Villaverde,
A., J. Ross, F. Morán, E. Balsa-Canto, J.R. Banga (2011) Use of a Generalized Fisher
Equation for Global Optimization in Chemical Kinetics. Journal of Physical Chemistry
A115(30):8426-8436. (article)
Balsa-Canto,
E. and Julio R. Banga (2011)
AMIGO, a toolbox for Advanced Model Identification in systems biology
using Global Optimization. Bioinformatics
27(16):2311-2313. (article) (*software*)
Balsa-Canto,
E., J.R. Banga, J.A. Egea, A. Fernandez-Villaverde and G.M. de
Hijas-Liste (2011)
Global optimization in systems biology: stochastic methods and their
applications.
Advances in Systems Biology, accepted, in press.
De
Hijas-Liste, G. M., Balsa-Canto, E., & Banga, J. R. (2011) Prediction of activation of
metabolic pathways via dynamic optimization. Computer Aided Chemical
Engineering 29:1386-1390. (article)
Rodriguez-Fernandez,
M., Cardelle-Cobas, A., Villamiel, M., & Banga, J. R. (2011) Detailed kinetic model
describing new oligosaccharides synthesis using different
ß-galactosidases.
Journal of Biotechnology 153(3-4):116-124. (article)
Ross,
J., A.F. Villaverde, J.R. Banga, S. Vazquez, F. Moran (2010) A generalized Fisher equation
and its utility in chemical kinetics. Proc. Natl. Acad. Sci. USA
107(29):12777-12781. (article)
Vera,
J., O. Rath, E. Balsa-Canto, J. R. Banga, W. Kolch and Olaf Wolkenhauer
(2010) Investigating
dynamics of inhibitory and feedback loops in ERK signalling using
power-law models.
Mol. BioSyst. 6:2174–2191. (article)
Rodriguez-Fernandez,
M. and J.R. Banga (2010).
SensSB: A software toolbox for the development and sensitivity analysis
of systems biology models. Bioinformatics
26(13):1675-1676. (article) (software)
Sendin,
J.O.H., O. Exler & J.R. Banga (2010). Multi-objective mixed integer
strategy for the optimisation of biological networks. IET Systems Biology
4(3):236-248. (article)
Balsa-Canto,
E., Alonso, A. A., & Banga, J. R. (2010). An iterative identification
procedure for dynamic modeling of biochemical networks. BMC Systems Biology
4:11. (article)
Otero,
I, J. R. Banga,
A. A. Alonso (2009)
Exploring
multiplicity
conditions
in enzymatic reaction networks. Biotechnology
Progress 25(3):619-631. (abstract)
Hirmajer,
T., E.
Balsa-Canto and J. R. Banga (2009)
DOTcvpSB, a software toolbox for dynamic optimization in systems
biology. BMC
Bioinformatics 10:199.
(
PDF ) (software)
Rodriguez-Fernandez,
M., & Banga, J. R. (2009). Global
sensitivity
analysis of a biochemical pathway model. Advances
in Soft Computing 49, pp. 233-242
Sendín,
J. -. H., Alonso, A. A., & Banga, J. R. (2009). Multi-objective
optimization of biological networks for prediction of intracellular
fluxes. Advances
in Soft
Computing 49, pp. 197-205 (abstract)
Banga, J.R. and E.
Balsa-Canto
(2008) Parameter
estimation and optimal experimental design. Essays
in
Biochemistry 45:195–210. (abstract+pdf)
Banga, J.R. (2008) Optimization in
computational
systems biology. BMC
Systems Biology,
2:47. (abstract + PDF)
Balsa-Canto, E., M.
Peifer,
J.R. Banga, J. Timmer, C. Fleck (2008) Hybrid optimization
method with
general switching strategy for parameter estimation. BMC
Systems Biology,
2:26. (abstract + PDF)
Balsa-Canto, E.,
A.A.
Alonso
and J.R. Banga (2008)
Computational Procedures for Optimal Experimental Design in Biological
Systems. IET
Systems Biology 2(4):
163-172. (abstract)
Vilas, C., M.R.
Garcia,
J.R.
Banga, A.A. Alonso (2008)
Robust Feed-Back Control of Travelling Waves in a Class of
Reaction-Diffusion Distributed Biological Systems. Physica D
237(18):2353-2364. (abstract
+ pdf)
Vera,
J., E.
Balsa-Canto, P.
Wellstead, J. R. Banga and O. Wolkenhauer (2007) Power-Law Models of
Signal Transduction Pathways. Cellular
Signalling 19(7):1531-1541.
Rodriguez-Fernandez,
M.,
J. A.
Egea
and J. R. Banga (2006) Novel
Metaheuristic for Parameter Estimation in
Nonlinear Dynamic Biological Systems. BMC
Bioinformatics 7:483. (PDF)
SOFTWARE
Sendín,
J.O.H., I.
