multisysbioPublicationsJournal papers

 The publications listed below are either directly or indirectly related to the project. Thus, publications in the fields of biomedicine and biotechnology have been included. Also, publications concerning methodologies of potential use in systems biology have been listed. 

Publications listed by year:   2010  2009  2008  2007  2006  2005

2010

  1. Ross, J., A.F. Villaverde, J.R. Banga, S. Vazquez, F. Moran. A generalized Fisher equation and its utility in chemical kinetics. Proc. Natl. Acad. Sci. USA 107(29):12777-12781, 2010.

  2. Tortajada M, Llaneras F, Picó J. Validation of a constraint-based model of Pichia pastoris growth under data scarcity. BMC Systems Biology, 4:115, 2010.

  3. Vera, J., O. Rath, E. Balsa-Canto, J. R. Banga, W. Kolch and Olaf Wolkenhauer , Investigating dynamics of inhibitory and feedback loops in ERK signalling using power-law models. Mol. BioSyst. 6:2174–2191, 2010.

  4. Llaneras F. and Picó J., Which Metabolic Pathways Generate and Characterize the Flux Space? A Comparison among Elementary Modes, Extreme Pathways and Minimal Generators, Journal of Biomedicine and Biotechnology, vol. 2010, Article ID 753904, 13 pages, 2010.

  5. Rodriguez-Fernandez, M. and J.R. Banga. SensSB: A software toolbox for the development and sensitivity analysis of systems biology models. Bioinformatics 26(13):1675-1676, 2010.

  6.  Sendin, J.O.H., O. Exler & J.R. Banga. Multi-objective mixed integer strategy for the optimisation of biological networks. IET Systems Biology 4(3):236-248.

  7. Balsa-Canto, E., Alonso, A. A., & Banga, J. R. An iterative identification procedure for dynamic modeling of biochemical networks. BMC Systems Biology 4:11, 2010.

  8. Egea, J.A., Martí, R., & Banga, J.R., An evolutionary method for complex-process optimization. Computers and Operations Research 37(2):315-324, 2010.

  9. A. Revert, R. Calm, J. Vehí, J. Bondia, Calculation of the best basal-bolus combination for postprandial glucose control in insulin pump therapy, IEEE Transactions on Biomedical Engineering, in press, 2010.

  10. A. Revert, P. Rossetti, R. Calm. J. Vehí, J. Bondia, Combining Basal-Bolus Insulin Infusion for Tight Postprandial Glucose Control. An In Silico Evaluation in Adults, Children and Adolescents, Journal of Diabetes Science and Technology, 4(6), 1424-1437, 2010.

  11. J. Camacho, J. Picó, A. Ferrer, Data understanding with PCA: Structural and Variance Information plots,  Chemometrics and Intelligent Laboratory Systems. Vol. 100, Issue 1, Pages 48-56, 2010.

  12. Arteaga, F.; Ferrer, A. (2010). How to simulate normal data sets with the desired correlation structure, Chemometrics and Intelligent Laboratory Systems, 101(1): 38-42.

  13. Barceló, S.; Vidal-Puig, S.; Ferrer, A. (2010). Comparison of Multivariate Statistical Mathods for Dynamic Systems Modelling, Quality and Reliability Engineering International, 27(1):107-124.

  14. Conesa, A; Prats-Montalbán, J.M.; Nueda, MJ.; Tarazona, S.; Ferrer, A. (2010). A multiway approach to data integration in systems biology based on Tucker3 and N-PLS, Chemometrics and Intelligent Laboratory Systems, 104(1):101-111.

  15. González-Martínez, J.M.; Ferrer, A.; Westerhuis, J. (2010), Real-time Synchronization of Batch Trajectories for On’line Multivariate Statistical Process Control using Dynamic Time Warping. Chemometrics and Intelligent Laboratory System, 105: 195-206.

  16. Prats-Montalbán, J.M.; Ferrer, A.;de Juan, A. (2010). A multivariate Image Analisys: a review with aplications, Chemometrics and Intelligent Laboratory Systems, DOI:10.1016/j.chemolab.2011.03.002

 

2009

  1. J. Picó, H. De Battista, F. Garelli,  Smooth sliding-mode observers for specific growth rate and substrate from biomass measurement, Journal of Process Control, 19, pp. 1314-1323, 2009.

  2. J. Picó, F. Garelli, H. De Battista, R.J. Mantz, Geometric invariance and reference conditioning for control of overflow metabolism, Journal of Process Control, 19 (10), pp. 1617-1626, 2009.

  3. F. Llaneras, A. Sala, J. Picó, A possibilistic framework for constrained-base metabolic flux analysis, BMC Systems Biology, 3:79, 2009.

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

  5. Hirmajer, T., E. Balsa-Canto and J. R. Banga, DOTcvpSB, a software toolbox for dynamic optimization in systems biology. BMC Bioinformatics 10:199, 2009.

