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 UarrotaPONTIFICIA UNIVERSIDAD CATOLICA DE VALPARAISOVerified email at posgrad.ufsc.br
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	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	290	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	244	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	163	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	161	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	157	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	122	2021
Evolving time series forecasting ARMA models P Cortez, M Rocha, J Neves Journal of Heuristics 10, 415-429, 2004	120	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

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