{"id":"https://openalex.org/W2073578638","doi":"https://doi.org/10.1186/1471-2105-8-97","title":"MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes","display_name":"MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes","publication_year":2007,"publication_date":"2007-03-16","ids":{"openalex":"https://openalex.org/W2073578638","doi":"https://doi.org/10.1186/1471-2105-8-97","mag":"2073578638","pmid":"https://pubmed.ncbi.nlm.nih.gov/17367537"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-8-97","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-97","pdf_url":"https://link.springer.com/content/pdf/10.1186/1471-2105-8-97.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://link.springer.com/content/pdf/10.1186/1471-2105-8-97.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060533782","display_name":"Huaiqiu Zhu","orcid":"https://orcid.org/0000-0002-6376-218X"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4391767778","display_name":"State Key Laboratory of Turbulence and Complex Systems","ror":"https://ror.org/04km98768","country_code":null,"type":"facility","lineage":["https://openalex.org/I20231570","https://openalex.org/I4391767778"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huaiqiu Zhu","raw_affiliation_strings":["State Key Lab for Turbulence and Complex Systems and Department of Biomedical Engineering, Peking University, Beijing 100871, China. hqzhu@pku.edu.cn <hqzhu@pku.edu.cn>","State Key Lab for Turbulence and Complex Systems and Department of Biomedical Engineering, Peking University, Beijing, 100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Lab for Turbulence and Complex Systems and Department of Biomedical Engineering, Peking University, Beijing 100871, China. hqzhu@pku.edu.cn <hqzhu@pku.edu.cn>","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"State Key Lab for Turbulence and Complex Systems and Department of Biomedical Engineering, Peking University, Beijing, 100871, China","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4391767778"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073225177","display_name":"Gangqing Hu","orcid":"https://orcid.org/0000-0001-5453-6888"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210125404","display_name":"Institute of Theoretical Physics","ror":"https://ror.org/02xtbq882","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210125404"]},{"id":"https://openalex.org/I4391767778","display_name":"State Key Laboratory of Turbulence and Complex Systems","ror":"https://ror.org/04km98768","country_code":null,"type":"facility","lineage":["https://openalex.org/I20231570","https://openalex.org/I4391767778"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gang-Qing Hu","raw_affiliation_strings":["Center for Theoretical Biology and Department of Physics, Peking University, Beijing, 100871, China","State Key Lab for Turbulence and Complex Systems and Department of Biomedical Engineering, Peking University, Beijing, 100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Theoretical Biology and Department of Physics, Peking University, Beijing, 100871, China","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4210125404"]},{"raw_affiliation_string":"State Key Lab for Turbulence and Complex Systems and Department of Biomedical Engineering, Peking University, Beijing, 100871, China","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4391767778"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022785507","display_name":"Yifan Yang","orcid":"https://orcid.org/0000-0001-6697-0198"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4391767778","display_name":"State Key Laboratory of Turbulence and Complex Systems","ror":"https://ror.org/04km98768","country_code":null,"type":"facility","lineage":["https://openalex.org/I20231570","https://openalex.org/I4391767778"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi-Fan Yang","raw_affiliation_strings":["State Key Lab for Turbulence and Complex Systems and Department of Biomedical Engineering, Peking University, Beijing, 100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Lab for Turbulence and Complex Systems and Department of Biomedical Engineering, Peking University, Beijing, 100871, China","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4391767778"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100346147","display_name":"Jin Wang","orcid":"https://orcid.org/0000-0002-2841-4913"},"institutions":[{"id":"https://openalex.org/I161716053","display_name":"China Pharmaceutical University","ror":"https://ror.org/01sfm2718","country_code":"CN","type":"education","lineage":["https://openalex.org/I161716053"]},{"id":"https://openalex.org/I881766915","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760","country_code":"CN","type":"education","lineage":["https://openalex.org/I881766915"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jin Wang","raw_affiliation_strings":["State Key Lab of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210093, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Lab of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210093, China","institution_ids":["https://openalex.org/I161716053","https://openalex.org/I881766915"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039451500","display_name":"Zhen-Su She","orcid":"https://orcid.org/0000-0001-7001-9995"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]},{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210125404","display_name":"Institute of Theoretical Physics","ror":"https://ror.org/02xtbq882","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210125404"]},{"id":"https://openalex.org/I4391767778","display_name":"State