• A data science approach for the identification of molecular signatures of aggressive cancers (https://zenodo.org/record/6368086#.Yois6OhByS4).

• Machine learning analysis of NCBI GSE studies for epigenomics. (https://zenodo.org/record/4291069#.YoisYehByS4)

• Piereck B, Oliveira-Lima M, Benko-Iseppon AM, et al. LAITOR4HPC: A text mining pipeline based on HPC for building interaction networks. BMC Bioinformatics. 2020;21(1):365. Published 2020 Aug 24. doi:10.1186/s12859-020-03620-4

• Barbosa-Silva A, Bratfalean D, Gu W, et al. Presenting and sharing clinical data using the eTRIKS Standards Master Tree for tranSMART. Bioinformatics. 2019;35(9):1562-1565. doi:10.1093/bioinformatics/bty809

• Herzinger S, Gu W, Satagopam V, et al. SmartR: an open-source platform for interactive visual analytics for translational research data. Bioinformatics. 2017;33(14):2229-2231. doi:10.1093/bioinformatics/btx137

• Wethmar K, Barbosa-Silva A, Andrade-Navarro MA, Leutz A. uORFdb--a comprehensive literature database on eukaryotic uORF biology. Nucleic Acids Res. 2014;42(Database issue):D60-D67. doi:10.1093/nar/gkt952

• Soldatos TG, O'Donoghue SI, Satagopam VP, et al. Caipirini: using gene sets to rank literature. BioData Min. 2012;5(1):1. Published 2012 Feb 1. doi:10.1186/1756-0381-5-1

• Barbosa-Silva A, Fontaine JF, Donnard ER, Stussi F, Ortega JM, Andrade-Navarro MA. PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. BMC Bioinformatics. 2011;12:435. Published 2011 Nov 9. doi:10.1186/1471-2105-12-435

• Fontaine JF, Priller F, Barbosa-Silva A, Andrade-Navarro MA. Génie: literature-based gene prioritization at multi genomic scale. Nucleic Acids Res. 2011;39(Web Server issue):W455-W461. doi:10.1093/nar/gkr246

• Barbosa-Silva A, Soldatos TG, Magalhães IL, et al. LAITOR--Literature Assistant for Identification of Terms co-Occurrences and Relationships. BMC Bioinformatics. 2010;11:70. Published 2010 Feb 1. doi:10.1186/1471-2105-11-70

• Soldatos TG, O'Donoghue SI, Satagopam VP, et al. Martini: using literature keywords to compare gene sets. Nucleic Acids Res. 2010;38(1):26-38. doi:10.1093/nar/gkp876

• Fontaine JF, Barbosa-Silva A, Schaefer M, Huska MR, Muro EM, Andrade-Navarro MA. MedlineRanker: flexible ranking of biomedical literature. Nucleic Acids Res. 2009;37(Web Server issue):W141-W146. doi:10.1093/nar/gkp353

• Barbosa-Silva A, Satagopam VP, Schneider R, Ortega JM. (SeedLinkage) Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence. BMC Bioinformatics. 2008;9:141. Published 2008 Mar 5. doi:10.1186/1471-2105-9-141

• Barbosa-Silva A, Pafilis E, Ortega JM, Schneider R. Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases. Genet Mol Res. 2007;6(4):1142-1150. Published 2007 Dec 11.

• Cestari IS, Haver NJ, Barbosa-Silva A, Ramirez MI. PROTOGIM: a novel tool to search motifs and domains in hypothetical proteins of protozoan genomes. Parasitol Res. 2006;98(4):375-377. doi:10.1007/s00436-005-0064-0

2022 (Recife/BR/Online) Oncogene 2020: Northeastern Seminar of Genetics

Organized by: UFPE/UFPI: https://www.instagram.com/oncogene.2022/ 

• Speaker: Identification of Aggressiveness Signatures in Cancer using Data Science and Machine Learning 

2022 (Salvador/BR/Online) I Summer course of Bioinformatics and Synthetic Biology

Organized by: CVBB: https://instagram.com/cvbb2022

• Speaker: Bioinformatics Round Table 

2021 (Recife/BR/Online) XI UFPE's Postgraduate in Genetics Programme Symposium

Organized by: UFPE: https://www.instagram.com/ppgg.ufpe 

• Speaker: One decade of text-mining analysis! Happy anniversary PESCADOR! What's next?

