{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,25]],"date-time":"2026-10-25T06:16:51Z","timestamp":1792909011890,"version":"4.5.0"},"reference-count":125,"publisher":"Elsevier BV","issue":"2","license":[{"start":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T00:00:00Z","timestamp":1769904000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T00:00:00Z","timestamp":1769904000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T00:00:00Z","timestamp":1765929600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100029374","name":"United Steelworkers","doi-asserted-by":"publisher","award":["States"],"award-info":[{"award-number":["States"]}],"id":[{"id":"10.13039\/100029374","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015751","name":"CQDM","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100015751","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"NSERC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005445","name":"National Science Foundation Division of Grants and Agreements","doi-asserted-by":"publisher","award":["U24 CA248138"],"award-info":[{"award-number":["U24 CA248138"]}],"id":[{"id":"10.13039\/100005445","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100019683","name":"Cole Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100019683","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100022706","name":"Cole Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100022706","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100023447","name":"CHU Sainte-Justine Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100023447","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000156","name":"Health Research Funds of Quebec","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000156","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000196","name":"Fondation canadienne pour l'innovation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000196","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008762","name":"Genome Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008762","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100016067","name":"Charles-Bruneau Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100016067","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["174924"],"award-info":[{"award-number":["174924"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["172712"],"award-info":[{"award-number":["172712"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["iScience"],"published-print":{"date-parts":[[2026,2]]},"DOI":"10.1016\/j.isci.2025.114512","type":"journal-article","created":{"date-parts":[[2025,12,24]],"date-time":"2025-12-24T08:14:53Z","timestamp":1766564093000},"page":"114512","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":1,"title":["The GF-NEO discovery platform unveils a [KQE][DG] sequence motif within fusion neoantigens in pediatric cancer"],"prefix":"10.1016","volume":"29","author":[{"given":"Christopher","family":"Savoie","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhaoguan","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frederic","family":"Saab","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tristan","family":"St-Laurent","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lou Nielly","family":"Thibault","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles B.","family":"Beauparlant","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc-Andr\u00e9","family":"D\u00e9ry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nehme","family":"El-Hachem","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bayrem","family":"Gharsallaoui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel-Joseph","family":"Tremblay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Sabouret","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nadia Emely","family":"Chauca Torres","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M\u00e9lanie","family":"Bilodeau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u00c9ric","family":"Bonneil","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Sidney","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alessandro","family":"Sette","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arnaud","family":"Droit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierre","family":"Thibault","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sonia","family":"Cellot","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u00c9tienne","family":"Caron","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6929-1761","authenticated-orcid":false,"given":"Isabelle","family":"Sirois","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.isci.2025.114512_bib1","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1038\/nrc2091","article-title":"The impact of translocations and gene fusions on cancer causation","volume":"7","author":"Mitelman","year":"2007","journal-title":"Nat. Rev. Cancer"},{"key":"10.1016\/j.isci.2025.114512_bib2","doi-asserted-by":"crossref","first-page":"1315","DOI":"10.1002\/cncr.32649","article-title":"Targeting fusions for improved outcomes in oncology treatment","volume":"126","author":"Nikanjam","year":"2020","journal-title":"Cancer"},{"key":"10.1016\/j.isci.2025.114512_bib3","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1158\/1078-0432.CCR-22-1851","article-title":"Oncogenic Addiction of Fibrolamellar Hepatocellular Carcinoma to the Fusion Kinase DNAJB1-PRKACA","volume":"29","author":"Neumayer","year":"2023","journal-title":"Clin. Cancer Res."