{"id":"https://openalex.org/W4376618342","doi":"https://doi.org/10.1093/bioinformatics/btad322","title":"LENS: Landscape of Effective Neoantigens Software","display_name":"LENS: Landscape of Effective Neoantigens Software","publication_year":2023,"publication_date":"2023-05-01","ids":{"openalex":"https://openalex.org/W4376618342","doi":"https://doi.org/10.1093/bioinformatics/btad322","pmid":"https://pubmed.ncbi.nlm.nih.gov/37184881"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad322","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad322","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad322/50329709/btad322.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/btad322/50329709/btad322.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071255263","display_name":"Steven Vensko","orcid":"https://orcid.org/0000-0001-9399-5999"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]},{"id":"https://openalex.org/I4390039329","display_name":"UNC Lineberger Comprehensive Cancer Center","ror":"https://ror.org/043ehm030","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I114027177","https://openalex.org/I4390039329"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Steven P Vensko","raw_affiliation_strings":["Lineberger Comprehensive Cancer Center, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"],"raw_orcid":"https://orcid.org/0000-0001-9399-5999","affiliations":[{"raw_affiliation_string":"Lineberger Comprehensive Cancer Center, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States","institution_ids":["https://openalex.org/I114027177","https://openalex.org/I4390039329"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077507722","display_name":"Kelly Olsen","orcid":"https://orcid.org/0000-0001-7215-7654"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kelly Olsen","raw_affiliation_strings":["Department of Microbiology and Immunology, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Immunology, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071654126","display_name":"Dante S. Bortone","orcid":"https://orcid.org/0000-0002-3215-5440"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]},{"id":"https://openalex.org/I4390039329","display_name":"UNC Lineberger Comprehensive Cancer Center","ror":"https://ror.org/043ehm030","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I114027177","https://openalex.org/I4390039329"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dante Bortone","raw_affiliation_strings":["Lineberger Comprehensive Cancer Center, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lineberger Comprehensive Cancer Center, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States","institution_ids":["https://openalex.org/I114027177","https://openalex.org/I4390039329"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069323471","display_name":"Christof C. Smith","orcid":"https://orcid.org/0000-0001-6517-0439"},"institutions":[{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christof C Smith","raw_affiliation_strings":["Department of Medicine, Brigham and Women\u2019s Hospital , Boston, MA, United States"],"raw_orcid":"https://orcid.org/0000-0001-6517-0439","affiliations":[{"raw_affiliation_string":"Department of Medicine, Brigham and Women\u2019s Hospital , Boston, MA, United States","institution_ids":["https://openalex.org/I1283280774"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068320484","display_name":"Shengjie Chai","orcid":"https://orcid.org/0000-0002-6445-9457"},"institutions":[{"id":"https://openalex.org/I2946016260","display_name":"Uber AI (United States)","ror":"https://ror.org/05vm0ed18","country_code":"US","type":"company","lineage":["https://openalex.org/I2946016260"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shengjie Chai","raw_affiliation_strings":["Uber Technologies, Inc. , San Francisco, CA, United States"],"raw_orcid":"https://orcid.org/0000-0002-6445-9457","affiliations":[{"raw_affiliation_string":"Uber Technologies, Inc. , San Francisco, CA, United States","institution_ids":["https://openalex.org/I2946016260"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052618311","display_name":"Wolfgang Beckabir","orcid":"https://orcid.org/0000-0001-7458-7033"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wolfgang Beckabir","raw_affiliation_strings":["Department of Microbiology and Immunology, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Immunology, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035625682","display_name":"Misha Fini","orcid":"https://orcid.org/0000-0002-3063-6064"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Misha Fini","raw_affiliation_strings":["Department of Microbiology and Immunology, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Immunology, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036590638","display_name":"Othmane Jadi","orcid":"https://orcid.org/0000-0002-2675-1916"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]},{"id":"https://openalex.org/I4390039329","display_name":"UNC Lineberger Comprehensive Cancer Center","ror":"https://ror.org/043ehm030","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I114027177","https://openalex.org/I4390039329"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Othmane Jadi","raw_affiliation_strings":["Lineberger Comprehensive Cancer Center, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lineberger Comprehensive Cancer Center, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States","institution_ids":["https://openalex.org/I114027177","https://openalex.org/I4390039329"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074035362","display_name":"Alex