{"id":"https://openalex.org/W4376609880","doi":"https://doi.org/10.1093/bioinformatics/btad323","title":"uORF4u: a tool for annotation of conserved upstream open reading frames","display_name":"uORF4u: a tool for annotation of conserved upstream open reading frames","publication_year":2023,"publication_date":"2023-05-01","ids":{"openalex":"https://openalex.org/W4376609880","doi":"https://doi.org/10.1093/bioinformatics/btad323","pmid":"https://pubmed.ncbi.nlm.nih.gov/37184890"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad323","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad323","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad323/50329707/btad323.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad323/50329707/btad323.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013872096","display_name":"Artyom A. Egorov","orcid":"https://orcid.org/0000-0001-5578-5384"},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Artyom A Egorov","raw_affiliation_strings":["Department of Experimental Medical Science, Lund University , S\u00f6lvegatan 19 , Lund, 223 62, Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Experimental Medical Science, Lund University , S\u00f6lvegatan 19 , Lund, 223 62, Sweden","institution_ids":["https://openalex.org/I187531555"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013054326","display_name":"Gemma C. Atkinson","orcid":"https://orcid.org/0000-0002-4861-4584"},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Gemma C Atkinson","raw_affiliation_strings":["Department of Experimental Medical Science, Lund University , S\u00f6lvegatan 19 , Lund, 223 62, Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Experimental Medical Science, Lund University , S\u00f6lvegatan 19 , Lund, 223 62, Sweden","institution_ids":["https://openalex.org/I187531555"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5013054326","https://openalex.org/A5013872096"],"corresponding_institution_ids":["https://openalex.org/I187531555"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.8271,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.85041436,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"39","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9998000264167786,"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":0.994700014591217,"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/orfs","display_name":"ORFS","score":0.8319419622421265},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6952410340309143},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5735030174255371},{"id":"https://openalex.org/keywords/open-reading-frame","display_name":"Open reading frame","score":0.5689124464988708},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5460224151611328},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5135786533355713},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5112791061401367},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4756942689418793},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.47295519709587097},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.47145968675613403},{"id":"https://openalex.org/keywords/start-codon","display_name":"Start codon","score":0.4474126696586609},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.34849226474761963},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.28449079394340515},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17912140488624573},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.14148366451263428}],"concepts":[{"id":"https://openalex.org/C2780530800","wikidata":"https://www.wikidata.org/wiki/Q7072921","display_name":"ORFS","level":5,"score":0.8319419622421265},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6952410340309143},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5735030174255371},{"id":"https://openalex.org/C47289529","wikidata":"https://www.wikidata.org/wiki/Q908550","display_name":"Open reading frame","level":4,"score":0.5689124464988708},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5460224151611328},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5135786533355713},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5112791061401367},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4756942689418793},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.47295519709587097},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.47145968675613403},{"id":"https://openalex.org/C176990463","wikidata":"https://www.wikidata.org/wiki/Q1854186","display_name":"Start codon","level":4,"score":0.4474126696586609},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.34849226474761963},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.28449079394340515},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17912140488624573},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.14148366451263428},{"id":"https://openalex.org/C512185932","wikidata":"https://www.wikidata.org/wiki/Q28745","display_name":"Nucleotide","level":3,"score":0.0}],"mesh":[{"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":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","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":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":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btad323","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad323","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad323/50329707/btad323.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37184890","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37184890","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10219788","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10219788","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10219788/pdf/btad323.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:lup.lub.lu.se:4f1d08b4-e4ed-4660-819f-2b857bffea76","is_oa":false,"landing_page_url":"https://lup.lub.lu.se/record/4f1d08b4-e4ed-4660-819f-2b857bffea76","pdf_url":null,"source":{"id":"https://openalex.org/S4306400536","display_name":"Lund University Publications (Lund University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I187531555","host_organization_name":"Lund University","host_organization_lineage":["https://openalex.org/I187531555"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1367-4803","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad323","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad323","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad323/50329707/btad323.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2366370763","display_name":null,"funder_award_id":"2019-01085","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G6352601823","display_name":null,"funder_award_id":"2022-01603","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G8597555680","display_name":null,"funder_award_id":"2020-0037","funder_id":"https://openalex.org/F4320322327","funder_display_name":"Knut och Alice Wallenbergs Stiftelse"},{"id":"https://openalex.org/G8683756101","display_name":null,"funder_award_id":"support","funder_id":"https://openalex.org/F4320322327","funder_display_name":"Knut och Alice Wallenbergs Stiftelse"}],"funders":[{"id":"https://openalex.org/F4320322327","display_name":"Knut och Alice Wallenbergs Stiftelse","ror":"https://ror.org/004hzzk67"},{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4376609880.pdf"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1980438612","https://openalex.org/W2011301426","https://openalex.org/W2056067932","https://openalex.org/W2079517684","https://openalex.org/W2101010252","https://openalex.org/W2102050179","https://openalex.org/W2114850508","https://openalex.org/W2142482793","https://openalex.org/W2142678478","https://openalex.org/W2145292712","https://openalex.org/W2162417400","https://openalex.org/W2171875574","https://openalex.org/W2173732482","https://openalex.org/W2175136759","https://openalex.org/W2519500331","https://openalex.org/W2520675467","https://openalex.org/W2755662361","https://openalex.org/W2776644290","https://openalex.org/W2792251295","https://openalex.org/W2973179166","https://openalex.org/W2987349979","https://openalex.org/W2995997429","https://openalex.org/W3010073072","https://openalex.org/W3082191894","https://openalex.org/W3121878354","https://openalex.org/W3137968765","https://openalex.org/W3202941569","https://openalex.org/W4282835389","https://openalex.org/W4295242737","https://openalex.org/W4296690682","https://openalex.org/W4310035789","https://openalex.org/W4353112026","https://openalex.org/W6838743993"],"related_works":["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/W2072439611","https://openalex.org/W3148570048","https://openalex.org/W2107647518"],"abstract_inverted_index":{"uORF4u":[0,60],"is":[1,35,61],"written":[2],"in":[3],"Python3":[4],"and":[5,9,30],"runs":[6],"on":[7],"Linux":[8],"MacOS.":[10],"The":[11],"command-line":[12],"interface":[13],"covers":[14],"most":[15],"practical":[16],"use":[17],"cases,":[18],"while":[19],"the":[20,38,51],"provided":[21],"Python":[22,28],"API":[23],"allows":[24],"usage":[25],"within":[26],"a":[27],"program":[29],"additional":[31],"customization.":[32],"Source":[33],"code":[34],"available":[36,49,62],"from":[37],"GitHub":[39],"page:":[40,54],"github.com/GCA-VH-lab/uorf4u.":[41],"Detailed":[42],"documentation":[43],"that":[44],"includes":[45],"an":[46],"example-driven":[47],"guide":[48],"at":[50,63],"software":[52],"home":[53],"gca-vh-lab.github.io/uorf4u.":[55],"A":[56],"web":[57],"version":[58],"of":[59],"server.atkinson-lab.com/uorf4u.":[64]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
