24/09/2026 - A new doctor in the group!
Today, Xabier Rey Barreiro has successfully defended his PhD thesis - Congratulations, Xabier!
The dissertation, titled "Computational modelling of the dynamics of immune reactions: methodologies for identifiability and robustness analysis", was supervised by Jose Faro and Alejandro F. Villaverde.
It was presented as a collection of published articles and received the maximum grade (sobresaliente), as well as an international distinction.
Many thanks to the PhD committee for their service: Eva Balsa Canto, María Teresa Sánchez Rúa, and Gleb Pogudin.
18/09/2026 - New preprint
In "A Hierarchical Framework for Inverse Problems in Biological Cybernetics: Opportunities and Limitations", Julio R. Banga and Alejandro F. Villaverde discuss inverse problems in biology.
Specifically, we discuss how to reconstruct the mechanisms that govern living systems from experimental data.
To this end, we propose a four-level hierarchy of inverse problems in systems biology, from the relatively mature to the still speculative.
The paper can be found here.
04/09/2026 - Participation in the Jornadas de Automática
One more year, our group is attending the Jornadas de Automática.
This year it is Mahmoud Shams Falavarjani who is in Córdoba, to present our work titled "Symmetry-Based Structural Identifiability and Observability Analysis of PDE and ODE Models in STRIKE-GOLDD".
The paper is already available here.
26/08/2026 - Visitor from Freiburg
Today, Mio Heinrich, from Jens Timmer's group at the University of Freiburg, is visiting our group.
We've already had great discussions about identifiability and related analyses, and their role in biological modelling.
Looking forward to opportunities to collaborate in this topic!.
03-04/06/2026 - Participation in the workshop on "Model discovery for engineering Biology"
Last week, Adriana, Xabier, and Alex attended the workshop on "Model discovery for engineering Biology", held at the Royal Academy of Engineering in London, UK.
We are grateful to the organiser, Prof. Alex Darlington (University of Warwick), for his generous invitation to participate.
It was a real pleasure to showcase our work in front of a wonderful audience, and to engage in many interesting discussions.
08/05/2026 - A second paper on T-cell activation models
We have published the second of two connected papers.
In the first one, we derived equations linking experimentally measurable response metrics to the current mathematical models of T-cell activation.
In the second, we use these results to assess when these models can be reliably calibrated and used for prediction.
The new paper, written again by Xabier and Alejandro in collaboration with Jose Faro, is now published in PLOS Computational Biology and can be read here.
25/03/2026 - New paper on T-cell activation models
A number of T-cell activation models have been proposed to describe how antigens trigger an immune response.
To analyse their identifiability, observability and sensitivity, it is necessary to have formulas relating their measurable outputs to model parameters.
In this paper we derive such formulas for models for which they were yet unknown, thus enabling their exploitation to understand and control the immune response.
The paper, written by Xabier and Alejandro in collaboration with Jose Faro, can be read here.
13/03/2026 - New release of STRIKE-GOLDD
We have added a new algorithm to our STRIKE-GOLDD toolbox.
Called 'SIM_PDE', it searches for scaling symmetries that lead to unidentifiability and/or unobservability in PDE models.
It has been implemented by Mahmoud.
The new release also contains minor improvements, such as fixing a number of bugs.
01/12/2025 - New paper on accessibility and observability analysis
Mahmoud's first paper, "Assessment of Computational Tools for Analysing the Observability and Accessibility of Nonlinear Models", has just been published
in Computation. Check it out here.
Co-written by Adriana and Alejandro, it provides a systematic comparison of two MATLAB tools, StrucID and STRIKE-GOLDD.
It features research carried out in the DYNAMO-bio project.
