orcid publication

Metabolic engineering with multi-objective optimization of kinetic models

orcid publication

On the relationship between sloppiness and identifiability

orcid publication

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

orcid publication

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

orcid publication

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

orcid publication

Evaluation of parallel differential evolution implementations on MapReduce and spark

orcid publication

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

orcid publication

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

orcid publication

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

orcid publication

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

orcid publication

Automated Design Framework for Synthetic Biology Exploiting Pareto Optimality

orcid publication

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

orcid publication

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

orcid publication

Sufficiently Exciting Inputs for Structurally Identifiable Systems Biology Models

orcid publication

Optimization-based prediction of fold bifurcations in nonlinear ODE models

orcid publication

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

orcid publication

Multimethod optimization for reverse engineering of complex biological networks

orcid publication

Mixed Integer Multiobjective Optimization Approaches for Systems and Synthetic Biology

orcid publication

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

orcid publication

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

orcid publication

Critical Assessment of Parameter Estimation Methods in Models of Biological Oscillators

orcid publication

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

orcid publication

Benchmarking optimization methods for parameter estimation in large kinetic models

orcid publication

PREMER: A Tool to Infer Biological Networks

orcid publication

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

orcid publication

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

orcid publication

Multiobjective optimization of gene circuits for metabolic engineering

orcid publication

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

orcid publication

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

orcid publication

A Comparison of Methods for Quantifying Prediction Uncertainty in Systems Biology

orcid publication

Distilling Robust Design Principles of Biocircuits Using Mixed Integer Dynamic Optimization

orcid publication

Input-Dependent Structural Identifiability of Nonlinear Systems

orcid publication

Computational Methods Enabling Next-Generation Bioprocesses

orcid publication

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

orcid publication

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

orcid publication

Using optimal control to understand complex metabolic pathways

orcid publication

Synthetic Gene Circuit Analysis and Optimization

orcid publication

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

orcid publication

PEtab - Interoperable specification of parameter estimation problems in systems biology

orcid publication

Editorial: Biological Control Systems and Disease Modeling

orcid publication

Automated Biocircuit Design with SYNBADm

orcid publication

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

orcid publication

A protocol for dynamic model calibration

orcid publication

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

orcid publication

Automated design of synthetic biocircuits in the stochastic regime

orcid publication

An efficient ant colony optimization framework for HPC environments

orcid publication

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

orcid publication

Parallel ant colony optimization for the training of cell signaling networks

orcid publication

Improving dynamic predictions with ensembles of observable models

orcid publication

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

orcid publication

Assessment of Prediction Uncertainty Quantification Methods in Systems Biology

orcid publication

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

orcid publication

Distilling identifiable and interpretable dynamic models from biological data

orcid publication

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

orcid publication

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

orcid publication

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

orcid publication

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

orcid publication

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

orcid publication

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

orcid publication

Conformal prediction for uncertainty quantification in dynamic biological systems

orcid publication

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

project

Deep Learning-based 3D Virtual Multiplexing to explore microenvironmental drivers of brain tumor progression

tool

BEHAV3D Tumor Profiler

BEHAV3D Tumor Profiler (BEHAV3D-TP) is a cloud-based computational platform designed to comprehensively map and analyze...

tool

MorphoTrack-merger

MorphoTrack-Merger is a Python-based tool designed to extract morphological features from segmented images and merge...

tool

BEHAVIORAL GUIDED TRANSCRIPTOMICS

Behavior-Guided Transcriptomics (BGT) is an extension of the BEHAV3D platform that links T cell live...

orcid publication

Adult-Onset Hypothyroidism Enhances Fear Memory and Upregulates Mineralocorticoid and Glucocorticoid Receptors in the Amygdala

orcid publication

Glioblastoma Therapy with Cytotoxic Mesenchymal Stromal Cells Optimized by Bioluminescence Imaging of Tumor and Therapeutic Cell Response

orcid publication

911 Bioluminescence Imaging of Glioblastoma Therapy with Cytotoxic Human Mesenchymal Stroma Cells that Differentiate to Endothelial Lineage

orcid publication

In Vivo Bioluminescence Imaging of Cell Differentiation in Biomaterials: A Platform for Scaffold Development

orcid publication

Calcium phosphate glass improves angiogenesis capacity of poly(lactic acid) scaffolds and stimulates differentiation of adipose tissue-derived mesenchymal stromal cells to the endothelial lineage

orcid publication

Endothelial Differentiation of Adipose Tissue-Derived Mesenchymal Stromal Cells in Glioma Tumors: Implications for Cell-Based Therapy

orcid publication

Bioluminescence imaging of cardiomyogenic and vascular differentiation of cardiac and subcutaneous adipose tissue-derived progenitor cells in fibrin patches in a myocardium infarct model

orcid publication

Imaging windows for long-term intravital imaging

orcid publication

Fast-Proliferating Adipose Tissue Mesenchymal-Stromal-Like Cells for Therapy

orcid publication

Abstract A84: Intravital microscopy reveals biopsy induced local wound-healing response

orcid publication

OS06.3 Characterisation of human brain tumour initiating cells leading invasion

orcid publication

ANGI-06. CHARACTERISATION OF INVASION OF HUMAN BRAIN TUMOUR INITIATING CELLS IN HUMAN GLIOBLASTOMA

orcid publication

Preventing inflammation inhibits biopsy-mediated changes in tumor cell behavior

orcid publication

Potential impact of invasive surgical procedures on primary tumor growth and metastasis

orcid publication

Longitudinal Intravital Imaging of Brain Tumor Cell Behavior in Response to an Invasive Surgical Biopsy

orcid publication

High-resolution 3D imaging of fixed and cleared organoids

orcid publication

Intravital imaging of glioma border morphology reveals distinctive cellular dynamics and contribution to tumor cell invasion

orcid publication

Invaders Exposed: Understanding and Targeting Tumor Cell Invasion in Diffuse Intrinsic Pontine Glioma

orcid publication

Behavioral-transcriptomic landscape of engineered T cells targeting human cancer organoids

orcid publication

Revealing the spatio-phenotypic patterning of cells in healthy and tumor tissues with mLSR-3D and STAPL-3D

orcid publication

3D imaging for driving cancer discovery

orcid publication

Uncovering the mode of action of engineered T cells in patient cancer organoids

orcid publication

Neutrophils Promote Glioblastoma Tumor Cell Migration after Biopsy

orcid publication

Multispectral confocal 3D imaging of intact healthy and tumor tissue using mLSR-3D

orcid publication

BEHAV3D: an imaging and transcriptomics platform that unravels T cell antitumor activity

orcid publication

Bridging live-cell imaging and next-generation cancer treatment

orcid publication

BEHAV3D: a 3D live imaging platform for comprehensive analysis of engineered T cell behavior and tumor response