{"id":"https://openalex.org/W4310703193","doi":"https://doi.org/10.1371/journal.pcbi.1010733","title":"Regional mutational signature activities in cancer genomes","display_name":"Regional mutational signature activities in cancer genomes","publication_year":2022,"publication_date":"2022-12-05","ids":{"openalex":"https://openalex.org/W4310703193","doi":"https://doi.org/10.1371/journal.pcbi.1010733"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1010733","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010733","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1010733","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054079335","display_name":"Caitlin Timmons","orcid":"https://orcid.org/0000-0003-4118-4902"},"institutions":[{"id":"https://openalex.org/I202524275","display_name":"Smith College","ror":"https://ror.org/0497crr92","country_code":"US","type":"education","lineage":["https://openalex.org/I202524275"]},{"id":"https://openalex.org/I39965400","display_name":"Kettering University","ror":"https://ror.org/03rcspa57","country_code":"US","type":"education","lineage":["https://openalex.org/I39965400"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Caitlin Timmons","raw_affiliation_strings":["Computational and Systems Biology Program, Sloan Kettering Institute, New York, New York, United States of America","Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-4118-4902","affiliations":[{"raw_affiliation_string":"Computational and Systems Biology Program, Sloan Kettering Institute, New York, New York, United States of America","institution_ids":["https://openalex.org/I39965400"]},{"raw_affiliation_string":"Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America","institution_ids":["https://openalex.org/I202524275"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035010657","display_name":"Quaid Morris","orcid":"https://orcid.org/0000-0002-2760-6999"},"institutions":[{"id":"https://openalex.org/I39965400","display_name":"Kettering University","ror":"https://ror.org/03rcspa57","country_code":"US","type":"education","lineage":["https://openalex.org/I39965400"]},{"id":"https://openalex.org/I4210127509","display_name":"Vector Institute","ror":"https://ror.org/03kqdja62","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210127509"]}],"countries":["CA","US"],"is_corresponding":true,"raw_author_name":"Quaid Morris","raw_affiliation_strings":["Computational and Systems Biology Program, Sloan Kettering Institute, New York, New York, United States of America","Vector Institute for Artificial Intelligence, Toronto, Canada"],"raw_orcid":"https://orcid.org/0000-0002-2760-6999","affiliations":[{"raw_affiliation_string":"Computational and Systems Biology Program, Sloan Kettering Institute, New York, New York, United States of America","institution_ids":["https://openalex.org/I39965400"]},{"raw_affiliation_string":"Vector Institute for Artificial Intelligence, Toronto, Canada","institution_ids":["https://openalex.org/I4210127509"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053775979","display_name":"Caitlin F. Harrigan","orcid":"https://orcid.org/0000-0002-9243-9648"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I4210127509","display_name":"Vector Institute","ror":"https://ror.org/03kqdja62","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210127509"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Caitlin F. Harrigan","raw_affiliation_strings":["Department of Computer Science, University of Toronto, Toronto, Canada","Vector Institute for Artificial Intelligence, Toronto, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Toronto, Toronto, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Vector Institute for Artificial Intelligence, Toronto, Canada","institution_ids":["https://openalex.org/I4210127509"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5035010657"],"corresponding_institution_ids":["https://openalex.org/I39965400","https://openalex.org/I4210127509"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.17206081,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"18","issue":"12","first_page":"e1010733","last_page":"e1010733"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.9987000226974487,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9987000226974487,"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/genome","display_name":"Genome","score":0.7432506084442139},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6537415385246277},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5860682725906372},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5361748933792114},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.5170691609382629},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4983396530151367},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4477340579032898},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.42320334911346436},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.36157697439193726},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2793273329734802}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7432506084442139},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6537415385246277},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5860682725906372},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5361748933792114},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.5170691609382629},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4983396530151367},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4477340579032898},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.42320334911346436},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.36157697439193726},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2793273329734802},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1371/journal.pcbi.1010733","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010733","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:74cf33fa231544038a08ee6674f0d92d","is_oa":true,"landing_page_url":"https://doaj.org/article/74cf33fa231544038a08ee6674f0d92d","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 18, Iss 12, p e1010733 