Research Group

Detalle de: Computational Biology Lab at MBG

Title	Computational Biology Lab at MBG
Description	Our research is focused in computational systems and synthetic biology. We use mathematical modelling, simulation and optimization to understand complex biological systems and processes. Current research topics include: Reverse engineering: systems identification (dynamic modelling) of biological networks Forward engineering: computer-aided design in synthetic biology Optimality principles in biological systems Dynamics and optimal control of biosystems
Home Page	https://www.bangalab.org/
Contact Email	j.r.banga@csic.es
Collaborating Companies
Spin Off
Patents
Hpc Resources
Institution	MBG
Ontology	Computational Methods, Artificial Intelligence, Machine Learning in Biology, Computational models and simulations, Biosystems Modeling, Gene regulatory networks, Metabolic modelling, High-performance Computing, Parallel Computing, Systems Biology, Microbial communities, Cloud Computing, Dynamical systems, Mathematical optimization, Synthetic biology
Tools	saCeSS, MEIGO, AMIGO2: Advanced model identification using global optimization, GEARS, GenSSI 2.0, PREMER, VisId, SYNBADm, saCMM, saCeSS2, asynPDE
Service Units
Research Lines	Reverse engineering: systems identification (dynamic modelling) of biological networks, Forward engineering: computer-aided design in synthetic biology, Optimality principles in biological systems, Dynamics and optimal control of biosystems
Funded Projects	DATA-DRIVEN MECHANISTIC MODELLING, UNCERTAINTY QUANTIFICATION AND OPTIMISATION IN SYSTEMS BIOLOGY (DYNAMO-bio), ENHANCING THE COMPUTATIONAL BIOLOGY OF MICROORGANISMS AND PLANTS WITH NEW METHODS OF ARTIFICIAL INTELLIGENCE AND SUPERCOMPUTING (SuperBioComp), LARGE SCALE GLOBAL OPTIMIZATION IN SYSTEMS BIOLOGY (LarGO), DYNAMIC REGULATION ACROSS METABOLIC ENGINEERING SCALES. MULTI-MODEL INFERENCE AND DYNAMIC OPTIMALITY (BIODYNAMICS), Ensemble modelling in systems biology - from identification to uncertainty quantification in predictions and structure, Design, analysis and optimization of biochemical pathways and genetic regulatory networks using stochastic models, Generation of the CanPath prototype - a platform for predictive cancer pathway modeling, Systematic Models for Biological Systems Engineering Training Network, Design, characterization and optimal tuning of synthetic biocircuits for bioproduction with control of the metabolic load, Synthetic biology to improve bioprocesses: design, optimization, monitoring and control, From data to models: new bioinformatics methods and tools for data-driven predictive dynamic modelling in biotechnological applications, Network for integrated cellular homeostasis, Towards an understanding of dynamic transcriptional regulation at global scale in bacteria: a systems biology approach
Selected Publications	Conformal prediction for uncertainty quantification in dynamic biological systems Article · 12 May 2025 Parameter estimation in a whole-brain network model of epilepsy: Comparison of parallel global optimization solvers Article · 11 Jul 2024 Population based metaheuristics in Spark: Towards a general framework using PSO as a case study Article · Mar 2024 Improved cooperative Ant Colony Optimization for the solution of binary combinatorial optimization applications Article · 29 Jan 2024 Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells Article · 8 Jan 2024 View all (213 more) IDESS: a toolbox for identification and automated design of stochastic gene circuits Article · 1 Nov 2023 Distilling identifiable and interpretable dynamic models from biological data Article · 18 Oct 2023 Automated Design of Synthetic Gene Circuits in the Presence of Molecular Noise Article · 9 Oct 2023 Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants Article · 6 Jul 2023 Global Optimization Approach for Parameter Estimation in Stochastic Dynamic Models of Biosystems Article · 1 May 2023 Assessment of Prediction Uncertainty Quantification Methods in Systems Biology Article · 1 May 2023 Parallel ant colony optimization for the training of cell signaling networks Article · Dec 2022 Improving dynamic predictions with ensembles of observable models Article · 23 Nov 2022 OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production Article · 7 Apr 2022 Editorial overview: ‘Mathematical modelling of high-throughput