Personal Publicaciones Proyectos y contratos Tesis Web del grupo

2017

  • ALONSO A.A, OTERO-MURAS I. 2017. Wegscheider’s condition and passivity of open chemical reaction systems. IFAC-PapersOnLine , 50 (1): 564-569. DOI: 10.1016/j.ifacol.2017.08.075.
  • BALSA-CANTO E, VILAS C, LÓPEZ-NÚÑEZ A, MOSQUERA-FERNÁNDEZ M, BRIANDET R, CABO M.L, VÁZQUEZ C. 2017. Modeling reveals the role of aging and glucose uptake impairment in L1A1 Listeria monocytogenes biofilm life cycle. Frontiers in Microbiology , 8(1): 2118. DOI:10.3389/fmicb.2017.02118.
  • ALONSO A.A, OTERO-MURAS I. 2017. Wegscheider’s condition and passivity of open chemical reaction systems. IFAC-PapersOnLine 50(1):564-569 DOI: 10.1016/j.ifacol.2017.08.075.
  • DA-ROCHA J.M., PRELLEZO R., SEMPERE J., TABOADA ANTELO L. 2017. A dynamic economic equilibrium model for the economic assessment of the fishery stock-rebuilding policies Marine Policy 81:185-195. DOI: 10.1016/j.marpol.2017.03.029
  • VILAS C., ALONSO A.A., HERRERA J.R., GARCÍA-BLANCO A., GARCÍA M.R. 2017. A model for the biochemical degradation of inosine monophosphate in hake (Merluccius merluccius) Journal of Food Engineering 200:95-101 DOI: 10.1016/j.jfoodeng.2016.12.016
  • OTERO-MURAS I., YORDANOV P., STELLING J. 2017. Chemical Reaction Network Theory elucidates sources of multistability in interferon signaling PLoS Computational Biology 13(4) DOI: 10.1371/journal.pcbi.1005454
  • HENRIQUES D., VILLAVERDE A.F., ROCHA M., SAEZ-RODRÍGUEZ J., BANGA J.R. 2017. Data-driven reverse engineering of signaling pathways using ensembles of dynamic models PLoS Computational Biology 13(2) DOI: 10.1371/journal.pcbi.1005379
  • BALSA-CANTO E., LÓPEZ-NÚÑEZ A., VÁZQUEZ C. 2017. Numerical methods for a nonlinear reaction–diffusion system modelling a batch culture of biofilm Applied Mathematical Modelling 18:164-179 DOI:  10.1016/j.apm.2016.08.020
  • PENAS, D.R., GONZÁLEZ, P., EGEA, J.A., DOALLO, R., BANGA, J.R. 2017. Parameter estimation in large-scale systems biology models: A parallel and self-adaptive cooperative strategy BMC Bioinformatics 18(1) DOI: 10.1186/s12859-016-1452-4
  • ATTILA GÁBOR, Alejandro F. VILLAVERDE, Julio R. BANGA. 2017 Parameter identifiability analysis and visualization in large-scale kinetic models of Biosystems BMC Systems Biology 11 DOI: 10.1186/s12918-017-0428-y
  • GARCÍA M.R., CABO M.L., HERRERA, J.R., RAMILO-FERNÁNDEZ, G., ALONSO, A.A., BALSA-CANTO, E. 2017. Smart sensor to predict retail fresh fish quality under ice storage Journal of Food Engineering 8:87-97 DOI: 10.1016/j.jfoodeng.2016.11.006 
  • PENAS, D.R., HENRIQUES, D., GONZÁLEZ, P., DOALLO, R., SAEZ-RODRÍGUEZ, J., BANGA, J.R. 2017. A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology PLoS ONE 12(8) DOI: 10.1371/journal.pone.0182186
  • OTERO-MURAS, I., BANGA, J.R. 2017. Automated Design Framework for Synthetic Biology Exploiting Pareto Optimality ACS Synthetic Biology 6(7):1180-1193 DOI: 10.1021/acssynbio.6b00306
  • GARCÍA, M.R., ALONSO, A.A., BALSA-CANTO, E. 2017. A normalisation strategy to optimally design experiments in computational biology. Advances in Intelligent Systems and Computing 616:136-136 DOI: 10.1007/978-3-319-60816-7_16
  • TEIJEIRO, D., PARDO, X.C., PENAS, D.R., GONZÁLEZ, P., BANGA, J.R., DOALLO, R. 2017. Evaluation of parallel differential evolution implementations on MapReduce and spark Lecture Notes in Computer Science 10104:397-408 DOI: 10.1007/978-3-319-58943-5_32

