PRAIRIE VIEW, Texas (January 26, 2023) – Last spring, Princeton University launched a program in partnership with the United Negro College Fund (UNCF) and five historically Black colleges and universities (HBCUs) – including Prairie View A&M University (PVAMU) – to cultivate diversity and participation across research, innovation and entrepreneurship within the academic community.
The Princeton Alliance for Collaborative Research and Innovation (PACRI) is an initiative that provides funding for research projects co-led by principal investigators from Princeton and one of its five HBCU partnering institutions. Spearheading one of these projects is a professor at PVAMU with extensive experience studying and teaching data science, computational biology, and algorithm development.
Noushin Ghaffari, assistant professor, Department of Computer Science
Noushin Ghaffari, Ph.D., an assistant professor in PVAMU’s Department of Computer Science, was awarded $235,687 by PACRI for her research project, “Exploring Applications of Machine Learning for DNA Methylation Experiments with the Goal of Trait Discoveries.” Her Princeton collaborator is principal investigator (PI) Bridgett vonHoldt, an associate professor in the Department of Ecology and Evolutionary Biology. Also involved in the project will be a diverse team of faculty, post-docs, graduate and undergraduate students. These students will learn how to collect, analyze and present large volumes of biological assay-based data.
“Data science continues to be one of the fastest-growing fields driving innovation across a variety of industries,” said PVAMU Vice President of Research & Innovation Magesh Rajan, Ph.D., P.E., MBA. “Dr. Ghaffari’s research and this award from PACRI will allow our students to gain the critical skills and hands-on experience required to address the present and future needs of industry and society.”
“I am very excited to start this multidisciplinary research,” said Dr. Ghaffari. “We will look into effects of molecular-level genome changes and their impact on health, behavior, and possibly social interactions in sea mammals. We will focus on sea lions and will study their genomes through DNAm experiments and will tackle their immune response and few visible phenotypes.”
DNA methylation (DNAm) is the most common epigenetic modification that affects gene expression and other important genomic elements. Dr. Ghaffari and her team are learning how the presence of DNAm can change the behavior of genes, proteins and chromosomes.
To tackle the statistical challenge that comes with learning about DNAm and its impact, Dr. Ghaffari’s field is using current machine learning (ML) approaches, or developing new ones, that allow researchers to analyze the differences among mammals. ML is still new to evolutionary genomics, but its techniques are designed to understand the data in hand and to make predictions for an unseen dataset. Dr. Ghaffari and her partners are hoping to establish a successful collaboration that merges the expertise of computational ML methods with evolutionary and population genomics with respect to DNAm data obtained from wild populations.
“This is a perfect example of a data science project where the computer science, analytical and engineering skills and techniques can be applied to a life science domain to expand our understanding of nature,” said Dr. Ghaffari.
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By Leigh Badrigian