Julio R. Banga

We are very interested in applying a systems approach (i.e. model-based concepts and related computational tools) to problems from the biological domain. In particular, we are doing research in computational systems biology, targetting the following topics:

• Parameter estimation (inverse problems, model calibration) in biochemical pathways
• Optimal experimental design (optimal dynamic experiments) for Systems Biology
• Dynamic optimization (optimal control) of biosystems and bioprocesses
• Nonlinear analysis of biochemical reaction networks
  
• Robust control of diffusion-reaction systems, with applications in biosystems
  

We are also developing software toolboxes to solve problems from these classes above. If you want more information e-mail me. 

We are (or have been) involved in the following  projects:

1. EU project "COSBICS"  ("Computational Systems Biology of Cell Signalling", see partners here), coordinated by Prof. Olaf Wolkenhauer (Univ. Rostock, Germany). (project finished)
2. EU project "BaSysBio" ("Towards an understanding of dynamic transcriptional regulation at global scale in bacteria: a systems biology approach"), coordinated by Prof. P. Noirot (INRA, France). (press release)
3. EU project SysMO-KOSMOBAC ("Ion and solute homeostasis in enteric bacteria: an integrated view generated from the interface of modelling and biological experimentation"), coordinated by Prof. Ian R. Booth (Univ. of Aberdeen, UK)
4. MULTISYSBIO ("Multi-scale modelling approach to systems biology: application to bioprocess monitoring, optimization and control"), joint project with UPV (Valencia,Spain) (see research team )

Currently we have active collaborations with the following groups:

• John Ross at Stanford and Federico Moran at UCM (Fisher equations in chemical kinetics)
• Joerg Stelling at ETH (network inference, in BaSysBio Project)
• Edda Klipp at Humbolt University (parameter estimation, in BaSysBio Project)
• Andreas Kremling at MPI Magdeburg (model discrimination and identification, in KOSMOBAC Project)
• Jesús Picó at UPV, Valencia (multi-scale modelling, in MULTISYSBIO Project)
• Frank Doyle at UCSB (parameter estimation, identifiability)

Further, recently we have had collaborations with:


• Pedro Mendes (parameter estimation)
• Nestor V. Torres (multi-objective optimization of pathways)

Julio R. Banga is a member of the Spanish Systems Biology Network,

member of IFAC's Technical Committee on BioSystems and BioProcesses,

and a member of the Editorial Board of BMC Systems Biology

1. Szederkenyi G., Banga J.R., Alonso A.A. (2011) Inference of complex biological networks: distinguishability issues and optimization-based solutions. BMC Systems Biology 5:177.  (article)

2. Oana Chis, Julio R. Banga, and Eva Balsa-Canto (2011) Structural Identifiability of Systems Biology Models: A Critical Comparison of Methods. PLoS ONE 27(18):2610-2611.  (article)

3. Oana Chis, Julio R. Banga, and Eva Balsa-Canto (2011) GenSSI: a software toolbox for structural identifiability analysis of biological models. Bioinformatics 27(18):2610-2611.  (article) (*software*)

4. 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)

5. 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*)

6. 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. 

7. 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)

8. 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)

9. 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)

10. 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)

11. 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)

12. 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)

13. 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)

14. Otero, I, J. R. Banga, A. A. Alonso (2009) Exploring multiplicity conditions in enzymatic reaction networks. Biotechnology Progress 25(3):619-631. (abstract)

15. 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)

16. Rodriguez-Fernandez, M., & Banga, J. R. (2009). Global sensitivity analysis of a biochemical pathway model. Advances in Soft Computing 49, pp. 233-242

17. 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)

18. Banga, J.R. and E. Balsa-Canto (2008) Parameter estimation and optimal experimental design. Essays in Biochemistry 45:195–210. (abstract+pdf)

19. Banga, J.R. (2008) Optimization in computational systems biology. BMC Systems Biology, 2:47. (abstract + PDF)

20. 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)

21. 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)

22. 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)

23. 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.

24. 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

25. 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.

26. 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.

27. 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.

28. 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.

29. 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.

30. 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.

31. 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.

32. Banga,J. R., E. Balsa-Canto, M. Rodríguez and A. A. Alonso (2005) Model calibration in Systems Biology. BioForum Europe 9:42-43.

33. 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.

34. 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

35. 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.

36. 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.

37. 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.

38. 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.

39. 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

40. 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. 

