{"id":"https://openalex.org/W2140558049","doi":"https://doi.org/10.1093/bioinformatics/btg434","title":"SEPON, a Selection and Evaluation Pipeline for OligoNucleotides based on ESTs with a non-target <i>T</i>m algorithm for reducing cross-hybridization in microarray gene expression experiments","display_name":"SEPON, a Selection and Evaluation Pipeline for OligoNucleotides based on ESTs with a non-target <i>T</i>m algorithm for reducing cross-hybridization in microarray gene expression experiments","publication_year":2004,"publication_date":"2004-01-22","ids":{"openalex":"https://openalex.org/W2140558049","doi":"https://doi.org/10.1093/bioinformatics/btg434","mag":"2140558049","pmid":"https://pubmed.ncbi.nlm.nih.gov/14960473"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg434","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg434","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/3/428/48905089/bioinformatics_20_3_428.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/20/3/428/48905089/bioinformatics_20_3_428.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103378699","display_name":"Henrik Hornsh\u00f8j","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Henrik Hornsh\u00f8j","raw_affiliation_strings":["Department of Animal Breeding and Genetics, Danish Institute of Agricultural Sciences, Research Center Foulum, DK-8830 Tjele, Denmark. henrikh.jensen@agrsci.dk","Department of Animal Breeding and Genetics, Danish Institute of Agricultural Sciences, Research Center Foulum, DK-8830 Tjele, Denmark#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Animal Breeding and Genetics, Danish Institute of Agricultural Sciences, Research Center Foulum, DK-8830 Tjele, Denmark. henrikh.jensen@agrsci.dk","institution_ids":[]},{"raw_affiliation_string":"Department of Animal Breeding and Genetics, Danish Institute of Agricultural Sciences, Research Center Foulum, DK-8830 Tjele, Denmark#TAB#","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077947702","display_name":"Henrik Stengaard","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Henrik Stengaard","raw_affiliation_strings":["Department of Animal Breeding and Genetics, Danish Institute of Agricultural Sciences, Research Center Foulum, DK-8830 Tjele, Denmark#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Animal Breeding and Genetics, Danish Institute of Agricultural Sciences, Research Center Foulum, DK-8830 Tjele, Denmark#TAB#","institution_ids":[]}]},{"author_position":"middle","author":{"id":null,"display_name":"Frank Panitz","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Frank Panitz","raw_affiliation_strings":["Department of Animal Breeding and Genetics, Danish Institute of Agricultural Sciences, Research Center Foulum, DK-8830 Tjele, Denmark#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Animal Breeding and Genetics, Danish Institute of Agricultural Sciences, Research Center Foulum, DK-8830 Tjele, Denmark#TAB#","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101160130","display_name":"Christian Bendixen","orcid":"https://orcid.org/0000-0002-6909-5162"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Christian Bendixen","raw_affiliation_strings":["Department of Animal Breeding and Genetics, Danish Institute of Agricultural Sciences, Research Center Foulum, DK-8830 Tjele, Denmark#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Animal Breeding and Genetics, Danish Institute of Agricultural Sciences, Research Center Foulum, DK-8830 Tjele, Denmark#TAB#","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5103378699"],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8407,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.7101528,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"20","issue":"3","first_page":"428","last_page":"429"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9998000264167786,"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":0.9998000264167786,"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/T10015","display_name":"Genomics and Phylogenetic Studies","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"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9966999888420105,"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/oligonucleotide","display_name":"Oligonucleotide","score":0.8266955614089966},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5287144780158997},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.48166048526763916},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.4799135625362396},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4508783221244812},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4399125277996063},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4302462339401245},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4180997908115387},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32244473695755005},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1513957381248474}],"concepts":[{"id":"https://openalex.org/C129312508","wikidata":"https://www.wikidata.org/wiki/Q133686","display_name":"Oligonucleotide","level":3,"score":0.8266955614089966},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5287144780158997},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.48166048526763916},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.4799135625362396},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4508783221244812},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4399125277996063},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4302462339401245},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4180997908115387},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32244473695755005},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1513957381248474},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D015342","descriptor_name":"DNA Probes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015342","descriptor_name":"DNA Probes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015342","descriptor_name":"DNA Probes","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":"Q000737","qualifier_name":"chemistry","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/btg434","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg434","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/3/428/48905089/bioinformatics_20_3_428.pdf","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:14960473","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14960473","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:pure.atira.dk:openaire/d8fa56b0-cc26-11db-8e26-000ea68e967b","is_oa":true,"landing_page_url":"https://pure.au.dk/portal/en/publications/d8fa56b0-cc26-11db-8e26-000ea68e967b","pdf_url":null,"source":null,"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Hornsh\u00f8j, H, Stengaard, H, Panitz, F & Bendixen, C 2004, 'SEPON, a Selection and Evaluation Pipeline for OligoNucleotides based on ESTs with a non-target Tm algorithm for reducing cross-hybridization in microarray gene expression experiments', Bioinformatics, vol. 20, no. 3, pp. 428-429. https://doi.org/10.1093/bioinformatics/btg434","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btg434","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg434","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/3/428/48905089/bioinformatics_20_3_428.pdf","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"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2140558049.pdf","grobid_xml":"https://content.openalex.org/works/W2140558049.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1519185585","https://openalex.org/W1595877216","https://openalex.org/W2097383747","https://openalex.org/W2103123883","https://openalex.org/W2118782342","https://openalex.org/W2130494035","https://openalex.org/W2132048031","https://openalex.org/W2132285289","https://openalex.org/W2135995702","https://openalex.org/W2158714788"],"related_works":["https://openalex.org/W2159038264","https://openalex.org/W2840367830","https://openalex.org/W2168160406","https://openalex.org/W1974344026","https://openalex.org/W2027177155","https://openalex.org/W2024398706","https://openalex.org/W2050630975","https://openalex.org/W1990057240","https://openalex.org/W1509371698","https://openalex.org/W2087429349"],"abstract_inverted_index":{"SEPON,":[0],"Selection":[1],"and":[2,42,70,73],"Evaluation":[3],"Pipeline":[4],"for":[5,18,76],"OligoNucleotide":[6],"generates":[7],"n-mer":[8],"oligonucleotide":[9,35],"sequences":[10],"from":[11],"expressed":[12],"sequence":[13],"tags":[14],"of":[15,34],"non-annotated":[16],"genomes":[17],"microarray":[19],"gene-expression":[20],"profiling.":[21],"A":[22],"non-target":[23,46,71],"melting":[24],"temperature":[25],"(T(m))":[26],"algorithm":[27],"will":[28],"reduce":[29],"cross-hybridization":[30],"by":[31],"estimating":[32],"T(m)":[33,47,69,72],"hybridization":[36],"to":[37],"non-specific":[38],"targets":[39],"(non-target":[40],"T(m))":[41],"discard":[43],"oligonucleotides":[44,75],"with":[45],"estimate":[48],"above":[49],"user-defined":[50,54],"threshold.":[51],"SEPON":[52],"allows":[53],"filtering,":[55],"predicts":[56],"exon":[57],"location,":[58],"assigns":[59],"penalty":[60],"based":[61],"on":[62],"3'":[63],"distance,":[64],"GC":[65],"content,":[66],"secondary":[67],"structure":[68],"ranks":[74],"optimal":[77],"selection.":[78]},"counts_by_year":[{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-03-25T23:56:10.502304","created_date":"2016-06-24T00:00:00"}