Miguel Rocha

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Isabel RochaITQB NOVA - Universidade NOVA de LisboaVerified email at itqb.unl.pt
Eugénio Campos FerreiraProfessor of Biological Engineering, Universidade do MinhoVerified email at deb.uminho.pt
Paulo CortezFull Professor, ALGORITMI, Department Information Systems, University of MinhoVerified email at dsi.uminho.pt
Jose Carlos Ferreira Maia NevesProfessor of Computer Science, The University of MinhoVerified email at di.uminho.pt
Paulo MaiaSilicoLife SAVerified email at silicolife.com
Marcelo MaraschinUniversidade Federal de Santa CatarinaVerified email at ufsc.br
Miguel RioProfessor of Computer NetworksVerified email at ucl.ac.uk
Oscar DiasUniversity of MinhoVerified email at deb.uminho.pt
Florentino Fdez-RiverolaProfessor, Computer Science Department, University of VigoVerified email at uvigo.es
Rui MendesAlgoritmi, DI, Universidade do MinhoVerified email at di.uminho.pt
Virgilio Gavicho UarrotaUniversidad de O´HigginsVerified email at uoh.cl
Kiran Raosaheb PatilMRC Toxicology Unit, University of CambridgeVerified email at cam.ac.uk
José P. FariaAssistant Computational BiologistVerified email at anl.gov
Julio Saez RodriguezHeidelberg UniversityVerified email at uni-heidelberg.de
Bruno M. CostaLife and Health Sciences Research Institute (ICVS), School of Medicine, University of MinhoVerified email at med.uminho.pt
Christopher HenryComputational Biologist, Argonne National LaboratoryVerified email at mcs.anl.gov
Daniel MachadoNorwegian University of Science and TechnologyVerified email at ntnu.no
Jens NielsenProfessor in Systems Biology, Chalmers University of Technology, SwedenVerified email at chalmers.se
Adam Paul ArkinDepartment of Bioengineering, University of California, Berkeley, Physical Biosciences Division, E.OVerified email at lbl.gov
Luis M. RochaGeorge J. Klir Professor of Systems Science and Industrial Engineering, Binghamton University (SUNY)Verified email at binghamton.edu

Miguel Rocha

Associate Professor, Dept. Informatics and Centre Biological Engineering, Universidade do Minho

Verified email at di.uminho.pt

Bioinformatics Evolutionary Computation Systems Biology Machine Learning Neural Networks


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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	492	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	425	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	310	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	258	2012
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
Deep learning for drug response prediction in cancer D Baptista, PG Ferreira, M Rocha Briefings in bioinformatics 22 (1), 360-379, 2021	189	2021
Reconstructing genome-scale metabolic models with merlin O Dias, M Rocha, EC Ferreira, I Rocha Nucleic acids research 43 (8), 3899-3910, 2015	184	2015
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	180	2006
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	167	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	164	2014
Evolution of neural networks for classification and regression M Rocha, P Cortez, J Neves Neurocomputing 70 (16-18), 2809-2816, 2007	149	2007
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	149	1999
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
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	134	2021
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
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	126	2021
Evolving time series forecasting ARMA models P Cortez, M Rocha, J Neves Journal of Heuristics 10, 415-429, 2004	123	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	118	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	113	2014
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	95	2018

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