{"id":"https://openalex.org/W4406363766","doi":"https://doi.org/10.1145/3700666.3700694","title":"An Ensemble Method for Calling and Ranking Somatic Structural Variants Using Long and Short Reads","display_name":"An Ensemble Method for Calling and Ranking Somatic Structural Variants Using Long and Short Reads","publication_year":2024,"publication_date":"2024-09-13","ids":{"openalex":"https://openalex.org/W4406363766","doi":"https://doi.org/10.1145/3700666.3700694"},"language":"en","primary_location":{"id":"doi:10.1145/3700666.3700694","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3700666.3700694","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3700666.3700694?download=true","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 11th International Conference on Bioinformatics Research and Applications","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3700666.3700694?download=true","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014729436","display_name":"Walter Gallego Gomez","orcid":"https://orcid.org/0009-0006-2956-6747"},"institutions":[{"id":"https://openalex.org/I177477856","display_name":"Politecnico di Torino","ror":"https://ror.org/00bgk9508","country_code":"IT","type":"education","lineage":["https://openalex.org/I177477856"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Walter Gallego Gomez","raw_affiliation_strings":["Department of Control and Computer Engineering, Politecnico di Torino, Turin, Piedmont, Italy"],"raw_orcid":"https://orcid.org/0009-0006-2956-6747","affiliations":[{"raw_affiliation_string":"Department of Control and Computer Engineering, Politecnico di Torino, Turin, Piedmont, Italy","institution_ids":["https://openalex.org/I177477856"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049648750","display_name":"Elena Grassi","orcid":"https://orcid.org/0000-0003-1066-927X"},"institutions":[{"id":"https://openalex.org/I4210151091","display_name":"Candiolo Cancer Institute","ror":"https://ror.org/04wadq306","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210151091","https://openalex.org/I4210153126","https://openalex.org/I4210167100"]},{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Elena Grassi","raw_affiliation_strings":["Candiolo Cancer Institute - FPO IRCCS, Turin, Piedmont, Italy","Department of Oncology, University of Torino, Turin, Piedmont, Italy"],"raw_orcid":"https://orcid.org/0000-0003-1066-927X","affiliations":[{"raw_affiliation_string":"Candiolo Cancer Institute - FPO IRCCS, Turin, Piedmont, Italy","institution_ids":["https://openalex.org/I4210151091"]},{"raw_affiliation_string":"Department of Oncology, University of Torino, Turin, Piedmont, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031287599","display_name":"Andrea Bertotti","orcid":"https://orcid.org/0000-0001-8196-7608"},"institutions":[{"id":"https://openalex.org/I4210151091","display_name":"Candiolo Cancer Institute","ror":"https://ror.org/04wadq306","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210151091","https://openalex.org/I4210153126","https://openalex.org/I4210167100"]},{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Andrea Bertotti","raw_affiliation_strings":["Candiolo Cancer Institute - FPO IRCCS, Turin, Piedmont, Italy","Department of Oncology, University of Torino, Turin, Piedmont, Italy"],"raw_orcid":"https://orcid.org/0000-0001-8196-7608","affiliations":[{"raw_affiliation_string":"Candiolo Cancer Institute - FPO IRCCS, Turin, Piedmont, Italy","institution_ids":["https://openalex.org/I4210151091"]},{"raw_affiliation_string":"Department of Oncology, University of Torino, Turin, Piedmont, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011857762","display_name":"Gianvito Urgese","orcid":"https://orcid.org/0000-0003-2672-7593"},"institutions":[{"id":"https://openalex.org/I177477856","display_name":"Politecnico di Torino","ror":"https://ror.org/00bgk9508","country_code":"IT","type":"education","lineage":["https://openalex.org/I177477856"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Gianvito Urgese","raw_affiliation_strings":["Interuniversity Department of Regional and Urban Studies and Planning, Politecnico di Torino, Turin, Piedmont, Italy"],"raw_orcid":"https://orcid.org/0000-0003-2672-7593","affiliations":[{"raw_affiliation_string":"Interuniversity Department of Regional and Urban Studies and Planning, Politecnico di Torino, Turin, Piedmont, Italy","institution_ids":["https://openalex.org/I177477856"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5014729436"],"corresponding_institution_ids":["https://openalex.org/I177477856"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.3074032,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"62","last_page":"69"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11674","display_name":"Sports Analytics and Performance","score":0.8776000142097473,"subfield":{"id":"https://openalex.org/subfields/2002","display_name":"Economics and Econometrics"},"field":{"id":"https://openalex.org/fields/20","display_name":"Economics, Econometrics and Finance"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11674","display_name":"Sports Analytics and Performance","score":0.8776000142097473,"subfield":{"id":"https://openalex.org/subfields/2002","display_name":"Economics and Econometrics"},"field":{"id":"https://openalex.org/fields/20","display_name":"Economics, Econometrics and Finance"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T12026","display_name":"Explainable Artificial Intelligence (XAI)","score":0.8557999730110168,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.705611526966095},{"id":"https://openalex.org/keywords/somatic-cell","display_name":"Somatic