FELTES, B. C. ; CHANDELIER, E. B. ; GRISCI, B. I. ; DORN, M . CuMiDa: An Extensively Curated Microarray Database for Benchmarking and Testing of Machine Learning Approaches in Cancer Research. Journal of Computational Biology, v. 26, p. 1, 2019. DOI: http://dx.doi.org/10.1089/cmb.2018.0238 ARANTES, P. R. ; POLÊTO, M. D. ; JOHN, E. B. O. ; PEDEBOS, C. ; GRISCI, B. I. ; DORN, M. ; VERLI, H . Development of GROMOS-Compatible Parameter Set for Simulations of Chalcones and Flavonoids. Journal of Physical Chemistry B, v. 123, p. 1-20, 2019. DOI: http://dx.doi.org/10.1021/acs.jpcb.8b10139 GRISCI, B. I. ; FELTES, B. C. ; DORN, M. . Neuroevolution as a Tool for Microarray Gene Expression Pattern Identification in Cancer Research. Journal of Biomedical Informatics, v. 89, p. 122-133, 2019. DOI: http://dx.doi.org/10.1016/j.jbi.2018.11.013 LEONHART, P. F. ; OLIVEIRA, E. S. ; BRAUN, R. L. ; DORN, M . A Biased Random Key Genetic Algorithm for the Protein-Ligand Docking Problem. Soft Computing, v. 22, p. 1, 2018. DOI: http://dx.doi.org/10.1007/s00500-018-3065-5 LIGABUE-BRAUN, R. ; BORGUESAN, B. ; VERLI, H. ; KRAUSE, M. J. ; DORN, M . Everyone Is a Protagonist: Residue Conformational Preferences in High-Resolution Protein Structures. Journal of Computational Biology, v. 25, p. 451-465, 2018. DOI: http://dx.doi.org/10.1089/cmb.2017.0182 CORRÊA, L. L.; BORGUESAN, B. ; FARFAN, C. ; INOSTROZA-PONTA, M. ; DORN, M . A Memetic Algorithm for 3D Protein Structure Prediction Problem. IEEE-ACM Transactions on Computational Biology and Bioinformatics, v. 15, p. 690-704, 2018. DOI: http://dx.doi.org/10.1109/TCBB.2016.2635143 KLEMENS, F. ; FORSTER, B. ; DORN, M. ; THATER, G. ; KRAUSE, M. J. . Solving Fluid Flow Domain Identification Problems with Adjoint Lattice Boltzmann Methods. Computer & Mathematics With Applications, v. 76, p. 1, 2018. DOI: http://dx.doi.org/10.1016/j.camwa.2018.07.010 PARRAGA-ALAVA, J. ; DORN, M. ; INOSTROZA, M. . A Multi-objective Gene Clustering Algorithm Guided by Apriori Biological Knowledge with Intensification and Diversification Strategies. BioData Mining, v. 11, p. 1, 2018. DOI: http://dx.doi.org/10.1186/s13040-018-0178-4 FELTES, B. C. ; GRISCI, B. I. ; POLONI, J. F. ; DORN, M . Perspectives and Applications of Machine Learning for Evolutionary Developmental Biology. Molecular BioSystems, v. 14, p. 1, 2018. DOI: http://dx.doi.org/10.1039/C8MO00111A POLÊTO, M. D. ; RUSU, V. H. ; GRISCI, B. I. ; DORN, M. ; LINS, R. D. ; VERLI, H. . Aromatic Rings Commonly Used in Medicinal Chemistry: Force Fields Comparison and Interactions With Water Toward the Design of New Chemical Entities. Frontiers in Pharmacology, v. 9, p. 395, 2018. DOI: http://dx.doi.org/10.3389/fphar.2018.00395 VILLALOBOS-CID, M. ; BRAUN, R. L. ; DORN, M ; INOSTROZA, M. . A Memetic Algorithm Based on an NSGA-II Scheme for Phylogenetic Tree Inference. IEEE Transactions on Evolutionary Computation, v. 22, p. 1-1, 2018. DOI: http://dx.doi.org/10.1109/tevc.2018.2883888 CORRÊA, L. L. ; BORGUESAN, B. ; KRAUSE, M. J. ; DORN, M . Three-dimensional Protein Structure Prediction Based on Memetic Algorithms. Computers & Operations Research, v. 91, p. 160-177, 2018. DOI: http://dx.doi.org/10.1016/j.cor.2017.11.015 GRISCI, B. I. ; DORN, M. . NEAT-FLEX: Predicting the