{"id":"https://openalex.org/W4410028126","doi":"https://doi.org/10.1093/bioinformatics/btaf138","title":"Detecting known neoepitopes, gene fusions, transposable elements, and circular RNAs in cell-free RNA","display_name":"Detecting known neoepitopes, gene fusions, transposable elements, and circular RNAs in cell-free RNA","publication_year":2025,"publication_date":"2025-04-30","ids":{"openalex":"https://openalex.org/W4410028126","doi":"https://doi.org/10.1093/bioinformatics/btaf138","pmid":"https://pubmed.ncbi.nlm.nih.gov/40315130"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf138","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf138","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf138/63045437/btaf138.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/btaf138/63045437/btaf138.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016662682","display_name":"Mayank Mahajan","orcid":"https://orcid.org/0000-0001-6548-5756"},"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"]},{"id":"https://openalex.org/I4210087915","display_name":"Massachusetts General Hospital","ror":"https://ror.org/002pd6e78","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087915","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mayank Mahajan","raw_affiliation_strings":["Gene Lay Institute of Immunology and Inflammation, Brigham and Women\u2019s Hospital, Massachusetts General Hospital and Harvard Medical School , Boston, MA 02115,","Massachusetts General Hospital, and Harvard Medical School Gene Lay Institute of Immunology and Inflammation, Brigham and Women\u2019s Hospital, , Boston, MA 02115,"],"affiliations":[{"raw_affiliation_string":"Gene Lay Institute of Immunology and Inflammation, Brigham and Women\u2019s Hospital, Massachusetts General Hospital and Harvard Medical School , Boston, MA 02115,","institution_ids":["https://openalex.org/I1283280774"]},{"raw_affiliation_string":"Massachusetts General Hospital, and Harvard Medical School Gene Lay Institute of Immunology and Inflammation, Brigham and Women\u2019s Hospital, , Boston, MA 02115,","institution_ids":["https://openalex.org/I1283280774","https://openalex.org/I136199984","https://openalex.org/I4210087915"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022843288","display_name":"Martin Hemberg","orcid":"https://orcid.org/0000-0001-8895-5239"},"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"]},{"id":"https://openalex.org/I4210087915","display_name":"Massachusetts General Hospital","ror":"https://ror.org/002pd6e78","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087915","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Martin Hemberg","raw_affiliation_strings":["Gene Lay Institute of Immunology and Inflammation, Brigham and Women\u2019s Hospital, Massachusetts General Hospital and Harvard Medical School , Boston, MA 02115,","Massachusetts General Hospital, and Harvard Medical School Gene Lay Institute of Immunology and Inflammation, Brigham and Women\u2019s Hospital, , Boston, MA 02115,"],"affiliations":[{"raw_affiliation_string":"Gene Lay Institute of Immunology and Inflammation, Brigham and Women\u2019s Hospital, Massachusetts General Hospital and Harvard Medical School , Boston, MA 02115,","institution_ids":["https://openalex.org/I1283280774"]},{"raw_affiliation_string":"Massachusetts General Hospital, and Harvard Medical School Gene Lay Institute of Immunology and Inflammation, Brigham and Women\u2019s Hospital, , Boston, MA 02115,","institution_ids":["https://openalex.org/I1283280774","https://openalex.org/I136199984","https://openalex.org/I4210087915"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5016662682"],"corresponding_institution_ids":["https://openalex.org/I1283280774","https://openalex.org/I136199984","https://openalex.org/I4210087915"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.9784,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.75108131,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"41","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11482","display_name":"RNA modifications and cancer","score":0.996999979019165,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9969000220298767,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5239477157592773},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5007762908935547},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.4616692364215851},{"id":"https://openalex.org/keywords/colorectal-cancer","display_name":"Colorectal cancer","score":0.4609636962413788},{"id":"https://openalex.org/keywords/cell-free-fetal-dna","display_name":"Cell-free fetal DNA","score":0.4561772048473358},{"id":"https://openalex.org/keywords/causes-of-cancer","display_name":"Causes of cancer","score":0.4259818196296692},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4113650918006897},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.407986044883728},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3202723264694214},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20297974348068237}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5239477157592773},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5007762908935547},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.4616692364215851},{"id":"https://openalex.org/C526805850","wikidata":"https://www.wikidata.org/wiki/Q188874","display_name":"Colorectal cancer","level":3,"score":0.4609636962413788},{"id":"https://openalex.org/C152110520","wikidata":"https://www.wikidata.org/wiki/Q14225730","display_name":"Cell-free fetal DNA","level":5,"score":0.4561772048473358},{"id":"https://openalex.org/C2777914349","wikidata":"https://www.wikidata.org/wiki/Q18205885","display_name":"Causes of