STIC AMSUD

AICaBI: Artificial Intelligence for Cancer Biomarkes Identification
Will the development and integration of meta-heuristics, machine learning and biological annotation data deliver high-quality solutions for the identification of cancer biomarkers?
January 2021 to December 2023
Researchers Students Study Missions Work Missions Thesis Publications

The current scenario is characterized by a technical capacity to produce large-scale data that goes beyond our analytical capacity for interpretation. The comprehensive characterization of genomic, epigenomic, transcriptomic and proteomic alterations in pathological states, especially when correlated with clinical characteristics, has a great potential to improve the diagnosis and prognosis of diseases, and especially, to enable the practice of personalized medicine in the reality of care activities. This project comprises four big areas: Computational Sciences, Molecular Biology, Bioinformatics and Health Sciences. The aim of this project is to contribute to the personalized medicine seeking, through the development of computational methods and strategies in a Bioinformatic context, to improve the creation of preventive measures for cancer, as well as to advance in diagnosis and prognosis precision of the disease. The main research question that leads this project is: "Will the development and integration of meta-heuristics, machine learning and biological annotation data deliver high-quality solutions for the identification of cancer biomarkers?"

Researchers

Dr. Márcio Dorn - Coordinator
INF/UFRGS - Brazil

Dr. Ana Lúcia Cetertich Bazzan - Researcher
INF/UFRGS - Brazil

Dr. Santiago Valdés Ravelo - Researcher
INF/UFRGS - Brazil

Dr. Bruno César Feltes - PosDoc
INF/UFRGS - Brazil

Dr. Joice de Faria Poloni - PosDoc
INF/UFRGS - Brazil

Dr. Clarice Sampaio Alho - Researcher
LGHM/PUCRS - Brazil

Dr. Mario Inostroza-Ponta - Coordinator
DIINF/USACH - Chile

Dr. Juliana Silva Bernardes - Coordinator
LCQB/UPMC - France

Dr. Eduardo Filipe Avila Silva - Researcher
INCT FORENSE/PUCRS - Brazil

Dr. Manuel Villalobos-Cid - Researcher
DIINF/USACH - Chile

Dr. Hugues Ripoche - Researcher
LCQB/UPMC - France

Dr. Manuel Escalona - PosDoc
INF/UFRGS - Brazil

Graduate Students/Collaborators

Pedro Henrique Narloch
Ph.D. finished in Nov, 2021.
PPGC/INF/UFRGS - Brazil

Mateus Boiani
Ph.D. Candidate
PPGC/INF/UFRGS - Brazil

Bruno Iochins Grisci
Ph.D. Candidate
PPGC/INF/UFRGS - Brazil

Bruna Missaggia
Ph.D. Candidate
PPGBM/IB/UFRGS - Brazil

Gabriel Dominico
Ph.D. Candidate
PPGC/INF/UFRGS - Brazil

Nika Abdollahi
Ph.D. Candidate
LCQB/UPMC - France

Flavielle B. Marques
Ph.D. Candidate
PPGC/INF/UFRGS - Brazil

Gabriela Flores Gonçalves
Ph.D. Candidate
PPGBCM/CBIOT/UFRGS - Brazil

Sebastián Aliaga-Rojas
Ph.D. Candidate
DIINF/USACH - Chile

Study Missions

chile  ✈  brazil
USACH/Chile to UFRGS/Brazil

Ph.D Candidate - DIINF/USACH - Juan Giglio Gutiérrez
July, 2022

Ph.D Candidate - DIINF/USACH - Pamela Landero Sepúlveda
July, 2022

Ph.D Candidate - DIINF/USACH - Sebastián Aliaga Rojas
July, 2022

brazil  ✈  france
UFRGS/Brazil to SU/France

Ph.D Candidate - PPGC/UFRGS - Gabriel Dominico
February, 2022 - March 2023

Ph.D Candidate - PPGBM/UFRGS - Bruna Missaggia
January, 2023 - November 2023

Work Missions

brazil  ✈  german
USACH/Chile to UFRGS/Brazil

Dr. Mario Inostroza-Ponta
July, 2022

Dr. Manuel Villalobos-Cid
July, 2022

Dr. Mario Inostroza-Ponta
September, 2023

Dr. Manuel Villalobos-Cid
September, 2023

brazil  ✈  chile
UFRGS/Brazil to USACH/Chile

Dr. Márcio Dorn
October, 2022 (Funding: USACH)

