Miguel Rocha
Miguel Rocha
Associate Professor, Dept. Informatics and Centre Biological Engineering, Universidade do Minho
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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, 1-12, 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
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
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
Modeling formalisms in systems biology
D Machado, RS Costa, M Rocha, EC Ferreira, B Tidor, I Rocha
AMB express 1, 1-14, 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
Reconstructing genome-scale metabolic models with merlin
O Dias, M Rocha, EC Ferreira, I Rocha
Nucleic acids research 43 (8), 3899-3910, 2015
Deep learning for drug response prediction in cancer
D Baptista, PG Ferreira, M Rocha
Briefings in bioinformatics 22 (1), 360-379, 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
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
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
Evolution of neural networks for classification and regression
M Rocha, P Cortez, J Neves
Neurocomputing 70 (16-18), 2809-2816, 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
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
Evolving time series forecasting ARMA models
P Cortez, M Rocha, J Neves
Journal of Heuristics 10, 415-429, 2004
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
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
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
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
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
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