{"id":"https://openalex.org/W2957367608","doi":"https://doi.org/10.1093/bioinformatics/btz340","title":"Modeling clinical and molecular covariates of mutational process activity in cancer","display_name":"Modeling clinical and molecular covariates of mutational process activity in cancer","publication_year":2019,"publication_date":"2019-05-09","ids":{"openalex":"https://openalex.org/W2957367608","doi":"https://doi.org/10.1093/bioinformatics/btz340","mag":"2957367608","pmid":"https://pubmed.ncbi.nlm.nih.gov/31510643"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz340","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz340","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/14/i492/30302615/btz340.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/14/i492/30302615/btz340.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059617425","display_name":"Welles Robinson","orcid":"https://orcid.org/0000-0001-9018-6811"},"institutions":[{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Welles Robinson","raw_affiliation_strings":["Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, MD, USA","Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, MD, USA","institution_ids":["https://openalex.org/I4210140884"]},{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046958549","display_name":"Roded Sharan","orcid":"https://orcid.org/0000-0001-8363-4882"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Roded Sharan","raw_affiliation_strings":["Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089144841","display_name":"Mark D.M. Leiserson","orcid":"https://orcid.org/0000-0002-1034-4363"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mark D M Leiserson","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA"],"raw_orcid":"https://orcid.org/0000-0002-1034-4363","affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA","institution_ids":["https://openalex.org/I66946132"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5089144841"],"corresponding_institution_ids":["https://openalex.org/I66946132"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7726,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.65955069,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"35","issue":"14","first_page":"i492","last_page":"i500"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.7656000256538391,"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":0.7656000256538391,"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/T11235","display_name":"Statistical Methods in Clinical Trials","score":0.0333000011742115,"subfield":{"id":"https://openalex.org/subfields/2613","display_name":"Statistics and Probability"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10392","display_name":"Cutaneous Melanoma Detection and Management","score":0.032600000500679016,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/covariate","display_name":"Covariate","score":0.7887527942657471},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.500568151473999},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.4780500531196594},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.477438747882843},{"id":"https://openalex.org/keywords/carcinogenesis","display_name":"Carcinogenesis","score":0.4525453746318817},{"id":"https://openalex.org/keywords/germline-mutation","display_name":"Germline mutation","score":0.4210847020149231},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4162311255931854},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3890892267227173},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.36293989419937134},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.18190976977348328},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17497113347053528}],"concepts":[{"id":"https://openalex.org/C119043178","wikidata":"https://www.wikidata.org/wiki/Q320723","display_name":"Covariate","level":2,"score":0.7887527942657471},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.500568151473999},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.4780500531196594},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.477438747882843},{"id":"https://openalex.org/C555283112","wikidata":"https://www.wikidata.org/wiki/Q1637543","display_name":"Carcinogenesis","level":3,"score":0.4525453746318817},{"id":"https://openalex.org/C13514818","wikidata":"https://www.wikidata.org/wiki/Q5552256","display_name":"Germline mutation","level":4,"score":0.4210847020149231},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4162311255931854},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3890892267227173},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.36293989419937134},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.18190976977348328},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17497113347053528}],"mesh":[{"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":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"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":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D063646","descriptor_name":"Carcinogenesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063646","descriptor_name":"Carcinogenesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063646","descriptor_name":"Carcinogenesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz340","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz340","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/14/i492/30302615/btz340.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31510643","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31510643","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:6612886","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6612886","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz340","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz340","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/14/i492/30302615/btz340.