{"id":"https://openalex.org/W3212743825","doi":"https://doi.org/10.1093/bioinformatics/btab759","title":"nextNEOpi: a comprehensive pipeline for computational neoantigen prediction","display_name":"nextNEOpi: a comprehensive pipeline for computational neoantigen prediction","publication_year":2021,"publication_date":"2021-11-09","ids":{"openalex":"https://openalex.org/W3212743825","doi":"https://doi.org/10.1093/bioinformatics/btab759","mag":"3212743825","pmid":"https://pubmed.ncbi.nlm.nih.gov/34788790"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab759","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab759","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":"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://doi.org/10.1093/bioinformatics/btab759","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066477976","display_name":"Dietmar Rieder","orcid":"https://orcid.org/0000-0003-1754-690X"},"institutions":[{"id":"https://openalex.org/I143397708","display_name":"Innsbruck Medical University","ror":"https://ror.org/03pt86f80","country_code":"AT","type":"education","lineage":["https://openalex.org/I143397708"]},{"id":"https://openalex.org/I190249584","display_name":"Universit\u00e4t Innsbruck","ror":"https://ror.org/054pv6659","country_code":"AT","type":"education","lineage":["https://openalex.org/I190249584"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Dietmar Rieder","raw_affiliation_strings":["Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria","institution_ids":["https://openalex.org/I143397708","https://openalex.org/I190249584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066001126","display_name":"Georgios Fotakis","orcid":"https://orcid.org/0000-0001-9659-4226"},"institutions":[{"id":"https://openalex.org/I143397708","display_name":"Innsbruck Medical University","ror":"https://ror.org/03pt86f80","country_code":"AT","type":"education","lineage":["https://openalex.org/I143397708"]},{"id":"https://openalex.org/I190249584","display_name":"Universit\u00e4t Innsbruck","ror":"https://ror.org/054pv6659","country_code":"AT","type":"education","lineage":["https://openalex.org/I190249584"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Georgios Fotakis","raw_affiliation_strings":["Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria","institution_ids":["https://openalex.org/I143397708","https://openalex.org/I190249584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088521746","display_name":"Markus Au\u00dferhofer","orcid":null},"institutions":[{"id":"https://openalex.org/I143397708","display_name":"Innsbruck Medical University","ror":"https://ror.org/03pt86f80","country_code":"AT","type":"education","lineage":["https://openalex.org/I143397708"]},{"id":"https://openalex.org/I190249584","display_name":"Universit\u00e4t Innsbruck","ror":"https://ror.org/054pv6659","country_code":"AT","type":"education","lineage":["https://openalex.org/I190249584"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Markus Ausserhofer","raw_affiliation_strings":["Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria","institution_ids":["https://openalex.org/I143397708","https://openalex.org/I190249584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015614968","display_name":"Ren\u00e9 Geyeregger","orcid":"https://orcid.org/0000-0002-5762-790X"},"institutions":[{"id":"https://openalex.org/I4210123554","display_name":"St Anna Children's Hospital","ror":"https://ror.org/02qb3f692","country_code":"AT","type":"healthcare","lineage":["https://openalex.org/I4210123554"]},{"id":"https://openalex.org/I4388891777","display_name":"St. Anna Children's Cancer Research Institute","ror":"https://ror.org/05bd7c383","country_code":null,"type":"nonprofit","lineage":["https://openalex.org/I4388891777"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Geyeregger Ren\u00e9","raw_affiliation_strings":["St. Anna Children\u2019s Cancer Research Institute , Vienna 1090, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"St. Anna Children\u2019s Cancer Research Institute , Vienna 1090, Austria","institution_ids":["https://openalex.org/I4210123554","https://openalex.org/I4388891777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057905121","display_name":"Wolfgang Paster","orcid":"https://orcid.org/0000-0002-5537-2886"},"institutions":[{"id":"https://openalex.org/I4210123554","display_name":"St Anna Children's Hospital","ror":"https://ror.org/02qb3f692","country_code":"AT","type":"healthcare","lineage":["https://openalex.org/I4210123554"]},{"id":"https://openalex.org/I4388891777","display_name":"St. Anna Children's Cancer Research