},{"key":"10.1016\/j.isci.2025.114512_bib4","doi-asserted-by":"crossref","first-page":"6604","DOI":"10.1038\/ncomms7604","article-title":"Rise and fall of subclones from diagnosis to relapse in pediatric B-acute lymphoblastic leukaemia","volume":"6","author":"Ma","year":"2015","journal-title":"Nat. Commun."},{"key":"10.1016\/j.isci.2025.114512_bib5","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1038\/nrc3947","article-title":"The emerging complexity of gene fusions in cancer","volume":"15","author":"Mertens","year":"2015","journal-title":"Nat. Rev. Cancer"},{"key":"10.1016\/j.isci.2025.114512_bib6","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.1056\/NEJM200104053441401","article-title":"Efficacy and Safety of a Specific Inhibitor of the BCR-ABL Tyrosine Kinase in Chronic Myeloid Leukemia","volume":"344","author":"Druker","year":"2001","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.isci.2025.114512_bib7","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1056\/NEJMoa1714448","article-title":"Efficacy of Larotrectinib in TRK Fusion-Positive Cancers in Adults and Children","volume":"378","author":"Drilon","year":"2018","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.isci.2025.114512_bib8","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1038\/s41586-023-05812-3","article-title":"The menin inhibitor revumenib in KMT2A-rearranged or NPM1-mutant leukaemia","volume":"615","author":"Issa","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.isci.2025.114512_bib9","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1007\/s10555-019-09839-9","article-title":"Targeting the undruggable: exploiting neomorphic features of fusion oncoproteins in childhood sarcomas for innovative therapies","volume":"38","author":"Knott","year":"2019","journal-title":"Cancer Metastasis Rev."},{"key":"10.1016\/j.isci.2025.114512_bib10","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/j.celrep.2018.03.050","article-title":"Driver Fusions and Their Implications in the Development and Treatment of Human Cancers","volume":"23","author":"Gao","year":"2018","journal-title":"Cell Rep."},{"key":"10.1016\/j.isci.2025.114512_bib11","article-title":"DNAJB1-PRKACA fusion neoantigens elicit rare endogenous T cell responses that potentiate cell therapy for fibrolamellar carcinoma","volume":"5","author":"Kirk","year":"2024","journal-title":"Cell Rep. Med."},{"key":"10.1016\/j.isci.2025.114512_bib12","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1007\/s40272-018-0297-x","article-title":"Pediatric Cancer Immunotherapy: Opportunities and Challenges","volume":"20","author":"Wedekind","year":"2018","journal-title":"Paediatr. Drugs"},{"key":"10.1016\/j.isci.2025.114512_bib13","doi-asserted-by":"crossref","first-page":"4845","DOI":"10.1038\/onc.2014.406","article-title":"The landscape and therapeutic relevance of cancer-associated transcript fusions","volume":"34","author":"Yoshihara","year":"2015","journal-title":"Oncogene"},{"key":"10.1016\/j.isci.2025.114512_bib14","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.aat8549","article-title":"Pediatric patients with acute lymphoblastic leukemia generate abundant and functional neoantigen-specific CD8+ T cell responses","volume":"11","author":"Zamora","year":"2019","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.isci.2025.114512_bib15","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1182\/blood-2010-12-325035","article-title":"The only proposed T-cell epitope derived from the TEL-AML1 translocation is not naturally processed","volume":"118","author":"Popovi\u0107","year":"2011","journal-title":"Blood"},{"key":"10.1016\/j.isci.2025.114512_bib16","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/j.canlet.2021.02.023","article-title":"Gene fusion neoantigens: Emerging targets for cancer immunotherapy","volume":"506","author":"Wang","year":"2021","journal-title":"Cancer Lett."},{"key":"10.1016\/j.isci.2025.114512_bib17","doi-asserted-by":"crossref","first-page":"6401","DOI":"10.1038\/s41467-022-33746-3","article-title":"The oncogenic fusion protein DNAJB1-PRKACA can be specifically targeted by peptide-based immunotherapy in fibrolamellar hepatocellular carcinoma","volume":"13","author":"Bauer","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.isci.2025.114512_bib18","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1016\/j.isci.2019.10.028","article-title":"The Landscape of Tumor Fusion Neoantigens: A Pan-Cancer Analysis","volume":"21","author":"Wei","year":"2019","journal-title":"iScience"},{"key":"10.1016\/j.isci.2025.114512_bib19","doi-asserted-by":"crossref","first-page":"5127","DOI":"10.1172\/JCI137723","article-title":"CBFB-MYH11 fusion neoantigen enables T cell recognition and killing of acute myeloid leukemia","volume":"130","author":"Biernacki","year":"2020","journal-title":"J. Clin. Investig."},{"key":"10.1016\/j.isci.2025.114512_bib20","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1038\/s41591-019-0434-2","article-title":"Immunogenic neoantigens derived from gene fusions stimulate T cell responses","volume":"25","author":"Yang","year":"2019","journal-title":"Nat. Med."