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Mario Romualdo Inostroza Ponta

Director

UNIVERSIDAD DE SANTIAGO DE CHILE

Santiago, Chile

bioinformatics; combinatorial optimization; graph modelling, multiobjective optimization

Ingeniero Civil en Informática, UNIVERSIDAD DE SANTIAGO DE CHILE. Chile, 2001
Magister en Ingeniería Informática, UNIVERSIDAD DE CHILE. Chile, 2001
Computer Science, The University of Newcastle. Australia, 2008
Docencia Universitaria, UNIVERSIDAD DE SANTIAGO DE CHILE. Chile, 2011

Profesor Asociado Full Time

UNIVERSIDAD DE SANTIAGO DE CHILE

Facultad de Ingeniería

Santiago, Chile

2016 - At present
Profesor Asistente Full Time

UNIVERSIDAD DE SANTIAGO DE CHILE

Ingeniería

Chile

2009 - 2016
Profesor Instructor Full Time

UNIVERSIDAD DE SANTIAGO DE CHILE

Ingeniería

Chile

2002 - 2009

Ingeniero de Proyectos Full Time

NorthSupply

Santiago, Chile

2001 - 2002

PhD supervisions:
completed: 2
ongoing: 1

Master supervision:
completed: 9
ongoing: 2

Undergraduate supervision:
completed: 20
ongoing: 2

Académico Destacado Fac Ingeniería

UNIVERSIDAD DE SANTIAGO DE CHILE

Chile, 2008

Reconocimiento que se entrega anualmente a los académicos que se destacan en su labor durante el año anterior