cancer","level":3,"score":0.4259818196296692},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4113650918006897},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.407986044883728},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3202723264694214},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20297974348068237},{"id":"https://openalex.org/C172680121","wikidata":"https://www.wikidata.org/wiki/Q26513","display_name":"Fetus","level":3,"score":0.0},{"id":"https://openalex.org/C2778258057","wikidata":"https://www.wikidata.org/wiki/Q1136569","display_name":"Prenatal diagnosis","level":4,"score":0.0},{"id":"https://openalex.org/C2779234561","wikidata":"https://www.wikidata.org/wiki/Q11995","display_name":"Pregnancy","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000073888","descriptor_name":"Cell-Free Nucleic Acids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000073888","descriptor_name":"Cell-Free Nucleic Acids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000073888","descriptor_name":"Cell-Free Nucleic Acids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000073888","descriptor_name":"Cell-Free Nucleic Acids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000073888","descriptor_name":"Cell-Free Nucleic Acids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000073888","descriptor_name":"Cell-Free Nucleic Acids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006528","descriptor_name":"Carcinoma, Hepatocellular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006528","descriptor_name":"Carcinoma, Hepatocellular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006528","descriptor_name":"Carcinoma, Hepatocellular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006528","descriptor_name":"Carcinoma, Hepatocellular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006528","descriptor_name":"Carcinoma, Hepatocellular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006528","descriptor_name":"Carcinoma, Hepatocellular","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":"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":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf138","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf138","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf138/63045437/btaf138.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:40315130","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40315130","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:12057812","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12057812","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/btaf138","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf138","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf138/63045437/btaf138.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":[{"score":0.8199999928474426,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410028126.pdf","grobid_xml":"https://content.openalex.org/works/W4410028126.grobid-xml"},"referenced_works_count":63,"referenced_works":["https://openalex.org/W1846631206","https://openalex.org/W1964807436","https://openalex.org/W1987264710","https://openalex.org/W1994547803","https://openalex.org/W2024947462","https://openalex.org/W2047285578","https://openalex.org/W2051615060","https://openalex.org/W2053343049","https://openalex.org/W2058835062","https://openalex.org/W2096064375","https://openalex.org/W2102172636","https://openalex.org/W2119180969","https://openalex.org/W2146146418","https://openalex.org/W2150131459","https://openalex.org/W2169456326","https://openalex.org/W2170551349","https://openalex.org/W2275486737","https://openalex.org/W2417483443","https://openalex.org/W2728365508","https://openalex.org/W2782116692","https://openalex.org/W2796292093","https://openalex.org/W2890085191","https://openalex.org/W2898389621","https://openalex.org/W2899311685","https://openalex.org/W2912017471","https://openalex.org/W2920848372","https://openalex.org/W2922870792","https://openalex.org/W2937238238","https://openalex.org/W2945153532","https://openalex.org/W2947989913","https://openalex.org/W2953065444","https://openalex.org/W2980759299","https://openalex.org/W2990636420","https://openalex.org/W2996796392","https://openalex.org/W3007378084","https://openalex.org/W3013833426","https://openalex.org/W3016853422","https://openalex.org/W3080815742","https://openalex.org/W3092076936","https://openalex.org/W3115898451","https://openalex.org/W3128858085","https://openalex.org/W3131055609","https://openalex.org/W3155038581","https://openalex.org/W3193943505","https://openalex.org/W3194757681","https://openalex.org/W4210348552","https://openalex.org/W4211216305","https://openalex.org/W4224865986","https://openalex.org/W4225883667","https://openalex.org/W4285032110","https://openalex.org/W4290546253","https://openalex.org/W4306406766","https://openalex.org/W4315628887","https://openalex.org/W4319763359","https://openalex.org/W4377965350","https://openalex.org/W4386324896","https://openalex.org/W4387865673","https://openalex.org/W4389367121","https://openalex.org/W4391818889","https://openalex.org/W4406494847","https://openalex.org/W6694635588","https://openalex.org/W6770221991","https://openalex.org/W6770471582"],"related_works":["https://openalex.org/W3012252867","https://openalex.org/W2104784390","https://openalex.org/W3000665244","https://openalex.org/W3082476907","https://openalex.org/W2040142885","https://openalex.org/W3039284339","https://openalex.org/W3122383771","https://openalex.org/W2406927386","https://openalex.org/W2910396248","https://openalex.org/W2025194427"],"abstract_inverted_index":{"The":[0,9],"FastNeo":[1,30],"package":[2],"is":[3],"available":[4,38],"at":[5],"https://github.com/yashumayank/FastNeo":[6],"and":[7,17,25,27],"https://zenodo.org/records/11521368.":[8],"benchmark":[10],"pipelines":[11],"to":[12,28],"detect":[13],"Immune":[14],"Epitope":[15],"database":[16,20],"Tumor-Specific":[18],"Neoantigen":[19],"neoepitopes":[21],"using":[22],"HaplotypeCaller,":[23],"bcftools,":[24],"Lofreq,":[26],"run":[29],"with":[31],"STAR":[32],"instead":[33],"of":[34],"Bowtie2":[35],"are":[36],"also":[37],"in":[39],"the":[40],"above":[41],"github":[42],"repository.":[43]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