  6. Prats-Montalbán, J.M.; Ferrer, A.; Bro, R.;Hancewicz, T.M., Prediction of skin quality properties by different Multivariate Image Analysis methodologies, Chemometrics and Intelligent Laboratory Systems, 96: 6-13, 2009.

  7. Camacho, J.; Picó, J.; Ferrer, A., On-line monitoring of batch processes based on PCA: Does the modelling structure matter?, Analytica Chimica Acta, 642: 59-68, 2009.

  8. Egea, J.A., Balsa-Canto, E., García, M.G., & Banga, J.R.,  Dynamic optimization of nonlinear processes with an enhanced scatter search method. Industrial and Engineering Chemistry Research 48(9):4388-4401,2009.

  9. Ferrer, A. (2009). "Discussion of Manuscript "Opportunities and Issues in Multiple Data Type Meta-Analyses", Journal of Quality Engineering, 21(3): 254-255.

  10. Martínez-Guijarro, R.; Romero, I.; Pachés, M.; del Río, J.G.; Martí, C.M.; Gila, G.; Ferrer-Riquelme, A.; Ferrer, J. (2009). "Determination of phytoplankton composition using absorption spectra.", Talanta, 78: 814-819.

  11. Nueda, M.J.; Sebastián, P.; Tarazona, S.; García, F.; Dopazo, J.; Ferrer, A.; Conesa,A. (2009). "Functional Assessment of Time Course Microarray Data",  Bioinfomatics, 10(Suppl 6:S9): 1-18.

  

2008

  1. J. Camacho, J. Picó,A. Ferrer, Multi-Phase Analysis Framework for handling Batch process Data, Journal of Chemometrics, 22(11-12), pp. 632-643, 2008.

  2. F. Llaneras, J. Picó, Stoichiometric Modelling of Cell Metabolism, Journal of Bioscience and Bioengineering, Vol. 105 (1), pp. 1-11,2008.
  3. J. Camacho, J. Picó,A. Ferrer, Bilinear modelling of Batch Processes. Part I: Theoretical Discussion, Journal of Chemometrics, 22(5), pp. 299-308, 2008.

  4. J. Camacho, J. Picó,A. Ferrer, Bilinear modelling of Batch Processes. Part II: A comparison of PLS soft-sensors, Journal of Chemometrics, 22(10), pp.533-547, 2008.

  5. Fernando López; José Miguel Valiente; José Manuel Prats; Alberto Ferrer  (2008). “Performance Evaluation of Soft Color Texture Descriptors for Surface Grading using Experimental Design and Logistic Regression”, Pattern Recognition 41 (5), 1761-1772.

  6. Ferrer, A.; Aguado, D.; Vidal, P.; Prats, J.M.; Zarzo, M. (2008). "PLS: A Versatile Tool for Industrial Process Improvement and Optimization", Applied Stochastic Models for Business and Industry, 24, 551-567.

  7. Prats-Montalbán, J.M.; López,F.; Valiente, J.M.; Ferrer, A. (2008). "Multivariate Statistical Methods to Perform Robust Feature Extraction and Classification in Surface Grading ", Journal of Electronic imaging, 17(3), 031106.

  8. Aguado, D.; Ferrer, A.; Seco, A.; Ferrer, J. (2008). "Using Unfold-PCA for batch-to-batch start-up process understanding and steaty-state identification in a sequencing batch reactor", Journal of Chemometrics 22(1), 81-90.

 

2007

  1. F. Llaneras, J. Picó, An Interval Approach for Dealing with Flux Distributions and Elementary Modes Activity Patterns, Journal of Theoretical Biology, vol. 246, pp.290-308, Springer Verlag

  2. J. L. Díez, J. L. Navarro, A. Sala, A fuzzy clustering algorithm enhancing local model interpretability, Soft Computing – A Fusion of Foundations, Methodologies and Applications, vol.11, pp. 973-983, Springer.

     

  3. J. Camacho, J. Picó,A. Ferrer, Self-tuning run to run optimization of fed-batch processes using unfolded-PLS,  AIChE, vol. 53, no. 7, pp. 1789-1803, American Chemical Society

  4. F. Llaneras, J. Picó, A procedure for the estimation over time of metabolic fluxes in scenarios where measurements are uncertain and/or insufficient, BMC Bioinformatics, 8:421, 2007.

  5. F. Llaneras, M. Tortajada, J. Picó, Structural analysis of metabolic pathways applied to heterologous protein production with Pichia pastoris. Journal of Biotechnology, 131 issue 2S, pp. 209, 2007.

  6. J. C. Dehesa, J. Picó, J. Bondia, E. Picó-Marco, Robust posibilistic control of nonlinear flat systems. Journal of Biotechnology, 131 issue 2S, pp. 105, 2007.