2009

ICSB 2009 THE 10TH INTERNATIONAL CONFERENCE ON SYSTEMS BIOLOGY. Stanford (USA), 30 August- 4 Sept 2009
BALSA-CANTO E., BANGA J.R. Dynamic model building using an iterative parametric identification procedure.
EGEA, J. A., LIEBERMEISTER, W., KLIPP, E., BANGA, J. R. Calibration of large-scale dynamic models in systems biology.
OTERO-MURAS I., BANGA J.R., ALONSO A.A., Parameter conditions for multistability in biochemical reaction networks: interval based search.
RODRIGUEZ-FERNANDEZ, M, BANGA, J. R. SensSB.- A software toolbox for sensitivity analysis in systems biology models.
RODRIGUEZ-FERNANDEZ, M., YURASZECK, T. M., DOYLE III, F. J., BANGA, J. R. A pseudo-global method for detecting parameters correlations in dynamic models of biological systems.

DATA ANALYSIS AND PARAMETER IDENTICATION. Lorentz Center, Leiden, Holland, 2-5 June 2009.
BALSA-CANTO E., BANGA J.R. Parametric identification using global optimization methods. Invited talk.

SYSID'09, IFAC INTERNATIONAL CONFERENCE ON SYSTEM IDENTIFICATION. Sant Malo, France, 6-8 July 2009
BALSA-CANTO E., BANGA J.R. Computacional procedures for optimal model identification in systems biology.

MATHMOD 2009 - 6TH VIENNA INTERNATIONAL CONFERENCE ON MATHEMATICAL MODELLING. Vienna (Austria), 10-13 Feb 2009
EGEA, J. A., BALSA-CANTO, E., BANGA, J. R. Dynamic optimization of chemical and bio-chemical processes using an efficient global optimization metaheuristic.

IET BIOSYSBIO CONFERENCE 2009 Cambridge (UK), 22-25 March 2009
EGEA, J. A., LIEBERMEISTER, W., KLIPP, E., BANGA, J. R. Parameter estimation in large-scale models from systems biology.
OTERO-MURAS I, BANGA JR, ALONSO AA, Parameter conditions for multistability in bio- chemical reaction networks.
RODRÍGUEZ-FERNÁNDEZ, M., EGEA, J. A., BANGA, J. R. Global optimal experimental design for parameter estimation in systems biology.
UHR, M., EGEA, J. A., BANGA, J. R., STELLING, J. Inference of transcriptional control design of metabolic networks.

II XORNADA GALEGA DE BIOINFORMÁTICA Universidad de Santiago de Compostela, Spain, 4 Dec 2009.
BANGA, J. R., Computational Systems Biology. Invited talk.

2008

10TH INTERNATIONAL CHEMICAL AND BIOLOGICAL ENGINEERING CONFERENCE (CHEMPOR 2008) Braga (Portugal), 4-6 Sept 2008
RODRÍGUEZ-FERNÁNDEZ M, BANGA JR. Methods and tools for global sensitivity analysis of dynamic models of biological systems. Keynote lecture. Invited talk. EGEA JA, GARCÍA MSG, BALSA-CANTO E, BANGA JR. Global dynamic optimization of chemical and bio-processes using the Scatter Search metaheuristic.

2ND INTERNATIONAL WORKSHOP ON PRACTICAL APPLICATIONS OF COMPUTATIONAL BIOLOGY & BIOINFORMATICS (IWPACBB'09) Salamanca (Spain), 22-24 Oct 2008
RODRÍGUEZ-FERNÁDEZ M, BANGA JR. Global sensitivity analysis of a biochemical pathway model.

IET CONFERENCE ON SYNTHETIC BIOLOGY, SYSTEMS BIOLOGY AND BIOINFORMATICS (BIOSYSBIO 2008) London (UK), 20-22 April 2008
RODRÍGUEZ-FERNÁNDEZ M, KREMLING A, BANGA JR. Global sensitivity methods for identifiability analysis and model reformulation in Systems Biology.

9TH INTERNATIONAL CONFERENCE ON SYSTEMS BIOLOGY. ICSB 2008 Göteborg (Sweden), 22-28 August 2008
RODRÍGUEZ-FERNÁNDEZ M, BANGA, JR. Global sensitivity analysis methods for dynamic models in systems biology.
SENDÍN JOH, ALONSO AA, BANGA JR. Multicriteria optimization in systems biology: application to metabolic engineering and flux balance analysis.
REHBERG M, RODRÍGUEZ-FERNÁNDEZ M, EGEA JA, KREMLING A, BANGA, JR. Simultaneous model discrimination and parameter estimation in dynamic models of biological systems.
HIRMAJER T, BALSA-CANTO E, BANGA JR. DOTcvp - a software toolbox for dynamic optimization in systems biology.
EGEA JA, SCHMIDT H, BANGA JR. A new tool for parameter estimation in nonlinear dynamic biological systems using global optimization.

2ND INTERNATIONAL WORKSHOP ON SYSTEMS BIOLOGY. IWSB2008 Maynooth (Ireland), 17-20 August 2008
EGEA JA, SCHMIDT H, BANGA JR. A new global optimization tool for parameter estimation in systems biology.

More conference papers here