Our group builds computational tools rooted in advanced optimization and machine learning to redesign and understand biological systems.
Genome-scale network reconstruction, construction and analysis of stoichiometric and kinetic models of cellular metabolism. Our flagship tools — GRASP, LooplessFluxSampler, and METACONE — underpin this research direction.
Related papersEngineering biological systems for sustainable production of food ingredients and high-value chemicals.
Related papersAdvanced optimization frameworks for bioreactor design, control, and process scale-up.
Related papersComputational statistics and ML techniques to infer, predict, and design biological behavior from sparse data.
Related papersPublicly released computational tools — METACONE, GRASP, LooplessFluxSampler, Fast-SNP, ll-ACHRB, among others.
Explore softwareGroup Leader
Faculty member at the Department of Chemical and Bioprocess Engineering and the Institute for Mathematical and Computational Engineering of PUC Chile. Interests include genome-scale network reconstruction and analysis, metabolic modelling and engineering, and bioprocess and biosystems optimization.
Education
PhD Students
Master Students
Alumni
Featured Works
All Papers
IEEE ICA-ACCA, Santiago, Chile
Synthetic Biology of Yeasts. Springer, Cham
Methods in Molecular Biology vol. 2399, Springer
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In Preparation
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Scalable framework for exploring the conversions cone of metabolic networks.
Efficient algorithm for sampling the loopless flux solution space of genome-scale metabolic models.
Computational platform for building thermodynamically consistent kinetic models of cell metabolism.
Matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models.
Scalable algorithm for sampling the feasible solution space of metabolic networks.
Browse all open-source repositories, models, datasets, and supporting code released by the lab.
2026
Official lunch of VitiScience
Our group leader was part of the official lunch of VitiScience at the Center for Research and Innovation of Viña Concha y Toro in Pencahue, Talca.
2026
New FONDECYT Regular ANID Grant Awarded — Principal Investigator
Grant No. 1262500 — Scalable prediction of metabolic fluxes using modelling frameworks informed by enzyme kinetics and omics data (2026–2029).
2026
New Paper: Beer Digital Twin
Congrats Colomba! Our group recently published in Journal of Food Engineering — a digital model integrating industrial process data for beer quality control.
2026
New Paper: METACONE released
Congrats Álvaro! Our group just published METACONE in Computational Biology and Chemistry — a scalable framework for computing metabolic conversions.
2025
New Avanza UC Grant Awarded — Principal Investigator
Grant No. AV25292 for optimizing EPS production in Sulfobacillus acidophilus using metabolic engineering.
2025
New ANID Center for Applied Research established
Joined the Center for Research and Innovation VitiScience as Adjunct Investigator.
2025
New Paper: Kinetic model of β-carotene in yeast
Congrats Benjamín! We just published a detailed kinetic model predicting β-carotene production in ACS Synthetic Biology.
2024
New Paper: LooplessFluxSampler released
We have recently published an efficient loopless flux sampling algorithm in BMC Bioinformatics.
Principal Investigator
Basal Center for Artificial Intelligence Research
2021–ongoing
Principal Investigator
FONDECYT Regular No. 1262500 — Scalable prediction of metabolic fluxes informed by enzyme kinetics and omics data.
2026–2029
Co-Investigator
FONDECYT Exploración No. 13250023 — Impact of GABA-producing bacterial consortia in neuroprotection
2025–2029
Co-Investigator
FONDECYT Regular No. 1230764 — Model-guided analysis of microbial interactions in gut microbiota
2023–2027
Principal Investigator
Avanza UC AV25292 — EPS production from mining waste via S. acidophilus
2026–2027
Adjunct Investigator
Center for Research and Innovation VitiScience
2025–ongoing
Our lab uses both wet and dry lab approaches to better understand biological systems. We welcome motivated students and researchers excited about developing new computational approaches for rediscovering biology. We have openings for domestic and international applicants at all levels.
Contact Prof. Pedro Saa directly at pnsaa@uc.cl · +56 2 2354 9674