Key Laboratory of Turbulence and Complex Systems","ror":"https://ror.org/04km98768","country_code":null,"type":"facility","lineage":["https://openalex.org/I20231570","https://openalex.org/I4391767778"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Zhen-Su She","raw_affiliation_strings":["Center for Theoretical Biology and Department of Physics, Peking University, Beijing, 100871, China","Department of Mathematics, UCLA, Los Angeles, CA, 90095, USA","State Key Lab for Turbulence and Complex Systems and Department of Biomedical Engineering, Peking University, Beijing, 100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Theoretical Biology and Department of Physics, Peking University, Beijing, 100871, China","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4210125404"]},{"raw_affiliation_string":"Department of Mathematics, UCLA, Los Angeles, CA, 90095, USA","institution_ids":["https://openalex.org/I161318765"]},{"raw_affiliation_string":"State Key Lab for Turbulence and Complex Systems and Department of Biomedical Engineering, Peking University, Beijing, 100871, China","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4391767778"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5039451500"],"corresponding_institution_ids":["https://openalex.org/I161318765","https://openalex.org/I20231570","https://openalex.org/I4210125404","https://openalex.org/I4391767778"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.2651,"has_fulltext":true,"cited_by_count":45,"citation_normalized_percentile":{"value":0.87892314,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"8","issue":"1","first_page":"97","last_page":"97"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.5778999924659729,"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":0.5778999924659729,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.3467000126838684,"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":0.01489999983459711,"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/genome","display_name":"Genome","score":0.7717318534851074},{"id":"https://openalex.org/keywords/gene-prediction","display_name":"Gene prediction","score":0.6683849692344666},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6043031215667725},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.569801926612854},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5438090562820435},{"id":"https://openalex.org/keywords/bacterial-genome-size","display_name":"Bacterial genome size","score":0.5265786051750183},{"id":"https://openalex.org/keywords/sulfolobus-solfataricus","display_name":"Sulfolobus solfataricus","score":0.44906842708587646},{"id":"https://openalex.org/keywords/orfs","display_name":"ORFS","score":0.44215846061706543},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4416203200817108},{"id":"https://openalex.org/keywords/archaea","display_name":"Archaea","score":0.39947232604026794},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.37280330061912537},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3670535683631897},{"id":"https://openalex.org/keywords/open-reading-frame","display_name":"Open reading frame","score":0.245501309633255}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7717318534851074},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.6683849692344666},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6043031215667725},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.569801926612854},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5438090562820435},{"id":"https://openalex.org/C3742359","wikidata":"https://www.wikidata.org/wiki/Q4839988","display_name":"Bacterial genome size","level":4,"score":0.5265786051750183},{"id":"https://openalex.org/C2780631447","wikidata":"https://www.wikidata.org/wiki/Q3503466","display_name":"Sulfolobus solfataricus","level":4,"score":0.44906842708587646},{"id":"https://openalex.org/C2780530800","wikidata":"https://www.wikidata.org/wiki/Q7072921","display_name":"ORFS","level":5,"score":0.44215846061706543},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4416203200817108},{"id":"https://openalex.org/C550995028","wikidata":"https://www.wikidata.org/wiki/Q10872","display_name":"Archaea","level":3,"score":0.39947232604026794},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.37280330061912537},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3670535683631897},{"id":"https://openalex.org/C47289529","wikidata":"https://www.wikidata.org/wiki/Q908550","display_name":"Open reading frame","level":4,"score":0.245501309633255},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"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":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":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020745","descriptor_name":"Genome, Archaeal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020745","descriptor_name":"Genome, Archaeal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020745","descriptor_name":"Genome, Archaeal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D039662","descriptor_name":"Prokaryotic Initiation Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D039662","descriptor_name":"Prokaryotic Initiation Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D039662","descriptor_name":"Prokaryotic Initiation Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-8-97","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-97","pdf_url":"https://link.springer.com/content/pdf/10.1186/1471-2105-8-97.