Rubinsteyn","orcid":"https://orcid.org/0000-0003-2839-2870"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alex Rubinsteyn","raw_affiliation_strings":["Computational Medicine Program, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States","Curriculum in Bioinformatics and Computational Biology, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States","Department of Genetics, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Medicine Program, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Curriculum in Bioinformatics and Computational Biology, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Department of Genetics, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020894945","display_name":"Benjamin G. Vincent","orcid":"https://orcid.org/0000-0002-1762-2282"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]},{"id":"https://openalex.org/I4390039329","display_name":"UNC Lineberger Comprehensive Cancer Center","ror":"https://ror.org/043ehm030","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I114027177","https://openalex.org/I4390039329"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Benjamin G Vincent","raw_affiliation_strings":["Computational Medicine Program, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States","Curriculum in Bioinformatics and Computational Biology, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States","Department of Microbiology and Immunology, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States","Division of Hematology, Department of Medicine, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States","Lineberger Comprehensive Cancer Center, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Medicine Program, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Curriculum in Bioinformatics and Computational Biology, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Department of Microbiology and Immunology, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Division of Hematology, Department of Medicine, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Lineberger Comprehensive Cancer Center, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States","institution_ids":["https://openalex.org/I114027177","https://openalex.org/I4390039329"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5020894945","https://openalex.org/A5036590638","https://openalex.org/A5071255263"],"corresponding_institution_ids":["https://openalex.org/I114027177","https://openalex.org/I4390039329"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.6163,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.89896692,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"39","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9941999912261963,"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":0.9941999912261963,"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/T10580","display_name":"Immunotherapy and Immune Responses","score":0.0032999999821186066,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.00039999998989515007,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"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/epitope","display_name":"Epitope","score":0.8104002475738525},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6098275780677795},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5320906043052673},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.529664933681488},{"id":"https://openalex.org/keywords/cancer-immunotherapy","display_name":"Cancer immunotherapy","score":0.41290947794914246},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.35016655921936035},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.28986087441444397},{"id":"https://openalex.org/keywords/immunotherapy","display_name":"Immunotherapy","score":0.27221232652664185}],"concepts":[{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.8104002475738525},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6098275780677795},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5320906043052673},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.529664933681488},{"id":"https://openalex.org/C2780674031","wikidata":"https://www.wikidata.org/wiki/Q2012719","display_name":"Cancer immunotherapy","level":4,"score":0.41290947794914246},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.35016655921936035},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.28986087441444397},{"id":"https://openalex.org/C2777701055","wikidata":"https://www.wikidata.org/wiki/Q1427096","display_name":"Immunotherapy","level":3,"score":0.27221232652664185}],"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":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad322","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad322","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad322/50329709/btad322.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:37184881","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37184881","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:10246587","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10246587","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10246587/pdf/btad322.pdf","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/btad322","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad322","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad322/50329709/btad322.