{"id":"https://openalex.org/W2559743355","doi":"https://doi.org/10.1145/2975167.2985684","title":"Exploration of regression models for cancer noncoding mutation recurrence","display_name":"Exploration of regression models for cancer noncoding mutation recurrence","publication_year":2016,"publication_date":"2016-10-02","ids":{"openalex":"https://openalex.org/W2559743355","doi":"https://doi.org/10.1145/2975167.2985684","mag":"2559743355"},"language":"en","primary_location":{"id":"doi:10.1145/2975167.2985684","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2975167.2985684","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"type":"article","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/A5074813952","display_name":"Tanjin Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tanjin Xu","raw_affiliation_strings":["Oregon State University, Electrical Engineering and Computer Science, Corvallis, OR"],"affiliations":[{"raw_affiliation_string":"Oregon State University, Electrical Engineering and Computer Science, Corvallis, OR","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091354698","display_name":"Stephen A. Ramsey","orcid":"https://orcid.org/0000-0002-2168-5403"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephen A. Ramsey","raw_affiliation_strings":["Oregon State University, Electrical Engineering and Computer Science, Corvallis, OR"],"affiliations":[{"raw_affiliation_string":"Oregon State University, Electrical Engineering and Computer Science, Corvallis, OR","institution_ids":["https://openalex.org/I131249849"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5074813952"],"corresponding_institution_ids":["https://openalex.org/I131249849"],"apc_list":null,"apc_paid":null,"fwci":0.1265,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.58550626,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"15","issue":null,"first_page":"546","last_page":"553"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9997000098228455,"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":0.9997000098228455,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9975000023841858,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9955000281333923,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/computational-biology","display_name":"Computational biology","score":0.6109669804573059},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6098255515098572},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.539136528968811},{"id":"https://openalex.org/keywords/germline-mutation","display_name":"Germline mutation","score":0.5368990898132324},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5158266425132751},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.49979400634765625},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.4899420142173767},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.48493626713752747},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3984372913837433}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6109669804573059},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6098255515098572},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.539136528968811},{"id":"https://openalex.org/C13514818","wikidata":"https://www.wikidata.org/wiki/Q5552256","display_name":"Germline mutation","level":4,"score":0.5368990898132324},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5158266425132751},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.49979400634765625},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.4899420142173767},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.48493626713752747},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3984372913837433},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2975167.2985684","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2975167.2985684","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6399999856948853,"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306799","display_name":"Pharmaceutical Research and Manufacturers of America Foundation","ror":"https://ror.org/01z88k350"},{"id":"https://openalex.org/F4320317250","display_name":"Animal Cancer