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Timothy O'Donnell
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Immunology of COVID-19: current state of the science
N Vabret, GJ Britton, C Gruber, S Hegde, J Kim, M Kuksin, R Levantovsky, ...
Immunity 52 (6), 910-941, 2020
14932020
Mapping systemic inflammation and antibody responses in multisystem inflammatory syndrome in children (MIS-C)
CN Gruber, RS Patel, R Trachtman, L Lepow, F Amanat, F Krammer, ...
Cell 183 (4), 982-995. e14, 2020
3952020
MHCflurry: open-source class I MHC binding affinity prediction
TJ O'Donnell, A Rubinsteyn, M Bonsack, AB Riemer, U Laserson, ...
Cell systems 7 (1), 129-132. e4, 2018
2762018
Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody
AG Schmidt, H Xu, AR Khan, T O’Donnell, S Khurana, LR King, ...
Proceedings of the National Academy of Sciences 110 (1), 264-269, 2013
2172013
MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen Processing
TJ O’Donnell, A Rubinsteyn, U Laserson
Cell Systems 11 (1), 42-48. e7, 2020
1202020
Shared Immunogenic Poly-Epitope Frameshift Mutations in Microsatellite Unstable Tumors
V Roudko, CC Bozkus, T Orfanelli, CB McClain, C Carr, T O’Donnell, ...
Cell 183 (6), 1634-1649. e17, 2020
892020
Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer
T O’Donnell, EL Christie, A Ahuja, J Buros, BA Aksoy, DDL Bowtell, ...
BMC cancer 18 (1), 1-11, 2018
342018
Landscape and selection of vaccine epitopes in SARS-CoV-2
CC Smith, KS Olsen, KM Gentry, M Sambade, W Beck, J Garness, ...
Genome medicine 13 (1), 1-23, 2021
292021
Key mutations stabilize antigen‐binding conformation during affinity maturation of a broadly neutralizing influenza antibody lineage
H Xu, AG Schmidt, T O'Donnell, MD Therkelsen, TB Kepler, MA Moody, ...
Proteins: Structure, Function, and Bioinformatics 83 (4), 771-780, 2015
252015
Bioinformatic methods for cancer neoantigen prediction
S Boegel, JC Castle, J Kodysh, T O'Donnell, A Rubinsteyn
Progress in Molecular Biology and Translational Science 164, 25-60, 2019
202019
Predicting Peptide-MHC Binding Affinities With Imputed Training Data
A Rubinsteyn, T O'Donnell, N Damaraju, J Hammerbacher
bioRxiv, 054775, 2016
172016
A Comprehensive Phenotypic and Functional Immune Analysis Unravels Circulating Anti–Phospholipase A2 Receptor Antibody Secreting Cells in Membranous Nephropathy Patients
C Cantarelli, M Jarque, A Angeletti, J Manrique, S Hartzell, T O’Donnell, ...
Kidney International Reports 5 (10), 1764-1776, 2020
122020
Estimating Local Costs Associated With Clostridium difficile Infection Using Machine Learning and Electronic Medical Records
TR Pak, KI Chacko, T O’Donnell, SS Huprikar, H van Bakel, A Kasarskis, ...
Infection Control & Hospital Epidemiology, 1-9, 2017
92017
Hammerlab/Fancyimpute: Version 0.2. 0
A Rubinsteyn, S Feldman, T O’Donnell, B Beaulieu-Jones
Zenodo. doi 10, 2017
72017
NKG2A and HLA-E define an alternative immune checkpoint axis in bladder cancer
B Salomé, JP Sfakianos, D Ranti, J Daza, C Bieber, A Charap, C Hammer, ...
Cancer Cell 40 (9), 1027-1043. e9, 2022
42022
TGM4: an immunogenic prostate-restricted antigen
ZA Lopez-Bujanda, A Obradovic, TR Nirschl, L Crowley, R Macedo, ...
Journal for Immunotherapy of Cancer 9 (6), 2021
42021
High-Throughput MHC I Ligand Prediction Using MHCflurry
T O’Donnell, A Rubinsteyn
Bioinformatics for Cancer Immunotherapy, 113-127, 2020
32020
A phase I study of the safety and immunogenicity of a multi-peptide personalized genomic vaccine in the adjuvant treatment of solid tumors and hematological malignancies.
A Blazquez, A Rubinsteyn, J Kodysh, JP Finnigan, TU Marron, M Meseck, ...
Journal of Clinical Oncology 37 (15_suppl), e14307-e14307, 2019
22019
Repeat elements amplify TLR signaling
T O’Donnell, N Vabret
Nature Reviews Immunology 21 (12), 760-760, 2021
12021
289 PGV-001: a phase 1 trial of a personalized neoantigen peptide vaccine for the treatment of malignancies in the adjuvant setting
T Marron, J Kodysh, A Rubinsteyn, J Finnigan, A Blazquez, M Saxena, ...
Journal for ImmunoTherapy of Cancer 8 (Suppl 3), 2020
12020
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