{"id":"https://openalex.org/W4408845443","doi":"https://doi.org/10.1093/bib/bbaf127","title":"deepTAD: an approach for identifying topologically associated domains based on convolutional neural network and transformer model","display_name":"deepTAD: an approach for identifying topologically associated domains based on convolutional neural network and transformer model","publication_year":2025,"publication_date":"2025-03-01","ids":{"openalex":"https://openalex.org/W4408845443","doi":"https://doi.org/10.1093/bib/bbaf127","pmid":"https://pubmed.ncbi.nlm.nih.gov/40131313"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf127","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf127","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf127/62700008/bbaf127.pdf","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","license_id":"https://openalex.org/licenses/cc-by","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://academic.oup.com/bib/article-pdf/26/2/bbaf127/62700008/bbaf127.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047533435","display_name":"Xiaoyan Wang","orcid":"https://orcid.org/0000-0003-3477-0102"},"institutions":[{"id":"https://openalex.org/I4210166499","display_name":"Henan Polytechnic University","ror":"https://ror.org/05vr1c885","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210166499"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaoyan Wang","raw_affiliation_strings":["School of Software, Henan Polytechnic University , 2001 Century Road, Jiaozuo 454003 ,"],"affiliations":[{"raw_affiliation_string":"School of Software, Henan Polytechnic University , 2001 Century Road, Jiaozuo 454003 ,","institution_ids":["https://openalex.org/I4210166499"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100422484","display_name":"Junwei Luo","orcid":"https://orcid.org/0000-0001-6841-9893"},"institutions":[{"id":"https://openalex.org/I4210166499","display_name":"Henan Polytechnic University","ror":"https://ror.org/05vr1c885","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210166499"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junwei Luo","raw_affiliation_strings":["School of Software, Henan Polytechnic University , 2001 Century Road, Jiaozuo 454003 ,"],"affiliations":[{"raw_affiliation_string":"School of Software, Henan Polytechnic University , 2001 Century Road, Jiaozuo 454003 ,","institution_ids":["https://openalex.org/I4210166499"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024617117","display_name":"Lili Wu","orcid":"https://orcid.org/0000-0003-0680-8716"},"institutions":[{"id":"https://openalex.org/I4210166499","display_name":"Henan Polytechnic University","ror":"https://ror.org/05vr1c885","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210166499"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lili Wu","raw_affiliation_strings":["School of Software, Henan Polytechnic University , 2001 Century Road, Jiaozuo 454003 ,"],"affiliations":[{"raw_affiliation_string":"School of Software, Henan Polytechnic University , 2001 Century Road, Jiaozuo 454003 ,","institution_ids":["https://openalex.org/I4210166499"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012174743","display_name":"Huimin Luo","orcid":"https://orcid.org/0000-0002-5066-5372"},"institutions":[{"id":"https://openalex.org/I173899330","display_name":"Henan University","ror":"https://ror.org/003xyzq10","country_code":"CN","type":"education","lineage":["https://openalex.org/I173899330"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huimin Luo","raw_affiliation_strings":["School of Computer and Information Engineering, Henan University , North Section of Jinming Avenue, Kaifeng 475001 ,"],"affiliations":[{"raw_affiliation_string":"School of Computer and Information Engineering, Henan University , North Section of Jinming Avenue, Kaifeng 475001 ,","institution_ids":["https://openalex.org/I173899330"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112879504","display_name":"Fei Guo","orcid":"https://orcid.org/0000-0002-9279-9547"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fei Guo","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University , 932 Lushan South Road, Changsha 410083 ,"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , 932 Lushan South Road, Changsha 410083 ,","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5047533435"],"corresponding_institution_ids":["https://openalex.org/I4210166499"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":3.7492,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.9272365,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":100},"biblio":{"volume":"26","issue":"2","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":0.9998999834060669,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9966999888420105,"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/T10604","display_name":"RNA Research and Splicing","score":0.9958000183105469,"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/computer-science","display_name":"Computer science","score":0.6907495856285095},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6372185945510864},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.5240647792816162},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4831477999687195},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.46337902545928955},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3505614399909973},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12872737646102905},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.09121376276016235}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6907495856285095},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6372185945510864},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.5240647792816162},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4831477999687195},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.46337902545928955},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3505614399909973},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12872737646102905},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.09121376276016235},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000098415","descriptor_name":"Convolutional Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098415","descriptor_name":"Convolutional Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098415","descriptor_name":"Convolutional