Publicações em Bioinformática com participação dos membros do laboratório.

Periódicos

  1. GONÇALVES-ALMEIDA, V.M. ; PIRES, D.E.V. ; MELO-MINARDI, R.C. ; DA SILVEIRA, C.H. ; MEIRA JR., W. ; SANTORO, M.M. . HydroPaCe: understanding and predicting cross-inhibition in serine proteases through hydrophobic patch centroids. Bioinformatics (Oxford. Print), v. 28, p. 342-349, 2012.



  2. PIRES, D.E.V. ; Totti, L. ; Moreira, R. ; Fazzion, E. ; Fonseca, O. ; MEIRA JR., W. ; MELO-MINARDI, R.C. ; Guedes, D. . FPCluster: an efficient out-of-core clustering strategy without a similarity metric. Journal of Information and Data Management - JIDM, v. 3, p. 132-141, 2012.



  3. Arumugam, M.R.J ; et al. Enterotypes of the human gut microbiome. Nature (London), p. 1-7, 2011.



  4. PIRES, D.E.V. ; MELO-MINARDI, R.C. ; SANTOS, M.A. ; DA 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, v. 12, p. S12, 2011.



  5. 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. . 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.



  6. Ribeiro, C. ; Togawa, R.C. ; Neshich, I.A.P. ; Mazoni, I. ; Mancini, A.L. ; MELO-MINARDI, R.C. ; SILVEIRA, C.H. ; Jardine, J.G. ; SANTORO, M.M. ; Neshich, G. . Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors. BMC Structural Biology (Online), v. 10, p. 36, 2010.



  7. MELO-MINARDI, R.C. ; Bastard, K. ; Artiguenave, F. . Identification of subfamily-specific sites based on active sites modeling and clustering. Bioinformatics (Oxford. Print), v. 26, 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. . A human gut microbial gene catalogue established by metagenomic sequencing. Nature (London), v. 464, p. 59-65, 2010.



  9. SILVEIRA, C.H. ; PIRES, D.E.V. ; MINARDI, R.C.M. ; Ribeiro, C. ; Veloso, C. J. M. ; Lopes, J. C. D. ; MEIRA JUNIOR, 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.



  10. Gomide, J. ; MELO-MINARDI, R.C. ; SANTOS, M.A. ; Neshich, G. ; MEIRA JUNIOR, 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.



  11. Araújo, R.B. ; Ferreira, G.H.T. ; Orair, G.H. ; MEIRA JUNIOR, W. ; Ferreira, R.A.C. ; Guedes Neto, D.O ; Zaki, M. . The ParTriCluster Algorithm for Gene Expression Analysis. International Journal of Parallel Programming, v. 36, p. 226-249, 2008.



  12. MELO, R.C. ; Ribeiro, C. ; Murray, C.S. ; Veloso, C.J.M. ; SILVEIRA, C.H. ; Neshich, G. ; MEIRA JUNIOR, 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.



  13. Veloso, C.J.M. ; SILVEIRA, C.H. ; MELO, R.C. ; Ribeiro, C. ; Lopes, J.C.D. ; Santoro, M.M. ; MEIRA JUNIOR, W. . On the characterization of energy networks of proteins. Genetics and Molecular Research, v. 6, p. 799-820, 2007.



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



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



  16. PAPPA, G.L. ; Freitas, A.A. ; Baines, A.J. . Predicting post-synaptic activity in proteins with data mining. Bioinformatics, v. 21, n. 2, p. ii19-ii25, 2005.



  17. Prado, T.A.K.L. ; MEIRA JUNIOR, W. ; Santoro, M.M. ; Carvalho, M.B. ; Carceroni, R.L. ; SILVEIRA, C.H. ; 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.