Institute","ror":"https://ror.org/05bd7c383","country_code":null,"type":"nonprofit","lineage":["https://openalex.org/I4388891777"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Wolfgang Paster","raw_affiliation_strings":["St. Anna Children\u2019s Cancer Research Institute , Vienna 1090, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"St. Anna Children\u2019s Cancer Research Institute , Vienna 1090, Austria","institution_ids":["https://openalex.org/I4210123554","https://openalex.org/I4388891777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084751312","display_name":"Zlatko Trajanoski","orcid":"https://orcid.org/0000-0002-0636-7351"},"institutions":[{"id":"https://openalex.org/I143397708","display_name":"Innsbruck Medical University","ror":"https://ror.org/03pt86f80","country_code":"AT","type":"education","lineage":["https://openalex.org/I143397708"]},{"id":"https://openalex.org/I190249584","display_name":"Universit\u00e4t Innsbruck","ror":"https://ror.org/054pv6659","country_code":"AT","type":"education","lineage":["https://openalex.org/I190249584"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Zlatko Trajanoski","raw_affiliation_strings":["Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria","institution_ids":["https://openalex.org/I143397708","https://openalex.org/I190249584"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033275131","display_name":"Francesca Finotello","orcid":"https://orcid.org/0000-0003-0712-4658"},"institutions":[{"id":"https://openalex.org/I143397708","display_name":"Innsbruck Medical University","ror":"https://ror.org/03pt86f80","country_code":"AT","type":"education","lineage":["https://openalex.org/I143397708"]},{"id":"https://openalex.org/I190249584","display_name":"Universit\u00e4t Innsbruck","ror":"https://ror.org/054pv6659","country_code":"AT","type":"education","lineage":["https://openalex.org/I190249584"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Francesca Finotello","raw_affiliation_strings":["Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria","Digital Science Center (DiSC), University Innsbruck , Innsbruck 6020, Austria","Institute of Molecular Biology, University Innsbruck , Innsbruck 6020, Austria"],"raw_orcid":"https://orcid.org/0000-0003-0712-4658","affiliations":[{"raw_affiliation_string":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria","institution_ids":["https://openalex.org/I143397708","https://openalex.org/I190249584"]},{"raw_affiliation_string":"Digital Science Center (DiSC), University Innsbruck , Innsbruck 6020, Austria","institution_ids":["https://openalex.org/I190249584"]},{"raw_affiliation_string":"Institute of Molecular Biology, University Innsbruck , Innsbruck 6020, Austria","institution_ids":["https://openalex.org/I190249584"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5033275131"],"corresponding_institution_ids":["https://openalex.org/I143397708","https://openalex.org/I190249584"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.4892,"has_fulltext":false,"cited_by_count":55,"citation_normalized_percentile":{"value":0.9417615,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"38","issue":"4","first_page":"1131","last_page":"1132"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9128999710083008,"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":0.9128999710083008,"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/T10158","display_name":"Cancer Immunotherapy and Biomarkers","score":0.033900000154972076,"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"}},{"id":"https://openalex.org/T10580","display_name":"Immunotherapy and Immune Responses","score":0.029100000858306885,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/immunogenicity","display_name":"Immunogenicity","score":0.7387697696685791},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6304121017456055},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6261491775512695},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6022820472717285},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5739452242851257},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4538215398788452},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.41595539450645447},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.2930361032485962},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2584434747695923},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2434404194355011},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.15045461058616638},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.1337129771709442},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.13119319081306458},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1294618546962738}],"concepts":[{"id":"https://