Carnegie Mellon University
Marcus Thomas standing in front of a body of water

Marcus Thomas

Describe your position and what is your current project?

I am a recent (Jan 2021) CPCB graduate and member of the Schwartz Lab at CMU. A major focus of my work over the past few years has been the development of simulation algorithms for molecular self-assembly and general reaction-diffusion systems. This research exists at the intersection of computer science, biology and physics, and is motivated by questions ranging from the long term and aspirational to the day-to-day.  For example, can we develop viral therapies based on an understanding of the kinetics of capsid assembly? How do we discover the assembly pathways available to self-assembling systems? What are appropriate computational representations for a biological system and how can we efficiently evolve its state over time while respecting the physics on a microscopic scale? And, how does stochasticity affect a simulation algorithm’s time complexity and physical accuracy? In a paper currently under review, we tackle some of these questions and present a novel simulation methodology.

Later this month I will be starting a postdoc position in the computational biology department at Mount Sinai in New York City. There, I will investigate evolution in cancer and in viruses.

What did you enjoy while researching this project?

I enjoyed having the time to become familiar with the field and the freedom to explore alternative approaches.

What is your dream job?

I am not sure my dream job exists, but my dream lifestyle would include doing computational biology research as part of an international collaboration. I would also like to do some teaching, and charity work in the effective altruism space. Ideally, there will be opportunities to work and live overseas periodically.

What is your favorite project or favorite things to do (this can be either about your education or personal interest).

My hobbies outside of academia include competitive ballroom dancing, playing chamber music and reading history. I’m a big fan of the late Roman empire.

Shuanger Li

Shuanger Li

Describe your position and what is your current project?

I'm a second-year student in the MSCB program and currently working with Professor Oana Carja. My project is to investigate the contribution of social interaction preferences to the evolution of virus strain diversity. We use population genetic models and computer simulations to explore a range of questions relevant to pathogen diversity and the current pandemics: How do social interaction preferences foster strain coexistence and how fast? How do social distancing and traveling alter such dynamics? What are the implications of our model on vaccination strategies?

I will join the Ecology and Evolution program at the University of Chicago for my PhD study and explore host-pathogen coevolution dynamics.


What did you enjoy while researching this project?

I loved the process of conceptualizing a model. It's fun to turn vague ideas into illustrations and equations on scratch paper, and then to scripts. My idea doesn't work most of the time, but that means I can work with more models.


What is your dream job?

A wildlife veterinarian. My "realistic dream job" is to work at the intersection of computational biology and evolutionary biology, and I'm working towards this goal.


What is your favorite project or favorite things to do?

I enjoy making tutorials for modeling, especially related to biological systems. Hopefully I can make some of my old tutorials publicly available someday. Recently I've been part of Professor Phillip Compeau's team developing an online course for multiscale biological modeling. I promise it will be fun when published!