Otero, A. A. Alonso and J. R. Banga (2006) Improved optimization
methods for the multiobjective design of bioprocesses. Ind.
& Engineering Chemistry Research 45(25):
8594-8603.
Vilas,
C., M. R. Garcia,
J. R.
Banga and A. A. Alonso (2006) Stabilization
of Inhomogeneous
Patterns in a Diffusion-reaction
System under Structural and Parametric Uncertainties. Journal
of Theoretical Biology 241 (2):
295-306.
Rodriguez-Fernandez,
M.,
P.
Mendes and J. R. Banga (2006) A
hybrid approach
for efficient and robust parameter estimation in biochemical pathways.
BioSystems,
83(2-3):248-265.
Sendin,
O. H., J. Vera,
N. V.
Torres and J. R. Banga (2006) Model
Based
Optimization of Biochemical Systems Using Multiple Objectives: A
Comparison
of Several Solution Strategies. Mathematical
and
Computer Modelling
of Dynamical Systems 12 (5):
469-487.
Balsa-Canto,
E.;
Rodríguez-Fernández, M.; Alonso, A.A.; Banga,
J.R. (2006) Computational
design of optimal dynamic experiments in systems biology: a case study
in cell signaling. In: Understanding
and Exploiting Systems Biology in Bioprocesses and Biomedicine.
(M. Cánovas, J. L. Iborra, A. Manjón eds.), pp.
103-117. Fundación Cajamurcia, Murcia.
Otero-Muras,
I.; Banga,
J.R.;
Alonso, A.A. (2006) A
method for detecting bifurcations in biochemical networks.
In: Understanding
and
Exploiting Systems Biology in Bioprocesses and Biomedicine.
(M. Cánovas, J. L. Iborra, A. Manjón eds.), pp.
71-78. Fundación Cajamurcia, Murcia.
Vilas,
C.;
García,
M.R.; Banga, J.R.; Alonso, A.A. (2006) Robust Stabilization of
Inhomogeneous Patterns in a Reaction-Diffusion Biological Systems.
In: Understanding
and
Exploiting Systems Biology in Bioprocesses and Biomedicine.
(M. Cánovas, J. L. Iborra, A. Manjón eds.), pp.
93-100. Fundación Cajamurcia, Murcia.
Banga,J.
R.,
E.
Balsa-Canto, M.
Rodríguez and A. A. Alonso (2005) Model
calibration in Systems Biology. BioForum
Europe 9:42-43.
Banga,
J. R., E.
Balsa-Canto,
C. G. Moles and A. A. Alonso (2005) Dynamic
optimization of
bioprocesses: Efficient and robust numerical strategies. Journal
of Biotechnology 117(4):407-419.
Moles,
C. G., Pedro
Mendes and
Julio R. Banga (2003) Parameter
estimation in biochemical
pathways: a comparison of global optimization methods.
Genome Research,
13(11):2467-2474.
pdf Supl.
info
Vera,
J., Carmen G.
Moles,
Julio R. Banga and Néstor V. Torres (2003) Integrated
non-linear optimization of bioprocesses via
linear programming. AIChE
Journal 49(12):3173-3187.
Banga,
J.R., Moles,
C.G.,
Alonso, A.A. (2003) Global
optimization of
bioprocesses using stochastic and hybrid methods.
In "Frontiers
In Global Optimization ", C.A.
Floudas and P. M. Pardalos,
(Eds.), Nonconvex Optimization and Its Applications, vol. 74, pp.
45-70, Kluwer Academic Publishers, ISBN 1-4020-7699-1.
Banga,
J. R., E.
Balsa-Canto,
C. G. Moles and A. A. Alonso (2003) Dynamic Optimization of
Bioreactors - a Review. Proc.
Ind. Natn. Science
Academy , 69A(3-4):257-265.
Banga,
J. R., K. J.
Versyck
and J. F. Van Impe (2002) Computation of optimal identification
experiments for nonlinear dynamic process models: an stochastic global
optimization approach. Industrial
& Engineering
Chemistry Research 41:2425-2430.
Balsa-Canto,
E., Banga
J.R.,
Alonso A.A. and Vassiliadis V.S. (2001) Dynamic optimization of
chemical and biochemical processes using restricted second order
information. Comp. & Chem. Eng.
25(4-6):539-546
Balsa-Canto,
E., J. R.
Banga,
A. A. Alonso and V. S. Vassiliadis (2000). Efficient optimal control of
bioprocesses using second order information. Ind.
Eng. Chem.
Res. 39:4287-4295
Complete
list of papers
here.