and high-content data’ Article · Mar 2022 An efficient ant colony optimization framework for HPC environments Article · Jan 2022 Automated design of synthetic biocircuits in the stochastic regime Article · 2022 AutoRepar: A method to obtain identifiable and observable reparameterizations of dynamic models with mechanistic insights Article · 18 Nov 2021 A protocol for dynamic model calibration Article · 9 Oct 2021 Editorial: Biological Control Systems and Disease Modeling Article · 9 Apr 2021 PEtab - Interoperable specification of parameter estimation problems in systems biology Article · 26 Jan 2021 Structural identifiability and observability of compartmental models of the COVID-19 pandemic Article · 2021 Automated Biocircuit Design with SYNBADm Book / chapter · 2021 Spark implementation of the enhanced Scatter Search metaheuristic: Methodology and assessment Article · Dec 2020 Synthetic Gene Circuit Analysis and Optimization Book / chapter · 13 Nov 2020 A dual-parameter identification approach for data-based predictive modeling of hybrid gene regulatory network-growth kinetics in Pseudomonas putida mt-2 Article · 6 May 2020 Full observability and estimation of unknown inputs, states and parameters of nonlinear biological models Article · Jul 2019 Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology Article · 8 May 2019 Computational Methods Enabling Next-Generation Bioprocesses Article · 12 Apr 2019 Input-Dependent Structural Identifiability of Nonlinear Systems Article · Apr 2019 Parameter estimation in models of biological oscillators: An automated regularised estimation approach Article · 15 Feb 2019 Distilling Robust Design Principles of Biocircuits Using Mixed Integer Dynamic Optimization Article · 13 Feb 2019 Multiobjective optimization of gene circuits for metabolic engineering Article · 2019 A Comparison of Methods for Quantifying Prediction Uncertainty in Systems Biology Article · 2019 Multimethod optimization for reverse engineering of complex biological networks Conference paper · 23 Sep 2018 CanPathPro-development of a platform for predictive pathway modelling using genetically engineered mouse models Article · 1 Jul 2018 PREMER: A Tool to Infer Biological Networks Software · 1 Jul 2018 Erratum: Optimality and identification of dynamic models in systems biology: an inverse optimal control framework (Bioinformatics (Oxford, England) (2018) 34 14 (2433-2440)) Article · 15 Jun 2018 Multimethod optimization in the cloud: A case-study in systems biology modelling Software · 30 Mar 2018 Optimality and identification of dynamic models in systems biology: an inverse optimal control framework Article · 7 Mar 2018 Sufficiently Exciting Inputs for Structurally Identifiable Systems Biology Models Article · 2018 Optimization-based prediction of fold bifurcations in nonlinear ODE models Article · 2018 Mixed Integer Multiobjective Optimization Approaches for Systems and Synthetic Biology Article · 2018 Critical Assessment of Parameter Estimation Methods in Models of Biological Oscillators Article · 2018 GenSSI 2.0: Multi-experiment structural identifiability analysis of SBML models Software · 30 Nov 2017 Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation Article · 29 Nov 2017 A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology Article · 15 Aug 2017 Structural Properties of Dynamic Systems Biology Models: Identifiability, Reachability, and Initial Conditions Article · 2 Jun 2017 Energy and society Book / chapter · 12 May 2017 Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems Software · 5 May 2017 Using the cloud for parameter estimation problems: comparing spark vs MPI with a case-study Conference paper · May 2017 A cloud-based enhanced differential evolution algorithm for parameter estimation problems in computational systems biology Article · 17 Apr 2017 Automated Design Framework for Synthetic Biology Exploiting Pareto Optimality Article · 12 Apr 2017 Data-driven reverse engineering of signaling pathways using ensembles of dynamic models Article · 6 Feb 2017 Parameter estimation in large-scale systems biology models: A parallel and self-adaptive cooperative strategy Software · 21 Jan 2017 Evaluation of parallel differential evolution implementations on MapReduce and spark Book / chapter · 2017 Design Principles of Biological Oscillators through Optimization: Forward and Reverse Analysis