{"id":"https://openalex.org/W4406271178","doi":"https://doi.org/10.1109/bibm62325.2024.10822031","title":"TADClam: overlapped and hierarchical topologically associating domains detection with community affiliation model","display_name":"TADClam: overlapped and hierarchical topologically associating domains detection with community affiliation model","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406271178","doi":"https://doi.org/10.1109/bibm62325.2024.10822031"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822031","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822031","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 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/A5101067202","display_name":"Zhao Ling","orcid":"https://orcid.org/0000-0003-0512-6369"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Zhao Ling","raw_affiliation_strings":["City University of Hong Kong,Department of Computer Science,Hong Kong,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"City University of Hong Kong,Department of Computer Science,Hong Kong,China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100680487","display_name":"Shiying Li","orcid":"https://orcid.org/0000-0003-0666-7634"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Shi Ying Li","raw_affiliation_strings":["City University of Hong Kong,Department of Computer Science,Hong Kong,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"City University of Hong Kong,Department of Computer Science,Hong Kong,China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Qiu Shi Liang","orcid":null},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Qiu Shi Liang","raw_affiliation_strings":["City University of Hong Kong,Department of Computer Science,Hong Kong,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"City University of Hong Kong,Department of Computer Science,Hong Kong,China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083428910","display_name":"Shuai Cheng Li","orcid":"https://orcid.org/0000-0001-6246-6349"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Shuai Cheng Li","raw_affiliation_strings":["City University of Hong Kong,Department of Computer Science,Hong Kong,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"City University of Hong Kong,Department of Computer Science,Hong Kong,China","institution_ids":["https://openalex.org/I168719708"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I168719708"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.28039988,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"54","last_page":"61"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11550","display_name":"Text and Document Classification Technologies","score":0.9789000153541565,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11550","display_name":"Text and Document Classification Technologies","score":0.9789000153541565,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9294000267982483,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10064","display_name":"Complex Network Analysis Techniques","score":0.9265000224113464,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5960249304771423},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3604618012905121}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5960249304771423},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3604618012905121}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822031","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822031","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Reduced inequalities","score":0.6000000238418579,"id":"https://metadata.un.org/sdg/10"}],"awards":[],"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":29,"referenced_works":["https://openalex.org/W1506343731","https://openalex.org/W1965863160","https://openalex.org/W1973062929","https://openalex.org/W2009576540","https://openalex.org/W2018658338","https://openalex.org/W2090037139","https://openalex.org/W2139694940","https://openalex.org/W2227178360","https://openalex.org/W2310342073","https://openalex.org/W2416744721","https://openalex.org/W2481029670","https://openalex.org/W2568062379","https://openalex.org/W2581883027","https://openalex.org/W2597274540","https://openalex.org/W2755736028","https://openalex.org/W2784063494","https://openalex.org/W2885386724","https://openalex.org/W2898514070","https://openalex.org/W2951765178","https://openalex.org/W2958578938","https://openalex.org/W2989228133","https://openalex.org/W2996196683","https://openalex.org/W3007651317","https://openalex.org/W3121637338","https://openalex.org/W3151083339","https://openalex.org/W3164534693","https://openalex.org/W4250589301","https://openalex.org/W4283156191","https://openalex.org/W4368361817"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Identifying":[0],"hierarchical":[1],"and":[2,75,88],"overlapped":[3,110],"topologically":[4],"associating":[5],"domains":[6],"(TADs)":[7],"from":[8,45,106],"high-throughput":[9],"chromosome":[10],"conformation":[11],"capture":[12],"(Hi-C)":[13],"contact":[14,47,64],"maps":[15,65],"is":[16],"an":[17,51],"ongoing":[18],"challenge.":[19],"Here,":[20],"we":[21],"present":[22],"TADClam,":[23],"a":[24,35],"novel":[25],"algorithm":[26],"designed":[27],"to":[28,40,55,78,102],"untangle":[29],"complex":[30,97,131],"TAD":[31,68,81,98,132],"architectures.":[32],"TADClam":[33,59,83,114,128],"employs":[34],"weighted":[36,89],"community":[37],"affiliation":[38],"model":[39],"efficiently":[41],"identify":[42],"candidate":[43],"TADs":[44,111],"Hi-C":[46,104],"maps,":[48],"followed":[49],"by":[50,113],"entropy-based":[52],"filtering":[53],"procedure":[54],"select":[56],"significant":[57],"domains.":[58],"was":[60],"evaluated":[61],"on":[62],"simulated":[63],"with":[66],"various":[67],"structures,":[69,133],"including":[70],"disjoint,":[71],"overlapped,":[72],"nested":[73],"TADs,":[74],"gaps.":[76],"Compared":[77],"six":[79],"state-of-the-art":[80],"callers,":[82],"achieved":[84],"the":[85],"highest":[86],"overlapping":[87],"similarity":[90],"ratios,":[91],"indicating":[92],"superior":[93],"performance":[94],"in":[95],"detecting":[96],"organizations.":[99],"When":[100],"applied":[101],"real":[103],"data":[105],"human":[107],"cell":[108],"lines,":[109],"identified":[112],"showed":[115],"significantly":[116],"greater":[117],"enrichment":[118],"of":[119],"structural":[120],"proteins":[121],"across":[122],"boundaries.":[123],"These":[124],"results":[125],"demonstrate":[126],"that":[127],"accurately":[129],"captures":[130],"providing":[134],"unprecedented":[135],"insights":[136],"into":[137],"3D":[138],"genome":[139],"organization.":[140]},"counts_by_year":[],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}