cell","score":0.6785524487495422},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6584155559539795},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3881509304046631},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.35563042759895325},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34980273246765137},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20427241921424866},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14916402101516724},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10362565517425537}],"concepts":[{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.705611526966095},{"id":"https://openalex.org/C134305767","wikidata":"https://www.wikidata.org/wiki/Q725508","display_name":"Somatic cell","level":3,"score":0.6785524487495422},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6584155559539795},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3881509304046631},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.35563042759895325},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34980273246765137},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20427241921424866},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14916402101516724},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10362565517425537}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3700666.3700694","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3700666.3700694","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3700666.3700694?download=true","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 11th International Conference on Bioinformatics Research and Applications","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3700666.3700694","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3700666.3700694","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3700666.3700694?download=true","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 11th International Conference on Bioinformatics Research and Applications","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4406363766.pdf","grobid_xml":"https://content.openalex.org/works/W4406363766.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1959574505","https://openalex.org/W2119180969","https://openalex.org/W2195724570","https://openalex.org/W2586169357","https://openalex.org/W2591633430","https://openalex.org/W2605897695","https://openalex.org/W2803750811","https://openalex.org/W2950121474","https://openalex.org/W2971559821","https://openalex.org/W2990344913","https://openalex.org/W3004584205","https://openalex.org/W3006653136","https://openalex.org/W3045587277","https://openalex.org/W3046401484","https://openalex.org/W3083468523","https://openalex.org/W3158106703","https://openalex.org/W3161096424","https://openalex.org/W3202634790","https://openalex.org/W3213101281","https://openalex.org/W4206662285","https://openalex.org/W4224000597","https://openalex.org/W4225624933","https://openalex.org/W4281983143","https://openalex.org/W4289515190","https://openalex.org/W4317034776","https://openalex.org/W4353060537","https://openalex.org/W4366716892","https://openalex.org/W4381252065","https://openalex.org/W4382537978"],"related_works":["https://openalex.org/W2060908277","https://openalex.org/W2048083752","https://openalex.org/W2438531772","https://openalex.org/W1992103432","https://openalex.org/W81105053","https://openalex.org/W4251027247","https://openalex.org/W1881137434","https://openalex.org/W3021321537","https://openalex.org/W2081894066","https://openalex.org/W2188500270"],"abstract_inverted_index":{"Structural":[0],"variants":[1,34],"(SVs)":[2],"are":[3,82],"a":[4,11,55,123,150],"class":[5],"of":[6,38,65,76,107,141,153,170,181],"genetic":[7],"alterations":[8],"that":[9,103,135],"play":[10],"crucial":[12],"role":[13],"in":[14,43,58,91],"cancer":[15],"development.Detecting":[16],"somatic":[17,28,93,154],"SVs":[18],"is":[19],"challenging,":[20],"as":[21,54],"it":[22,136],"requires":[23],"distinguishing":[24],"between":[25],"germline":[26],"and":[27,30,35,40,133,161,174],"events":[29],"dealing":[31],"with":[32,112],"subclonal":[33],"the":[36,63,74,105,129,139,168,171,179],"compresence":[37],"tumor":[39],"normal":[41],"cells":[42],"patient-derived":[44],"samples.SVs":[45],"callers":[46,111],"based":[47],"on":[48,122],"single-molecule":[49],"sequencing":[50],"technologies":[51],"have":[52],"emerged":[53],"powerful":[56],"tool":[57,143],"detecting":[59],"SVs,":[60],"thanks":[61],"to":[62,68,148,157],"ability":[64],"long":[66],"reads":[67],"span":[69],"large":[70],"genomic":[71],"regions,":[72],"allowing":[73],"detection":[75],"more":[77],"complex":[78],"rearrangements.However,":[79],"these":[80,96],"tools":[81,173],"still":[83],"affected":[84],"by":[85,128],"low":[86],"precision":[87],"and/or":[88],"recall,":[89],"especially":[90],"determining":[92],"SVs.To":[94],"overcome":[95],"limitations,":[97],"we":[98],"propose":[99],"an":[100],"ensemble":[101],"method":[102,121],"combines":[104],"results":[106],"three":[108],"long-read":[109],"variant":[110],"evidence":[113],"extracted":[114],"from":[115],"accompanying":[116],"short-read":[117],"alignments.We":[118],"evaluate":[119],"our":[120,182],"curated":[124],"truth":[125],"set":[126],"provided":[127],"Espejo":[130],"Valle-Inclan":[131],"benchmark":[132],"show":[134],"can":[137],"leverage":[138],"strengths":[140],"each":[142],"while":[144],"mitigating":[145],"their":[146],"weaknesses":[147],"produce":[149],"ranked":[151],"list":[152],"deletions,":[155],"useful":[156],"prioritize":[158],"downstream":[159],"analysis":[160],"experimental":[162],"validation.We":[163],"also":[164],"provide":[165],"insights":[166],"into":[167],"performance":[169],"individual":[172],"discuss":[175],"future":[176],"directions":[177],"for":[178],"extension":[180],"method.":[183]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}