Journal Articles 2019(4 publications) [publication]Pereira, G.C. and Pereira, S.P. and Pereira, F.B. and Lourenço, Nuno and Lumini, J.A. and Pereira, C.V. and Bjork, J.A. and Magalhães, J. and Ascensão, A. and Moreno, A.J. and Wallace, K.B. and Oliveira, P.J. , "Early Cardiac Mitochondrial Molecular and Functional Responses to Acute Anthracycline Treatment in Wistar Rats", Toxicological Sciences, 2019 [publication]Deus, C. and Pereira, S. and Cunha-Oliveira, T. and Pereira, F.B. and Oliveira, P.J. , "Mitochondrial remodeling in human skin fibroblasts from sporadic PD male patients uncovers metabolic and mitochondrial bioenergetics defects", Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 2019 [publication]Simões, R. and Cunha-Oliveira, T. and Kovarova, . and Neuzil, J. and Oliveira, P.J. and Pereira, F.B. , "Early mitochondrial metabolism and dynamics changes as predictors of neurodegeneration and neuronal cell death", European Journal of Clinical Investigation, vol. 49, pp. 180-181, 2019 [publication]Pereira, F.B. and Lourenço, Nuno and Jesus, W. and Prudente, F.V. and Marques, J.C. , "Discovering low-energy atomic clusters with machine learning", European Journal of Clinical Investigation, vol. 49, pp. 41, 2019 2018(2 publications) [publication]Jesus, W. and Marques, J.C. and Prudente, F.V. and Pereira, F.B. , "Exploring the First- and Second-shell Structures Arising in the Microsolvation of Li+ by Rare Gases", International Journal of Quantum Chemistry, 2018 [publication]Simões, R. and Cunha-Oliveira, T. and Oliveira, P.J. and Pereira, F.B. , "Optimization of experimental and computational processes to study mitochondrial trafficking and metabolic biomarkers", European Journal of Clinical Investigation, vol. 48, pp. 89, 2018 2017(3 publications) [publication]Marques, J.C. and Pereira, F.B. and Llanio-Trujillo, J.L. and Abreu, P.E. , "A global optimization perspective on molecular clusters", Philosophical Transactions of the Royal Society A, 2017 [publication]Rodri?guez-Ferna?ndez, R. and Pereira, F.B. and Marques, J.C. and Marti?nez-Nu?n?ez, E. and Va?zquez, S.A. , "GAFit: a general-purpose, user-friendly program for fitting potential energy surfaces", Computer Physics Communications, 2017 [publication]Prudente, F.V. and Marques, J.C. and Pereira, F.B. , "Solvation of Li+ by argon: How important are three-body forces?", Physical Chemistry Chemical Physics , 2017 2016(3 publications) [publication]Lourenço, Nuno and Pereira, F.B. and Costa, E. , "Unveiling the properties of structured grammatical evolution", Genetic Programming and Evolvable Machines , pp. 1-39, 2016 [citation][year=2018]Bartoli, A., Castelli, M., & Medvet, E. (2018). Weighted Hierarchical Grammatical Evolution. IEEE Transactions on Cybernetics. [citation][year=2018]Brum, A., & Ritt, M. (2018, July). Automatic Design of Heuristics for Minimizing the Makespan in Permutation Flow Shops. In 2018 IEEE Congress on Evolutionary Computation (CEC) (pp. 1-8). IEEE. Chicago [citation][year=2018]Brum, A., & Ritt, M. (2018, April). Automatic Algorithm Configuration for the Permutation Flow Shop Scheduling Problem Minimizing Total Completion Time. In European Conference on Evolutionary Computation in Combinatorial Optimization (pp. 85-100). Springer, Cham. [citation][year=2018]de Souza, M., & Ritt, M. (2018, July). An Automatically Designed Recombination Heuristic for the Test-Assignment Problem. In 2018 IEEE Congress on Evolutionary Computation (CEC) (pp. 1-8). IEEE [citation][year=2018]de Souza, M., & Ritt, M. (2018, April). Automatic Grammar-Based Design of Heuristic Algorithms for Unconstrained Binary Quadratic Programming. In European Conference on Evolutionary Computation in Combinatorial Optimization (pp. 67-84). Springer, Cham. [citation][year=2018]Nicolau, M., & Agapitos, A. (2018). Understanding