Article · 15 Dec 2016 On the relationship between sloppiness and identifiability Article · Dec 2016 Towards cloud-based parallel metaheuristics: A case study in computational biology with Differential Evolution and Spark Article · 28 Nov 2016 SYNBADm: A tool for optimization-based automated design of synthetic gene circuits Software · 8 Jul 2016 AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology Software · 4 Jul 2016 Metabolic engineering with multi-objective optimization of kinetic models Article · Mar 2016 PREMER: Parallel reverse engineering of biological networks with information theory Book / chapter · 2016 Implementing parallel differential evolution on spark Book / chapter · 2016 Exploring Design Principles of Gene Regulatory Networks via Pareto Optimality Article · 2016 Robust and efficient parameter estimation in dynamic models of biological systems Article · 29 Oct 2015 Enabling network inference methods to handle missing data and outliers Article · 3 Sep 2015 Enhanced parallel differential evolution algorithm for problems in computational systems biology Software · Aug 2015 Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach Article · 21 May 2015 Optimal programs of pathway control: Dissecting the influence of pathway topology and feedback inhibition on pathway regulation Article · 16 May 2015 Reaction network realizations of rational biochemical systems and their structural properties Article · 15 May 2015 A consensus approach for estimating the predictive accuracy of dynamic models in biology Article · Apr 2015 BioPreDyn-bench: A suite of benchmark problems for dynamic modelling in systems biology Article · 20 Feb 2015 Parallel metaheuristics in computational biology: An asynchronous Cooperative enhanced Scatter Search method Article · 2015 Multicriteria global optimization for biocircuit design Article · 24 Sep 2014 MEIGO: An open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics Software · 10 May 2014 MIDER: Network inference with mutual information distance and entropy reduction Article · 7 May 2014 Dynamics of an interactive network composed of a bacterial two-component system, a transporter and K+ as mediator Article · 28 Feb 2014 Reverse engineering and identification in systems biology: Strategies, perspectives and challenges Article · 6 Feb 2014 Global dynamic optimization approach to predict activation in metabolic pathways Article · 6 Jan 2014 Optimization based design of synthetic oscillators from standard biological parts Book / chapter · 2014 Improved parameter estimation in kinetic models: Selection and tuning of regularization methods Book / chapter · 2014 High-confidence predictions in systems biology dynamic models Book / chapter · 2014 A parallel differential evolution algorithm for parameter estimation in dynamic models of biological systems Book / chapter · 2014 Reverse-Engineering Post-Transcriptional Regulation of Gap Genes in Drosophila melanogaster Article · 31 Oct 2013 Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems Article · 12 Aug 2013 Computing all sparse kinetic structures for a Lorenz system using optimization Article · Aug 2013 Optimal regulatory programs for the control of metabolic pathways: The case of feedback inhibition Conference paper · Jun 2013 Reverse engineering cellular networks with information theoretic methods Article · 10 May 2013 Robust Identification in Nonlinear Dynamic Process Models Other · Mar 2013 Dynamic Optimization of Nonlinear Bioreactors Other · Mar 2013 Erratum: Characterizing multistationarity regimes in biochemical reaction networks (PLoS ONE (2013) 8:1 DOI: 10.1371/annotation/b5283cc5-5a93-4c96-abc4- c5112266fabe) Article · 15 Jan 2013 On the verification and correction of large-scale kinetic models in systems biology Book / chapter · 2013 Multi-criteria optimization of regulation in metabolic networks Article · 26 Jul 2012 Characterizing multistationarity regimes in biochemical reaction networks Article · 3 Jul 2012 Dynamic optimization of distributed biological systems using robust and efficient numerical techniques Article · 2 Jul 2012 Robust and efficient numerical methods for the optimal control of spatially distributed biological systems Conference paper · Jul 2012 A cooperative strategy for parameter estimation in large scale systems biology models Article · 22 Jun 2012 CRNreals: A toolbox for distinguishability