{"id":"https://openalex.org/W3162358070","doi":"https://doi.org/10.1093/bioinformatics/btab339","title":"ORFLine: a bioinformatic pipeline to prioritize small open reading frames identifies candidate secreted small proteins from lymphocytes","display_name":"ORFLine: a bioinformatic pipeline to prioritize small open reading frames identifies candidate secreted small proteins from lymphocytes","publication_year":2021,"publication_date":"2021-04-30","ids":{"openalex":"https://openalex.org/W3162358070","doi":"https://doi.org/10.1093/bioinformatics/btab339","mag":"3162358070","pmid":"https://pubmed.ncbi.nlm.nih.gov/33970232"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab339","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab339","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/19/3152/40556910/btab339.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":"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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/19/3152/40556910/btab339.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028139996","display_name":"Fengyuan Hu","orcid":"https://orcid.org/0000-0002-1756-7551"},"institutions":[{"id":"https://openalex.org/I1302113299","display_name":"Babraham Institute","ror":"https://ror.org/01d5qpn59","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1302113299","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Fengyuan Hu","raw_affiliation_strings":["Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus , Cambridge CB22 3AT, UK"],"affiliations":[{"raw_affiliation_string":"Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus , Cambridge CB22 3AT, UK","institution_ids":["https://openalex.org/I1302113299"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074284350","display_name":"Jia Lu","orcid":"https://orcid.org/0000-0003-3995-324X"},"institutions":[{"id":"https://openalex.org/I1302113299","display_name":"Babraham Institute","ror":"https://ror.org/01d5qpn59","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1302113299","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jia Lu","raw_affiliation_strings":["Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus , Cambridge CB22 3AT, UK"],"affiliations":[{"raw_affiliation_string":"Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus , Cambridge CB22 3AT, UK","institution_ids":["https://openalex.org/I1302113299"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038878668","display_name":"Louise S. Matheson","orcid":"https://orcid.org/0000-0002-9392-2519"},"institutions":[{"id":"https://openalex.org/I1302113299","display_name":"Babraham Institute","ror":"https://ror.org/01d5qpn59","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1302113299","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Louise S Matheson","raw_affiliation_strings":["Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus , Cambridge CB22 3AT, UK"],"affiliations":[{"raw_affiliation_string":"Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus , Cambridge CB22 3AT, UK","institution_ids":["https://openalex.org/I1302113299"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062442842","display_name":"Manuel D. D\u00edaz\u2010Mu\u00f1oz","orcid":"https://orcid.org/0000-0002-9227-7474"},"institutions":[{"id":"https://openalex.org/I1302113299","display_name":"Babraham Institute","ror":"https://ror.org/01d5qpn59","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1302113299","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Manuel D D\u00edaz-Mu\u00f1oz","raw_affiliation_strings":["Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus , Cambridge CB22 3AT, UK"],"affiliations":[{"raw_affiliation_string":"Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus , Cambridge CB22 3AT, UK","institution_ids":["https://openalex.org/I1302113299"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082818907","display_name":"Alexander Saveliev","orcid":"https://orcid.org/0000-0003-0840-4774"},"institutions":[{"id":"https://openalex.org/I1302113299","display_name":"Babraham Institute","ror":"https://ror.org/01d5qpn59","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1302113299","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Alexander Saveliev","raw_affiliation_strings":["Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus , Cambridge CB22 3AT, UK"],"affiliations":[{"raw_affiliation_string":"Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus , Cambridge CB22 3AT, UK","institution_ids":["https://openalex.org/I1302113299"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019398608","display_name":"Jinbo Xu","orcid":"https://orcid.org/0000-0001-7111-4839"},"institutions":[{"id":"https://openalex.org/I1302113299","display_name":"Babraham Institute","ror":"https://ror.org/01d5qpn59","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1302113299","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jinbo Xu","raw_affiliation_strings":["The Babraham Institute [Cambridge, UK] (Babraham Hall, Babraham, Cambridge CB22 3AT - Royaume-Uni)"],"affiliations":[{"raw_affiliation_string":"The Babraham Institute [Cambridge, UK] (Babraham Hall, Babraham, Cambridge CB22 3AT - Royaume-Uni)","institution_ids":["https://openalex.org/I1302113299"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031709180","display_name":"Martin Turner","orcid":"https://orcid.org/0000-0002-3801-9896"},"institutions":[{"id":"https://openalex.org/I1302113299","display_name":"Babraham Institute","ror":"https://ror.org/01d5qpn59","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1302113299","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Martin Turner","raw_affiliation_strings":["Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus , Cambridge CB22 3AT, UK"],"affiliations":[{"raw_affiliation_string":"Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus , Cambridge CB22 3AT, UK","institution_ids":["https://openalex.org/I1302113299"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5028139996","https://openalex.org/A5031709180","https://openalex.org/A5062442842"],"corresponding_institution_ids":["https://openalex.org/I1302113299"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.8115,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.70677087,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"37","issue":"19","first_page":"3152","last_page":"3159"},"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/T11668","display_name":"interferon and immune responses","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.9965999722480774,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/open-reading-frame","display_name":"Open reading