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PRIMES: Boryana Doyle's Story



PRIMES is an excellent program that allowed me to experience all stages of performing computational biology research, while focusing on learning about a single project. In my first year, I spent time becoming acquainted with background information before starting work on my project. This early stage was a challenge for me, because the material and the concepts were novel. However, once I received and began working on my project about polymer simulations of chromatinized DNA loops, I caught on and made initial progress quickly. Presenting at the 2012 PRIMES Conference allowed me to gain valuable experience by organizing my results and giving a talk.

Throughout the summer, I continued to work on my first project by deepening my initial findings and reading papers to understand how my project fit into previous and tangential work. This stage of research was difficult and uncertain at times, but in the end we were able to arrive at nice, satisfying conclusions. An abstract containing these results was selected for me to give a talk at the conference, Dynamic Organization of Nuclear Function, held at Cold Spring Harbor Laboratory, Cold Spring Harbor, New York in September, 2012. Presenting my research at the conference to 200 established scientists was a nerve-wracking but rewarding experience. The questions I received about my project following my talk were even more intriguing; I was excited that my work was interesting to others and gained new ideas to explore.

During the next year, I presented a poster at two conferences: Cells, Circuits, and Computation 2013: Physics of Living Systems at Harvard University in January, 2013 and Epigenetics and Chromatin: Interactions and Processes hosted at Harvard Medical School in March, 2013. I appreciated presenting a poster to explain my results because, in this discussion-based format, I learned which diagrams and plots were most useful to describe my project effectively. This, in turn, has proven to be very useful as I am writing up my results into a paper.

Meanwhile, I began a new and exciting project that involves data analysis rather than polymer simulations. It is interesting for me to be exposed to something a bit different, while still using previous knowledge from my first project. Both projects were presented at the 2013 PRIMES Conference, and I enjoyed the opportunity to practice giving a talk again.

Overall, my experience in PRIMES has been amazing; I did not really know what to expect since I had no previous experience with anything like this, but the hard-work and surprises were all pleasant. I enjoyed discussions with my mentors, Maxim Imakaev and Geoff Fudenberg, about my project and related work in the lab. Exchanging ideas and questions was an integral component of making progress on my project. Moreover, my mentors and other lab members were very useful resources for technical questions; a few minutes of help can save hours of confusion. Because of my participation in PRIMES, I am now considering a career in research.

There are many strengths to the PRIMES program, but I would like to especially note the benefits of having a long-term environment to perform research as much of this work would have been impossible in a short session. The best way to really learn about something is to try it; I strongly encourage anyone interested in learning about research itself or about computational biology (or math or computer science) to participate in PRIMES. Keep an open mind, stay in communication with your mentor(s), spend time thinking about your project, don't be afraid to take initiative, seize opportunities to organize/present your work, and have fun!

I thank my fellow PRIMES students in computational biology for all of the fun and learning we have had together; my parents for having the patience to provide transportation to and from MIT; my mentors, Maxim Imakaev and Geoffrey Fudenberg, as well as Professor Leonid Mirny for providing much needed guidance and encouragement; and PRIMES itself for making this all possible.


Boryana Doyle worked on the project Chromatin organization: from polymer loops to topological domains under the mentorship of Geoffrey Fudenberg and Maxim Imakaev.

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