{"id":"https://openalex.org/W7164745540","doi":"https://doi.org/10.1093/bib/bbag305","title":"GraphChIAr: genome-wide super-resolution reconstruction of protein-mediated remote chromatin interactions by augmenting hi-C interaction maps with multiple ChIP-seq profiles","display_name":"GraphChIAr: genome-wide super-resolution reconstruction of protein-mediated remote chromatin interactions by augmenting hi-C interaction maps with multiple ChIP-seq profiles","publication_year":2026,"publication_date":"2026-05-01","ids":{"openalex":"https://openalex.org/W7164745540","doi":"https://doi.org/10.1093/bib/bbag305","pmid":"https://pubmed.ncbi.nlm.nih.gov/42289051"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag305","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag305","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbag305","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100389360","display_name":"Hao Dong","orcid":"https://orcid.org/0009-0001-5308-0759"},"institutions":[{"id":"https://openalex.org/I132369690","display_name":"Tianjin University of Science and Technology","ror":"https://ror.org/018rbtf37","country_code":"CN","type":"education","lineage":["https://openalex.org/I132369690"]},{"id":"https://openalex.org/I136765683","display_name":"Tianjin University of Technology","ror":"https://ror.org/00zbe0w13","country_code":"CN","type":"education","lineage":["https://openalex.org/I136765683"]},{"id":"https://openalex.org/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Dong","raw_affiliation_strings":["School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University , Tianjin 300350 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University , Tianjin 300350 ,","institution_ids":["https://openalex.org/I132369690","https://openalex.org/I136765683","https://openalex.org/I162868743"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138614923","display_name":"Guo-Zheng Rao","orcid":null},"institutions":[{"id":"https://openalex.org/I132369690","display_name":"Tianjin University of Science and Technology","ror":"https://ror.org/018rbtf37","country_code":"CN","type":"education","lineage":["https://openalex.org/I132369690"]},{"id":"https://openalex.org/I136765683","display_name":"Tianjin University of Technology","ror":"https://ror.org/00zbe0w13","country_code":"CN","type":"education","lineage":["https://openalex.org/I136765683"]},{"id":"https://openalex.org/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guo-Zheng Rao","raw_affiliation_strings":["School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University , Tianjin 300350 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University , Tianjin 300350 ,","institution_ids":["https://openalex.org/I132369690","https://openalex.org/I136765683","https://openalex.org/I162868743"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100427208","display_name":"Haoyu Wang","orcid":"https://orcid.org/0009-0002-8101-6452"},"institutions":[{"id":"https://openalex.org/I132369690","display_name":"Tianjin University of Science and Technology","ror":"https://ror.org/018rbtf37","country_code":"CN","type":"education","lineage":["https://openalex.org/I132369690"]},{"id":"https://openalex.org/I136765683","display_name":"Tianjin University of Technology","ror":"https://ror.org/00zbe0w13","country_code":"CN","type":"education","lineage":["https://openalex.org/I136765683"]},{"id":"https://openalex.org/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao-Yu Wang","raw_affiliation_strings":["School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University , Tianjin 300350 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University , Tianjin 300350 ,","institution_ids":["https://openalex.org/I132369690","https://openalex.org/I136765683","https://openalex.org/I162868743"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110808186","display_name":"Xin-Ran Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I132369690","display_name":"Tianjin University of Science and Technology","ror":"https://ror.org/018rbtf37","country_code":"CN","type":"education","lineage":["https://openalex.org/I132369690"]},{"id":"https://openalex.org/I136765683","display_name":"Tianjin University of Technology","ror":"https://ror.org/00zbe0w13","country_code":"CN","type":"education","lineage":["https://openalex.org/I136765683"]},{"id":"https://openalex.org/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xin-Ran Wu","raw_affiliation_strings":["School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University , Tianjin 300350 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University , Tianjin 300350 ,","institution_ids":["https://openalex.org/I132369690","https://openalex.org/I136765683","https://openalex.org/I162868743"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138608695","display_name":"Tong Xian","orcid":null},"institutions":[{"id":"https://openalex.org/I132369690","display_name":"Tianjin University of Science and Technology","ror":"https://ror.org/018rbtf37","country_code":"CN","type":"education","lineage":["https://openalex.org/I132369690"]},{"id":"https://openalex.org/I136765683","display_name":"Tianjin University of Technology","ror":"https://ror.org/00zbe0w13","country_code":"CN","type":"education","lineage":["https://openalex.org/I136765683"]},{"id":"https://openalex.org/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tong