Conformational Flexibility of Amino Acids Using Neuroevolution of Augmenting Topologies. Journal of Bioinformatics and Computational Biology (Print), p. 1750009, 2017. DOI: http://dx.doi.org/10.1142/s0219720017500093 BORGUESAN, B. ; INOSTROZA-PONTA, M. ; DORN, M . NIAS-Server: Neighbors Influence of Amino Acids and Secondary Structures in Proteins. Journal of Computational Biology, v. 24, p. 255-265, 2017. DOI: http://dx.doi.org/10.1089/cmb.2016.0074 BORGUESAN, B. ; E SILVA, M. B. ; GRISCI, B. ; INOSTROZA-PONTA, M. ; DORN, M . APL: An Angle Probability List to Improve Knowledge-Based Metaheuristics for the Three-Dimensional Protein Structure Prediction. Computational Biology and Chemistry (Print), v. 59, p. 142-157, 2015. DOI: http://dx.doi.org/10.1016/j.compbiolchem.2015.08.006 DORN, M.; BURIOL, L.S. ; LAMB, L.C. . MOIRAE: A Computational Strategy to Extract and Represent Structural Information from Experimental Protein Templates. Soft Computing, v. 18, p. 773-795, 2014. DOI: http://dx.doi.org/10.1007/s00500-013-1087-6 DORN, M. ; E SILVA, M. B. ; BURIOL, L. S. ; LAMB, L. C. . Three-dimensional Protein Structure Prediction: Methods and Computational Strategies. Computational Biology and Chemistry (Print), v. 53, p. 251-276, 2014. DOI: http://dx.doi.org/10.1016/j.compbiolchem.2014.10.001 DORN, M.; BURIOL, L.S. ; LAMB, L. C. . A Molecular Dynamics and Knowledge-Based Computational Strategy to Predict Native-like Structures of Polypeptides. Expert Systems with Applications, v. 40, p. 698-706, 2013.
DOI: http://dx.doi.org/10.1016/j.eswa.2012.08.003 ANDRADES, R. K. ; DORN, M. ; FARENZENA, D. S. ; LAMB, L. C. . A Cluster-DEE-based Strategy to Empower Protein design. Expert Systems with Applications, v. 40, p. 5210-5218, 2013. DOI: http://dx.doi.org/10.1016/j.eswa.2013.03.011 DORN, M. ; SOUZA, O. N . An Interval-based Algorithm to Represent Conformational States of Experimentally Determined Polypeptide Templates and Fast Prediction of Approximated 3D Protein Structures. International Journal of Bioinformatics Research and Applications (Print), v. 9, p. 462, 2013. DOI: : http://dx.doi.org/10.1504/ijbra.2013.056075 COSTA, A. L. P. ; PAULI, I. ; DORN, M. ; SCHROEDER, E. K. ; ZHAN, C. G. ; SOUZA, O. N . Conformational Changes in 2-trans-enoyl-ACP (CoA) Reductase (InhA) from M. tuberculosis Induced by an Inorganic Complex: a Molecular Dynamics Simulation Study. Journal of Molecular Modeling (Online), v. 18, p. 1779-1790, 2012. DOI: http://dx.doi.org/10.1007/s00894-011-1200-7 DORN, M. ; BRAGA, A. L. S. ; LLANOS, C. H. ; COELHO, L. S. . A GMDH Polynomial Neural Network-based Method to Predict Approximate Three-dimensional Structures of Polypeptides. Expert Systems with Applications, v. 39, p. 12268-12279, 2012. DOI: http://dx.doi.org/10.1016/j.eswa.2012.04.046 DORN, M.; SOUZA, O. N . A3N: An Artificial Neural Network N-gram-based Method to Approximate 3-D Polypeptides Structure Prediction. Expert Systems with Applications, v. 37, p. 7497-7508, 2010. DOI: http://dx.doi.org/10.1016/j.eswa.2010.04.096 DORN, M. ; SOUZA, O. N . Mining the Protein Data Bank with CReF to Predict Approximate 3-D Structures of Polypeptides. International Journal of Data Mining and Bioinformatics, v. 4, p. 281, 2010. DOI: http://dx.doi.org/10.1504/ijdmb.2010.033521