},{"key":"10.1016\/j.isci.2025.114512_bib21","doi-asserted-by":"crossref","first-page":"1369","DOI":"10.1182\/blood.V81.5.1369.1369","article-title":"Human CD4 lymphocytes specifically recognize a peptide representing the fusion region of the hybrid protein pml\/RAR alpha present in acute promyelocytic leukemia cells","volume":"81","author":"Gambacorti-Passerini","year":"1993","journal-title":"Blood"},{"key":"10.1016\/j.isci.2025.114512_bib22","doi-asserted-by":"crossref","first-page":"1738","DOI":"10.1038\/sj.leu.2404354","article-title":"BCR-ABL fusion regions as a source of multiple leukemia-specific CD8+ T-cell epitopes","volume":"20","author":"Kessler","year":"2006","journal-title":"Leukemia"},{"key":"10.1016\/j.isci.2025.114512_bib23","doi-asserted-by":"crossref","first-page":"2400","DOI":"10.1038\/sj.leu.2402742","article-title":"Leukemia-associated fusion proteins, dek-can and bcr-abl, represent immunogenic HLA-DR-restricted epitopes recognized by fusion peptide-specific CD4+ T lymphocytes","volume":"16","author":"Makita","year":"2002","journal-title":"Leukemia"},{"key":"10.1016\/j.isci.2025.114512_bib24","doi-asserted-by":"crossref","first-page":"1818","DOI":"10.1158\/0008-5472.CAN-05-2549","article-title":"Identification and Epitope Enhancement of a PAX-FKHR Fusion Protein Breakpoint Epitope in Alveolar Rhabdomyosarcoma Cells Created by a Tumorigenic Chromosomal Translocation Inducing CTL Capable of Lysing Human Tumors","volume":"66","author":"van den Broeke","year":"2006","journal-title":"Cancer Res."},{"key":"10.1016\/j.isci.2025.114512_bib25","doi-asserted-by":"crossref","first-page":"1611","DOI":"10.4049\/jimmunol.169.3.1611","article-title":"Detection and Induction of CTLs Specific for SYT-SSX-Derived Peptides in HLA-A24+ Patients with Synovial Sarcoma1","volume":"169","author":"Sato","year":"2002","journal-title":"J. Immunol."},{"key":"10.1016\/j.isci.2025.114512_bib26","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1016\/j.cels.2019.08.009","article-title":"Neoantigen Dissimilarity to the Self-Proteome Predicts Immunogenicity and Response to Immune Checkpoint Blockade","volume":"9","author":"Richman","year":"2019","journal-title":"Cell Syst."},{"key":"10.1016\/j.isci.2025.114512_bib27","doi-asserted-by":"crossref","DOI":"10.3390\/cancers11070983","article-title":"Uncovering Potential Therapeutic Targets in Colorectal Cancer by Deciphering Mutational Status and Expression of Druggable Oncogenes","volume":"11","author":"Menyhart","year":"2019","journal-title":"Cancers"},{"key":"10.1016\/j.isci.2025.114512_bib28","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1182\/blood-2013-03-490565","article-title":"Cardiovascular toxicity and titin cross-reactivity of affinity-enhanced T cells in myeloma and melanoma","volume":"122","author":"Linette","year":"2013","journal-title":"Blood"},{"key":"10.1016\/j.isci.2025.114512_bib29","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1097\/CJI.0b013e3182829903","article-title":"Cancer Regression and Neurological Toxicity Following Anti-MAGE-A3 TCR Gene Therapy","volume":"36","author":"Morgan","year":"2013","journal-title":"J. Immunother."},{"key":"10.1016\/j.isci.2025.114512_bib30","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1186\/s13045-017-0515-y","article-title":"Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles","volume":"10","author":"Marincevic-Zuniga","year":"2017","journal-title":"J. Hematol. Oncol."},{"key":"10.1016\/j.isci.2025.114512_bib31","doi-asserted-by":"crossref","first-page":"6389","DOI":"10.1038\/s41467-023-42010-1","article-title":"KRAS G12V neoantigen specific T cell receptor for adoptive T cell therapy against tumors","volume":"14","author":"Lu","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.isci.2025.114512_bib32","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1038\/nature22991","article-title":"An immunogenic personal neoantigen vaccine for patients with melanoma","volume":"547","author":"Ott","year":"2017","journal-title":"Nature"},{"key":"10.1016\/j.isci.2025.114512_bib33","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1038\/s41586-023-06063-y","article-title":"Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer","volume":"618","author":"Rojas","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.isci.2025.114512_bib34","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1186\/s13045-019-0812-8","article-title":"Targeting cancers through TCR-peptide\/MHC interactions","volume":"12","author":"He","year":"2019","journal-title":"J. Hematol. Oncol."},{"key":"10.1016\/j.isci.2025.114512_bib35","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1038\/s41586-023-06706-0","article-title":"Targeting of intracellular oncoproteins with peptide-centric CARs","volume":"623","author":"Yarmarkovich","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.isci.2025.114512_bib36","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1097\/01.COT.0000265629.30194.8e","article-title":"Chronic Health Conditions in Adult Survivors of Childhood Cancer","volume":"29","author":"Oeffinger","year":"2007","journal-title":"Oncol. Times"},{"key":"10.1016\/j.isci.2025.114512_bib37","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1007\/BF00352198","article-title":"Review: Molecular analysis of the Philadelphia chromosome","volume":"100","author":"Dobrovic","year":"1991","journal-title":"Chromosoma"},{"key":"10.1016\/j.isci.2025.114512_bib38","doi-asserted-by":"crossref","first-page":"D1221","DOI":"10.1093\/nar\/gkab1056","article-title":"FusionGDB 2.0: fusion gene annotation updates aided by deep learning","volume":"50","author":"Kim","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.isci.2025.114512_bib39","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1016\/j.jmoldx.2019.05.006","article-title":"Development and Clinical Validation of a Large Fusion Gene Panel for Pediatric Cancers","volume":"21","author":"Chang","year":"2019","journal-title":"J. Mol. Diagn."