{"id":"https://openalex.org/W4383113554","doi":"https://doi.org/10.1109/jbhi.2023.3292299","title":"IChrom-Deep: An Attention-Based Deep Learning Model for Identifying Chromatin Interactions","display_name":"IChrom-Deep: An Attention-Based Deep Learning Model for Identifying Chromatin Interactions","publication_year":2023,"publication_date":"2023-07-04","ids":{"openalex":"https://openalex.org/W4383113554","doi":"https://doi.org/10.1109/jbhi.2023.3292299","pmid":"https://pubmed.ncbi.nlm.nih.gov/37402191"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2023.3292299","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2023.3292299","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5100653968","display_name":"Pengyu Zhang","orcid":"https://orcid.org/0000-0001-8696-4983"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]},{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pengyu Zhang","raw_affiliation_strings":["School of Software, Shandong University, Jinan, China","College of Information Engineering, Northwest A&F University, Yangling, China"],"raw_orcid":"https://orcid.org/0000-0001-8696-4983","affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"College of Information Engineering, Northwest A&F University, Yangling, China","institution_ids":["https://openalex.org/I89652312"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036176693","display_name":"Hao Wu","orcid":"https://orcid.org/0000-0003-2340-9258"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Wu","raw_affiliation_strings":["School of Software, Shandong University, Jinan, China"],"raw_orcid":"https://orcid.org/0000-0003-2340-9258","affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":6.8618,"has_fulltext":false,"cited_by_count":51,"citation_normalized_percentile":{"value":0.97571464,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"27","issue":"9","first_page":"4559","last_page":"4568"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9962999820709229,"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":0.9954000115394592,"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/chromatin","display_name":"Chromatin","score":0.9007670879364014},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.7252383232116699},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6920026540756226},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6332663297653198},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6283082962036133},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.45141956210136414},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.44118812680244446},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.42540451884269714},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.33051297068595886},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28753936290740967},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.2458001673221588},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.193536639213562},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17799833416938782}],"concepts":[{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.9007670879364014},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.7252383232116699},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6920026540756226},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6332663297653198},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6283082962036133},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.45141956210136414},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.44118812680244446},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.42540451884269714},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.33051297068595886},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28753936290740967},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.2458001673221588},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.193536639213562},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17799833416938782},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","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":"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}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2023.3292299","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2023.3292299","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:37402191","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37402191","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":"IEEE journal of biomedical and health informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.550000011920929,"display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G2698802062","display_name":null,"funder_award_id":"2021YFF0704103","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G3278557419","display_name":null,"funder_award_id":"62272278","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G715904284","display_name":"\u4e09\u7ef4\u57fa\u56e0\u7ec4\u8c03\u63a7\u5c42\u9762\u7684\u764c\u75c7\u81f4\u75c5\u901a\u8def\u6316\u6398\u65b9\u6cd5\u7814\u7a76","funder_award_id":"61972322","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"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":61,"referenced_works":["https://openalex.org/W1970831058","https://openalex.org/W1985621639","https://openalex.org/W2011463791","https://openalex.org/W2018363492","https://openalex.org/W2061412286","https://openalex.org/W2065006553","https://openalex.org/W2068315875","https://openalex.org/W2090037139","https://openalex.org/W2102619694","https://openalex.org/W2131186458","https://openalex.org/W2147947827","https://openalex.org/W2161212572","https://openalex.org/W2310342073","https://openalex.org/W2333286569","https://openalex.org/W2470513050","https://openalex.org/W2585635281","https://openalex.org/W2610240247","https://openalex.org/W2735099323","https://openalex.org/W2752211734","https://openalex.org/W2767749844","https://openalex.org/W2774733631","https://openalex.org/W2781657900","https://openalex.org/W2792734199","https://openalex.org/W2800857888","https://openalex.org/W2884561390","https://openalex.org/W2911079020","https://openalex.org/W2913199583","https://openalex.org/W2921983621","https://openalex.org/W2943761358","https://openalex.org/W2949423586","https://openalex.org/W2951218167","https://openalex.org/W2952763207","https://openalex.org/W2953462601","https://openalex.org/W2962862931","https://openalex.org/W2963398066","https://openalex.org/W2963733149","https://openalex.org/W2971769670","https://openalex.org/W2991091214","https://openalex.org/W3041895828","https://openalex.org/W3093812284","https://openalex.org/W3126352312","https://openalex.org/W3127410616","https://openalex.org/W3129125493","https://openalex.org/W3132963234","https://openalex.org/W3195330522","https://openalex.org/W3197375931","https://openalex.org/W4205478771","https://openalex.org/W4210880116","https://openalex.org/W4230875896","https://openalex.org/W4285405240","https://openalex.org/W4286373989","https://openalex.org/W4292263641","https://openalex.org/W4292722723","https://openalex.org/W4294990936","https://openalex.org/W4297257598","https://openalex.org/W4297263351","https://openalex.org/W4385245566","https://openalex.org/W6737947904","https://openalex.org/W6739901393","https://openalex.org/W6790335695","https://openalex.org/W6840655891"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W4286930115","https://openalex.org/W3004891660","https://openalex.org/W2969540308","https://openalex.org/W2414971881","https://openalex.org/W4206381471","https://openalex.org/W1886874180","https://openalex.org/W42421305","https://openalex.org/W2400987468","https://openalex.org/W1598419885"],"abstract_inverted_index":{"Identification":[0],"of":[1,10,18,65,88,105],"chromatin":[2,33,50,98,163],"interactions":[3,51],"is":[4,23,77,146],"crucial":[5],"for":[6,31,156],"advancing":[7],"our":[8],"knowledge":[9],"gene":[11],"regulation.":[12],"However,":[13],"due":[14],"to":[15,27,48,79,161],"the":[16,63,71,80,86,102],"limitations":[17],"high-throughput":[19],"experimental":[20,59],"techniques,":[21],"there":[22],"an":[24],"urgent":[25],"need":[26],"develop":[28],"computational":[29],"methods":[30],"predicting":[32],"interactions.":[34,164],"In":[35],"this":[36],"study,":[37],"we":[38,115],"propose":[39],"a":[40,117,153],"novel":[41],"attention-based":[42],"deep":[43],"learning":[44],"model,":[45],"termed":[46],"IChrom-Deep,":[47],"identify":[49,116,162],"using":[52,141],"sequence":[53,90,110],"features":[54,93,96,120,139],"and":[55,76,91,94,100,112,129],"genomic":[56,95,119,138,143],"features.":[57,144],"The":[58],"results":[60],"based":[61],"on":[62,97],"datasets":[64],"three":[66],"cell":[67,127],"lines":[68],"demonstrate":[69],"that":[70,121,148,159],"IChrom-Deep":[72,130,149],"achieves":[73,131],"satisfactory":[74],"performance":[75,133],"superior":[78],"previous":[81],"methods.":[82],"We":[83],"also":[84],"investigate":[85],"effect":[87],"DNA":[89],"associated":[92],"interactions,":[99],"highlight":[101],"applicable":[103],"scenarios":[104],"some":[106],"features,":[107],"such":[108],"as":[109,152],"conservation":[111],"distance.":[113],"Moreover,":[114],"few":[118],"are":[122],"extremely":[123],"important":[124],"across":[125],"different":[126],"lines,":[128],"comparable":[132],"with":[134],"only":[135],"these":[136],"significant":[137],"versus":[140],"all":[142],"It":[145],"believed":[147],"can":[150],"serve":[151],"useful":[154],"tool":[155],"future":[157],"studies":[158],"seek":[160]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":21},{"year":2024,"cited_by_count":20},{"year":2023,"cited_by_count":6}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