Foundation","ror":"https://ror.org/03d7wen40"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W1518897246","https://openalex.org/W1552247668","https://openalex.org/W1582121160","https://openalex.org/W1583862312","https://openalex.org/W1606347560","https://openalex.org/W1678356000","https://openalex.org/W1744771032","https://openalex.org/W1880949099","https://openalex.org/W1932714322","https://openalex.org/W1973628995","https://openalex.org/W1975846642","https://openalex.org/W1989919392","https://openalex.org/W1995837988","https://openalex.org/W2009720434","https://openalex.org/W2022495797","https://openalex.org/W2038473742","https://openalex.org/W2039877945","https://openalex.org/W2044433401","https://openalex.org/W2059191987","https://openalex.org/W2076154138","https://openalex.org/W2077026063","https://openalex.org/W2088544963","https://openalex.org/W2107949418","https://openalex.org/W2112293785","https://openalex.org/W2134508297","https://openalex.org/W2137297899","https://openalex.org/W2141820415","https://openalex.org/W2145094598","https://openalex.org/W2165064122","https://openalex.org/W2170798594","https://openalex.org/W2178844003","https://openalex.org/W2198606573","https://openalex.org/W2259938310","https://openalex.org/W2270152626","https://openalex.org/W2271238666","https://openalex.org/W2306570595","https://openalex.org/W2489578462","https://openalex.org/W2541389513","https://openalex.org/W2753666478","https://openalex.org/W2890339007","https://openalex.org/W2911964244","https://openalex.org/W2959792658","https://openalex.org/W2997574889","https://openalex.org/W4205947740","https://openalex.org/W4234212348","https://openalex.org/W4301029089","https://openalex.org/W6633658626"],"related_works":["https://openalex.org/W2086525401","https://openalex.org/W2006735166","https://openalex.org/W2079327011","https://openalex.org/W2053325634","https://openalex.org/W3178279768","https://openalex.org/W193851735","https://openalex.org/W2773861473","https://openalex.org/W2987420353","https://openalex.org/W1491897707","https://openalex.org/W2049713270"],"abstract_inverted_index":{"Cancer":[0],"initiation":[1],"and":[2,117,147,162,185,208,214,240,262],"progression":[3],"are":[4,8],"caused":[5],"by\"driver\"mutations":[6],"that":[7,15,141,250,263],"vastly":[9],"outnumbered":[10],"by":[11,83],"the":[12,47,80,120,125,155,159,182,216,237,246,251,256,259],"\"passenger\"":[13],"mutations":[14,27,43,57,101,140,227],"accumulate":[16],"due":[17],"to":[18,65,107,181],"cancer-associated":[19],"genome":[20,188],"instability.":[21],"With":[22],"genome-wide":[23],"detection":[24],"of":[25,49,56,74,99,115,124,137,158,165,222,232],"somatic":[26,100,111,167,226],"now":[28],"becoming":[29],"commonplace":[30],"for":[31,38,71,96,153,245,271],"moderate-sized":[32],"cancer":[33,50,76,143],"studies,":[34,54],"improvements":[35],"in":[36,131,196],"methods":[37],"discriminating":[39],"driver":[40,68],"from":[41,228],"passenger":[42],"would":[44],"significantly":[45],"advance":[46],"field":[48],"biology.":[51],"In":[52,89],"large-cohort":[53],"recurrence":[55,81],"within":[58,102,191],"a":[59,127,149,166,219,264],"regulatory":[60],"element":[61],"can":[62],"be":[63],"used":[64],"identify":[66],"probable":[67],"mutations;":[69],"but":[70,105],"small-cohort":[72],"studies":[73],"new":[75],"types":[77,231],"or":[78],"subtypes,":[79],"approach":[82,152],"itself":[84],"has":[85],"limited":[86],"statistical":[87],"power.":[88],"such":[90],"cases,":[91],"bioinformatic":[92],"approaches":[93],"work":[94],"well":[95],"functional":[97],"assessment":[98],"protein-coding":[103],"genes,":[104],"how":[106],"functionally":[108],"assess":[109],"noncoding":[110,139,225,273],"mutations--using":[112],"large-scale":[113],"datasets":[114],"measurements":[116],"information":[118],"about":[119],"local":[121,160],"genomic":[122,161,172],"context":[123,164],"mutation--is":[126],"fundamental":[128],"open":[129],"problem":[130],"bioinformatics.":[132],"Based":[133],"on":[134],"recent":[135],"reports":[136],"specific":[138],"drive":[142],"progression,":[144],"we":[145],"proposed":[146],"investigated":[148],"recurrence-based":[150],"regression":[151,194,253,260],"quantifying":[154],"cancer-promoting":[156],"potential":[157],"chromatin":[163],"mutation.":[168],"We":[169,212,234,248],"integrated":[170],"29":[171],"correlates":[173],"(from":[174],"sequence":[175,177],"conservation,":[176],"GC":[178],"content,":[179],"distance":[180],"nearest":[183],"gene,":[184],"ENCODE":[186],"project":[187],"location":[189],"datasets)":[190],"seven":[192],"different":[193,230],"models":[195,202,217,261],"three":[197],"model":[198,254],"classes":[199],"(generalized":[200],"linear":[201],"(GLMs),":[203],"ensemble":[204],"decision":[205],"tree":[206],"models,":[207],"neural":[209,266],"network":[210,267],"models).":[211],"trained":[213],"tested":[215],"using":[218],"combined":[220],"dataset":[221],"4.5":[223],"million":[224],"20":[229],"cancer.":[233],"then":[235],"characterized":[236],"models'":[238],"accuracies":[239],"obtained":[241],"relative":[242],"importance":[243],"scores":[244],"features.":[247],"found":[249],"Poisson":[252],"performs":[255],"best":[257],"among":[258],"deep":[265],"structure":[268],"is":[269],"promising":[270],"predicting":[272],"mutation":[274],"recurrence.":[275]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