 
2016

  • BALSA-CANTO E, ALONSO A.A, ARIAS-MÉNDEZ A, GARCÍA M.R, LÓPEZ-NÚÑEZ A, MOSQUERA-FERNÁNDEZ M, VÁZQUEZ C, VILAS C. 2016. Modeling and optimization techniques with applications in food processes, bio-processes and bio-systems. SEMA SIMAI Springer Series, 9 :187-216. DOI: 10.1007/978-3-319-32146-2_4.
  • ALONSO  AA,  SZEDERKÉNYI  G2016Uniqueness of feasible equilibria for mass action law (MAL) kinetic systems. Journal of Process Control , 48 pp. 41 – 71 .
  • BALSA-CANTO  E,  HENRIQUES  D,  GÁBOR  A,  BANGA  J.R.2016AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biologyBioinformatics ,32 ( 21 ) pp. 3357 – 3359
  • OTERO-MURAS  I,  HENRIQUES  D,  BANGA  JR.2016SYNBADm: A tool for optimization-based automated design of synthetic gene circuitsBioinformatics , 32 ( 21 ) pp. 3360 – 3362 .
  • ANTELO LT, ORDÓÑEZ-DEL PAZO T, LOPES C, FRANCO-URÍA A, PÉREZ-MARTÍN RI, ALONSO AA . 2016. Pollutant levels in discarded fish species by Spanish trawlers operating in the Great Sole Bank and the Atlantic coast of the Iberian Peninsula. Marine Pollution Bulletin,  108: 303-310 . DOI: 10.1016/j.marpolbul.. 2016..04.040
  • MOSQUERA-FERNÁNDEZ M, SANCHEZ-VIZUETE P, BRIANDET R, CABO ML, BALSA-CANTO E . 2016. Quantitative image analysis to characterize the dynamics of Listeria monocytogenes biofilms. International Journal of Food Microbiology, 236: 130-137 . DOI: 10.1016/j.ijfoodmicro.. 2016..07.015
  • OTERO-MURAS I, BANGA JR . 2016. Exploring Design Principles of Gene Regulatory Networks via Pareto Optimality. IFAC-PapersOnLine, 49(7): 809-814 . DOI: 10.1016/j.ifacol.. 2016..07.289
  • PÁJARO M, ALONSO AA . 2016. On the applicability of deterministic approximations to model genetic circuits. IFAC-PapersOnLine 49(7):206-211  . DOI: 10.1016/j.ifacol.. 2016..07.251
  • VILLAVERDE AF, BECKER K, BANGA JR . 2016. PREMER: Parallel reverse engineering of biological networks with information theory Lecture Notes in Computer Science (including subseries. Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics),  9859( LNCS): 323-329 . DOI: 10.1007/978-3-319-45177-0_21
  • VILLAVERDE A F, BONGARD  S, MAUCH K, BALSA-CANTO E, BANGA J R. 2016. Metabolic engineering with multi-objective optimization of kinetic models.  Journal of biotechnology 222: 1-8 (2016). DOI: 10.1016/j.jbiotec.. 2016..01.005
  • VILLAVERDE, A.F., BARREIRO, A., PAPACHRISTODOULOU. 2016. Structural Identifiability Analysis via Extended Observability and Decomposition  IFAC-PapersOnLine 49(26):171-177 DOI: 10.1016/j.ifacol.2016.12.121

 

2015

  • ANTELO LT, HIJAS-LISTE GM DE, FRANCO-URÍA A, ALONSO AA, PÉREZ-MARTÍN RI. 2015. Optimisation of processing routes for a marine biorefinery. Journal of Cleaner Production, 104: 489-501.
  • HIJAS-LISTE GM DE, BALSA-CANTO E, EWALD J, BARTL M, LI P, BANGA JR, KALETA C. 2015. Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation. BMC Bioinformatics, 16: 163.
  • LOPES C, ANTELO LT, FRANCO-URÍA A, ALONSO AA, PÉREZ-MARTÍN RI. 2015. Valorisation of fish by-products against waste management treatments: Comparison of environmental impacts. Waste Management, 46: 103-112.
  • GARCÍA MR, VILAS C, HERRERA JR, BERNÁRDEZ M, BALSA-CANTO E, ALONSO AA. 2015. Quality and shelf-life prediction for retail fresh hake (Merluccius merluccius). International Journal of Food Microbiology, 208: 65-74.
  • VILLAVERDE AF, 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 AND BANGA JR. 2015. BioPreDyn-bench: benchmark problems for kinetic modelling in systems biology. BMC Systems Biology, 9(1): 8.
  • VILLAVERDE AF, BONGARD S, MAUCH K, MÜLLER D, BALSA-CANTO E, SCHMID J, BANGA JR. 2015. A consensus approach for estimating the predictive accuracy of dynamic models in biology. Computer Methods and Programs in Biomedicine, 119: 17-28.
  • FOLCH-FORTUNY A, VILLAVERDE AF, FERRER A, BANGA JR. 2015. Enabling network inference methods to handle missing data and outliers. BMC Bioinformatics, 16: 283.
  • GABOR A, BANGA JR. 2015. Robust and efficient parameter estimation in dynamic models of biological systems. BMC Systems Biology, 9: 74
  • GABOR A, HANGOS KM, BANGA JR, SZEDERKENYI G. 2015. Reaction Network Realizations of Rational Biochemical Systems and Their Structural Properties. Journal of Mathematical Chemistry, 53: 1657-1686.
  • PÁJARO M, ALONSO AA, VÁZQUEZ C. 2015. Shaping protein distributions in stochastic self-regulated gene expression networks. Physical Review E, 92: 032712.
  • PENAS DR, BANGA JR, GONZÁLEZ P, DOALLO R. 2015. Enhanced parallel Differential Evolution algorithm for problems in computational systems biology. Applied Soft Computing, 33: 86-99.
  • HENRIQUES D, ROCHA M, SAEZ-RODRIGUEZ J, BANGA JR. 2015. Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach. Bioinformatics, 31(18): 2999-3007.
  • PENAS DR, GONZALEZ P, EGEA JA, BANGA JR, DOALLO R. 2015. Parallel Metaheuristics in Computational Biology: An Asynchronous Cooperative Enhanced Scatter Search Method. Procedia Computer Science, 51: 630-639