Trabalhos completos em anais de eventos

  1. E.B. DE LIMA ; MELO-MINARDI, R. C. ; M. Zaki ; MEIRA JUNIOR, 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.


  2. MINARDI, R.C.M. ; Artiguenave, F. ; Neshich, G. . Large scale protein function prediction tools. In: Colloque d Informatique: Brésil / INRIA, Coopérations, Avancées et Défis, 2009, Bento Gonçalves. Anais do Colóquio em Informática: Brasil / INRIA, Cooperações, Avanços e Desafios, 2009.

  3. MELO, R.C. ; Gomide, J.S. ; Dias, P.S. ; MEIRA JUNIOR, W. ; Santoro, M.M. . Mining structural signatures of proteins. III Workshop de Algoritmos e Aplicações em Mineração de Dados, 2007.



  4. Araújo, R.B. ; Ferreira, G.H.T. ; Orair, G.H. ; MEIRA JUNIOR, W. ; Ferreira, R.A.C. ; Guedes Neto, D.O. . ParTriCluster: A Scalable Parallel Algorithm for Gene Expression Analysis. In: XVIII International Symposium on Computer Architecture and High Performance Computing, 2006, Ouro Preto, MG. Proc. of XVIII International Symposium on Computer Architecture and High Performance Computing, 2006. p. 3-10.

  5. MELO, R.C. ; Lopes, C.E.R. ; Fernandes Jr., F.A. ; SILVEIRA, C.H. ; Santoro, M.M. ; Carceroni, R.L. ; MEIRA JUNIOR, W. ; Araújo A. A. . A contact map matching approach to protein structure similarity analysis. In: II International Conference on Bioinformatics and Computational Biology, 2004, Angra dos Reis. Proceedings of the II International Conference on Bioinformatics and Computational Biology, 2004.

  6. Fernandes Jr., F.A. ; Lopes, C.E.R. ; MELO, R.C. ; Santoro, M.M. ; Carceroni, R.L. ; MEIRA JUNIOR, W. ; Araújo, A.A. ; SILVEIRA, C.H. . An image-matching approach to protein similarity analysis. In: XVII Brazilian Symposium on Computer Graphics and Image Processing, 2004, Curitiba. Proceedings of the XVII Brazilian Symposium on Computer Graphics and Image Processing, 2004.

  7. Veloso, C. ; MEIRA JUNIOR, W. ; Santoro, M. ; SILVEIRA, C. . Application of Information Theory Principles to Mine Relationships in Globins Helices. In: 1st International Conference on Bionformatics and Computacional Biology, 2003, Ribeirão Preto. Proceedings of the 1st International Conference on Bionformatics and Computacional Biology, 2003.

  8. MEIRA JUNIOR, W. ; Carvalho, M.L.B. . Neural Networks In Biological Taxonomy. In: Proceedings of International Joint Conference of Neural Networks - 1993, 1993, Nagoya. Anais do Proceedings of International Joint Conference of Neural Networks - 1993, 1993. p. 33-36.


Resumos expandidos

  1. Veloso, C.J.M. ; SANTOS, M.A. ; MEIRA JUNIOR, W. . Using Linear Algebra for Predicting Alpha-Helix in Proteins. In: International Conference on Bioinformatics and Computational Biology, 2004, Angra dos Reis/RJ. Proceedings of the International Conference on Bioinformatics and Computacional Biology, 2004. v. 1. p. 205-206.


Resumos em anais de eventos

  1. Bellinzoni, M. ; Zaparucha, A. ; Perret, A. ; Vergne, C. ; Bastard, K. ; Berardinis, V. ; MELO-MINARDI, R.C. ; Wagner, T. ; Kreimeyer, A. ; Artiguenave, F. ; Weissenbach, J. ; Cohen, G.N. ; Salanoubat, M. ; Alzari, P.M. . 3-keto-5-aminohexanoate cleavage enzyme: a common fold for an uncommon reaction. In: EMBO Conference Series: Catalytic mechanisms by biological systems: Catalytic mechanisms by biological systems at the interface between chemistry and biology, 2010, Hamburg. EMBO Conference Series: Catalytic mechanisms by biological systems: Catalytic mechanisms by biological systems at the interface between chemistry and biology, 2010.

