While visiting her family in Philadelphia last fall, Gowri Nayar received an email she had been waiting for over a year. After she read it, she began jumping up and down with great excitement and her niece and nephew joined in, even though they had no idea why.
After applying for the Ruth L. Kirschstein Predoctoral Individual National Research Service Award (F31), Nayar learned she had been honored with the prestigious fellowship.
The award is structured to enable predoctoral students to develop into productive research scientists while receiving mentored training, and will fund her training until their doctorate is complete. It is notorious for its gauntlet of rigorous peer reviews, and few students apply for it. Of those who do, less than 50 percent secure the honor on their second application. Nayar was successful on the first try. Prior to joining the Department of Biomedical Data Science as a Ph.D. candidate, she spent four years building the largest bacterial and viral sequences genomics database at IBM Research after completing her master’s at Georgia Tech. She was at IBM when the pandemic began, which gave her the opportunity to repurpose her platform to be able to study the SARS Co V2 genome.
“Gowri has very deep understanding of computer science and especially machine learning,” Russ Altman, Professor of Biomedical Data Science and Nayar’s mentor, said. “She has taken classes widely and was introduced to Reinforcement Learning, which she found powerful and exciting. At the same time, she noticed that many proteins have not been assembled into pathways and that there is a real need to have algorithms to discover new pathways that can be related to both health and disease.”
Nayar, who has worked in Altman’s lab for several years, focused her research on protein pathways and how they react with pharmaceuticals.
“My work specifically focuses on this idea that we don’t actually know of all of the ways that a drug works in our body or all the ways that a disease occurs in our body,” she explains. “Protein pathways are sequences of proteins that can cause either normal behavior or diseased behavior. For example, one common pathway, glycolosis, is how you turn food or sugar into energy.”
But there are only a handful of these pathways that are very well studied and very well characterized, Nayar explained. Therefore, when a drug is developed, only a limited set of proteins are targeted.
This can cause unanticipated results when a drug is released for patient use, because only certain proteins may be identified that interact with the drug. Proteins that are not identified can cause the drug to be ineffective or have side effects that render it ineffective or produce side effects that are too consequential to be implemented in clinical care.
“My research is in trying to broaden the scope of what types of pathways we know about,” she added. “How many proteins we know, and which types of interactions are actually causing specific diseases. I take a computational approach to try to identify pathways protein pathways across the human proteome.”
In Altman’s lab, Nayar’s research fits in like a puzzle piece. The lab focuses on the molecular factors underlying disease and health. With that knowledge, opportunities can be discovered for new drugs and treatments for disease, as well as novel diagnostics, Altman explained. “Gowri’s work fits generally into our interest in understanding both normal and abnormal physiology at the molecular level,” he added.
He also underscores the importance and impact Nayar’s research may have with future pharmaceuticals and patient outcomes.
“If we are able to discover novel pathways, this will almost certainly suggest novel treatment opportunities. We have such a powerful way to deliver therapies now — small molecule drugs, protein biologics, CRISPR knockouts, RNA knockdowns, gene therapy — that the real challenge is finding the right targets involved in the pathways that are critical in disease,” he said. “Gowri’s work will contribute to the creation of novel methods for linking proteins together in pathways so that we can understand how they work together to create phenotypes of interest.”
The Kirschstein Award will fund Nayar up to her doctoral defense. After that, Nayar hopes to continue her research work in an academic setting.
“In academia, you definitely have more freedom to explore, and you have a larger scope,” Nayar said. “You see professors here at Stanford; they collaborate so much across departments, across disciplines and I think that’s what I’m most excited by.”
—Laurie Notaro, DBDS Communications