1],"Hi-C":[2,16,88,102,240],"contact":[3,30,41,103,258],"matrices":[4,42],"reveal":[5],"the":[6,11,100,122,125,151,163,171,202,220,233,256],"detailed":[7],"three-dimensional":[8],"architecture":[9],"of":[10,99,124,205,222,264],"genome,":[12],"but":[13,46],"high-coverage":[14,115,153,234],"experimental":[15],"data":[17],"are":[18,49,276],"expensive":[19],"to":[20,38,112,179,193,213,229,247],"generate.":[21],"Simultaneously,":[22],"chromatin":[23,94,147,249],"structure":[24],"analyses":[25],"struggle":[26],"with":[27],"extremely":[28],"sparse":[29],"matrices.":[31],"To":[32],"address":[33],"this":[34,206,274],"problem,":[35],"computational":[36],"methods":[37,48,55,134],"enhance":[39],"low-coverage":[40,257],"have":[43],"been":[44],"developed,":[45],"existing":[47,133,180,196],"largely":[50],"based":[51],"on":[52,132],"resolution":[53,89,241],"enhancement":[54,90,242],"for":[56,87,146,269],"natural":[57],"images":[58],"and":[59,75,105,141,166,199,217,266],"hence":[60],"often":[61],"employ":[62],"models":[63],"that":[64,91,119,158,185,219,244,251],"do":[65],"not":[66],"distinguish":[67],"between":[68],"biologically":[69],"meaningful":[70],"contacts,":[71],"such":[72],"as":[73,96],"loops":[74,216,224],"other":[76],"stochastic":[77],"contacts.":[78],"RESULTS:":[79],"We":[80,117,155,182],"present":[81],"Capricorn,":[82],"a":[83,107,114,128,238],"machine":[84],"learning":[85],"model":[86,110],"incorporates":[92],"small-scale":[93],"features":[95,250],"additional":[97],"views":[98],"input":[101],"matrix":[104],"leverages":[106],"diffusion":[108],"probability":[109],"backbone":[111],"generate":[113],"matrix.":[116,259],"show":[118,184],"Capricorn":[120,159,226,236,265],"outperforms":[121],"state":[123],"art":[126],"in":[127,137,143,162,255,273],"cross-cell-line":[129,168],"setting,":[130,169],"improving":[131,170],"by":[135,176],"17%":[136],"mean":[138],"squared":[139],"error":[140],"26%":[142],"F1":[144,174],"score":[145,175],"loop":[148,173],"identification":[149],"from":[150,225,232],"generated":[152],"data.":[154,235],"also":[156,190],"demonstrate":[157],"performs":[160],"well":[161],"cross-chromosome":[164],"setting":[165],"cross-chromosome,":[167],"downstream":[172],"14%":[177],"relative":[178],"methods.":[181],"further":[183],"our":[186],"multiview":[187],"idea":[188],"can":[189],"be":[191,253],"used":[192],"improve":[194],"several":[195],"methods,":[197],"HiCARN":[198],"HiCNN,":[200],"indicating":[201],"wide":[203],"applicability":[204],"approach.":[207],"Finally,":[208],"we":[209],"use":[210],"DNA":[211],"sequence":[212],"validate":[214],"discovered":[215],"find":[218,248],"fraction":[221],"CTCF-supported":[223],"is":[227,237],"similar":[228],"those":[230],"identified":[231,254],"powerful":[239],"method":[243],"enables":[245],"scientists":[246],"cannot":[252],"AVAILABILITY":[260],"AND":[261],"IMPLEMENTATION:":[262],"Implementation":[263],"source":[267],"code":[268],"reproducing":[270],"all":[271],"figures":[272],"paper":[275],"available":[277],"at":[278],"https://github.com/CHNFTQ/Capricorn.":[279]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}