{"id":"https://openalex.org/W7166814450","doi":"https://doi.org/10.1093/bioinformatics/btag478","title":"Primer design through submodular function estimation","display_name":"Primer design through submodular function estimation","publication_year":2026,"publication_date":"2026-06-30","ids":{"openalex":"https://openalex.org/W7166814450","doi":"https://doi.org/10.1093/bioinformatics/btag478","pmid":"https://pubmed.ncbi.nlm.nih.gov/42378440"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag478","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag478","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag478","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072374914","display_name":"Y.-M. Chen","orcid":"https://orcid.org/0000-0001-8611-2828"},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yixin Chen","raw_affiliation_strings":["Department of Computer Science and Engineering, College of Engineering, Texas A&M University , College Station, TX 77843-3112,"],"raw_orcid":"https://orcid.org/0000-0001-8611-2828","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, College of Engineering, Texas A&M University , College Station, TX 77843-3112,","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014884281","display_name":"Yunheng Han","orcid":"https://orcid.org/0000-0003-0200-5924"},"institutions":[{"id":"https://openalex.org/I94062374","display_name":"Florida College","ror":"https://ror.org/010bgev76","country_code":"US","type":"education","lineage":["https://openalex.org/I94062374"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yunheng Han","raw_affiliation_strings":["Department of Computer and Information Science and Engineering, Herbert Wertheim College of Engineering, University of Florida , Gainesville, FL 32611,"],"raw_orcid":"https://orcid.org/0000-0003-0200-5924","affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science and Engineering, Herbert Wertheim College of Engineering, University of Florida , Gainesville, FL 32611,","institution_ids":["https://openalex.org/I94062374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5139401554","display_name":"Ao wang","orcid":"https://orcid.org/0009-0009-8152-612X"},"institutions":[{"id":"https://openalex.org/I94062374","display_name":"Florida College","ror":"https://ror.org/010bgev76","country_code":"US","type":"education","lineage":["https://openalex.org/I94062374"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ao Wang","raw_affiliation_strings":["Department of Computer and Information Science and Engineering, Herbert Wertheim College of Engineering, University of Florida , Gainesville, FL 32611,"],"raw_orcid":"https://orcid.org/0009-0009-8152-612X","affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science and Engineering, Herbert Wertheim College of Engineering, University of Florida , Gainesville, FL 32611,","institution_ids":["https://openalex.org/I94062374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057139651","display_name":"Aaron Hong","orcid":null},"institutions":[{"id":"https://openalex.org/I94062374","display_name":"Florida College","ror":"https://ror.org/010bgev76","country_code":"US","type":"education","lineage":["https://openalex.org/I94062374"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aaron Hong","raw_affiliation_strings":["Department of Computer and Information Science and Engineering, Herbert Wertheim College of Engineering, University of Florida , Gainesville, FL 32611,"],"raw_orcid":"https://orcid.org/0009-0001-7138-182X","affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science and Engineering, Herbert Wertheim College of Engineering, University of Florida , Gainesville, FL 32611,","institution_ids":["https://openalex.org/I94062374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085522942","display_name":"Adam R. Rivers","orcid":"https://orcid.org/0000-0002-3703-834X"},"institutions":[{"id":"https://openalex.org/I1308724467","display_name":"Florida Department of Agriculture and Consumer Services","ror":"https://ror.org/058nbms57","country_code":"US","type":"government","lineage":["https://openalex.org/I1308724467"]},{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adam R Rivers","raw_affiliation_strings":["United States Department of Agriculture , Gainesville, FL 32608,"],"raw_orcid":"https://orcid.org/0000-0002-3703-834X","affiliations":[{"raw_affiliation_string":"United States Department of Agriculture , Gainesville, FL 32608,","institution_ids":["https://openalex.org/I1308724467","https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083575259","display_name":"Alan Kuhnle","orcid":"https://orcid.org/0000-0001-6506-1902"},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alan