and identifiability analysis of biochemical reaction networks Article · 6 Apr 2012 Novel global sensitivity analysis methodology accounting for the crucial role of the distribution of input parameters: Application to systems biology models Article · 6 Mar 2012 9th IFAC International Symposium on Dynamics and Control of Process Systems (DYCOPS) & 11th IFAC International Symposium on Computer Applications in Biotechnology (CAB): Leuven, Belgium, July 5-7, 2010 and July 7-9, 2010 Article · Dec 2011 Structural identifiability of systems biology models: A critical comparison of methods Article · 22 Nov 2011 Global optimization in systems biology: Stochastic methods and their applications Book / chapter · 18 Nov 2011 GenSSI: A software toolbox for structural identifiability analysis of biological models Article · 22 Jul 2011 Use of a generalized fisher equation for global optimization in chemical kinetics Article · 14 Jul 2011 AMIGO, a toolbox for advanced model identification in systems biology using global optimization Article · 17 Jun 2011 Detailed kinetic model describing new oligosaccharides synthesis using different β-galactosidases Article · May 2011 Fuzzy finite element analysis of heat conduction problems with uncertain parameters Article · Mar 2011 Methods for checking structural identifiability of nonlinear biosystems: A critical comparison Article · Jan 2011 Inference of transcriptional control design of metabolic networks Article · Jan 2011 Prediction of activation of metabolic pathways via dynamic optimization Book / chapter · 2011 Inference of complex biological networks: Distinguishability issues and optimization-based solutions Article · 2011 Process Systems Engineering Book / chapter · 27 Oct 2010 Preface: Volume 7: Dynamic Process Modeling Other · 27 Oct 2010 Investigating dynamics of inhibitory and feedback loops in ERK signalling using power-law models Article · 18 Aug 2010 A generalized Fisher equation and its utility in chemical kinetics Article · 6 Jul 2010 Efficient and robust multi-objective optimization of food processing: A novel approach with application to thermal sterilization Article · Jun 2010 Multi-objective mixed integer strategy for the optimisation of biological networks Article · 13 May 2010 SensSB: a software toolbox for the development and sensitivity analysis of systems biology models Article · 5 May 2010 An iterative identification procedure for dynamic modeling of biochemical networks Article · 17 Feb 2010 An evolutionary method for complex-process optimization Article · Feb 2010 Parametric condition for multistationarity in biochemical reaction networks Article · 2010 Computational Procedures for Model Identification Book / chapter · 2010 AMIGO: A model identification toolbox based on global optimization and its applications in biosystems Article · 2010 Extended ant colony optimization for non-convex mixed integer nonlinear programming Article · Jul 2009 DOTcvpSB, a software toolbox for dynamic optimization in systems biology Article · 29 Jun 2009 An extended ant colony optimization algorithm for integrated process and control system design Article · 9 Jun 2009 Exploring Multiplicity Conditions in Enzymatic Reaction Networks Article · May 2009 Dynamic optimization of nonlinear processes with an enhanced scatter search method Article · 3 Apr 2009 Extensions of a multistart clustering algorithm for constrained global optimization problems Article · 10 Feb 2009 Multi-objective optimization of biological networks for prediction of intracellular fluxes Book / chapter · 2009 Global sensitivity analysis of a biochemical pathway model Book / chapter · 2009 A Library of Software Components for the Operation of Thermal Food Processing Plants Article · Dec 2008 Exponential observers for distributed tubular (bio)rteactors Article · 7 Oct 2008 Optimal tuning of thermodynamic-based decentralized PI control loops: Application to the tennessee eastman process Article · 6 Oct 2008 Parameter estimation and optimal experimental design Article · 30 Sep 2008 Robust feed-back control of travelling waves in a class of reaction-diffusion distributed biological systems Article · Sep 2008 Hierarchical design of decentralized control structures for the Tennessee Eastman Process Article · Sep 2008 A Tabu search-based algorithm for mixed-integer nonlinear problems and its application to integrated process