Periódicos

22. Soardi, F. C. ; Machado-Silva, A. ; Linhares, N. D. ; Zheng, G. E. ; Qu, Q. ; Pena, H. B. ; Martins, T. M. M. ; Vieira, H. G. S. ; Pereira, N. B. ; DE MELO-MINARDI, R. C. ; Gomes, C. C. ; Gomez, R. S. ; Gomes, D. A. ; Pires, D. E. V. ; Ascher, D. B. ; YU, H. ; Pena, S. D. J. . Familial STAG2 germline mutation defines a new human cohesinopathy. npj Genomic Medicine, v. 2, p. 1-11, 2017.


21. Mariano, D. C. B. ; Leite, C. ; Santos, L. H. S. ; Marins, L. F. ; Machado, K. S. ; Wehrli, A. V. ; Lima, L. H. F. ; DE MELO-MINARDI, R. C. . Characterization of glucose-tolerant β-glucosidases used in biofuel production under the bioinformatics perspective: a systematic review. Genetics and Molecular Research, v. 16, p. gmr16039740, 2017.


20. Fassio, A. V. ; Martins, P. M. ; Guimarães, S. DA S. ; Junior, S. S. A. ; Ribeiro, V. S. ; DE MELO-MINARDI, R. C. ; Silveira, S. DE A. . Vermont: a multi-perspective visual interactive platform for mutational analysis. BMC BIOINFORMATICS, v. 18, p. 51-79, 2017.


19. de Lima, E. B. ; Meira Jr., W. ; DE MELO-MINARDI, R.C. . Isofunctional protein subfamily detection using data integration and spectral clustering. PLOS Computational Biology (Online), v. 12, p. e1005001, 2016.


18. Gonçalves, W. R. S. ; Gonçalves-Almeida, V. M. ; Arruda, A. L. ; Meira Jr., W. ; da Silveira, C. H. ; Pires, D. E. V. ; DE MELO-MINARDI, R. C. . PDBest: a user-friendly platform for manipulating and enhancing protein structures. Bioinformatics (Oxford. Print), v. 1, p. 1, 2015.


17. Silveira, S. A. ; DE MELO-MINARDI, R. C. ; Silveira, C. H. ; Santoro, M. M. ; Meira Jr., W. . ENZYMAP: Exploiting protein annotation for modeling and predicting EC number changes in UniProt/Swiss-Prot. Plos One, v. 9, p. e89162, 2014.


16. Izidoro, S. C. ; DE MELO-MINARDI, R. C. ; Pappa, G. L. . GASS: Identifying enzyme active sites with genetic algorithms. Bioinformatics (Oxford. Print), v. 1, p. 1, 2014.


15. Pires, D. E. V. ; DE MELO-MINARDI, R. C. ; da Silveira, C. H. ; Campos, F. F. ; Meira, W. . aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction. Bioinformatics (Oxford. Print), v. 29, p. 855-861, 2013.


14. Bastard, K. ; SMITH, A. A. T. ; Vergne-Vexelaire, C. ; Perret, A. ; Zaparucha, A. ; DE MELO-MINARDI, R. C. ; Mariage, A. ; Boutard, M. ; Debard, A. ; Lechaplais, C. ; Pelle, C. ; Pellouin, V. ; Perchat, N. ; Petit, J. L. ; Kreimeyer, A. ; Médigue, C. ; Weissenbach, J. ; Artiguenave, F. ; De Berandinis, V. ; Vallenet, D. ; Salanoubat, M. . Revealing the hidden functional diversity of an enzyme family. Nature Chemical Biology, v. 10, p. 42-49, 2013.


13. Gonçalves-Almeida, V. M. ; Pires, D. E. V. ; DE MELO-MINARDI, R. C. ; Silveira, C. H. ; Meira Jr., W. ; Santoro, M.M. . HydroPaCe: understanding and predicting cross-inhibition in serine proteases through hydrophobic patch centroids. Bioinformatics, 2012, in press.


12. Pires, D. E. V. ; DE MELO-MINARDI, R. C. ; Santos, M. A. ; Silveira, C. H. ; Santoro, M. M. ; Meira Jr., W. . Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns. BMC Genomics, 2011, in press.


