Publications

Journal articles

2020

  • Parraga-Alava, J. and Inostroza-Ponta, M. Influence of the go-based semantic similarity measures in multi-objective gene clustering algorithm performance, Journal of Bioinformatics and Computational Biology, Vol. 18, No. 6, 2020 doi.org/10.1142/S0219720020500389

  • Villalobos-Cid, M. Salinas, F., Inostroza-Ponta, M. Total evidence or taxonomic congruence? A comparison of methods for combining biological evidence. Journal of Bioinformatics and Computational Biology, Vol. 18, No. 6, 2020, doi.org/10.1142/S0219720020500407.

  • Inostroza-Ponta, M., Dorn, M. Escobar, I., de Lima Correa, L. Rosas, E., Hidalgo, N., Marin, M. Exploring the high selectivity of 3-D protein structures using distributed memetic algorithms, Journal of Computational Science, Volume 41, 2020, 101087, doi.org/10.1016/j.jocs.2020.101087.

  • Román, J. and González, D. and Inostroza, M. and Mahn, A., Molecular Modeling of Epithiospecifier and Nitrile-Specifier Proteins of Broccoli and Their Interaction with Aglycones, Molecules, Volume 25, number 4, 2020, doi.org/10.3390/molecules25040772.

  • Villalobos-Cid, M., Salinas, F., Kessi-Pérez, E. I., De Chiara, M., Liti, M., Inostroza-Ponta, M., Martínez, C. Comparison of phylogenetic tree topologies for nitrogen associated genes partially reconstruct the evolutionary history of Saccharomyces cerevisiae, Microorganisms 2020, 8, 32 doi:10.3390/microorganisms8010032.

2019

  • M. Villalobos-Cid, M. Dorn, R. Ligabue-Braun and M. Inostroza-Ponta, A Memetic Algorithm Based on an NSGA-II Scheme for Phylogenetic Tree Inference, in IEEE Transactions on Evolutionary Computation, vol. 23, no. 5, pp. 776-787, Oct. 2019. doi:10.1109/TEVC.2018.2883888.

2018

  • L. Correa, B. Borguesan, C. Farf an, M. Inostroza-Ponta and M. Dorn, A Memetic Algorithm for 3D Protein Structure Prediction Problem, in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 15, no. 3, pp. 690-704, 1 May-June, 2018. doi:10.1109/TCBB.2016.2635143.

  • 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 11, 16, 2018 doi:10.1186/s13040-018-0178-4.

2017

  • Bruno Borguesan, Mario Inostroza-Ponta, Marcio Dorn, NIAS-Server: Neighbors Influence of Amino acids and Secondary Structures in Proteins, Journal of Computational Biology 24(3): 255-265, 2017 doi:10.1089/cmb.2016.0074.

2016

  • Manuel Villalobos-Cid; Max Chacón; Pedro Zitko; Mario Inostroza-Ponta. A New Strategy to Evaluate Technical Efficiency in Hospitals Using Homogeneous Groups of Casemix - How to Evaluate When There is Not DRGs?, J. Medical Systems 40(4): 103:1-103:1, 2016. doi:10.1007/s10916-016-0458-9.

2015

  • Borguesan, Bruno; E Silva, Mariel Barbachan; Grisci, Bruno; Inostroza-Ponta, Mario; Dorn, Marcio. APL: An angle probability list to improve knowledge-based metaheuristics for the threedimensional protein structure prediction. Computational Biology and Chemistry (Print), v. 59, p.142-157, 2015. doi:10.1016/j.compbiolchem.2015.08.006.

<2015

  • Ramirez-Castrill on, M; Mendes, S; Inostroza-Ponta, Mario; Valente, P. (GTG)5 MSP-PCR Fingerprinting as a Technique for Discrimination of Wine Associated Yeasts?. Plos One, v. 9, p. e105870, 2014. doi:10.1371/journal.pone.0105870.

  • Clark, M. B.; Johnston, R. L.; Inostroza-Ponta, M.; Fox, A. H.; Fortini, E.; Moscato, P.; Dinger, M. E.; Mattick, J. S. Genome-wide analysis of long noncoding RNA stability. Genome Research, v. 22, p. 885-898, 2012. doi:10.1101/gr.131037.111.

  • Inostroza-Ponta, M; Berretta, R; Moscato, P (2011) QAPgrid: A Two Level QAP-Based Approach for Large-Scale Data Analysis and Visualization. PLoS ONE 6(1): e14468. doi:10.1371/journal.pone.0014468 .

  • C Riveros, D Mellor, KS Gandhi, FC McKay, MB Cox, R Berretta, SY Vaezpour, M Inostroza-Ponta, SA Broadley, RN Heard, S Vucic, GJ Stewart, DW Williams, RJ Scott, J Lechner-Scott, DR Booth, P Moscato. (2010) A Transcription Factor Map as Revealed by a Genome-Wide Gene Expression Analysis of Whole-Blood mRNA Transcriptome in Multiple Sclerosis. PLoS ONE 5(12): e14176. doi:10.1371/journal.pone.0014176.

