{"id":"https://openalex.org/W3196811047","doi":"https://doi.org/10.1093/bioinformatics/btab628","title":"pepsickle rapidly and accurately predicts proteasomal cleavage sites for improved neoantigen identification","display_name":"pepsickle rapidly and accurately predicts proteasomal cleavage sites for improved neoantigen identification","publication_year":2021,"publication_date":"2021-09-03","ids":{"openalex":"https://openalex.org/W3196811047","doi":"https://doi.org/10.1093/bioinformatics/btab628","mag":"3196811047","pmid":"https://pubmed.ncbi.nlm.nih.gov/34478497"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab628","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab628","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036788659","display_name":"Benjamin R. Weeder","orcid":"https://orcid.org/0000-0002-4128-5861"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin R Weeder","raw_affiliation_strings":["Computational Biology Program, Oregon Health & Science University , Portland, OR 97239, USA","Department of Biomedical Engineering, Oregon Health & Science University , Portland, OR 97239, USA"],"affiliations":[{"raw_affiliation_string":"Computational Biology Program, Oregon Health & Science University , Portland, OR 97239, USA","institution_ids":["https://openalex.org/I165690674"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Oregon Health & Science University , Portland, OR 97239, USA","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060420733","display_name":"Mary A. Wood","orcid":"https://orcid.org/0000-0003-4011-3811"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mary A Wood","raw_affiliation_strings":["Phase Genomics Inc. , Seattle, WA 98109, USA"],"affiliations":[{"raw_affiliation_string":"Phase Genomics Inc. , Seattle, WA 98109, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055886116","display_name":"Ellysia Li","orcid":null},"institutions":[{"id":"https://openalex.org/I4210149261","display_name":"Pacific University","ror":"https://ror.org/059z5w858","country_code":"US","type":"education","lineage":["https://openalex.org/I4210149261"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ellysia Li","raw_affiliation_strings":["Pacific University , Forest Grove, OR 97116, USA"],"affiliations":[{"raw_affiliation_string":"Pacific University , Forest Grove, OR 97116, USA","institution_ids":["https://openalex.org/I4210149261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028455102","display_name":"Abhinav Nellore","orcid":"https://orcid.org/0000-0001-8145-1484"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Abhinav Nellore","raw_affiliation_strings":["Computational Biology Program, Oregon Health & Science University , Portland, OR 97239, USA","Department of Biomedical Engineering, Oregon Health & Science University , Portland, OR 97239, USA","Department of Surgery, Oregon Health & Science University , Portland, OR 97239, USA"],"affiliations":[{"raw_affiliation_string":"Computational Biology Program, Oregon Health & Science University , Portland, OR 97239, USA","institution_ids":["https://openalex.org/I165690674"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Oregon Health & Science University , Portland, OR 97239, USA","institution_ids":["https://openalex.org/I165690674"]},{"raw_affiliation_string":"Department of Surgery, Oregon Health & Science University , Portland, OR 97239, USA","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088872826","display_name":"Reid F. Thompson","orcid":"https://orcid.org/0000-0003-3661-5296"},"institutions":[{"id":"https://openalex.org/I4210144745","display_name":"VA Portland Health Care System","ror":"https://ror.org/054484h93","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1322918889","https://openalex.org/I2799886695","https://openalex.org/I4210144745"]},{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Reid F Thompson","raw_affiliation_strings":["Computational Biology Program, Oregon Health & Science University , Portland, OR 97239, USA","Department of Biomedical Engineering, Oregon Health & Science University , Portland, OR 97239, USA","Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University , Portland, OR 97239, USA","Department of Radiation Medicine, Oregon Health & Science University , Portland, OR 97239, USA","Division of Hospital and Specialty Medicine, VA Portland Healthcare System , Portland, OR 97239, USA"],"affiliations":[{"raw_affiliation_string":"Computational Biology Program, Oregon Health & Science University , Portland, OR 97239, USA","institution_ids":["https://openalex.org/I165690674"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Oregon Health & Science University , Portland, OR 97239, USA","institution_ids":["https://openalex.org/I165690674"]},{"raw_affiliation_string":"Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University , Portland, OR 97239, USA","institution_ids":["https://openalex.org/I165690674"]},{"raw_affiliation_string":"Department of Radiation Medicine, Oregon Health & Science University , Portland, OR 97239, USA","institution_ids":["https://openalex.org/I165690674"]},{"raw_affiliation_string":"Division of Hospital and Specialty Medicine, VA Portland Healthcare System , Portland, OR 97239, USA","institution_ids":["https://openalex.org/I4210144745"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5088872826"],"corresponding_institution_ids":["https://openalex.org/I165690674","https://openalex.org/I4210144745"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6489,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.6714054,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"37","issue":"21","first_page":"3723","last_page":"3733"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","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/T12576","display_name":"vaccines and immunoinformatics approaches","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/T11041","display_name":"Ubiquitin and proteasome pathways","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/T12505","display_name":"Peptidase Inhibition and Analysis","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cleavage","display_name":"Cleavage (geology)","score":0.7369775772094727},{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.6390286684036255},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6389111876487732},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.6095271110534668},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5375617742538452},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.43797796964645386},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.35050085186958313},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2296839952468872},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.1701606810092926},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.131953626871109},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07701727747917175}],"concepts":[{"id":"https://openalex.org/C175156509","wikidata":"https://www.wikidata.org/wiki/Q1990218","display_name":"Cleavage (geology)","level":3,"score":0.7369775772094727},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.6390286684036255},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6389111876487732},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.6095271110534668},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5375617742538452},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.43797796964645386},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.35050085186958313},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2296839952468872},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.1701606810092926},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.131953626871109},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07701727747917175},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C43369102","wikidata":"https://www.wikidata.org/wiki/Q2307625","display_name":"Fracture (geology)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000941","descriptor_name":"Antigens","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000941","descriptor_name":"Antigens","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000941","descriptor_name":"Antigens","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":"D046988","descriptor_name":"Proteasome Endopeptidase Complex","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D046988","descriptor_name":"Proteasome Endopeptidase Complex","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D046988","descriptor_name":"Proteasome Endopeptidase Complex","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D059748","descriptor_name":"Proteolysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059748","descriptor_name":"Proteolysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059748","descriptor_name":"Proteolysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btab628","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab628","pdf_url":null,"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:34478497","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34478497","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":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":90,"referenced_works":["https://openalex.org/W1438791329","https://openalex.org/W1528487587","https://openalex.org/W1894683288","https://openalex.org/W1964684295","https://openalex.org/W1965167575","https://openalex.org/W1967731044","https://openalex.org/W1977142804","https://openalex.org/W1993652875","https://openalex.org/W1994048581","https://openalex.org/W1995741768","https://openalex.org/W1996498079","https://openalex.org/W1999119754","https://openalex.org/W2004157941","https://openalex.org/W2005993899","https://openalex.org/W2006617902","https://openalex.org/W2007903646","https://openalex.org/W2008421541","https://openalex.org/W2009265507","https://openalex.org/W2010177704","https://openalex.org/W2010239849","https://openalex.org/W2010371508","https://openalex.org/W2021289499","https://openalex.org/W2026043555","https://openalex.org/W2033531531","https://openalex.org/W2040874036","https://openalex.org/W2042632472","https://openalex.org/W2055043387","https://openalex.org/W2055821710","https://openalex.org/W2058126719","https://openalex.org/W2071191421","https://openalex.org/W2071591384","https://openalex.org/W2071708791","https://openalex.org/W2085760247","https://openalex.org/W2089892946","https://openalex.org/W2093150133","https://openalex.org/W2093505872","https://openalex.org/W2100656989","https://openalex.org/W2101234009","https://openalex.org/W2103675269","https://openalex.org/W2103980159","https://openalex.org/W2104759527","https://openalex.org/W2107198699","https://openalex.org/W2108035024","https://openalex.org/W2108279225","https://openalex.org/W2110241531","https://openalex.org/W2112002514","https://openalex.org/W2116595225","https://openalex.org/W2117333383","https://openalex.org/W2118592492","https://openalex.org/W2118617212","https://openalex.org/W2123206156","https://openalex.org/W2132905138","https://openalex.org/W2132925083","https://openalex.org/W2132972924","https://openalex.org/W2137917591","https://openalex.org/W2142129114","https://openalex.org/W2143625068","https://openalex.org/W2147880582","https://openalex.org/W2157186692","https://openalex.org/W2340267638","https://openalex.org/W2355140549","https://openalex.org/W2514929667","https://openalex.org/W2547542486","https://openalex.org/W2555228033","https://openalex.org/W2580614520","https://openalex.org/W2583666712","https://openalex.org/W2597129987","https://openalex.org/W2605808699","https://openalex.org/W2620578360","https://openalex.org/W2728365508","https://openalex.org/W2782708334","https://openalex.org/W2783423953","https://openalex.org/W2791483720","https://openalex.org/W2809880448","https://openalex.org/W2898389621","https://openalex.org/W2912850482","https://openalex.org/W2914962392","https://openalex.org/W2939259633","https://openalex.org/W2948567032","https://openalex.org/W2970971581","https://openalex.org/W2995389725","https://openalex.org/W2998313390","https://openalex.org/W3091991776","https://openalex.org/W3129223620","https://openalex.org/W4237142329","https://openalex.org/W4242320431","https://openalex.org/W4295312788","https://openalex.org/W6675354045","https://openalex.org/W6763600569","https://openalex.org/W6766978945"],"related_works":["https://openalex.org/W1979044599","https://openalex.org/W2021824670","https://openalex.org/W2009867644","https://openalex.org/W2363997565","https://openalex.org/W1981120125","https://openalex.org/W3036615648","https://openalex.org/W2408448169","https://openalex.org/W2182598264","https://openalex.org/W2075879923","https://openalex.org/W2060253881"],"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":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2}],"updated_date":"2026-03-11T14:59:36.786465","created_date":"2025-10-10T00:00:00"}