An evolutionary algorithm based on parsimony for the multiobjective phylogenetic network inference problem Villalobos-Cid, Manuel; Dorn, Marcio; Contreras, Angela; Inostroza-Ponta, Mario Article ISI APPLIED SOFT COMPUTING (2023)
A multi-modal algorithm based on an NSGA-II scheme for phylogenetic tree inference Villalobos-Cid, Manuel; Rivera, Cesar; Kessi-Perez, Eduardo I.; Inostroza-Ponta, Mario Article ISI BIOSYSTEMS (2022)
Improving solution diversity on NSGA-II for multi-objective clustering problems Rivera-Rebolledo, Vicente; Villalobos-Cid, Manuel; Inostroza-Ponta, Mario Article SCOPUS 2018 37TH INTERNATIONAL CONFERENCE OF THE CHILEAN COMPUTER SCIENCE SOCIETY (SCCC) (2022)
Comparison of Phylogenetic Tree Topologies for Nitrogen Associated Genes Partially Reconstruct the Evolutionary History of Saccharomyces cerevisiae Villalobos-Cid, Manuel; Salinas, Francisco; Kessi-Pérez, Eduardo I.; De Chiara, Matteo; Liti, Gianni; Inostroza-Ponta, Mario; Martínez, Claudio Article ISI SCOPUS Microorganisms (2020)
Exploring the high selectivity of 3-D protein structures using distributed memetic algorithms Inostroza-Ponta, Mario; Dorn, Márcio; Escobar, Iván; de Lima Correa, Leonardo; Rosas, Erika; Hidalgo, Nicolás; Marin, Mauricio Article ISI SCOPUS Journal of Computational Science (2020)
Molecular Modeling of Epithiospecifier and Nitrile-Specifier Proteins of Broccoli and Their Interaction with Aglycones Román, Juan; González, Dorian; Inostroza-Ponta, Mario; Mahn, Andrea Article ISI MOLECULES (2020)
A Memetic Algorithm Based on an NSGA-II Scheme for Phylogenetic Tree Inference Villalobos-Cid, M; Dorn, M; Ligabue-Braun, R; Inostroza-Ponta, M Article ISI IEEE TRANSACTIONS ON EVOLUTIONARY COMPUTATION (2019)
A Memetic Algorithm for 3D Protein Structure Prediction Problem Correa, L.; Borguesan B.; Farfan, C; Inostroza-Ponta, M; Dorn, M Article ISI SCOPUS IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2018)
A multi-objective gene clustering algorithm guided by apriori biological knowledge with intensification and diversification strategies Parraga-Alava, J; Dorn, M; Inostroza-Ponta, M Article ISI SCOPUS BIODATA MINING (2018)
Performance Comparison of Multi-Objective Local Search Strategies to Infer Phylogenetic Trees Villalobos-Cid, Manuel; Dorn, Marcio; Inostroza-Ponta, Mario Article 2018 IEEE Congress on Evolutionary Computation (CEC) (2018)
Understanding the Relationship Between Decision and Objective Space in the Multi-Objective Phylogenetic Inference Problem Villalobos-Cid, Manuel; Dorn, Marcio; Inostroza-Ponta, Mario Article 2018 IEEE Congress on Evolutionary Computation (CEC) (2018)
An evolutionary multi-agent algorithm to explore the high degree of selectivity in three-dimensional protein structures Correa, Leonardo de Lima; Inostroza-Ponta, Mario; Dorn, Marcio; IEEE Article ISI 2017 IEEE CONGRESS ON EVOLUTIONARY COMPUTATION (CEC) (2017)
NIAS-Server: Neighbors Influence of Amino acids and Secondary Structures in Proteins Borguesan B.; Inostroza-Ponta M.; Dorn M. Article ISI SCOPUS JOURNAL OF COMPUTATIONAL BIOLOGY (2017)
A New Strategy to Evaluate Technical Efficiency in Hospitals Using Homogeneous Groups of Casemix Villalobos-Cid, M; Chacon M.; Zitko P.; Inostroza-Ponta, M Article ISI SCOPUS JOURNAL OF MEDICAL SYSTEMS (2016)
Evaluation of a combined energy fitness function for a distributed memetic algorithm to tackle the 3D protein structure prediction problem Escobar, I; Hidalgo, N; Inostroza-Ponta, M; Marín, M; Rosas, E; Dorn, M Article International Conference of the Chilean Computer Science Society (SCCC) (2016)
A Memetic Algorithm for Protein Structure Prediction based on Conformational Preferences of Aminoacid Residues Mario Inostroza-Ponta, Camilo Farfán and Marcio Dorn Article Proceedings of the Companion Publication of the 2015 on Genetic and Evolutionary Computation Conference (2015)
APL: An angle probability list to improve knowledge-based metaheuristics for the three-dimensional protein structure prediction Borguesan B.; Silva, MBE; Grisci, B; Inostroza-Ponta, M; Dorn, M Article ISI SCOPUS Computational Biology and Chemistry (2015)
(GTG)(5) MSP-PCR Fingerprinting as a Technique for Discrimination of Wine Associated Yeasts? Ramirez-Castrillon, M; Mendes, SDC; Inostroza-Ponta, M; Valente, P. Article ISI PLOS ONE (2014)
A knowledge-based genetic algorithm to predict three-dimensional structures of polypeptides Dorn, M.; Inostroza-Ponta, M.; Buriol, L.S.; Verli, H. Article IEEE Congress on Evolutionary Computation (CEC), 2013 (2013)
Genome-wide analysis of long noncoding RNA stability Clark M.B.; Johnston R.L.; Inostroza-Ponta, M; Fox A.H.; Fortini E.; Moscato P.; Dinger M.E.; Mattick J.S. Article ISI SCOPUS Genome Research (2012)
Clustering Nodes in Large-Scale Biological Networks Using External Memory Algorithms Ahmed Shamsul Arefin ; Inostroza-Ponta, Mario ; Luke Mathieson ; Berretta, Regina ; Moscato, Pablo Article Lecture Notes in Computer Science (2011)
Evaluating Memory Schemas in a Memetic Algorithm for the Quadratic Assignment Problem Meneses, H and Inostroza-Ponta Article Computer Science Society (SCCC), 2011 30th International Conference of the Chilean (2011)
QAPgrid: A Two Level QAP-Based Approach for Large-Scale Data Analysis and Visualization Inostroza-Ponta, M; Moscato, P; Berretta, R Article PLOS ONE (2011)
A Transcription Factor Map as Revealed by a Genome-Wide Gene Expression Analysis of Whole-Blood mRNA Transcriptome in Multiple Sclerosis Riveros, C; Mellor, D; Gandhi, KS; McKay, FC; Cox, MB; Berretta R.; Vaezpour, SY; Inostroza-Ponta, M; Broadley, SA; Heard, RN; Vucic, S.; Stewart, GJ; Williams, DW; Scott, RJ; Lechner-Scott, J; Booth, DR; Moscato P. Article ISI SCOPUS PLOS ONE (2010)
Is there more than one proctitis syndrome? A revisitation using data from the TROG 96.01 trial Denham, James W.; Matthews, John; Capp, Anne; Atkinson, Chris; Bill, Dana; North, John; Lai, Chi; Poulsen, Michael; Lamb, David; Spry, Nigel A.; Joseph, David; Tai, Keen-Hun; Moscato, Pablo; Wynne, Chris; Turner, Sandra; Duchesne, Gillian; Christie, David; Steigler, Allison; Inostroza-Ponta, Mario Article ISI RADIOTHERAPY AND ONCOLOGY (2009)
Is there more than one proctitis syndrome? A revisitation using data from the TROG 96.01 trial. Radiotherapy and Oncology, v. 90, p. 400-407, 2009. Capp, Anne ; Inostroza-Ponta, Mario ; Bill, Dana ; Moscato, Pablo ; Lai, Chi ; Christie, David ; Lamb, David ; Turner, Sandra ; Joseph, David ; Matthews, John ; Atkinson, Chris ; North, John ; Poulsen, Michael ; Spry, Nigel A. ; Tai, Keen-Hun ; Wynne, Chris ; Duchesne, Gillian ; Steigler, Allison ; Denham, James W. Article Radiotherapy and Oncology (2009)
An integrated QAP-based approach to visualize patterns of gene expression similarity Inostroza-Ponta, Mario ; Mendes, Alexandre; Berretta, Regina; Moscato, Pablo Article Progress in Artificial Life, Lecture Notes in Computer Science (2007)
An automatic graph layout procedure to visualize correlated data Inostroza-Ponta, Mario; Berretta, Regina ; Mendes, Alexandre ; Moscato, Pablo Article Artificial Intelligence in Theory and Practice (2006)
A scheduling algorithm to optimize real-world applications Solar, Mauricio; Inostroza, Mario Article Distributed Computing Systems Workshops, Proceedings. 24th International Conference on (2004)
Using Genetic Algorithms and Tabu Search Parallel Models to Solve the Scheduling Problem Pinacho, Pedro; Solar, Mauricio; Inostroza, Mario; Muñoz, Rosa Article IFIP Advances in Information and Communication Technology (2004)
An automatic scheduler for parallel machines Solar M.; Inostroza, M. Article ISI BIO-INSPIRED SYSTEMS AND APPLICATIONS: FROM ROBOTICS TO AMBIENT INTELLIGENCE, PT II (2002)
A parallel compiler scheduler Solar, Mauricio; Inostroza, Mario Article Computer Science Society, 2001. SCCC'01. Proceedings. XXI Internatinal Conference of the Chilean (2001)


