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Global optimization in systems biology: Stochastic methods and their applications


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Dynamic optimization of distributed biological systems using robust and efficient numerical techniques


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Characterizing multistationarity regimes in biochemical reaction networks


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CRNreals: A toolbox for distinguishability and identifiability analysis of biochemical reaction networks


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A cooperative strategy for parameter estimation in large scale systems biology models


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Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems


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Robust Identification in Nonlinear Dynamic Process Models


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Reverse-Engineering Post-Transcriptional Regulation of Gap Genes in Drosophila melanogaster


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Reverse engineering cellular networks with information theoretic methods


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Optimal regulatory programs for the control of metabolic pathways: The case of feedback inhibition


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On the verification and correction of large-scale kinetic models in systems biology


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Erratum: Characterizing multistationarity regimes in biochemical reaction networks (PLoS ONE (2013) 8:1 DOI: 10.1371/annotation/b5283cc5-5a93-4c96-abc4- c5112266fabe)


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Dynamic Optimization of Nonlinear Bioreactors


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Computing all sparse kinetic structures for a Lorenz system using optimization


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Reverse engineering and identification in systems biology: Strategies, perspectives and challenges


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Preface: Volume 7: Dynamic Process Modeling


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Optimization based design of synthetic oscillators from standard biological parts


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Multicriteria global optimization for biocircuit design


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MIDER: Network inference with mutual information distance and entropy reduction


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MEIGO: An open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics


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Improved parameter estimation in kinetic models: Selection and tuning of regularization methods


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High-confidence predictions in systems biology dynamic models


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Global dynamic optimization approach to predict activation in metabolic pathways


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Dynamics of an interactive network composed of a bacterial two-component system, a transporter and K+ as mediator


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A parallel differential evolution algorithm for parameter estimation in dynamic models of biological systems


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Robust and efficient parameter estimation in dynamic models of biological systems


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Reaction network realizations of rational biochemical systems and their structural properties


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Parallel metaheuristics in computational biology: An asynchronous Cooperative enhanced Scatter Search method


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Optimal programs of pathway control: Dissecting the influence of pathway topology and feedback inhibition on pathway regulation


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Enhanced parallel differential evolution algorithm for problems in computational systems biology


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Enabling network inference methods to handle missing data and outliers


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BioPreDyn-bench: A suite of benchmark problems for dynamic modelling in systems biology


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A consensus approach for estimating the predictive accuracy of dynamic models in biology


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Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach


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SYNBADm: A tool for optimization-based automated design of synthetic gene circuits


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PREMER: Parallel reverse engineering of biological networks with information theory


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Implementing parallel differential evolution on spark


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Exploring Design Principles of Gene Regulatory Networks via Pareto Optimality


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Design Principles of Biological Oscillators through Optimization: Forward and Reverse Analysis


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AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology


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Metabolic engineering with multi-objective optimization of kinetic models


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On the relationship between sloppiness and identifiability


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Using the cloud for parameter estimation problems: comparing spark vs MPI with a case-study


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Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems


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Parameter estimation in large-scale systems biology models: A parallel and self-adaptive cooperative strategy


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Evaluation of parallel differential evolution implementations on MapReduce and spark


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Data-driven reverse engineering of signaling pathways using ensembles of dynamic models


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A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology


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A cloud-based enhanced differential evolution algorithm for parameter estimation problems in computational systems biology


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Structural Properties of Dynamic Systems Biology Models: Identifiability, Reachability, and Initial Conditions


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Automated Design Framework for Synthetic Biology Exploiting Pareto Optimality


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Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation


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Towards cloud-based parallel metaheuristics: A case study in computational biology with Differential Evolution and Spark


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Sufficiently Exciting Inputs for Structurally Identifiable Systems Biology Models


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Optimization-based prediction of fold bifurcations in nonlinear ODE models


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Multimethod optimization in the cloud: A case-study in systems biology modelling


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Multimethod optimization for reverse engineering of complex biological networks


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Mixed Integer Multiobjective Optimization Approaches for Systems and Synthetic Biology


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GenSSI 2.0: Multi-experiment structural identifiability analysis of SBML models


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Erratum: Optimality and identification of dynamic models in systems biology: an inverse optimal control framework (Bioinformatics (Oxford, England) (2018) 34 14 (2433-2440))


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Critical Assessment of Parameter Estimation Methods in Models of Biological Oscillators


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CanPathPro-development of a platform for predictive pathway modelling using genetically engineered mouse models


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Benchmarking optimization methods for parameter estimation in large kinetic models


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PREMER: A Tool to Infer Biological Networks


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Optimality and identification of dynamic models in systems biology: an inverse optimal control framework


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Parameter estimation in models of biological oscillators: An automated regularised estimation approach


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Multiobjective optimization of gene circuits for metabolic engineering


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Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology


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Full observability and estimation of unknown inputs, states and parameters of nonlinear biological models


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A Comparison of Methods for Quantifying Prediction Uncertainty in Systems Biology


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Distilling Robust Design Principles of Biocircuits Using Mixed Integer Dynamic Optimization


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Input-Dependent Structural Identifiability of Nonlinear Systems


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Computational Methods Enabling Next-Generation Bioprocesses


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Spark implementation of the enhanced Scatter Search metaheuristic: Methodology and assessment


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A dual-parameter identification approach for data-based predictive modeling of hybrid gene regulatory network-growth kinetics in Pseudomonas putida mt-2


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Using optimal control to understand complex metabolic pathways


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Synthetic Gene Circuit Analysis and Optimization


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Structural identifiability and observability of compartmental models of the COVID-19 pandemic


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PEtab - Interoperable specification of parameter estimation problems in systems biology


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Editorial: Biological Control Systems and Disease Modeling


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Automated Biocircuit Design with SYNBADm


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AutoRepar: A method to obtain identifiable and observable reparameterizations of dynamic models with mechanistic insights


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A protocol for dynamic model calibration


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Editorial overview: ‘Mathematical modelling of high-throughput and high-content data’


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Automated design of synthetic biocircuits in the stochastic regime


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An efficient ant colony optimization framework for HPC environments


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OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production


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Parallel ant colony optimization for the training of cell signaling networks


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Improving dynamic predictions with ensembles of observable models


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Global Optimization Approach for Parameter Estimation in Stochastic Dynamic Models of Biosystems


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Assessment of Prediction Uncertainty Quantification Methods in Systems Biology


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Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants


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Distilling identifiable and interpretable dynamic models from biological data


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Automated Design of Synthetic Gene Circuits in the Presence of Molecular Noise


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IDESS: a toolbox for identification and automated design of stochastic gene circuits


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Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells


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Improved cooperative Ant Colony Optimization for the solution of binary combinatorial optimization applications


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Population based metaheuristics in Spark: Towards a general framework using PSO as a case study


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Parameter estimation in a whole-brain network model of epilepsy: Comparison of parallel global optimization solvers


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Conformal prediction for uncertainty quantification in dynamic biological systems


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