openalex.org/C2780868878","wikidata":"https://www.wikidata.org/wiki/Q1660197","display_name":"Immunogenicity","level":3,"score":0.7387697696685791},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6304121017456055},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6261491775512695},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6022820472717285},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5739452242851257},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4538215398788452},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.41595539450645447},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.2930361032485962},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2584434747695923},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2434404194355011},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.15045461058616638},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.1337129771709442},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.13119319081306458},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1294618546962738}],"mesh":[{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab759","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab759","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":"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:34788790","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34788790","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:8796378","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8796378","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab759","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab759","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":"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":0.4300000071525574,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G5197713679","display_name":null,"funder_award_id":"18496","funder_id":"https://openalex.org/F4320322325","funder_display_name":"Oesterreichische Nationalbank"}],"funders":[{"id":"https://openalex.org/F4320322325","display_name":"Oesterreichische Nationalbank","ror":"https://ror.org/00nkcmy90"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W2089041106","https://openalex.org/W2150056019","https://openalex.org/W2605820408","https://openalex.org/W2605897695","https://openalex.org/W2938148515","https://openalex.org/W2953065444","https://openalex.org/W2972438906","https://openalex.org/W2990636420","https://openalex.org/W2998313390","https://openalex.org/W3042910002","https://openalex.org/W3088005314","https://openalex.org/W3091991776","https://openalex.org/W4254055122"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W1581415616","https://openalex.org/W1552738310","https://openalex.org/W4250292386","https://openalex.org/W2030908446","https://openalex.org/W2470318958","https://openalex.org/W2428121789","https://openalex.org/W4205567707","https://openalex.org/W3042894437","https://openalex.org/W2403806215"],"abstract_inverted_index":{"SUMMARY:":[0],"Somatic":[1],"mutations":[2],"and":[3,39,64,76,85,92,102],"gene":[4],"fusions":[5],"can":[6],"produce":[7],"immunogenic":[8],"neoantigens":[9,72],"mediating":[10],"anticancer":[11],"immune":[12],"responses.":[13],"However,":[14],"their":[15,52],"computational":[16,23],"prediction":[17,60],"from":[18,73],"sequencing":[19,78],"data":[20,115],"requires":[21],"complex":[22],"workflows":[24],"to":[25,43,69,94],"identify":[26],"tumor-specific":[27],"aberrations,":[28],"derive":[29],"the":[30],"resulting":[31],"peptides,":[32],"infer":[33],"patients'":[34],"Human":[35],"Leukocyte":[36],"Antigen":[37],"types":[38],"predict":[40,70],"neoepitopes":[41],"binding":[42],"them,":[44],"together":[45],"with":[46,89],"a":[47,62],"set":[48],"of":[49],"features":[50,87],"underlying":[51],"immunogenicity.":[53],"Here,":[54],"we":[55],"present":[56],"nextNEOpi":[57,82,99],"(nextflow":[58],"NEOantigen":[59],"pipeline)":[61],"comprehensive":[63],"fully":[65],"automated":[66],"bioinformatic":[67],"pipeline":[68],"tumor":[71,90],"raw":[74],"DNA":[75],"RNA":[77],"data.":[79],"In":[80],"addition,":[81],"quantifies":[83],"neoepitope-":[84],"patient-specific":[86],"associated":[88],"immunogenicity":[91],"response":[93],"immunotherapy.":[95],"AVAILABILITY":[96],"AND":[97],"IMPLEMENTATION:":[98],"source":[100],"code":[101],"documentation":[103],"are":[104,116],"available":[105,117],"at":[106,118],"https://github.com/icbi-lab/nextNEOpi.":[107],"CONTACT:":[108],"dietmar.rieder@i-med.ac.at":[109],"or":[110],"francesca.finotello@uibk.ac.at.":[111],"SUPPLEMENTARY":[112],"INFORMATION:":[113],"Supplementary":[114],"Bioinformatics":[119],"online.":[120]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
