How to apply to and thrive in quantitative biology REUs

By Annamarie Leske and John T. Nardini

Every summer, many undergraduate students spend 8 weeks conducting projects as part of a Research Experience for Undergraduates (REU) program. Many colleges and universities host their own REU programs and invite several students from all over the nation to participate. Once students come to campus, they are often paired with a research mentor and assigned on a project, which they may work on individually or in groups.

During the summer of 2021, Annamarie Leske participated in Northwestern University’s Quantitative Biology REU, which was hosted by the NSF-Simons Center for Quantitative Biology. Due to the ongoing Covid-19 pandemic, this program was hosted virtually. Annamarie and I recently talked about her experience in this program, her advice for future REU applicants, and what’s coming next in her career.

Annamarie, please tell us a little bit about yourself.
Sure! My name is Annamarie and I am a junior at North Carolina State University (NC State). I study applied mathematics and physics (my new minor!). In November of 2020, I began undergraduate research in the Belmonte Lab at NC State. When I am not in class or researching, I am performing on the football field as one of the Pack Twirlers, here at State. Sushi is my favorite food. Yellow is my favorite color. Most importantly, my favorite karaoke song is “I Will Survive” by Gloria Gaynor (check this out if you ever need performance tips and/or outfit inspiration).

Could you tell us a little more about Quantitative Biology and Northwestern’s Quantitative Biology REU program?
Quantitative Biology is an exciting field that involves attacking biological problems from a mathematical or statistical point of view. Historically, much of biological research has been done qualitatively, presumably due to the overwhelming complexity of life. Today’s technology and big data processing capabilities have opened up biology’s horizons for new, more robust means of research. An example of a booming field in computational biology is the mathematical modeling of gene regulation, which is a highly complex system involving many, many components. We are getting better at quantifying gene regulation with the help of computers and big data processing (but it’s still a very complex task). Northwestern’s Quantitative Biology Undergraduate Summer Research Program aims to expose undergraduate students from all backgrounds and fields to mathematical techniques that they can use to further our understanding of such biological phenomena. For more info on this REU, check out this link as well as the NSF-Simons Center for Quantitative Biology webpage to learn more about the awesome work that’s being done there!

There are so many REUs held each year. How did you approach finding REU programs, and what excited you about Northwestern’s Quantitative Biology Program?
It can be a little overwhelming to navigate the REU application process. I began searching for REU programs when I started undergraduate research in the fall of 2020. I had some mathematics research experience at that point, but I felt very drawn to biological applications. For example, I had recently undergone a tonsillectomy and became beyond interested in the body’s healing process as well as intercellular function! I searched through some relevant keywords in The National Science Foundation’s REU Site Search tool and found many programs that fit my interests of biological applications in mathematics.

I also planted the REU bug in some of my professors’ ears: I mentioned being interested in research and somehow applying math to solve biological problems. Sure enough, one of my professors came across Northwestern’s Quantitative Biology REU program and sent the information my way. The rest was history!

What is the typical timeline for an REU application, and what materials did you have to send to each program? How did you ensure your application stood out from the others?
I sent in my application on January 19th and heard back on March 11th! The application materials were straightforward: a standard questionnaire containing the usual logistics (name, age, year, etc.), a few essay questions pertaining to what my research interests were and why, university transcripts, a resumé, and one letter of recommendation. All programs were a little different however; some required two or three letters of recommendation, and others required short answer questions instead of essays.

I think the most important things that helped me stand out from other applicants were (a) my letter of recommendation and (b) my essays expressing my intentions for the program. I was fortunate enough to have my research advisor write my letter of recommendation, which I think helped demonstrate that I was familiar with research, though that is not necessary for an REU. Lots of students participate with no previous research experience! More importantly, my research advisor was able to write about how passionate I am about quantitative biology from our work together on the analysis of cytoskeletal dynamics with mathematical models!

The essays were also important because they gave me the chance to share my goals for an REU and why Northwestern’s Quantitative Biology was the right choice to help me achieve these goals. I knew that I wanted more interdisciplinary experience and was looking for a program that would expose me to new fields of biology, cutting-edge mathematical methods and how to apply my previous experience to these areas. I made sure to highlight this goal in my essays with special emphasis on what meaningful progress means to me: having the ability to grow to understand concepts that were once foreign and complex. I also spent ample time researching the program’s participating faculty so that I could confidently write about those who I felt would best help me reach my goals. I referenced multiple faculty in my essays and wrote about why I was interested in their work or mentorship. I even ended up having the chance to work with a few of my choices over the course of the summer, even if they were not my principal mentor!

In terms of the writing process, some of my advisors and professors from NC State graciously looked over my essays. They helped me refine my message into exactly what I wanted to portray. Asking for help from trusted faculty definitely made a huge difference!

What is one piece of advice you would give any future REU applicants?
Ask for help! I always feel bad asking professors or advisors to look over essays or write recommendation letters because I know how much they have on their plates. Truth is, many faculty want to help you in any way they can. As my research mentor, Dr. Belmonte, put it, “We wouldn’t be where we are if our professors and advisors hadn’t written us letters of recommendations!”

Once the program started, how did you find your project and mentor? Did you work individually or as part of a team? How did you navigate all of this over Zoom?
My mentors and projects for the summer were assigned to me at the beginning. One of our essay questions prompted us to explain which participating faculty we’d be most interested in working with and why. Once the program started, I ended up working directly under three mentors (one graduate student, one post-doc student and the head PI). Some students in the REU cohort worked in the same lab group on joint projects, but most of us had our own individual tasks. It was a little tough to adjust to a new project, especially virtually, but daily Zoom meetings and frequent Slack messages made it all possible and surprisingly comfortable! Surely, the REU faculty played the largest role in creating an effortless virtual environment.

