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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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Mechanistic dynamic modelling of biological systems: The road ahead

project

Spatial crosstalk in immune-oncology HORIZON-MSCA-2024-DN-01-01

project

Exploring the significance of the pontine brain microenvironment in shaping pediatric glioma invasive properties

project

Unraveling the microenvironmental niches driving pediatric glioma infiltration in the brain.

project

Guiding personalized immunotherapy strategies through exploration of cellular dynamics in live imaging data

PID2023-146455OA-I00

project

Exploring tumor heterogeneity with morphocynetic analysis: tools for live imaging  

El mencionado proyecto se enmarca en el Programa Momentum cuya financiación procede del Mecanismo de...

project

Developing an organoid Dynamic Screening Platform to Evaluate Immuno-Oncology Drug activities in a Clinically Relevant Preclinical Model

project

PEJ_2023__CM23_IIBM_M1_13

project

DCODER: Unravelling cell Dynamics to deCODE tumor cell Resistance to immunotherapy

Core Funding