112 citations · 161 across the 12 of their papers we have counts for
15 papers
Structural Identifiability and Discrete Symmetries
Xabier Rey Barreiro, Nick Baberuxki, Meskerem Abebaw Mebratie +2
We discuss the use of symmetries for analysing the structural identifiability and observability of control systems. Special emphasis is put on the role of discrete symmetries, in c…
Analysing control-theoretic properties of nonlinear synthetic biology circuits
Antón Pardo, Sandra Díaz Seoane, Dorin A. Ionescu +2
Synthetic biology is a recent area of biological engineering, whose aim is to provide cells with novel functionalities. A number of important results regarding the development of c…
Employing observability rank conditions for taking into account experimental information a priori
Alejandro F. Villaverde
The concept of identifiability describes the possibility of inferring the parameters of a dynamic model by observing its output. It is common and useful to distinguish between stru…
STRIKE-GOLDD 4.0: user-friendly, efficient analysis of structural identifiability and observability
Sandra Díaz-Seoane, Xabier Rey-Barreiro, Alejandro F. Villaverde
Structural identifiability and observability are desirable properties of systems biology models. Many software toolboxes have been developed for their analysis in the last decades.…
Benchmarking tools for a priori identifiability analysis
Xabier Rey Barreiro, Alejandro F. Villaverde
The structural identifiability and the observability of a model determine the possibility of inferring its parameters and states by observing its outputs. These properties should b…
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…
Nonlinear observability algorithms with known and unknown inputs: analysis and implementation
Nerea Martínez, Alejandro F. Villaverde
The observability of a dynamical system is affected by the presence of external inputs, either known (such as control actions) or unknown (disturbances). Inputs of unknown magnitud…
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…
Observability and Structural Identifiability of Nonlinear Biological Systems
Alejandro F. Villaverde
Observability is a modelling property that describes the possibility of inferring the internal state of a system from observations of its output. A related property, structural ide…
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…
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…