Assistant Professor

Dr. Bernstein is an Assistant Professor in Electrical and Biomedical Engineering with a secondary appointment in Microbiology and Molecular Genetics. He earned his BS in Mechanical Engineering from the University of Vermont and PhD in Biomedical Engineering from Boston University. Prior to joining UVM, he was a postdoctoral researcher at the University of California, Berkeley. His research in the field of systems biology combines bioinformatics, computational modeling, and machine learning to gain quantitative understanding of microbial ecosystems. His work is at the forefront of genome-scale metabolic modeling where he has published in leading journals and presented at international conferences. Applications of his work focus on understanding the role of microbial organisms in environmental and human health.

Research and/or Creative Works

The Microbiome Metabolic Modeling (“M-cubed”) lab develops computational tools to better understand microbial ecosystems. Microbial organisms are ubiquitous in nature, forming complex ecosystems that influence human health and environmental processes. Our goal is to improve quantitative understanding of these microbial systems to leverage control points of environmental processes and design treatments for human diseases. We focus primarily on metabolism, and genome-scale metabolic models, through which we can link genomic data to multi-scale computational models of microbial physiology. Current research projects in the lab relate to general improvement of genome-scale metabolic model accuracy through experimental validation, and development of dynamic computational models of the infant gut microbiome.

david bernstein photo

Areas of Expertise and/or Research

Computational Biology, Systems Biology, Genome-Scale Metabolic Modeling, Microbiome, Machine Learning


  • B.S., Mechanical Engineering, University of Vermont
  • Ph.D., Biomedical Engineering, Boston University


Office Location:

Votey 309B

  1. Microbiome Metabolic Modeling Lab