{"id":"https://openalex.org/W2170119516","doi":"https://doi.org/10.1186/1471-2105-8-295","title":"Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation","display_name":"Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation","publication_year":2007,"publication_date":"2007-08-08","ids":{"openalex":"https://openalex.org/W2170119516","doi":"https://doi.org/10.1186/1471-2105-8-295","mag":"2170119516","pmid":"https://pubmed.ncbi.nlm.nih.gov/17686169"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-8-295","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-295","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-295","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://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-295","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026743647","display_name":"Marija Cvijovi\u0107","orcid":"https://orcid.org/0000-0002-5142-5100"},"institutions":[{"id":"https://openalex.org/I881427289","display_name":"University of Gothenburg","ror":"https://ror.org/01tm6cn81","country_code":"SE","type":"education","lineage":["https://openalex.org/I881427289"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Marija Cvijovi\u0107","raw_affiliation_strings":["Department of Cell and Molecular Biology, Lundberg Laboratory, G\u00f6teborg University, PO Box 462 SE-405 30 G\u00f6teborg, Sweden. cvijovic@molgen.mpg.de","Department of Cell and Molecular Biology, Lundberg Laboratory, G\u00f6teborg University, PO Box 462, SE-405 30, G\u00f6teborg, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell and Molecular Biology, Lundberg Laboratory, G\u00f6teborg University, PO Box 462 SE-405 30 G\u00f6teborg, Sweden. cvijovic@molgen.mpg.de","institution_ids":["https://openalex.org/I881427289"]},{"raw_affiliation_string":"Department of Cell and Molecular Biology, Lundberg Laboratory, G\u00f6teborg University, PO Box 462, SE-405 30, G\u00f6teborg, Sweden","institution_ids":["https://openalex.org/I881427289"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081024973","display_name":"Daniel Dalevi","orcid":null},"institutions":[{"id":"https://openalex.org/I66862912","display_name":"Chalmers University of Technology","ror":"https://ror.org/040wg7k59","country_code":"SE","type":"education","lineage":["https://openalex.org/I66862912"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Daniel Dalevi","raw_affiliation_strings":["Department of Computer Science and Engineering, Chalmers University of Technology, SE-412 96, G\u00f6teborg, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Chalmers University of Technology, SE-412 96, G\u00f6teborg, Sweden","institution_ids":["https://openalex.org/I66862912"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063640880","display_name":"Elizabeth Bilsland","orcid":"https://orcid.org/0000-0002-8697-3553"},"institutions":[{"id":"https://openalex.org/I881427289","display_name":"University of Gothenburg","ror":"https://ror.org/01tm6cn81","country_code":"SE","type":"education","lineage":["https://openalex.org/I881427289"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB","SE"],"is_corresponding":false,"raw_author_name":"Elizabeth Bilsland","raw_affiliation_strings":["Biochemistry Department, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK","Department of Cell and Molecular Biology, Lundberg Laboratory, G\u00f6teborg University, PO Box 462, SE-405 30, G\u00f6teborg, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biochemistry Department, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Department of Cell and Molecular Biology, Lundberg Laboratory, G\u00f6teborg University, PO Box 462, SE-405 30, G\u00f6teborg, Sweden","institution_ids":["https://openalex.org/I881427289"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103582650","display_name":"Graham JL Kemp","orcid":null},"institutions":[{"id":"https://openalex.org/I66862912","display_name":"Chalmers University of Technology","ror":"https://ror.org/040wg7k59","country_code":"SE","type":"education","lineage":["https://openalex.org/I66862912"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Graham JL Kemp","raw_affiliation_strings":["Department of Computer Science and Engineering, Chalmers University of Technology, SE-412 96, G\u00f6teborg, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Chalmers University of Technology, SE-412 96, G\u00f6teborg, Sweden","institution_ids":["https://openalex.org/I66862912"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047513730","display_name":"Per Sunnerhagen","orcid":"https://orcid.org/0000-0002-0967-8729"},"institutions":[{"id":"https://openalex.org/I881427289","display_name":"University of Gothenburg","ror":"https://ror.org/01tm6cn81","country_code":"SE","type":"education","lineage":["https://openalex.org/I881427289"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Per Sunnerhagen","raw_affiliation_strings":["Department of Cell and Molecular Biology, Lundberg Laboratory, G\u00f6teborg University, PO Box 462, SE-405 30, G\u00f6teborg, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell and Molecular Biology, Lundberg Laboratory, G\u00f6teborg University, PO Box 462, SE-405 30, G\u00f6teborg, Sweden","institution_ids":["https://openalex.org/I881427289"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5026743647"],"corresponding_institution_ids":["https://openalex.org/I881427289"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.4801,"has_fulltext":true,"cited_by_count":50,"citation_normalized_percentile":{"value":0.81701118,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"8","issue":"1","first_page":"295","last_page":"295"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9803000092506409,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9803000092506409,"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/T10604","display_name":"RNA