112 citations · 158 across the 12 of their papers we have counts for
14 papers
A Hybrid Framework for Uncertainty Quantification in Partially Observed Dynamic Biological Systems
Alberto Portela, Julio R. Banga
Mechanistic ordinary differential equation (ODE) models are widely used in systems biology, but uncertainty quantification (UQ) remains difficult when only a subset of state variab…
Conformal Prediction in Dynamic Biological Systems
Alberto Portela, Julio R. Banga, Marcos Matabuena
Uncertainty quantification (UQ) is the process of systematically determining and characterizing the degree of confidence in computational model predictions. In the context of syste…
Generalized Inverse Optimal Control and its Application in Biology
Julio R. Banga, Sebastian Sager
Living organisms exhibit remarkable adaptations across all scales, from molecules to ecosystems. We believe that many of these adaptations correspond to optimal solutions driven by…
Parameter estimation in ODEs: assessing the potential of local and global solvers
M. Fernández de Dios, Ángel M. González-Rueda, Julio R. Banga +2
We consider the problem of parameter estimation in dynamic systems described by ordinary differential equations. A review of the existing literature emphasizes the need for determi…
A protocol for dynamic model calibration
Alejandro F. Villaverde, Dilan Pathirana, Fabian Fröhlich +2
Ordinary differential equation models are nowadays widely used for the mechanistic description of biological processes and their temporal evolution. These models typically have man…
Repairing dynamic models: a method to obtain identifiable and observable reparameterizations with mechanistic insights
Gemma Massonis, Julio R. Banga, Alejandro F. Villaverde
Mechanistic dynamic models allow for a quantitative and systematic interpretation of data and the generation of testable hypotheses. However, these models are often over-parameteri…
Structural Identifiability and Observability of Compartmental Models of the COVID-19 Pandemic
Gemma Massonis, Julio R. Banga, Alejandro F. Villaverde
The recent coronavirus disease (COVID-19) outbreak has dramatically increased the public awareness and appreciation of the utility of dynamic models. At the same time, the dissemin…
PEtab -- interoperable specification of parameter estimation problems in systems biology
Leonard Schmiester, Yannik Schälte, Frank T. Bergmann +26
Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been -- so far -- no broadly supported format for the specification of p…
Dynamical compensation and structural identifiability: analysis, implications, and reconciliation
Alejandro F. Villaverde, Julio R. Banga
The concept of dynamical compensation has been recently introduced to describe the ability of a biological system to keep its output dynamics unchanged in the face of varying param…
Dynamical compensation in biological systems as a particular case of structural non-identifiability
Alejandro F. Villaverde, Julio R. Banga
Dynamical compensation (DC) has been recently defined as the ability of a biological system to keep its output dynamics unchanged in the face of varying parameters. This concept is…
BioPreDyn-bench: benchmark problems for kinetic modelling in systems biology
Alejandro F Villaverde, David Henriques, Kieran Smallbone +10
Dynamic modelling is one of the cornerstones of systems biology. Many research efforts are currently being invested in the development and exploitation of large-scale kinetic model…
Sloppy models can be identifiable
Oana-Teodora Chis, Julio R. Banga, Eva Balsa-Canto
Dynamic models of biochemical networks typically consist of sets of non-linear ordinary differential equations involving states (concentrations or amounts of the components of the…
Multicriteria global optimization for biocircuit design
Irene Otero-Muras, Julio R. Banga
One of the challenges in Synthetic Biology is to design circuits with increasing levels of complexity. While circuits in Biology are complex and subject to natural tradeoffs, most…
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics
Jose A Egea, David Henriques, Thomas Cokelaer +3
Optimization is key to solve many problems in computational biology. Global optimization methods provide a robust methodology, and metaheuristics in particular have proven to be th…