YURKOVICH LAB
Lab focus
The Yurkovich Lab applies cutting-edge systems science and computational methods to understand human health, disease, and aging. Our primary goal is to leverage vast, multi-modal datasets—ranging from genomics and epigenomics to proteomics, metabolomics, and real-world digital health data—to build predictive computational models. These models allow us to move beyond simple correlations, identifying causal mechanisms and enabling a deeper, mechanistic understanding of the intricate biological networks that govern human physiology.
A key thrust of our research involves defining the baseline for phenomic signals in humans, accounting for inherent biological variability and known cycles (e.g., circadian rhythms) to ensure accurate interpretation of dynamic health states. We work to identify robust and cost-effective proxies for complex phenomic signals, exploring the utility of non-invasive devices like wearables in capturing data that correlates with traditional molecular measurements. We are dedicated to exploring the role of red blood cells (RBCs) in human health and aging, integrating molecular data with clinical observations to connect physiological-scale phenomena with underlying molecular mechanisms.
We explore molecular mechanisms through whole-cell simulation, building comprehensive computational models that represent biological systems in their entirety. While red blood cells serve as an ideal, simple model for developing systems biology approaches due to the extensive availability of data, we also use bacteria and other cell types to pioneer simulation methodologies and computational techniques. These models integrate molecular data to account for the intricate mechanisms governing cellular function. By simulating the interactions and dynamic behavior of these systems, we strive to predict their responses to perturbations, unravel complex genotype-phenotype relationships, and gain deeper insights into fundamental biological processes applicable across diverse organisms.
Why it matters
Our research is not just about health and disease; it is about redefining health itself and bringing it from the clinic directly into your home. We are on a mission to transform healthcare from a reactive system—where we wait for illness to strike—to a proactive one, focused on predicting and preventing diseases before they even manifest. By diving deep into the intricate biological networks of the human body and other model systems, we are unlocking the secrets to personalized wellness that adapts as you age. We are working to create a future that enriches the human healthspan; where you have the power to manage your health proactively and affordably.
Project SIMBA: Simulating Microbial Behavior
The Yurkovich Lab is leading a groundbreaking new project awarded by the Defense Advanced Research Projects Agency (DARPA). The Simulation and Inference of Microbial Behavior and Adaptation (SIMBA) project is a comprehensive computational effort to predict the behavior of E. coli with unprecedented accuracy. By integrating multi-dimensional data, our team will build a digital twin of this complex bacterium, offering a new frontier in understanding microbial life at the single-cell level. The resulting platform will have broad applications—from optimizing biomanufacturing to forecasting antimicrobial efficacy—and push the boundaries of what is possible in synthetic biology.
Life is subject to constraints—modeling these constraints mathematically allows us to unlock a future where data empowers us to understand, predict, and optimize health.
James Yurkovich, PhD
CENTER DETAILS
The Yurkovich lab is pleased to acknowledge the generous support of the following major funders:
Advanced Projects Research Agency for Health (ARPA-H)
Defense Advanced Research Projects Agency (DARPA)
James T Yurkovich, PhD is a Research Assistant Professor at the Buck Institute for Research on Aging. After receiving his BS in Electrical Engineering from the University of Notre Dame, James obtained his PhD in Bioinformatics and Systems Biology from the University of California San Diego under the supervision of Prof Bernhard Palsson. From there, James completed a Translational Research Fellowship at the Institute for Systems Biology in Seattle under the supervision of Leroy Hood and Nathan Price. James then transitioned into the biotech industry by joining the pharmaceutical company Biosplice Therapeutics (formerly Samumed) to build and lead a systems biology division focused on understanding the healthy functioning and aging of the human musculoskeletal system.
At the Buck, the Yurkovich Lab works to bridge the gap between computer science and biology, blending mechanistic models of biological systems with AI. James’ interdisciplinary background spans mechanistic modeling, machine learning, network analysis, and dynamical systems theory. His experience in the pharma industry and at multiple tech and biotech startups has built a strong foundation in machine learning and various mathematical modeling approaches applied to human health and disease. He developed and teaches the world’s first graduate-level course on digital health and wearable devices at the University of Texas at Dallas, where James is an adjunct faculty and on the Industrial Advisory Committee in the Department of Bioengineering.
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Emma Glass, PhD Research ScientistEmma Glass, PhD, is a Research Scientist in the Yurkovich lab whose focus is on developing computational tools that connect microbial biology with age-related disease. Her research integrates systems biology, genome-scale metabolic network modeling, and machine learning to simulate cellular processes and better understand microbial threats to human health. Emma holds a BS in Computational and Applied Mathematics and Statistics from William & Mary and a PhD in Biomedical Engineering from the University of Virginia. At the Buck, she is particularly interested in applying AI-enabled approaches to disentangle the complex interplay between microbes, the human phenome, and the biology of longevity.
EGlass@buckinstitute.org
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Vangelis Simeonidis, PhD, PMP Senior Project ManagerDr. Vangelis Simeonidis is Senior Project Manager in the Yurkovich Lab, bringing expertise in clinical research, vaccine and drug development, systems biology, and project governance, with a focus on applying innovative solutions that improve human health. Prior to joining the Buck, Vangelis managed multidisciplinary programs at PATH, Lumen Bioscience, and the Institute for Systems Biology. He holds a PhD in Optimization of Biochemical Systems, as well as master’s degrees in Chemical Engineering and Process Systems Engineering. Vangelis has extensive experience in both the application of project management best practices, and the integration of computational approaches for the study of metabolic behavior.
VSimeonidis@buckinstitute.org
