Reset control for injecting dissipation into port-hamiltonian systems. - Cesáreo Raimúndez; Antonio Barreiro; Alejandro Fernández Villaverde (ECC, 2009)

Passive position error correction in Internet-based teleoperation. - Alejandro Fernández Villaverde; Antonio Barreiro; Cesáreo Raimúndez (Autom., 2010)

Thermodynamics and Fluctuations Far From Equilibrium. - John Ross 002; Alejandro Fernández Villaverde (Entropy, 2010)

Reset Control for Passive Bilateral Teleoperation. - Alejandro Fernández Villaverde; Antonio Barreiro Blas; Joaquín Carrasco; Alfonso Baños Torrico (IEEE Trans. Ind. Electron., 2011)

A cooperative strategy for parameter estimation in large scale systems biology models. - Alejandro Fernández Villaverde; Jose A. Egea; Julio R. Banga (BMC Syst. Biol., 2012)

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. - Jose A. Egea; David Henriques; Thomas Cokelaer; Alejandro Fernández Villaverde; Julio R. Banga; Julio Saez-Rodriguez (CoRR, 2013)

High-Confidence Predictions in Systems Biology Dynamic Models. - Alejandro Fernández Villaverde; Sophia Bongard; Klaus Mauch; Dirk Müller 004; Eva Balsa-Canto; Joachim Schmid 004; Julio R. Banga (PACBB, 2014)

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. - Jose A. Egea; David Henriques; Thomas Cokelaer; Alejandro Fernández Villaverde; Aidan MacNamara; Diana-Patricia Danciu; Julio R. Banga; Julio Saez-Rodriguez (BMC Bioinform., 2014)

BioPreDyn-bench: benchmark problems for kinetic modelling in systems biology. - Alejandro Fernández Villaverde; David Henriques; Kieran Smallbone; Sophia Bongard; Joachim Schmid 004; Damjan Cicin-Sain; Anton Crombach; Julio Saez-Rodriguez; Klaus Mauch; Eva Balsa-Canto; Pedro Mendes 001; Johannes Jaeger; et al. (CoRR, 2014)

Enabling network inference methods to handle missing data and outliers. - Abel Folch-Fortuny; Alejandro Fernández Villaverde; Alberto Ferrer 001; Julio R. Banga (BMC Bioinform., 2015)

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. - Alejandro Fernández Villaverde; David Henriques; Kieran Smallbone; Sophia Bongard; Joachim Schmid 004; Damjan Cicin-Sain; Anton Crombach; Julio Saez-Rodriguez; Klaus Mauch; Eva Balsa-Canto; Pedro Mendes 001; Johannes Jaeger; et al. (BMC Syst. Biol., 2015)

A consensus approach for estimating the predictive accuracy of dynamic models in biology. - Alejandro Fernández Villaverde; Sophia Bongard; Klaus Mauch; Dirk Müller 004; Eva Balsa-Canto; Joachim Schmid 004; Julio R. Banga (Comput. Methods Programs Biomed., 2015)

PREMER: Parallel Reverse Engineering of Biological Networks with Information Theory. - Alejandro Fernández Villaverde; Kolja Becker; Julio R. Banga (CMSB, 2016)

Structural Identifiability of Dynamic Systems Biology Models. - Alejandro Fernández Villaverde; Antonio Barreiro; Antonis Papachristodoulou (PLoS Comput. Biol., 2016)

Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems. - Attila Gábor; Alejandro Fernández Villaverde; Julio R. Banga (BMC Syst. Biol., 2017)

Dynamical compensation in biological systems as a particular case of structural non-identifiability. - Alejandro Fernández Villaverde; Julio R. Banga (CoRR, 2017)

Dynamical compensation and structural identifiability: analysis, implications, and reconciliation. - Alejandro Fernández Villaverde; Julio R. Banga (CoRR, 2017)

Data-driven reverse engineering of signaling pathways using ensembles of dynamic models. - David Henriques; Alejandro Fernández Villaverde; Miguel Rocha 001; Julio Saez-Rodriguez; Julio R. Banga (PLoS Comput. Biol., 2017)

Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation. - Alejandro Fernández Villaverde; Julio R. Banga (PLoS Comput. Biol., 2017)

PREMER: A Tool to Infer Biological Networks. - Alejandro Fernández Villaverde; Kolja Becker; Julio R. Banga (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Benchmarking optimization methods for parameter estimation in large kinetic models. - Alejandro Fernández Villaverde; Fabian Fröhlich; Daniel Weindl; Jan Hasenauer; Julio R. Banga (Bioinform., 2019)