Xian","raw_affiliation_strings":["School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University , Tianjin 300350 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University , Tianjin 300350 ,","institution_ids":["https://openalex.org/I132369690","https://openalex.org/I136765683","https://openalex.org/I162868743"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044603287","display_name":"B Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I132369690","display_name":"Tianjin University of Science and Technology","ror":"https://ror.org/018rbtf37","country_code":"CN","type":"education","lineage":["https://openalex.org/I132369690"]},{"id":"https://openalex.org/I136765683","display_name":"Tianjin University of Technology","ror":"https://ror.org/00zbe0w13","country_code":"CN","type":"education","lineage":["https://openalex.org/I136765683"]},{"id":"https://openalex.org/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo-Qiang Wang","raw_affiliation_strings":["School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University , Tianjin 300350 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University , Tianjin 300350 ,","institution_ids":["https://openalex.org/I132369690","https://openalex.org/I136765683","https://openalex.org/I162868743"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011271652","display_name":"Pu-Feng Du","orcid":"https://orcid.org/0000-0001-9897-3932"},"institutions":[{"id":"https://openalex.org/I132369690","display_name":"Tianjin University of Science and Technology","ror":"https://ror.org/018rbtf37","country_code":"CN","type":"education","lineage":["https://openalex.org/I132369690"]},{"id":"https://openalex.org/I136765683","display_name":"Tianjin University of Technology","ror":"https://ror.org/00zbe0w13","country_code":"CN","type":"education","lineage":["https://openalex.org/I136765683"]},{"id":"https://openalex.org/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Pu-Feng Du","raw_affiliation_strings":["School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University , Tianjin 300350 ,"],"raw_orcid":"https://orcid.org/0000-0001-9897-3932","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University , Tianjin 300350 ,","institution_ids":["https://openalex.org/I132369690","https://openalex.org/I136765683","https://openalex.org/I162868743"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5011271652"],"corresponding_institution_ids":["https://openalex.org/I132369690","https://openalex.org/I136765683","https://openalex.org/I162868743"],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":{"value":3885,"currency":"USD","value_usd":3885},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.54382918,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"3","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":0.9951000213623047,"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":0.9951000213623047,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0010000000474974513,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.00039999998989515007,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.7985000014305115},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.5619000196456909},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4666999876499176},{"id":"https://openalex.org/keywords/chia-pet","display_name":"ChIA-PET","score":0.4343999922275543},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4172999858856201},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.39820000529289246},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.3587000072002411}],"concepts":[{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.7985000014305115},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6675999760627747},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.600600004196167},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.5619000196456909},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4666999876499176},{"id":"https://openalex.org/C67258246","wikidata":"https://www.wikidata.org/wiki/Q5065897","display_name":"ChIA-PET","level":5,"score":0.4343999922275543},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4172999858856201},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.39820000529289246},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.3587000072002411},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3495999872684479},{"id":"https://openalex.org/C138268822","wikidata":"https://www.wikidata.org/wiki/Q1051925","display_name":"Resolution (logic)","level":2,"score":0.3456000089645386},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34380000829696655},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.3091999888420105},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.2978000044822693},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.2883000075817108},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2775000035762787},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.2727000117301941},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.26820001006126404},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.26669999957084656},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.2590000033378601},{"id":"https://openalex.org/C3020199158","wikidata":"https://www.wikidata.org/wiki/Q210521","display_name":"High