Jonathan Monk, Ph.D.

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.

April 2025 – Present

Vice President of Bioinformatics

Avellino Labs

April 2023 – April 2025

Co-Founder and Head of Bioinformatics

Palmona Pathogenomics

January 2020 – April 2023

Research Scientist and Scientific Consultant

Sinopia Biosciences

January 2016 – January 2020

Graduate Student Researcher

Systems Biology Research Group, UC San Diego

September 2010 – December 2015

Education

University of California, San Diego

Ph.D., Chemical Engineering

September 2010 – December 2015

University of California, San Diego

M.S., Chemical Engineering

September 2010 – December 2012

Princeton University

B.S.E., Chemical Engineering

Minors: Computer Science and Engineering Biology

September 2004 – June 2008

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

2015

National Science Foundation Fellow

EAPSI

2013