},{"key":"10.1016\/j.isci.2025.114512_bib40","article-title":"Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector","volume":"3","author":"Haas","year":"2023","journal-title":"Cell Rep. Methods"},{"key":"10.1016\/j.isci.2025.114512_bib41","doi-asserted-by":"crossref","DOI":"10.3389\/fmolb.2023.1141310","article-title":"Fusion InPipe, an integrative pipeline for gene fusion detection from RNA-seq data in acute pediatric leukemia","volume":"10","author":"Vicente-Garc\u00e9s","year":"2023","journal-title":"Front. Mol. Biosci."},{"key":"10.1016\/j.isci.2025.114512_bib42","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1038\/s41467-023-37438-4","article-title":"Etiology of oncogenic fusions in 5,190 childhood cancers and its clinical and therapeutic implication","volume":"14","author":"Liu","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.isci.2025.114512_bib43","doi-asserted-by":"crossref","first-page":"D1276","DOI":"10.1093\/nar\/gkad922","article-title":"FusionNeoAntigen: a resource of fusion gene-specific neoantigens","volume":"52","author":"Kumar","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.isci.2025.114512_bib44","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1038\/nm.4439","article-title":"The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions","volume":"24","author":"Bolouri","year":"2018","journal-title":"Nat. Med."},{"key":"10.1016\/j.isci.2025.114512_bib45","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1186\/s13073-017-0468-3","article-title":"The neoepitope landscape in pediatric cancers","volume":"9","author":"Chang","year":"2017","journal-title":"Genome Med."},{"key":"10.1016\/j.isci.2025.114512_bib46","first-page":"675","article-title":"Mapping of HLA class I binding motifs in forty-four fusion proteins involved in human cancers","volume":"3","author":"Gambacorti-Passerini","year":"1997","journal-title":"Clin. Cancer Res."},{"key":"10.1016\/j.isci.2025.114512_bib47","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giy062","article-title":"Massive NGS data analysis reveals hundreds of potential novel gene fusions in human cell lines","volume":"7","author":"Gioiosa","year":"2018","journal-title":"GigaScience"},{"key":"10.1016\/j.isci.2025.114512_bib48","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/nature11003","article-title":"The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity","volume":"483","author":"Barretina","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.isci.2025.114512_bib49","article-title":"Arginine Signaling and Cancer Metabolism","volume":"13","author":"Chen","year":"2021","journal-title":"Cancers"},{"key":"10.1016\/j.isci.2025.114512_bib50","doi-asserted-by":"crossref","DOI":"10.3390\/cancers13246274","article-title":"Arginine Depletion in Human Cancers","volume":"13","author":"Nelakurti","year":"2021","journal-title":"Cancers"},{"key":"10.1016\/j.isci.2025.114512_bib51","doi-asserted-by":"crossref","DOI":"10.1126\/scisignal.aam9931","article-title":"Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins","volume":"10","author":"White","year":"2017","journal-title":"Sci. Signal."},{"key":"10.1016\/j.isci.2025.114512_bib52","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.1056\/NEJMp1607591","article-title":"Toward a Shared Vision for Cancer Genomic Data","volume":"375","author":"Grossman","year":"2016","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.isci.2025.114512_bib53","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.pcl.2014.09.004","article-title":"Biology of childhood acute lymphoblastic leukemia","volume":"62","author":"Bhojwani","year":"2015","journal-title":"Pediatr. Clin. North Am."},{"key":"10.1016\/j.isci.2025.114512_bib54","doi-asserted-by":"crossref","first-page":"1376","DOI":"10.1038\/s41588-022-01159-z","article-title":"The genomic landscape of pediatric acute lymphoblastic leukemia","volume":"54","author":"Brady","year":"2022","journal-title":"Nat. Genet."},{"key":"10.1016\/j.isci.2025.114512_bib55","doi-asserted-by":"crossref","first-page":"E1754","DOI":"10.1073\/pnas.1500973112","article-title":"TCR contact residue hydrophobicity is a hallmark of immunogenic CD8+ T cell epitopes","volume":"112","author":"Chowell","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.isci.2025.114512_bib56","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1003266","article-title":"Properties of MHC Class I Presented Peptides That Enhance Immunogenicity","volume":"9","author":"Calis","year":"2013","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.isci.2025.114512_bib57","doi-asserted-by":"crossref","first-page":"W449","DOI":"10.1093\/nar\/gkaa379","article-title":"NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data","volume":"48","author":"Reynisson","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.isci.2025.114512_bib58","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/j.cels.2020.06.010","article-title":"MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen Processing","volume":"11","author":"O\u2019Donnell","year":"2020","journal-title":"Cell Syst."