Jonathan Karr

Jonathan Karr, PhD

  • ASSISTANT PROFESSOR | Genetics and Genomic Sciences

Research Topics:

Bioinformatics, Biomechanics/Bioengineering, Biophysics, Cell Biology, Computational Biology, Computer Simulation, Genomics, Metabolism, Microbiology, Systems Biology, Theoretical Biology

Jonathan is an Assitant Professor for the Department of Genetics and Genomic Sciences. The goal of Jonathan's research is to develop a predictive foundation for medicine and bioengineering analogous to the Newtonian foundation for mechanical engineering. Such a predictive foundation could enable clinical decision support tools that help clinicians personalize medicine, as well as enable Bio-CAD tools that help bioengineers rationally design microorganisms for a wide range of medical and industrial functions.   Toward this goal, Jonathan's research group is developing "whole-cell" dynamical models that predict the phenotype of individual cells from their genotype by representing all of the biochemical activity inside cells. To enable comprehensive whole-cell models, Jonathan's group is also developing the computational methods and software tools needed to build, simulate, and apply whole-cell models to medicine and bioengineering.   Currently, Jonathan's group is developing an expanded model of Mycoplasma pneumoniae, as well as prototyping the first whole-cell model of a human cell. In addition, Jonathan's group is developing tools for discovering, aggregating, and integrating the data needed for cell modeling; scalably designing large models from large datasets; describing mixed-grain models; simulating multi-algorithmic models; and rigorously verifying models. All of Jonathan's research is available open-source.   Jonathan's group is an interdisciplinary group of scientists and engineers. The group currently includes one PhD student, three postdoctoral scholars, one staff member, and three faculty members. The group is always looking for talented, motivated individuals to join the team. Interested candidates should contact Jonathan for more information.   More information:

Multi-Disciplinary Training Areas

Cancer Biology [CAB], Genetics and Genomic Sciences [GGS], Microbiology [MIC], Pharmacology and Therapeutics Discovery [PTD]


MS, Stanford University

PhD, Stanford University

SB, Massachusetts Institute of Technology