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MHCflurry: Open-Source Class I MHC Binding Affinity Prediction.
O'Donnell TJ, Rubinsteyn A, Bonsack M, Riemer AB, Laserson U, Hammerbacher J. O'Donnell TJ, et al. Among authors: bonsack m. Cell Syst. 2018 Jul 25;7(1):129-132.e4. doi: 10.1016/j.cels.2018.05.014. Epub 2018 Jun 27. Cell Syst. 2018. PMID: 29960884 Free article.
The shared frameshift mutation landscape of microsatellite-unstable cancers suggests immunoediting during tumor evolution.
Ballhausen A, Przybilla MJ, Jendrusch M, Haupt S, Pfaffendorf E, Seidler F, Witt J, Hernandez Sanchez A, Urban K, Draxlbauer M, Krausert S, Ahadova A, Kalteis MS, Pfuderer PL, Heid D, Stichel D, Gebert J, Bonsack M, Schott S, Bläker H, Seppälä T, Mecklin JP, Ten Broeke S, Nielsen M, Heuveline V, Krzykalla J, Benner A, Riemer AB, von Knebel Doeberitz M, Kloor M. Ballhausen A, et al. Among authors: bonsack m. Nat Commun. 2020 Sep 21;11(1):4740. doi: 10.1038/s41467-020-18514-5. Nat Commun. 2020. PMID: 32958755 Free PMC article.
High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets.
Shao XM, Bhattacharya R, Huang J, Sivakumar IKA, Tokheim C, Zheng L, Hirsch D, Kaminow B, Omdahl A, Bonsack M, Riemer AB, Velculescu VE, Anagnostou V, Pagel KA, Karchin R. Shao XM, et al. Among authors: bonsack m. Cancer Immunol Res. 2020 Mar;8(3):396-408. doi: 10.1158/2326-6066.CIR-19-0464. Epub 2019 Dec 23. Cancer Immunol Res. 2020. PMID: 31871119 Free PMC article.