AFV research

Publications

Under review

    G Massonis, AF Villaverde. On testing structural identifiability by a simple scaling method: relying on scaling symmetries can be misleading. Preprint: doi:10.1101/2020.11.30.403956

    G Massonis, JR Banga, AF Villaverde. Repairing dynamic models: a method to obtain identifiable and observable reparameterizations with mechanistic insights. Preprint: arXiv:2012.09826 [eess.SY]

Journal papers

    35. L Schmiester, Y Schälte, F Bergmann , T Camba, E Dudkin, J Egert, F Fröhlich, L Fuhrmann, AL Hauber, S Kemmer, P Lakrisenko, C Loos, S Merkt, D Pathirana, E Raimúndez, L Refisch, M Rosenblatt, PL Stapor, P Städter, D Wang, F-G Wieland, JR Banga, J Timmer, AF Villaverde, S Sahle, C Kreutz, J Hasenauer, D Weindl (2021) PEtab — Interoperable Specification of Parameter Estimation Problems in Systems Biology. PLOS Computational Biology, 17(1): e1008646 doi:10.1371/journal.pcbi.1008646

    34. G Massonis, JR Banga, AF Villaverde (2020) Structural identifiability and observability of compartmental models of the COVID-19 pandemic. Annual Reviews in Control, doi:10.1016/j.arcontrol.2020.12.001

    33. N Martínez, AF Villaverde (2020) Nonlinear observability algorithms with known and unknown inputs: analysis and implementation. Mathematics, 8, 1876 doi:10.3390/math8111876

    32. G Massonis, AF Villaverde (2020) Finding and breaking Lie symmetries: implications for structural identifiability and observability in biological modelling. Symmetry, 12(3), 469 doi:10.3390/sym12030469

    31. AF Villaverde, NTsiantis, JR Banga (2019) Full observability and estimation of unknown inputs, states, and parameters of nonlinear biological models. Journal of the Royal Society Interface, 16:20190043 doi:10.1098/rsif.2019.0043

    30. AF Villaverde (2019) Observability and structural identifiability of nonlinear biological systems. Complexity, vol. 2019, article ID 8497093, 12 pages doi:10.1155/2019/8497093

    29. AF Villaverde, ND Evans, MJ Chappell, JR Banga (2019) Input-dependent structural identifiability of nonlinear systems. IEEE Control Systems Letters, 3(2):1–6 doi:10.1109/LCSYS.2018.2868608

    28. AF Villaverde, F Froehlich, D Weindl, J Hasenauer, JR Banga (2018) Benchmarking optimization methods for parameter estimation in large kinetic models. Bioinformatics, 35 (5): 830–838 doi:10.1093/bioinformatics/bty736

    27. AF Villaverde, K Becker, JR Banga (2018) PREMER: a Tool to Infer Biological Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15(4):1193 - 1202 doi:10.1109/TCBB.2017.2758786

    26. AF Villaverde, JR Banga (2017) Dynamical compensation and structural identifiability in biological models: analysis, implications, and reconciliation. PLOS Computational Biology, 13(11): e1005878 doi:10.1371/journal.pcbi.1005878

    25. AF Villaverde, JR Banga (2017) Structural properties of dynamic systems biology models: identifiability, reachability, and initial conditions. Processes, 5(2), 29 doi:10.3390/pr5020029

    24. D Henriques, AF Villaverde, M Rocha, J Sáez-Rodriguez, JR Banga (2017) Data-driven reverse engineering of signaling pathways using ensembles of dynamic models. PLOS Computational Biology, 13(2):e1005379 doi:10.1371/journal.pcbi.1005379

    23. A Gabor, AF Villaverde, JR Banga (2017) Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems. BMC Systems Biology, 11:54 doi:10.1186/s12918-017-0428-y

    22. AF Villaverde, A Barreiro, A Papachristodoulou (2016) Structural identifiability of dynamic systems biology models. PLOS Computational Biology, 12(10):e1005153 doi:10.1371/journal.pcbi.1005153

    21. O-T Chis, AF Villaverde, JR Banga, E Balsa-Canto (2016) On the relationship between sloppiness and identifiability. Mathematical Biosciences, 282:147-161 doi:10.1016/j.mbs.2016.10.009

    20. AF Villaverde, A Barreiro (2016) Identifiability of Large Nonlinear Biochemical Networks. MATCH Communications in Mathematical and in Computer Chemistry, 76(2):259-296

    19. AF Villaverde, S Bongard, K Mauch, E Balsa-Canto, JR Banga (2016) Metabolic engineering with multi-objective optimization of kinetic models. Journal of Biotechnology, 222:1–8, doi:10.1016/j.jbiotec.2016.01.005

    18. A Folch-Fortuny, AF Villaverde, A Ferrer, JR Banga (2015) Enabling network inference methods to handle missing data and outliers. BMC Bioinformatics 16(1), 283, doi:10.1186/s12859-015-0717-7

