{"id":"https://openalex.org/W2737819809","doi":"https://doi.org/10.1109/memea.2017.7985889","title":"Nonconvex regularization for sparse genomic variant signal detection","display_name":"Nonconvex regularization for sparse genomic variant signal detection","publication_year":2017,"publication_date":"2017-05-01","ids":{"openalex":"https://openalex.org/W2737819809","doi":"https://doi.org/10.1109/memea.2017.7985889","mag":"2737819809"},"language":"en","primary_location":{"id":"doi:10.1109/memea.2017.7985889","is_oa":false,"landing_page_url":"https://doi.org/10.1109/memea.2017.7985889","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 IEEE International Symposium on Medical Measurements and Applications (MeMeA)","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/A5082681242","display_name":"Mario Ba\u00f1uelos","orcid":null},"institutions":[{"id":"https://openalex.org/I156087764","display_name":"University of California, Merced","ror":"https://ror.org/00d9ah105","country_code":"US","type":"education","lineage":["https://openalex.org/I156087764"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mario Banuelos","raw_affiliation_strings":["Applied Mathematics, University of California, Merced, Merced, CA, USA"],"affiliations":[{"raw_affiliation_string":"Applied Mathematics, University of California, Merced, Merced, CA, USA","institution_ids":["https://openalex.org/I156087764"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003506092","display_name":"Lasith Adhikari","orcid":"https://orcid.org/0000-0002-3252-8972"},"institutions":[{"id":"https://openalex.org/I156087764","display_name":"University of California, Merced","ror":"https://ror.org/00d9ah105","country_code":"US","type":"education","lineage":["https://openalex.org/I156087764"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lasith Adhikari","raw_affiliation_strings":["Applied Mathematics, University of California, Merced, Merced, CA, USA"],"affiliations":[{"raw_affiliation_string":"Applied Mathematics, University of California, Merced, Merced, CA, USA","institution_ids":["https://openalex.org/I156087764"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001635770","display_name":"Rubi Almanza","orcid":null},"institutions":[{"id":"https://openalex.org/I156087764","display_name":"University of California, Merced","ror":"https://ror.org/00d9ah105","country_code":"US","type":"education","lineage":["https://openalex.org/I156087764"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rubi Almanza","raw_affiliation_strings":["Applied Mathematics, University of California, Merced, Merced, CA, USA"],"affiliations":[{"raw_affiliation_string":"Applied Mathematics, University of California, Merced, Merced, CA, USA","institution_ids":["https://openalex.org/I156087764"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071568479","display_name":"Andrew Fujikawa","orcid":null},"institutions":[{"id":"https://openalex.org/I43522216","display_name":"California State University, Sacramento","ror":"https://ror.org/03e26wv14","country_code":"US","type":"education","lineage":["https://openalex.org/I43522216"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew Fujikawa","raw_affiliation_strings":["California State University, Sacramento, Sacramento, CA, USA"],"affiliations":[{"raw_affiliation_string":"California State University, Sacramento, Sacramento, CA, USA","institution_ids":["https://openalex.org/I43522216"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086933118","display_name":"Jonathan Sahagun","orcid":null},"institutions":[{"id":"https://openalex.org/I27825529","display_name":"California State University Los Angeles","ror":"https://ror.org/0294hxs80","country_code":"US","type":"education","lineage":["https://openalex.org/I27825529"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan Sahagun","raw_affiliation_strings":["California State University Los Angeles, Los Angeles, CA, US"],"affiliations":[{"raw_affiliation_string":"California State University Los Angeles, Los Angeles, CA, US","institution_ids":["https://openalex.org/I27825529"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067647428","display_name":"Katharine Sanderson","orcid":null},"institutions":[{"id":"https://openalex.org/I23732399","display_name":"Montana State University","ror":"https://ror.org/02w0trx84","country_code":"US","type":"education","lineage":["https://openalex.org/I23732399","https://openalex.org/I4210126032"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Katharine Sanderson","raw_affiliation_strings":["Montana State University, Bozeman, MT, USA"],"affiliations":[{"raw_affiliation_string":"Montana State University, Bozeman, MT, USA","institution_ids":["https://openalex.org/I23732399"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045718155","display_name":"Melissa Spence","orcid":null},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Melissa Spence","raw_affiliation_strings":["University of California, Davis, Davis, CA, USA"],"affiliations":[{"raw_affiliation_string":"University of California, Davis, Davis, CA, USA","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027970835","display_name":"Suzanne Sindi","orcid":"https://orcid.org/0000-0003-2742-4332"},"institutions":[{"id":"https://openalex.org/I156087764","display_name":"University of California, Merced","ror":"https://ror.org/00d9ah105","country_code":"US","type":"education","lineage":["https://openalex.org/I156087764"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Suzanne Sindi","raw_affiliation_strings":["Applied Mathematics, University of California, Merced, Merced, CA, USA"],"affiliations":[{"raw_affiliation_string":"Applied Mathematics, University of California, Merced, Merced, CA, USA","institution_ids":["https://openalex.org/I156087764"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005703929","display_name":"Roummel F. Marcia","orcid":"https://orcid.org/0000-0001-6838-140X"},"institutions":[{"id":"https://openalex.org/I156087764","display_name":"University of California, Merced","ror":"https://ror.org/00d9ah105","country_code":"US","type":"education","lineage":["https://openalex.org/I156087764"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Roummel F. Marcia","raw_affiliation_strings":["Applied Mathematics, University of California, Merced, Merced, CA, USA"],"affiliations":[{"raw_affiliation_string":"Applied Mathematics, University of