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LEONHART, P. F. ; DORN, M . A Biased Random Key Genetic Algorithm with Local Search Chains for Molecular Docking. In: 22nd International Conference on the Applications of Evolutionary Computation, 2019, Leipzig. Proceedings of the 22nd International Conference on the Applications of Evolutionary Computation, 2019. v. 11454. p. 360-376. DOI: http://dx.doi.org/10.1007/978-3-030-16692-2_24 NARLOCH, P. H. ; DORN, M . A Knowledge Based Differential Evolution Algorithm for Protein Structure Prediction. In: 22nd International Conference on the Applications of Evolutionary Computation, 2019, Leipzig. Proceedings of the 22nd International Conference on the Applications of Evolutionary Computation, 2019. v. 11454. p. 343-359. DOI: http://dx.doi.org/10.1007/978-3-030-16692-2_23 LEONHART, P. F. ; NARLOCH, P. H. ; DORN, M . A Self-Adaptive Local Search Coordination in Multimeme Memetic Algorithm for Molecular Docking (aceito para apresentação). In: International Conference on Computational Science (ICCS 2019), 2019, Faro. Proceedings of the International Conference on Computational Science, 2019. p. 1. CORRÊA, L. L. ; DORN, M . A Multi-Objective Artificial Bee Colony Algorithm for the 3-D Protein Structure Prediction Problem (aceito para apresentação). In: International Conference on Computational Science (ICCS 2019), 2019, Faro. Proceedings of the International Conference on Computational Science, 2019. p. 1. NARLOCH, P. H. ; DORN, M . A Knowledge Based Self-Adaptive Differential Evolution Algorithm for Protein Structure Prediction (aceito para apresentação). In: International Conference on Computational Science (ICCS 2019), 2019, Faro. Proceedings of the International Conference on Computational Science, 2019. p. 1. BORGUESAN, B ; NARLOCH, P. H. ; INOSTROZA-PONTA, MARIO ; DORN, M . A Genetic Algorithm Based on Restricted Tournament Selection for the 3D-PSP Problem. In: 2018 IEEE Congress on Evolutionary Computation (CEC), 2018, Rio de Janeiro. 2018 IEEE Congress on Evolutionary Computation (CEC), 2018. p. 1. DOI: http://dx.doi.org/10.1109/CEC.2018.8477721 CORRÊA, L. L. ; DORN, M . A Knowledge-Based Artificial Bee Colony Algorithm for the 3-D Protein Structure Prediction Problem. In: 2018 IEEE Congress on Evolutionary Computation (CEC), 2018, Rio de Janeiro. 2018 IEEE Congress on Evolutionary Computation (CEC), 2018. p. 1. DOI: http://dx.doi.org/10.1109/CEC.2018.8477863 GRISCI, B. I. ; FELTES, B. C. ; DORN, M . Microarray Classification and Gene Selection with FS-NEAT. In: 2018 IEEE Congress on Evolutionary Computation (CEC), 2018, Rio de Janeiro. 2018 IEEE Congress on Evolutionary Computation (CEC), 2018. p. 1. DOI: http://dx.doi.org/10.1109/cec.2018.8477813 VILLALOBOS-CID, M. ; DORN, M. ; INOSTROZA-PONTA, M. . Performance Comparison of Multi-Objective Local Search Strategies to Infer Phylogenetic Trees. In: 2018 IEEE Congress on Evolutionary Computation (CEC), 2018, Rio de Janeiro. 2018 IEEE Congress on Evolutionary Computation (CEC), 2018. p. 1. DOI: http://dx.doi.org/10.1109/CEC.2018.8477666 PARRAGA-ALAVA, J. ; DORN, M ; INOSTROZA-PONTA, M . Using Local Search Strategies to Improve the Performance of NSGA-II for the Multi-Criteria Minimum Spanning Tree problem. In: 2017 IEEE Congress on Evolutionary Computation (CEC), 2017, Donostia. 