Paulo Maia
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OptFlux: an open-source software platform for in silico metabolic engineering
I Rocha, P Maia, P Evangelista, P Vilaça, S Soares, JP Pinto, J Nielsen, ...
BMC systems biology 4 (1), 1-12, 2010
Natural computation meta-heuristics for the in silico optimization of microbial strains
M Rocha, P Maia, R Mendes, JP Pinto, EC Ferreira, J Nielsen, KR Patil, ...
BMC bioinformatics 9 (1), 1-16, 2008
In silico constraint-based strain optimization methods: the quest for optimal cell factories
P Maia, M Rocha, I Rocha
Microbiology and Molecular Biology Reviews 80 (1), 45-67, 2016
MEMOTE for standardized genome-scale metabolic model testing
C Lieven, ME Beber, BG Olivier, FT Bergmann, M Ataman, P Babaei, ...
Nature biotechnology 38 (3), 272-276, 2020
@ Note: a workbench for biomedical text mining
A Lourenço, R Carreira, S Carneiro, P Maia, D Glez-Peña, ...
Journal of biomedical informatics 42 (4), 710-720, 2009
AIBench: a rapid application development framework for translational research in biomedicine
D Glez-Peña, M Reboiro-Jato, P Maia, M Rocha, F Díaz, F Fdez-Riverola
Computer methods and programs in biomedicine 98 (2), 191-203, 2010
Memote: A community driven effort towards a standardized genome-scale metabolic model test suite
C Lieven, ME Beber, BG Olivier, FT Bergmann, P Babaei, JA Bartell, ...
BioRxiv, 350991, 2018
A review of dynamic modeling approaches and their application in computational strain optimization for metabolic engineering
OD Kim, M Rocha, P Maia
Frontiers in microbiology 9, 1690, 2018
Implementing metaheuristic optimization algorithms with jecoli
P Evangelista, P Maia, M Rocha
2009 Ninth International Conference on Intelligent Systems Design and …, 2009
Evaluating evolutionary multiobjective algorithms for the in silico optimization of mutant strains
P Maia, I Rocha, EC Ferreira, M Rocha
2008 8th IEEE International Conference on BioInformatics and BioEngineering, 1-6, 2008
CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data
R Carreira, P Evangelista, P Maia, P Vilaça, M Pont, JF Tomb, I Rocha, ...
BMC systems biology 8 (1), 1-10, 2014
A platform for the selection of genes in DNA microarraydata using evolutionary algorithms
M Rocha, R Mendes, P Maia, D Glez-Peña, F Fdez-Riverola
Proceedings of the 9th annual conference on Genetic and evolutionary …, 2007
OptGene: a framework for in silico metabolic engineering
I Rocha, P Maia, M Rocha, EC Ferreira
Metaheuristics for strain optimization using transcriptional information enriched metabolic models
P Vilaça, P Maia, I Rocha, M Rocha
European Conference on Evolutionary Computation, Machine Learning and Data …, 2010
An integrated framework for strain optimization
P Maia, I Rocha, M Rocha
2013 IEEE Congress on Evolutionary Computation, 198-205, 2013
An integrated computational environment for elementary modes analysis of biochemical networks
P Maia, P Vilaça, I Rocha, M Pont, JF Tomb, M Rocha
International journal of data mining and bioinformatics 6 (4), 382-395, 2012
OptFerm-a computational platform for the optimization of fermentation processes
O Rocha, P Maia, I Rocha, M Rocha
Evaluating simulated annealing algorithms in the optimization of bacterial strains
M Rocha, R Mendes, P Maia, JP Pinto, I Rocha, EC Ferreira
Portuguese Conference on Artificial Intelligence, 473-484, 2007
Analyzing and designing cell factories with OptFlux
P Vilaça, P Maia, H Giesteira, I Rocha, M Rocha
Metabolic Network Reconstruction and Modeling, 37-76, 2018
Development of an integrated framework for minimal cut set enumeration in constraint-based models
V Vieira, P Maia, I Rocha, M Rocha
International Conference on Practical Applications of Computational Biology …, 2016
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