resolution","level":2,"score":0.25760000944137573}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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":"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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbag305","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag305","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42289051","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42289051","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":"Briefings in bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13376144","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13376144/","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbag305","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag305","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3111514414","display_name":null,"funder_award_id":"NSFC 62372320","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7221642899","display_name":null,"funder_award_id":"NSFC 61872268","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":52,"referenced_works":["https://openalex.org/W1660678623","https://openalex.org/W1951112263","https://openalex.org/W1985621639","https://openalex.org/W2056482755","https://openalex.org/W2070021921","https://openalex.org/W2076936580","https://openalex.org/W2089894746","https://openalex.org/W2090037139","https://openalex.org/W2108234281","https://openalex.org/W2111288554","https://openalex.org/W2118258530","https://openalex.org/W2145619687","https://openalex.org/W2152605077","https://openalex.org/W2159164310","https://openalex.org/W2161212572","https://openalex.org/W2195190137","https://openalex.org/W2259938310","https://openalex.org/W2341539131","https://openalex.org/W2481029670","https://openalex.org/W2493763501","https://openalex.org/W2530292798","https://openalex.org/W2584394140","https://openalex.org/W2600121124","https://openalex.org/W2781657900","https://openalex.org/W2792734199","https://openalex.org/W2920852097","https://openalex.org/W2967697632","https://openalex.org/W3013411594","https://openalex.org/W3014261926","https://openalex.org/W3046151504","https://openalex.org/W3091921516","https://openalex.org/W3092624702","https://openalex.org/W4220688679","https://openalex.org/W4225279860","https://openalex.org/W4226349074","https://openalex.org/W4280512834","https://openalex.org/W4292722723","https://openalex.org/W4313893501","https://openalex.org/W4379536676","https://openalex.org/W4384130138","https://openalex.org/W4390790903","https://openalex.org/W4392861070","https://openalex.org/W4396999856","https://openalex.org/W4401084367","https://openalex.org/W4401960401","https://openalex.org/W4403478939","https://openalex.org/W4405265005","https://openalex.org/W4406250204","https://openalex.org/W4409157646","https://openalex.org/W4409190772","https://openalex.org/W4409383149","https://openalex.org/W4415707321"],"related_works":[],"abstract_inverted_index":{"Protein-mediated":[0],"chromatin":[1,59,88],"interactions":[2,89,114],"are":[3,20,32],"fundamental":[4],"to":[5,94,111,151],"gene":[6],"regulation.":[7],"However,":[8],"experimental":[9,153],"approaches":[10],"such":[11,133],"as":[12,134],"Chromatin":[13],"Interaction":[14],"Analysis":[15],"by":[16,22,34,62],"Paired-End":[17],"Tag":[18],"sequencing":[19],"limited":[21,35],"data":[23,154],"scarcity":[24],"and":[25,37,71,155],"high":[26,126],"cost,":[27],"while":[28],"existing":[29],"computational":[30,149],"models":[31],"constrained":[33],"resolution":[36,97],"challenges":[38],"in":[39,106],"effectively":[40],"integrating":[41,140],"heterogeneous":[42],"genomic":[43,72,103,117,142],"data.":[44],"To":[45],"address":[46],"these":[47],"issues,":[48],"we":[49,108],"propose":[50],"GraphChIAr,":[51,107],"a":[52,120],"regression-based":[53],"deep":[54],"learning":[55],"framework":[56],"that":[57],"estimates":[58],"interaction":[60],"strength":[61],"augmenting":[63],"Hi-C":[64],"contact":[65],"maps":[66],"with":[67],"various":[68],"ChIP-seq":[69],"profiles":[70],"sequence":[73],"information.":[74],"A":[75],"key":[76,130],"advantage":[77],"of":[78,87,139,159,166],"GraphChIAr":[79,145,167],"is":[80,168],"its":[81],"super-resolution":[82],"capability,":[83],"enabling":[84],"accurate":[85],"estimations":[86],"from":[90],"conventional":[91],"resolutions":[92],"down":[93],"ultra-high":[95],"near-nucleosome":[96],"(e.g.":[98],"200":[99],"bp).":[100],"By":[101],"introducing":[102],"shift":[104],"distance":[105],"enabled":[109],"it":[110],"predict":[112],"remote":[113],"between":[115],"distant":[116],"loci":[118],"at":[119,170],"genome-wide":[121],"scale.":[122],"Cross-referencing":[123],"results":[124],"demonstrate":[125],"predictive":[127],"accuracy":[128],"for":[129],"mediating":[131],"proteins":[132],"CTCF,":[135],"highlighting":[136],"the":[137,157],"benefits":[138],"complementary":[141],"features.":[143],"Together,":[144],"provides":[146],"an":[147],"effective":[148],"tool":[150],"augment":[152],"advance":[156],"study":[158],"3D":[160],"genome":[161],"organization.":[162],"The":[163],"source":[164],"code":[165],"available":[169],"(https://github.com/don194/GraphChIAr).":[171]},"counts_by_year":[],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2026-06-15T00:00:00"}