    17. AF Villaverde, D Henriques, K Smallbone, S Bongard, J Schmid, D Cicin-Sain, A Crombach, J Saez-Rodriguez, K Mauch, E Balsa-Canto, P Mendes, J Jaeger, JR Banga (2015) BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. BMC Systems Biology, 9:8, doi:10.1186/s12918-015-0144-4

    16. AF Villaverde, S Bongard, K Mauch, D Muller, E Balsa-Canto, J Schmid, JR Banga (2015) A consensus approach for estimating the predictive accuracy of dynamic models in biology. Computer Methods and Programs in Biomedicine, 119(1):17-28, doi:10.1016/j.cmpb.2015.02.001

    15. JA Egea, D Henriques, T Cokelaer, AF Villaverde, A MacNamara, D Danciu, JR Banga, J Saez-Rodriguez (2014) MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. BMC Bioinformatics, 15:136, doi:10.1186/1471-2105-15-136

    14. AF Villaverde, J Ross, F Morán, JR Banga (2014) MIDER: network inference with Mutual Information Distance and Entropy Reduction. PLOS ONE, 9(5):e96732, doi:10.1371/journal.pone.0096732

    13. C Raimúndez, AF Villaverde, A Barreiro (2014) Adaptive tracking in mobile robots with input-output linearization. Journal of Dynamic Systems, Measurement, and Control, Transactions of the ASME, 136:054503-1, doi:10.1115/1.4027369

    12. AF Villaverde, JR Banga (2014) Reverse engineering and identification in systems biology: strategies, perspectives, and challenges. Journal of the Royal Society Interface, 11:20130505, doi:10.1098/rsif.2013.0505

    11. AF Villaverde, J Ross, JR Banga (2013) Reverse engineering cellular networks with information theoretic methods. Cells, 2(2):306–329, doi:10.3390/cells2020306

    10. C Higuera, AF Villaverde, JR Banga, J Ross, F Morán (2012) Multi-criteria optimization of regulation in metabolic networks. PLOS ONE, 7(7):e41122, doi:10.1371/journal.pone.0041122

    9. AF Villaverde, JA Egea, JR Banga (2012) A cooperative strategy for parameter estimation in large scale systems biology models. BMC Systems Biology, 6:75, doi:10.1186/1752-0509-6-75

    8. AF Villaverde, C Raimúndez, A Barreiro (2012) Passive internet-based crane teleoperation with haptic aids. International Journal of Control, Automation, and Systems, 10(1):78–87, doi:10.1007/s12555-012-0109-y

    7. E Balsa-Canto, JR Banga, JA Egea, AF Villaverde, GM de Hijas-Liste (2012) Global optimization in systems biology: stochastic methods and their applications. Advances in Experimental Medicine and Biology, 736:409–425, doi:10.1007/978-1-4419-7210-1_24

    6. AF Villaverde, J Ross, F Morán, E Balsa, JR Banga (2011) Use of a generalized Fisher equation for global optimization in chemical kinetics. Journal of Physical Chemistry A, 115 (30):8426-8436, doi:10.1021/jp203158r

    5. C Raimúndez, A Barreiro, AF Villaverde (2011) Damping injection by reset control. Journal of Dynamic Systems, Measurement, and Control, Transactions of the ASME, 134(2):024504 (5 pages), doi:10.1115/1.4005369

    4. AF Villaverde, A Blas, A Torrico, J Carrasco (2011) Reset control for passive bilateral teleoperation. IEEE Transactions on Industrial Electronics, 58(7):3037–3045, doi:10.1109/TIE.2010.2077610

    3. AF Villaverde, A Barreiro, C Raimúndez (2010) Passive position error correction in Internet-based teleoperation. Automatica, 46(11):1884–1890, doi:10.1016/j.automatica.2010.07.009

    2. J Ross, AF Villaverde (2010) Thermodynamics and fluctuations far from equilibrium. Entropy, 12(10):2199–2243, doi:10.3390/e12102199

    1. J Ross, AF Villaverde, S Vázquez, JR Banga, F Morán (2010) A generalized Fisher equation and its utility in chemical kinetics. Proceedings of the National Academy of Sciences of the USA, 107(29):12777–12781, doi:10.1073/pnas.1008257107

Conference papers

    21. AF Villaverde, E Raimúndez, J Hasenauer, JR Banga (2019) A comparison of methods for quantifying prediction uncertainty in systems biology. 8th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE), València, España, October 15-18, 2019. IFAC-PapersOnLine, 52(26):45-51, doi:10.1016/j.ifacol.2019.12.234

    20. AF Villaverde, JR Banga (2019) Análisis de observabilidad e identificabilidad estructural de un modelo de la vía de señalización JAK/STAT. XL Jornadas de Automática (JA'19), Ferrol, Spain, September 4-6, 2019, pp. 631-638.