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17367537","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17367537","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:041165b362aa4e5db4aaba626cae2878","is_oa":false,"landing_page_url":"https://doaj.org/article/041165b362aa4e5db4aaba626cae2878","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 8, Iss 1, p 97 (2007)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:1818302","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1847833","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-8-97","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-97","pdf_url":"https://link.springer.com/content/pdf/10.1186/1471-2105-8-97.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.6299999952316284,"id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G6637634347","display_name":null,"funder_award_id":"2003CB715905","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2073578638.pdf","grobid_xml":"https://content.openalex.org/works/W2073578638.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1562379515","https://openalex.org/W1669459870","https://openalex.org/W1873623553","https://openalex.org/W1969028360","https://openalex.org/W1972875046","https://openalex.org/W1985588605","https://openalex.org/W1993071991","https://openalex.org/W1993158258","https://openalex.org/W2000436194","https://openalex.org/W2015546264","https://openalex.org/W2018962053","https://openalex.org/W2019261103","https://openalex.org/W2026570450","https://openalex.org/W2027031393","https://openalex.org/W2032838501","https://openalex.org/W2032870665","https://openalex.org/W2039680623","https://openalex.org/W2091560728","https://openalex.org/W2103919457","https://openalex.org/W2106090237","https://openalex.org/W2123153443","https://openalex.org/W2130291362","https://openalex.org/W2131185306","https://openalex.org/W2133253129","https://openalex.org/W2149629850","https://openalex.org/W2154478075","https://openalex.org/W2158714788","https://openalex.org/W2163023575","https://openalex.org/W2166064969","https://openalex.org/W2168846269","https://openalex.org/W2170909437","https://openalex.org/W4247462717"],"related_works":["https://openalex.org/W2091106247","https://openalex.org/W2000357831","https://openalex.org/W2340204314","https://openalex.org/W1992744443","https://openalex.org/W1976545601","https://openalex.org/W2139837231","https://openalex.org/W2112744958","https://openalex.org/W2002422491","https://openalex.org/W2154478075","https://openalex.org/W2073578638"],"abstract_inverted_index":{"BACKGROUND:":[0],"Despite":[1],"a":[2,15,61,68,89,117,140,147,172,252],"remarkable":[3],"success":[4],"in":[5,11,130,176,247],"the":[6,101,109,131,153,158,177,189,198,211,220,260,265],"computational":[7],"prediction":[8,159,179,255],"of":[9,17,20,28,54,72,96,149,160,164,197,223,256],"genes":[10],"Bacteria":[12],"and":[13,79,100,144,183,207,226,264],"Archaea,":[14],"lack":[16],"comprehensive":[18,69],"understanding":[19,222],"prokaryotic":[21,55,63,192,224],"gene":[22,154,178,193,262],"structures":[23],"prevents":[24],"from":[25],"further":[26],"elucidation":[27],"differences":[29],"among":[30],"genomes.":[31,56,209],"It":[32],"continues":[33],"to":[34,37,108,115,138,145,188,241,259],"be":[35],"interesting":[36],"develop":[38,139],"new":[39,62],"ab":[40],"initio":[41],"algorithms":[42],"which":[43],"not":[44],"only":[45],"accurately":[46],"predict":[47],"genes,":[48],"but":[49],"also":[50],"facilitate":[51],"comparative":[52,232],"studies":[53],"RESULTS:":[57],"This":[58],"paper":[59],"describes":[60],"genefinding":[64],"algorithm":[65],"based":[66,87],"on":[67,88],"statistical":[70],"model":[71,95],"protein":[73],"coding":[74,97],"Open":[75],"Reading":[76],"Frames":[77],"(ORFs)":[78],"Translation":[80],"Initiation":[81],"Sites":[82],"(TISs).":[83],"The":[84,134,195],"former":[85],"is":[86,201,239],"linguistic":[90],"\"Entropy":[91],"Density":[92],"Profile\"":[93],"(EDP)":[94],"DNA":[98],"sequence":[99],"latter":[102],"comprises":[103],"several":[104,128],"relevant":[105],"features":[106],"related":[107],"translation":[110,244],"initiation.":[111],"They":[112],"are":[113],"combined":[114],"form":[116],"so-called":[118],"Multivariate":[119],"Entropy":[120],"Distance":[121],"(MED)":[122],"algorithm,":[123],"MED":[124,169,199,216,237],"2.0,":[125],"that":[126,168],"incorporates":[127],"strategies":[129],"iterative":[132],"program.":[133],"iterations":[135],"enable":[136],"us":[137],"non-supervised":[141],"learning":[142],"process":[143],"obtain":[146],"set":[148],"genome-specific":[150,212],"parameters":[151,213],"for":[152,180,204,231],"structure,":[155],"before":[156],"making":[157,251],"genes.":[161],"CONCLUSION:":[162],"Results":[163],"extensive":[165],"tests":[166],"show":[167],"2.0":[170,200,217,238],"achieves":[171],"competitive":[173],"high":[174],"performance":[175],"both":[181],"5'":[182],"3'":[184],"end":[185],"matches,":[186],"compared":[187,258],"current":[190,221,266],"best":[191],"finders.":[194],"advantage":[196],"particularly":[202],"evident":[203],"GC-rich":[205],"genomes":[206,225,249],"archaeal":[208,248],"Furthermore,":[210],"given":[214],"by":[215],"match":[218],"with":[219],"may":[227],"serve":[228],"as":[229],"tools":[230],"genomic":[233],"studies.":[234],"In":[235],"particular,":[236],"shown":[240],"reveal":[242],"divergent":[243],"initiation":[245],"mechanisms":[246],"while":[250],"more":[253],"accurate":[254],"TISs":[257],"existing":[261],"finders":[263],"GenBank":[267],"annotation.":[268]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":5}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}