Matthew Muller

I am a PhD candidate in Biomedical Engineering at New York University, co-mentored by Dr. Kelly Ruggles and Dr. Jeffrey Berger at the NYU Tandon School of Engineering and NYU Langone Health. My research sits at the intersection of multi-omic computational biology and cardiovascular medicine, with a focus on discovering translational biomarkers and molecular disease subtypes in high-risk patient populations.

My work integrates whole-genome sequencing, bulk and single-cell RNA-seq, DNA methylomics, and proteomics to characterize the molecular landscape of chronic coronary disease—primarily through analysis of the ISCHEMIA trials biorepository. In parallel, I develop and prospectively validate platelet-based RNA and protein scoring tools (PRESS, TIPS, PROSPER) that stratify cardiovascular risk across diverse inflammatory disease contexts. I have contributed to 25+ peer-reviewed publications, including 7 first-author papers, and hold two U.S. provisional patents for platelet biomarker tools.

Prior to my PhD, I spent four years at the Knight Cardiovascular Institute at OHSU investigating therapeutic and diagnostic ultrasound, characterizing shear-dependent vasoactive pathways and VWF-mediated thromboinflammatory mechanisms in peripheral artery disease and aortic stenosis.

My research program spans two complementary areas:

Multi-omic cardiovascular genomics. I lead computational analyses of the ISCHEMIA trials biorepository, applying multi-layered omics (WGS, RNA-seq, methylomics, proteomics) to identify molecularly distinct subtypes of chronic coronary disease with differential clinical outcomes. Using whole-genome sequencing, I established that clonal hematopoiesis of indeterminate potential (CHIP) is prevalent in this cohort and independently associated with adverse cardiovascular events. I subsequently integrated whole-blood epigenomics and transcriptomics to define vulnerable molecular subtypes with precision stratification potential.

Platelet biology & biomarker discovery. I develop platelet transcriptomic and proteomic scoring tools—PRESS (Platelet Reactivity ExpreSsion Score), TIPS (platelet Transcriptomic signature of thrombInflammation and Platelet reactivity Score), and PROSPER (PROtein Signature of PlatelEt Reactivity)—validated across patients with peripheral artery disease, systemic lupus erythematosus, and chronic coronary disease. These tools predict cardiovascular events prospectively and are the basis of two U.S. provisional patents.

• Muller M, Cornwell MG, Rajkumar S, Chen Z, et al. "Whole blood epigenomic and transcriptomic characterization identifies vulnerable molecular subtypes of chronic coronary disease." Nature Communications, 2026. Accepted
• Muller M, Liu R, Shah F, Hu J, et al. "Clonal Hematopoiesis of Indeterminate Potential in Chronic Coronary Disease: A Report From the ISCHEMIA Trials Biorepository." Circulation: Genomic and Precision Medicine, 2025.
• Berger JS, Cornwell MG, Xia Y, Muller MA, et al. "A Platelet Reactivity ExpreSsion Score derived from patients with peripheral artery disease predicts cardiovascular risk." Nature Communications, 2024.

• Muller MA, Luttrell-Williams E, Bash H, Cornwell MG, et al. "Platelet Gene Expression in Systemic Lupus Erythematosus and Cardiovascular Health." JACC: Basic to Translational Science, 2025.
• Beitzen-Heineke A, Muller MA, Xia Y, Luttrell-Williams E, et al. "A platelet transcriptomic signature of thromboinflammation predicts cardiovascular risk." JCI Insight, 2025.
• Muller M, Hamo CE, Luttrell-Williams E, Ruggles KV, Barrett TJ, Berger JS. "A PROtein Signature of PlatelEt Reactivity (PROSPER) Associated with Cardiovascular Events." Under Review. Under Review (Presented at AHA Scientific Sessions 2025)

• Muller MA, Ozawa K, Hodovan J, Hagen MW, et al. "Treatment of Limb Ischemia with Conducted Effects of Catheter-Based Endovascular Ultrasound." Ultrasound in Medicine & Biology, 2021.
• Muller MA, Xie A, Qi Y, Zhao Y, et al. "Regional and Conducted Vascular Effects of Endovascular Ultrasound Catheters." Ultrasound in Medicine & Biology, 2020.
• Ozawa K, Muller MA, Varlamov O, Hagen MW, et al. "Reduced Proteolytic Cleavage of von Willebrand Factor Leads to Aortic Valve Stenosis and Load-Dependent Ventricular Remodeling." JACC: Basic to Translational Science, 2022.
• Ozawa K, Muller MA, Varlamov O, Tavori H, et al. "Proteolysis of Von Willebrand Factor Influences Inflammatory Endothelial Activation and Vascular Compliance in Atherosclerosis." JACC: Basic to Translational Science, 2020.

Complete publication list on Google Scholar.