{"id":"https://openalex.org/W2747648606","doi":"https://doi.org/10.1145/3107411.3107414","title":"CERENKOV","display_name":"CERENKOV","publication_year":2017,"publication_date":"2017-08-20","ids":{"openalex":"https://openalex.org/W2747648606","doi":"https://doi.org/10.1145/3107411.3107414","mag":"2747648606"},"language":"en","primary_location":{"id":"doi:10.1145/3107411.3107414","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3107414","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th 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/A5100389441","display_name":"Yao Yao","orcid":"https://orcid.org/0000-0002-8218-8638"},"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":"Yao Yao","raw_affiliation_strings":["Oregon State University, Corvallis, OR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Oregon State University, Corvallis, OR, USA","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100423669","display_name":"Zheng Liu","orcid":"https://orcid.org/0000-0002-0405-2348"},"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":"Zheng Liu","raw_affiliation_strings":["Oregon State University, Corvallis, OR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Oregon State University, Corvallis, OR, USA","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031593358","display_name":"Satpreet H. Singh","orcid":"https://orcid.org/0000-0003-1867-4401"},"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":"Satpreet Singh","raw_affiliation_strings":["Oregon State University, Corvallis, OR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Oregon State University, Corvallis, OR, USA","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046136400","display_name":"Qi Wei","orcid":"https://orcid.org/0000-0002-1481-2304"},"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":"Qi Wei","raw_affiliation_strings":["Oregon State University, Corvallis, OR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Oregon State University, Corvallis, OR, USA","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, Corvallis, OR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Oregon State University, Corvallis, OR, USA","institution_ids":["https://openalex.org/I131249849"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.4487,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.63755048,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"526","issue":null,"first_page":"79","last_page":"88"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9599000215530396,"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9599000215530396,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9581999778747559,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9550999999046326,"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/computer-science","display_name":"Computer science","score":0.46794384717941284},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.32826149463653564}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46794384717941284},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.32826149463653564}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3107411.3107414","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3107414","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities","score":0.6399999856948853}],"awards":[{"id":"https://openalex.org/G7282970069","display_name":null,"funder_award_id":"1557605-DMS, 1553728-DBI","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/F4320306799","display_name":"Pharmaceutical Research and Manufacturers of America Foundation","ror":"https://ror.org/01z88k350"},{"id":"https://openalex.org/F4320311401","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":61,"referenced_works":["https://openalex.org/W1533942137","https://openalex.org/W1544691147","https://openalex.org/W1680392829","https://openalex.org/W1964963969","https://openalex.org/W1965170928","https://openalex.org/W1969761972","https://openalex.org/W1984068087","https://openalex.org/W1991381389","https://openalex.org/W1996760543","https://openalex.org/W2001554877","https://openalex.org/W2011582941","https://openalex.org/W2012627860","https://openalex.org/W2018189081","https://openalex.org/W2019983262","https://openalex.org/W2020302515","https://openalex.org/W2033201031","https://openalex.org/W2038473742","https://openalex.org/W2038774969","https://openalex.org/W2041460881","https://openalex.org/W2069520341","https://openalex.org/W2078059415","https://openalex.org/W2078663610","https://openalex.org/W2104549677","https://openalex.org/W2105071916","https://openalex.org/W2106306904","https://openalex.org/W2106848050","https://openalex.org/W2112814753","https://openalex.org/W2114880905","https://openalex.org/W2116868464","https://openalex.org/W2118596665","https://openalex.org/W2122732537","https://openalex.org/W2123958887","https://openalex.org/W2124514674","https://openalex.org/W2128476271","https://openalex.org/W2131515457","https://openalex.org/W2134755636","https://openalex.org/W2136124952","https://openalex.org/W2136707328","https://openalex.org/W2142570576","https://openalex.org/W2144141448","https://openalex.org/W2145191876","https://openalex.org/W2146013776","https://openalex.org/W2153087859","https://openalex.org/W2160995259","https://openalex.org/W2161978970","https://openalex.org/W2169674658","https://openalex.org/W2198606573","https://openalex.org/W2212528563","https://openalex.org/W2220384803","https://openalex.org/W2225726427","https://openalex.org/W2295598076","https://openalex.org/W2336509392","https://openalex.org/W2415245143","https://openalex.org/W2475229214","https://openalex.org/W2509668036","https://openalex.org/W2911964244","https://openalex.org/W2997591727","https://openalex.org/W3102027041","https://openalex.org/W3102476541","https://openalex.org/W4213327946","https://openalex.org/W4230266413"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2935759653","https://openalex.org/W3105167352","https://openalex.org/W54078636","https://openalex.org/W2954470139","https://openalex.org/W1501425562","https://openalex.org/W2902782467","https://openalex.org/W3084825885","https://openalex.org/W2298861036","https://openalex.org/W3148032049"],"abstract_inverted_index":{"We":[0,85,160,175],"describe":[1],"a":[2,39,42,49,62,91,127,164],"novel":[3,50,63,151],"computational":[4],"approach,":[5],"CERENKOV":[6,28,89,123,149,181,236,253],"(Computational":[7],"Elucidation":[8],"of":[9,38,41,78,94,180,207,209],"the":[10,36,73,79,177,204,210,242,252],"REgulatory":[11],"NonKOding":[12],"Variome),":[13],"for":[14,32,72,166,173,186,235,249],"discriminating":[15],"regulatory":[16],"single":[17],"nucleotide":[18],"polymorphisms":[19],"(rSNPs)":[20],"from":[21,142],"non-regulatory":[22],"SNPs":[23,96],"within":[24],"noncoding":[25],"genetic":[26],"loci.":[27],"is":[29,103,124,203,237],"specifically":[30],"designed":[31,116],"recognizing":[33],"rSNPs":[34],"in":[35],"context":[37],"post-analysis":[40,81],"genome-wide":[43],"association":[44],"study":[45],"(GWAS);":[46],"it":[47],"includes":[48,150],"accuracy":[51],"scoring":[52],"metric":[53],"(which":[54],"we":[55,115,140,213],"call":[56],"average":[57],"rank,":[58],"or":[59],"AVGRANK)":[60],"and":[61,87,110,146,157,195,197,227,241],"cross-validation":[64],"strategy":[65],"(locus-based":[66],"sampling)":[67],"that":[68,114,139,162,199,212],"both":[69,216],"correctly":[70],"account":[71],"\"sparse":[74],"positive":[75],"bag\"":[76],"nature":[77],"GWAS":[80,121],"rSNP":[82,187],"recognition":[83,188],"problem.":[84],"trained":[86],"validated":[88],"using":[90],"reference":[92],"set":[93],"15,331":[95],"(the":[97],"OSU17":[98],"SNP":[99,136,243],"set)":[100],"whose":[101],"composition":[102],"based":[104,125,153],"on":[105,126,154,239],"selection":[106],"criteria":[107],"(linkage":[108],"disequilibrium":[109],"minor":[111],"allele":[112],"frequency)":[113],"to":[117,120,182],"ensure":[118],"relevance":[119],"post-analysis.":[122],"machine-learning":[128],"algorithm":[129],"(gradient":[130],"boosted":[131],"decision":[132],"trees)":[133],"incorporating":[134],"246":[135],"annotation":[137],"features":[138,152],"extracted":[141],"genomic,":[143],"epigenomic,":[144],"phylogenetic,":[145],"chromatin":[147],"datasets.":[148],"replication":[155],"timing":[156],"DNA":[158],"shape.":[159],"found":[161,198],"tuning":[163],"classifier":[165],"AUPVR":[167],"performance":[168,179,202],"does":[169],"not":[170],"guarantee":[171],"optimality":[172],"AVGRANK.":[174],"compared":[176],"validation":[178,201],"nine":[183],"other":[184],"methods":[185],"(including":[189],"GWAVA,":[190],"RSVP,":[191],"DeltaSVM,":[192],"DeepSEA,":[193],"Eigen,":[194],"DANQ),":[196],"CERENKOV's":[200],"strongest":[205],"out":[206],"all":[208],"classifiers":[211],"tested,":[214],"by":[215],"traditional":[217],"global":[218],"rank-based":[219],"measures":[220],"(\u3008AUPVR\u3009":[221],"=":[222,225,230],"0.506;":[223],"\u3008AUROC\u3009":[224],"0.855)":[226],"AVGRANK":[228],"(\u3008AVGRANK\u3009":[229],"3.877).":[231],"The":[232],"source":[233],"code":[234],"available":[238,248],"GitHub":[240],"feature":[244],"data":[245],"files":[246],"are":[247],"download":[250],"via":[251],"website.":[254]},"counts_by_year":[{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2017-08-31T00:00:00"}