  • Capp A, Inostroza-Ponta M, Bill D, Moscato P, Lai C, Christie D, Lamb D, Turner S, Joseph D, Matthews J, Atkinson C, North J, Poulsen M, Spry NA, Tai KH, Wynne C, Duchesne G, Steigler A, Denham JW. (2009) Is there more than one proctitis syndrome? A revisitation using data from the TROG 96.01 trial, Radiotherapy & Oncology, Mar;90(3):400-407. doi:10.1016/j.radonc.2008.09.019.

Conferences papers

2020

2019

  • Troncoso, N., Rojo-González, R. Villalobos-Cid, M., Vásquez, O. C, Chavez. H. Economic decision-making tool for distributed solar photovoltaic panels and storage: The case of Chile. Energy Procedia 159:388 - 393, March 2019. DOI: 10.1016/j.egypro.2018.12.071.

  • Giglio, J., Inostroza-Ponta, M., Villalobos-Cid, M. A multi-objective optimisation evolutionary approach for the Multidimensional Scaling Problem (2019) Proceedings - International Conference of the Chilean Computer Science Society, SCCC, 2019-November, doi:10.1109/SCCC49216.2019.8966433.

  • Parraga-Alava, J., Caicedo, R.A., Gomez, J.M., Inostroza-Ponta, M. An Unsupervised Learning Approach for Automatically to Categorize Potential Suicide Messages in Social Media (2019) Proceedings - International Conference of the Chilean Computer Science Society, SCCC, 2019-November, doi:10.1109/SCCC49216.2019.8966443.

  • Villalobos-Cid, M., Orellana, M., Vasquez, O.C., Pinto-Sothers, E., Inostroza-Ponta, M. Dealing with the Balanced Academic Curriculum Problem considering the Chilean Academic Credit Transfer System (2019) Proceedings - International Conference of the Chilean Computer Science Society, SCCC, 2019-November, .doi:10.1109/SCCC49216.2019.8966411.

2018

  • Manuel Villalobos-Cid, M arcio Dorn, Mario Inostroza-Ponta (2018) Understanding the Relationship Between Decision and Objective Space in the Multi-Objective Phylogenetic Inference Problem, 2018 IEEE Congress on Evolutionary Computation (CEC), Rio de Janeiro, pp. 1-8.

  • M. Villalobos-Cid, M. Dorn and M. Inostroza-Ponta (2018) Performance Comparison of Multi-Objective Local Search Strategies to Infer Phylogenetic Trees, 2018 IEEE Congress on Evolutionary Computation (CEC), Rio de Janeiro, pp. 1-8.

  • B. Borguesan, P. H. Narloch, M. Inostroza-Ponta and M. Dorn, (2018) A Genetic Algorithm Based on Restricted Tournament Selection for the 3D-PSP Problem, 2018 IEEE Congress on Evolutionary Computation (CEC), Rio de Janeiro, pp. 1-8.

  • J. Parraga-Alava, G. M. Garz on, R. Alc var Cevallos and M. Inostroza-Ponta (2018) Unsupervised Pattern Recognition for Geographical Clustering of Seismic Events Post MW 7.8 Ecuador Earthquake, 2018 37th International Conference of the Chilean Computer Science Society (SCCC), Santiago, Chile, pp. 1-8.

2017

  • M. Villalobos-Cid, D. Vega-Araya and M. Inostroza-Ponta, (2017) Application of different multiobjective decision making techniques in the phylogenetic inference problem, 2017 36th International Conference of the Chilean Computer Science Society (SCCC), Arica, pp. 1-9.

  • R. Sandoval-Soto, M. Villalobos-Cid and M. Inostroza-Ponta, (2017) Tackling the bi-objective quadratic assignment problem by characterizing different memory strategies in a memetic algorithm, 2017 36th International Conference of the Chilean Computer Science Society (SCCC), Arica, pp. 1-12.

  • B. Ruiz-Tagle, M. Villalobos-Cid, M. Dorn and M. Inostroza-Ponta, (2017) Evaluating the use of local search strategies for a memetic algorithm for the protein-ligand docking problem, 2017 36th International Conference of the Chilean Computer Science Society (SCCC), Arica, 2017, pp. 1-12.

  • J. P arraga- Alava, M. Dorn and M. Inostroza-Ponta, (2017) 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), San Sebastian, 2017, pp. 1119-1126.

  • L. de Lima Correa, M. Inostroza-Ponta and M. Dorn, (2017) An evolutionary multi-agent algorithm to explore the high degree of selectivity in three-dimensional protein structures, 2017 IEEE Congress on Evolutionary Computation (CEC), San Sebastian, 2017, pp. 1111-1118.

2016

  • Parraga- Alava J., Inostroza-Ponta M. (2016). A bi-objective model for gene clustering combining expression data and external biological knowledge. CLEI 2016: 1-12.

  • Escobar I., Hidalgo N., Inostroza-Ponta M., Mar n M., Rosas E. , Dorn M. (2016) Evaluation of a combined energy tness function for a distributed memetic algorithm to tackle the 3D protein structure prediction problem. SCCC 2016: 1-10.