Evaluating the incorporation of Biological Knowledge in multiobjective clustering of gene expression data Mariangel, Nicolas; Giglio, Juan; Aliaga-Rojas, Sebastián; Villalobos-Cid, Manuel; Inostroza-Ponta, Mario ConferencePaper (2023)
A Genetic Algorithm Based on Restricted Tournament Selection for the 3D-PSP Problem Borguesan B.; Narloch P.H.; Inostroza-Ponta M.; Dorn M. ConferencePaper ISI SCOPUS (2018)
Application of different multi-objective decision making techniques in the phylogenetic inference problem Villalobos-Cid M.; Vega-Araya D.; Inostroza-Ponta M. ConferencePaper SCOPUS Proceedings - International Conference of the Chilean Computer Science Society, SCCC (2018)
Evaluating the use of local search strategies for a memetic algorithm for the protein-ligand docking problem Ruiz-Tagle B.; Villalobos-Cid M.; Dorn M.; Inostroza-Ponta M. ConferencePaper SCOPUS Proceedings - International Conference of the Chilean Computer Science Society, SCCC (2018)
Performance Comparison of Multi-Objective Local Search Strategies to Infer Phylogenetic Trees Villalobos-Cid M.; Dorn M.; Inostroza-Ponta M. ConferencePaper ISI SCOPUS (2018)
Tackling the bi-objective quadratic assignment problem by characterizing different memory strategies in a memetic algorithm Sandoval-Soto R.; Villalobos-Cid M.; Inostroza-Ponta M. ConferencePaper SCOPUS Proceedings - International Conference of the Chilean Computer Science Society, SCCC (2018)
A bi-objective model for gene clustering combining expression data and external biological knowledge Parraga-Alava J.; Inostroza-Ponta M. ConferencePaper SCOPUS Proceedings of the 2016 42nd Latin American Computing Conference, CLEI 2016 (2017)
Evaluation of a combined energy fitness function for a distributed memetic algorithm to tackle the 3D protein structure prediction problem Escobar, I; Hidalgo, N; Inostroza-Ponta, M; Marin, M; Rosas, E; Dorn, M ConferencePaper ISI 2020 39TH INTERNATIONAL CONFERENCE OF THE CHILEAN COMPUTER SCIENCE SOCIETY (SCCC) (2016)
A scheduling algorithm to optimize real-world applications Solar M.; Inostroza, M. ConferencePaper ISI 24TH INTERNATIONAL CONFERENCE ON DISTRIBUTED COMPUTING SYSTEMS WORKSHOPS, PROCEEDINGS (2004)
A parallel compiler scheduler Solar M.; Inostroza, M. ConferencePaper ISI SCCC 2001: XXI INTERNATIONAL CONFERENCE OF THE CHILEAN COMPUTER SCIENCE SOCIETY, PROCEEDINGS (2001)