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/G3398986676","display_name":null,"funder_award_id":"1F30CA268748","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7701681286","display_name":null,"funder_award_id":"R37 CA247676","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G8148934282","display_name":null,"funder_award_id":"F30 CA268748","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4376618342.pdf"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W1602627378","https://openalex.org/W2000336618","https://openalex.org/W2007026865","https://openalex.org/W2072047081","https://openalex.org/W2098357256","https://openalex.org/W2114104545","https://openalex.org/W2119180969","https://openalex.org/W2134121541","https://openalex.org/W2171892226","https://openalex.org/W2276333078","https://openalex.org/W2408851413","https://openalex.org/W2471645096","https://openalex.org/W2562592234","https://openalex.org/W2567441703","https://openalex.org/W2605219687","https://openalex.org/W2605808699","https://openalex.org/W2605897695","https://openalex.org/W2606588635","https://openalex.org/W2724264513","https://openalex.org/W2728365508","https://openalex.org/W2801185119","https://openalex.org/W2867868648","https://openalex.org/W2888593931","https://openalex.org/W2891169704","https://openalex.org/W2892300772","https://openalex.org/W2897615585","https://openalex.org/W2909021353","https://openalex.org/W2938148515","https://openalex.org/W2953065444","https://openalex.org/W2954615294","https://openalex.org/W2964569119","https://openalex.org/W2972612455","https://openalex.org/W2979330780","https://openalex.org/W2980759299","https://openalex.org/W2998313390","https://openalex.org/W3004279987","https://openalex.org/W3088005314","https://openalex.org/W3091991776","https://openalex.org/W3111170609","https://openalex.org/W3122472315","https://openalex.org/W3132948359","https://openalex.org/W3135148976","https://openalex.org/W3157007328","https://openalex.org/W3165500155","https://openalex.org/W3183254943","https://openalex.org/W3184105584","https://openalex.org/W3212743825","https://openalex.org/W4210297691","https://openalex.org/W4210348552","https://openalex.org/W4226063992","https://openalex.org/W4285192462","https://openalex.org/W6694647680","https://openalex.org/W6754829260","https://openalex.org/W6755601280","https://openalex.org/W6790047902"],"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/W2205639271"],"abstract_inverted_index":{"MOTIVATION:":[0],"Elimination":[1],"of":[2,12,26,67,107,140,148,151,164,168,183,193],"cancer":[3,16,22,41],"cells":[4,7,20,23],"by":[5,24,34,54],"T":[6,19,27,206],"is":[8,142],"a":[9,82,200],"critical":[10],"mechanism":[11],"anti-tumor":[13],"immunity":[14],"and":[15,69,115,123,134,166,172,203,240],"immunotherapy":[17],"response.":[18],"recognize":[21],"engagement":[25],"cell":[28,42,207],"receptors":[29],"with":[30,214],"peptide":[31],"epitopes":[32,45,64,76,220],"presented":[33],"major":[35],"histocompatibility":[36],"complex":[37],"molecules":[38],"on":[39,75],"the":[40,101,146,191],"surface.":[43],"Peptide":[44],"can":[46,242],"be":[47,199,243],"derived":[48,77],"from":[49,78,89,118,221],"antigen":[50],"proteins":[51],"coded":[52],"for":[53,205],"multiple":[55,176],"genomic":[56,91,149,177,223],"sources.":[57,92,178],"Bioinformatics":[58],"tools":[59],"used":[60],"to":[61,189],"identify":[62],"tumor-specific":[63,114,219],"via":[65],"analysis":[66,182],"DNA":[68],"RNA-sequencing":[70],"data":[71],"have":[72,85],"largely":[73],"focused":[74],"somatic":[79,216],"variants,":[80,121,128],"though":[81],"smaller":[83],"number":[84],"evaluated":[86],"potential":[87],"antigens":[88,117,154],"other":[90],"RESULTS:":[93],"We":[94,179,195],"report":[95],"here":[96],"an":[97,181,226],"open-source":[98],"workflow":[99,104,238],"utilizing":[100],"Nextflow":[102],"DSL2":[103],"manager,":[105],"Landscape":[106],"Effective":[108],"Neoantigens":[109],"Software":[110],"(LENS),":[111],"which":[112],"predicts":[113],"tumor-associated":[116],"single":[119],"nucleotide":[120],"insertions":[122],"deletions,":[124],"fusion":[125],"events,":[126],"splice":[127],"cancer-testis":[129],"antigens,":[130],"overexpressed":[131],"self-antigens,":[132],"viruses,":[133],"endogenous":[135],"retroviruses.":[136],"The":[137],"primary":[138],"advantage":[139],"LENS":[141,197],"that":[143],"it":[144],"expands":[145],"breadth":[147],"sources":[150,224],"discoverable":[152],"tumor":[153],"using":[155],"genomics":[156],"data.":[157],"Other":[158],"advantages":[159],"include":[160],"modularity,":[161],"extensibility,":[162],"ease":[163],"use,":[165],"harmonization":[167],"relative":[169],"expression":[170],"level":[171],"immunogenicity":[173],"prediction":[174],"across":[175],"present":[180],"115":[184],"acute":[185],"myeloid":[186],"leukemia":[187],"samples":[188],"demonstrate":[190],"utility":[192],"LENS.":[194],"expect":[196],"will":[198],"valuable":[201],"platform":[202],"resource":[204],"epitope":[208],"discovery":[209],"bioinformatics,":[210],"especially":[211],"in":[212],"cancers":[213],"few":[215],"variants":[217],"where":[218],"alternative":[222],"are":[225],"elevated":[227],"priority.":[228],"AVAILABILITY":[229],"AND":[230],"IMPLEMENTATION:":[231],"More":[232],"information":[233],"about":[234],"LENS,":[235],"including":[236],"code,":[237],"documentation,":[239],"instructions,":[241],"found":[244],"at":[245],"(https://gitlab.com/landscape-of-effective-neoantigens-software).":[246]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-01T08:55:40.977307","created_date":"2025-10-10T00:00:00"}