frame","score":0.733905553817749},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6672050356864929},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5814955234527588},{"id":"https://openalex.org/keywords/signal-peptide","display_name":"Signal peptide","score":0.5797410607337952},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5638791918754578},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5479446053504944},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.529764711856842},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.42764461040496826},{"id":"https://openalex.org/keywords/secretion","display_name":"Secretion","score":0.42659616470336914},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.423300176858902},{"id":"https://openalex.org/keywords/reading","display_name":"Reading (process)","score":0.41883593797683716},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2314450442790985},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.22951936721801758},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1613609790802002},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09518605470657349}],"concepts":[{"id":"https://openalex.org/C47289529","wikidata":"https://www.wikidata.org/wiki/Q908550","display_name":"Open reading frame","level":4,"score":0.733905553817749},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6672050356864929},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5814955234527588},{"id":"https://openalex.org/C10858879","wikidata":"https://www.wikidata.org/wiki/Q899790","display_name":"Signal peptide","level":4,"score":0.5797410607337952},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5638791918754578},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5479446053504944},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.529764711856842},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.42764461040496826},{"id":"https://openalex.org/C49039625","wikidata":"https://www.wikidata.org/wiki/Q84230","display_name":"Secretion","level":2,"score":0.42659616470336914},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.423300176858902},{"id":"https://openalex.org/C554936623","wikidata":"https://www.wikidata.org/wiki/Q199657","display_name":"Reading (process)","level":2,"score":0.41883593797683716},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2314450442790985},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.22951936721801758},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1613609790802002},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09518605470657349},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btab339","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab339","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/19/3152/40556910/btab339.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":"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:33970232","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33970232","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:HAL:hal-03778860v1","is_oa":true,"landing_page_url":"https://ut3-toulouseinp.hal.science/hal-03778860","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2021, 37 (19), pp.3152-3159. &#x27E8;10.1093/bioinformatics/btab339&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:pubmedcentral.nih.gov:8504629","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8504629","pdf_url":null,"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/btab339","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab339","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/19/3152/40556910/btab339.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":"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":[{"score":0.7799999713897705,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G1990583613","display_name":null,"funder_award_id":"BBS/E/B/000C0428","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G552273675","display_name":"Develop a mechanistic understanding of how transcriptional and posttranscriptional regulation of gene expression is coordinated by signal transduction pathways.","funder_award_id":"BBS/E/B/000C0428","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G6160911136","display_name":null,"funder_award_id":"BBS/E/B/000C0427","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G7465016671","display_name":"Immune homeostasis and the immune response","funder_award_id":"BBS/E/B/000C0427","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3162358070.pdf","grobid_xml":"https://content.openalex.org/works/W3162358070.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1749737319","https://openalex.org/W1970569349","https://openalex.org/W1978417963","https://openalex.org/W1986705163","https://openalex.org/W1988622164","https://openalex.org/W2016450373","https://openalex.org/W2029173942","https://openalex.org/W2033492309","https://openalex.org/W2055043387","https://openalex.org/W2078266900","https://openalex.org/W2079517684","https://openalex.org/W2094201044","https://openalex.org/W2113224683","https://openalex.org/W2152974197","https://openalex.org/W2153521373","https://openalex.org/W2160343816","https://openalex.org/W2193904848","https://openalex.org/W2205343347","https://openalex.org/W2262417550","https://openalex.org/W2267382996","https://openalex.org/W2282922301","https://openalex.org/W2398612826","https://openalex.org/W2559953833","https://openalex.org/W2567665210","https://openalex.org/W2579217144","https://openalex.org/W2581437033","https://openalex.org/W2606627603","https://openalex.org/W2615953964","https://openalex.org/W2734798616","https://openalex.org/W2761249484","https://openalex.org/W2768144926","https://openalex.org/W2777171598","https://openalex.org/W2905456928","https://openalex.org/W2913230339","https://openalex.org/W2937932584","https://openalex.org/W2951280166","https://openalex.org/W2971297443","https://openalex.org/W2990682473","https://openalex.org/W2992003657","https://openalex.org/W2998667423","https://openalex.org/W3011599364","https://openalex.org/W3028519422","https://openalex.org/W3046357967","https://openalex.org/W3112376646","https://openalex.org/W6732654142"],"related_works":["https://openalex.org/W2023004010","https://openalex.org/W1968702305","https://openalex.org/W2156604464","https://openalex.org/W2895816064","https://openalex.org/W2111815711","https://openalex.org/W1900806339","https://openalex.org/W2019978236","https://openalex.org/W1581561389","https://openalex.org/W4312065197","https://openalex.org/W1998633373"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":5},{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
