URPs together strong: My summer at CSHL in summary

I really enjoyed my time with the CSHL URP (Cold Spring Harbor Laboratory Undergraduate Research Program) this summer! I learned a lot and had a lot of fun with my cohort. Honestly, this may have been my favorite summer ever and if not, it’s certainly way up there. Let me elaborate.

I feel like the URP was a really formative experience for me. Previously, my research experiences were all in developmental biology even if the model organisms were not necessarily the same and were very organismal biology-focused. While I genuinely love organismal biology, being able to learn more about computational biology and to pick up coding in a project concerning machine learning was very empowering for me. It not only made me feel better about my computational skills as a biologist but also made me feel more comfortable with the process of learning how to adapt to a new way of thinking. In short, it was a great opportunity for me to learn how to learn in an environment of mentors who were patient with me when I struggled with certain concepts.

This summer, I tried to develop and use methods for visualizing how the neural network Akita makes predictions about genome architecture from DNA sequences. I looked into methods for visualizing what happens to the model’s predictions when important sites for the model’s predictions or meaningful motifs for genome architecture like CTCF are disrupted. I also did some “genome context analysis”, where I looked into whether the context in which nucleotides are situated in affects how these nucleotides are interpreted by the model. There was certainly a learning curve in figuring out how to use Python and how to create new functions to randomize nucleotides/find motifs, but I got through it thanks to the help of my mentors and PIs. If there’s anything I’d give as advice on this front, I’d say it would be good if you could talk to grad students and postdocs in your lab besides your assigned mentor (assuming you are assigned a mentor). During the program, my main mentor was abroad for a month with a significant time difference, which made getting timely feedback on my code difficult. I reached out to another grad student in the lab and that really expedited the process of writing code. Don’t be afraid to reach out to others if you need help!

I also really enjoyed getting to know the cohort of URPs who came from a diverse range of backgrounds. Getting to know others who are as curious about science as I am was a real fun experience and I feel like I’m more curious about neuroscience and plant biology due to the time I spent at CSHL. We were able to see a Broadway show together and otherwise spend time in NYC seeing museums and trying good food. CSHL also hosts a lot of events for its employees like happy hours, picnics, and dinners, which we as a cohort made full use of.

As part of the program, we had to prepare two presentations: one near the beginning of the program to get us up to speed with our research topics and one at the end to present our findings to the other URPs. My mentor and PIs were really supportive throughout this process and I felt like my presentations went pretty well due to all of their feedback!

Overall, I highly recommend this program if you’re interested in quantitative biology or other disciplines like cancer biology/plant biology/neuroscience. Please reach out to me if you have any further questions! (My email is pzhou24@amherst.edu.)