},{"key":"10.1016\/j.isci.2025.114512_bib59","first-page":"6868","article-title":"Antigenicity of Fusion Proteins from Sarcoma-associated Chromosomal Translocations1","volume":"61","author":"Worley","year":"2001","journal-title":"Cancer Res."},{"key":"10.1016\/j.isci.2025.114512_bib60","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1172\/JCI3126","article-title":"Cytotoxic T cell response against the chimeric ETV6-AML1 protein in childhood acute lymphoblastic leukemia","volume":"102","author":"Yotnda","year":"1998","journal-title":"J. Clin. Investig."},{"key":"10.1016\/j.isci.2025.114512_bib61","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1007\/s00428-022-03448-8","article-title":"International Consensus Classification of acute lymphoblastic leukemia\/lymphoma","volume":"482","author":"Duffield","year":"2023","journal-title":"Virchows Arch."},{"key":"10.1016\/j.isci.2025.114512_bib62","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1038\/s41588-023-01640-3","article-title":"A new genomic framework to categorize pediatric acute myeloid leukemia","volume":"56","author":"Umeda","year":"2024","journal-title":"Nat. Genet."},{"key":"10.1016\/j.isci.2025.114512_bib63","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/leu.2011.227","article-title":"ETV6-RUNX1-positive childhood acute lymphoblastic leukemia: improved outcome with contemporary therapy","volume":"26","author":"Bhojwani","year":"2012","journal-title":"Leukemia"},{"key":"10.1016\/j.isci.2025.114512_bib64","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1111\/bjh.15725","article-title":"CBFA2T3-GLIS2-positive acute myeloid leukaemia. A peculiar paediatric entity","volume":"184","author":"Masetti","year":"2019","journal-title":"Br. J. Haematol."},{"key":"10.1016\/j.isci.2025.114512_bib65","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1111\/ijlh.12641","article-title":"Clinicopathologic and molecular characterization of myeloid neoplasms with isolated t(6;9)(p23;q34)","volume":"39","author":"Visconte","year":"2017","journal-title":"Int. J. Lab. Hematol."},{"key":"10.1016\/j.isci.2025.114512_bib66","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1016\/j.canlet.2019.11.005","article-title":"KMT2A rearranged acute lymphoblastic leukaemia: Unravelling the genomic complexity and heterogeneity of this high-risk disease","volume":"469","author":"Forgione","year":"2020","journal-title":"Cancer Lett."},{"key":"10.1016\/j.isci.2025.114512_bib67","doi-asserted-by":"crossref","DOI":"10.3390\/cancers12102766","article-title":"Targeted Inhibition of the NUP98-NSD1 Fusion Oncogene in Acute Myeloid Leukemia","volume":"12","author":"Mohanty","year":"2020","journal-title":"Cancers"},{"key":"10.1016\/j.isci.2025.114512_bib68","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1010976","article-title":"A multispecies framework for modeling adaptive immunity and immunotherapy in cancer","volume":"19","author":"Qi","year":"2023","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.isci.2025.114512_bib69","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2023.1142573","article-title":"CrossDome: an interactive R package to predict cross-reactivity risk using immunopeptidomics databases","volume":"14","author":"Fonseca","year":"2023","journal-title":"Front. Immunol."},{"key":"10.1016\/j.isci.2025.114512_bib70","doi-asserted-by":"crossref","first-page":"2276","DOI":"10.1007\/s13346-021-00923-8","article-title":"Overcoming biological barriers to improve solid tumor immunotherapy","volume":"11","author":"Ukidve","year":"2021","journal-title":"Drug Deliv. Transl. Res."},{"key":"10.1016\/j.isci.2025.114512_bib71","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1038\/s41587-023-01945-y","article-title":"Systematic discovery of neoepitope\u2013HLA pairs for neoantigens shared among patients and tumor types","volume":"42","author":"Gurung","year":"2024","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.isci.2025.114512_bib72","doi-asserted-by":"crossref","DOI":"10.1016\/j.mcpro.2021.100178","article-title":"MhcVizPipe: A Quality Control Software for Rapid Assessment of Small- to Large-Scale Immunopeptidome Datasets","volume":"21","author":"Kovalchik","year":"2022","journal-title":"Mol. Cell. Proteomics"},{"key":"10.1016\/j.isci.2025.114512_bib73","doi-asserted-by":"crossref","first-page":"e151","DOI":"10.1038\/bcj.2013.48","article-title":"The impact of TEL-AML1 (ETV6-RUNX1) expression in precursor B cells and implications for leukaemia using three different genome-wide screening methods","volume":"3","author":"Linka","year":"2013","journal-title":"Blood Cancer J."},{"key":"10.1016\/j.isci.2025.114512_bib74","series-title":"The Proteomics Protocols Handbook","first-page":"571","article-title":"Protein Identification and Analysis Tools on the ExPASy Server","author":"Gasteiger","year":"2005"},{"key":"10.1016\/j.isci.2025.114512_bib75","first-page":"e63052","article-title":"Immunopeptidomics: isolation of mouse and human MHC class I-and II-associated peptides for mass spectrometry analysis","author":"Sirois","year":"2021","journal-title":"J. Vis. Exp."