Research

My background is in applied mathematics. I specialized in systems biology modeling during my Ph.D. After that, I did research on machine learning applications in genomics.

Check out my Ph.D. thesis, “In pursuit of mathematical principles in systems biology” PDF

Better ways to perform mitochondrial DNA association studies

I study the variations in the mitochondrial genome. I am interested in determining the pathogenicity of mtDNA variants and their role in the etiology of chronic disease, cancer treatment, and healthy aging. I am developing methods to perform Genome-Wide Association Studies for mitochondrial DNA. The goal is to overcome the limitations of traditional methods, such as haplogroup association studies that are underpowered to detect subtle changes when dealing with a moderate sample size.

Systems biology approach to sensory adaptation

Chapters 2, 3, 4, and 5 of this my are inspired by a biological behavior called sensory adaptation. We can briefly define it as the continuous recalibration of biological sensors as a response to the changes in their environment. I explore the capabilities of different classes of biochemical reaction networks in showing sensory adaptation. Under certain constraints on the structure and thermodynamics of these biochemical reactions, I prove that the functionality is limited. I prove that those limitations can be characterized by the properties of the graph of the reactions. I further show how relaxing the constraints allows these networks to exhibit arbitrarily strong adaptation.

Synthetic Biology

Finding design principles in Synthetic biology is the subject of Chapter 6 of my Ph.D. thesis. I study a specific synthetic biology toolbox called the PEN-DNA toolbox, which is used to make DNA-based circuits that mimic the cellular signaling pathways. We find general design principles in terms of mathematical theorems that shed light on the global properties of the toolbox. I also analyze different ways of reducing the complexity of the mathematical models of this toolbox.

Systems Pharmacology

Systems pharmacology, the quantitative and data-integrated approach to studying the interaction of the body with drugs, is the subject of Chapter 7 of my thesis. We deal with the mathematical modeling, fitting, and interpreting of clinical trial data related to blood glucose regulation in human subjects. We study the effect of a new drug on the number of glucagon receptors in the liver, as well as its impact on the action of the hormone glucagon in the blood glucose regulation.