Dr. Greenbaum is a theoretical physicist who applies tools from the fields of computer science, mathematics, and physics to difficult problems in cancer biology. Immunotherapy has proven to be a groundbreaking strategy for cancer therapy, with incredible success for some patients. In part due to the complex systems involved – interactions between tumor cells, normal cells, immune system cells, and the surrounding environment – it is difficult to predict which patients will benefit from immunotherapy. Dr. Greenbaum’s lab is developing a computational model that takes these complexities into account to more accurately predict response of cancer patients to immunotherapy. Dr. Greenbaum is Program Leader in Computational Immuno-Oncology at Memorial Sloan Kettering Cancer Center.
PUBLISHED RESEARCH
Nogalski MT, Solovyov A, Kulkarni AS, Desai N, Oberstein A, Levine AJ, Ting DT, Shenk T, Greenbaum BD. A tumor-specific endogenous repetitive element is induced by herpesviruses. Nat Commun. 2019.
Perumal D, Imai N, Laganà A, Finnigan J, Melnekoff D, Leshchenko VV, Solovyov A, Madduri D, Chari A, Cho HJ, Dudley JT, Brody JD, Jagannath S, Greenbaum B, Gnjatic S, Bhardwaj N, Parekh S. Mutation-derived Neoantigen-specific T-cell Responses in Multiple Myeloma. Clin Cancer Res. 2020.
Roudko V, Greenbaum B, Bhardwaj N. Computational Prediction and Validation of Tumor-Associated Neoantigens. Front Immunol. 2020.
Maura F, Rustad EH, Yellapantula V, Łuksza M, Hoyos D, Maclachlan KH, Diamond BT, Greenbaum BD, Morgan G, Lesokhin A, Papaemmanuil E, Landgren O. Role of AID in the temporal pattern of acquisition of driver mutations in multiple myeloma. Leukemia. 2020.
Luo J, Rizvi H, Preeshagul IR, Egger JV, Hoyos D, Bandlamudi C, McCarthy CG, Falcon CJ, Schoenfeld AJ, Arbour KC, Chaft JE, Daly RM, Drilon A, Eng J, Iqbal A, Lai WV, Li BT, Lito P, Namakydoust A, Ng K, Offin M, Paik PK, Riely GJ, Rudin CM, Yu HA, Zauderer MG, Donoghue MTA, Łuksza M, Greenbaum BD, Kris MG, Hellmann MD. COVID-19 in patients with lung cancer. Ann Oncol. 2020.
Desai N, Neyaz A, Szabolcs A, Shih AR, Chen JH, Thapar V, Nieman LT, Solovyov A, Mehta A, Lieb DJ, Kulkarni AS, Jaicks C, Xu KH, Raabe MJ, Pinto CJ, Juric D, Chebib I, Colvin RB, Kim AY, Monroe R, Warren SE, Danaher P, Reeves JW, Gong J, Rueckert EH, Greenbaum BD, Hacohen N, Lagana SM, Rivera MN, Sholl LM, Stone JR, Ting DT, Deshpande V. Temporal and spatial heterogeneity of host response to SARS-CoV-2 pulmonary infection. Nat Commun. 2020.
Roudko V, Bozkus CC, Orfanelli T, McClain CB, Carr C, O’Donnell T, Chakraborty L, Samstein R, Huang KL, Blank SV, Greenbaum B, Bhardwaj N. Shared Immunogenic Poly-Epitope Frameshift Mutations in Microsatellite Unstable Tumors. Cell. 2020.
Di Gioacchino A, Šulc P, Komarova AV, Greenbaum BD, Monasson R, Cocco S. The heterogeneous landscape and early evolution of pathogen-associated CpG dinucleotides in SARS-CoV-2. Mol Biol Evol. 2021.
Bravi B, Balachandran VP, Greenbaum BD, Walczak AM, Mora T, Monasson R, Cocco S. Probing T-cell response by sequence-based probabilistic modeling. PLoS Comput Biol. 2021.
Rajurkar M, Parikh AR, Solovyov A, You E, Kulkarni AS, Chu C, Xu KH, Jaicks C, Taylor MS, Wu C, Alexander KA, Good CR, Szabolcs A, Gerstberger S, Tran AV, Xu N, Ebright RY, Van Seventer EE, Vo KD, Tai EC, Lu C, Joseph-Chazan J, Raabe MJ, Nieman LT, Desai N, Arora KS, Ligorio M, Thapar V, Cohen L, Garden PM, Senussi Y, Zheng H, Allen JN, Blaszkowsky LS, Clark JW, Goyal L, Wo JY, Ryan DP, Corcoran RB, Deshpande V, Rivera MN, Aryee MJ, Hong TS, Berger SL, Walt DR, Burns KH, Park PJ, Greenbaum BD, Ting DT. Reverse Transcriptase Inhibition Disrupts Repeat Element Life Cycle in Colorectal Cancer. Cancer Discov. 2022.
Hoyos D, Zappasodi R, Schulze I, Sethna Z, de Andrade KC, Bajorin DF, Bandlamundi C, Callahan MK, Funt SA, Hadrup SR, Holm JS, Rosenberg JE, Shah SP, Vázquez-García I, Weigelt B, Wu M, Zamarin D, Campitelli LF, Osborne EJ, Klinger M, Robins HS, Khincha PP, Savage SA, Balachandran VP, Wolchok JD, Hellmann MD, Merghoub T, Levine AJ, Łuksza M, Greenbaum BD. Fundamental immune-oncogenicity trade-offs define driver mutation fitness. Nature. 2022.
Vabret N, Najburg V, Solovyov A, Gopal R, McClain C, Šulc P, Balan S, Rahou Y, Beauclair G, Chazal M, Varet H, Legendre R, Sismeiro O, Sanchez David RY, Chauveau L, Jouvenet N, Markowitz M, van der Werf S, Schwartz O, Tangy F, Bhardwaj N, Greenbaum BD, Komarova AV. Y RNAs are conserved endogenous RIG-I ligands across RNA virus infection and are targeted by HIV-1. iScience. 2022.