I’d love to hear a bit more about the project you were working on. Could you tell us the project your worked on, the long-term goal, and why math is necessary to answer this biological problem?
The title of my research project this year was “Topological Variation in Ommatidial Precluster Formation.” In simpler terms, my group and I were interested in how the compound eye of the fruit fly is able to develop highly organized photoreceptor patterns. We used bifurcation theory to try to uncover where bifurcation might exist within data obtained from image processing. The data involved in this project is very high dimensional and consists of vectorized pixel matrices from movies of photoreceptor clustering. Bifurcations in the data exist when the principal covariance eigenvalue of the data is significantly different from the null (randomized re-sampling) data. This data usually forms a peak in bifurcation events, but appears plateau-like in null data. This bifurcation is indicative of a state change (from an unorganized structure to an organized structure) that may hint at the mechanism causing patterning in the first place. Uncovering said mechanism is the long-term goal of this project! If, eventually, we can understand this driving force, we may be able to understand what happens in instances of “mispatterning” and thus know how and where to direct reparation efforts. This would be helpful way beyond fly eyes because patterning plays a critical role in ALL organisms’ development, including us! Mutations in patterning can affect the overall function of an organism for the worse, so learning to identify mechanisms associated with said mutations could be significant. Attacking this problem mathematically allows us to view the phenomena from a different vantage point and provides a more feasible way to determine the mechanisms causing patterning (as opposed to expressing every individual gene involved in this patterning, for example).

You mentioned you had conducted research previously. Was this project related to your previous work? Did your previous experience help you during this new project?
Technically, no. But maybe I should say not yet? My previous research with the Belmonte Lab has been on cytoskeletal dynamics, where the cytoskeleton is a network of fibrous filaments located in the cytoplasm that gives rise to cell structure and function. It’s very different from quantifying morphological differentiation in fly eyes. However, one of my Northwestern REU mentors is quite versed in cytoskeleton networks and did admit (to my excitement) that there are components of the photoreceptor clustering system where understanding cytoskeletal dynamics may be especially important! For example, there are areas of cellular contraction in the fly eye tissue with interesting dynamics – this is where there’s room for cytoskeletal dynamics analysis!

While my work in Dr. Belmonte’s lab is not directly related to what I did over the summer, the programming abilities that I learned with him and other courses proved to be extremely helpful. In fact, I was able to nearly skip over the“learning a new programming language” portion of the REU and started working on my project, thanks to my previous experience in Matlab, Unix, Python, etc. Also, the self-efficacy I developed in Dr. Belmonte’s lab became a critical feature of my summer program at Northwestern; learning to be self-sufficient was tremendously helpful for working on a research project virtually!

What does undergraduate research look like for you one a day-to-day basis? Do you spend a lot of time reading books and research articles, putting pen to paper, and/or coding on the computer?
My experience in undergraduate research has been solely computational so far. I started research at the height of the COVID pandemic where computer work was part of my daily life, so computational work was a logical option. I am lucky that I love it despite previously despising both coding and computers. A lot of my day-to-day work in research involves coding,running scripts on the high performance computer, Henry2, at NC State, and analyzing results with a combination of Python and Matlab scripts (Matlab will always have my heart, sorry Python junkies). During the academic year, I meet with my mentor every week, and we all meet with my entire lab group every few months or so.

A huge part of REUs is getting to know a cohort of your peers in the program. How did you and your peers bond during a virtual program?
The Northwestern Quantitative Biology faculty, namely Dr. Bill Kath and Tiffany Leighton-Ozmina, were incredible in providing our cohort with many opportunities to communicate and collaborate together. We had meetings every day, which were themed. For example, Mondays were seminar days, Wednesdays we did co-working, Thursdays were “Tea with Faculty” days, and we had social hours on Fridays where we got to bond, play games, and chat about life! Our cohort shared phone numbers and created a group chat to meet at other times outside of those planned. It was always great to have people to relate, vent, brag, joke, and work with!

Did you have a final report or research presentation that you gave at the conclusion of your program?
Yes! Because our cohort (QBio REU) combined forces with the Synthetic Biology REU at Northwestern, we had a large symposium to share our summer’s findings! Each student had 15 minutes to present with 5 minutes allotted for questions. It was a little intimidating to present in front of all of my very successful mentors and peers; however, my mentors made sure to help me thoroughly prepare beforehand so I knew deep down that I would be okay! The hardest part was answering the audience’s questions as you never fully know what they will ask. Despite everyone’s nerves, I think all the mentees did well! It was really impressive to hear all the progress we made over just eight short weeks.

How do you see your experience in this REU program shaping your career as a Mathematician?
This REU gave me so much more than just the tools to succeed in mathematical research – it gave me the confidence to brazenly start my career! I becameclose with and learned so much from all my peers, mentors and participating faculty in the program. I learned important new scientific and quantitative skills during the program and participating in the REU energized me and has helped me gain a new sense of trust within myself. The participants, faculty, and mentors at Northwestern made me feel like an important contributor to not only their program, but the future of research as a whole.

Now that the program has concluded, what is next for you? Will you return to your research lab at NC State, continue collaborating on this project at Northwestern, or something entirely different?
I am excited to return to Dr. Belmonte’s Lab at NC State this fall to pick up where I left off! I look forward to integrating some of the skills I have learned in Dr. Carthew’s Lab to my work with cytoskeletal networks. Who knows where it will take me!

Annamarie Leske

Biography. Annamarie Leske is a junior at North Carolina State University (NC State) studying applied mathematics and physics. When Annamarie is not in class or researching, she performs on the football field as one of the Pack Twirlers at NC State. Sushi is her favorite food, and yellow is her favorite color.

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