and control system design Article · Aug 2008 Computational procedures for optimal experimental design in biological systems Article · 14 Jul 2008 Optimization in computational systems biology Article · 28 May 2008 Hybrid optimization method with general switching strategy for parameter estimation Article · 24 Mar 2008 Computing optimal dynamic experiments for model calibration in predictive microbiology Article · 24 Feb 2008 Quality and safety models and optimization as part of computer-integrated manufacturing Article · Jan 2008 Optimal dynamic heat generation profiles for simultaneous estimation of thermal food properties using a hotwire probe: Computation, implementation and validation Article · Jan 2008 Development of a library of components in ecosimpro for the operation of thermal processing plants,Desarrollo de una librería de componentes en ecosimpro para la operación de plantas de procesamiento térmico de alimentos Article · Jan 2008 TECHNOLOGY AND SOCIETY Book / chapter · 2008 Identifiability and robust parameter estimation in food process modeling: Application to a drying model Article · Dec 2007 The GLOBAL optimization method revisited Article · 30 Nov 2007 Optimal design of dynamic experiments for improved estimation of kinetic parameters of thermal degradation Article · Sep 2007 Improved scatter search for the global optimization of computationally expensive dynamic models Article · 7 Jul 2007 Power-law models of signal transduction pathways Article · Jul 2007 Welcome and introduction Article · Jun 2007 Robust feed-back control of distributed chemical reaction systems Article · Jun 2007 Network theory in control engineering: Applications in dynamic analysis and process control,La teoría de redes en ingeniería de control: Aplicación al análisis dinámico y al control de procesos Article · Jan 2007 Optimal dynamic experimental design in systems biology: Applications in cell signaling Article · 2007 Optimal control of the Simulated Moving Bed (SMB) chromatographic separation process Article · 2007 NBI-RPRGM for multi-objective optimization design of bio-processes Article · 2007 Optimal field reconstruction of distributed process systems from partial measurements Article · 21 Dec 2006 Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems Article · 2 Nov 2006 Scatter search for chemical and bio-process optimization Article · 7 Oct 2006 Model based optimization of biochemical systems using multiple objectives: A comparison of several solution strategies Article · Oct 2006 Improved optimization methods for the multiobjective design of bioprocesses Article · 2 Sep 2006 Robust parameter estimation in a model for glucose kinetics in type 1 diabetes subjects Conference paper · Aug 2006 Stabilization of inhomogeneous patterns in a diffusion-reaction system under structural and parametric uncertainties Article · Jul 2006 Computing optimal operating policies for the food industry Article · May 2006 A hybrid approach for efficient and robust parameter estimation in biochemical pathways Article · Feb 2006 A thermodynamic based plant-wide control design procedure of the tennessee eastman process Book / chapter · 2006 Dynamic optimization of complex distributed process systems Article · Jun 2005 Dynamic optimization of bioprocesses: Efficient and robust numerical strategies Article · Jun 2005 Dynamic optimization of single- and multi-stage systems using a hybrid Stochastic-deterministic method Article · 27 Jan 2005 State reconstruction in spatially distributed BioProcess systems using reduced order models: Application to the gluconic acid production Conference paper · 2005 An efficient real-time dynamic optimization architecture for the control of non-isothermal tubular reactors Book / chapter · 2005 A systematic approach to plant-wide control based on thermodynamics Book / chapter · 2005 A software toolbox for the dynamic optimization of nonlinear processes Book / chapter · 2005 Solving nonconvex climate control problems: Pitfalls and algorithm performances Article · Dec 2004 A model-based approach to develop periodic thermal treatments for surface decontamination of strawberries Article · Oct 2004 Dynamic optimization of distributed parameter systems using second-order directional derivatives Article · 21 Sep 2004 Reduced-order models for nonlinear distributed process systems and their application in dynamic optimization