11. Arumugam, M. ; Raes, J. ; Pelletier, E. ; Le Paslier, D. ; Yamada, T. ; Mende, D. R. ; Fernandes, G. R. ; Tap, J. ; Bruls, T. ; Batto, J. M. ; Bertalan, M. ; Borruel, N. ; Casellas, F. ; Fernandez, L. ; Gautier, L. ; Hansen, T. ; Hattori, M. ; Hayashi, T. ; Kleerebezem, M. ; Kurokawa, K. ; Leclerc, M. ; Levenez, F. ; Manichanh, C. ; Nielsen, H. B. ; Nielsen, T. ; Pons, N. ; Poulain, J. ; Qin, J. ; Sicheritz-Ponten, T. ; Tims, S. ; Torrents, D. ; Ugarte, E. ; Zoetendal, E. G. ; Wang, J. ; Guarner, F. ; Pedersen, O. ; de Vos, W. M. ; Brunak, S. ; Doré;, F. ; DE MELO-MINARDI, R.C. no Consórcio MetaHit. Enterotypes of the human gut microbiome. Nature (London), p. 1-7, 2011.


10. Bellinzoni, M. ; Bastard, K. ; Perret, A. ; Zaparucha, A. ; Perchat, N. ; Vergne, C. ; Wagner, T. ; MELO-MINARDI, R. C. ; Artiguenave, F. ; Cohen, G. N. ; Weissenbach, J. ; Salanoubat, M. ; Alzari, P. M. ; MELO-MINARDI, R. C. . 3-keto-5-aminohexanoate cleavage enzyme: a common fold for an uncommon Claisen-type condensation. The Journal of Biological Chemistry (Print), v. 286, p. 27399-27405, 2011.


9. MELO-MINARDI, R. C. ; Bastard, K. ; Artiguenave, F. . Identification of subfamily-specific sites based on active sites modeling and clustering. Bioinformatics, v. 26, n. 24, p. 3075-3082, 2010.


8. Qin, J. ; Li, R. ; Raes, J. ; Arumugam, M. ; Burgdorf, K. S. ; Manichanh, C. ; Nielsen, T. ; Pons, N. ; Levenez, F. ; Yamada, T. ; Mende, D. R. ; Li, J. ; Xu, J. ; Li, S. ; Li, D. ; Cao, J. ; Wang, B. ; Liang, H. ; Zheng, H. ; Xie, Y. ; Tap, J. ; Lepage, P. ; Bertalan, M. ; Batto, J. M. ; Hansen, T. ; Le Paslier, D. ; Linneberg, A. ; Nielsen, H. B. ; Pelletier, E. ; Renault, P. ; Sicheritz-Ponten, T. ; Turner, K. ; Zhu, H. ; Yu, C. ; Li, S. ; Jian, M. ; Zhou, Y. ; Li, Y. ; Zhang, X. ; Li, S. ; MELO-MINARDI, R. C. no Consórcio MetaHit. A human gut microbial gene catalogue established by metagenomic sequencing. Nature (London), v. 464, p. 59-65, 2010.


7. da Silveira, C. H. ; Pires, D. E. V. ; MINARDI, R. C. M. ; Ribeiro, C. ; Veloso, C. J. M. ; Lopes, J. C. D. ; Meira Jr., W. ; Neshich, G. ; Ramos, C. H. I. ; Habesch, R. ; Santoro, M. M. . Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins. Proteins, v. 74, p. 727-743, 2009.


6. Gomide, J. ; DE MELO-MINARDI, R. ; Santos, M. A. ; Neshich, G. ; Meira Jr., W. ; Lopes, J. C. D. ; Santoro, M. M. . Using linear algebra for protein structural comparison and classification. Genetics and Molecular Biology (Impresso), v. 32, p. 645-651, 2009.


5. DE MELO, R. C. ; Ribeiro, C. ; Murray, C. S. ; Veloso, C. J. M. ; Silveira, C. H. ; Neshich, G. ; Meira Jr., W. ; Carceroni, R. L. ; Santoro, M. M. . Finding protein-protein interaction patterns by contact map matching. Genetics and Molecular Research, v. 6, p. 1-10, 2007.


4. Veloso, C. J. M. ; Silveira, C. H. ; DE MELO, R. C. ; Ribeiro, C. ; Lopes, J. C. D. ; Santoro, M. M. ; Meira Jr., W. . On the characterization of energy networks of proteins. Genetics and Molecular Research, v. 6, p. 799-820, 2007.


3. DE MELO, R. C. ; Lopes, C. E. R. ; Fernandes Jr., F. A. ; Silveira, C. H. ; Santoro, M. M. ; Carceroni, R. L. ; Meira Jr., W. ; Araújo, A. A. . A contact map matching approach to protein structure similarity analysis. Genetics and Molecular Research, v. 5, p. 284-308, 2006.


