Undergraduate Research

Congratulations to the June Undergraduate Researcher of the Month, Joseph Cagle! 

Joseph Cagle, a senior majoring in computer science with a minor in math, works with Drs. Indika Kahanda and Anirban Ghosh from the UNF School of Computing. Their current research focuses on automated protein function prediction, an area within bioinformatics that uses machine learning and neural networks to determine the roles of different proteins. Using 3D structures from Google’s AlphaFold model, their team analyzes patterns in protein shapes, specifically fully connected subgraphs, to improve machine learning predictions of protein function, with the goal of further enhancing accuracy by combining this approach with other methods. Their research is supported by an O.U.R. Undergraduate Research Scholarship and Creative Activities (U-RSCA) Training Grant. This past spring, their work was presented at the 2025 Florida Undergraduate Research Conference (FURC) in Tampa and at the UNF2025 Showcase of Osprey Advancements in Research and Scholarship (SOARS). Now, they are preparing a manuscript for submission to a bioinformatics journal.

After graduating this December, Joseph plans to begin a career in software development in Jacksonville, where he hopes to continue learning from senior developers. He is also considering pursuing a master’s degree in computer science and eventually launching his own tech products as an entrepreneur. Through his research, Joseph has gained experience with machine learning techniques, neural networks architecture design, and protein analysis tools, while also learning how to read academic literature, design posters, and maintain detailed documentation.

His advice to aspiring researchers is to start by talking to professors, and to take meticulous notes. “[Write] with enough detail that someone else could understand what you’re doing from your documentation alone,” which is especially important when it’s time to write a paper summarizing your work.