  2. Couto, B.R.G.M. ; Santoro, M.M. ; CAMPOS, F.F. ; SANTOS, M.A. . Unrevealing biological process with linear algebra: extracting patterns from noisy data. In: International Conference of the Brazilian Association for Bioinformatics and Computational Biology, 2009, Angra dos Reis-RJ. Anais da International Conference of the Brazilian Association for Bioinformatics and Computacional Biology 2009, 2009.

  3. Gomide, J.S. ; MELO, R.C. ; MEIRA JUNIOR, W. ; Santoro, M.M. . Measuring protein structure similarity using the Levenshtein distance. In: BIOMAT, 2008, Campos do Jordao. BIOMAT, 2008.

  4. ALMEIDA, V.M.G. ; Silveira, S.A. ; Crepalde, M.A. ; SANTOS, M.A. ; MELO, R.C. ; SILVEIRA, C.H. ; Lopes, J.C.D. ; Santoro, M.M. . Using singular value decomposition and latent semactic indexing to search structural signatures in subtilase protein family. In: BIOMAT, 2008, Campos do Jordao. BIOMAT, 2008.

  5. MELO-MINARDI, R.C. ; Gomide, J.S. ; SILVEIRA, C.H. ; Neshich, G. ; Lopes, J.C.D. ; MEIRA JUNIOR, W. ; Santoro, M.M. . Protein family structural classification based on intra-chain contacts. In: X-Meeting 2008 (Quarto Encontro da Associação Brasileira de Bioinformática e Biologia Computonal), 2008, Fortaleza. Anais do X-Meeting 2008 (Quarto Encontro da Associação Brasileira de Bioinformática e Biologia Computaciona 2008.

  6. MELO, R.C. ; Gomide, J.S. ; MEIRA JUNIOR, W. ; Lopes, J.C.D. ; Neshich, G. ; Santoro, M.M. . Mining structural signatures in proteins using intrachain interactions. In: X-Meeting 2007 (Terceiro Encontro da Associação Brasileira de Bioinformática e Biologia Computacional), 2007, São Paulo. Anais do AB3C 3rd International Conference, 2007.

  7. Gomide, J.S. ; Dias, P.S. ; MELO, R.C. ; SANTOS, M.A. ; Santoro, M.M. ; MEIRA JUNIOR, W. . Using principal component analysis to classify protein structures. In: AB3C 3rd International Conference, 2007, São Paulo. Anais do AB3C 3rd International Conference, 2007

  8. MELO, R.C. ; Manzoni, I. ; Neshich, G. ; Santoro, M.M. ; MEIRA JUNIOR, W. . Contacts and the key elements for comparing two protein structures. In: X-Meeting 2006 (Segundo Encontro da Associação Brasileira de Bioinformática e Biologia Computacional), 2006, Fortaleza. Anais do Segundo Encontro da Associação Brasileira dBioinformática e Biologia Computacion 2006.

  9. MELO, R.C. ; Mazoni, I. ; Neshich, G. ; Santoro, M.M. ; MEIRA JUNIOR, W. . Protein topology comparison based on contact maps. In: X-Meeting 2006 (Segundo Encontro da Associação Brasileira de Bioinformática e Biologia Computacional), 2006, Fortaleza. Anais do Segundo Encontro da Associação Brasileira de Bioinformática e Biologia Computacional, 2006.

  10. MELO, R.C. ; Murray, C.S. ; Alvim Jr., M.S.F. ; SILVEIRA, C.H. ; Carceroni, R.L. ; MEIRA JUNIOR, W. ; Santoro, M.M. . Predicting globin folding pathways using and unfolding heuristic. In: X-Meeting 2005 (Primeiro Encontro da Associação Brasileira de Bioinformática e Biologia Computacional), 2005, Caxambú. Anais do Primeiro Encontro da Associação Brasileira de Bioinformática e Biologia Computacional, 2005.