Kuhnle","raw_affiliation_strings":["Department of Computer Science and Engineering, College of Engineering, Texas A&M University , College Station, TX 77843-3112,"],"raw_orcid":"https://orcid.org/0000-0001-6506-1902","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, College of Engineering, Texas A&M University , College Station, TX 77843-3112,","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021635660","display_name":"Christina Boucher","orcid":"https://orcid.org/0000-0001-9509-9725"},"institutions":[{"id":"https://openalex.org/I94062374","display_name":"Florida College","ror":"https://ror.org/010bgev76","country_code":"US","type":"education","lineage":["https://openalex.org/I94062374"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christina Boucher","raw_affiliation_strings":["Department of Computer and Information Science and Engineering, Herbert Wertheim College of Engineering, University of Florida , Gainesville, FL 32611,"],"raw_orcid":"https://orcid.org/0000-0001-9509-9725","affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science and Engineering, Herbert Wertheim College of Engineering, University of Florida , Gainesville, FL 32611,","institution_ids":["https://openalex.org/I94062374"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.79698997,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"7","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.16089999675750732,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.16089999675750732,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.06870000064373016,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.06419999897480011,"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/submodular-set-function","display_name":"Submodular set function","score":0.7960000038146973},{"id":"https://openalex.org/keywords/heuristics","display_name":"Heuristics","score":0.7020999789237976},{"id":"https://openalex.org/keywords/correctness","display_name":"Correctness","score":0.5758000016212463},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5282999873161316},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5224999785423279},{"id":"https://openalex.org/keywords/primer","display_name":"Primer (cosmetics)","score":0.4982999861240387},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.44999998807907104},{"id":"https://openalex.org/keywords/multiplex","display_name":"Multiplex","score":0.3921999931335449}],"concepts":[{"id":"https://openalex.org/C178621042","wikidata":"https://www.wikidata.org/wiki/Q7631710","display_name":"Submodular set function","level":2,"score":0.7960000038146973},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.7020999789237976},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6504999995231628},{"id":"https://openalex.org/C55439883","wikidata":"https://www.wikidata.org/wiki/Q360812","display_name":"Correctness","level":2,"score":0.5758000016212463},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5282999873161316},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5224999785423279},{"id":"https://openalex.org/C2777563447","wikidata":"https://www.wikidata.org/wiki/Q7243397","display_name":"Primer (cosmetics)","level":2,"score":0.4982999861240387},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.44999998807907104},{"id":"https://openalex.org/C2781188995","wikidata":"https://www.wikidata.org/wiki/Q6934982","display_name":"Multiplex","level":2,"score":0.3921999931335449},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.385699987411499},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.373199999332428},{"id":"https://openalex.org/C108710211","wikidata":"https://www.wikidata.org/wiki/Q11538","display_name":"Mathematical proof","level":2,"score":0.3610000014305115},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35280001163482666},{"id":"https://openalex.org/C2776330181","wikidata":"https://www.wikidata.org/wiki/Q18358244","display_name":"Maximization","level":2,"score":0.3522999882698059},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.3400999903678894},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3224000036716461},{"id":"https://openalex.org/C51823790","wikidata":"https://www.wikidata.org/wiki/Q504353","display_name":"Greedy algorithm","level":2,"score":0.3167000114917755},{"id":"https://openalex.org/C137836250","wikidata":"https://www.wikidata.org/wiki/Q984063","display_name":"Optimization