  | Herzinger, S., Gu, W., Satagopam, V., Eifes, S., Rege, K., Barbosa Da Silva, A., & Schneider, R. (2017). SmartR: An open-source platform for interactive visual analytics for translational research data. Bioinformatics. doi:10.1093/bioinformatics/btx137  Peer reviewed |
  | Trindade, D., Orsine, L. A., Barbosa Da Silva, A., Donnard, E. R., & Ortega, J. M. (2015). A guide for building biological pathways along with two case studies: hair and breast development. Methods, 74, 16-35. doi:10.1016/j.ymeth.2014.10.006 Peer Reviewed verified by ORBi |
 | Wethmar, K., Barbosa Da Silva, A., Andrade-Navarro, M. A., & Leutz, A. (2014). uORFdb--a comprehensive literature database on eukaryotic uORF biology. Nucleic Acids Research, 42 (1), 60-7. doi:10.1093/nar/gkt952 Peer Reviewed verified by ORBi |
 | Donnard, E., Barbosa Da Silva, A., Guedes, R. L. M., Fernandes, G. R., Velloso, H., Kohn, M. J., Andrade-Navarro, M. A., & Ortega, J. M. (2011). Preimplantation development regulatory pathway construction through a text-mining approach. BMC Genomics, 12 Suppl 4, 3. doi:10.1186/1471-2164-12-S4-S3 Peer Reviewed verified by ORBi |
 | Barbosa Da Silva, A., Fontaine, J.-F., Donnard, E. R., Stussi, F., Ortega, J. M., & Andrade-Navarro, M. A. (2011). PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. BMC Bioinformatics, 12, 435. doi:10.1186/1471-2105-12-435 Peer Reviewed verified by ORBi |
 | Fontaine, J.-F., Priller, F., Barbosa Da Silva, A., & Andrade-Navarro, M. A. (2011). Genie: literature-based gene prioritization at multi genomic scale. Nucleic Acids Research, 39 (Web Server issue), 455-61. doi:10.1093/nar/gkr246 Peer Reviewed verified by ORBi |
 | Barbosa Da Silva, A., Soldatos, T. G., Magalhaes, I. L. F., Pavlopoulos, G. A., Fontaine, J.-F., Andrade-Navarro, M. A., Schneider, R., & Ortega, J. M. (2010). LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships. BMC Bioinformatics, 11, 70. doi:10.1186/1471-2105-11-70 Peer Reviewed verified by ORBi |
 | Pavlopoulos, G. A., Soldatos, T. G., Barbosa Da Silva, A., & Schneider, R. (2010). A reference guide for tree analysis and visualization. BioData Mining, 3 (1), 1. doi:10.1186/1756-0381-3-1 Peer Reviewed verified by ORBi |
 | Soldatos, T. G., O'Donoghue, S. I., Satagopam, V., Jensen, L. J., Brown, N. P., Barbosa Da Silva, A., & Schneider, R. (2010). Martini: using literature keywords to compare gene sets. Nucleic Acids Research, 38 (1), 26-38. doi:10.1093/nar/gkp876 Peer Reviewed verified by ORBi |
 | Fontaine, J.-F., Barbosa Da Silva, A., Schaefer, M., Huska, M. R., Muro, E. M., & Andrade-Navarro, M. A. (2009). MedlineRanker: flexible ranking of biomedical literature. Nucleic Acids Research, 37 (Web Server issue), 141-6. doi:10.1093/nar/gkp353 Peer Reviewed verified by ORBi |
 | Barbosa Da Silva, A., Satagopam, V., Schneider, R., & Ortega, J. M. (2008). Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence. BMC Bioinformatics, 9, 141. doi:10.1186/1471-2105-9-141 Peer Reviewed verified by ORBi |
 | Fernandes, G. R., Barbosa Da Silva, A., Prosdocimi, F., Pena, I. A., Santana-Santos, L., Coelho Junior, O., Barbosa-Silva, A., Velloso, H. M., Mudado, M. A., Natale, D. A., Faria-Campos, A. C., Aguiar, S. C. V., & Ortega, J. M. (2008). A procedure to recruit members to enlarge protein family databases--the building of UECOG (UniRef-Enriched COG Database) as a model. Genetics and Molecular Research, 7 (3), 910-24. doi:10.4238/vol7-3X-Meeting008 Peer Reviewed verified by ORBi |
 | Wanderley-Nogueira, A. C., Soares-Cavalcanti, N. M., Morais, D. A. L., Belarmino, L. C., Barbosa Da Silva, A., & Benko-Iseppon, A. M. (2007). Abundance and diversity of resistance genes in the sugarcane transcriptome revealed by in silico analysis. Genetics and Molecular Research, 6 (4), 866-89. Peer Reviewed verified by ORBi |
Barbosa Da Silva, A., Pafilis, E., Ortega, J. M., & Schneider, R. (2007). Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases. Genetics and Molecular Research, 6 (4), 1142-1150. Peer Reviewed verified by ORBi |
 | Nascimento, D. G., Rates, B., Santos, D. M., Verano-Braga, T., Barbosa Da Silva, A., Dutra, A. A. A., Biondi, I., Martin-Eauclaire, M. F., De Lima, M. E., & Pimenta, A. M. C. (2006). Moving pieces in a taxonomic puzzle: venom 2D-LC/MS and data clustering analyses to infer phylogenetic relationships in some scorpions from the Buthidae family (Scorpiones). Toxicon : official journal of the International Society on Toxinology, 47 (6), 628-39. doi:10.1016/j.toxicon.2006.01.015 Peer reviewed |
 | Cestari, I. S., Haver, N. J., Barbosa Da Silva, A., & Ramirez, M. I. (2006). PROTOGIM: a novel tool to search motifs and domains in hypothetical proteins of protozoan genomes. Parasitology research, 98 (4), 375-7. doi:10.1007/s00436-005-0064-0 Peer reviewed |