Students

Gisele Lopes Nunes, Ph.D. (CV Lattes),

Postdoc: DNA barcoding, metabarcoding, comparative analysis, databases. [start: 2017/3, end: 2018/10 ] [CAPES/ITV nº 20/2016]

Researcher Assistant at ITV.

NUNES et al. Quillworts from the Amazon: A multidisciplinary populational study on Isoetes serracarajensis and Isoetes cangae. PLoS One. 2018. [pdf]
OLIVEIRA et al. PIPEBAR and OverlapPER: tools for a fast and accurate DNA barcoding analysis and paired-end assembly. BMC BIOINFORMATICS. 2018. [pdf]

Luciano de Almeida Alves. (CV Lattes)

Master's student : statistics, multivariate data analysis, anomaly detection. [start: 2017/3 end 2018/5]

Senior Engineer at Vale.

Luciano de Almeida Alves. Testes em Resíduo de Estéril e Minério para Prevenção na Geração de Drenagem Ácida na Mina do Sossego, Carajás - Pará. Dissertação apresentada ao Mestrado Profissional, Uso Sustentável de Recursos Naturais em Regiões Tropicais. Instituto Tecnológico Vale (ITV). Belém, Maio/2018.

Computer Science Graduate's Program (PPGCC) at UFPA

José de Sousa Ribeiro Filho (CV Lattes),

Ph.D. Candidate: machine learning, explainable AI, classification, crime detection. [start: 2020/3]

Lucas Felipe Ferraro Cardoso (CV Lattes),

Master's student: machine learning, classification, item response theory. [start: 2020/3]

Andre do Rosário Quadros (CV Lattes),

Master's student: reinforcement learning, machine learning, optmization. [start: 2020/3]

Vitor Cirilo Araujo Santos (CV Lattes),

Ph.D. Candidate: machine learning, item response theory, latent learning abilities, instance hardness [start: 2019/3]

Researcher Assistant at ITV.

Master's student: clustering analysis, comparative analysis, metagenomics. [start: 2016/3 end: 2018/5 ]

Vitor Santos, Leandro Correa, Bianchi Meiguins, Guilherme Oliveira and Ronnie Alves. Metagenomics-based signature clustering and interactive visualization analysis. In The International Joint Conference on Neural Networks (IJCNN) 2018, Rio de Janeiro, Brazil, July 8-13, 2018. [pdf]
Vitor Cirilo Araujo Santos. MGCOMP: Sistema computacional multiplataforma para análise comparativa de metagenomas. Dissertação apresentada ao Programa de Pós-Graduação em Ciência da Computação (PPGCC). Instituto de Ciências Exatas e Naturais (ICEN). Universidade Federal do Pará (UFPA). Belém, Maio/2018.

Kleber Padovani de Souza (CV Lattes),

Ph.D. Candidate: machine learning, deep learning, reinforcement learning, assembly, metagenomics. [start: 2017/8]

SOUZA, K. P. ; SETUBAL, J. C. ; CARVALHO, A. P. L. ; CHATEAU, A. ; Alves, R. Machine learning meets genome assembly. Briefings in Bioinformatics, v. 1, p. 1, 2018. [pdf]

Raissa Lorena Silva da Silva (CV Lattes),

Master's student: metagenomics, classification, gene predictions, ensemble learning. [start: 2018/3, end: 2020/2]

Raissa Silva, Kleber Padovani, Fabiana Góes. A Random Forest Classifier for Prokaryotes Gene Prediction. In the 8th Brazilian Conference on Intelligent System (BRACIS). Salvador, BA, Brazil, October 15-18, 2019. [pdf]
Raissa Silva. Um classificador random forest para a predição de genes em procariotos. Dissertação apresentada ao Programa de Pós-Graduação em Ciência da Computação (PPGCC). Instituto de Ciências Exatas e Naturais (ICEN). Universidade Federal do Pará (UFPA). Belém, Fevereiro/2020.
-->Área de Concentração: Sistemas Inteligentes; Bioinformática. [dissertacao]

Roberto Brito Xavier Junior (CV Lattes),

Master's student: machine learning, deep learning, assembly, metagenomics. [start: 2018/3, end:2020/2]

Roberto Xavier, Kleber Souza and Ronnie Alves. Genome Assembly using Reinforcement Learning. In the Brazilian Symposium on Bioinformatics (BSB), Fortaleza, CE, Brazil, October 7-10, 2019. [pdf]
- Roberto Xavier. Montagem de genomas usando aprendizado por reforço. Dissertação apresentada ao Programa de Pós-Graduação em Ciência da Computação (PPGCC). Instituto de Ciências Exatas e Naturais (ICEN). Universidade Federal do Pará (UFPA). Belém, Fevereiro/2020.
- -->Área de Concentração: Sistemas Inteligentes; Bioinformática. [dissertacao]

Pedro Paulo Furtado Oliveira Junior (CV Lattes),

Master's student: clustering analysis, binning, taxonomic analysis, metagenomics. [start: 2017/3]

Paulo Oliveira, Kleber Padovani and Ronnie Alves. On Clustering Validation in Metagenomics Sequence Binning. In the Brazilian Symposium on Bioinformatics (BSB), Fortaleza, CE, Brazil, October 7-10, 2019. [pdf]

Alessandra Priscila Alves de Oliveira (CV Lattes),

Master's student: metatranscriptomic, classification, functional analysis. [start: 2015/3 end: 2018/2]

Alessandra Alves, Ronnie Alves. Um pipeline para predição de genes em dados metatranscriptômicos. In the 14 Encontro Nacional de Inteligência Artificial e Computacional (ENIAC). The 6th Brazilian Conference on Intelligent Systems (BRACIS), Uberlandia, Brazil, Outubro 2-5, 2017. [pdf]

Alessandra Alves. GENEFINDER-TR: Um pipeline para a predição de genes em dados metatranscriptômicos. Dissertação apresentada ao Prog`rama de Pós-Graduação em Ciência da Computação (PPGCC). Instituto de Ciências Exatas e Naturais (ICEN). Universidade Federal do Pará (UFPA). Belém, Fevereiro/2018.