Dr. Márcio Dorn
December, 2022

france  ✈  brazil
SU/France to UFRGS/Brazil

Dr. Juliana Bernardes
July, 2022

brazil  ✈  france
UFRGS/Brazil to SU/France

Dr. Márcio Dorn
October, 2023

Undergraduate Students

Name: Diego Salinas
Title: Sistema para incorporar conocimiento biológico en processo de clustering multiobjectivo
Level: Undergraduate
Date of Defense: August/2021
University: University of Santiago de Chile
Country: Chile
Advisor: Mario Inostroza-Ponta

Name: Nicolás Mariangel
Title: Clustering multiobjetivo de datos de expresión génica de cáncer incorporando búsqueda local y conocimiento biológico a priori
Level: Undergraduate
Date of Defense: August/2021
University: University of Santiago de Chile
Country: Chile
Advisor: Mario Inostroza-Ponta

Name: Vicente Rivera
Title: Aumentando la diversidad de soluciones en problemas multimodales: operadores de búsqueda sobre el espacio de decisión para clustering multiobjetivo
Level: Undergraduate
Date of Defense: July/2022
University: University of Santiago de Chile
Country: Chile
Advisor: Mario Inostroza-Ponta

Name: Daniel Gómez
Title: Algoritmo de Evolución Diferencial para clustering de datos de expresión génica
Level: Undergraduate
Date of Defense: July/2022
University: University of Santiago de Chile
Country: Chile
Advisor: Mario Inostroza-Ponta

Doctoral and Master Thesis

Name: Bruna Missaggia
Title: Machine Learning for Skin Color Prediction in Admixed Latin American Populations
Level: PhD
Date of Defense: ongoing
University: Federal University of Rio Grande do Sul
Country: Brazil
Advisor: Maria Cátira Bortolini
Co-Advisor: Márcio Dorn

Name: Gabriela Flores Gonçalves
Title: Análise do repertório de linfócitos B em neoplasias linfohematopoieticas
Level: PhD
Date of Defense: ongoing
University: Federal University of Rio Grande do Sul
Country: Brazil
Advisor: Márcio Dorn
Co-Advisor: Joice de Faria Poloni

Name: Nika Abdollahi
Title: B cell receptor repertoire analysis in clinical context: new approaches for clonal grouping, intra-clonal diversity studies, and repertoire visualization
Level: PhD
Date of Defense: 08/07/2021
University: University Pierre et Marie Curie
Country: France
Advisor: Juliana Bernardes

Name: Jorge Cubillos
Title: Multiobjective Feature Selection for Biomarker prediction of Colorectal Cancer
Level: Master
Date of Defense: ongoing
University: University of Santiago de Chile
Country: Chile
Advisor: Mario Inostroza-Ponta
Co-Advisor: Márcio Dorn

Name: Christian Manriquez
Title: Deep Memetic Algorithm for Multiobjective clustering of gene expression Data
Level: Master
Date of Defense: April/2022
University: University of Santiago de Chile
Country: Chile
Advisor: Mario Inostroza-Ponta

Name: Gabriel Dominico
Title: Machine Learning and Metaheuristics for Feature Selection in Biological Problems
Level: PhD
Date of Defense: ongoing
University: Federal University of Rio Grande do Sul
Country: Brazil
Advisor: Márcio Dorn

Name: Flavielle Blanco Marques
Title: Mechanism of attention for the identification of genes relevant to the tumor process
Level: PhD
Date of Defense: ongoing
University: Federal University of Rio Grande do Sul
Country: Brazil
Advisor: Márcio Dorn
Co-Advisor: Bruno César Feltes

STIC AMSUD Workshops

2021 - STIC AmSud Workshop

On October 14, 2021, researchers from groups involved with the Stic Amsud project from Chile, Brazil, and France participated in an online and open-to-community workshop.

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2022 - STIC AmSud Workshop

From July 18 to 21, 2022, the second Workshop of the AICABI Project was held at the Institute of Informatics/ Center for Biotechnology of the Federal University of Rio Grande do Sul, Porto Alegre, Brazil. The event was realized in a hybrid way with the participation of students and researchers from Chile, France, and Brazil

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STIC AMSUD Meetings / Presentations

2021 - First Meeting

Objective: Planning Meeting

2021 - Second Meeting

Objective: Presentation of ongoing projects at DIINF/USACH (Chile)

2021 - Third Meeting

Objective: presentation of ongoing work

2021 - Fourth Meeting

Objective: sandwich PhD plan; Gabriel Dominico Study mission; workshop organization; work missions 2021 and 2022;

2022 - Fifth Meeting

Objective: presentation of ongoing work, Research Meeting at USACH

2022 - Sixth Meeting

Objective: presentation of ongoing work, Research Meeting at USACH

Participation in Events

Tools and Datasets

Publications



Photos Gallery