Article · 18 May 2004 Global optimization of bioprocesses using stochastic and hybrid methods Book / chapter · 2004 On systematic model reduction techniques for dynamic optimization and robust control of distributed process systems Book / chapter · 2004 Chapter D4 Multi-objective integrated design and control using stochastic global optimization methods Book / chapter · 2004 Dissipative systems: From physics to robust nonlinear control Article · 11 Dec 2003 Integrated Nonlinear Optimization of Bioprocesses via Linear Programming Article · Dec 2003 Dynamic optimization of double-sided cooking of meat patties Article · Jun 2003 Improving food processing using modern optimization methods Article · Apr 2003 Parameter estimation in biochemical pathways: A comparison of global optimization methods Article · 1 Jan 2003 Global optimization of climate control problems using evolutionary and stochastic algorithms Book / chapter · 2003 From irreversible thermodynamics to a robust control theory for distributed process systems Article · Jun 2002 Computation of optimal identification experiments for nonlinear dynamic process models: a stochastic global optimization approach Article · 17 Apr 2002 Restricted second order information for the solution of optimal control problems using control vector parameterization Article · Feb 2002 A COMBINED ELECTROMAGNETIC AND HEAT TRANSFER MODEL FOR HEATING OF FOODS IN MICROWAVE COMBINATION OVENS Article · Jan 2002 Robust nonlinear control design of distributed process systems with input constraints Article · 2002 Optimal control of distributed processes using reduced order models Conference paper · Sep 2001 Integrated process design and control via global optimization: A wastewater treatment plant case study Conference paper · Sep 2001 On the optimal control of contact-cooking processes Article · Jun 2001 Temperature control in microwave combination ovens Article · Oct 2000 Optimization of hybrid discrete/continuous dynamic systems Article · Oct 2000 Efficient optimal control of bioprocesses using second-order information Article · 29 Sep 2000 Passive control design for distributed process systems: Theory and applications Article · Aug 2000 Numerical strategies for optimal experimental design for parameter identification of non-linear dynamic (Bio-)chemical processes Book / chapter · 2000 Second-order sensitivities of general dynamic systems with application to optimal control problems Article · Sep 1999 Modeling and adaptive control for batch sterilization Article · Feb 1998 Rebuttal to the comments of Rein Luus on "Dynamic optimization of batch reactors using adaptive stochastic algorithms" Article · 1 Jan 1998 Design of a class of stabilizing nonlinear state feedback controllers with bounded inputs Article · 1 Jan 1998 Stochastic optimization for optimal and model-predictive control Article · 1998 A hybrid method for the optimal control of chemical processes Conference paper · 1998 A complete dynamic model for the thermal processing of bioproducts in batch units and its application to controller design Article · Apr 1997 Time-temperature effects on microbial, chemical and sensory changes during cooling and aging of cheddar cheese Book / chapter · 1995 Optimal control of heat and mass transfer in food and bioproducts processing Article · Jan 1994 OPTIMIZATION OF AIR-DRYING OF FOODS Article · Jan 1994 ICRS/DS: A computer package for the optimization of batch processes and its applications in food processing Book / chapter · 1994 Different strategies for controlling pressure during the cooling stage in batch retorts Book / chapter · 1994 Computer aided design and optimization of sterilization of canned tuna Book / chapter · 1994 Kinetics of thermal degradation of thiamine and surface colour in canned tuna Article · Aug 1993 MATHEMATICAL-MODELING AND SIMULATION OF THE THERMAL-PROCESSING OF ANISOTROPIC AND NONHOMOGENEOUS CONDUCTION-HEATED CANNED FOODS - APPLICATION TO CANNED TUNA Article · Jan 1993 DEGRADATION KINETICS OF PROTEIN DIGESTIBILITY AND AVAILABLE LYSINE DURING THERMAL-PROCESSING OF TUNA Article · Jul 1992 Determination of thermal conductivity, specific heat and thermal diffusivity of albacore (Thunnus alalunga) Article · Dec 1989
Researchers	Julio Rodriguez Banga, Ana Paredes Vázquez, Andrea Polo Rodríguez, David Rodríguez Penas

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