2017 IEEE Congress on Evolutionary Computation (CEC), 2017. p. 1119. DOI: http://dx.doi.org/10.1109/CEC.2017.7969432 CORREA, L. L. ; INOSTROZA-PONTA, MARIO ; DORN, M . An Evolutionary Multi-Agent Algorithm to Explore the High Degree of Selectivity in Three-Dimensional Protein Structures. In: 2017 IEEE Congress on Evolutionary Computation (CEC), 2017, Donostia. 2017 IEEE Congress on Evolutionary Computation (CEC), 2017. p. 1111. DOI: http://dx.doi.org/10.1109/cec.2017.7969431 OLIVEIRA, M. ; BORGUESAN, B. ; DORN, M . SADE-SPL: A Self-Adapting Differential Evolution algorithm with a loop Structure Pattern Library for the PSP problem. In: 2017 IEEE Congress on Evolutionary Computation (CEC), 2017, Donostia. 2017 IEEE Congress on Evolutionary Computation (CEC), 2017. p. 1095. DOI: http://dx.doi.org/10.1109/cec.2017.7969429 ALIXANDRE, B. F. F. ; DORN, M . D-BRKGA: A Distributed Biased Random-Key Genetic Algorithm. In: 2017 IEEE Congress on Evolutionary Computation (CEC), 2017, Donostia. 2017 IEEE Congress on Evolutionary Computation (CEC), 2017. p. 1398. DOI: http://dx.doi.org/10.1109/cec.2017.7969467 RUIZ-TAGLE, B. ; VILLALOBOS-CID, M. ; DORN, M. ; INOSTROZA-PONTA, M . Evaluating the Use of Local Search Strategies for a Memetic Algorithm for the Protein-Ligand Docking Problem. In: 2017 36th International Conference of the Chilean Computer Science Society (SCCC), 2017, Arica. 2017 36th International Conference of the Chilean Computer Science Society (SCCC), 2017. p. 1. DOI: http://dx.doi.org/10.1109/SCCC.2017.8405141 GRISCI, B. I. ; DORN, M . Predicting Protein Structural Features with NeuroEvolution of Augmenting Topologies. In: International Joint Conference on Neural Networks, 2016, Vancouver. Proceedings of the International Joint Conference on Neural Networks (IJCNN 2016), 2016. DOI: http://dx.doi.org/10.1109/IJCNN.2016.7727291 BORGUESAN, B. ; BOHRER, J. S. ; BARBACHAN e SILVA, M. ; CORREA, L. L. ; DORN, M . Improving Protein Tertiary Structure Prediction with Conformational Propensities of Amino Acid Residues. In: IEEE Congress on Evolutionary Computation, 2016, vancouver. Proceedings of the IEEE Congress on Evolutionary Computation (IEEE CEC 2016), 2016. DOI: http://dx.doi.org/10.1109/CEC.2016.7743772 BIAZUS, M. ; DORN, M. ; THOM, L. . Modelagem e Análise de Conformidade do Processo de Atracamento Molecular. In: X BreSci - Brazilian e-Science Workshop, 2016, Porto Alegre. Anais do XXXVI Congresso da Sociedade Brasileira de Computação, 2016. ESCOBAR, I. ; HIDALGO, N. ; INOSTROZA-PONTA, M. ; MARIN, M. ; ROSAS, E. ; DORN, M . Evaluation of a Combined Energy Fitness Function for a Distributed Memetic Algorithm to Tackle the 3D Protein Structure Prediction Problem. In: 2016 35th International Conference of the Chilean Computer Science Society (SCCC), 2016, Valparaíso. 