},{"key":"10.1016\/j.isci.2025.114512_bib76","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1158\/2159-8290.CD-22-0523","article-title":"Cellular Senescence Is Immunogenic and Promotes Antitumor Immunity","volume":"13","author":"Marin","year":"2023","journal-title":"Cancer Discov."},{"key":"10.1016\/j.isci.2025.114512_bib77","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1373\/clinchem.2015.250563","article-title":"Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry\u2013Based Assays","volume":"62","author":"Hoofnagle","year":"2016","journal-title":"Clin. Chem."},{"key":"10.1016\/j.isci.2025.114512_bib78","series-title":"Quantitative Methods in Proteomics","first-page":"145","article-title":"Targeted ProteinQuantificationproteinsQuantification Using Parallel Reaction Monitoring (PRM)","author":"Barkovits","year":"2021"},{"key":"10.1016\/j.isci.2025.114512_bib79","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1038\/s41568-019-0181-1","article-title":"Challenging (immunogenically) silent assumptions","volume":"19","author":"Bradley","year":"2019","journal-title":"Nat. Rev. Cancer"},{"key":"10.1016\/j.isci.2025.114512_bib80","doi-asserted-by":"crossref","first-page":"4487","DOI":"10.1093\/nar\/gkw282","article-title":"Discovering and understanding oncogenic gene fusions through data intensive computational approaches","volume":"44","author":"Latysheva","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.isci.2025.114512_bib81","doi-asserted-by":"crossref","first-page":"3104","DOI":"10.1158\/0008-5472.CAN-13-2235","article-title":"Identification and Characterization of Small Molecules That Inhibit Nonsense-Mediated RNA Decay and Suppress Nonsense p53 Mutations","volume":"74","author":"Martin","year":"2014","journal-title":"Cancer Res."},{"key":"10.1016\/j.isci.2025.114512_bib82","doi-asserted-by":"crossref","first-page":"720","DOI":"10.1038\/s41375-024-02166-1","article-title":"Enhanced Risk Stratification for Children and Young Adults with B-Cell Acute Lymphoblastic Leukemia: A Children\u2019s Oncology Group Report","volume":"38","author":"DelRocco","year":"2024","journal-title":"Leukemia"},{"key":"10.1016\/j.isci.2025.114512_bib83","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1016\/j.ccell.2020.03.006","article-title":"Response and Resistance to BCR-ABL1-Targeted Therapies","volume":"37","author":"Braun","year":"2020","journal-title":"Cancer Cell"},{"key":"10.1016\/j.isci.2025.114512_bib84","doi-asserted-by":"crossref","first-page":"4814","DOI":"10.1093\/nar\/gkv407","article-title":"Splice junctions are constrained by protein disorder","volume":"43","author":"Smithers","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.isci.2025.114512_bib85","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1002\/pro.2206","article-title":"Linkers in the structural biology of protein\u2013protein interactions","volume":"22","author":"Reddy Chichili","year":"2013","journal-title":"Protein Sci."},{"key":"10.1016\/j.isci.2025.114512_bib86","doi-asserted-by":"crossref","first-page":"1357","DOI":"10.1016\/j.addr.2012.09.039","article-title":"Fusion protein linkers: property, design and functionality","volume":"65","author":"Chen","year":"2013","journal-title":"Adv. Drug Deliv. Rev."},{"key":"10.1016\/j.isci.2025.114512_bib87","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2020.563800","article-title":"Elucidation of the Signatures of Proteasome-Catalyzed Peptide Splicing","volume":"11","author":"Paes","year":"2020","journal-title":"Front. Immunol."},{"key":"10.1016\/j.isci.2025.114512_bib88","doi-asserted-by":"crossref","first-page":"2709","DOI":"10.1021\/acs.jproteome.4c00973","article-title":"To Fly, or Not to Fly, That Is the Question: A Deep Learning Model for Peptide Detectability Prediction in Mass Spectrometry","volume":"24","author":"Abdul-Khalek","year":"2025","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.isci.2025.114512_bib89","doi-asserted-by":"crossref","DOI":"10.1084\/jem.20221654","article-title":"A cell-free antigen processing system informs HIV-1 epitope selection and vaccine design","volume":"220","author":"Sengupta","year":"2023","journal-title":"J. Exp. Med."},{"key":"10.1016\/j.isci.2025.114512_bib90","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1007\/BF02592307","article-title":"Immunogenicity of fusion proteins","volume":"23","author":"Gambacorti-Passerini","year":"1993","journal-title":"Int. J. Clin. Lab. Res."},{"key":"10.1016\/j.isci.2025.114512_bib91","doi-asserted-by":"crossref","first-page":"539","DOI":"10.4049\/jimmunol.1901173","article-title":"Impact of Cysteine Residues on MHC Binding Predictions and Recognition by Tumor-Reactive T Cells","volume":"205","author":"Sachs","year":"2020","journal-title":"J. Immunol."},{"key":"10.1016\/j.isci.2025.114512_bib92","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1038\/s41587-022-01464-2","article-title":"Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors","volume":"41","author":"Kacen","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.isci.2025.114512_bib93","series-title":"RUNX Proteins in Development and Cancer","first-page":"201","article-title":"Mechanism of ETV6-RUNX1 Leukemia","author":"Sundaresh","year":"2017"},{"key":"10.1016\/j.isci.2025.114512_bib94","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1124\/pr.118.016972","article-title":"Challenges and Opportunities for Childhood Cancer Drug Development","volume":"71","author":"Houghton","year":"2019","journal-title":"Pharmacol. Rev."