UNIVERSITY PARK, Pa. — One Penn State professor is seeking to merge physical bioinformatics, which is the science of collecting and analyzing complex biological data, to create analysis tools to better understand the behaviors of protein synthesis, influence and protein expression.
Edward O’Brien, assistant professor of chemistry and Penn State Institute for CyberScience faculty co-hire, has received $687,883 from the National Science Foundation (NSF) for his new research based in the interdisciplinary fields of chemistry, physics and bioinformatics.
“O’Brien’s new study showcases the importance of merging fields to develop new tools and methods of analyses,” ICS Director and Professor of Meteorology and Atmospheric Science Jenni Evans said. “Interdisciplinary study is at the heart of the ICS mission and O’Brien is using these three fields to answer significant questions on a molecular scale.”
O’Brien’s project, which will span three years, will collaborate with Penn State’s Upward Bound Math and Science Program (UBMS). UBMS assists participating students from local schools in identifying and developing their abilities in the fields of math or science. This program encourages the students to pursue postsecondary degrees in STEM. O’Brien has been working with UBMS since 2016, and has had four different students in his lab. O’Brien will have two students for this project.
Utilizing computationally intensive research methods provided by the ICS Advanced CyberInfrastructure, O’Brien will explore this data and protein behavior to answer two fundamental biological questions: what controls protein translations and their speeds, and if evolution has encoded translation rates to control certain processes.
“Bioinformatics is an approach for analyzing large biological datasets and it has largely been dominated by computer scientists and molecular biologists,” O’Brien said. “We’re bringing physical sciences to bioinformatics by developing analysis tools motivated by the chemistry and the physics of the underlying system that is being measured.”
O’Brien research is motivated by protein synthesis, which occurs at certain rates, such as how quickly proteins are produced. This project will work to design analysis tools to make the measurement of those rates “easy and rigorous.”
“In principle, an experimentalist can take a cell they’re interested in, carry out studies, produce their data, and then the analysis tools will look at the data to report information such as the initiation rate of protein synthesis and the elongation rate of protein synthesis across all of the genes in the cell,” O’Brien said.
Along with developing new methods and analysis tools, O’Brien is looking to take these tools and apply them in Galaxy, a web-based platform for comprehensible and reproducible computational biomedical research. By using Galaxy, researchers with no coding knowledge are able to take their data and run tests with pre-programmed analysis tools.
O’Brien said that his research ultimately aims to aid in the study of certain mutations and their linkage to cancer. He hopes to use these tools to look at certain translation speeds to discover what mutations contribute to cancer.