Sheaffer '24 Unwinds Protein Networks in Brain with Computer Science
July 26, 2023
BLOOMINGTON, Ill. 鈥� Eckley Summer Scholar Anna Sheaffer '24 is on a mission to combine her computer science major and psychology minor to delve into the mysteries of the human brain.
鈥淭here鈥檚 a lot that we don鈥檛 know about the brain, so thinking about how a computer might be able to help us explore further, even if it might not be able to create a perfect representation, is exciting to me,鈥� Sheaffer said.
Sheaffer, through her research project 鈥淲eb-Based Application for Visualizing Protein-Protein Interaction Network Alignment,鈥� is creating a new software tool that will enable others to more efficiently and effectively research one of the most vastly complex and important aspects of neurology 鈥� molecular protein interactions.
The idea for her project began when Sheaffer first spoke to Assistant Professor of Computer Science Brian Law about switching her major from psychology. Law has a background in computational biology, and he explained to Sheaffer the utility of interdisciplinary computer science . Sheaffer first started doing research with Law in the summer of 2022.
鈥淭he point [of computational biology] is to take something that鈥檚 really difficult and time-consuming for biologists, like collecting and studying all the necessary evidence on their own, and automate it using computation,鈥� Sheaffer explained.
In this case, she plans to help researchers determine the biological purpose of proteins by identifying their molecular partners.
鈥淧roteins that interact with one another carry out similar functions, so, if you don鈥檛 know what a particular protein is supposed to do, you can interpret the function of an unknown protein by finding known proteins that it interacts with,鈥� Sheaffer said. 鈥淚t鈥檚 a topic within computational biology that a lot of biologists and computer scientists are looking at.鈥�
The application that Sheaffer is programming will create visual representations of 鈥減rotein interaction networks鈥� and the 鈥渁lignment of networks between multiple [protein] species.鈥� Sheaffer plans to construct it as a useful tool for visually organizing and exploring protein interactions in the brain, where there are countless vital and sensitive protein interactions.
Ideally, Sheaffer would be able to finish the summer with a working product for public use by any interested neuroscientists, though doing so in that time is an ambitious goal.
鈥淩ight now, I鈥檓 working on creating a pipeline from the back-end, where all the data is stored, that will bring the interpreted data to the front-end display,鈥� she said.
Sheaffer has gone through several iterations of a visual network, with hopes of avoiding what she refers to as 鈥渢he hairball problem.鈥�
鈥淵ou have hundreds of thousands of proteins, and if you try to visualize all of them, you get a giant hairball of connections that鈥檚 not useful,鈥� she said.
The novelty Sheaffer hopes to achieve is in unraveling the hairball to help researchers find useful patterns of alignment within a system that鈥檚 almost as complex as the brains it will help us understand.
Established by the late 含羞草传媒 President Emeritus Robert Eckley and his wife Nell , the Eckley award provides a stipend of $4,000 for each scholar to spend the summer conducting academic research or artistic activity under the mentorship of a faculty member. The program is designed to develop and deepen a student鈥檚 creative and research competencies.
By Chris Francis '13