{"id":"https://openalex.org/W2169629105","doi":"https://doi.org/10.1093/bioinformatics/18.suppl_1.s128","title":"Microarray synthesis through multiple-use PCR primer design","display_name":"Microarray synthesis through multiple-use PCR primer design","publication_year":2002,"publication_date":"2002-07-01","ids":{"openalex":"https://openalex.org/W2169629105","doi":"https://doi.org/10.1093/bioinformatics/18.suppl_1.s128","mag":"2169629105","pmid":"https://pubmed.ncbi.nlm.nih.gov/12169540"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/18.suppl_1.s128","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/18.suppl_1.s128","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045228830","display_name":"Rohan J. Fernandes","orcid":null},"institutions":[{"id":"https://openalex.org/I1327163397","display_name":"State University of New York","ror":"https://ror.org/01q1z8k08","country_code":"US","type":"education","lineage":["https://openalex.org/I1327163397"]},{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rohan J. Fernandes","raw_affiliation_strings":["Applied Algorithm Laboratory, Department of Computer Science, State University of New York Stony Brook, NY, 11794-4400, USA","Applied Algorithm Laboratory, Department of Computer Science, State University of New York\nStony Brook, NY, 11794-4400, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Applied Algorithm Laboratory, Department of Computer Science, State University of New York Stony Brook, NY, 11794-4400, USA","institution_ids":["https://openalex.org/I59553526"]},{"raw_affiliation_string":"Applied Algorithm Laboratory, Department of Computer Science, State University of New York\nStony Brook, NY, 11794-4400, USA","institution_ids":["https://openalex.org/I59553526","https://openalex.org/I1327163397"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060741187","display_name":"Steven Skiena","orcid":"https://orcid.org/0000-0003-0397-7514"},"institutions":[{"id":"https://openalex.org/I1327163397","display_name":"State University of New York","ror":"https://ror.org/01q1z8k08","country_code":"US","type":"education","lineage":["https://openalex.org/I1327163397"]},{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steven S. Skiena","raw_affiliation_strings":["Applied Algorithm Laboratory, Department of Computer Science, State University of New York Stony Brook, NY, 11794-4400, USA","Applied Algorithm Laboratory, Department of Computer Science, State University of New York\nStony Brook, NY, 11794-4400, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Applied Algorithm Laboratory, Department of Computer Science, State University of New York Stony Brook, NY, 11794-4400, USA","institution_ids":["https://openalex.org/I59553526"]},{"raw_affiliation_string":"Applied Algorithm Laboratory, Department of Computer Science, State University of New York\nStony Brook, NY, 11794-4400, USA","institution_ids":["https://openalex.org/I59553526","https://openalex.org/I1327163397"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.0355,"has_fulltext":false,"cited_by_count":24,"citation_normalized_percentile":{"value":0.75924545,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"18","issue":"suppl_1","first_page":"S128","last_page":"S135"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9995999932289124,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9995999932289124,"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":0.9987999796867371,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9984999895095825,"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/primer","display_name":"Primer (cosmetics)","score":0.8804618716239929},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.6490515470504761},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6098541021347046},{"id":"https://openalex.org/keywords/applications-of-pcr","display_name":"Applications of PCR","score":0.5827310681343079},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5435913801193237},{"id":"https://openalex.org/keywords/in-silico-pcr","display_name":"In silico PCR","score":0.5045439004898071},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4688614010810852},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4608864486217499},{"id":"https://openalex.org/keywords/polymerase-chain-reaction","display_name":"Polymerase chain reaction","score":0.45622333884239197},{"id":"https://openalex.org/keywords/primer-dimer","display_name":"Primer dimer","score":0.41740158200263977},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4041450023651123},{"id":"https://openalex.org/keywords/multiplex-polymerase-chain-reaction","display_name":"Multiplex polymerase chain reaction","score":0.20867517590522766},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19923052191734314},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.08460894227027893}],"concepts":[{"id":"https://openalex.org/C2777563447","wikidata":"https://www.wikidata.org/wiki/Q7243397","display_name":"Primer (cosmetics)","level":2,"score":0.8804618716239929},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.6490515470504761},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6098541021347046},{"id":"https://openalex.org/C28134486","wikidata":"https://www.wikidata.org/wiki/Q176996","display_name":"Applications of PCR","level":5,"score":0.5827310681343079},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5435913801193237},{"id":"https://openalex.org/C200658500","wikidata":"https://www.wikidata.org/wiki/Q4112082","display_name":"In silico PCR","level":5,"score":0.5045439004898071},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4688614010810852},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4608864486217499},{"id":"https://openalex.org/C49105822","wikidata":"https://www.wikidata.org/wiki/Q176996","display_name":"Polymerase chain reaction","level":3,"score":0.45622333884239197},{"id":"https://openalex.org/C52001828","wikidata":"https://www.wikidata.org/wiki/Q2902493","display_name":"Primer dimer","level":5,"score":0.41740158200263977},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4041450023651123},{"id":"https://openalex.org/C90583042","wikidata":"https://www.wikidata.org/wiki/Q1952456","display_name":"Multiplex polymerase chain reaction","level":4,"score":0.20867517590522766},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19923052191734314},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.08460894227027893},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004867","descriptor_name":"Equipment Design","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004867","descriptor_name":"Equipment Design","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004867","descriptor_name":"Equipment Design","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017076","descriptor_name":"Computer-Aided Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017076","descriptor_name":"Computer-Aided Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017076","descriptor_name":"Computer-Aided Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/18.suppl_1.s128","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/18.suppl_1.s128","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:12169540","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12169540","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":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.20.5389","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.20.5389","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.sunysb.edu/~skiena/papers/rohan.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337345","display_name":"Office of Naval Research","ror":"https://ror.org/00rk2pe57"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1484881582","https://openalex.org/W1535144194","https://openalex.org/W1970156673","https://openalex.org/W2010787744","https://openalex.org/W2011546759","https://openalex.org/W2013469283","https://openalex.org/W2015569722","https://openalex.org/W2032279394","https://openalex.org/W2085781250","https://openalex.org/W2103453943","https://openalex.org/W2125811524","https://openalex.org/W2142460132","https://openalex.org/W2143996311","https://openalex.org/W2146264532","https://openalex.org/W2206848221"],"related_works":["https://openalex.org/W2319030365","https://openalex.org/W2019810109","https://openalex.org/W2418893447","https://openalex.org/W2922644496","https://openalex.org/W2046606471","https://openalex.org/W2064206660","https://openalex.org/W3200892774","https://openalex.org/W3084381115","https://openalex.org/W2365302609","https://openalex.org/W390510863"],"abstract_inverted_index":{"A":[0],"substantial":[1],"percentage":[2],"of":[3,15,85],"the":[4,13,17,22,47,59,83],"expense":[5],"in":[6,46,74],"constructing":[7],"full-genome":[8],"spotted":[9],"microarrays":[10],"comes":[11],"from":[12],"cost":[14,84],"synthesizing":[16],"PCR":[18,36],"primers":[19,37,88],"to":[20,30,81],"amplify":[21],"desired":[23],"DNA.":[24],"We":[25,69],"propose":[26],"a":[27,75],"computationally-based":[28],"method":[29],"substantially":[31],"reduce":[32],"this":[33],"cost.":[34],"Historically,":[35],"are":[38],"designed":[39],"so":[40],"that":[41,71],"each":[42,64],"primer":[43,60],"occurs":[44],"uniquely":[45],"genome.":[48],"This":[49],"condition":[50],"is":[51],"unnecessarily":[52],"strong":[53],"for":[54],"selective":[55],"amplification,":[56],"since":[57],"only":[58],"pair":[61],"associated":[62],"with":[63],"amplification":[65,77],"need":[66],"be":[67],"unique.":[68],"demonstrate":[70],"careful":[72],"design":[73],"genome-level":[76],"project":[78],"permits":[79],"us":[80],"save":[82],"several":[86],"thousand":[87],"over":[89],"conventional":[90],"approaches.":[91]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}