Ronnie Alves received his PhD in Computer Science (Artificial Intelligence) from the University of Minho at Braga (Portugal) in April'2008, under the supervision of Prof. Dr. Orlando Belo. While pursuing his PhD studies, he also served as a Visiting Researcher in the Data Mining Group at DAIS Lab in the University of Illinois at Urbana-Champaign, USA) led by Prof. Dr. Jiawei Han and in the Bioinformatics Research Group at Pablo de Olavide University – Sevilla, Spain) led by Prof. Dr. Jesus Aguilar-Ruiz

Before starting his Ph.D, he also worked as IT Consultant on several industrial data mining projects (From Retail to Telecommunications) in Brazil and Portugal. He was awarded a Postdoctoral Fellowship (Transcriptomics) from the French National Center for Scientific Research (CNRS) in the Virtual Biology Lab at the Institute of Biology Valrose (iBV) at Nice from September'2008 to March'2010. Followed by another two-year postdoc position on Machine Learning and Bioinformatics at the Institute of Informatics at the Federal University of Rio Grande do Sul (UFRGS). Being also a Collaborating Professor in the Department of Theoretical Informatics.

He worked as Researcher Fellow (Jeune Chercheur) in the Lab. of Computer Science, Robotics and Microelectronics of Montpellier (LIRMM), being a member of the Computational Biology Institute (IBC) at the Université Montpellier (UM) and the Institute for Regenerative Medicine and Biotherapy - CHRU de Montpellier (with the bioinformatics team led by Prof. Thérèse Commes) from September'2014 to February'2016.

He is an Adjunct Researcher in the Environmental Genomics Research Group at the Instituto Tecnologico Vale (ITV).

He holds the position of Collaborating Professor in the Computer Science Graduate's Program of UFPA (PPGCC-UFPA) and in the Professional Master's in Sustainable Use of Natural Resources in Tropical Regions (MProf-ITV). He supervises Ph.D and MSc students in the research area of Intelligent Systems, focusing on bioinformatics and machine learning. He was also a member of the Special Committee on Computational Biology (CE-BioComp) of the Brazilian Computer Society (SBC), from 2014 to 2015.

My research interests include: bioinformatics, machine learning and data mining.

CV: Lattes, Linkedin.

Conferences: X-meeting + BSB'15 , BIOKDD-DEXA'16, BIOKDD-DEXA'17, BRACIS'17

Tutorials: [ECML-PKDD'14, SBSI'12BSB'11]

Projects:

Methods for High-throughput Sequencing AnalysisBioanalysis of cancer genomes and transcriptomes, funding by IBC [2014-2016].

BioFlows: Computational modeling for pattern mining discovery on experimental metagenomics data, funding by the Brazilian National Research Council (CNPq, Universal 14/2012) [2013-2015]

CESM: Center of Excellence on Software for Mining Business [challenge 1: Control & Automation, challenge 2: Logistics, challenge 3: Biodiversity], funding by the Brazilian National Research Council (CNPq, Call MCTI/CT-Info/CNPq Nº 59/2013) [2013-2015]

NEW: Open positions for: a postdoc and a Ph.D. candidate in data science/bioinformatics.

Publications [log]


-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.

-RICHARD, F.D.; ALVES, R.; KAJAVA, A.V. A scoring tool for boundary determination between repetitive and non-repetitive protein sequences. Bioinformatics. 2016.

-LIRA, W.P.; GAMA, F.; BARBOSA, H.; ALVES, R.; SOUZA, C.R.B.: VCloud: adding interactiveness to word clouds for knowledge exploration in large unstructured texts. ACM SAC 2016: 193-198

-JUNIOR, J.F.D.; ALVES, R.; COMMES, T. 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]

-CORREA, L., GOES, F.; ALVES, A.; ALVES, R. Functional network-oriented analysis of environmental metagenomics data. In the 3ème Colloque de Génomique Environnementale Montpellier (GE2015). Montpellier, October 26-28, 2015.

-BEAUMEUNIER, S.; AUDOUX, J.; BOUREAUX, 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] Best Paper Award at BIOKDD-DEXA'15

-LIRA, W. P. ; ALVES, R.; COSTA, J.M.R. ; PESSIN, G. GALVAO, L.; CARDOSO, A.C. ; DE SOUZA, C.R.B. A Visual-Analytics System for Railway Safety Management. IEEE Computer Graphics and Applications, v. 34, p. 52-57, 2014.
-GUIMARAES, J.T.F; SOUZA-FILHO, P.W.M ; ALVES, R; DE SOUZA, E.B; DA COSTA, F.R; REIS, L. S.; SAHOO, P.K.; DE OLIVEIRA MANES, C-L.; SILVA JUNIOR, R.O.; OTI, D.; DALL'AGNOL, R. Source and distribution of pollen and spores in surface sediments of a plateau lake in southeastern Amazonia. Quaternary International, v. xx, p. 1-16, 2014.

-LICHTNOW, D.; ALVES, R.; PASTOR, O.; BURRIEL, V.; OLIVEIRA, J.P.M.: BION2SEL: An Ontology-Based Approach for the Selection of Molecular Biology Databases. 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. 83-90.
-GOES, F.; ALVES, R.; CORREA, L.; CHAPARRO, C; and THOM, L. 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.

-CORREA, L.; ALVES, R.; GOES, F.; CHAPARRO, C; and THOM, L. 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.

-ALVES, R.; MENDES, MARCUS; BONNATO, DIEGO. A Network-Based Meta-analysis Strategy for the Selection of Potential Gene Modules in Type 2 Diabetes. In: 8th Brazilian Symposium on Bioinformatics, 2013, Recife. Advances in Bioinformatics and Computational Biology - Lecture Notes in Computer Science. New York: Springer International Publishing, 2013. v. 8213. p. 160-169.

-MENDOZA, MARIANA R. ; DA FONSECA, GUILHERME C. ; LOSS-MORAIS, GUILHERME ; ALVES, R; MARGIS, ROGERIO ; BAZZAN, ANA L. C. . RFMirTarget: Predicting Human MicroRNA Target Genes with a Random Forest Classifier. Plos One, v. 8, p. e70153, 2013.

-ALVES, R.; FERREIRA, P.; RIBEIRO, J.; BELO, O. Detecting Abnormal Patterns in Call Graphs based on the Aggregation of Relevant Vertex Measures In: 12th Industrial Conference on Data Mining, 2012, Berlin.
-SIMAO, E.M.; SINIGAGLIA, M.; BUGS, C.A., CASTRO, M.A.A.; LIBRELOTTO, G. R.; ALVES, R.; MOMBACH, J. C. M. Induced genome maintenance pathways in pre-cancer tissues describe an anti-cancer barrier in tumor development. Molecular Biosystems (Print), 2012.
-ALVES, R. ; RODRIGUEZ-BAENA, D. S. ; AGUILAR-RUIZ, J. S. Gene Association Analysis: A Survey of Frequent Pattern Mining from Gene Expression Data. Briefings in Bioinformatics, p. 210-224, 2010.