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Putting computational models of immunity to the test - an invited challenge to predict B. pertussis vaccination outcomes.
Shinde P, Willemsen L, Anderson M, Aoki M, Basu S, Burel JG, Cheng P, Dastidar SG, Dunleavy A, Einav T, Forschmiedt J, Fourati S, Garcia J, Gibson W, Greenbaum JA, Guan L, Guan W, Gygi JP, Ha B, Hou J, Hsiao J, Huang Y, Jansen R, Kakoty B, Kang Z, Kobie JJ, Kojima M, Konstorum A, Lee J, Lewis SA, Li A, Lock EF, Mahita J, Mendes M, Meng H, Neher A, Nili S, Olsen LR, Orfield S, Overton JA, Pai N, Parker C, Qian B, Rasmussen M, Reyna J, Richardson E, Safo S, Sorenson J, Srinivasan A, Thrupp N, Tippalagama R, Trevizani R, Ventz S, Wang J, Wu CC, Ay F, Grant B, Kleinstein SH, Peters B. Shinde P, et al. Among authors: greenbaum ja. bioRxiv [Preprint]. 2024 Sep 8:2024.09.04.611290. doi: 10.1101/2024.09.04.611290. bioRxiv. 2024. PMID: 39282381 Free PMC article. Preprint.
Linked CD4 + /CD8 + T cell neoantigen vaccination overcomes immune checkpoint blockade resistance and enables tumor regression.
Dolina JS, Lee J, Brightman SE, McArdle S, Hall SM, Thota RR, Lanka M, Premlal ALR, Greenbaum JA, Cohen EEW, Peters B, Schoenberger SP. Dolina JS, et al. Among authors: greenbaum ja. bioRxiv [Preprint]. 2023 May 7:2023.05.06.539290. doi: 10.1101/2023.05.06.539290. bioRxiv. 2023. Update in: J Clin Invest. 2023 Sep 1;133(17):e164258. doi: 10.1172/JCI164258 PMID: 37205330 Free PMC article. Updated. Preprint.
A systems vaccinology resource to develop and test computational models of immunity.
Shinde P, Soldevila F, Reyna J, Aoki M, Rasmussen M, Willemsen L, Kojima M, Ha B, Greenbaum JA, Overton JA, Guzman-Orozco H, Nili S, Orfield S, Gygi JP, da Silva Antunes R, Sette A, Grant B, Olsen LR, Konstorum A, Guan L, Ay F, Kleinstein SH, Peters B. Shinde P, et al. Among authors: greenbaum ja. bioRxiv [Preprint]. 2023 Aug 29:2023.08.28.555193. doi: 10.1101/2023.08.28.555193. bioRxiv. 2023. Update in: Cell Rep Methods. 2024 Mar 25;4(3):100731. doi: 10.1016/j.crmeth.2024.100731 PMID: 37693565 Free PMC article. Updated. Preprint.
A multi-omics systems vaccinology resource to develop and test computational models of immunity.
Shinde P, Soldevila F, Reyna J, Aoki M, Rasmussen M, Willemsen L, Kojima M, Ha B, Greenbaum JA, Overton JA, Guzman-Orozco H, Nili S, Orfield S, Gygi JP, da Silva Antunes R, Sette A, Grant B, Olsen LR, Konstorum A, Guan L, Ay F, Kleinstein SH, Peters B. Shinde P, et al. Among authors: greenbaum ja. Cell Rep Methods. 2024 Mar 25;4(3):100731. doi: 10.1016/j.crmeth.2024.100731. Epub 2024 Mar 14. Cell Rep Methods. 2024. PMID: 38490204 Free PMC article.
Next-generation IEDB tools: a platform for epitope prediction and analysis.
Yan Z, Kim K, Kim H, Ha B, Gambiez A, Bennett J, de Almeida Mendes MF, Trevizani R, Mahita J, Richardson E, Marrama D, Blazeska N, Koşaloğlu-Yalçın Z, Nielsen M, Sette A, Peters B, Greenbaum JA. Yan Z, et al. Among authors: greenbaum ja. Nucleic Acids Res. 2024 Jul 5;52(W1):W526-W532. doi: 10.1093/nar/gkae407. Nucleic Acids Res. 2024. PMID: 38783079 Free PMC article.
The Immune Epitope Database (IEDB): 2024 update.
Vita R, Blazeska N, Marrama D; IEDB Curation Team Members; Duesing S, Bennett J, Greenbaum J, De Almeida Mendes M, Mahita J, Wheeler DK, Cantrell JR, Overton JA, Natale DA, Sette A, Peters B. Vita R, et al. Among authors: greenbaum j. Nucleic Acids Res. 2025 Jan 6;53(D1):D436-D443. doi: 10.1093/nar/gkae1092. Nucleic Acids Res. 2025. PMID: 39558162 Free PMC article.
80 results