112 citations · 158 across the 12 of their papers we have counts for
7 papers · 1 filter
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…
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…
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…
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…