Publications

papers

Generated by DALL·E

Preprints

  • XR Barreiro, AF Villaverde (2022). Benchmarking tools for a priori identifiability analysis. arXiv preprint, arXiv:2207.09745

Journal papers

  • 43. G Massonis, AF Villaverde, JR Banga (2022). Improving dynamic predictions with ensembles of observable models. Bioinformatics, 39(1), btac755, doi:10.1093/bioinformatics/btac755
  • 42. S Díaz-Seoane, X Rey-Barreiro, AF Villaverde (2022). STRIKE-GOLDD 4.0: user-friendly, efficient analysis of structural identifiability and observability. Bioinformatics, 39(1), btac748, doi:10.1093/bioinformatics/btac748
  • 41. AF Villaverde, E Raimúndez, J Hasenauer, JR Banga (2022). Assessment of prediction uncertainty quantification methods in systems biology. IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press, doi:10.1109/TCBB.2022.3213914
  • 40. G Massonis, JR Banga, AF Villaverde (2022). AutoRepar: A method to obtain identifiable and observable reparameterizations of dynamic models with mechanistic insights. International Journal of Robust and Nonlinear Control, in press, doi:10.1002/rnc.5887
  • 39. AF Villaverde (2022). Symmetries in dynamic models of biological systems: mathematical foundations and implications. Symmetry, 14(3), 467 doi:10.3390/sym14030467
  • 38. AF Villaverde, D Pathirana, F Fröhlich, J Hasenauer, JR Banga (2021). A protocol for dynamic model calibration. Briefings in Bioinformatics, 23(1), bbab387, doi:10.1093/bib/bbab387
  • 37. JAG Prieto, AF Villaverde (2021). Smooth Non Linear High Gain Observers for a Class of Dynamical Systems. IEEE Access, doi:10.1109/ACCESS.2021.3137650
  • 36. AF Villaverde, G Massonis (2021). On testing structural identifiability by a simple scaling method: relying on scaling symmetries can be misleading. PLOS Computational Biology, 17(10): e1009032 doi:10.1371/journal.pcbi.1009032
  • 35. L Schmiester, Y Schälte, ..., 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 (2021). Structural identifiability and observability of compartmental models of the COVID-19 pandemic. Annual Reviews in Control, 51:440-459 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

  • 22. D Rey Rostro, AF Villaverde (2022). StrikePy: Nonlinear observability analysis of inputs, states, and parameters in Python. XLIII Jornadas de Automática (JA'22), Logroño, Spain, September 7-9, 2022. Libro de actas: pp. 430-435 http://hdl.handle.net/2183/31455
  • 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