Fabiana Rodrigues de Góes (CV Lattes),

Master's student: metagenomics, classification, gene predictions, ensemble learning. [start: 2014/3 end: 2016/2]

PhD candidate at ICMC-USP.

Fabiana Góes, Ronnie Alves, Leandro Corrêa, Cristian Chaparro and Lucinéia Thom. A comparison of classification methods for gene prediction in metagenomics. In the International Workshop on New Frontiers in Mining Complex Patterns (NFmcp). The European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD), Nancy, France, September 15-19, 2014. [pdf]
Fabiana Góes, Ronnie Alves, Leandro Corrêa, Cristian Chaparro and Lucinéia Thom. Towards an ensemble learning strategy for metagenomic gene prediction. In the Brazilian Symposium on Bioinformatics (BSB), Belo Horizonte, MG, Brazil, October 28-30, 2014. To appear in the Lecture Notes in Bioinformatics (LNBI), vol. 8826 Springer, pp.17-24. [pdf]
Fabiana Góes. GENEFINDER-MG: Um pipeline para a predição de genes em dados metagenômicos. Dissertação apresentada ao Programa de Pós-Graduação em Ciência da Computação (PPGCC). Instituto de Ciências Exatas e Naturais (ICEN). Universidade Federal do Pará (UFPA). Belém, Fevereiro/2016.
- -->Área de Concentração: Sistemas Inteligentes; Bioinformática. [dissertacao]

Leandro Henrique Santos Corrêa (CV Lattes),

Master's student: metagenomics, clustering, graph mining, functional analysis, system biology. [start: 2014/3, end: 2016/2]

PhD Candidate at I3S@Unice (France)

Leandro Corrêa, Ronnie Alves, Fabiana Góes, Cristian Chaparro and Lucinéia Thom. A pipeline for functional and visual analytics of microbial genetic networks. In the 2nd International Workshop on Dynamic Networks and Knowledge Discovery (DyNaK). The European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD), Nancy, France, September 15-19, 2014. [pdf]
Leandro Corrêa, Ronnie Alves, Fabiana Góes, Cristian Chaparro and Lucinéia Thom. FUNN-MG: A metagenomic systems biology computational framework. In the Brazilian Symposium on Bioinformatics (BSB), Belo Horizonte, MG, Brazil, October 28-30, 2014. To appear in the Lecture Notes in Bioinformatics (LNBI), vol. 8826 Springer, pp.25-32. [pdf]
Leandro Corrêa, Fabiana Góes, Alessandra Alves and Ronnie Alves. Functional network-oriented analysis of environmental metagenomics data. In the 3ème Colloque de Génomique Environnementale Montpellier (GE2015). Montpellier, October 26-28, 2015. [pdf]
Leandro Corrêa. FUNN-MG: Um pipeline para análise funcional e visual de metagenomas. Dissertação de Mestrado apresentada ao Programa de Pós-Graduação em Ciência da Computação (PPGCC). Instituto de Ciências Exatas e Naturais (ICEN). Universidade Federal do Pará (UFPA). Belém, Fevereiro/2016.
- -->Área de Concentração: Sistemas Inteligentes; Bioinformática.[dissertacao]

José Flávio de Souza Dias Júnior (CV Lattes),

Master's student: transcriptomics, interactomics, clustering, graph mining, system biology, biomarkers. [start: 2014/3, end: 2016/9]

IT Analyst at IFPA - Campus Tucuruí.

José Flávio de Souza Dias Júnior, Ronnie Alves and Therese Commes. A module-based approach for evaluating differential genome-wide expression profiles. In the 5th Brazilian Conference on Intelligent System (BRACIS). Recife, PE, Brazil, October 9-12, 2016. [pdf]
- José Flávio de Souza Dias Júnior. Uma abordagem baseada em módulos para análise de perfis de expressão diferencial de genoma completo. Dissertação de Mestrado apresentada ao Programa de Pós-Graduação em Ciência da Computação (PPGCC). Instituto de Ciências Exatas e Naturais (ICEN). Universidade Federal do Pará (UFPA). Belém, Setembro/2016.
  - -->Área de Concentração: Sistemas Inteligentes; Bioinformática [dissertacao]
- TGRAMS: Tools for Transcriptograms Analysis and Visualization [GitHub], Transmod [GitHub]

Master STIC pour la Santé -- Spécialité (Bioinformatique, Connaissances, Données)

Sacha Beaumeunier, Master's student: [l'UE GMIN115 du Master 2 STIC]

Sacha Beaumeunier, Ronnie Alves. Projet des M1. Étude bibliographique autour de l'analyse des ARN chimères. Montpellier, le 13 janvier 2015.
Beaumeunier, S., Audoux, J., Boureux, A., Commes, T., Philippe, N., Alves, R. The Role of Machine Learning in Finding Chimeric RNAs. 6th International Workshop on Biological Knowledge Discovery and Data Mining (BIOKDD 2015), Valencia, Spain, September 1-4, 2015. [site] [JOBIM'15 poster] Best Paper Award at BIOKDD-DEXA'15

Beaumeunier, S.; Audoux, J.; Boureux, A.; Commes, T.; Fruffle, F.; Alves, R. On the evaluation of the fidelity of supervised classifiers in the prediction of chimeric RNAs. BioData Mining, 2016. [pdf]

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