Memorial Hospital Research Laboratories

The Benjamin Greenbaum Lab

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Research

Benjamin Greenbaum
Benjamin Greenbaum, PhD

Our goal is to quantify how the immune system impacts tumor evolution and to use that understanding to advance the reach and breadth of cancer immunotherapies. We do so by using approaches from disciplines such as statistical physics, evolutionary dynamics, machine learning and information theory to infer the mechanisms by which the immune system alters the fitness of tumors and viruses in both therapeutic and non-therapeutic settings. Much of our lab’s work draws inspiration from fundamental theoretical questions related to the evolution of viruses and cancer, self versus non-self discrimination, and the role of repetitive elements in cancer. We work with clinical and experimental investigators to assemble datasets where questions about the immune system’s role in cancer be well-posed and insights gained can be translated into clinically impactful work. Towards this end, we recently formed the Program in Computational Immuno-oncology to bridge the Computational Oncology Service and the Parker Institute for Cancer Immunotherapy.

Research Projects

The Benjamin Greenbaum lab group

Publications

Łuksza M, Sethna ZM, Rojas LA, Lihm J, Bravi B, Elhanati Y, Soares K, Amisaki M, Dobrin A, Hoyos D, Guasp P, Zebboudj A, Yu R, Chandra AK, Waters T, Odgerel Z, Leung J, Kappagantula R, Makohon-Moore A, Johns A, Gill A, Gigoux M, Wolchok J, Merghoub T, Sadelain M, Patterson E, Monasson R, Mora T, Walczak AM, Cocco S, Iacobuzio-Donahue C, Greenbaum BD*, Balachandran VP*. Neoantigen quality predicts immunoediting in survivors of pancreatic cancer. Nature. 2022 Jun;606(7913):389-395. doi: 10.1038/s41586-022-04735-9. Epub 2022 May 19. PMID: 35589842; PMCID: PMC9177421.

Hoyos D, Zappasodi R, Schulze I, Sethna Z, de Andrade KC, Bajorin DF, Bandlamudi 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 Jun;606(7912):172-179. doi: 10.1038/s41586-022-04696-z. Epub 2022 May 11. Erratum in: Nature. 2022 May 31;: PMID: 35545680; PMCID: PMC9159948.

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 Jun 2;12(6):1462-1481. doi: 10.1158/2159-8290.CD-21-1117. PMID: 35320348; PMCID: PMC9167735.

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 183:1634-1649 (2020).

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. 10:90 (2019).

Solovyov A*, Vabret N*, Arora KS, Snyder A, Funt SA, Bajorin DF, Rosenberg JE, Bhardwaj N, Ting DT*, Greenbaum BD*. Global cancer transcriptome quantifies repeat element polarization between immunotherapy responsive and T cell suppressive classes. Cell Reports 23:512-521 (2018).

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People

Benjamin Greenbaum

Benjamin Greenbaum, PhD

  • The Greenbaum lab utilizes techniques from statistical physics, information theory, and evolutionary biology to better understand the role of self/non-self discrimination in tumor evolution, model response to immunotherapies, and quantify drivers of virus and cancer evolution.
  • PhD in theoretical physics, Columbia University
[email protected]
Email Address

Members

Alex Chu
Alex Chu

Computational Biologist I

Yuval Elhanati
Yuval Elhanati

Senior Research Scientist

David Hoyos
David Hoyos

Computational Biologist II

Hao Li
Hao Li

Bioinformatics Software Engineer II

Jayon Lihm
Jayon Lihm

Senior Computational Biologist II

Olga Lyudovyk
Olga Lyudovyk

Bioinformatics Technician

Stephen Martis
Stephen Martis

Postdoctoral Research Scholar

Jahan Rahman
Jahan Rahman

Computational Biologist II

Zachary Sethna, PhD
Zachary Sethna

Research Associate

Alexander Solovyov
Alexander Solovyov

Senior Research Scientist

Siyu Sun
Siyu Sun

Postdoctoral Research Scholar

Rami Vanguri
Rami Vanguri

Senior Computational Biologist II

Lab Affiliations

Achievements

  • Invited Professor, Statistical Physics, École Normale Supérieure (2022)
  • The Mark Foundation for Cancer Research ASPIRE Award (2021)
  • Pancreatic Cancer Collective Phillip A. Sharp Challenge Award (2021)
  • Pershing Square Foundation COVID-19 Award (2020)
  • NextGen Innovator, HemOnc Today (2019)
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  • Pershing Square Sohn Prize for Young Investigators in Cancer Research (2018)
  • Mark Foundation Investigator Award (2018)
  • Phillip A. Sharp Award for Innovation in Collaboration, Stand Up to Cancer (2016)

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Disclosures

Doctors and faculty members often work with pharmaceutical, device, biotechnology, and life sciences companies, and other organizations outside of MSK, to find safe and effective cancer treatments, to improve patient care, and to educate the health care community.

MSK requires doctors and faculty members to report (“disclose”) the relationships and financial interests they have with external entities. As a commitment to transparency with our community, we make that information available to the public.

Benjamin Greenbaum discloses the following relationships and financial interests:

  • DarwinHealth Inc.
    Provision of Services
  • Icahn School of Medicine at Mount Sinai
    Intellectual Property Rights
  • Merck Sharp & Dohme
    Provision of Services
  • Rome Therapeutics
    Intellectual Property Rights; Ownership / Equity Interests; Provision of Services
  • Shennon Biotechnologies Inc.
    Ownership / Equity Interests
  • Sibyl Analytics LLC
    Fiduciary Role/Position; Ownership / Equity Interests; Provision of Services (uncompensated)
  • Zonklers, LLC
    Provision of Services (uncompensated)

The information published here is for a specific annual disclosure period. There may be differences between information on this and other public sites as a result of different reporting periods and/or the various ways relationships and financial interests are categorized by organizations that publish such data.

This page and data include information for a specific MSK annual disclosure period (January 1, 2021 through disclosure submission in spring 2022). This data reflects interests that may or may not still exist. This data is updated annually.

Learn more about MSK’s COI policies here. For questions regarding MSK’s COI-related policies and procedures, email MSK’s Compliance Office at [email protected].


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