2020           (Rio de Janeiro/BR/Online) I Workshop On-line of Bioinformatics

Organized by: UFMG, https://ufmg.br/ 

• Speaker: Bioinformatics Round Table 

2020           (Rio de Janeiro/BR/Online) 1st international school on Big Data and Epigenomics applied to Public Health 

Organized by: FIOCRUZ, https://portal.fiocruz.br/ 

• Speaker: Transnational Data Integration for Translational Data Science.

2020           (London/UK/Online) London Bioinformatics e-talks series 

Organized by: Imperial College London, https://www.imperial.ac.uk

• Speaker: Machine learning for the stratification of Sjögren’s Syndrome patients using clinical and molecular data.

2020           (London/UK/Online) SMD COVID Research Seminar

Organized by: QMUL/SMD, https://www.qmul.ac.uk/smd/ 

• Speaker: Comorbidities, Co-infections and COVID-19: systems biology approaches to find effective targets for antimicrobial peptides from Brazilian plants to fight the pandemic.

2020           (Brussels/BE) 4th Annual General Meeting - Final Open Meeting

Organized by: CORBEL, https://www.corbel-project.eu/ 

• Speaker: Integrating EU-wide cardiovascular research datasets

2019           (Montevideo/UY) Personalised Medicine Technical Workshop

Organized by: EULAC, www.eulac-permed.eu

• Speaker: Multimodal patient data integration to foster machine-learning aided personalized medicine

2019           (Heidelberg/DE) CORBEL Service Operator and User Meeting

Organized by: CORBEL, https://www.corbel-project.eu

2019           (London/UK) ELIXIR Bioinformatics Suppliers Forum 2019

Organized by: ELIXIR, https://elixir-europe.org/

• Speaker: Clinical, OMICs and Imaging Data Integration

2017            (Barcelona/ES) BioTransR Meeting

Organized by: eTRIKS, http://etriks.org/

·   Speaker: Data exploration using the eTRIKS/ tranSMART platform

2016           (San Diego/USA) The 2016 tranSMART Foundation Annual Meeting

Organized by: tranSMART Foundation, http://transmartfoundation.org/

·   Speaker: Linking tranSMART to brain imaging, connectivity data and vis-tools

2016           (Barcelona/ES) NGS’16 – Next Generation Sequencing Meeting 2016

Organized by: ISCB, http://www.iscb.org

·  Delegate

2015           (Luxembourg/LU) 3rd LCSB International Systems Biomedicine Symposium: Big data in Health Care

Organized by: University of Luxembourg http://www.uni.lu

·  Delegate

2015           (Leuven/BE) EMBL Alumini Meeting

Organized by: EMBL Alumini Association, http://portal.fiocruz.br

·  Speaker: UL Bioinformatics Core Approaches for Translational Bioinformatics

2014           (Rio de Janeiro/BR) International Course on Systems Biology Applied to Parasitology

Organized by: IOC/FIOCRUZ, http://portal.fiocruz.br

·  Lecturer

2014           (Michigan/US) The 2014 tranSMART Foundation Annual Meeting

Organized by: tranSMART Foundation, http://transmartfoundation.org/

·  Delegate

2014           (Boston/US) Intelligent Systems for Molecular Biology (ISMB)

Organized by: ISCB, http://www.iscb.org

·  Delegate

2014           (Toronto/CAN) 7th International Biocuration Conference

Organized by OICR and ISB: http://biocuration2014.events.oicr.on.ca

·   Eifes S, Barbosa-Silva A, Gu W, Satagopam VP, Schneider R (2014) Clinical cata curation in the framework of eTRIKS. In: Proceedings of the 7th International Biocuration Conference. Toronto, Canada.

2014           (Rio Grande do Norte/BR) Europe-Brazil Meeting on Systems and Synthetic Biology (2nd SB-Meeting)

Organized by UFRN and DKFZ: http://www.sb-meeting.com.br 

·  Speaker: Systems biology data integration to speed up the development of better and safer medicines for patients

·   Chair: Symposium 2

2013           (Berlin/DE) Workshop on Molecular Interactions

Organized by: Univ. Potsdam, http://molecularinteractions.de

·  Speaker: Text mining approaches to mine biological knowledge for systems biology

2013           (Berlin/DE) Intelligent Systems for Molecular Biology (ISMB)

Organized by: ISCB, http://www.iscb.org

·  Delegate

2013           (Heidelberg/DE) International Conference on Systems Biology of Human Diseases (SBHD)

Organized by: DKFZ and Harvard Med. School, http://www.sbhd2013.org

·   Delegate

2013           (Luxembourg/LU) 2nd International Systems Biomedicine Symposium

Organized by: Univ. of Luxembourg, http://www.uni.lu  

·  Delegate

2012           (Pernambuco/BR) Brazilian Northeastern Genetics Meeting

Organized by: UNIVASF, http://www.engene.univasf.edu.br/ 

·   Tutor: Mini-course: web-resources applied to the study of biological systems

2012           (Brasilia/BR) Brazilian-German Frontiers in Science and Technology

Organized by: CAPES and AvH Foundation

http://www.humboldt-foundation.de/web/bragfost-2012.html

·   Delegate

2012           (São Paulo/BR) 8th International Conference of the Brazilian Association of Bioinformatics and Computational Biology (X- Meeting)

Organized by: AB3C, http://www.x-meeting.com

·   Speaker: Text Mining for Biological Knowledge Extraction.