Grammatical Evolution: Grammar Design. In Handbook of Grammatical Evolution (pp. 23-53). Springer, Cham. [citation][year=2017]Shunya Maruta and Yi Zuo and Masahiro Nagao and Eisuke Kita (2017). Grammati- cal Evolution Using Tree Representation Learning. In Neural Information Processing (pp.346-355) [citation][year=2017]Medvet, E., Daolio, F., and Tagliapietra, D. (2017). Evolvability in Grammatical Evolu- tion. In Proceedings of the Genetic and Evolutionary Computation Conference, GECCO. [citation][year=2017]Medvet, E., and Tušar, T. (2017). The DU Map: A Visualization to Gain Insights into Genotype-Phenotype Mapping and Diversity. [citation][year=2017]Nicolau, M. (2017). Understanding grammatical evolution: initialisation. Genetic Pro- gramming and Evolvable Machines, 1-41. [citation][year=2017]Klotz, D., Herrnegger, M., & Schulz, K. (2017). Symbolic regression for the estimation of transfer functions of hydrological models. Water Resources Research, 53(11), 9402-9423. [citation][year=2017]Medvet, Eric. "A Comparative Analysis of Dynamic Locality and Redundancy in Grammatical Evolution." Harvard [publication]Maryam Abbasi and Paquete, L. and Pereira, F.B. , "Heuristics for multiobjective multiple sequence alignment", BioMedical Engineering Online, vol. 15, 2016 [citation][year=2016]Franscisco M. OrtuñoEmail author, Olga Valenzuela, Peter Glösekötter and Ignacio Rojas, Main findings and advances in biomedical engineering and bioinformatics from IWBBIO 2015, BioMedical Engineering OnLine 2016, 15(Suppl 1):79 [citation][year=2016]R. Ranjani Rani, D. Ramyachitra, Multiple sequence alignment using multi-objective based bacterial foraging optimization algorithm, Biosystems, Volume 150, December 2016, Pages 177-189 [citation][year=2016]Cristian Zambrano-Vega, Miriam Cárdenas-Zea, Ricardo Aguirre-Pérez, A Multi-Objective approach to the optimization of Multiple Sequence Alignment (MSA), Latin American Journal of Computing, Vol 3, number 1. [publication]Cruz, S. and Marques, J.C. and Pereira, F.B. , "Improved evolutionary algorithm for the global optimization of clusters with competing attractive and repulsive interactions", Journal of Chemical Physics, vol. 145, pp. 154109, 2016 2015(2 publications) [publication]Marques, J.C. and Pereira, F.B. , "Colloidal Clusters from a Global Optimization Perspective", Journal of Molecular Liquids, 2015 [publication]Leitão, A.P.d.A. and Pereira, F.B. and Penousal Machado , "Island Models for Cluster Geometry Optimization: How Design Options Impact Effectiveness and Diversity", Journal of Global Optimization, vol. 63, pp. 677-707, 2015 2013(1 publication) [publication]Llanio-Trujillo, J.L. and Marques, J.C. and Pereira, F.B. , "New insights on lithium-cation microsolvation by solvents forming hydrogen-bonds: Water versus methanol", Computational and Theoretical Chemistry, 2013 2012(1 publication) [publication]Marques, J.C. and Pereira, F.B. , "A detailed investigation on the global minimum structures of mixed rare-gas clusters: geometry, energetics and site occupancy", Journal of Computational Chemistry , 2012 [citation][year=2015]Low?energy structures of benzene clusters with a novel accurate potential surface M Bartolomei, F Pirani… - Journal of computational …, 2015 - Wiley Online Library [citation][year=2015]Ternary and quaternary Lennard-Jones atomic clusters: The effects of atomic sizes on the compositions, geometries, and relative stability H Takeuchi - Chemical Physics, 2015 - Elsevier [citation][year=2015]Pure and Hybrid Evolutionary Computing in Global Optimization of Chemical Structures: from Atoms and Molecules to Clusters and Crystals K Sarkar, SP Bhattacharyya - arXiv preprint arXiv:1509.00028, 2015 - arxiv.org 2011(4 publications) [publication]Llanio-Trujillo, J.L. and