Student Research Spotlight
laura tung
Describe your position and what is your current project.I am a member of the Kingsford group, and I just got my PhD degree in computational biology. My current research project is de novo error correction for RNA-seq long reads using deep learning.
What did you enjoy while researching this project?
I enjoyed trying out different ideas and experimenting with different approaches. I enjoyed the process of figuring out a solution from free exploration and stimulating discussions.
What is your dream job?
My dream job is one where I can contribute to bettering people's health (especially related to life-threatening diseases) while also being able to exercise creativity in our work.
What is your favorite project or favorite things to do? (this can be either about your education and/or personal interests).
I love art and music with my favorite activities being drawing and playing piano. I like working with charcoal and playing ragtime music the most.
Yutong Qiu
Describe your position and what is your current project?
I am finishing my fourth year of Ph.D. in the CPCB program. My current research project is enabling large-scale genomes to genomes comparison using genome graphs.
What did you enjoy while researching this project?
I enjoyed the process of identifying and formulating the computational problem underlying the biological questions. Having the concrete computational problem formulated always helps me bridge concepts from computer science to solve challenges in biology.
What is your dream job?
My dream job is where I get paid for using my knowledge and skills to create inspiring works that will benefit the world.
What is your favorite project or favorite things to do? (this can be either about your education or personal interest).
I love traveling and enjoy taking photographs during vacations. During work weeks, I enjoy indoor climbing.
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
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!
Trevor Frisby
Describe your position and what is your current project?I work with Chris Langmead, and am entering the fifth year of my Ph.D. My most recent work focuses on automating experimental science. This means using machine learning and artificial intelligence to create systems that are capable of formulating hypotheses, designing and carrying out wet-lab experiments to test these hypotheses, and updating them based on experimental results. While this might sound somewhat like science fiction, Cloud Laboratories already exist and are the perfect environment to actualize these types of systems. A cloud lab gives you the power to fully specify wet-lab experiments by writing computer programs, so what you can achieve is only limited by what you can dream up and write in code.
Most recently, I worked with Emerald Cloud Labs to automate the optimization of experimental designs in their cloud lab setting- a first step towards the larger goal of total closed-loop science. (Shameless plug: I'll present this work at ISMB later this month, come check it out!)
What did you enjoy while researching this project?
I'm not a wet-lab experimentalist at all, so learning how to configure wet-lab experiments through the cloud lab is quite the experience. It's pretty cool to think about how code I write from the comfort of my home is actually guiding real-life experiments being carried out on the opposite side of the country. On the other hand, it can be a bit nerve-racking as well- not totally knowing the intricate details of sophisticated equipment that I'm using always leaves me a little afraid that I'll end up breaking something (I'm not saying I did it, but something like this did happen!).
What is your dream job?
I don’t know that I have a dream job per se, but I hope to work at some intersection of machine learning and medicine/biology. I like environments where I am exposed to new things and able to learn as I go. I want to feel like I am contributing to some greater good, rather than stuffing the pockets of some already rich person.
To be honest, when I think of a “dream future,” I don’t typically think about a job. I think about having the autonomy to do things I want to do when I want to do them. Whether it’s traveling or picking up a new skill, it sometimes feels that work can get in the way of these things- as if somehow focusing on non-work-related tasks is a misuse of time. I want to have a job that emphasizes striking some balance here.
What is your favorite project or favorite things to do?
I have some simple hobbies that I enjoy, like playing my Switch, solving chess puzzles, and playing my bass guitar. I enjoy going out and trying new foods, though my life has been deprived of this as of late. I like going to hockey games, and hope to do more of that next season as well!