Paulo Maia

发表

OptFlux: an open-source software platform for in silico metabolic engineering

Miguel Rocha, Eugénio C. Ferreira, Jens Nielsen, 2010, BMC Systems Biology.

In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories

I. Rocha, Paulo Maia, Miguel Rocha, 2015, Microbiology and Molecular Reviews.

On the effects of phenotype prediction methods over strain design algorithms. A multi-objective approach

Miguel Rocha, Paulo Maia, Isabel Rocha, 2014 .

A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic Engineering

Miguel Rocha, Paulo Maia, Osvaldo D. Kim, 2018, Front. Microbiol..

Model‐guided development of an evolutionarily stable yeast chassis

P. Kötter, P. Jouhten, K. Patil, 2021, Molecular systems biology.

Comparison of pathway analysis and constraint-based methods for cell factory design

Miguel Rocha, Isabel Rocha, Paulo Maia, 2019, BMC Bioinformatics.

Turnover Dependent Phenotypic Simulation: A Quantitative Constraint-Based Simulation Method That Accommodates All Main Strain Design Strategies.

Isabel Rocha, Paulo Maia, Paulo Vilaça, 2015, ACS synthetic biology.

Analyzing and Designing Cell Factories with OptFlux.

Miguel Rocha, Isabel Rocha, Paulo Maia, 2018, Methods in molecular biology.

Identification of robust strain designs via tandem pFBA/LMOMA phenotype prediction

Miguel Rocha, Paulo Maia, Isabel Rocha, 2017, GECCO.

CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data

Miguel Rocha, Paulo Maia, Isabel Rocha, 2014, BMC Systems Biology.

OptGene: a framework for in silico metabolic engineering

E. Ferreira, I. Rocha, Paulo Maia, 2008 .

Natural computation meta-heuristics for the in silico optimization of microbial strains

Miguel Rocha, Eugénio C. Ferreira, Jens Nielsen, 2008, BMC Bioinformatics.

Evaluating evolutionary multiobjective algorithms for the in silico optimization of mutant strains

Miguel Rocha, Eugénio C. Ferreira, Paulo Maia, 2008, 2008 8th IEEE International Conference on BioInformatics and BioEngineering.

A Software Platform for Evolutionary Computation with Pluggable Parallelism and Quality Assurance

Miguel Rocha, Paulo Maia, Emanuel J. V. Gonçalves, 2011, EANN/AIAI.

An integrated framework for strain optimization

Miguel Rocha, Paulo Maia, Isabel Rocha, 2013, 2013 IEEE Congress on Evolutionary Computation.

An integrated computational environment for elementary modes analysis of biochemical networks

Miguel Rocha, Paulo Maia, Isabel Rocha, 2012, Int. J. Data Min. Bioinform..

OptFlux: a software for metabolic engineering

Jens Nielsen, Paulo Maia, Isabel Rocha, 2009 .

Enhancing Elementary Flux Modes Analysis Using Filtering Techniques in an Integrated Environment

Miguel Rocha, Paulo Maia, Isabel Rocha, 2010, IWPACBB.

Development of a Framework for Metabolic Pathway Analysis-Driven Strain Optimization Methods

I. Rocha, Paulo Maia, Miguel Rocha, 2017, Interdisciplinary Sciences: Computational Life Sciences.

Development of an Integrated Framework for Minimal Cut Set Enumeration in Constraint-Based Models

Miguel Rocha, Paulo Maia, Isabel Rocha, 2016, PACBB.

Comparison of pathway analysis and constraint-based methods for cell factory design

I. Rocha, Paulo Maia, Miguel Rocha, 2019, BMC Bioinformatics.

Implementing Metaheuristic Optimization Algorithms with JECoLi

Miguel Rocha, Paulo Maia, Pedro Evangelista, 2009, 2009 Ninth International Conference on Intelligent Systems Design and Applications.

Analyzing and Designing Cell Factories with OptFlux.

I. Rocha, Paulo Maia, Paulo Vilaça, 2018, Methods in molecular biology.

Turnover Dependent Phenotypic Simulation: A Quantitative Constraint-Based Simulation Method That Accommodates All Main Strain Design Strategies.

J. Nielsen, I. Rocha, Paulo Maia, 2019, ACS synthetic biology.

Metaheuristics for Strain Optimization Using Transcriptional Information Enriched Metabolic Models

Miguel Rocha, Paulo Maia, Isabel Rocha, 2010, EvoBIO.

Evaluating Simulated Annealing Algorithms in the Optimization of Bacterial Strains

Miguel Rocha, Eugénio C. Ferreira, Paulo Maia, 2007, EPIA Workshops.