Postdoctoral Scholar · San Diego State University
Genome-scale modeling & data analytics for biology.
I’m a computational systems biologist with 14 peer-reviewed publications and six years building predictive genome-scale models of microbial metabolism. I currently apply metabolism-and-expression (ME) modeling to plant rhizosphere bacteria for bioenergy applications, and I specialize in translating multi-omics data into models that guide strain engineering.
Quick links
Postdoctoral Scholar at San Diego State University. Alongside that work I take on selective independent contracting in genome-scale modeling and biological data analytics.
About
I’m a Postdoctoral Scholar in the Computational Biotechnology Research Group at San Diego State University, where I build metabolism-and-expression (ME) models for plant rhizosphere bacteria with integrated pH- and temperature-stress mechanisms. I validate these reconstructions against large-scale phenotypic screens across pH and temperature gradients, integrate model predictions with multi-omics and biogeochemical data from the Earth Microbiome Project, NMDC, and NEON, and contribute to federally funded research programs (DOE, NSF) on metabolic modeling of bioenergy-relevant microbial systems.
My PhD work at UC San Diego combined unsupervised machine learning on large multi-omics datasets with genome-scale metabolism and expression models to study proteome allocation and stress response in E. coli. I also built and deployed a web-based platform that makes ME-model tools accessible to the broader scientific community.
Alongside my postdoctoral position, I consult for academic research groups under an independent contractor agreement — ME-model reconstruction, constraint-based modeling methods, multi-omics analysis, and modeling infrastructure.
Services
Selective independent contracting for academic labs, biotech, and industry R&D, taken on alongside my postdoctoral research.
Genome-scale modeling
Build, curate, and analyze GEMs and ME-models; condition-specific constraints; gene knockouts; and interpretable model-based predictions.
Constraint-based analysis
FBA / ME optimization, resource allocation analyses, and workflow automation with clear documentation and reproducible outputs.
Multi-omics integration
Integrate transcriptomics, proteomics, and metabolomics with modeling frameworks; quality control, normalization, and structured compendia.
Data analytics
Statistics and ML for high-dimensional biology (dimensionality reduction, clustering, regression) with an emphasis on interpretability.
Reproducible pipelines
Python + Git + Docker-based pipelines for analyses you can hand off to a team and maintain over time.
Engagement types
- Short consult — one or two calls + written recommendations
- Fixed-scope project — defined deliverables and timeline
- Ongoing support — weekly hours for modeling/analytics work
Selected work
Representative artifacts that show capabilities end-to-end.
COBRAme.org
A web platform I built and deployed to make ME-model tools accessible to outside research groups — run and explore genome-scale metabolism & expression workflows without a local install.
↗PhD Dissertation
UC San Diego, 2025. Integrating multi-omics knowledge with constraint-based modeling to improve predictive physiology — machine learning on transcriptomes and proteomes coupled to genome-scale ME-models of E. coli.
↗Google Scholar
Complete publication list, citations, and links.
↗GitHub
Open-source tools, pipelines, and modeling code.
↗Publications
14 peer-reviewed publications. Full metrics and links on Google Scholar .
2026
- A systems-level atlas of carbon-response transcriptional states in Escherichia coli. Proceedings of the National Academy of Sciences 123(27), e2531884123.
- Aerobicity stimulon in Escherichia coli revealed using multi-scale computational systems biology of respiratory variants. iScience 29(2), 114715.
2025
- Laboratory evolution reveals transcriptional mechanisms underlying thermal adaptation of Escherichia coli. Genome Biology and Evolution 2025 Sep 30;17(10):evaf171.
- Extracellular respiration is a latent energy metabolism in Escherichia coli. Cell 188(11), 2907–2924.e23.
- iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets. Nucleic Acids Research 53(D1), D99–D106.
- Trade-off between resistance and persistence in high cell density Escherichia coli cultures. mSystems 10(7), e0032325.
2024
- Proteome allocation is linked to transcriptional regulation through a modularized transcriptome. Nature Communications 15(1), 5234.
- The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. mSystems 9(7), e00305-24.
2023
- Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance. Cell Reports 42(9):113105.
- TCA cycle tailoring facilitates optimal growth of proton-pumping NADH dehydrogenase-dependent Escherichia coli. Microbiology Spectrum 11(6), e02225-23.
2022
- Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity. Nature Communications 13(1), 3682.
2021
- Restoration of fitness lost due to dysregulation of the pyruvate dehydrogenase complex is triggered by ribosomal binding site modifications. Cell Reports 35(1), 108961.
2020
- The expanding computational toolbox for engineering microbial phenotypes at the genome scale. Microorganisms 8(12), 2050.
2018
- Ethical considerations in the translation of CAR-T cell therapies. Immuno-oncology Insights
CV
Education
- PhD, Bioengineering — University of California, San Diego (Nov 2025) — GPA: 3.833
- BS, Biomedical Engineering — Georgia Institute of Technology (May 2019), minor in Engineering and Business — GPA: 4.0
Focus areas
- Genome-scale metabolic and expression (ME) modeling (COBRAme, DynamicME, StressME)
- Stress-integrated ME-models (AcidifyME, FoldME) for pH and temperature response
- Constraint-based modeling workflows (FBA/ME), resource allocation, condition-specific modeling
- Multi-omics integration and interpretable ML for regulatory structure discovery
- Software engineering for reproducible modeling pipelines (Python, Docker, GitHub)
Experience (condensed)
- Postdoctoral Scholar — San Diego State University, Computational Biotechnology Research Group (2026–present)
ME-models for plant rhizosphere bacteria under pH and temperature stress; bioenergy applications; DOE/NSF proposals. - Scientific Consultant — independent contractor (2026–present)
Computational systems biology consulting for academic research groups. - Graduate Student Researcher — UC San Diego, Systems Biology Research Group (Palsson Lab) (2019–2025)
Genome-scale modeling + multi-omics analytics; tool development and collaborations across projects.
Selected highlights
- 14 peer-reviewed publications, including first-author papers in Nature Communications and iScience
- Invited flash talk and first-author poster, Center for Bioenergy Innovation 2026 Annual Science Meeting; first-author poster, GLBRC 2026
- Invited lectures at Tata Institute of Fundamental Research, Mumbai (2025, 2026) and San Diego State University (2026)
- Hosted and organized the pre-conference COBRA methods workshop, COBRA 2024
- Patent WO2018045287 — Solid Particulate Measuring Devices, Systems and Methods
Download
The on-page CV is intentionally condensed for readability; the PDF contains the full academic CV.