{"id":"https://openalex.org/W2036989119","doi":"https://doi.org/10.1109/bibe.2008.4696662","title":"Faster greedy algorithms for Multiple Degenerate Primer Selection","display_name":"Faster greedy algorithms for Multiple Degenerate Primer Selection","publication_year":2008,"publication_date":"2008-10-01","ids":{"openalex":"https://openalex.org/W2036989119","doi":"https://doi.org/10.1109/bibe.2008.4696662","mag":"2036989119"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2008.4696662","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2008.4696662","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2008 8th IEEE International Conference on BioInformatics and BioEngineering","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/A5108536575","display_name":"Sudha Balla","orcid":null},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sudha Balla","raw_affiliation_strings":["Research Fellow, the Sloan-Kettering Institute, Memorial Sloan Kettering Cancer Center, NY, USA","Sloan-Kettering Cancer Center, Sloan-Kettering Inst., York Avenue, NY"],"affiliations":[{"raw_affiliation_string":"Research Fellow, the Sloan-Kettering Institute, Memorial Sloan Kettering Cancer Center, NY, USA","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"Sloan-Kettering Cancer Center, Sloan-Kettering Inst., York Avenue, NY","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034177039","display_name":"Sanguthevar Rajasekaran","orcid":null},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sanguthevar Rajasekaran","raw_affiliation_strings":["Department of Computer Science & Engineering, University of Connecticut, Storrs, CT, USA","Dept. of Computer Science and Engineering, University of Connecticut, Storrs, CT"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science & Engineering, University of Connecticut, Storrs, CT, USA","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"Dept. of Computer Science and Engineering, University of Connecticut, Storrs, CT","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014788373","display_name":"Ion M\u0103ndoiu","orcid":"https://orcid.org/0000-0002-4818-0237"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ion I. Mandoiu","raw_affiliation_strings":["Department of Computer Science & Engineering, University of Connecticut, Storrs, CT, USA","Dept. of Computer Science and Engineering, University of Connecticut, Storrs, CT"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science & Engineering, University of Connecticut, Storrs, CT, USA","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"Dept. of Computer Science and Engineering, University of Connecticut, Storrs, CT","institution_ids":["https://openalex.org/I140172145"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5108536575"],"corresponding_institution_ids":["https://openalex.org/I1334819555"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.08915384,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.998199999332428,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.998199999332428,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9976999759674072,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9972000122070312,"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":0.6563476920127869},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.6367177963256836},{"id":"https://openalex.org/keywords/greedy-algorithm","display_name":"Greedy algorithm","score":0.5170419812202454},{"id":"https://openalex.org/keywords/primer","display_name":"Primer (cosmetics)","score":0.5031935572624207},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3416389226913452},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24484741687774658}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6563476920127869},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6367177963256836},{"id":"https://openalex.org/C51823790","wikidata":"https://www.wikidata.org/wiki/Q504353","display_name":"Greedy algorithm","level":2,"score":0.5170419812202454},{"id":"https://openalex.org/C2777563447","wikidata":"https://www.wikidata.org/wiki/Q7243397","display_name":"Primer (cosmetics)","level":2,"score":0.5031935572624207},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3416389226913452},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24484741687774658},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibe.2008.4696662","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2008.4696662","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2008 8th IEEE International Conference on BioInformatics and BioEngineering","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1571979946","https://openalex.org/W1580213736","https://openalex.org/W2011546759","https://openalex.org/W2026820283","https://openalex.org/W2047755806","https://openalex.org/W2071190510","https://openalex.org/W2084507708","https://openalex.org/W2093172707","https://openalex.org/W2116714101","https://openalex.org/W2147244812","https://openalex.org/W2168338748","https://openalex.org/W6634719314"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W4387497383","https://openalex.org/W3183948672","https://openalex.org/W3173606202","https://openalex.org/W3110381201","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2758277628","https://openalex.org/W2748952813","https://openalex.org/W1531601525"],"abstract_inverted_index":{"To":[0],"achieve":[1],"increased":[2],"throughput,":[3],"amplification":[4,53],"of":[5,31,42,59,70,82,99,104,112,138,189,204,210,217,228,243],"multiple":[6],"DNA":[7,40],"sequences":[8],"is":[9,65,207,247],"often":[10],"performed":[11],"using":[12,89],"a":[13,61,109],"single":[14],"Polymerase":[15],"Chain":[16],"Reaction":[17],"(PCR)":[18],"called":[19,34],"Multiplex":[20],"PCR":[21],"(MP-PCR).":[22],"Successful":[23],"MP-PCR":[24],"requires":[25],"efficient":[26],"methods":[27],"for":[28,47,169],"selecting":[29,100],"sets":[30],"synthetic":[32],"oligonucleotides":[33],"primers":[35,71,84,90,106],"that":[36,107,153,188,197,237],"collectively":[37],"amplify":[38,74,108],"all":[39,75],"loci":[41],"interest.":[43],"Since":[44,135],"the":[45,57,68,80,101,117,131,139,198,215,222,226,229,239],"potential":[46],"forming":[48],"primer-dimer":[49],"pairs":[50],"and":[51,174,177,183,201,241],"unintended":[52],"products":[54],"increases":[55],"with":[56,91,187],"number":[58,69,81,103],"primers,":[60],"common":[62],"optimization":[63],"objective":[64],"to":[66,73,115,144],"minimize":[67],"required":[72,83],"targets.":[76],"Significant":[77],"reductions":[78],"in":[79,130],"can":[85],"be":[86,145],"achieved":[87],"by":[88],"degenerate":[92,95,105],"bases,":[93],"or":[94],"primers.":[96],"The":[97,245],"problem":[98,140],"minimum":[102],"given":[110],"set":[111],"loci,":[113],"referred":[114],"as":[116],"Multiple":[118],"Degenerate":[119],"Primer":[120],"Selection":[121],"Problem":[122],"(MDPSP)":[123],"has":[124,148],"received":[125],"much":[126],"attention":[127],"from":[128],"researchers":[129],"past":[132],"few":[133],"years.":[134],"several":[136],"variants":[137],"have":[141],"been":[142],"proved":[143],"NP-Complete,":[146],"research":[147],"focused":[149],"on":[150,156,181,232],"heuristic":[151],"algorithms":[152,168,206,224,231],"perform":[154],"well":[155],"real":[157,184],"biological":[158,185],"data.":[159],"In":[160],"this":[161],"paper,":[162],"we":[163],"present":[164],"two":[165,190],"new":[166,223],"greedy":[167],"MDPSP,":[170],"analyze":[171],"their":[172,179],"time":[173,200],"space":[175],"complexities":[176],"compare":[178],"performance":[180],"random":[182],"data":[186],"previously":[191],"reported":[192],"algorithms.":[193],"Our":[194],"results":[195],"show":[196],"execution":[199],"memory":[202],"requirement":[203],"proposed":[205],"less":[208],"than":[209],"existing":[211],"algorithms,":[212],"thus":[213],"enabling":[214],"processing":[216],"larger":[218],"input":[219,235],"sets.":[220],"Also,":[221],"eliminate":[225],"dependency":[227],"previous":[230],"an":[233],"empirical":[234],"parameter":[236],"affects":[238],"runtime":[240],"quality":[242],"output.":[244],"software":[246],"downloadable":[248],"at":[249],"http://www.engr.uconn.edu/\u02dcsub02005/software.html":[250]},"counts_by_year":[{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
