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Projects:
DNA barcoding of plants that form the Flora of Carajás: sequencing and computational tools, funding by the Coordination for the Improvement of Higher Education Personnel (CAPES/ITV nº 20/2016) [2016-2018]
Methods for High-throughput Sequencing Analysis: Bioanalysis of cancer genomes and transcriptomes, funding by IBC [2014-2016].
- with Prof. Thérèse Commes at the Institute for Regenerative Medicine and Biotherapy (CHU, Montpellier).
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]
NEWs:
Brazilian Symposium on Bioinformatics (BSB) 2019
Montpellier Omics Days (MOD) 2019
Machine learning course at PPGCC-UFPA, Kaggle InClass Competition 2018
Master's Programme (PPGCC-UFPA): [Call] [Research]
-- Machine learning, 2016/2 (available in portuguese): [Site] [Competition]
Profissional Master's course (ITV)
-- Applied Statistics, 2016/2 (available in portuguese): [Site]
Current projects [log]
Methods for High-throughput Sequencing Analysis: Bioanalysis of cancer genomes and transcriptomes, funding by IBC [2014-2016].
- with Prof. Thérèse Commes at the Institute for Research in Biotherapy.
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]
(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. Link for the paper to review.
(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. (May-2014) The Brazilian Symposium on Bioinformatics (BSB) 2014 will take place in Belo Horizonte, MG, Brazil, October 28-30, 2014. This year BSB will be co-located with the X-meeting and the ISCB Latin America Conference 2014.
(May-2014) Seminar entitled “Modelagem computacional para a descoberta de padrões e tendências em dados experimentais gerados em estudos metagenômicos”, às 12h45min, 7 de maio, no Auditório Prof. Castilho do INF-UFRGS, Porto Alegre, RS, Brazil.
(April-2014) Our Tutorial entitled "The Pervasiveness of Machine Learning in Omics Science" has been accepted for the ECML/PKDD 2014.
(February-2014) I am now a member of the Special Committee on Computational Biology (CE-BioComp) of the Brazilian Computer Society (SBC). (information available only in Portuguese)
(PPGCC-2013) Machine Learning (ML) course (only in Portuguese) [PPGCC-UFPA], collaboration with Prof. Jefferson Morais. [2013--2]
- Graduate students in the ML course must submit their solution to our Kaggle competition up to 11:59 pm, Monday 9 December 2013 UTC.
(November-2013) I am now holding a position of Collaborating Professor in the Computer Science Master's Program of UFPA. (information available only in Portuguese)
- I am able to supervise up to three graduate students on Machine Learning in Bioinformatics. Candidates must have a basic background on machine learning, theory of computation and bioinformatics.
(July-2013) Our paper presenting a network-based meta-analysis strategy for the selection of potential gene regulatory modules in Type 2 Diabetes (T2D) has been accepted to the Brazilian Symposium on Bioinformatics (BSB & X-Meeting 2013). The basis to retrieve such potential gene modules relies on the proper inference of weighted gene co-expression networks from associated T2D transcriptomic studies.
- ALVES et al. A Network-based Meta-analysis Strategy for the Selection of Potential Gene Modules in Type 2 Diabetes.
(June-2013) Our framework RFMirTarget for predicting human MicroRNA target genes with a random forest classifier has been accepted to the PLOS ONE journal. Experiments have shown that RFMirTarget outperforms several well-known classifiers with statistical significance, and that its performance is not impaired by the class imbalance problem or features correlation.
- MENDOZA et al. Predicting Human MiRNA Targets with Random Forests.
(Mar-2013) Our paper presenting a temporal analysis of the the main hydrodynamic processes acting on tidal flats of the coast of Amapá near the mouth of the Amazon River has been accepted to the Earth Surface Processes and Landforms journal.
- GUIMARÃES et al.Recent effects of tidal and hydro-meteorological changes on coastal plains near the mouth of the Amazon River.
(Mar-2013) ITV DS is offering a Master program on Sustainable Use of Natural Resources in Tropical Regions. (information available only in Portuguese).
- I am able to supervise one candidate either on Environmental Monitoring [predictive analytics] or Biodiversity [metagenomic data-mining] (2013-2014). Candidates must have a good background on machine learning, theory of computation and econometrics.
(Jan-2013) The following entries will be published in the Encyclopedia of System Biology by Springer in 2013. Editors-in-chief: Werner Dubitzky; Olaf Wolkenhauer; Kwang-Hyun Cho; Hiroki Yokota, Springer (print and online).
- ALVES, R. Biomarkers, Ranking.
- ALVES, R. Gene Expression Biomarkers, Ranking.
(Jan-2013) Our paper describing a gene clustering research on hypothesizing the alterations of pre-cancer samples comprise a possible barrier of cancer development has been accepted to the Molecular BioSystems journal.
- SIMAO et al. Induced genome maintenance pathways in pre-cancer tissues describe an anti-cancer barrier in tumor development.
(Dec-2012) Be invited to the Program Commitee of the book Data Mining Applications with R by Elsevier.
(May -2012) Short course on Introduction to Business Process Management and Artificial Intelligence on Bioinformatics at the Braziliam Symposium on Information Systems SBSI'2012 (Sao Paulo, Brazil, May.16-18,2012)
(Aug-2011) Short course on Transcriptome Data Mining at the Braziliam Symposium on Bioinformatics BSB-EBB'2011 (Brasilia, Brazil, Aug.7-9,2011)