},{"key":"10.1016\/j.isci.2025.114512_bib95","doi-asserted-by":"crossref","DOI":"10.1080\/2162402X.2018.1532759","article-title":"Affinity-enhanced T-cell receptors for adoptive T-cell therapy targeting MAGE-A10: strategy for selection of an optimal candidate","volume":"8","author":"Border","year":"2019","journal-title":"OncoImmunology"},{"key":"10.1016\/j.isci.2025.114512_bib96","article-title":"Divergent HLA variations and heterogeneous expression but recurrent HLA loss-of- heterozygosity and common HLA-B and TAP transcriptional silencing across advanced pediatric solid cancers","volume":"14","author":"Lim","year":"2023","journal-title":"Front. Immunol."},{"key":"10.1016\/j.isci.2025.114512_bib97","doi-asserted-by":"crossref","first-page":"3058","DOI":"10.1074\/mcp.M116.060350","article-title":"Human Leukocyte Antigen (HLA) Peptides Derived from Tumor Antigens Induced by Inhibition of DNA Methylation for Development of Drug-facilitated Immunotherapy","volume":"15","author":"Shraibman","year":"2016","journal-title":"Mol. Cell. Proteomics"},{"key":"10.1016\/j.isci.2025.114512_bib98","article-title":"CTAT-LR-fusion: accurate fusion transcript identification from long and short read isoform sequencing at bulk or single cell resolution","author":"Qin","year":"2024","journal-title":"bioRxiv"},{"key":"10.1016\/j.isci.2025.114512_bib99","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1074\/mcp.RA119.001846","article-title":"Immunopeptidomic Analysis Reveals That Deamidated HLA-bound Peptides Arise Predominantly from Deglycosylated Precursors","volume":"19","author":"Mei","year":"2020","journal-title":"Mol. Cell. Proteomics"},{"key":"10.1016\/j.isci.2025.114512_bib100","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1002\/mas.21905","article-title":"Exploring the dynamic landscape of immunopeptidomics: Unravelling posttranslational modifications and navigating bioinformatics terrain. Mass Spectrometry Reviews n\/a","volume":"44","author":"Flender","year":"2025","journal-title":"Mass Spectrom. Rev."},{"key":"10.1016\/j.isci.2025.114512_bib101","doi-asserted-by":"crossref","first-page":"W281","DOI":"10.1093\/nar\/gks469","article-title":"Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion","volume":"40","author":"Thomsen","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.isci.2025.114512_bib102","doi-asserted-by":"crossref","first-page":"D339","DOI":"10.1093\/nar\/gky1006","article-title":"The Immune Epitope Database (IEDB): 2018 update","volume":"47","author":"Vita","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.isci.2025.114512_bib103","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1002\/0471142735.im1803s100","article-title":"Measurement of MHC\/Peptide Interactions by Gel Filtration or Monoclonal Antibody Capture","volume":"100","author":"Sidney","year":"2013","journal-title":"Curr. Protoc. Immunol."},{"key":"10.1016\/j.isci.2025.114512_bib104","doi-asserted-by":"crossref","first-page":"D1188","DOI":"10.1093\/nar\/gkac1072","article-title":"The UCSC Genome Browser database: 2023 update","volume":"51","author":"Nassar","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.isci.2025.114512_bib105","doi-asserted-by":"crossref","first-page":"3307","DOI":"10.1182\/bloodadvances.2019030981","article-title":"Human models of NUP98-KDM5A megakaryocytic leukemia in mice contribute to uncovering new biomarkers and therapeutic vulnerabilities","volume":"3","author":"Cardin","year":"2019","journal-title":"Blood Adv."},{"key":"10.1016\/j.isci.2025.114512_bib106","doi-asserted-by":"crossref","first-page":"3232","DOI":"10.1093\/bioinformatics\/bts617","article-title":"Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript","volume":"28","author":"Benelli","year":"2012","journal-title":"Bioinformatics"},{"key":"10.1016\/j.isci.2025.114512_bib107","doi-asserted-by":"crossref","first-page":"R72","DOI":"10.1186\/gb-2011-12-8-r72","article-title":"TopHat-Fusion: an algorithm for discovery of novel fusion transcripts","volume":"12","author":"Kim","year":"2011","journal-title":"Genome Biol."},{"key":"10.1016\/j.isci.2025.114512_bib108","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/s13073-015-0167-x","article-title":"JAFFA: High sensitivity transcriptome-focused fusion gene detection","volume":"7","author":"Davidson","year":"2015","journal-title":"Genome Med."},{"key":"10.1016\/j.isci.2025.114512_bib109","article-title":"FusionCatcher \u2013 a tool for finding somatic fusion genes in paired-end RNA-sequencing data","author":"Nicorici","year":"2014","journal-title":"bioRxiv"},{"key":"10.1016\/j.isci.2025.114512_bib110","doi-asserted-by":"crossref","first-page":"2539","DOI":"10.1093\/bioinformatics\/btt445","article-title":"Oncofuse: a computational framework for the prediction of the oncogenic potential of gene fusions","volume":"29","author":"Shugay","year":"2013","journal-title":"Bioinformatics"},{"key":"10.1016\/j.isci.2025.114512_bib111","doi-asserted-by":"crossref","first-page":"D941","DOI":"10.1093\/nar\/gky1015","article-title":"COSMIC: the Catalogue Of Somatic Mutations In Cancer","volume":"47","author":"Tate","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.isci.2025.114512_bib112","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1101\/gr.257246.119","article-title":"Accurate and efficient detection of gene fusions from RNA sequencing data","volume":"31","author":"Uhrig","year":"2021","journal-title":"Genome Res."