Marques, J.C. and Pereira, F.B. , "An Evolutionary Algorithm for the Global Optimization of Molecular Clusters: Application to Water, Benzene, and Cation-benzene", Journal of Physical Chemistry A, 2011 [citation][year=2015]Low?energy structures of benzene clusters with a novel accurate potential surface M Bartolomei, F Pirani… - Journal of computational …, 2015 - Wiley Online Library [citation][year=2015]Phase changes of the water hexamer and octamer in the gas phase and adsorbed on polycyclic aromatic hydrocarbons LFL Oliveira, J Cuny, M Morinière, L Dontot… - Physical Chemistry …, 2015 - pubs.rsc.org [citation][year=2015]Pure and Hybrid Evolutionary Computing in Global Optimization of Chemical Structures: from Atoms and Molecules to Clusters and Crystals K Sarkar, SP Bhattacharyya - arXiv preprint arXiv:1509.00028, 2015 - arxiv.org [citation][year=2014]Exploring energy landscapes: from molecular to mesoscopic systems D Chakrabarti, H Kusumaatmaja, V Rühle… - Physical Chemistry …, 2014 - pubs.rsc.org [citation][year=2014]Quantum chemical investigations on molecular clusters SR Gadre, SD Yeole, N Sahu - Chemical reviews, 2014 - ACS Publications [citation][year=2014]Structure, spectroscopy and electronic properties of neutral lattice-like (MgO) n clusters: a study based on a blending of DFT with stochastic algorithms inspired by … SG Neogi, P Chaudhury - Structural Chemistry, 2014 - Springer [citation][year=2014]Hydration of HNO 3–HOCl clusters: Bonding properties FM Balc?, N Uras-Aytemiz, R Escribano… - Computational and …, 2014 - Elsevier [citation][year=2014]Activation of Pt–O and Pt–H bonds: DFT studies on adsorption of [Gd (H 2 O) n] 3+(n= 8–9) with Ptn (n= 3–7) cluster M Carmona-Pichardo, RL Camacho-Mendoza… - Computational and …, 2014 - Elsevier [citation][year=2014]Potassium ion surrounded by aromatic rings: molecular dynamics of the first solvation shell M Albertí, A Aguilar, JMC Marques - The European Physical Journal D, 2014 - Springer [citation][year=2013]PDECO: Parallel differential evolution for clusters optimization Z Chen, X Jiang, J Li, S Li… - Journal of computational …, 2013 - Wiley Online Library [citation][year=2013]Competitive solvation of K+ by C6H6 and H2O in the K+-(C6H6) n-(H2O) m (n= 1–4; m= 1–6) aggregates M Albertí, NF Lago - The European Physical Journal D, 2013 - Springer [citation][year=2013]A sphere-cut-splice crossover for the evolution of cluster structures Z Chen, X Jiang, J Li, S Li - The Journal of chemical physics, 2013 - scitation.aip.org [citation][year=2013]Structures, stability, and growth sequence patterns of small homoclusters of naphthalene, anthracene, phenanthrene, phenalene, naphthacene, and pyrene H Takeuchi - Computational and Theoretical Chemistry, 2013 - Elsevier [citation][year=2013]Double ?–? 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[publication]Abreu, P.E. and Marques, J.C. and Pereira, F.B. , "Electronic Structure Calculations on the Ar-C6H12 Interaction: Application to the Microsolvation of the Chair Conformer", Computational and Theoretical Chemistry, 2011 [publication]Lourenço, Nuno and Pereira, F.B. , "PSO-CGO: A Particle Swarm Algorithm for Cluster Geometry Optimization", International Journal of Natural Computing Research, 2011 [citation][year=2018]Vengadeswaran, S., & Balasundaram, S. R. (2018). An Optimal Data Placement Strategy for Improving System Performance of Massive Data Applications Using Graph Clustering. International Journal of Ambient Computing and Intelligence (IJACI), 9(3), 15-30. [citation][year=2016]Omran, Mohsen Samet. "Computing of the Ground State Energy of a Hydrogen Like Impurity in a Spherical Quantum Dot using QPSO Algorithm." International Journal of Energy Optimization and Engineering (IJEOE) 5.4 (2016): 48-61. 