·   Covre RA, Lopes KP, Monteiro RA, Brusamarello LCC, Souza EM, Pedrosa FO, Barbosa-Silva A (2012) Wedring: a pipeline for analysis of differential gene expression in RNA-Seq. In: Proceedings of the 8th International Conference of the Brazilian Association of Bioinformatics and Computational Biology (X- Meeting). Campinas – SP, Brazil.

·   Lopes KP, Covre RA, Brusamarello LCC, Wassem R, Souza EM, Pedrosa FO, Barbosa-Silva A (2012) Identification of rice alternatively spliced and new transcripts in response to diazotrophic inoculation using RNA-Seq data. In: Proceedings of the 8th International Conference of the Brazilian Association of Bioinformatics and Computational Biology (X- Meeting). Campinas – SP, Brazil.

·   Lopes KP, Covre RA, Brusamarello LCC, Wassem R, Souza EM, Pedrosa FO, Barbosa-Silva A (2012) RNA-Seq based identification of alternative splicing in transcription start sites of rice mRNAs. In: Proceedings of the 8th International Conference of the Brazilian Association of Bioinformatics and Computational Biology (X- Meeting). Campinas – SP, Brazil.

·   Stussi F, Guedes RLM, Barbosa-Silva A, Ortega JM (2012) Depicting the origin of sumoylation network in Arabdopsis thaliana with text-mining and orthologue clustering tools. In: Proceedings of the 8th International Conference of the Brazilian Association of Bioinformatics and Computational Biology (X- Meeting). Campinas – SP, Brazil.

·   Barbosa-Silva, A. (2010) Integrating biological concepts into protein-protein interactions using text mining. In: Proceedings of the Brasil-Deutschland Systems Biology Meeting (SB-Meeting). Ouro Preto – MG, Brasil.

2011           (Santa Catarina/BR) 7th International Conference of the Brazilian Association of Bioinformatics and Computational Biology (X- Meeting)

Organized by: AB3C, http://www.x-meeting.com

·   Chair: Full paper presentation session.

·   Stussi, F., Guedes, R., Velloso, H., Donnard, E., Ribeiro, H., Fernandes, G., Barbosa-Silva, A., Andrade-Navarro, M., Ortega, J.M. (2011) Depicting the origin of drought response in Arabidopsis thaliana with text-mining and orthologue clustering tools. In: Proceedings of the 6th International Conference of the Brazilian Association of Bioinformatics and Computational Biology (X- Meeting). Florianopolis – SC, Brazil.

·   Barbosa-Silva, A., Fontaine., J.F., Donnard, E., Stussi, F., Ortega, J.M., Andrade-Navarro, M. (2011) Efficient network curation using the text-mining tool PESCADOR. In: Proceedings of the 6th International Conference of the Brazilian Association of Bioinformatics and Computational Biology (X- Meeting). Florianopolis – SC, Brazil.

·   Lopes, K.P., Covre, R.A., Brusamarello-Santos, L.C.C., Wassem, R., Souza, E.M., Pedrosa, F.O., Barbosa-Silva, A. (2011) Initial mapping of rice cDNA short-sequences created by RNA-Seq. In: Proceedings of the 6th International Conference of the Brazilian Association of Bioinformatics and Computational Biology (X- Meeting). Florianopolis – SC, Brazil.

·  Covre, R.A., Lopes, K.P., Brusamarello-Santos, L.C.C., Wassem, R., Souza, E.M., Pedrosa, F.O., Barbosa-Silva, A. (2011) Pipeline for analysis of RNA-Seq short-sequences using open source softwares. In: Proceedings of the 6th International Conference of the Brazilian Association of Bioinformatics and Computational Biology (X- Meeting). Florianopolis – SC, Brazil.

2010           Brasil-Deutschland Systems Biology Meeting (SB- Meeting)

·   Speaker: Learning from homologs.

·   Chair: Best-posters oral presentation.

