{"id":"https://openalex.org/W7126046672","doi":"https://doi.org/10.1109/bibm66473.2025.11356431","title":"Leveraging scHi-C Data for Integrated Single-Cell Omics Analysis","display_name":"Leveraging scHi-C Data for Integrated Single-Cell Omics Analysis","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126046672","doi":"https://doi.org/10.1109/bibm66473.2025.11356431"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11356431","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356431","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5121237668","display_name":"Weixin Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Weixin Liu","raw_affiliation_strings":["Vanderbilt University,Nashville,Tennessee,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vanderbilt University,Nashville,Tennessee,USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100403642","display_name":"Rui Chen","orcid":"https://orcid.org/0000-0002-4341-2908"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rui Chen","raw_affiliation_strings":["Vanderbilt University,Nashville,Tennessee,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vanderbilt University,Nashville,Tennessee,USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124232536","display_name":"Yang Li","orcid":null},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yang Li","raw_affiliation_strings":["Vanderbilt University,Nashville,Tennessee,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vanderbilt University,Nashville,Tennessee,USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042786517","display_name":"Yuting Tan","orcid":"https://orcid.org/0000-0002-3605-1307"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuting Tan","raw_affiliation_strings":["Vanderbilt University,Nashville,Tennessee,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vanderbilt University,Nashville,Tennessee,USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Xue Zhong","orcid":null},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xue Zhong","raw_affiliation_strings":["Vanderbilt University,Nashville,Tennessee,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vanderbilt University,Nashville,Tennessee,USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015400531","display_name":"Bo Li","orcid":"https://orcid.org/0000-0002-7294-6888"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bingshan Li","raw_affiliation_strings":["Vanderbilt University,Nashville,Tennessee,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vanderbilt University,Nashville,Tennessee,USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5124231830","display_name":"Zhijun Yin","orcid":null},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhijun Yin","raw_affiliation_strings":["Vanderbilt University,Nashville,Tennessee,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vanderbilt University,Nashville,Tennessee,USA","institution_ids":["https://openalex.org/I200719446"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I200719446"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"39","last_page":"44"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9939000010490417,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9939000010490417,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.0010999999940395355,"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/T10505","display_name":"Pluripotent Stem Cells Research","score":0.000699999975040555,"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/data-integration","display_name":"Data integration","score":0.7854999899864197},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.478300005197525},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.4377000033855438},{"id":"https://openalex.org/keywords/neuroinformatics","display_name":"Neuroinformatics","score":0.4244999885559082},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.373199999332428},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.3691999912261963},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.3368000090122223}],"concepts":[{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.7854999899864197},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.580299973487854},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48980000615119934},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.478300005197525},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.4377000033855438},{"id":"https://openalex.org/C205427263","wikidata":"https://www.wikidata.org/wiki/Q1931480","display_name":"Neuroinformatics","level":2,"score":0.4244999885559082},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.373199999332428},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3691999912261963},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36820000410079956},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.3368000090122223},{"id":"https://openalex.org/C33326189","wikidata":"https://www.wikidata.org/wiki/Q17092450","display_name":"Information integration","level":2,"score":0.3239000141620636},{"id":"https://openalex.org/C2780980858","wikidata":"https://www.wikidata.org/wiki/Q110022","display_name":"Dual (grammatical number)","level":2,"score":0.3212999999523163},{"id":"https://openalex.org/C19527686","wikidata":"https://www.wikidata.org/wiki/Q1665453","display_name":"System integration","level":2,"score":0.31360000371932983},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.305400013923645},{"id":"https://openalex.org/C75684735","wikidata":"https://www.wikidata.org/wiki/Q858810","display_name":"Big data","level":2,"score":0.3005000054836273},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.29269999265670776},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.2687999904155731}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356431","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356431","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1567168821","https://openalex.org/W1973605976","https://openalex.org/W2046165140","https://openalex.org/W2068359053","https://openalex.org/W2069977787","https://openalex.org/W2123403527","https://openalex.org/W2551092411","https://openalex.org/W2803562279","https://openalex.org/W2949177718","https://openalex.org/W2979911343","https://openalex.org/W3045703643","https://openalex.org/W3124454906","https://openalex.org/W3207880742","https://openalex.org/W4225278475","https://openalex.org/W4379792586","https://openalex.org/W4386471322","https://openalex.org/W4400140791","https://openalex.org/W4403519940","https://openalex.org/W4406146175","https://openalex.org/W4406155921","https://openalex.org/W4406844902"],"related_works":[],"abstract_inverted_index":{"The":[0],"integration":[1,28,38,75,131],"of":[2,48,76],"single-cell":[3,15,36],"multi-omics":[4,27,37,157],"data":[5,50,101,155],"is":[6],"essential":[7],"for":[8,152],"deciphering":[9],"complex":[10],"gene":[11,63,174],"regulatory":[12,64,166],"programs.":[13],"While":[14],"Hi-C":[16],"(scHi-C)":[17],"provides":[18],"insight":[19],"into":[20,138],"3D":[21,170],"genome":[22,171],"architecture,":[23],"its":[24,122],"utilization":[25],"in":[26,82,124,156],"remains":[29],"underexplored.":[30],"Here,":[31],"we":[32,58,89],"use":[33,59],"mouse":[34],"brain":[35],"as":[39,61,98],"a":[40,52,62,68,99,110,125,134,160],"case":[41],"study":[42],"to":[43,66,163],"demonstrate":[44,121],"the":[45,92],"dual":[46],"utility":[47],"scHiC":[49],"within":[51],"knowledge":[53],"graph-based":[54],"integrative":[55],"framework.":[56],"First,":[57],"scHi-C":[60,97,114,154],"prior":[65],"construct":[67],"Hi-C-driven":[69],"guidance":[70],"graph.":[71],"This":[72,129],"approach":[73],"enhances":[74],"scRNA-seq":[77,112],"and":[78,113,120,143],"scATAC-seq":[79],"data,":[80],"resulting":[81],"an":[83,149],"improved":[84],"alignment":[85],"score":[86],"(FOSCTTM$=0.0356)$.":[87],"Second,":[88],"show":[90],"that":[91],"framework":[93],"can":[94],"directly":[95],"integrate":[96],"primary":[100],"modality":[102],"with":[103,173],"scRNA-seq.":[104],"We":[105],"validate":[106],"this":[107],"method":[108],"on":[109],"paired":[111],"dataset,":[115],"achieving":[116],"85.0%":[117],"mapping":[118],"accuracy,":[119],"power":[123],"cross-modal":[126],"labeltransfer":[127],"application.":[128],"direct":[130],"successfully":[132],"refines":[133],"broader":[135],"neuronal":[136],"cluster":[137],"finer,":[139],"distinct":[140],"hippocampal":[141],"granule":[142],"pyramidal":[144],"subtypes.":[145],"Our":[146],"work":[147],"presents":[148],"effective":[150],"strategy":[151],"leveraging":[153],"integration,":[158],"providing":[159],"powerful":[161],"tool":[162],"dissect":[164],"cellular":[165],"programs":[167],"through":[168],"combining":[169],"organization":[172],"expression.":[175]},"counts_by_year":[],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2026-01-30T00:00:00"}