2015

  • Mario Inostroza-Ponta, Camilo Farf an, M arcio Dorn. (2015) A Memetic Algorithm for Protein Structure Prediction based on Conformational Preferences of Aminoacid Residues. GECCO (Companion) 2015: 1403-1404.

  • Harris, Matthew; Berretta, Regina; Inostroza-Ponta, Mario; Moscato, Pablo. (2015) A memetic algorithm for the quadratic assignment problem with parallel local search. In: 2015 IEEE Congress on Evolutionary Computation (CEC), 2015, Sendai. 2015 IEEE Congress on Evolutionary Computation (CEC), 2015. p. 838-845.

<2015

  • Dorn, M.; Inostroza-Ponta, M.; Buriol, L.S.; Verli, H. (2013), A knowledge-based genetic algorithm to predict three-dimensional structures of polypeptides, Evolutionary Computation (CEC), 2013 IEEE Congress on, vol., no., pp.1233,1240, 20-23 June 2013. doi: 10.1109/CEC.2013.6557706

  • Ahmed Shamsul Are n; Inostroza-Ponta, Mario; Luke Mathieson; Berretta, R; Moscato, Pablo (2011) Clustering Nodes in Large-Scale Biological Networks Using External Memory Algorithms. Lecture Notes in Computer Science, v. 7017, p. 375-386. doi:10.1007/978-3-642-24669-2 36

  • Meneses, H.; Inostroza-Ponta, M., (2011) Evaluating Memory Schemas in a Memetic Algorithm for the Quadratic Assignment Problem, Computer Science Society (SCCC), 2011 30th International Conference of the Chilean , vol., no., pp.14,18, 9-11 Nov. 2011. doi: 10.1109/SCCC.2011.3

  • M. Inostroza-Ponta, A. Mendes, R. Berretta and P. Moscato. (2007) An integrated QAPbased approach to visualize patterns of gene expression similarity. ACAL 2007 C The Third Australian Conference on Arti cial Life. Lecture Notes in Artificial Intelligence, vol 4828, pp 156-167.

  • M. Inostroza-Ponta, R. Berretta, A. Mendes, and P. Moscato (2006), An automatic graph layout procedure to visualize correlated data. IFIP 19th World Computer Congress. In Artificial Intelligence in Theory and Practice ser. IFIP International Federation for Information Processing, M. Bramer, Ed., vol. 217. Springer, pp. 179-188.

  • M. Solar and M. Inostroza (2004), A Scheduling Algorithm to Optimize Real-World Applications. ICDCSW 04: Proceedings of the 24th International Conference on Distributed Computing Systems Workshops-W7: EC (ICDCSW04). IEEE Computer Society, pp. 858-862.

Theses

2020

  • Master thesis - Metaheurística basada en el algoritmo NSGA-II para el problema de predicción de la estructura terciaria de proteínas. Aliaga, S. (2020)

2019

  • Graduate thesis - Algoritmo genérico para el problema de escalamiento multidimensional multi-objetivo. Giglio, J. (2019)

  • Graduate thesis - Caracterización de la clasificación de los establecimientos públicos de salud en Chile según complejidad mediante la identificación de variables asociadas a casuística hospitalaria. Carlier-González, Á. (2019)

2018

  • Graduate thesis - Método de clustering multi-objetivo para el análisis de datos de expresión génica. Villagrán, A. (2017)

2017

  • Phd thesis - Clustering difuso multi-objetivo de genes basado en información biológica externa y datos de expresión génica. Párraga-Álava, J. (2017)

  • Phd thesis - Inferencia filogenética multi-objetivo considerando fenómenos reticulares. Villalobos-Cid, M. (2017)

  • Master thesis - Metaheurística basada en conocimiento para el problema de docking molecular. Ruiz-Tagle, B. (2017)

  • Master thesis - Algoritmo memético para el problema de asignación cuadrática Bi-Objetivo. Sandoval, R. (2017)

  • Graduate thesis - Aplicación móvil para apoyar la comunicación entre apoderados y transportistas escolares. Vergara, A. (2017)

2016

  • Master thesis - Algoritmo memético para problema de docking de proteina rígida y ligando flexible. González, F. (2016)

  • Graduate thesis - Algoritmo basado en GPU para apoyar el diseño de primers con enzimas de restricción para clonación molecular. Moreno, C. (2016)

2015

  • Master thesis - Algoritmo de agrupamiento para datos de expresión génica de RNA-Seg con la incorporación de anotaciones biológicas. Cornejo C. (2015)

<2015

  • Graduate thesis - Construcción de un framework para pipeline de aplicaciones de bioinformática. Figueroa, A. (2014)

  • Graduate thesis - Algoritmo memético para el problema de predicción de la estructura tridimensional de una proteína. Farfán-Pérez, C. (2014)

  • Master thesis - Incorporación de anotaciones géneticas en el algoritmo de agrupamiento MST-KNN. Pavéz-Sandoval, D. (2013)

  • Master thesis - Resolución de situaciones de Ko utilizando heurísticas en Montecarlo Go. Acosta, C. (2012)

  • Graduate thesis - Algoritmo híbrido para el problema de visualización de datos. Bustamante, V. (2011)