| 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, 1-12, 2010 | 473 | 2010 |
| 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 | 339 | 2020 |
| Memote: A community driven effort towards a standardized genome-scale metabolic model test suite C Lieven, ME Beber, BG Olivier, FT Bergmann, M Ataman, P Babaei, ... BioRxiv, 350991, 2018 | 59 | 2018 |
| Sequence based heuristics for two-dimensional bin packing problems F Alvelos, TM Chan, P Vilaça, T Gomes, E Silva, JM Valério de Carvalho Engineering Optimization 41 (8), 773-791, 2009 | 29 | 2009 |
| A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information P Vilaca, I Rocha, M Rocha Biosystems 103 (3), 435-441, 2011 | 28 | 2011 |
| Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z B Pereira, J Miguel, P Vilaça, S Soares, I Rocha, S Carneiro BMC systems biology 12, 1-12, 2018 | 27 | 2018 |
| Genome-wide semi-automated annotation of transporter systems O Dias, D Gomes, P Vilaça, J Cardoso, M Rocha, EC Ferreira, I Rocha IEEE/ACM transactions on computational biology and bioinformatics 14 (2 …, 2016 | 20 | 2016 |
| Discovery and implementation of a novel pathway for n-butanol production via 2-oxoglutarate S Ferreira, R Pereira, F Liu, P Vilaça, I Rocha Biotechnology for biofuels 12, 1-14, 2019 | 16 | 2019 |
| Development and application of efficient pathway enumeration algorithms for metabolic engineering applications F Liu, P Vilaça, I Rocha, M Rocha Computer methods and programs in biomedicine 118 (2), 134-146, 2015 | 13 | 2015 |
| 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, 1-10, 2014 | 12 | 2014 |
| An integrated network visualization framework towards metabolic engineering applications A Noronha, P Vilaça, M Rocha BMC bioinformatics 15, 1-13, 2014 | 8 | 2014 |
| Analyzing and designing cell factories with OptFlux P Vilaça, P Maia, H Giesteira, I Rocha, M Rocha Metabolic Network Reconstruction and Modeling: Methods and Protocols, 37-76, 2018 | 7 | 2018 |
| Metaheuristics for strain optimization using transcriptional information enriched metabolic models P Vilaça, P Maia, I Rocha, M Rocha Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics …, 2010 | 7 | 2010 |
| Memote: A Community-Driven Effort towards a Standardized Genome-Scale Metabolic Model Test Suite bioRxiv 350991 C Lieven, ME Beber, BG Olivier, FT Bergmann, M Ataman, P Babaei, ... | 5 | 2018 |
| An algorithm to assemble gene-protein-reaction associations for genome-scale metabolic model reconstruction J Cardoso, P Vilaça, S Soares, M Rocha Pattern Recognition in Bioinformatics: 7th IAPR International Conference …, 2012 | 5 | 2012 |
| A critical evaluation of automatic atom mapping algorithms and tools N Osório, P Vilaça, M Rocha 11th International Conference on Practical Applications of Computational …, 2017 | 4 | 2017 |
| 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 | 4 | 2012 |
| Network Visualization Tools to Enhance Metabolic Engineering Platforms A Noronha, P Vilaça, M Rocha 7th International Conference on Practical Applications of Computational …, 2013 | 2 | 2013 |
| Turnover dependent phenotypic simulation: a quantitative constraint-based simulation method that accommodates all main strain design strategies R Pereira, P Vilaça, P Maia, J Nielsen, I Rocha ACS Synthetic Biology 8 (5), 976-988, 2019 | 1 | 2019 |
| MIYeastK: The Metabolic Integrated Yeast Knowledgebase S Santos, F Liu, C Costa, P Vilaça, M Rocha, I Rocha | 1 | 2016 |