Incorporación de optimización multiobjetivo en WGCNA para el análisis de datos de RNAseq Mario Inostroza-Ponta Proyecto (2024)
A NOVEL MULTIOBJECTIVE STRATEGY TO IDENTIFY SIGNIFICANT GROUPS OF GENES USING HIGH THROUGHPUT DATA AND BIOLOGICAL KNOWLEDGE Inostroza-Ponta, Mario; Villalobos-Cid, Manuel Proyecto (2023)
Ciência de Dados para Aplicações Biotecnológicas: resolvendo desafios de larga escala utilizando aprendizagem de máquina explicável, metaheurísticas e computação de alto desempenho Dorn, Márcio; Inostroza-Ponta, Mario Proyecto (2022)
Interpretabilidade e Métodos de Busca Heurística para Seleção de Features em Dados Biológicos com Alta Dimensionalidade Dorn, Márcio; Inostroza-Ponta, Mario Proyecto (2022)
BIG DATA ANALYTICS TOOL TO ASSESS THE DYNAMIC SECURITY OF INERTIAL AND FREQUENCY RESPONSE IN THE CHILEAN POWER SYSTEM Chavez Oróstica, Héctor; Inostroza-Ponta, Mario Proyecto (2021)
AICaBI: Artificial Intelligence for Cancer Biomarkes Identification Inostroza-Ponta, Mario; Dorn, Márcio; Bernardes, Juliana S. Proyecto (2020)
Biological guided algorithms for multi-objective clustering in bioinformatics Inostroza-Ponta, Mario Proyecto DICYT USACH Regular (2019)
Diseño de modelos multi-objetivo para inferencia filogenética considerando fenómenos reticulares Inostroza-Ponta, Mario; Villalobos-Cid, Manuel Proyecto Proyecto para contratar POSTDOC (2019)
Bioinformática aplicada à medicina personalizada=> do diagnóstico ao tratamento de doenças FAPERGS, Brasil (16/2551-0000 520-6) Proyecto 2017-2018 Investigador(a)
PadMetBio: Parallel and Distributed Metaheuristics for Structural Bioinformatics Inostroza-Ponta, Mario; Dorn, Marcio; Arantes, Luciana; Gil-Costa, Verónica Proyecto (2017)
Parallel and Distributed Metaheuristics for structural bioinformatics PCI (17-STIC-05) Proyecto 2017-2018 Inv. Principal
Centro de Biotecnología y Bioingeniería FONDAP (FB001) Proyecto 2014-2019 Investigador(a)
Aplicação de Técnicas de Aprendizagem de Máquina e Otimização no Desenvolvimento de Estratégias Computacionais para a Predição em Silico da Estrutura Tridimensional de Proteínas FAPERGS, Brasil (002021-25.51/13-7) Proyecto 2013-2015 Investigador(a)
Desenvolvimento de métodos e estratégias computacionais para a predição da estrutura tridimensional de polipeptídeos CNPQ, Brasil (473692/2013-9) Proyecto 2013-2016 Investigador(a)
Federated Cloud Computing for Bioinformatics=> Infrastructure, Algorithms and Applications PCI (13STIC-09) Proyecto 2013-2014 Inv. Responsable
DESIGNING AND CONSTRUCTING A SCALABLE PIPELINE OF GRAPH-BASED METHODS FOR THE ANALYSIS OF GENE EXPRESSION DATA FONDECYT (11121288) Proyecto 2012-2015 Inv. Responsable
SELECCION AUTOMATICA DE ALGORITMO DE ASIGNACION PARA GENERAR CODIGO PARALELO EFICIENTE FONDECYT (1000074) Proyecto 2000-2003 Tesista