Trainees
2026-2027 SBDS Trainees
Caelli Bagalkotkar, Biomedical Engineering
Identifying metabolic features associated with distant progression in melanoma
Melanoma accounts for a disproportionate share of skin-cancer-related deaths due to its propensity to metastasize to distant organs. To survive the metastatic process, melanoma cells rely on phenotypic and metabolic plasticity to adapt to diverse stressors along the metastatic cascade. My research uses genome-scale metabolic models (GEMs) to identify metabolic pathways and functions that may support this adaptation by comparing inferred metabolic activity in primary melanoma tumors from patients with and without evidence of metastatic progression.
Primary Mentor: Mohammad Fallahi-Sichani
Secondary Mentor: Jason Papin
Alex DeWalle, Biomedical Engineering
Evaluating a Link Between Macropinocytosis and Epithelial-Mesenchymal Transition in Pancreatic Ductal Adenocarcinoma
RAS-driven pancreatic ductal adenocarcinoma (PDAC) cells employ both macropinocytosis, a bulk endocytic process used for nutrient uptake, and epithelial-mesenchymal transition (EMT), a pro-migratory phenotypic change that drives chemoresistance, to survive and escape a nutrient-depleted tumor microenvironment. Since these processes are both RAS-driven, mediated by cytoskeletal reorganization, and associated with worse outcomes in mouse models, I hypothesize that EMT and macropinocytosis are causally linked. My prior work has established a correlation between these two processes in vitro, and my ongoing work aims to investigate it ex vivo and establish a directionality.
Primary Mentor: Matthew Lazzara
Secondary Mentor: Eli Zunder
Ben Dahl, Biomedical Engineering
Systems analyses to understand mechanisms of dosage sensitivity in signaling networks.
I use mathematical modeling and systems-level approaches to characterize genes like GDF11 and various protein kinases and quantify how the network of interactions leads to dosage sensitivity and genetic disease when mutated.
Primary Mentor: Sameer Bajikar
Secondary Mentor: Kristen Naegle
Ryan Smith, Biomedical Engineering
Elucidating the Role of Metabolic State Heterogeneity in Melanoma Metastasis
Melanoma is a curable form of skin cancer, but if it metastasizes, there is a sharp decline in patient survival. My work uses spatially resolved, multiplexed, single-cell imaging and data-driven computational modeling to profile heterogenous metabolic states and their determinants in human primary melanoma tumors and lymph node metastases. Additionally, my work aims to identify metabolic features that predict sentinel lymph node metastasis.
Primary Mentor: Mohammad Fallahi-Sichani
Secondary Mentor: David Kashatus
Rashmi Mohotti, Chemical Engineering
Systems biology framework for engineering of kinase-adaptive oncolytic virus therapy
My research seeks to improve oncolytic virus (OV) therapy for glioblastoma (GBM) by developing a mechanistic mathematical model of the mammalian cellular response to viral infection. By integrating the regulation of antiviral signaling pathways, protein expression, and kinase activity, I investigate how these molecular networks influence viral replication and therapeutic efficacy. Using this model, I would then be able to identify pharmacological kinase targets that can be modulated to enhance the effectiveness of oncolytic viral therapy against GBM.
Primary Mentor: Matthew Lazzara
Secondary Mentor: Shayn-Pierce Cottler
Patrick Hart, Experimental Pathology
Multi-modal characterization of comorbid diabetic-atherosclerosis
Diabetes (T1D & T2D) is an independent risk factor for atherosclerosis, enhancers several disease features, and is associated with poor clinical outcomes. My project seeks to identify shared genetic risk in diabetes and atherosclerosis and will leverage single cell multi-omic (ATAC, RNA) profiling to identify the gene programs and cell types which govern altered disease progression and establishment. Using primary human coronary vascular tissue, this work aims to describe the major effectors of atherosclerotic plaque instability in diabetic populations, which can cause life-threatening cardiovascular events such as myocardial infarction, with the ultimate goal of informing new therapeutic approaches for prevention of adverse cardiovascular events.
Primary Mentor: Clint L. Miller, PhD
Secondary Mentor: Chongzhi Zang, PhD
Prerak Thakkar, Biomedical Engineering
Characterizing the role of tumor-intrinsic MHC II in the immune response to non-small cell lung cancer
My research focuses on the interactions between immune cells and cancer cells in the tumor microenvironment of non-small cell lung cancer. Through the use of experimental approaches alongside computational analyses of patient data, I aim to establish prognostic biomarkers of immune response and outcomes of immunotherapies.
Primary Mentor: Sepideh Dolatshahi
Secondary Mentor: Ryan Gentzler
Andrew Croitoru, Biology
Cell-type Level Metabolic Modeling of the response to a High Fructose Diet in C. elegans
I am interested in better understanding the molecular mechanisms by which high sugar diets promote obesity and its many negative effects on health across tissues. My research uses the nematode C. elegans as a model of diet induced obesity and its negative effects on organismal health and cellular function. Using a combination of single-cell RNA sequencing analysis and high throughput RNA interference genetic screens, I aim to identify how obesity affects specific cell types differently and how effects are coordinated across cell types. I am using metabolic modeling to develop hypotheses about how a high fructose diet alters metabolic networks in a cell type specific manner, with the ultimate goal of identifying targets for the treatment of obesity and its comorbidities.
Primary Mentor: Dr. Eyleen O'Rourke
Secondary Mentor: Dr. Jason Papin
Past Year Cohorts
2025
Lucia Wagner, Pathology, Experimental Pathology
Anna Grace Dickerson, Neuroscience
Caitlin Sullivan, Biomedical Engineering
Samuel Doak, Chemical Engineering
Robert Heussner, Biomedical Engineering
Adam Bates, Biomedical Engineering
Ify Nwolah, Biomedical Engineering
2024
Jeffrey Hsu, Biochemistry & Molecular Genetics
Audrey Kidd, Biomedical Engineering
Lavie Ngo, Biomedical Engineering
Mary O'Sullivan, Biomedical Engineering
William Shao, Biomedical Engineering
Madison Turner, Microbiology, Immunology, and Cancer Biology (MIC)
Yasmina Zeineddine, Biomedical Engineering
2023
Gabe Hanson, Biomedical Engineering
Russell Hawes, Biomedical Engineering
Shay Ladd, Biomedical Engineering
Kris Pas, Biomedical Engineering
Jamel Simpson, Biophysics
Lionel Watkins, Biomedical Engineering
Yonatan Degefu, Biomedical Engineering
Candace Lei, Biomedical Engineering
2022
Catalina Alvarez Yela, Biomedical Engineering
Tien Comlekoglu, Biomedical Engineering
Remziye Erdogan, Biomedical Engineering
Mario Garcia, Biomedical Engineering
Emma Glass, Biomedical Engineering
Nathan LeRoy, Biomedical Engineering
Conner Moore, Biomedical Engineering
Contact Us
Connie Pace
Administrator, Systems & Biolecular Data Science Training Program
UVA BME | MR5 Room 2010
Phone: 434 243-7660