Publications SBCB Lab

Journals    » Proceedings    » Book Chapter



Journals
  • 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

Proceedings
  • 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

  • VILLALOBOS-CID, M. ; DORN, M. ; INOSTROZA-PONTA, M . Understanding the Relationship Between Decision and Objective Space in the Multi-Objective Phylogenetic Inference 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.2018.8477689

  • 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

Book Chapter
  • NARLOCH, P.H. ; DORN, M. A Knowledge Based Self-Adaptive Differential Evolution Algorithm for Protein Structure Prediction. Lecture Notes in Computer Science. 1ed.: Springer International Publishing, 2019, v. 11538, p. 87-100. DOI: http://dx.doi.org/10.1007/978-3-030-22744-9_7

  • LEONHART, P.F.; NARLOCH, P.H. ; DORN, M. A Self-adaptive Local Search Coordination in Multimeme Memetic Algorithm for Molecular Docking. Lecture Notes in Computer Science. 1ed.: Springer International Publishing, 2019, v. 11538, p. 145-159. DOI: http://dx.doi.org/10.1007/978-3-030-22744-9_11

  • CORRÊA, L. L. ; DORN, M. A Multi-objective Swarm-Based Algorithm for the Prediction of Protein Structures. Lecture Notes in Computer Science. 1ed.: Springer International Publishing, 2019, v. 11538, p. 101-115. DOI: http://dx.doi.org/10.1007/978-3-030-22744-9_8

  • NARLOCH, P. H. ; DORN, M. A Knowledge Based Differential Evolution Algorithm for Protein Structure Prediction. Lecture Notes in Computer Science. 1ed.: Springer International Publishing, 2019, v. 11454, p. 343-359. DOI: http://dx.doi.org/10.1007/978-3-030-16692-2_23

  • LEONHART, P. F. ; DORN, M. A Biased Random Key Genetic Algorithm with Local Search Chains for Molecular Docking. Lecture Notes in Computer Science. 1ed.: Springer International Publishing, 2019, v. 11454, p. 360-376. DOI: http://dx.doi.org/10.1007/978-3-030-16692-2_24

  • CORRÊA, L. L. ; DORN, M. Multi-Agent Systems in Three-dimensional Protein Structure Prediction. In: Diana Adamatti. (Org.). Multi-Agent-Based Simulations Applied to Biological and Environmental Systems. 10ed.Hershey: IGI Global, 2016, v. , p. 241-278. DOI: http://dx.doi.org/10.4018/978-1-5225-1756-6.ch011