Observability and Structural Identifiability of Nonlinear Biological Systems. - Alejandro Fernández Villaverde (Complex., 2019)

Computational Methods for Identification and Modelling of Complex Biological Systems. - Alejandro Fernández Villaverde; Carlo Cosentino; Attila Gábor; Gábor Szederkényi (Complex., 2019)

Input-Dependent Structural Identifiability of Nonlinear Systems. - Alejandro Fernández Villaverde; Neil D. Evans; Michael J. Chappell; Julio R. Banga (IEEE Control. Syst. Lett., 2019)

Nonlinear observability algorithms with known and unknown inputs: analysis and implementation. - Nerea Martínez; Alejandro Fernández Villaverde (CoRR, 2020)

Repairing dynamic models: a method to obtain identifiable and observable reparameterizations with mechanistic insights. - Gemma Massonis; Julio R. Banga; Alejandro Fernández Villaverde (CoRR, 2020)

Finding and Breaking Lie Symmetries: Implications for Structural Identifiability and Observability in Biological Modelling. - Gemma Massonis; Alejandro Fernández Villaverde (Symmetry, 2020)

Structural identifiability and observability of compartmental models of the COVID-19 pandemic. - Gemma Massonis; Julio R. Banga; Alejandro Fernández Villaverde (Annu. Rev. Control., 2021)

PEtab - Interoperable specification of parameter estimation problems in systems biology. - Leonard Schmiester; Yannik Schälte; Frank T. Bergmann; Tacio Camba; Erika Dudkin; Janine Egert; Fabian Fröhlich; Lara Fuhrmann; Adrian L. Hauber; Svenja Kemmer; Polina A. Lakrisenko; Carolin Loos; et al. (PLoS Comput. Biol., 2021)

On testing structural identifiability by a simple scaling method: Relying on scaling symmetries can be misleading. - Alejandro Fernández Villaverde; Gemma Massonis (PLoS Comput. Biol., 2021)

Smooth Non Linear High Gain Observers for a Class of Dynamical Systems. - José Antonio González-Prieto; Alejandro Fernández Villaverde (IEEE Access, 2022)

A protocol for dynamic model calibration. - Alejandro F. Villaverde; Dilan Pathirana; Fabian Fröhlich; Jan Hasenauer; Julio R. Banga (Briefings Bioinform., 2022)

Symmetries in Dynamic Models of Biological Systems: Mathematical Foundations and Implications. - Alejandro F. Villaverde (Symmetry, 2022)

On the Origins and Rarity of Locally but Not Globally Identifiable Parameters in Biological Modeling. - Xabier Rey-Barreiro; Alejandro F. Villaverde (IEEE Access, 2023)

Assessment of Prediction Uncertainty Quantification Methods in Systems Biology. - Alejandro F. Villaverde; Elba Raimúndez-Álvarez; Jan Hasenauer; Julio R. Banga (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

STRIKE-GOLDD 4.0: user-friendly, efficient analysis of structural identifiability and observability. - Sandra Díaz-Seoane; Xabier Rey-Barreiro; Alejandro F. Villaverde (Bioinform., 2023)

Improving dynamic predictions with ensembles of observable models. - Gemma Massonis; Alejandro F. Villaverde; Julio R. Banga (Bioinform., 2023)

Benchmarking tools for a priori identifiability analysis. - Xabier Rey-Barreiro; Alejandro F. Villaverde (Bioinform., 2023)

Distilling identifiable and interpretable dynamic models from biological data. - Gemma Massonis; Alejandro F. Villaverde; Julio R. Banga (PLoS Comput. Biol., 2023)

Controllability and accessibility analysis of nonlinear biosystems. - Sandra Díaz-Seoane; Antonio Barreiro Blas; Alejandro F. Villaverde (Comput. Methods Programs Biomed., 2023)

Corrigendum to "Controllability and accessibility analysis of nonlinear biosystems" [Computer Methods and Programs in Biomedicine 242 (2023) 107837]. - Sandra Díaz-Seoane; Antonio Barreiro Blas; Alejandro Fernández Villaverde (Comput. Methods Programs Biomed., 2024)

Observability rank conditions for analysing practical identifiability a priori. - Alejandro F. Villaverde (CoRR, 2024)

Analysing control-theoretic properties of nonlinear synthetic biology circuits. - Antón Pardo; Sandra Díaz-Seoane; Dorin A. Ionescu; Antonis Papachristodoulou; Alejandro F. Villaverde (CoRR, 2024)