    19. AF Villaverde, N Evans, M Chappell, JR Banga (2018) Sufficiently exciting inputs for structurally identifiable systems biology models. 7th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE), Chicago, IL, USA, August 5–8 2018. IFAC-PapersOnLine, 51(19):16-19, doi:10.1016/j.ifacol.2018.09.015

    18. AF Villaverde, A Barreiro, A Papachristodoulou (2016) Structural identifiability analysis via extended observability and decomposition. 6th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE), Magdeburg, Germany. IFAC-PapersOnLine, 49(26), 171-177, doi:10.1016/j.ifacol.2016.12.121

    17. AF Villaverde, K Becker, JR Banga (2016) PREMER: parallel reverse engineering of biological networks with information theory. Computational Methods in Systems Biology: 14th International Conference, CMSB 2016, Cambridge, UK. Lecture Notes in Computer Science, 9859:323–329, doi:10.1007/978-3-319-45177-0_21

    16. AF Villaverde, S Bongard, K Mauch, D Muller, E Balsa-Canto, J Schmid, JR Banga (2014) High-confidence predictions in systems biology dynamic models. Advances in Intelligent and Soft-Computing, 294:161–171 (Proc. 8th PACBB, Salamanca, Spain), doi:10.1007/978-3-319-07581-5_20

    15. AF Villaverde, JA Egea, JR Banga (2013) Búsqueda dispersa cooperativa para problemas de alta dimensión en el contexto de biología de sistemas. XV CAEPIA – IX MAEB, pp. 348–357, Madrid, Spain

    14. AF Villaverde, JA Egea, JR Banga (2012) Calibrado de modelos en biología de sistemas mediante búsqueda dispersa paralelizada y cooperativa. XXXIII Jornadas de Automática, pp. 677-682, Vigo, Spain

    13. M Uhr, AF Villaverde, JA Egea, JR Banga, J Stelling (2011) Inference of transcriptional control design of metabolic networks. 18th IFAC World Congress, pp. 10448-10453, Milano, Italy, doi:10.3182/20110828-6-IT-1002.01588

    12. C Raimúndez, A Barreiro, A Fernández (2009) Reset control for injecting dissipation into port-hamiltonian systems. European Control Conference, pp. 4919–4924, Budapest, Hungary, doi:10.23919/ECC.2009.7075179

    11. A Fernández, A Barreiro, AJ van der Schaft (2009) Control por interconexión de una clase de sistemas subactuados. XXX Jornadas de Automática, P14, Valladolid, Spain

    10. A Fernández, A Barreiro, A Baños, J Carrasco (2008) Reset control for passive teleoperation. 34th Annual Conference IEEE Industrial Electronics Society, pp. 2935–2940, Orlando, FL, USA, doi:10.1109/IECON.2008.4758426

    9. M Díaz-Cacho, A Fernández, M García, A Barreiro (2008) Internet emulation system for UDP-based teleoperation. 16th IEEE Mediterranean Conference on Control & Automation, pp. 1417–1422, Ajaccio, France, doi:10.1109/MED.2008.4601986

    8. M Díaz-Cacho, AF Villaverde, A Barreiro (2008) Sistema de teleoperación cooperativa grúa-cámara con retorno de estado. XXIX Jornadas de Automática, P271, Tarragona, Spain

    7. C Raimúndez, AF Villaverde (2008) Adaptive tracking control for a quad-rotor. 6th EUROMECH Nonlinear Oscillations Conference, pp. 1630–1635, Saint Petersbourg, Russia

    6. AF Villaverde, A Barreiro, C Raimúndez (2008) Passive correction of position error in Internet-based teleoperation. 17th IFAC World Congress, pp. 14998–15003, Seoul, Korea, doi:10.3182/20080706-5-KR-1001.02538

    5. AF Villaverde, M Díaz-Cacho, A Barreiro, C Raimúndez (2008) Virtual haptic interface for crane teleoperation. 8th Portuguese Conference on Automatic Control, pp. 46–51, Vila Real, Portugal

    4. AF Villaverde, C Raimúndez, A Barreiro (2007) Digital passive teleoperation of a gantry crane. IEEE International Symposium on Industrial Electronics, pp. 56–61, Vigo, Spain, doi:10.1109/ISIE.2007.4374573

    3. AF Villaverde, C Raimúndez, A Barreiro (2007) Passive teleoperation of a gantry crane. European Control Conference, pp. 3479–3485, Kos, Greece, doi:10.23919/ECC.2007.7068688

    2. AF Villaverde, M Santos (2006) Control de una grúa pórtico mediante redes neuronales. XXVII Jornadas de Automática, pp. 1006–1011, Almeria, Spain

    1. A Barreiro, AF Villaverde, C Raimúndez (2006) Teleoperación háptica de un puente-grúa. XXVII Jornadas de Automática, pp. 136–143, Almeria, Spain

    Departamento de Enxeñaría de Sistemas e Automática | Campus universitario Lagoas-Marcosende | C.P. 36310 Vigo (Galicia) | Spain