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9754594","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9754594","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1010733","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010733","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1514215252","display_name":null,"funder_award_id":"P30 CA008748","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3845656875","display_name":null,"funder_award_id":"R25 CA233208","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4102770861","display_name":null,"funder_award_id":"CA008748","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G5110314844","display_name":null,"funder_award_id":"P30 CA008748","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G5171646378","display_name":null,"funder_award_id":"R25 CA233208","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5390211282","display_name":null,"funder_award_id":"Grant P30 CA008748","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G6403603385","display_name":null,"funder_award_id":"Support Grant P30 CA008748","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320309949","display_name":"Canadian Institute for Advanced Research","ror":"https://ror.org/01sdtdd95"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1595906092","https://openalex.org/W1896708637","https://openalex.org/W1973568247","https://openalex.org/W1975684011","https://openalex.org/W1985690171","https://openalex.org/W1989456683","https://openalex.org/W2009720434","https://openalex.org/W2042793731","https://openalex.org/W2070021921","https://openalex.org/W2079314031","https://openalex.org/W2086239585","https://openalex.org/W2090527870","https://openalex.org/W2101836667","https://openalex.org/W2106452314","https://openalex.org/W2129136620","https://openalex.org/W2142160913","https://openalex.org/W2152061559","https://openalex.org/W2156988725","https://openalex.org/W2158264171","https://openalex.org/W2159973050","https://openalex.org/W2161212572","https://openalex.org/W2266041843","https://openalex.org/W2281629727","https://openalex.org/W2586629973","https://openalex.org/W2610240247","https://openalex.org/W2896872272","https://openalex.org/W2898215009","https://openalex.org/W2898789672","https://openalex.org/W2924903871","https://openalex.org/W2958845386","https://openalex.org/W2964698118","https://openalex.org/W2991196083","https://openalex.org/W2996426546","https://openalex.org/W3004480399","https://openalex.org/W3004613412","https://openalex.org/W3004647847","https://openalex.org/W3005327280","https://openalex.org/W3006500278","https://openalex.org/W3016284863","https://openalex.org/W3022071200","https://openalex.org/W3045153201","https://openalex.org/W3126332871","https://openalex.org/W3142571537","https://openalex.org/W3159766141","https://openalex.org/W3166192807","https://openalex.org/W3177051364","https://openalex.org/W3186397855","https://openalex.org/W3212488818","https://openalex.org/W3214152292","https://openalex.org/W4226224747","https://openalex.org/W4255375128"],"related_works":["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","https://openalex.org/W2005362630"],"abstract_inverted_index":{"Cancer":[0],"genomes":[1,72,117,134,148],"harbor":[2],"a":[3,215],"catalog":[4],"of":[5,13,40,45,65,84,139,149,176,217,222,257],"somatic":[6,228],"mutations.":[7],"The":[8,193],"type":[9,179],"and":[10,20,108,132,180,241,260,263,269],"genomic":[11,46,268],"context":[12],"these":[14,165],"mutations":[15],"depend":[16],"on":[17],"their":[18,22],"causes":[19],"allow":[21],"attribution":[23],"to":[24,95,100],"particular":[25,168],"mutational":[26,33,50,66,128,223],"signatures.":[27],"Previous":[28],"work":[29,60],"has":[30],"shown":[31],"that":[32,115,212,236,272],"signature":[34,67,103,129,169],"activities":[35,68,130],"change":[36,126],"over":[37,69],"the":[38,81,96,109,150,167,177,254],"course":[39],"tumor":[41,75,120,152,162],"development,":[42],"but":[43,182],"investigations":[44],"region":[47],"variability":[48],"in":[49,127,227,233,243],"signatures":[51,188],"have":[52],"been":[53],"limited.":[54],"Here,":[55],"we":[56,195],"expand":[57],"upon":[58],"this":[59],"by":[61,80,144,160,187,201],"constructing":[62],"regional":[63,102,225,255],"profiles":[64,104],"2,203":[70],"whole":[71],"across":[73,174],"25":[74],"types,":[76],"using":[77,105],"data":[78],"aggregated":[79],"Pan-Cancer":[82],"Analysis":[83],"Whole":[85],"Genomes":[86],"(PCAWG)":[87],"consortium.":[88],"We":[89,113,210],"present":[90],"GenomeTrackSig":[91],"as":[92],"an":[93],"extension":[94],"TrackSig":[97],"R":[98],"package":[99],"construct":[101],"optimal":[106],"segmentation":[107],"expectation-maximization":[110],"(EM)":[111],"algorithm.":[112],"find":[114],"426":[116],"from":[118],"20":[119],"types":[121],"display":[122],"at":[123,136],"least":[124,137],"one":[125,138],"(changepoint),":[131],"306":[133],"contain":[135],"54":[140],"recurrent":[141,155],"changepoints":[142,194],"shared":[143,159],"seven":[145],"or":[146,206],"more":[147],"same":[151,178],"type.":[153],"Five":[154],"changepoint":[156],"locations":[157],"are":[158,171,185],"multiple":[161],"types.":[163],"Within":[164],"regions,":[166],"changes":[170,232,242,271],"often":[172],"consistent":[173],"samples":[175],"some,":[181],"not":[183],"all,":[184],"characterized":[186],"associated":[189],"with":[190],"subclonal":[191,247],"expansion.":[192,248],"found":[196],"cannot":[197],"strictly":[198],"be":[199,238],"explained":[200],"gene":[202],"density,":[203,205],"mutation":[204,229],"cell-of-origin":[207],"chromatin":[208,234,244],"state.":[209],"hypothesize":[211],"they":[213],"reflect":[214],"confluence":[216],"factors":[218],"including":[219],"evolutionary":[220],"timing":[221],"processes,":[224,262],"differences":[226],"rate,":[230],"large-scale":[231],"state":[235],"may":[237,264],"tissue":[239],"type-specific,":[240],"accessibility":[245],"during":[246,274],"These":[249],"results":[250],"provide":[251],"insight":[252],"into":[253],"effects":[256],"DNA":[258],"damage":[259],"repair":[261],"help":[265],"us":[266],"localize":[267],"epigenomic":[270],"occur":[273],"cancer":[275],"development.":[276]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2022-12-16T00:00:00"}