2. Neshich, G. ; Mazoni, I. ; Oliveira, S. R. M. ; Yamagushi, M. E. B. ; Kuser-Falcão, P. R. ; Borro, L. C. ; Morita, D. U. ; Souza, K. R. R. ; Almeida, G. V. ; DE MELO, R. C. . Star STING server: a multiplatform environment for protein structure analysis. Genetics and Molecular Research, v. 5, p. 717-722, 2006.


1. Prado, T. A. K. L. ; Meira Jr., W. ; Santoro, M. M. ; Carvalho, M. B. ; Carceroni, R. L. ; Silveira, C. H. ; DE MELO, R. C. ; Fonseca, J. A. . Using structural signatures for identifying globins: the intrasubunit electrostatics interactions. Revista Tecnologia da Informação, v. 3, p. 115-118, 2003.

Conferências

20. Fassio, A. V. ; Santana, C. A. ; Cerqueira, F. R. ; Silveira, C. H. ; Romanelli, J. P. R. ; DE MELO-MINARDI, R. C. ; Silveira, S. A. . visGReMLIN: an interactive strategy to visualize common subgraphs in protein-ligand interaction. In: International Work Conference on Bioinformatics and Biomedical Enginnering, 2018, Granada. In Proceedings of the International Work Conference on Bioinformatics and Biomedical Enginnering, 2018.

19. Martins, P. M. ; Mayrink, V. ; Silveira, S. A. ; Silveira, C. H. ; Lima, L. H. F. ; DE MELO-MINARDI, R. C. . How to more accurately compute protein residue contacts?. In: ACM Symposium on Applied Computing - TRACK ON BIOINFORMATICS (BIO), 2017, Pau. Proceedings of the ACM Symposium on Applied Computing - TRACK ON BIOINFORMATICS (BIO), 2018.

18. Fassio, A. V. ; Martins, P. M. ; Guimarães, S. ; Araújo Junior, S. ; Ribeiro, V. ; DE MELO-MINARDI, R. C. ; Silveira, S. A. . Vermont: multi perspective visual interactive platform for mutational analysis. In: IEEE Biological Data Visualization (BioVis), 2017, Praga. Proceedings of the IEEE Biological Data Visualization (BioVis), 2017.

17. Franciscani JR., G. ; Bernardina, P. D. ; Boaventura, M. ; Santos, R. L. T. ; Meira Jr., W. ; DE MELO-MINARDI, R. C. . Experimental Evaluation of Crowdsourcing on the Characterization of Data Visualization Techniques. In: Brazilian Conference on Intelligent Systems, 2017, Uberlândia. Proceedings of the Brazilian Conference on Intelligent Systems, 2017.

16. Medina, S. ; Fassio, A. V. ; Silveira, S. A. ; Silveira, C. H. ; DE MELO-MINARDI, R. C. . CALI: a novel visual model for frequent pattern mining in protein-ligand-graphs. In: 17th International IEEE Conference on Bioinformatics and Bioengineering, 2017, Herndon. Proceedings of the 17th International IEEE Conference on Bioinformatics and Bioengineering, 2017.

15. Sen, S. ; Ribeiro, M. H. ; DE MELO-MINARDI, R. C. ; Meira Jr., W. ; Nygard, M. . Portinari: a data exploration tool to personalize cervical cancer screening. In: 39th International Conference on Software Engineering: Software Engineering in Society Track, 2017, Buenos Aires. Proceedings of the 39th International Conference on Software Engineering: Software Engineering in Society Track, 2017.

14. Santana, C. A. ; Cerqueira, F. R. ; Silveira, C. H. ; Fassio, A. V. ; DE MELO-MINARDI, R. C. ; Silveira, S. A. . GReMLIN: a graph mining strategy to infer protein-ligand interaction patterns. In: IEEE 16th International Conference on BioInformatics and BioEngineering, 2016, Taichung. Proceedings of the IEEE 16th International Conference on BioInformatics and BioEngineering, 2016.

13. Araújo, M. ; Nascimento, I. ; Rafael, G. C. ; MELO-MINARDI, R. C. ; Benevenuto, F. . Assinatura Emocional de Autores em Obras Literárias. In: 22o. Simpósio Brasileiro de Multimídia e Web (WebMedia), 2016, Teresina. Anais do 22o. Simpósio Brasileiro de Multimídia e Web (WebMedia), 2016.

12. Villela, M. L. B. ; Ferreira, L. S. ; Barros, D. A. F. ; Prates, R. O. ; DE MELO-MINARDI, R. C. . PryMeVis: Uma ferramenta para modelagem de design de privacidade. In: Simpósio Brasileiro de Sistemas Colaborativos, 2016, Porto Alegre. Anais do Simpósio Brasileiro de Sistemas Colaborativos, 2016.

