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Alejandro Fernández Villaverde

Post-Doc



  • 2015 - 2016: Computational tools for improving predictions of dynamic models in systems biology


Recent Publications

1
Data-driven reverse engineering of signaling pathways using ensembles of dynamic models
  • PLoS Computational Biology, 13(2), 1-25, 2017
2
Metabolic engineering with multi-objective optimization of kinetic models
  • Journal of Biotechnology, 222, 1-8, 2016
3
PREMER: Parallel reverse engineering of biological networks with information theory
  • Lecture Notes in Computer Science, 9859 (Computational Methods in Systems Biology), 323-329, 2016
4
Identifiability of large nonlinear biochemical networks
  • Match - Communications in Mathematical and in Computer Chemistry, 76(2), 359-376, 2016
5
Structural identifiability of dynamic systems biology models
  • PLoS Computational Biology, 12(10), 2016
6
On the relationship between sloppiness and identifiability
  • Mathematical Biosciences, 282, 147-161, 2016
7
  • Villaverde, Alejandro F.; Henriques, D.; Smallbone, K.; Bongard, S.; Schmid, J.; Cicin-Sain, D.; Crombach, A.; Saez-Rodriguez, J.; Mauch, K.; Balsa-Canto, E.; Mendes, P.; Jaeger, J.; Banga, J.R.
BioPreDyn-bench: A suite of benchmark problems for dynamic modelling in systems biology
  • BMC Systems Biology, 9(1), 2015
8
A consensus approach for estimating the predictive accuracy of dynamic models in biology
  • Computer Methods and Programs in Biomedicine, 119(1), 17-28, 2015
9
Enabling network inference methods to handle missing data and outliers
  • BMC Bioinformatics, 16(1), 2015
10
MIDER: Network inference with mutual information distance and entropy reduction
  • PLoS One, 9(5), 2014
11
Reverse engineering and identification in systems biology: Strategies, perspectives and challenges
  • Journal of the Royal Society Interface, 11(91), 2014
12
High-confidence predictions in systems biology dynamic models
  • Advances in Intelligent Systems and Computing, 294, 161-171, 2014
13
Adaptive tracking in mobile robots with input-output linearization
  • Journal of Dynamic Systems, Measurement and Control - Transactions of the ASME, 136(5), 2014
14
  • Egea, J.A.; Henriques, D.; Cokelaer, T.; Villaverde, Alejandro F.; MacNamara, A.; Danciu, D.-P.; Banga, J.R.; Saez-Rodriguez, J.
MEIGO: An open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics
  • BMC Bioinformatics, 15(1), 2014
15
  • Villaverde, A.F., Egea, J.A., Banga, J.R.
A cooperative strategy for parameter estimation in large scale systems biology models
  • BMC Systems Biology, 6(75), 2012
16
Passive internet-based crane teleoperation with haptic aids
  • International Journal of Control, Automation and Systems, 10(1), 78-87, 2012
17
Multi-criteria optimization of regulation in metabolic networks
  • PLoS One, 7(7), 2012
18
  • Raimúndez, C., Barreiro, A., Villaverde, A.F.
Damping injection by reset control
  • Journal of Dynamic Systems, Measurement and Control - Transactions of the ASME, 134(2), 2012
19
Global optimization in systems biology: Stochastic methods and their applications
  • Advances in Experimental Medicine and Biology, 736, 409-424, 2012
20
Use of a generalized Fisher equation for global optimization in chemical kinetics
  • Journal of Physical Chemistry A, 115(30), 8426-8436, 2011
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