{"id":"https://openalex.org/W2156116529","doi":"https://doi.org/10.1093/bioinformatics/btq601","title":"PPO: Predictor for Prokaryotic Operons","display_name":"PPO: Predictor for Prokaryotic Operons","publication_year":2010,"publication_date":"2010-10-28","ids":{"openalex":"https://openalex.org/W2156116529","doi":"https://doi.org/10.1093/bioinformatics/btq601","mag":"2156116529","pmid":"https://pubmed.ncbi.nlm.nih.gov/21030461"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq601","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq601","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/24/3127/16897824/btq601.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/26/24/3127/16897824/btq601.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034774683","display_name":"Li\u2010Yeh Chuang","orcid":"https://orcid.org/0000-0002-9817-5102"},"institutions":[{"id":"https://openalex.org/I128514506","display_name":"Toko University","ror":"https://ror.org/01k2qqb14","country_code":"TW","type":"education","lineage":["https://openalex.org/I128514506"]},{"id":"https://openalex.org/I89178830","display_name":"National Kaohsiung University of Applied Sciences","ror":"https://ror.org/04wydzr61","country_code":"TW","type":"education","lineage":["https://openalex.org/I89178830"]},{"id":"https://openalex.org/I98298690","display_name":"I-Shou University","ror":"https://ror.org/04d7e4m76","country_code":"TW","type":"education","lineage":["https://openalex.org/I98298690"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Li-Yeh Chuang","raw_affiliation_strings":["1 Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, 2Department of Computer Science and Information Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, 3Department of Network Systems, Toko University, Chiayi and 4Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, 2Department of Computer Science and Information Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, 3Department of Network Systems, Toko University, Chiayi and 4Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan","institution_ids":["https://openalex.org/I128514506","https://openalex.org/I89178830","https://openalex.org/I98298690"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086638580","display_name":"Jui-Hung Tsai","orcid":null},"institutions":[{"id":"https://openalex.org/I128514506","display_name":"Toko University","ror":"https://ror.org/01k2qqb14","country_code":"TW","type":"education","lineage":["https://openalex.org/I128514506"]},{"id":"https://openalex.org/I89178830","display_name":"National Kaohsiung University of Applied Sciences","ror":"https://ror.org/04wydzr61","country_code":"TW","type":"education","lineage":["https://openalex.org/I89178830"]},{"id":"https://openalex.org/I98298690","display_name":"I-Shou University","ror":"https://ror.org/04d7e4m76","country_code":"TW","type":"education","lineage":["https://openalex.org/I98298690"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Jui-Hung Tsai","raw_affiliation_strings":["1 Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, 2Department of Computer Science and Information Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, 3Department of Network Systems, Toko University, Chiayi and 4Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, 2Department of Computer Science and Information Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, 3Department of Network Systems, Toko University, Chiayi and 4Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan","institution_ids":["https://openalex.org/I128514506","https://openalex.org/I89178830","https://openalex.org/I98298690"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065832977","display_name":"Cheng\u2010Hong Yang","orcid":"https://orcid.org/0000-0002-2741-0072"},"institutions":[{"id":"https://openalex.org/I128514506","display_name":"Toko University","ror":"https://ror.org/01k2qqb14","country_code":"TW","type":"education","lineage":["https://openalex.org/I128514506"]},{"id":"https://openalex.org/I89178830","display_name":"National Kaohsiung University of Applied Sciences","ror":"https://ror.org/04wydzr61","country_code":"TW","type":"education","lineage":["https://openalex.org/I89178830"]},{"id":"https://openalex.org/I98298690","display_name":"I-Shou University","ror":"https://ror.org/04d7e4m76","country_code":"TW","type":"education","lineage":["https://openalex.org/I98298690"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Cheng-Hong Yang","raw_affiliation_strings":["1 Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, 2Department of Computer Science and Information Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, 3Department of Network Systems, Toko University, Chiayi and 4Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, 2Department of Computer Science and Information Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, 3Department of Network Systems, Toko University, Chiayi and 4Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan","institution_ids":["https://openalex.org/I128514506","https://openalex.org/I89178830","https://openalex.org/I98298690"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5065832977"],"corresponding_institution_ids":["https://openalex.org/I128514506","https://openalex.org/I89178830","https://openalex.org/I98298690"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3735,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.61060468,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"26","issue":"24","first_page":"3127","last_page":"3128"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.6151999831199646,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.6151999831199646,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.12250000238418579,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.06859999895095825,"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/operon","display_name":"Operon","score":0.7679430246353149},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5579351782798767},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.42247438430786133},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40744322538375854},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2581077218055725},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2162928283214569},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1901874542236328},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1603015661239624},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.09739547967910767}],"concepts":[{"id":"https://openalex.org/C203075996","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operon","level":4,"score":0.7679430246353149},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5579351782798767},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.42247438430786133},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40744322538375854},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2581077218055725},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2162928283214569},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1901874542236328},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1603015661239624},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.09739547967910767}],"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":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009876","descriptor_name":"Operon","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":"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":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btq601","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq601","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/24/3127/16897824/btq601.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:21030461","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21030461","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btq601","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq601","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/24/3127/16897824/btq601.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":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W1497256448","https://openalex.org/W2029112298","https://openalex.org/W2101292724","https://openalex.org/W2107337820","https://openalex.org/W2118576272","https://openalex.org/W2144795887","https://openalex.org/W2145091349","https://openalex.org/W2148973980","https://openalex.org/W2152195021","https://openalex.org/W2166406784","https://openalex.org/W2402846924"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W1608194938","https://openalex.org/W2572774164","https://openalex.org/W2061086355","https://openalex.org/W2111346700","https://openalex.org/W2090900888","https://openalex.org/W1541592150","https://openalex.org/W1546742425","https://openalex.org/W2145489399","https://openalex.org/W2089533157"],"abstract_inverted_index":{"SUMMARY:":[0],"We":[1],"present":[2],"an":[3],"operon":[4,51],"predictor":[5,52],"for":[6],"prokaryotic":[7,17],"operons":[8,13],"(PPO),":[9],"which":[10],"can":[11],"predict":[12,48],"in":[14,23,44],"the":[15,26,45,58,75,83],"entire":[16],"genome.":[18],"The":[19,50,67],"prediction":[20,76,84],"algorithm":[21,37],"used":[22],"PPO":[24,108],"allows":[25],"user":[27],"to":[28,47,63],"select":[29],"binary":[30],"particle":[31],"swarm":[32],"optimization":[33],"(BPSO),":[34],"a":[35],"genetic":[36],"(GA)":[38],"or":[39],"some":[40],"other":[41],"methods":[42],"introduced":[43],"literature":[46],"operons.":[49],"on":[53],"our":[54],"web":[55],"server":[56],"and":[57,65,101],"provided":[59],"database":[60,93],"are":[61],"easy":[62],"access":[64],"use.":[66],"main":[68],"features":[69],"offered":[70],"are:":[71],"(i)":[72],"selection":[73],"of":[74,82,89,97],"algorithm;":[77,85],"(ii)":[78],"adjustable":[79],"parameter":[80],"settings":[81],"(iii)":[86],"graphic":[87],"visualization":[88],"results;":[90],"(iv)":[91],"integrated":[92],"queries;":[94],"(v)":[95],"listing":[96],"experimentally":[98],"verified":[99],"operons;":[100],"(vi)":[102],"related":[103],"tools.":[104],"AVAILABILITY":[105],"AND":[106],"IMPLEMENTATION:":[107],"is":[109],"freely":[110],"available":[111],"at":[112],"http://bio.kuas.edu.tw/PPO/.":[113]},"counts_by_year":[{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