  7. Aguado, D.; Zarzo, M.; Seco, A.; Ferrer, A. (2007). “Process understanding of a wastewater batch reactor with block-wise PLS”, Environmetrics .18(5) 551-560

  8. Nueda, M.J.; Conesa, A.; Westerhuis, J.A.; Hoefsloot, H.C.J.; Smilde, A.K.; Talón, M.; Ferrer, A. (2007). “Discovering gene expression patterns in Time Course Microarray Experiments by ANOVA-SCA”, Bioinformatics 23(14) 1792-1800

  9. Ferrer, A. (2007), “Multivariate Statistical Process Control based on Principal Component Analysis (MSPC-PCA): Some Reflections and a Case Study in an Autobody Assembly Process”, Journal of Quality Engineering 19 311 – 325

  10. Aguado, D.; Ferrer, A.; Seco, A.; Ferrer, J. (2007). “Multivariate SPC of a sequencing batch reactor for wastewater treatment”, Chemometrics and Intelligent Laboratory Systems 85 (1), 82-93.

  11. Prats-Montalbán, J.M.; Ferrer, A. (2007). “Integration of colour and textural information in multivariate image analysis: defect detection and classification issues”, Journal of Chemometrics 21, 10-23

 

2006

  1. J.L. Díez,  A. Sala, J.L. Navarro, Target-shaped possibilistic clustering applied to local-model identification, Engineering Applications of Artificial Intelligence, Vol.19, pp. 201 – 208, 2006.

  2. E. Picó-Marco, J.L. Navarro, J.M. Bruno-Bárcena, A closed loop exponential feeding law: invariant and global stability analysis, Journal of Process control, vol.16, no.4, pp.395-402, 2006.

  3. Camacho,J., Picó,J. Multi-phase Principal Components Analysis for Batch Processes Modelling,  Chemometrics and Intelligent Laboratory Systems, vol.81, pp.127-136, 2006.

  4. H. De Battista, J.Picó, E. Picó-Marco, Globally Stabilizing Control of Fed-Batch Processes with Haldane Kinetics Using Growth Rate Estimation Feedback, Journal of Process Control, 16, pp. 865-875, 2006.

  5. Camacho,J., Picó,J. Online Monitoring of Batch Processes using phase Principal Components Analysis, Journal of Process Control, 16(10), pp. 1021-1035, 2006.

  6. Picó, J., Picó-Marco, E., Navarro,J.L., De Battista,H. Control of fedbatch bioreactors. Part I. in Nonlinear and adaptive control: theory and algorithms for the user, A. Astolfi (London) Editor, Imperial College Press, pp.207-238, 2006.

  7. Aguado, D.; Ferrer, A.; Seco, A.; Ferrer, J. (2006). “Comparison of different predictive models for nutrient estimation in a sequencing batch reactor for wastewater treatment”, Chemometrics and Intelligent Laboratory Systems 84, 75-81.

  8. Prats-Montalbán, J.M., Ferrer, A., Malo, J.L., Gorbeña, J. (2006). “A comparison of several classification techniques in a steel-industry welding process”, Chemometrics and Intelligent Laboratory Systems 80, 109-119.

  9. Fernando López; José Manuel Prats; Alberto Ferrer; José Miguel Valiente (2006). “Defect Detection in Random Colour Textures using the MIA T2 Defect Maps”, Lecture Notes in Computer Science 4142, 752-763. 

  10. Conesa, A.; Nueda, M.J.; Ferrer, A.; Talón, M. (2006). “maSigPro: a Method to Identify Significant Differential Expression Profiles in Time-Course Microarray Experiments”, Bioinformatics 22 (9), 1096-1102.

 

2005

  1. C. Tarín, E. Teufel, J. Picó, J. Bondia, H.-J. Pfleiderer. Comprehensive pharmacokinetic model of insulin Glargine and other insulin formulations, IEEE Transactions on Biomedical Engineering, pp.1994-2005, Vol.12, 2005.

  2. H. De Battista, E. Picó-Marco, J.Picó, On ‘Feedback Stabilization of Fed-Batch Bioreactors: Non-Monotonic Growth Kinetics’, Biotechnology Progress, American Chemical Society Publications, Vol.21, No. 3, pp.651-652, 2005.

  3. E. Picó-Marco, J.Picó, H. De Battista, Sliding Mode Scheme for Adaptive Specific Growth Rate Control in Biotechnological Fed-batch Processes, International Journal of Control, Taylor&Francis, Vol.78, No.2, pp.128-141, 2005.

  4. Arteaga, F,; Ferrer A. (2005). “Framework for regression-based missing data imputation methods in on-line MSPC”, Journal of Chemometrics 19, 439-447.

  5. López, F. Valiente, J.M., Prats-Montalbán, J.M. (2005). “Surface grading using soft colour-texture descriptors”, Lecture Notes in Computer Science 3773, 13-23.

  6. García-Díaz, J.C.; Prats-Montalbán, J.M. (2005). “Characterization of soils irrigated with untreated urban wastewater using multiway techniques”, Chemometrics and Intelligent Laboratory Systems, 76, 15-24.