{"id":"https://openalex.org/W4323036830","doi":"https://doi.org/10.1093/bioinformatics/btad112","title":"peaks2utr: a robust Python tool for the annotation of 3\u2032 UTRs","display_name":"peaks2utr: a robust Python tool for the annotation of 3\u2032 UTRs","publication_year":2023,"publication_date":"2023-03-01","ids":{"openalex":"https://openalex.org/W4323036830","doi":"https://doi.org/10.1093/bioinformatics/btad112","pmid":"https://pubmed.ncbi.nlm.nih.gov/36864613"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad112","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad112","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad112/49512482/btad112.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/article-pdf/39/3/btad112/49512482/btad112.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010911533","display_name":"William Haese-Hill","orcid":"https://orcid.org/0000-0002-1393-0966"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"William Haese-Hill","raw_affiliation_strings":["School of Infection & Immunity, MVLS, University of Glasgow , Glasgow G12 8TA, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Infection & Immunity, MVLS, University of Glasgow , Glasgow G12 8TA, United Kingdom","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019794734","display_name":"Kathryn Crouch","orcid":"https://orcid.org/0000-0001-9310-4762"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Kathryn Crouch","raw_affiliation_strings":["School of Infection & Immunity, MVLS, University of Glasgow , Glasgow G12 8TA, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Infection & Immunity, MVLS, University of Glasgow , Glasgow G12 8TA, United Kingdom","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012004257","display_name":"Thomas D. Otto","orcid":"https://orcid.org/0000-0002-1246-7404"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Thomas D Otto","raw_affiliation_strings":["School of Infection & Immunity, MVLS, University of Glasgow , Glasgow G12 8TA, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Infection & Immunity, MVLS, University of Glasgow , Glasgow G12 8TA, United Kingdom","institution_ids":["https://openalex.org/I7882870"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5012004257"],"corresponding_institution_ids":["https://openalex.org/I7882870"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.8669,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.90770828,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"39","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9987999796867371,"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/T11482","display_name":"RNA modifications and cancer","score":0.9987999796867371,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9987000226974487,"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":0.9986000061035156,"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/python","display_name":"Python (programming language)","score":0.9401588439941406},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.9185149073600769},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7767185568809509},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.48073673248291016},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.373150110244751},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3369433581829071},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.28083860874176025}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9401588439941406},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.9185149073600769},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7767185568809509},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.48073673248291016},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.373150110244751},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3369433581829071},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.28083860874176025}],"mesh":[{"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":"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":"D020413","descriptor_name":"3' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020413","descriptor_name":"3' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020413","descriptor_name":"3' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020413","descriptor_name":"3' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020413","descriptor_name":"3' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btad112","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad112","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad112/49512482/btad112.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:36864613","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36864613","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:eprints.gla.ac.uk:293224","is_oa":true,"landing_page_url":null,"pdf_url":"https://eprints.gla.ac.uk/293224/1/293224.pdf","source":{"id":"https://openalex.org/S4210235606","display_name":"ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam)","issn_l":"2622-8912","issn":["2622-8912","2622-8920"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Articles"},{"id":"pmh:oai:pubmedcentral.nih.gov:10008064","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10008064","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10008064/pdf/btad112.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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad112","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad112","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad112/49512482/btad112.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/G2955975842","display_name":null,"funder_award_id":"104111/Z/14/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G4219695895","display_name":null,"funder_award_id":"104111","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G4673607756","display_name":null,"funder_award_id":"218288/Z/19/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4323036830.pdf"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W2026663202","https://openalex.org/W2099753867","https://openalex.org/W2171808845","https://openalex.org/W2338978258","https://openalex.org/W2767898033","https://openalex.org/W2890344905","https://openalex.org/W2905306575","https://openalex.org/W3131055609","https://openalex.org/W3134111171","https://openalex.org/W3197560622","https://openalex.org/W4225286307"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2341492732","https://openalex.org/W2377979023","https://openalex.org/W3080200277","https://openalex.org/W2207495067","https://openalex.org/W1906486629","https://openalex.org/W2557718140","https://openalex.org/W67092138","https://openalex.org/W4225687299"],"abstract_inverted_index":{"peaks2utr":[0],"is":[1,8,19],"implemented":[2],"in":[3],"Python":[4],"3":[5],"(\u22653.8).":[6],"It":[7,18],"available":[9],"via":[10],"PyPI":[11],"at":[12,16],"https://pypi.org/project/peaks2utr":[13],"and":[14],"GitHub":[15],"https://github.com/haessar/peaks2utr.":[17],"licensed":[20],"under":[21],"GNU":[22],"GPLv3.":[23]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-10-10T00:00:00"}