Neural Networks","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":"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":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","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":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":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":true},{"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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":true},{"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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":true},{"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":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf127","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf127","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf127/62700008/bbaf127.pdf","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40131313","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40131313","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":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11934553","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11934553","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf127","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf127","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf127/62700008/bbaf127.pdf","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","license_id":"https://openalex.org/licenses/cc-by","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/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3085993365","display_name":null,"funder_award_id":"(Grant No.","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G391238517","display_name":null,"funder_award_id":", and","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5939423041","display_name":null,"funder_award_id":"Technology","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6221982799","display_name":null,"funder_award_id":"62372156","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7726157001","display_name":null,"funder_award_id":"Grant No.","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8252935001","display_name":null,"funder_award_id":"32102211","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/F4320327051","display_name":"Science and Technology Department of Henan Province","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4408845443.pdf"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1859117663","https://openalex.org/W1973062929","https://openalex.org/W1984827465","https://openalex.org/W2064537118","https://openalex.org/W2070021921","https://openalex.org/W2090037139","https://openalex.org/W2102368172","https://openalex.org/W2107866789","https://openalex.org/W2132089243","https://openalex.org/W2222531233","https://openalex.org/W2227178360","https://openalex.org/W2303393194","https://openalex.org/W2519117646","https://openalex.org/W2530292798","https://openalex.org/W2568062379","https://openalex.org/W2581883027","https://openalex.org/W2738924259","https://openalex.org/W2765865112","https://openalex.org/W2885386724","https://openalex.org/W2889421335","https://openalex.org/W2904120442","https://openalex.org/W2935837958","https://openalex.org/W2943761358","https://openalex.org/W2951322997","https://openalex.org/W2951765178","https://openalex.org/W2996196683","https://openalex.org/W2998689926","https://openalex.org/W3007651317","https://openalex.org/W3010360466","https://openalex.org/W3014699737","https://openalex.org/W3094502228","https://openalex.org/W3121637338","https://openalex.org/W3175495956","https://openalex.org/W3208802390","https://openalex.org/W4210385976","https://openalex.org/W4210880116","https://openalex.org/W4226214329","https://openalex.org/W4294647486","https://openalex.org/W4311589580","https://openalex.org/W4368361817","https://openalex.org/W4379599698","https://openalex.org/W4380848954","https://openalex.org/W4387108095","https://openalex.org/W4387460953","https://openalex.org/W4391253080","https://openalex.org/W4396672869","https://openalex.org/W6784333009"],"related_works":["https://openalex.org/W4391621807","https://openalex.org/W4321487865","https://openalex.org/W4313906399","https://openalex.org/W4391621790","https://openalex.org/W4239306820","https://openalex.org/W4391266461","https://openalex.org/W2590798552","https://openalex.org/W2811106690","https://openalex.org/W2033914206","https://openalex.org/W2042327336"],"abstract_inverted_index":{"In":[0],"this":[1],"paper,":[2],"a":[3,14,100,128],"novel":[4],"method":[5],"is":[6,10,140],"proposed,":[7],"deepTAD,":[8],"which":[9],"developed":[11],"based":[12,23],"on":[13,24],"convolutional":[15],"neural":[16],"network":[17],"(CNN)":[18],"and":[19,55,81,111,121],"transformer":[20,45],"model.":[21],"First,":[22],"Hi-C":[25],"contact":[26],"matrix,":[27],"deepTAD":[28,40,61,73,98,126,139],"utilizes":[29],"CNN":[30],"to":[31,47,67,85],"directly":[32],"extract":[33],"features":[34,51],"associated":[35],"with":[36,132],"TAD":[37,53,58,79,83,94],"boundaries.":[38,59,71],"Next,":[39],"takes":[41],"advantage":[42],"of":[43,103,123,138],"the":[44,49,57,63,119],"model":[46],"analyze":[48],"variation":[50],"around":[52],"boundaries":[54,80,84,95],"determines":[56],"Second,":[60],"uses":[62],"Wilcoxon":[64],"rank-sum":[65],"test":[66],"further":[68],"identify":[69],"false-positive":[70],"Finally,":[72],"computes":[74],"cosine":[75],"similarity":[76],"among":[77],"identified":[78,96,124],"assembles":[82],"obtain":[86],"hierarchical":[87],"TADs.":[88],"The":[89,135],"experimental":[90],"results":[91],"show":[92],"that":[93],"by":[97],"have":[99],"significant":[101],"enrichment":[102],"biological":[104],"features,":[105],"including":[106],"structural":[107],"proteins,":[108],"histone":[109],"modifications,":[110],"transcription":[112],"start":[113],"site":[114],"loci.":[115],"Additionally,":[116],"when":[117],"evaluating":[118],"completeness":[120],"accuracy":[122],"TADs,":[125],"has":[127],"good":[129],"performance":[130],"compared":[131],"other":[133],"methods.":[134],"source":[136],"code":[137],"available":[141],"at":[142],"https://github.com/xiaoyan-wang99/deepTAD.":[143]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2025-10-10T00:00:00"}
