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Methods in Molecular Biology (Clifton, N.J.)|March 4, 2020
High-Throughput MHC I Ligand Prediction Using MHCflurryTimothy O'Donnell, Alex RubinsteynProgress in Molecular Biology and Translational Science|August 7, 2019
Bioinformatic methods for cancer neoantigen predictionSebastian Boegel, John C Castle, Julia Kodysh, et al.Methods in Molecular Biology (Clifton, N.J.)|March 4, 2020
OpenVax: An Open-Source Computational Pipeline for Cancer Neoantigen PredictionJulia Kodysh, Alex RubinsteynCell Systems|July 27, 2020
MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen ProcessingTimothy J O'Donnell, Alex Rubinsteyn, Uri LasersonBriefings in Bioinformatics|January 5, 2024
ACE configurator for ELISpot: optimizing combinatorial design of pooled ELISpot assays with an epitope similarity modelJin Seok Lee, Dhuvarakesh Karthikeyan, Misha Fini, et al.Cell Systems|July 2, 2018
MHCflurry: Open-Source Class I MHC Binding Affinity PredictionTimothy J O'Donnell, Alex Rubinsteyn, Maria Bonsack, et al.Nature Machine Intelligence|September 29, 2025
Conditional generation of real antigen-specific T cell receptor sequencesDhuvarakesh Karthikeyan, Sarah N Bennett, Amy G Reynolds, et al.Nature Cancer|May 9, 2025
Atezolizumab plus personalized neoantigen vaccination in urothelial cancer: a phase 1 trialMansi Saxena, Jonathan F Anker, Julia Kodysh, et al.Frontiers in Immunology|February 7, 2018
Computational Pipeline for the PGV-001 Neoantigen Vaccine TrialAlex Rubinsteyn, Julia Kodysh, Isaac Hodes, et al.Biorxiv : the Preprint Server for Biology|June 25, 2020
Landscape and Selection of Vaccine Epitopes in SARS-CoV-2Christof C Smith, Sarah Entwistle, Caryn Willis, et al.Pageof 4