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 | 479 | 2010 |
Particle swarms for feedforward neural network training R Mendes, P Cortez, M Rocha, J Neves Proceedings of the 2002 International Joint Conference on Neural Networks …, 2002 | 424 | 2002 |
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen MP Menden, D Wang, MJ Mason, B Szalai, KC Bulusu, Y Guan, T Yu, ... Nature communications 10 (1), 2674, 2019 | 287 | 2019 |
Multi‐scale Internet traffic forecasting using neural networks and time series methods P Cortez, M Rio, M Rocha, P Sousa Expert Systems 29 (2), 143-155, 2012 | 250 | 2012 |
Modeling formalisms in systems biology D Machado, RS Costa, M Rocha, EC Ferreira, B Tidor, I Rocha AMB express 1, 1-14, 2011 | 243 | 2011 |
Internet traffic forecasting using neural networks P Cortez, M Rio, M Rocha, P Sousa The 2006 IEEE international joint conference on neural network proceedings …, 2006 | 178 | 2006 |
Reconstructing genome-scale metabolic models with merlin O Dias, M Rocha, EC Ferreira, I Rocha Nucleic acids research 43 (8), 3899-3910, 2015 | 174 | 2015 |
Deep learning for drug response prediction in cancer D Baptista, PG Ferreira, M Rocha Briefings in bioinformatics 22 (1), 360-379, 2021 | 162 | 2021 |
Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open … J Guinney, T Wang, TD Laajala, KK Winner, JC Bare, EC Neto, SA Khan, ... The Lancet Oncology 18 (1), 132-142, 2017 | 160 | 2017 |
Metabolomics combined with chemometric tools (PCA, HCA, PLS-DA and SVM) for screening cassava (Manihot esculenta Crantz) roots during postharvest physiological deterioration VG Uarrota, R Moresco, B Coelho, E da Costa Nunes, LAM Peruch, ... Food Chemistry 161, 67-78, 2014 | 156 | 2014 |
Preventing premature convergence to local optima in genetic algorithms via random offspring generation M Rocha, J Neves Multiple Approaches to Intelligent Systems: 12th International Conference on …, 1999 | 146 | 1999 |
Evolution of neural networks for classification and regression M Rocha, P Cortez, J Neves Neurocomputing 70 (16-18), 2809-2816, 2007 | 142 | 2007 |
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 | 139 | 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 |
Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses A Dugourd, C Kuppe, M Sciacovelli, E Gjerga, A Gabor, KB Emdal, ... Molecular Systems Biology 17 (1), e9730, 2021 | 118 | 2021 |
Evolving time series forecasting ARMA models P Cortez, M Rocha, J Neves Journal of Heuristics 10, 415-429, 2004 | 118 | 2004 |
Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models E Gonçalves, J Bucher, A Ryll, J Niklas, K Mauch, S Klamt, M Rocha, ... Molecular BioSystems 9 (7), 1576-1583, 2013 | 113 | 2013 |
Transcript level and sequence determinants of protein abundance and noise in Escherichia coli JC Guimaraes, M Rocha, AP Arkin Nucleic acids research 42 (8), 4791-4799, 2014 | 112 | 2014 |
Generative deep learning for targeted compound design T Sousa, J Correia, V Pereira, M Rocha Journal of chemical information and modeling 61 (11), 5343-5361, 2021 | 97 | 2021 |
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 | 91 | 2018 |