},{"key":"10.1016\/j.isci.2025.114512_bib113","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1186\/s13059-020-02043-x","article-title":"CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data","volume":"21","author":"Tian","year":"2020","journal-title":"Genome Biol."},{"key":"10.1016\/j.isci.2025.114512_bib114","doi-asserted-by":"crossref","first-page":"5961","DOI":"10.1038\/s41467-021-26213-y","article-title":"Cancer gene mutation frequencies for the U.S. population","volume":"12","author":"Mendiratta","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.isci.2025.114512_bib115","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1158\/2326-6066.CIR-19-0401","article-title":"pVACtools: A Computational Toolkit to Identify and Visualize Cancer Neoantigens","volume":"8","author":"Hundal","year":"2020","journal-title":"Cancer Immunol. Res."},{"key":"10.1016\/j.isci.2025.114512_bib116","doi-asserted-by":"crossref","first-page":"D1062","DOI":"10.1093\/nar\/gkad1068","article-title":"The SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics","volume":"52","author":"Huang","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.isci.2025.114512_bib117","doi-asserted-by":"crossref","DOI":"10.1136\/jitc-2020-002071","article-title":"HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy","volume":"9","author":"Marcu","year":"2021","journal-title":"J. Immunother. Cancer"},{"key":"10.1016\/j.isci.2025.114512_bib118","doi-asserted-by":"crossref","first-page":"W526","DOI":"10.1093\/nar\/gkae407","article-title":"Next-generation IEDB tools: a platform for epitope prediction and analysis","volume":"52","author":"Yan","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.isci.2025.114512_bib119","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1186\/1471-2105-7-153","article-title":"Predicting population coverage of T-cell epitope-based diagnostics and vaccines","volume":"7","author":"Bui","year":"2006","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.isci.2025.114512_bib120","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/0022-2836(82)90515-0","article-title":"A simple method for displaying the hydropathic character of a protein","volume":"157","author":"Kyte","year":"1982","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.isci.2025.114512_bib121","doi-asserted-by":"crossref","DOI":"10.1001\/jamanetworkopen.2019.2906","article-title":"Molecular Profiling of Hard-to-Treat Childhood and Adolescent Cancers","volume":"2","author":"Khater","year":"2019","journal-title":"JAMA Netw. Open"},{"key":"10.1016\/j.isci.2025.114512_bib122","doi-asserted-by":"crossref","first-page":"12086","DOI":"10.1021\/acs.analchem.2c02056","article-title":"Proteogenomics and Differential Ion Mobility Enable the Exploration of the Mutational Landscape in Colon Cancer Cells","volume":"94","author":"Wu","year":"2022","journal-title":"Anal. Chem."},{"key":"10.1016\/j.isci.2025.114512_bib123","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1002\/mas.21540","article-title":"The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics","volume":"39","author":"Pino","year":"2020","journal-title":"Mass Spectrom. Rev."},{"key":"10.1016\/j.isci.2025.114512_bib124","doi-asserted-by":"crossref","first-page":"3099","DOI":"10.1016\/0006-2952(73)90196-2","article-title":"Relationship between the inhibition constant (KI) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction","volume":"22","author":"Yung-Chi","year":"1973","journal-title":"Biochem. Pharmacol."},{"key":"10.1016\/j.isci.2025.114512_bib125","doi-asserted-by":"crossref","first-page":"1258","DOI":"10.1006\/jmbi.1997.0937","article-title":"Two complementary methods for predicting peptides binding major histocompatibility complex molecules11Edited by B. Honig","volume":"267","author":"Gulukota","year":"1997","journal-title":"J. Mol. Biol."}],"container-title":["iScience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2589004225027737?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2589004225027737?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T01:25:14Z","timestamp":1791336314000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2589004225027737"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2]]},"references-count":125,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2026,2]]}},"alternative-id":["S2589004225027737"],"URL":"https:\/\/doi.org\/10.1016\/j.isci.2025.114512","relation":{},"ISSN":["2589-0042"],"issn-type":[{"value":"2589-0042","type":"print"}],"subject":[],"published":{"date-parts":[[2026,2]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"The GF-NEO discovery platform unveils a [KQE][DG] sequence motif within fusion neoantigens in pediatric cancer","name":"articletitle","label":"Article Title"},{"value":"iScience","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.isci.2025.114512","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"114512"}}