Research and Splicing","score":0.008500000461935997,"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":0.00279999990016222,"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/biology","display_name":"Biology","score":0.7628746032714844},{"id":"https://openalex.org/keywords/orfs","display_name":"ORFS","score":0.7396577000617981},{"id":"https://openalex.org/keywords/open-reading-frame","display_name":"Open reading frame","score":0.5803369283676147},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5247055292129517},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5231060981750488},{"id":"https://openalex.org/keywords/conserved-sequence","display_name":"Conserved sequence","score":0.5125126838684082},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.502410888671875},{"id":"https://openalex.org/keywords/saccharomyces-cerevisiae","display_name":"Saccharomyces cerevisiae","score":0.46145710349082947},{"id":"https://openalex.org/keywords/ribosome-profiling","display_name":"Ribosome profiling","score":0.4492000937461853},{"id":"https://openalex.org/keywords/translation","display_name":"Translation (biology)","score":0.4267818331718445},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.42025846242904663},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.17679676413536072},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.06175240874290466}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7628746032714844},{"id":"https://openalex.org/C2780530800","wikidata":"https://www.wikidata.org/wiki/Q7072921","display_name":"ORFS","level":5,"score":0.7396577000617981},{"id":"https://openalex.org/C47289529","wikidata":"https://www.wikidata.org/wiki/Q908550","display_name":"Open reading frame","level":4,"score":0.5803369283676147},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5247055292129517},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5231060981750488},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.5125126838684082},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.502410888671875},{"id":"https://openalex.org/C2777576037","wikidata":"https://www.wikidata.org/wiki/Q719725","display_name":"Saccharomyces cerevisiae","level":3,"score":0.46145710349082947},{"id":"https://openalex.org/C182325514","wikidata":"https://www.wikidata.org/wiki/Q7322425","display_name":"Ribosome profiling","level":5,"score":0.4492000937461853},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.4267818331718445},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.42025846242904663},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.17679676413536072},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.06175240874290466}],"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":"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":"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":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","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":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1186/1471-2105-8-295","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-295","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-295","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:17686169","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17686169","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:04b647239178441f9dab8a2daf802511","is_oa":false,"landing_page_url":"https://doaj.org/article/04b647239178441f9dab8a2daf802511","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 295 (2007)","raw_type":"article"},{"id":"pmh:oai:publications.lib.chalmers.se:63150","is_oa":false,"landing_page_url":"http://publications.lib.chalmers.se/publication/63150-identification-of-putative-regulatory-upstream-orfs-in-the-yeast-genome-using-heuristics-and-evoluti","pdf_url":null,"source":{"id":"https://openalex.org/S4377196470","display_name":"Chalmers Publication Library (Chalmers University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66862912","host_organization_name":"Chalmers University of Technology","host_organization_lineage":["https://openalex.org/I66862912"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text.Article.Journal.PeerReviewed"},{"id":"pmh:oai:pubmedcentral.nih.gov:1964767","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1964767","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:research.chalmers.se:63150","is_oa":false,"landing_page_url":"https://research.chalmers.se/en/publication/63150","pdf_url":null,"source":{"id":"https://openalex.org/S4306402469","display_name":"Chalmers Research (Chalmers University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66862912","host_organization_name":"Chalmers University of Technology","host_organization_lineage":["https://openalex.org/I66862912"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:www.repository.cam.ac.uk:1810/238021","is_oa":true,"landing_page_url":"http://www.dspace.cam.ac.uk/handle/1810/238021","pdf_url":null,"source":{"id":"https://openalex.org/S4306401777","display_name":"Apollo (University of Cambridge)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I241749","host_organization_name":"University of Cambridge","host_organization_lineage":["https://openalex.org/I241749"],"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":"Article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-8-295","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-295","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-295","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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2170119516.pdf","grobid_xml":"https://content.openalex.org/works/W2170119516.