 

2014

  • ALONSO A, MOLINA I, THEODOROPOULOS K. 2014. Modeling bacteria population growth from stochastic single-cell dynamics.Applied and Environmental Microbiology, 80 (17), 5241-5253
  • ARIAS-MENDEZ A, VILAS C, ALONSO AA, BALSA-CANTO E. 2014. Time temperature integrators as predictive temperature sensors. Food Control, 44: 258-266.
  • DE HIJAS-LISTE GM, KLIPP E, BALSA-CANTO E, BANGA JR. 2014. Global dynamic optimization approach to predict activation in metabolic pathways. BMC Systems Biology,8:1.
  • EGEA JA, HENRIQUES D, COKELAER T, VILLAVERDE AF, MACNAMARA A, DANCIU D, BANGA JR, SAEZ-RODRIGUEZ J. 2014. MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. BMC Bioinformatics,15: 136.
  • HEERMANN R, ZIGANN K, GAYER S, RODRIGUEZ-FERNANDEZ M, BANGA JR, KREMLING A, JUNG K. 2014. Dynamics of an Interactive Network Composed of a Bacterial Two-Component System, a Transporter and K+ as Mediator. PLoS ONE, 9(2):e89671.
  • LÓPEZ-CAAMAL F, OYARZÚN DA, MIDDLETON RH, GARCÍA MR. 2014. Spatial quantification of cytosolic Ca2+ accumulation in nonexcitable cells: Ananalytical study. IEEE/ACM Transactions on Computational Biolgy and Bioinformatics, 11 (3): 592-603.
  • MOSQUERA-FERNÁNDEZ M, RODRÍGUEZ-LÓPEZ P, CABO ML, BALSA-CANTO E. 2014. Numerical spatio-temporal characterization of Listeria mono cytogenes biofilms.International Journal of Food Microbiology, 182, 26-36.
  • ORDÓÑEZ-DEL PAZO T, ANTELO LT, FRANCO-URÍA A, PÉREZ-MARTÍN RI, SOTELO CG, ALONSO AA. 2014. Fish discards management in selected Spanish and Portuguese métiers: Identification and potential valorisation. Trends in Food Science and Technology, 36 (1), 29-43.
  • OTERO MURAS I, BANGA JR. 2014. Multicriteria global optimization for biocircuit design. BMC Systems Biology,8:113.
  • OTERO MURAS I, YORDANOV P, STELLING J. 2014. A method for inverse bifurcation of biochemical switches: inferring parameters from dose response curves. BMC Systems Biology, 8:114.
  • RAIMÚNDEZ C, VILLAVERDE AF, BARREIRO A. 2014. Adaptive tracking in mobile robots with input-output linearization. Journal of Dynamic Systems, easurement, and Control, Transactions of the ASME,136: 054503-1.
  • VILLAVERDE AF, ROSS J, MORÁN F, BANGA JR. 2014. MIDER: network inference with Mutual Information Distance and Entropy Reduction. PLOS ONE, 9(5): e96732.
  • VILLAVERDE AF, BANGA JR. 2014. Reverse engineering and identification in systems biology: strategies, perspectives, and challenges.
  • Journal of the Royal Society Interface, 11: 20130505.

