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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 Developmental Biology and Cancer (IBDC) 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.

From April'2012 to August'2014, he was an Adjunct Researcher leading Data Analytics projects in the Environmental Monitoring Research Group at the Vale Institute of Technology (ITV Vale).

He holds the position of Collaborating Professor in the Computer Science Master's Program of UFPA (PPGCC-UFPA) and in the Professional Master’s Program – ITV Vale. He supervises graduate students in the research area of Intelligent Systems, focusing on Machine Learning and Bioinformatics.

He is a member of the Committee on Computational Biology (CE-BioComp) of the Brazilian Computer Society (SBC).

Currently he is a Researcher Fellow in the Lab. of Computer Science, Robotics and Microelectronics of Montpellier (LIRMM), being a member of the team Methods and Algorithms for Bioinformatics (MAB) and the Institute of Computational Biology (IBC) at the Université Montpellier 2 (UM2). I am focusing on developing computational methods for Scientific Data Analysis.

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

Tutorials: [ECML-PKDD'14, BSB'11] 

Current projects

Methods for High-throughput Sequencing Analysis:  Bioanalysis of cancer genomes and transcriptomes, funding by IBC [2014-2015].

BioFlows: Computational modeling for pattern mining discovery on experimental metagenomics data, funding by the Brazilian National Research Council (CNPq, Universal 14/2012) [2013-2014]

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]

  • Six(6) Research fellowships are available in the Young Talents Program and several other DTI-TIC positions at many levels (depends on professional experience). See the CESM call here. 

Social Nets: LinkedIn, ResearcherID , ResearchGate.

Curriculum: Lattes[br], CV, TeachingStatement, ResearchStatement.

NEWS [log]


(October-2014) Call (Processo Seletivo 2015) for the Computer Science Master's Program of UFPA (PPGCC-UFPA).
  • I am able to supervise one student on machine learning and computational biology.
(October-2014) Seminar entitled "The Pervasiveness of Machine Learning in Omics Science" presented at the plenary sessions of the IBC.

(August-2014) Three papers accepted at the Brazilian Symposium on Bioinformatics (BSB) 2014. Congrats Daniel, Leandro e Fabiana!
  • Lichtnow et al. BION2SEL: An Ontology-based Approach for the Selection of Molecular Biology Databases.
  • Corrêa et al. FUNN-MG: A Metagenomic Systems Biology Computational Framework.
  • Góes et al. Towards an Ensemble Learning Strategy for Metagenomic Gene Prediction.
(July-2014) Two papers accepted at Dynamic Networks and Knowledge Discovery (DyNaK II) and New Frontiers in Mining Complex Patterns (NFmcp) workshops of the ECML/PKDD 2014. Congrats Leandro e Fabiana!
  • Corrêa et al. A pipeline for functional and visual analytics of microbial genetic networks.
  • Góes et al. A comparison of classification methods for gene prediction in metagenomics.
(April-2014) Our Tutorial entitled "The Pervasiveness of Machine Learning in Omics Science" has been accepted for the ECML/PKDD 2014.

Publications


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

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

-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.

-GUIMARAES, J. T. F. ; COHEN, M. C. L. ; FRANCA, M. C. ; PESSENDA, L.C.R ; SOUZA, E.J. ; NOGUEIRA, A.C.R. ; ALVES, R. . Recent effects of tidal and hydro-meteorological changes on coastal plains near the mouth of the Amazon River. Earth Surface Processes and Landforms (Print), v. 1, p. n/a-n/a, 2013.

-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.
-LICHTNOW, D.; LEVIN, A.; ALVES, R.; CASTELLO, I. M.; PULIDO, L.; DOPAZO, J.; PASTOR, O.; OLIVEIRA, J.P.M. Using Metadata and Web Metrics to Create a Ranking of Genomic Databases. In: IADIS WWW/Internet 2011, 2011, Rio de Janeiro. IADIS WWW/Internet 2011.
-LICHTNOW, D.; ALVES, R. ; OLIVEIRA, J.P.M.; LEVIN, A.; PASTOR, O.; CASTELLO, I. M.; DOPAZO, J. Using Papers Citations for Selecting The Best Genomic Databases. In: 30th International Conference of the Chilean Computer Science Society, 2011, Curico. The Jornadas Chilenas de Computación (JCC), 2011.
-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.