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.8600000143051147,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G3710101564","display_name":null,"funder_award_id":"DGE-1632976","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"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":50,"referenced_works":["https://openalex.org/W1880262756","https://openalex.org/W1973268287","https://openalex.org/W1996127194","https://openalex.org/W2008255210","https://openalex.org/W2100163972","https://openalex.org/W2105100844","https://openalex.org/W2110065044","https://openalex.org/W2110417468","https://openalex.org/W2121443461","https://openalex.org/W2124977765","https://openalex.org/W2133775154","https://openalex.org/W2147629880","https://openalex.org/W2152061559","https://openalex.org/W2158065648","https://openalex.org/W2173818354","https://openalex.org/W2174706414","https://openalex.org/W2276335691","https://openalex.org/W2294814189","https://openalex.org/W2306119308","https://openalex.org/W2343368549","https://openalex.org/W2344657883","https://openalex.org/W2346025119","https://openalex.org/W2347107809","https://openalex.org/W2481795101","https://openalex.org/W2512945549","https://openalex.org/W2547187744","https://openalex.org/W2558715006","https://openalex.org/W2587610309","https://openalex.org/W2596164112","https://openalex.org/W2597577045","https://openalex.org/W2604024577","https://openalex.org/W2622499649","https://openalex.org/W2749641460","https://openalex.org/W2764292139","https://openalex.org/W2767034994","https://openalex.org/W2795993993","https://openalex.org/W2796153844","https://openalex.org/W2796403467","https://openalex.org/W2901987494","https://openalex.org/W2951181641","https://openalex.org/W2953163445","https://openalex.org/W3004480399","https://openalex.org/W4231510805","https://openalex.org/W6639619044","https://openalex.org/W6674922813","https://openalex.org/W6676591658","https://openalex.org/W6678343836","https://openalex.org/W6725919554","https://openalex.org/W6751101798","https://openalex.org/W6756870129"],"related_works":["https://openalex.org/W2985746494","https://openalex.org/W4206042385","https://openalex.org/W2511384863","https://openalex.org/W2080773131","https://openalex.org/W2096089271","https://openalex.org/W2923628599","https://openalex.org/W2014100433","https://openalex.org/W2024289194","https://openalex.org/W2049713270","https://openalex.org/W2511537300"],"abstract_inverted_index":{"MOTIVATION:":[0],"Somatic":[1],"mutations":[2],"result":[3],"from":[4,141,256],"processes":[5,18,41],"related":[6],"to":[7,79,99,107,122,145,203,210,248],"DNA":[8,100],"replication":[9],"or":[10,94],"environmental/lifestyle":[11],"exposures.":[12],"Knowing":[13],"the":[14,113,119,125,147,172,199,285,288],"activity":[15,77],"of":[16,30,39,52,58,74,127,175],"mutational":[17,40],"in":[19,43,166,197,215,224,232,271,287],"a":[20,50,155,233,243,280],"tumor":[21],"can":[22],"inform":[23],"personalized":[24],"therapies,":[25],"early":[26],"detection,":[27],"and":[28,65,169,180,192,218,236,274],"understanding":[29],"tumorigenesis.":[31],"Computational":[32],"methods":[33,85,140,162],"have":[34,61,69],"revealed":[35],"30":[36],"validated":[37],"signatures":[38,60,68,214,231],"active":[42],"human":[44],"cancers,":[45],"where":[46],"each":[47],"signature":[48,76,83,151],"is":[49,269],"pattern":[51],"single":[53],"base":[54],"substitutions.":[55],"However,":[56],"half":[57],"these":[59,109],"no":[62],"known":[63],"etiology,":[64],"some":[66],"similar":[67,204],"distinct":[70],"etiologies,":[71],"making":[72],"patterns":[73],"mutation":[75,82,132,213],"hard":[78],"interpret.":[80],"Existing":[81],"detection":[84],"do":[86],"not":[87],"consider":[88],"tumor-level":[89,129],"clinical/demographic":[90],"(e.g.":[91,97],"smoking":[92],"history)":[93],"molecular":[95],"features":[96],"inactivations":[98],"damage":[101],"repair":[102,222],"genes).":[103],"RESULTS:":[104],"To":[105,134],"begin":[106],"address":[108],"challenges,":[110],"we":[111,183],"present":[112],"Tumor":[114],"Covariate":[115],"Signature":[116],"Model":[117],"(TCSM),":[118],"first":[120],"method":[121],"directly":[123],"model":[124,138],"effect":[126],"observed":[128,157],"covariates":[130,165],"on":[131,150,154],"signatures.":[133,205],"this":[135],"end,":[136],"our":[137],"uses":[139],"Bayesian":[142],"topic":[143,193],"modeling":[144],"change":[146],"prior":[148],"distribution":[149],"exposure":[152,202],"conditioned":[153],"tumor's":[156],"covariates.":[158],"We":[159,206,227],"also":[160,228],"introduce":[161],"for":[163,170,283],"imputing":[164],"held-out":[167,225],"data":[168,281,293],"evaluating":[171],"statistical":[173,246],"significance":[174],"signature-covariate":[176],"associations.":[177],"On":[178],"simulated":[179],"real":[181],"data,":[182],"find":[184],"that":[185,252],"TCSM":[186,209,268],"outperforms":[187],"both":[188],"non-negative":[189],"matrix":[190],"factorization":[191],"modeling-based":[194],"approaches,":[195],"particularly":[196],"recovering":[198],"ground":[200],"truth":[201],"then":[207],"use":[208],"discover":[211,229],"five":[212],"breast":[216],"cancer":[217,238,240],"predict":[219],"homologous":[220],"recombination":[221],"deficiency":[223],"tumors.":[226],"four":[230],"combined":[234],"melanoma":[235],"lung":[237,254],"cohort-using":[239],"type":[241],"as":[242],"covariate-and":[244],"provide":[245],"evidence":[247],"support":[249],"earlier":[250],"claims":[251],"three":[253],"cancers":[255],"The":[257],"Cancer":[258],"Genome":[259],"Atlas":[260],"are":[261,294],"misdiagnosed":[262],"metastatic":[263],"melanomas.":[264],"AVAILABILITY":[265],"AND":[266],"IMPLEMENTATION:":[267],"implemented":[270],"Python":[272],"3":[273],"available":[275,295],"at":[276,296],"https://github.com/lrgr/tcsm,":[277],"along":[278],"with":[279],"workflow":[282],"reproducing":[284],"experiments":[286],"paper.":[289],"SUPPLEMENTARY":[290],"INFORMATION:":[291],"Supplementary":[292],"Bioinformatics":[297],"online.":[298]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}