11. Constantino, K. ; Figueiredo, E. M. L. ; DE MELO-MINARDI, R. C. ; Carneiro, G. F. . Multiple view interactive environment to analyze software product line tools. In: Simpósio Brasileiro de Sistemas de Informação, 2016, Florianópolis. Anais do Simpósio Brasileiro de Sistemas de Informação, 2016.

10. Silveira, S. A. ; Fassio, A. V. ; Silveira, C. H. ; MELO-MINARDI, R. C. DE. Revealing Protein-Ligand Interaction Patterns Through Frequent Subgraph Mining. In: The 2015 International Conference on Bioinformatics & Computational Biology, 2015, Las Vegas. The Proceedings of the 2015 International Conference on Bioinformatics & Computational Biology, 2015.

9. Franciscani Jr., G. ; Santos, R. L. T. ; Ottoni, R. ; Pesce, J. P. ; Meira Jr., W. ; DE MELO-MINARDI, R.C.. An annotation process for data visualization techniques. In: DATA ANALYTICS 2014, The Third International Conference on Data Analytics, 2014, Roma. Proceedins of the Third International Conference on Data Analytics, 2014.

8. Fassio, A. V. ; Silveira, S. A. ; DE MELO-MINARDI, R.C. . Visual and interactive strategies to reveal patterns of protein-ligand interactions. In: ISCB-LA X-Meeting 2014, 2014, Belo Horizonte. Anais do ISCB-LA X-Meeting 2014, 2014.

7. Magalhães, T. R. ; Dewan, P. ; Kumaraguru, P. ; DE MELO-MINARDI, R. C. ; Almeida, V. . uTrack: Track Yourself! Monitoring Information on Online Social Media. In: International World Wide Web Conference, 2013, Rio De Janeiro. Proceedings of the 2nd International World Wide Web Conference, 2013.

6. Rodrigues, A. O. ; Meira Jr., W. ; DE MELO-MINARDI, R. C.. Como nos Sentimos: Uma Ferramenta de Mineração Visual de Sentimentos no Twitter. In: II Brazilian Workshop on Social Network Analysis and Mining, 2013, Maceió. Proceedings of the II Brazilian Workshop on Social Network Analysis and Mining, 2013.

5. DE MELO-MINARDI, R. C.; Digiampietri, L. A. ; Vaz de Melo, P. O. S. ; Franciscani Jr., G. ; Oliveira, L. B. . Caracterização dos programas de pós-graduação em Bioinformática no Brasil. In: II Brazilian Workshop on Social Network Analysis and Mining, 2013, Maceió. proceedings of the II Brazilian Workshop on Social Network Analysis and Mining, 2013.

4. Silveira, S. A. ; Gonçalves-Almeida, V. M. ; Barcelos, Y. ; Lima, E. B. ; Aburjaile, F. ; Rodrigues, L. M. ; Meira Jr., W. ; DE MELO-MINARDI, R. C.. VERMONT: Visualizing mutations and their effects on protein physicochemical and topological property conservation. In: IEEE Symposium on Biological Data Visualization, 2013, Atlanta. Proceedins of the 3rd IEEE Symposium on Biological Data Visualization, 2013.

3. Saraiva, L. A. ; Silva, R. C. ; Camps, I. ; DE MELO-MINARDI, R. C.; Veloso, M. P. . Docking studies of a new series of analgesic and anti-inflamatory compounds (NSAIDs) with cyclooxigenases. In: International Society for Computational Bioogy - Latin America 2012 Conference on Bioinformatics, 2012, Santiago. Proceedings of the ISCB Latin America 2012, 2012.

2. Silveira, S. A. ; Rodrigues, A. O. ; Silveira, C. H. ; DE MELO-MINARDI, R. C.; Meira Jr., W. . ADVISe: Visualizing the dynamics of enzyme annotations in UniProt/SwissProt. In: IEEE Symposium on Biological Data Visualization, 2012, Seattle. Proceedings of the 2nd IEEE Symposium on Biological Data Visualization, 2012.

1. Lima, E. B. ; DE MELO-MINARDI, R. C. ; Zaki, M. ; Meira Jr., W. . Data integration via constrained clustering: an application to enzyme clustering. In: Eleventh SIAM International Conference on Data Mining, 2011, Phoenix/Mesa. Proceedings of the Eleventh SIAM International Conference on Data Mining, 2011.