·   Barbosa-Silva, A. (2010) Integrating biological concepts into protein-protein interactions using text mining. In: Proceedings of the Brasil-Deutschland Systems Biology Meeting (SB-Meeting). Ouro Preto – MG, Brasil.

Organized by UFMG and DKFZ: http://www.sb-meeting.com

2009           5th International Conference of the Brazilian Association of Bioinformatics and Computational Biology (X- Meeting)

·   Chair: Lecture 4: Comparative Metagenomics. Peer Bork – EMBL Heidelberg.

·   Speaker: PESCADOR: concepts associated to co-occurrences relationships.

·   Guedes, R.L.M., Fernandes, G.D.R., Coelho-Junior, O.S., Ribeiro, H.A.L., Barbosa-Silva, A., Ortega, J.M. (2009) Survey of phosphate kinases in 17.65 million metagenomics sequences using clusters of homologues built with SeedServer. In: Proceedings of the 5th International Conference of the Brazilian Association of Bioinformatics and Computational Biology (X- Meeting). Angra dos Reis – RJ, Brasil.

·   Donnard, E., Barbosa-Silva, A., Ortega, J.M. (2009) In pursuit of a KEGG-like pathway for the preimplantation development using the text mining tool LAITOR to reveal biointeractions. In: Proceedings of the 5th International Conference of the Brazilian Association of Bioinformatics and Computational Biology (X- Meeting). Angra dos Reis – RJ, Brasil.

Organized by AB3C: http://www.x-meeting.com

2009           I Pernambuco Bioinformatics Workshop

·   Speaker

2009           6th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics – CIBB

·   Chair

Organized by Univ. of Genova (Italy): http://cibb09.disi.unige.it/

2009           2nd German National Genome Research Network (NGFN) Meeting

·   Fontaine, J.-F., Barbosa-Silva, A.; Spruth, E., Priller, J., Andrade-Navarro, M.A. Hypothesis generation for neurodegenerative diseases pathogenesis using text-mining

Organized by BMBF: http://www.bmbf.de/

2008           1st German National Genome Research Network (NGFN) Meeting

·   Fontaine, J.-F., Barbosa-Silva, A.; Andrade-Navarro, M.A. Ranking the biomedical Literature for optimized experimental designs

Organized by BMBF: http://www.bmbf.de/

2007           53° Brazilian Congress of Genetics

·   Barbosa-Silva, A.; Satagopam, V.P.; Schneider, R.; Ortega, J.M. Clustering of inparalog and co-ortholog proteins in clusters founded by single seeds.

Organized by SBG: http://www.sbg.org.br

2007           I Workshop of the UFMG’s Bioinformatics PhD Course.

·   Speaker: Mineração de texto, agrupamento de seqüências e integração de dados para contrução de uma base de dados on-line de proteínas de defesa em plantas.

Organized by Bioinformática - UFMG: http://www.bioinfo.icb.ufmg.br

2005           I International Workshop on Genomic Databases

·   Cestari, I.S.; Barbosa-Silva, A.; Araya, M.I.R. Functional Analyses of Trypanosomatids Hypothetical Proteins.  

Organized by FIOCRUZ: http://www.biowebdb.org/iwgd05/

2005           1st International Conference of the Brazilian Association of Bioinformatics and Computational Biology (X- Meeting)

·   Committee member;

·   Barbosa-Silva, A., Mudado, M., Ortega, J. M. (2005). Plant Defense Mechanisms Database (PDM): Building and Evaluation. In: Proceedings of the 1st International Conference of the Brazilian Association of Bioinformatics and Computational Biology (X- Meeting). Caxambu – MG, Brasil.

·   Casanova, F. M., Andrade, P. P., Kido, E. A., Cavalcanti, E. S., Rayol, C. A., Barbosa, A. (2005). Patterns of gene expression from Leishmania ProGeNE cDNA libraries. In: Proceedings of the 1st International Conference of the Brazilian Association of Bioinformatics and Computational Biology (X- Meeting). Caxambu – MG, Brasil.

·   Rates, B. Barbosa-Silva, A., Nascimento, D. G., Santos, D. M., Braga, T. V., Dutra, A. A. A., Lima, M. E., Pimenta, A. M. C. (2005). Machine learning-based clustering analysis of venom 2D-LC/MS data to infer phylogenetic relationships in scorpions from the Buthidae family. In: Proceedings of the 1st International Conference of the Brazilian Association of Bioinformatics and Computational Biology (X- Meeting). Caxambu - MG, Brasil.