California, Merced, Merced, CA, USA","institution_ids":["https://openalex.org/I156087764"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5082681242"],"corresponding_institution_ids":["https://openalex.org/I156087764"],"apc_list":null,"apc_paid":null,"fwci":1.261,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.82044932,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"281","last_page":"286"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9997000098228455,"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"}},"topics":[{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9997000098228455,"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"}},{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.9958999752998352,"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"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9934999942779541,"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":0.6508637070655823},{"id":"https://openalex.org/keywords/regularization","display_name":"Regularization (linguistics)","score":0.537834882736206},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5030953288078308},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49172499775886536},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.43254154920578003},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4221726059913635},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3993165194988251},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3329885005950928},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.33232206106185913},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3308162987232208},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3293982744216919},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.30512499809265137},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.24128401279449463},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.20829999446868896}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6508637070655823},{"id":"https://openalex.org/C2776135515","wikidata":"https://www.wikidata.org/wiki/Q17143721","display_name":"Regularization (linguistics)","level":2,"score":0.537834882736206},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5030953288078308},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49172499775886536},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.43254154920578003},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4221726059913635},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3993165194988251},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3329885005950928},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33232206106185913},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3308162987232208},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3293982744216919},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30512499809265137},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.24128401279449463},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20829999446868896}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/memea.2017.7985889","is_oa":false,"landing_page_url":"https://doi.org/10.1109/memea.2017.7985889","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 IEEE International Symposium on Medical Measurements and Applications (MeMeA)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions","score":0.6100000143051147}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1512279564","https://openalex.org/W1514579811","https://openalex.org/W1523139359","https://openalex.org/W1966711026","https://openalex.org/W1990139627","https://openalex.org/W2050892949","https://openalex.org/W2057516806","https://openalex.org/W2082473969","https://openalex.org/W2096791516","https://openalex.org/W2102119022","https://openalex.org/W2103559027","https://openalex.org/W2124682210","https://openalex.org/W2125852763","https://openalex.org/W2127230157","https://openalex.org/W2133112449","https://openalex.org/W2135046866","https://openalex.org/W2135236030","https://openalex.org/W2142058898","https://openalex.org/W2171777347","https://openalex.org/W2204914826","https://openalex.org/W2323327415","https://openalex.org/W2400919359","https://openalex.org/W2512642942","https://openalex.org/W2535543414","https://openalex.org/W2616754551","https://openalex.org/W3100489614","https://openalex.org/W3106237033","https://openalex.org/W6678669296"],"related_works":["https://openalex.org/W1965280193","https://openalex.org/W2521866209","https://openalex.org/W3023271652","https://openalex.org/W2101115907","https://openalex.org/W2093610003","https://openalex.org/W2084576922","https://openalex.org/W2412321833","https://openalex.org/W2061338306","https://openalex.org/W1965856472","https://openalex.org/W3126673655"],"abstract_inverted_index":{"Recent":[0],"research":[1],"suggests":[2],"an":[3,33,78,120],"overwhelming":[4],"proportion":[5],"of":[6,14,55,59,77,112,152,167,188],"humans":[7],"have":[8],"genomic":[9],"structural":[10],"variants":[11],"(SVs):":[12],"rearrangements":[13],"regions":[15],"in":[16,32,42,66,101,145,150],"the":[17,40,52,67,75,159,186],"genome":[18,35,41],"such":[19],"as":[20],"inversions,":[21],"insertions,":[22],"deletions":[23],"and":[24,50,70,134,173,184],"duplications.":[25],"The":[26],"standard":[27],"approach":[28,91],"to":[29,46,81,93,147],"detecting":[30],"SVs":[31,62,100,143],"unknown":[34],"involves":[36],"sequencing":[37,172],"paired-reads":[38],"from":[39,86,98,169],"question,":[43],"mapping":[44],"them":[45],"a":[47,107,113,164],"reference":[48],"genome,":[49,69],"analyzing":[51],"resulting":[53],"configuration":[54],"fragments":[56],"for":[57],"evidence":[58],"rearrangements.":[60],"Because":[61],"occur":[63],"relatively":[64],"infrequently":[65],"human":[68],"erroneous":[71],"read-mappings":[72],"may":[73],"suggest":[74],"presence":[76],"SV,":[79],"approaches":[80],"SV":[82,189],"detection":[83],"typically":[84],"suffer":[85],"high":[87],"false-positive":[88],"rates.":[89],"Our":[90,155],"aims":[92],"more":[94],"accurately":[95],"distinguish":[96],"true":[97],"false":[99,160],"two":[102],"ways:":[103],"First,":[104],"we":[105,128,140,179],"solve":[106],"constrained":[108],"optimization":[109],"equation":[110],"consisting":[111],"negative":[114],"Poisson":[115],"log-likelihood":[116],"objective":[117],"function":[118],"with":[119],"additive":[121],"penalty":[122],"term":[123],"that":[124],"promotes":[125],"sparsity.":[126],"Second,":[127],"analyze":[129],"multiple":[130],"related":[131],"individuals":[132],"simultaneously":[133],"enforce":[135],"familial":[136],"constraints.":[137],"That":[138],"is,":[139],"require":[141],"any":[142],"predicted":[144],"children":[146],"be":[148],"present":[149],"one":[151],"their":[153],"parents.":[154],"problem":[156],"formulation":[157,183],"decreases":[158],"positive":[161],"rate":[162],"despite":[163],"large":[165],"amount":[166],"error":[168],"both":[170],"DNA":[171],"mapping.":[174],"By":[175],"incorporating":[176],"additional":[177],"information,":[178],"improve":[180],"our":[181],"model":[182],"increase":[185],"accuracy":[187],"prediction":[190],"methods.":[191]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}