List of works by Julio R. Banga

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

scientific article

A generalized Fisher equation and its utility in chemical kinetics

scientific article

A hybrid approach for efficient and robust parameter estimation in biochemical pathways

scientific article published on 19 October 2005

A protocol for dynamic model calibration

scientific article published on 08 September 2021

A systematic approach to plant-wide control based on thermodynamics

article

A systematic approach to plant-wide control based on thermodynamics

A thermodynamic based plant-wide control design procedure of the tennessee eastman process

article

AMIGO, a toolbox for advanced model identification in systems biology using global optimization

scientific article published on 17 June 2011

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

scientific article published on 4 July 2016

An iterative identification procedure for dynamic modeling of biochemical networks

scientific article

Automated Design Framework for Synthetic Biology Exploiting Pareto Optimality

scientific article published on 28 March 2017

Benchmarking optimization methods for parameter estimation in large kinetic models.

scientific article published in March 2019

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

scientific article

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

scientific article published on 06 April 2012

Characterizing multistationarity regimes in biochemical reaction networks

scientific article

Correction: Characterizing Multistationarity Regimes in Biochemical Reaction Networks

scientific article (publication date: 15 January 2013)

DOTcvpSB, a software toolbox for dynamic optimization in systems biology

scientific article published on 29 June 2009

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

scientific article

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

scientific article

Dynamic Optimization of Nonlinear Bioreactors

Dynamic optimization of bioprocesses: efficient and robust numerical strategies

scientific article

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

scientific article

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

scientific article published on 29 November 2017

Efficient and robust multi-objective optimization of food processing: A novel approach with application to thermal sterilization

Enabling network inference methods to handle missing data and outliers

scientific article

Exploring multiplicity conditions in enzymatic reaction networks.

scientific article published in May 2009

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

scientific article published on 03 July 2019

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

scientific article published on 30 November 2017

GenSSI: a software toolbox for structural identifiability analysis of biological models

scientific article

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

scientific article published on 01 December 2022

Global dynamic optimization approach to predict activation in metabolic pathways

scientific article

Hybrid optimization method with general switching strategy for parameter estimation

scientific article

Improved Optimization Methods for the Multiobjective Design of Bioprocesses

Inference of complex biological networks: distinguishability issues and optimization-based solutions

scientific article

Investigating dynamics of inhibitory and feedback loops in ERK signalling using power-law models

scientific article published on 18 August 2010

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

scientific article

MIDER: network inference with mutual information distance and entropy reduction

scientific article (publication date: 2014)

Metabolic engineering with multi-objective optimization of kinetic models.

scientific article published on 27 January 2016

Multi-criteria optimization of regulation in metabolic networks

scientific article

Multicriteria global optimization for biocircuit design

scientific article

Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems

scientific article

On the relationship between sloppiness and identifiability

scientific article published on 24 October 2016

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

scientific article published on 16 May 2015

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

scientific article published on 01 July 2018

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

scientific article published on 01 November 2018

Optimization in computational systems biology

scientific article

PREMER: a Tool to Infer Biological Networks

scientific article published on 4 October 2017

Parameter estimation and optimal experimental design.

scientific article published on January 2008

Parameter estimation in biochemical pathways: a comparison of global optimization methods

scientific article

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

scientific article

Power-law models of signal transduction pathways

scientific article (publication date: July 2007)

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

scientific article

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

scientific article

Reverse-engineering post-transcriptional regulation of gap genes in Drosophila melanogaster

scientific article

Robust and efficient parameter estimation in dynamic models of biological systems

scientific article

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

scientific article

Stabilization of inhomogeneous patterns in a diffusion-reaction system under structural and parametric uncertainties

scientific article published on 10 January 2006

Structural identifiability of systems biology models: a critical comparison of methods

scientific article

Use of a generalized fisher equation for global optimization in chemical kinetics.

scientific article published on 14 July 2011

Using optimal control to understand complex metabolic pathways

scientific article published on 21 October 2020

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