David R. Penas

Large-scale analysis of optimisation methods for parameter estimation problems in the life sciences

The paper benchmarks optimization methods for parameter estimation in life sciences, identifying performance tiers and proposing a hybrid strategy that improves solution quality and robustness.

An adaptive multi-strategy metaheuristic for robust model calibration in large-scale systems biology

This paper introduces eLSHADE+, a metaheuristic for robust model calibration in systems biology, showing improved convergence and accuracy over existing methods.

Host-aware Identification of Intrinsic Gene Expression Biopart Parameters from Combinatorial Libraries

The paper introduces a host-aware framework to identify transferable gene expression biopart parameters from combinatorial libraries, revealing intrinsic properties of transcriptional units.

Parameter estimation in a whole-brain network model of epilepsy: comparison of parallel global optimization solvers

This paper compares parallel global optimization solvers for parameter estimation in whole-brain epilepsy models, showing improved scalability and performance with Bayesian optimization and uncertainty quantification.

Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells

This paper develops a rule-based cell cycle model for RPE-1 cells that explains 16 observables and improves model reusability through PEtab specification.

Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants

This paper develops a method to evaluate energy yield and driving force in microbial metabolic pathways using thermodynamic principles and multi-objective optimization, applied to propionate oxidation and reverse TCA cycle.