{"id":"https://openalex.org/W2121857350","doi":"https://doi.org/10.1093/bioinformatics/btn004","title":"Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction","display_name":"Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction","publication_year":2008,"publication_date":"2008-01-10","ids":{"openalex":"https://openalex.org/W2121857350","doi":"https://doi.org/10.1093/bioinformatics/btn004","mag":"2121857350","pmid":"https://pubmed.ncbi.nlm.nih.gov/18187439"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn004","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn004","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/5/597/49051279/bioinformatics_24_5_597.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/24/5/597/49051279/bioinformatics_24_5_597.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100318580","display_name":"Qian Liu","orcid":"https://orcid.org/0000-0002-4517-6443"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Qian Liu","raw_affiliation_strings":["1 Department of Computer and Information Science, 2Department of Biology and 3Penn Genomics Institute, University of Pennsylvania, Philadelphia PA 19104, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer and Information Science, 2Department of Biology and 3Penn Genomics Institute, University of Pennsylvania, Philadelphia PA 19104, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074405433","display_name":"Aaron J. Mackey","orcid":"https://orcid.org/0000-0003-4734-5324"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aaron J. Mackey","raw_affiliation_strings":["1 Department of Computer and Information Science, 2Department of Biology and 3Penn Genomics Institute, University of Pennsylvania, Philadelphia PA 19104, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer and Information Science, 2Department of Biology and 3Penn Genomics Institute, University of Pennsylvania, Philadelphia PA 19104, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038050740","display_name":"David S. Roos","orcid":"https://orcid.org/0000-0001-6725-4089"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David S. Roos","raw_affiliation_strings":["1 Department of Computer and Information Science, 2Department of Biology and 3Penn Genomics Institute, University of Pennsylvania, Philadelphia PA 19104, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer and Information Science, 2Department of Biology and 3Penn Genomics Institute, University of Pennsylvania, Philadelphia PA 19104, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103620421","display_name":"Fernando C. N. Pereira","orcid":null},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fernando C. N. Pereira","raw_affiliation_strings":["1 Department of Computer and Information Science, 2Department of Biology and 3Penn Genomics Institute, University of Pennsylvania, Philadelphia PA 19104, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer and Information Science, 2Department of Biology and 3Penn Genomics Institute, University of Pennsylvania, Philadelphia PA 19104, USA","institution_ids":["https://openalex.org/I79576946"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100318580"],"corresponding_institution_ids":["https://openalex.org/I79576946"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.6934,"has_fulltext":false,"cited_by_count":122,"citation_normalized_percentile":{"value":0.90359184,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"24","issue":"5","first_page":"597","last_page":"605"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10015","display_name":"Genomics and Phylogenetic Studies","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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9988999962806702,"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":0.9918000102043152,"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/annotation","display_name":"Annotation","score":0.7183520793914795},{"id":"https://openalex.org/keywords/gene-prediction","display_name":"Gene prediction","score":0.6677020788192749},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5985023975372314},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.5973392724990845},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.5902153253555298},{"id":"https://openalex.org/keywords/bayes-theorem","display_name":"Bayes' theorem","score":0.5600407123565674},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5485705137252808},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5447408556938171},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5020742416381836},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.49090296030044556},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4836026728153229},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4694397449493408},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.460946649312973},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.45618098974227905},{"id":"https://openalex.org/keywords/genome-project","display_name":"Genome project","score":0.442362904548645},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3354892432689667},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.33109229803085327}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7183520793914795},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.6677020788192749},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5985023975372314},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.5973392724990845},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.5902153253555298},{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.5600407123565674},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5485705137252808},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5447408556938171},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5020742416381836},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.49090296030044556},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4836026728153229},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4694397449493408},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.460946649312973},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.45618098974227905},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.442362904548645},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3354892432689667},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.33109229803085327},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btn004","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn004","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/5/597/49051279/bioinformatics_24_5_597.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:18187439","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18187439","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/btn004","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn004","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/5/597/49051279/bioinformatics_24_5_597.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":[{"id":"https://metadata.un.org/sdg/14","score":0.8700000047683716,"display_name":"Life below water"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306135","display_name":"Ellison Medical Foundation","ror":"https://ror.org/01pqy3846"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2121857350.pdf","grobid_xml":"https://content.openalex.org/works/W2121857350.grobid-xml"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W1512702007","https://openalex.org/W1524975733","https://openalex.org/W1560512119","https://openalex.org/W1746680969","https://openalex.org/W1979083306","https://openalex.org/W2009570821","https://openalex.org/W2019573310","https://openalex.org/W2049633694","https://openalex.org/W2055043387","https://openalex.org/W2064946726","https://openalex.org/W2086240273","https://openalex.org/W2101904700","https://openalex.org/W2110400205","https://openalex.org/W2110575115","https://openalex.org/W2113000643","https://openalex.org/W2114452806","https://openalex.org/W2114759476","https://openalex.org/W2117179531","https://openalex.org/W2118300412","https://openalex.org/W2118930999","https://openalex.org/W2120815702","https://openalex.org/W2121840477","https://openalex.org/W2125415845","https://openalex.org/W2125838338","https://openalex.org/W2129623502","https://openalex.org/W2130395351","https://openalex.org/W2131074700","https://openalex.org/W2132372375","https://openalex.org/W2135146027","https://openalex.org/W2138379687","https://openalex.org/W2139133899","https://openalex.org/W2141572089","https://openalex.org/W2142418779","https://openalex.org/W2143801061","https://openalex.org/W2144921226","https://openalex.org/W2145133577","https://openalex.org/W2154269509","https://openalex.org/W2155144061","https://openalex.org/W2156296160","https://openalex.org/W2159512882","https://openalex.org/W2160053034","https://openalex.org/W2160649592","https://openalex.org/W2161162976","https://openalex.org/W2166187656","https://openalex.org/W2247766769","https://openalex.org/W4245668478","https://openalex.org/W4253573210","https://openalex.org/W6633434192","https://openalex.org/W6666611129","https://openalex.org/W6676404962","https://openalex.org/W6678615056","https://openalex.org/W7048738093"],"related_works":["https://openalex.org/W2117179531","https://openalex.org/W2980998232","https://openalex.org/W4388524370","https://openalex.org/W2101269698","https://openalex.org/W2294108133","https://openalex.org/W2059565715","https://openalex.org/W2078942911","https://openalex.org/W4231584750","https://openalex.org/W2319942811","https://openalex.org/W2955310315"],"abstract_inverted_index":{"The":[0],"source":[1],"code":[2],"is":[3],"available":[4],"at":[5],"http://www.seas.upenn.edu/~strctlrn/evigan/evigan.html.":[6]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":67},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":7}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