 

2013

  •  ALONSO AA, ARIAS-MÉNDEZ A, BALSA-CANTO E, GARCÍA MR, MOLINA JI, VILAS C, VILLAFÍN M. 2013. Real time optimization for quality control of batch thermal sterilization of  prepackaged foods. Food Control, 32 (2): 392-403.
  • ARIAS-MENDEZ A, WARNING A, DATTA AK, BALSA-CANTO E. 2013. Quality and safety driven optimal operation of deep-fat frying of potato chips. Journal of Food Engineering, 119 (1): 125–134.
  • BECKER K, BALSA-CANTO E, CICIN-SAIN D, HOERMANN A, JANSSENS H, BANGA JR, JAEGER J. 2013. Reverse-Engineering Post-Transcriptional Regulation of Gap Genes in Drosophila melanogaster. PLoS Computational Biology, 9 (10): e1003281.
  • EGEA JA, HENRIQUES D, COKELAER T, VILLAVERDE AF, BANGA JR, SAEZ-RODRIGUEZ J. 2013. MEIGO: an open-source software suite based on metaheuristics for global optimization  in systems biology and bioinformatics. ArXiv, 1311.5735.
  • HANNEMANN-TAMÁS R, GÁBOR A, SZEDERKÉNYI G, HANGOS KM. 2013. Model complexity reduction of chemical reaction networks using mixed-integer quadratic programming. Computers and Mathematics with Applications, 65 (10): 1575-1595.
  • LOPES C, ANTELO LT, FRANCO-URÍA A, BOTANA C, ALONSO AA. 2013. Sustainability of port activities within the framework of the fisheries sector: Port of Vigo (NW Spain). Ecological  Indicators, 30: 45-51.
  • RIVAS D, VILAS C, VARAS F, ALONSO AA. 2013. Derivation of postharvest fruit behavior reduced order models for on-line monitoring and control of quality parameters during refrigeration. Journal of Food Process Engineering, 36 (4): 480-491.
  • ROCHA JM, GUTIÉRREZ MJ, ANTELO LT. 2013. Selectivity, Pulse Fishing and Endogenous Lifespan in Beverton-Holt Models. Environmental and Resource Economics, 54 (1) 139-154, doi: 10.1007/s10640-012-9.
  • RODRIGUEZ-FERNANDEZ M, REHBERG M, KREMLING A, BANGA JR. 2013. Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems. BMC  Systems Biology, 7: 76.
  • TUZA ZA, SZEDERKENYI G, HANGOS KM, ALONSO  AA, BANGA JR. 2013. Computing all Sparse Kinetic Structures for a Lorenz System Using Optimization. Int. Journal of Bifurcation and Chaos, 23 (8): 1350141.
  • VILLAVERDE AF ROSS J, BANGA JR. 2013. Reverse engineering cellular networks with information theoretic methods. Cells, 2 (2): 306–329.
  • BALSA-CANTO E, BANGA J.R. 2013. Optimal dynamic experiments. En: Encyclopedia of Systems Biology. (W. Dubitzky, O. Wolkenhauer, K.-H. Cho, H. Yokota, eds.), pp. 1569-1572. Springer Science+Business Media.
  • DE HIJAS-LISTE GM, BALSA-CANTO E, BANGA JR, KALETA C. 2013. Optimal regulatory programs for the control of metabolic pathways: The case of feedback inhibition. En: 21st  Mediterranean Conference on Control and Automation, MED 2013- Conference Proceedings, pp. 237 – 242, (http:// dx.doi.org/10.1109/MED.2013.6608728).
  • BALSA-CANTO E, ALONSO AA, ANTELO LT, ARIAS-MENDEZ A, LÓPEZ-QUIROGA E, RIVAS D, VILAS C. 2013. Model identification and on-line optimal control of food processes. En:  Computational Methods for Coupled problems in Science and Engineering V. (S. Idelsohn, M. Papadrakakis and B. Schrefler, eds.), pp. 1395-1406, ISBN: 978-84-941407-6-1.
  • GÁBOR A, HANGOS KM, SZEDERKÉNYI G, BANGA JR. 2013. On the Verification and Correction of Large-Scale Kinetic Models in Systems Biology. En: Computational Methods in Systems  biology. Lecture Notes in Computer Science, 8130: 206-219.
  • GARCÍA M-SG, BALSA-CANTO E, ALONSO AA, BANGA JR. 2013. Dynamic Optimization of Nonlinear Bioreactors. En: Taming Heterogeneity and Complexity of Embedded Control,            307 -327 (http://dx.doi.org/10.1002/9780470612217.ch18).
  • MACNAMARA A, HENRIQUES D, SAEZ-RODRIGUEZ J. 2013. Modeling Signaling Networks with Different Formalisms: A Preview. En: In Silico Systems Biology, pp. 89-105. Humana Press.

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