About
Jonathan Monk
Data Scientist & Research Scientist
I am a Translational Systems Biologist and R&D Leader with over 15 years of experience driving precision diagnostics through the integration of multi-omics data, pathogen pangenomics, and genome-scale metabolic modeling. My work centers on applying systems biology and machine learning to deconstruct complex biological networks, build strain-resolved predictive models, and uncover novel vulnerabilities within highly adaptable pathogen populations. I hold a Ph.D. in Chemical Engineering with a focus on Systems Biology from UC San Diego and a B.S.E. in Chemical Engineering from Princeton University. Currently, I serve as the Co-Founder & Chief Technology Officer at Pastor21 AI, Inc., where I lead the architecture of predictive pangenome engines. In this role, I implement advanced AI/ML workflows—such as non-negative matrix factorization, LLMs, and knowledge graphs—to link vast genetic diversity directly to phenotypes for biomarker and target discovery. Previously, I co-founded Palmona Pathogenomics, a startup dedicated to infectious disease surveillance, virulence factor analysis, and diagnostics, which was successfully acquired by Avellino Labs. Throughout my career, I have been passionate about translating high-dimensional pangenomic datasets and in silico systems predictions into actionable insights, bridging the critical gap between computational models and wet-lab experimental validation.
Experience
Co-Founder & Chief Technology Officer
Pastor21 AI, Inc.
Vice President of Bioinformatics
Avellino Labs
Co-Founder and Head of Bioinformatics
Palmona Pathogenomics
Research Scientist and Scientific Consultant
Sinopia Biosciences
Graduate Student Researcher
Systems Biology Research Group, UC San Diego
Education
University of California, San Diego
Ph.D., Chemical Engineering
University of California, San Diego
M.S., Chemical Engineering
Princeton University
B.S.E., Chemical Engineering
Minors: Computer Science and Engineering Biology
Publications
Research spanning genome-scale metabolic modeling, systems biology, bacterial genomics, antibiotic resistance, and computational biology — with over 90 peer-reviewed publications from 2011 to present.
Awards & Honors
Outstanding Graduate Student Award
UC San Diego
National Science Foundation Fellow
EAPSI