Researcher of the Month
Biochemistry, Applied Mathematics & Statistics majors; Honors College, Class of 2016
Research Mentor: Dr. David Green, Applied Math & Statistics
was selected from over 100 applicants to the 2014 URECA summer program as the recipient
of this year’s Chhabra-URECA Fellowship, an award which recognizes undergraduate researchers
with tremendous potential who have a passion and talent for science. A rising junior
in the Honors College, with a double major in Applied Mathematics & Statistics, and Biochemistry,
Corey has been working for almost a year under the mentorship of Dr. David F. Green (
Dept. of Applied Mathematics & Statistics). His project involves modeling the reaction network between HIV (gp120), CD4 and
CCR5 proteins to understand the initial stages of HIV infection, using Gillespie’s
algorithm for stochastic simulation of chemical kinetics. He is currently the only
undergraduate in his research group. And to enhance his skills for this challenging
project, Corey enrolled in two graduate courses last semester in his sophomore year
(AMS 533-Numerical Methods and Algorithms, AMS 534-Introduction to Systems Biology)--courses
that turned out to be invaluable for his current research. He also is a regular attendee
of computational / mathematical biology talks at the Laufer Center.
Asked about his predilection for the field of systems biology, Corey explains, “ I have always loved making connections between physics, biology and chemistry to see the bigger picture. My interest in systems biology stems from its fundamental focus on the human body as a network of interactions…..I love the field of systems biology – I like to see how everything is connected. ” Corey plans to continue in the Green research group, using mathematical models and systems biological methods to find potential drug targets in the HIV infection pathway, and will be developing his senior thesis topic for the Honors College from this research. Farther down the road, he plans to complete a Ph.D. in the field of mathematical/ computational biology.
Corey is a member of the national and SB chapters of the American Chemical Society. His hobbies include drumming, singing, and skiing. Corey was a top graduate of Pennsbury High School in Yardley, PA, prior to coming to SB. Below are excerpts of his interview with Karen Kernan, URECA Director.
Karen . What’s your research about?
Corey: I have always loved making connections between physics, biology and chemistry to see the bigger picture. My interest in systems biology stems from its fundamental focus on the human body as a network of interactions. In the research group of Dr. David Green (AMS), I’m working on developing a model of the initial stages of HIV infection, using the Gillespie Stochastic Simulation Algorithm to calculate infection trajectories based on an initial probability distribution that is proportional to the concentration of reactants and the experimentally determined rate constants for each reaction in the network. We’re looking at hundreds upon hundreds of chemical reactions- running them through the computer, and then seeing how changing the kinetics of each of those reactions affects HIV infection. By modeling the bonding of HIV to its receptors, we hope to identify good targets for a future drug, and to optimize the prevention of HIV by interfering with HIV receptor-co-receptor binding. I really like the overall research focus of my lab – on HIV. I want to be able to help people.
How did you first get involved with the lab?
In my freshman year, I had contacted Dr. Leon Moore because I was interested in his research. It turned out the Dr. Moore was going to retire in the near future….but he asked me about what I was really interested in and suggested that Dr. Green’s research group in AMS would be perfect for me. So I set up with a meeting with Dr. David Green and we really hit it off. We arranged for me to start doing research in his group in the beginning of my sophomore year. I’m the only undergrad in the group- and a lot of the research is still in early phases. For example, with one of the receptors – the structure was literally discovered just in the last month – which is really cool.
When you first came to Stony Brook, did you know that you wanted to do work in the field of systems biology?
Not at all. I found my niche in systems bio after I started working in it. And I really only first discovered that it was a field in my freshman year of college. But I was always interested in math in high school. And I wanted to use my expertise in math to help people. And when I first learned about this field, I thought, “This seems interesting.” Then I started learning more about it, and working in it --and I’m loving it! ...I really love the lab I’m in. And I love the field of systems biology – I like to see how everything is connected.
What was your background coming in to the lab?
When I first started in the research group of Dr. Green, I spent some time learning the ropes….doing a lot of reading. There’s a lot of material to learn for what I have to do.
Did you need to learn any computer programming skills for your research?
In my freshman year, through the Honors College, I had taken a one credit mini course on Python, a language that I didn’t know that much about …but it taught me the basics of programming. From that, I was able to learn Matlab pretty easily by just teaching myself as I went along, something I have continued to use it in my research. Then in my sophomore year, in the spring semester, I took a graduate class, AMS 534, with Dr. MacCarthy – and I learned something called Rulebender; also BioNetGen, R – a statistical language. And I’m using A LOT of what I learned in that course to do my research right now. If I never had taken that class, my research would be impossible right now. I’ve learned an immense amount of tools that I would never have learned in undergrad classes.
What do you like most about the research you do?
I really like using math to apply to things. I really like being able to use all the math tools I have and apply them to one thing. You’re doing kinetics, differential equations, programming – but everything comes together to do the research and I have to use all the tools to solve one problem.
What are your future plans?
A PhD, definitely somewhere in the physical biology, systems biology area. I’m very interested in systems biology. I’ve learned a lot about the field from the Laufer Center here. My mentor is affiliated with the Laufer Center and I go to lectures there. I go over there quite frequently. There are two grad courses that I’m really looking forward to taking that are taught at the Laufer Center, on Biological Networks, and Physical Biology. I really enjoy talking to the grad students; they seem to know so much and I want to catch up to them.
What advice about research would you give to other undergrads?
You have to love what you’re doing. If you don’t love it- you’re not going to do good research.
And be interested! When I was in high school, I was always reading papers, trying to solve problems. It was helpful for me that I started early. I like working independently, and I was able to teach myself a lot of the math I was interested in exploring in high school. .. But I’d say in general the way to develop your skills is just to do problems and keep practicing. Keep reading things over and over until you understand. If you practice enough and keep solving them on your own, you’ll get better as you keep going.
Are there any particular qualities that are valuable for doing the kind of research that you do?
For my research specifically, you want to be able to be very careful to not make mistakes. You have to try to go very slow. The problem that I was getting into initially was that I was getting very excited and had a tendency to make my model too complicated. There are a lot of things going on and you need to know the connections between everything. I had to learn to make sure that every step is careful, and that we don’t add stuff before the backbone makes sense from physics, from chemistry, and from biology…otherwise it is a useless model.
With the type of work you do, are you getting continual feedback? Or are you waiting a lot of the time for data?
Because my project involves all this computer programming, I don’t have to be physically there in the lab all the time though I enjoy being there; it’s a fun place to hang out. But the research does involve a lot of waiting and waiting. The good thing is I found a way to speed up my simulations. I was sampling way too much in the beginning. I realized that I don’t need to do that as much. So I’m learning to be more efficient. Sometimes I have trouble seeing what the next step will be– and I have to talk to David Green to get guidance on where to go.
How does your mentor help you?
Dr David Green - he’s brilliant. He always knows exactly what I need to do. I just follow his instructions.
Will you continue with this research for your senior honors thesis with the Honors College?
Yes –and we’re also planning to present at a meeting in Boston, about a year from now. I’m glad I still have some time over the next year to really develop the topic before I write up my thesis.
Do you enjoy being part of the Honors College?
Yes, the Honors College has been great. I really like that I have all the contact – that I made a lot of friends really quickly. We have a lot of very small classes with generally renowned professors. And I like the ability to network that it has provided for me.
So SBU has been working out for you?