{"id":"https://openalex.org/W7171503357","doi":"https://doi.org/10.1145/3807503.3820172","title":"Generative genome modeling for simulation","display_name":"Generative genome modeling for simulation","publication_year":2026,"publication_date":"2026-06-30","ids":{"openalex":"https://openalex.org/W7171503357","doi":"https://doi.org/10.1145/3807503.3820172"},"language":null,"primary_location":{"id":"doi:10.1145/3807503.3820172","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3820172","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1145/3807503.3820172","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077802994","display_name":"Timothy Becker","orcid":"https://orcid.org/0000-0001-9784-5664"},"institutions":[{"id":"https://openalex.org/I4498119","display_name":"Connecticut College","ror":"https://ror.org/01hpqfm28","country_code":"US","type":"education","lineage":["https://openalex.org/I4498119"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Timothy James Becker","raw_affiliation_strings":["Computer Science, Connecticut College, New London, Connecticut, USA"],"raw_orcid":"https://orcid.org/0000-0001-9784-5664","affiliations":[{"raw_affiliation_string":"Computer Science, Connecticut College, New London, Connecticut, USA","institution_ids":["https://openalex.org/I4498119"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5077802994"],"corresponding_institution_ids":["https://openalex.org/I4498119"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"2"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.5318999886512756},{"id":"https://openalex.org/keywords/chromothripsis","display_name":"Chromothripsis","score":0.5087000131607056},{"id":"https://openalex.org/keywords/measure","display_name":"Measure (data warehouse)","score":0.5038999915122986},{"id":"https://openalex.org/keywords/structural-variation","display_name":"Structural variation","score":0.47850000858306885},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.4406000077724457},{"id":"https://openalex.org/keywords/variation","display_name":"Variation (astronomy)","score":0.4041999876499176},{"id":"https://openalex.org/keywords/interpretation","display_name":"Interpretation (philosophy)","score":0.361299991607666}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6797000169754028},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.5318999886512756},{"id":"https://openalex.org/C99983632","wikidata":"https://www.wikidata.org/wiki/Q1087765","display_name":"Chromothripsis","level":5,"score":0.5087000131607056},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.5038999915122986},{"id":"https://openalex.org/C151020129","wikidata":"https://www.wikidata.org/wiki/Q7625067","display_name":"Structural variation","level":4,"score":0.47850000858306885},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.4406000077724457},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43220001459121704},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4219000041484833},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.4041999876499176},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.36719998717308044},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.361299991607666},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.33709999918937683},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.31839999556541443},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.3165999948978424},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.3160000145435333},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.3160000145435333},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.30059999227523804},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.30000001192092896},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.2964000105857849},{"id":"https://openalex.org/C12713177","wikidata":"https://www.wikidata.org/wiki/Q1900281","display_name":"Perspective (graphical)","level":2,"score":0.2542000114917755}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3807503.3820172","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3820172","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3807503.3820172","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3820172","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G854341550","display_name":null,"funder_award_id":"R03DE033083","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":4,"referenced_works":["https://openalex.org/W2038840669","https://openalex.org/W2411835530","https://openalex.org/W2796038592","https://openalex.org/W4414629493"],"related_works":[],"abstract_inverted_index":{"Somatic":[0],"structural":[1,51],"variations":[2],"(SVs)":[3],"are":[4,118],"commonly":[5],"observed":[6],"in":[7,59,147],"cancer":[8],"tissue,":[9],"but":[10],"remain":[11],"challenging":[12],"to":[13,22,55,64,80,109,120,133,140],"discover":[14],"with":[15,28,78,100],"short":[16],"and":[17,57,92,112,139],"long":[18],"read":[19],"sequencing":[20,24],"due":[21],"technical":[23],"factors.":[25],"Only":[26],"SVs":[27],"a":[29,131],"sufficient":[30],"fraction":[31],"of":[32,47,67,104],"reads":[33],"spanning":[34],"the":[35,45,96,101,122,142,148],"event":[36],"will":[37],"be":[38],"detectable,":[39],"while":[40],"issues":[41],"like":[42],"chromothripsis":[43],"increase":[44],"complexity":[46],"interpretation":[48],"significantly.":[49],"Because":[50],"variation":[52,136],"is":[53,62,84],"difficult":[54,124],"measure":[56,134],"reproduce":[58],"vivo,":[60],"it":[61],"logical":[63],"make":[65],"use":[66],"simulation":[68],"frameworks.":[69],"The":[70],"SoMaCX":[71],"framework":[72],"provides":[73,130],"superior":[74],"generative":[75],"modeling":[76,129],"performance":[77,138],"respect":[79],"real":[81],"data.":[82],"This":[83],"achieved":[85],"by":[86],"utilizing":[87],"biological":[88,102],"relevant":[89],"positions":[90],"(genes":[91],"regulatory":[93],"elements)":[94],"as":[95],"distribution":[97],"controls":[98],"along":[99],"modulations":[103],"known":[105],"pathways":[106],"(end-joining)":[107],"leading":[108],"more":[110],"detailed":[111],"realistic":[113],"simulated":[114],"genomes.":[115],"Generative":[116],"methods":[117],"needed":[119,146],"explore":[121],"most":[123],"genomic":[125],"conditions,":[126],"where":[127],"our":[128],"means":[132],"germline":[135],"calling":[137],"calibrate":[141],"rare":[143],"variant":[144],"detection":[145],"clinical":[149],"setting.":[150]},"counts_by_year":[],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2026-07-29T00:00:00"}