2016 35th International Conference of the Chilean Computer Science Society (SCCC). p. 1. DOI: http://dx.doi.org/10.1109/SCCC.2016.7836019 SIMONETTI, V. ; DORN, M. . Escalonamento de Equipes de Enfermagem Utilizando Busca Tabu. In: XLVI Simpósio Brasileiro de Pesquisa Operacional, 2014, Salvador. Anais do XLVI Simpósio Brasileiro de Pesquisa Operacional, 2014. DOI: http://dx.doi.org/10.13140/RG.2.1.4570.6960 GRISCI, B. I. ; BORGUESAN, B. ; DORN, M. ; INOSTROZA, M. . Using Conformational Preferences of Amino Acid Residues and Meta-Heuristics to Predict 3-D Protein Structures. In: Third International Society for Computational Biology Latin America, 2014, Belo Horizonte. Proceedings of third International Society for Computational Biology Latin America. La Jolla: International Society for Computational Biology, 2014. v. 1. p. 20-35. DORN, M. ; INOSTROZA-PONTA, M. ; BURIOL, L. S. ; VERLI, H. . A Knowledge-Based Genetic Algorithm to Predict Three-Dimensional Structures of Polypeptides. In: 2013 IEEE Congress on Evolutionary Computation (CEC), 2013, Cancun. 2013 IEEE Congress on Evolutionary Computation. p. 1233-8. DOI: http://dx.doi.org/10.1109/CEC.2013.6557706 BRAGA, A.L.S. ; ARIAS-GARCIA, J. ; LLANOS, C. ; DORN, M. ; FOLTRAN, A. ; COELHO, L. S. . Hardware Implementation of GMDH-type Artificial Neural Networks and Its Use to Predict Approximate Three-Dimensional Structures of Proteins. In: 7th International Workshop on Reconfigurable and CommunicationCentric SystemsonChip (ReCoSoC), 2012, York. Proceedings of the 7th International Workshop on Reconfigurable and Communication-Centric Systems-on-Chip (ReCoSoC), 2012. v. 1. p. 1-8. DOI: http://dx.doi.org/10.1109/ReCoSoC.2012.6322907 DORN, M.; BURIOL, L.S. ; LAMB, L. C. . A Hybrid Genetic Algorithm for the 3-D Protein Structure Prediction Problem Using a Path-Relinking Strategy. In: IEEE Congress on Evolutionary Computation, 2011, New Orleans. Proceedings of the 2011 IEEE Congress on Evolutionary Computation. Los Alamitos: IEEE Press, 2011. v. 1. p. 2709-2716. DOI: http://dx.doi.org/10.1109/CEC.2011.5949957 GONÇALVES, W.W. ; DORN, M. ; BURIOL, L.S. ; LAMB, L. C. . A Structured-Population Genetic Algorithm for the 3-D Protein Structure Prediction Problem. In: Brazilian Symposium on Bioinformatics, 2011, Brasilia. Proceedings of BSB 2011. Porto Alegre: SBC, 2011. v. 1. p. 17-24. DOI: http://dx.doi.org/10.13140/RG.2.1.5094.9848 DORN, M.; SOUZA, O. N . CReF: A Central-Residue-Fragment-Based Method for Predicting Approximate 3-D Polypeptides Structures. In: Annual ACM Symposium on Applied Computing, 2008, Fortaleza. SAC '08: Proceedings of the 2008 ACM symposium on Applied computing. New York, NY, USA: ACM Press, 2008. p. 1261-1267. DOI: http://dx.doi.org/10.1145/1363686.1363979 DORN, M.; BREDA, A. E. ; SOUZA, O. N . A Hybrid Method for the Protein Structure Prediction Problem. In: Brazilian Symposium on Bioinformatics, 2008, Santo André, São Paulo, Brazil. Lecture Notes in Computer Science, Advances in Bioinformatics and Computational Biology. Heidelberg, Germany: Springer, 2008. v. 5167. p. 47-56. DOI: http://dx.doi.org/10.1007/978-3-540-85557-6_5 KOLBERG, M. L. ; DORN, M. ; DORN, M. ; BOHLENDER, G. ; FERNANDES, L. G. L. . Parallel Verified Linear System Solver for Ucertain Input Data. In: 20th International Symposium on Computer Architecture and High Performance Computing, 2008, Campo Grande. Proceedings of the 20th International Symposium on Computer Architecture and High Performance Computing. Los Alamitos, CA: EEE Press, 2008. v. 1. p. 89-96. DOI: http://dx.doi.org/10.1109/SBAC-PAD.2008.10
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