·   Barbosa, D. V. C., Faria-Campos, A. C., Barbosa, A., Ortega, J. M. (2005). Identification of the divergent genes in group of paralogs from microorganisms with complete genome. In: Proceedings of the 1st International Conference of the Brazilian Association of Bioinformatics and Computational Biology (X-Meeting). Caxambu - MG, Brasil.

Organized by AB3C: http://www.x-meeting.com

2005           VIII ICB Research Meeting / III Annual Meeting for Research in Biochemistry and Immunology (ENAPEBI)

Organized by ICB/UFMG: http://www.icb.ufmg.br

2005           51° Brazilian Congress of Genetics

·   Barbosa, A., Mudado, M. A., Ortega, J. M. (2005) PDM, A Plant Defense Mechanism Database Suitable For Automatic Annotation and Classification. In: Anais do 51° Congresso Brasileiro de Genética. Águas de Lindóia – SP, Brasil.

Organized by SBG: http://www.sbg.org.br

2004           II International Conference on Bioinformatics and Computational Biology

·   Mudado, M. A., Pinto, S. A. P., Barbosa, A. S., et al. (2004). A Picture of the Sampling of Gene Expression In Model Metazoa Using EST And KOG Proteins. In: II International Conference on Bioinformatics and Computational Biology. Angra dos Reis – RJ, Brasil.

·   Barbosa, A., Benko-Iseppon, A. M. (2004). In silico screening of tomato disease resistance pathway in sugarcane transcriptome. In: II ICOBICOBI - International Conference on Bioinformatics and Computational Biology. Angra dos Reis – RJ, Brasil.

Organized by AB3C: http://www.ab3c.org

2003           III Brazilian Biosafety Conference and III Latin-American Symposia on GMO Products .

·   Committee member;

Organized by the Brazilian Biosafety Association: http://www.anbio.org.br

2003           49° Brazilian Congress of Genetics

·   Barbosa, A., Morais, D. A. L., Benko-Iseppon, A. M. (2003). Data mining approach used to characterize putative disease resistance gene Pti1 on sugarcane transcriptome. In: Anais do 49° Congresso Brasileiro de Genética. Águas de Lindóia – SP, Brasil.

Organized by SBG: http://www.sbg.org.br

2002           XXXV Phytopathology Brazilian Congress

·   Barbosa, A., Morais, D. A. L., Benko-Iseppon, A. M. (2002). Sugarcane ESTs Data Mining revels homolog sequences to Lr10 gene from wheat. In: Anais do XXXV Congresso Brasileiro de Fitopatologia. Recife – PE, Brasil.

Organized by Brazilian Society of Phytopathology: http://www.sbfito.com.br/

2002           48° Brazilian Genetics Congress

·   Barbosa, A., Morais, D. A. L., Benko-Iseppon, A. M. (2003). In silico screening of sugarcane homolog sequences to tomato Pto R-gene. In: Proceedings of the 48th Brazilian Congress of Genetics. Águas de Lindóia – SP, Brasil.

Organized by SBG: http://www.sbg.org.br

2002           I Brazilian Congress of University Extension.

Organized by the Forum of the pro-rectories for extension of the Brazilian public universities: http://www.renex.org.br/

2001           IX UFPE’s Scientific Initiation Conference

·   Barbosa, A., Morais, D. A. L., Benko-Iseppon, A. M. (2001). Análise comparativa de genes de resistência a bactéria Pseudomonas syringae de Arabidopsis thaliana no genoma da cana-de-açúcar. In: Anais do XI Congresso de Iniciação Científica da UFPE. Recife – PE, Brasil.

Organized by UFPE: http://www.ufpe.br

2001           Workshop of the technology-based enterprises of the Pernambuco state.

Organized by FACEPE: http://www.facepe.br

2001           Parasitic Proteomics Workshop

Organized by FACEPE: http://www.facepe.br

2001           Workshop: Research, venture-capital and the Brazilian biotechnology industries, the experience of FK-Biotecnologia S.A.

Organized by FACEPE: http://www.facepe.br

2001           Workshop: Pernambuco State Biotechnology Program

Organized by FACEPE: http://www.facepe.br

2001           V UPE’s Scientific Initiation Workshop

Organized by FACEPE: http://www.facepe.br

2001           Workshop: Technologic opportunities of Genomics

Organized by FACEPE: http://www.facepe.br

2000           Building the pedagogic Project of the UFPE

Organized by UFPE: http://www.ufpe.br

2000           VIII UFPE’s Scientific Initiation Conference

Organized by UFPE: http://www.ufpe.br

2000           X EREB-NE: National Meeting of the Brazilian North-eastern Students

Organized by UFPI: http://www.ufpi.br