| Evolutionary programming as a platform for in silico metabolic engineering KR Patil, I Rocha, J Förster, J Nielsen BMC bioinformatics 6, 1-12, 2005 | 561 | 2005 |
| 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 | 493 | 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 | 403 | 2020 |
| Modeling formalisms in systems biology D Machado, RS Costa, M Rocha, EC Ferreira, B Tidor, I Rocha AMB express 1, 1-14, 2011 | 249 | 2011 |
| Galacto-oligosaccharides production during lactose hydrolysis by free Aspergillus oryzae β-galactosidase and immobilized on magnetic polysiloxane-polyvinyl alcohol DFM Neri, VM Balcão, RS Costa, ICAP Rocha, EMFC Ferreira, ... Food Chemistry 115 (1), 92-99, 2009 | 216 | 2009 |
| Reconstructing genome-scale metabolic models with merlin O Dias, M Rocha, EC Ferreira, I Rocha Nucleic acids research 43 (8), 3899-3910, 2015 | 185 | 2015 |
| Virtual laboratories in (bio) chemical engineering education L Domingues, I Rocha, F Dourado, M Alves, EC Ferreira Education for chemical engineers 5 (2), e22-e27, 2010 | 145 | 2010 |
| 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 | 140 | 2016 |
| 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, 1-16, 2008 | 130 | 2008 |
| Metabolic responses to recombinant bioprocesses in Escherichia coli S Carneiro, EC Ferreira, I Rocha Journal of biotechnology 164 (3), 396-408, 2013 | 125 | 2013 |
| Ecological modelling approaches for predicting emergent properties in microbial communities NI van den Berg, D Machado, S Santos, I Rocha, J Chacón, W Harcombe, ... Nature ecology & evolution 6 (7), 855-865, 2022 | 117 | 2022 |
| New improved method for fructooligosaccharides production by Aureobasidium pullulans A Dominguez, C Nobre, LR Rodrigues, AM Peres, D Torres, I Rocha, ... Carbohydrate Polymers 89 (4), 1174-1179, 2012 | 105 | 2012 |
| Integration of biomass formulations of genome-scale metabolic models with experimental data reveals universally essential cofactors in prokaryotes JC Xavier, KR Patil, I Rocha Metabolic engineering 39, 200-208, 2017 | 98 | 2017 |
| Design and application of genome-scale reconstructed metabolic models I Rocha, J Förster, J Nielsen Microbial Gene Essentiality: Protocols and Bioinformatics, 409-431, 2008 | 85 | 2008 |
| Comparison of adsorption equilibrium of fructose, glucose and sucrose on potassium gel-type and macroporous sodium ion-exchange resins C Nobre, MJ Santos, A Dominguez, D Torres, O Rocha, AM Peres, ... Analytica chimica acta 654 (1), 71-76, 2009 | 78 | 2009 |
| Genome-scale modeling of yeast: chronology, applications and critical perspectives H Lopes, I Rocha FEMS yeast research 17 (5), fox050, 2017 | 77 | 2017 |
| Optimization of fed-batch fermentation processes with bio-inspired algorithms M Rocha, R Mendes, O Rocha, I Rocha, EC Ferreira Expert Systems with Applications 41 (5), 2186-2195, 2014 | 77 | 2014 |
| Random sampling of elementary flux modes in large-scale metabolic networks D Machado, Z Soons, KR Patil, EC Ferreira, I Rocha Bioinformatics 28 (18), i515-i521, 2012 | 77 | 2012 |
| Systems biology perspectives on minimal and simpler cells JC Xavier, KR Patil, I Rocha Microbiology and Molecular Biology Reviews 78 (3), 487-509, 2014 | 75 | 2014 |
| @ Note: a workbench for biomedical text mining A Lourenço, R Carreira, S Carneiro, P Maia, D Glez-Pena, ... Journal of biomedical informatics 42 (4), 710-720, 2009 | 70 | 2009 |
