Structural bioinformatics deals with problems where the rules that govern the biochemical processes and relations are partially known which makes hard to design efficient computational strategies for these problems. There is a wide range of unanswered questions, which cannot be answered neither by experiments nor by classical modeling and simulation approaches. Specifically, there are several problems that still do not have a computational method that can guarantee a minimum quality of solution. The general goal of this project is to develop metaheuristics models based on robust and scalable parallel and distributed computing for structural bioinformatic problems. International Project (Stic-Amsud 2016) between the Federal University of Rio Grande do Sul (UFRGS, Brazil), University of Nacional de San Luis (UNSL, Argentine), University of Santiago de Chile (USACH, Chile), University of Pierre et Marie Currie (UPMC, LIP6, INRIA, France).
Researchers
Dr. Márcio Dorn - Coordinator
PPGC/INF/UFRGS - Brazil
Dr. Mario Inostroza-Ponta - Coordinator
DIINF/USACH - Chile
Dr. Verónica Gil-Costa - Coordinator
LIDIC/UNSL - Argentine
Dr. Luciana Arantes - Coordinator
LIP6/INRIA/UPMC - France
Dr. Rodrigo Ligabue Braun
DF/UFCSPA - Brazil
Dr. Hugo Verli
PPGBCM/CBIOT/UFRGS - Brazil
Dr. Nicolás Hidalgo
UDP - Chile
Dr. Erika Rosas
DI/UTFSM-Chile
Dr. Marcela Printista
LIDIC/UNSL - Argentine
Dr. Sébastien Monnet
LIP6/INRIA - France
Dr. Julien Sopena
LIP6/INRIA - France
Dr. Pierre Sens
LIP6/INRIA - France
Graduate Students/Collaborators
Bruno Borguesan
Ph.D. Candidate
PPGC/INF/UFRGS - Brazil
Leonardo de Lima Corrêa
Ph.D. Candidate
PPGC/INF/UFRGS - Brazil
Eduardo Spieler
MS.c. Candidate
PPGC/INF/UFRGS - Brazil
Manuel Villalobos Cid
Ph.D. Candidate
DIINF/USACH - Chile
Jorge Párraga-Alava
Ph.D. Candidate
DIINF/USACH - Chile
Benjamín Ruiz-Tagle
MS.C. Candidate
DIINF/USACH - Chile
Luis Celedón
MS.C. Candidate
DIINF/USACH - Chile
Sergio Hernandez
Ph.D. Candidate
LIDIC/UNSL - Argentine
Romina Molina
Ph.D. Candidate
LIDIC/UNSL - Argentine
Jair Lobos
MS.c. Candidate
LIDIC/UNSL - Argentine
Gruillermo Trabes
MS.c. Candidate
LIDIC/UNSL - Argentine
João Paulo de Araujo
Ph.D. Candidate
LIP6/INRIA - France
Denis Jeanneau
Ph.D. Candidate
LIP6/INRIA - France
Study Missions
✈
INF/UFRGS/Brazil to LIP6/UPMC/France
Ph.D. (c) - Leonardo de Lima Correa
October, 2018 to September, 2019
Work Missions
✈
INF/UFRGS/Brazil to LIP6/UPMC/France
Dr. Márcio Dorn
December, 2017
✈
INF/UFRGS/Brazil to LIP6/UPMC/France
Dr. Rodrigo Ligabue-Braun
August, 2018
✈
LIP6/UPMC/France to INF/UFRGS/Brazil
Dr. Luciana Arantes
April, 2017
✈
DIINF/USACH to INF/UFRGS/Brazil
Dr. Mario Inostroza-Ponta
April, 2017
✈
LIDIC/UNSL to INF/UFRGS/Brazil
Dr. Verónica Gil-Costa
April, 2017
✈
DIINF/USACH to INF/UFRGS/Brazil
Dr. Mario Inostroza-Ponta
December, 2018
✈
UDP to INF/UFRGS/Brazil
Dr. Nicolás Hidalgo
December, 2018
✈
INF/UFRGS/Brazil to DIINF/USACH
Dr. Márcio Dorn
April, 2018
✈
LIP6/UPMC/France to INF/UFRGS/Brazil
Dr. Luciana Arantes
December, 2018
✈
LIP6/UPMC/France to INF/UFRGS/Brazil
Dr. Piere Sens
December, 2018
PROBRAL Meetings / Presentations
2017 - First Meeting
2017 - Second meeting
2018 - Third meeting
2018 - Fourth meeting
Publications
- Borguesan, B.; Narloch, P.H.; Inostroza-Ponta, M.; Dorn, M. A Genetic Algorithm Based on Restricted Tournament Selection for the 3D-PSP Problem. 2018 IEEE Congress on Evolutionary Computation (CEC), 2018, Rio de Janeiro.
- Villalobos-Cid, M.; Dorn, M.; Inostroza-Ponta, M. Understanding the Relationship Between Decision and Objective Space in the Multi-Objective Phylogenetic Inference Problem. 2018 IEEE Congress on Evolutionary Computation (CEC), 2018, Rio de Janeiro.
- Villalobos-Cid, M.; Dorn, M.; Inostroza-Ponta, M. Performance Comparison of Multi-Objective Local Search Strategies to Infer Phylogenetic Trees. 2018 IEEE Congress on Evolutionary Computation (CEC), 2018, Rio de Janeiro.
- 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. 2017 IEEE Congress on Evolutionary Computation (CEC), 2018, Donostia.
- Correa, L.C.; Inostroza-Ponta, M.; Dorn, M. An evolutionary multi-agent algorithm to explore the high degree of selectivity in three-dimensional protein structures. 2017 IEEE Congress on Evolutionary Computation (CEC), 2018, Donostia.
- Sepulveda, V.; Solar, R.; Inostrosa, A.; Gil-Costa, V.; Marin, M. Towards Rapid Population Genetics Forward-in-time Simulations. 2017 Winter Simulation Conference, 2017, Las Vegas.
- Solar, R.; Sepulveda, V.; Inostrosa-Psijas, A.; Rojas, O.; Gil-Costa, V. and Marin, M. A Service-Oriented Platform for Approximate Bayesian Computation in Population Genetics. Journal of Computational Biology, ahead of print, 2019
- Correa, 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.
- Parraga-Alava, J.; Dorn, M.; Inostroza-Ponta, M. A multi-objective gene clustering algorithm guided by apriori biological knowledge with intensification and diversification strategies. BioData Mining, v. 11, p. 1, 2018.
- Villalobos-Cid, M.; Ligabue-Braun, R.; Dorn, M; Inostroza-Ponta, 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.
- 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.