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W188378287","https://openalex.org/W604176439","https://openalex.org/W1596013564","https://openalex.org/W1604959358","https://openalex.org/W1808776909","https://openalex.org/W1899601083","https://openalex.org/W1972102260","https://openalex.org/W1982980697","https://openalex.org/W1987339939","https://openalex.org/W1989230236","https://openalex.org/W1996423252","https://openalex.org/W2009064016","https://openalex.org/W2010091762","https://openalex.org/W2015009994","https://openalex.org/W2015497228","https://openalex.org/W2018590530","https://openalex.org/W2020850864","https://openalex.org/W2027195993","https://openalex.org/W2054624670","https://openalex.org/W2058682865","https://openalex.org/W2068714525","https://openalex.org/W2073575016","https://openalex.org/W2092904290","https://openalex.org/W2097040991","https://openalex.org/W2097409962","https://openalex.org/W2113206920","https://openalex.org/W2114474174","https://openalex.org/W2120366160","https://openalex.org/W2123850024","https://openalex.org/W2127201083","https://openalex.org/W2129178024","https://openalex.org/W2134597218","https://openalex.org/W2136674643","https://openalex.org/W2140183291","https://openalex.org/W2141200742","https://openalex.org/W2149960535","https://openalex.org/W2154031143","https://openalex.org/W2157611510","https://openalex.org/W2163977024","https://openalex.org/W2740652466","https://openalex.org/W4236806237","https://openalex.org/W4243704526","https://openalex.org/W4253223841","https://openalex.org/W4254228246","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2017477982","https://openalex.org/W1978801575","https://openalex.org/W2029252138","https://openalex.org/W4306784270","https://openalex.org/W2101899141","https://openalex.org/W3031046715","https://openalex.org/W2017335389","https://openalex.org/W2358544099","https://openalex.org/W1976390578","https://openalex.org/W2072439611"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,309],"translational":[2,32,98],"efficiency":[3],"of":[4,25,95,112,125,128,139,156,169,199,246,255,266,278,284,295,307,332,345],"an":[5,282],"mRNA":[6],"can":[7,22,299,339],"be":[8,239,249,300,340],"modulated":[9],"by":[10,29,42,76],"upstream":[11],"open":[12],"reading":[13],"frames":[14],"(uORFs)":[15],"present":[16],"in":[17,44,47,89,110,114,224,287,297],"certain":[18,313],"genes.":[19],"A":[20,253],"uORF":[21],"attenuate":[23],"translation":[24,113],"the":[26,35,45,58,126,132,154,157,190,244,325,333],"main":[27,36,158,326],"ORF":[28,159],"interfering":[30],"with":[31,91,184,186,203,263,315],"reinitiation":[33],"at":[34],"start":[37,155,327],"codon.":[38],"uORFs":[39,63,75,88,130,185,198,202,231,262,296,311],"also":[40],"occur":[41],"chance":[43],"genome,":[46],"which":[48],"case":[49],"they":[50],"do":[51],"not":[52,65,195],"have":[53,81,312],"a":[54,92,97,108,144,151,167,211,221,267],"regulatory":[55,99],"role.":[56,100],"Since":[57],"sequence":[59,77],"determinants":[60],"for":[61,117,137],"functional":[62,72,140,268],"are":[64,181,273],"understood,":[66],"it":[67],"is":[68],"difficult":[69],"to":[70,85,106,189,238,248,303,317,342],"discriminate":[71],"from":[73,141,153,232,320,324],"spurious":[74,142],"analysis.":[78],"RESULTS:":[79],"We":[80,101],"used":[82,341],"comparative":[83],"genomics":[84],"identify":[86],"novel":[87],"yeast":[90],"high":[93,204],"likelihood":[94],"having":[96],"examined":[102],"uORFs,":[103],"previously":[104],"shown":[105],"play":[107],"role":[109],"regulation":[111],"Saccharomyces":[115,122],"cerevisiae,":[116,226],"evolutionary":[118,214],"conservation":[119,215,294],"within":[120,251],"seven":[121],"species.":[123],"Inspection":[124],"set":[127,280],"conserved":[129,230,261,310,347],"yielded":[131],"following":[133],"three":[134],"characteristics":[135,314,338],"useful":[136],"discrimination":[138],"uORFs:":[143],"length":[145],"between":[146,160],"4":[147],"and":[148,162,165,172,193,290,323,329],"6":[149],"codons,":[150],"distance":[152,319],"50":[161],"150":[163],"nucleotides,":[164],"finally":[166],"lack":[168],"overlap":[170],"with,":[171],"clear":[173],"separation":[174],"from,":[175],"neighbouring":[176],"uORFs.":[177,219,348],"These":[178,335],"derived":[179],"rules":[180,209],"inherently":[182],"associated":[183],"properties":[187,264],"similar":[188],"GCN4":[191],"locus,":[192],"may":[194],"detect":[196],"most":[197],"other":[200,322,346],"types.":[201],"scores":[205],"based":[206],"on":[207],"these":[208,247],"showed":[210,243],"much":[212],"higher":[213],"than":[216],"randomly":[217],"selected":[218],"In":[220],"genome-wide":[222],"scan":[223],"S.":[225],"we":[227,236],"found":[228,259,337],"34":[229],"32":[233],"genes":[234,257,285],"that":[235],"predict":[237],"functional;":[240],"subsequent":[241],"analysis":[242,277],"majority":[245],"located":[250],"transcripts.":[252],"total":[254],"252":[256],"were":[258],"containing":[260],"indicative":[265],"role;":[269],"all":[270],"but":[271],"7":[272],"novel.":[274],"Functional":[275],"content":[276],"this":[279],"identified":[281],"overrepresentation":[283],"involved":[286],"transcriptional":[288],"control":[289],"development.":[291],"CONCLUSION:":[292],"Evolutionary":[293],"yeasts":[298],"traced":[301],"up":[302],"100":[304],"million":[305],"years":[306],"separation.":[308],"respect":[316],"length,":[318],"each":[321],"codon,":[328],"folding":[330],"energy":[331],"sequence.":[334],"newly":[336],"facilitate":[343],"detection":[344]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}