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The Ground State of RbCs", Journal of Physics B: Atomic, Molecular & Optical Physics, 2011 2010(2 publications) [publication]Marques, J.C. and Pereira, F.B. , "An evolutionary algorithm for global minimum search of binary atomic clusters", Chemical Physics Letters, vol. 485, pp. 211-216, 2010 [citation][year=2015]Geometrical and energetic properties in 38-atom trimetallic Au Pd Pt clusters GH Wu, QM Liu, X Wu - Chemical Physics Letters, 2015 - Elsevier [citation][year=2015]Exploring the MP2 energy surface of nanoalloy clusters with a genetic algorithm: Application to sodium–potassium FT Silva, BRL Galvão, GP Voga, MX Silva… - Chemical Physics …, 2015 - Elsevier [citation][year=2015]Low?energy structures of benzene clusters with a novel accurate potential surface M Bartolomei, F Pirani… - Journal of computational …, 2015 - Wiley Online Library [citation][year=2015]Ternary and quaternary Lennard-Jones atomic clusters: The effects of atomic sizes on the compositions, geometries, and relative stability H Takeuchi - Chemical Physics, 2015 - Elsevier [citation][year=2015]Pure and Hybrid Evolutionary Computing in Global Optimization of Chemical Structures: from Atoms and Molecules to Clusters and Crystals K Sarkar, SP Bhattacharyya - arXiv preprint arXiv:1509.00028, 2015 - arxiv.org [citation][year=2014]Fast optimization of binary clusters using a novel dynamic lattice searching method X Wu, W Cheng - The Journal of chemical physics, 2014 - scitation.aip.org [citation][year=2014]On the lowest-energy structure of binary Zn–Cd nanoparticles: Size and composition CMA Zanvettor, JMC Marques - Chemical Physics Letters, 2014 - Elsevier [citation][year=2014]Theoretical studies of structures and energies of Pd, Au–Pd, and Au–Pd–Pt clusters X Wu, Y Dong - New Journal of Chemistry, 2014 - pubs.rsc.org [citation][year=2014]Binary Lennard-Jones atomic clusters: Structural features induced by large-sized atoms H Takeuchi - Computational and Theoretical Chemistry, 2014 - Elsevier [citation][year=2013]Liquid-Drop-Like Multi-Orbit Topology Versus Ring Topology in PSO for Lennard-Jones Problem K Deep - Proceedings of Seventh International Conference on …, 2013 - Springer [citation][year=2013]Performance of modified Lennard–Jones potential to seed ab initio calculations of small cadmium clusters M Muñoz, A Varas, C Cárdenas, J Rogan… - Computational and …, 2013 - Elsevier [citation][year=2013]Novas ideias para o Método de Basin-Hopping Monte Carlo aplicado à otimização global de Clusters e Nanopartículas GG Rondina - teses.usp.br [citation][year=2012]X Wu, Y Sun, C Li, W Yang. 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Complexity, 2012 - Wiley Online Library 2009(1 publication) [publication]Pereira, F.B. and Marques, J.C. , "A Study on Diversity for Cluster Geometry Optimization", Evolutionary Intelligence, vol. 2, pp. 121-140, 2009 [citation][year=2015]Pure and Hybrid Evolutionary Computing in Global Optimization of Chemical Structures: from Atoms and Molecules to Clusters and Crystals K Sarkar, SP Bhattacharyya - arXiv preprint arXiv:1509.00028, 2015 - arxiv.org 2008(3 publications) [publication]Tavares, J. and Pereira, F.B. and Costa, E. , "Multidimensional Knapsack Problem: A Fitness Landscape Analysis", IEEE Transactions on Systems, Man and Cybernetics - Part B, vol. 38, pp. 604-616, 2008 [citation][year=2015]A case study of controlling crossover in a selection hyper-heuristic framework using the multidimensional knapsack problem JH Drake, E Özcan, EK Burke - Evolutionary computation, 2015 - MIT Press [citation][year=2015]BOOSTING SIMULATED ANNEALING WITH FITNESS LANDSCAPE PARAMETERS FOR BETTER OPTIMALITY S Gupta, S Arora - 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