Tim O'Donnell

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I am a computational immunologist and software engineer. I work as an independent consultant helping clients develop better vaccines and biologics using machine learning. I also develop open source software, often as part of the OpenVax project.

From 2020-2022, I was a senior scientist at the Tisch Cancer Institute at the Icahn School of Medicine at Mount Sinai. I worked on therapeutic cancer vaccines with Nina Bhardwaj’s group with the goal of helping these emerging therapies benefit more patients through better antigen selection. We ultimately launched four Phase I clinical trials at Mount Sinai to evaluate our platform for a fully personalized peptide vaccine targeting tumor neoantigens.

From 2017-2020, I was a PhD student advised by Uri Laserson. My dissertation introduced new methods for T cell epitope prediction, which are implemented in the MHCflurry package. I also did some work on antibody responses using phage immunoprecipitation sequencing (PhIP-seq).

In 2018, Alex Rubinsteyn, Julia Kodysh, Tavi Nathanson and I launched the OpenVax project to develop open source tools for selecting cancer vaccines. This grew out of work with Jeff Hammerbacher (2014-2017). The OpenVax tools continue to be extended and have seen wide adoption by research groups and companies worldwide.

Prior to Mount Sinai, I worked at D.E. Shaw Research (2009-2014) developing analysis software for molecular dynamics simulations. Before this, I worked as a software engineer, helped put together engineering teams for several internet startups, and spent a summer interning at Google. I hold a B.S. in Math & Computer Science from Brown University and a PhD in Immunology from the Icahn School of Medicine at Mount Sinai.

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