problem","level":2,"score":0.3140999972820282},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.29330000281333923},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.26910001039505005},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.2572000026702881},{"id":"https://openalex.org/C117251300","wikidata":"https://www.wikidata.org/wiki/Q1849855","display_name":"Parametric statistics","level":2,"score":0.2547000050544739},{"id":"https://openalex.org/C68781425","wikidata":"https://www.wikidata.org/wiki/Q2052203","display_name":"Multi-objective optimization","level":2,"score":0.25290000438690186}],"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D060885","descriptor_name":"Multiplex Polymerase Chain Reaction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D060885","descriptor_name":"Multiplex Polymerase Chain Reaction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag478","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag478","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42378440","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42378440","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13378452","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13378452/","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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag478","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag478","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1384730477","display_name":null,"funder_award_id":"6064-32000-001-009S","funder_id":"https://openalex.org/F4320332605","funder_display_name":"Agricultural Research Service"},{"id":"https://openalex.org/G988613421","display_name":null,"funder_award_id":"58-6064-4-016","funder_id":"https://openalex.org/F4320332605","funder_display_name":"Agricultural Research Service"}],"funders":[{"id":"https://openalex.org/F4320309170","display_name":"Florida State University","ror":"https://ror.org/05g3dte14"},{"id":"https://openalex.org/F4320332605","display_name":"Agricultural Research Service","ror":"https://ror.org/02d2m2044"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W2032019813","https://openalex.org/W2048662221","https://openalex.org/W2127774996","https://openalex.org/W2137089963","https://openalex.org/W2140721386","https://openalex.org/W2143434226","https://openalex.org/W2162098634","https://openalex.org/W2171719398","https://openalex.org/W2338281719","https://openalex.org/W2396849069","https://openalex.org/W2568029223","https://openalex.org/W2801615337","https://openalex.org/W2952045272","https://openalex.org/W4223591415","https://openalex.org/W4226133184","https://openalex.org/W4280574735","https://openalex.org/W4387197532"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"Multiplex":[1],"PCR-based":[2],"enrichment":[3],"is":[4,133],"widely":[5],"used":[6,145],"in":[7,128,146],"viral":[8,100],"genome":[9,22,82,101],"sequencing":[10],"and":[11,38,84,87,115,122,135,143],"pathogen":[12],"surveillance.":[13],"However,":[14],"designing":[15],"large":[16],"sets":[17],"of":[18,125],"primers":[19],"that":[20,64,80,104],"maximize":[21],"coverage":[23,83],"while":[24],"minimizing":[25],"primer-primer":[26],"interactions":[27],"remains":[28],"a":[29,44,61,70,89,94],"major":[30],"computational":[31],"challenge.":[32],"Existing":[33],"methods":[34],"such":[35],"as":[36,69],"SADDLE":[37],"Olivar":[39],"use":[40],"heuristics":[41],"to":[42,112],"optimize":[43],"Badness":[45,109],"score":[46],"for":[47],"primer":[48,67,129],"dimers":[49],"but":[50],"lack":[51],"theoretical":[52,123],"guarantees":[53],"on":[54,99,151],"solution":[55],"quality.":[56],"RESULTS:":[57],"We":[58],"introduce":[59],"PRISM,":[60],"new":[62],"framework":[63],"formulates":[65],"multiplex":[66],"design":[68],"constrained":[71],"submodular":[72,126],"maximization":[73],"problem.":[74],"Our":[75],"method":[76],"defines":[77],"an":[78],"objective":[79],"balances":[81],"dimer":[85],"risk,":[86],"applies":[88],"local":[90],"search":[91],"algorithm":[92],"with":[93],"constant-factor":[95],"approximation":[96],"guarantee.":[97],"Evaluations":[98],"datasets":[102],"demonstrate":[103],"PRISM":[105,132],"consistently":[106],"achieves":[107],"lower":[108],"scores":[110],"compared":[111],"PrimalScheme,":[113],"Olivar,":[114],"primerJinn.":[116],"These":[117],"results":[118,144],"highlight":[119],"the":[120],"scalability":[121],"rigor":[124],"optimization":[127],"design.":[130],"AVAILABILITY:":[131],"open-source":[134],"available":[136],"at":[137,153],"https://github.com/yhhan19/PRISM-new.":[138],"The":[139],"experimental":[140],"data,":[141],"scripts,":[142],"this":[147],"paper":[148],"are":[149],"archived":[150],"Figshare":[152],"https://doi.org/10.6084/m9.figshare.32806499.":[154]},"counts_by_year":[],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2026-07-02T00:00:00"}
