Book chapter

  1. Fujita A, Sato JR, Demasi MAA, Miyano S, Sogayar MC, Ferreira CE. An introduction to time-varying connectivity estimation for gene regulatory networks. In: Frank Emmert-Streib; Matthias Dehmer. (Org.). Medical Biostatistics for complex diseases. Weinheim, Germany: Wiley VCH Verlag, p.205-230, 2010.

Publication List

  1. Kasparek T, Thomaz CE, Sato JR, Schwarz D, Janousova E,Marecek R, Prikryl R, Vanicek J, Fujita A, Ceskova E. Maximum-uncertainty linear discrimination analysis of first-episode schizophrenia subjects. Psychiatry Research: Neuroimaging. 2011 (in press).
  2. Niida A, Imoto S, Yamaguchi R, Nagasaki M, Fujita A, Shimamura T, Miyano S. Model-free unsupervised gene set screening based on information enrichment in expression profiles. Bioinformatics. 26:3090-3097, 2010.
  3. Fujita A, Kojima, K, Patriota AG, Sato JR, Severino P, Miyano S. A fast and robust statistical test based on Likelihood ratio with Bartlett correction to identify Granger causality between gene sets. Bioinformatics. 26:2349-2351, 2010.
  4. Fujita A, Severino P, Sato JR, Miyano S. Granger causality in systems biology: modeling gene networks in time series microarray data using vector autoregressive models. Lecture Notes in Bioinformatics. 6268:13-24, 2010.
  5. Sato JR, Fujita A, Cardoso EF, Thomaz CE, Brammer MJ, Amaro Jr E. Analyzing the connectivity between regions of interest: an approach based on cluster Granger causality for fMRI data analysis. NeuroImage. 52:1444-1455, 2010.
  6. Shimamura T, Imoto S, Nagasaki M, Yamauchi M, Yamaguchi R, Fujita A, Tamada Y, Gotoh N, Miyano S. Collocation-based sparse estimation for constructing dynamic gene networks. Genome Informatics. 24:164-178, 2010.
  7. Fujita A, Nagasaki, M, Imoto S, Saito A, Ikeda E, Shimamura T, Yamaguchi R, Hayashizaki Y, Miyano S. Comparison of gene expression profiles produced by CAGE, illumina microarray and Real Time RT-PCR. Genome Informatics. 24:56-68, 2010.
  8. Fujita A, Sato JR, Kojima K, Gomes LR, Nagasaki M, Sogayar MC, Miyano S. Identification of Granger causality between gene sets. Journal of Bioinformatics and Computational Biology. 8:679-701, 2010.
  9. Fujita A, Patriota AG, Sato JR, Miyano S. The impact of measurement error in the identification of regulatory networks. BMC Bioinformatics. 10:412, 2009.
  10. Fujita A, Sato JR, da Silva FHL, Galvao MC, Sogayar MC, Miyano S. Quality control and reproducibility in DNA microarray experiments. Genome Informatics. 23:21-31, 2009.
  11. Fujita A, Sato JR, Demasi MAA, Yamaguchi R, Shimamura T, Ferreira CE, Sogayar MC, Miyano S. Inferring contagion in regulatory networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2009 (in press).
  12. Shimamura T, Imoto S, Yamaguchi R, Fujita A, Nagasaki M, Miyano S. Recursive regularization for inferring gene networks from time-course gene expression profiles. BMC Systems Biology 3:41, 2009.
  13. Fujita A, Sato JR, Demasi MAA, Sogayar MC, Ferreira CE, Miyano S. Comparing Pearson, Spearman and Hoeffding's D measure for gene expression association analysis. Journal of Bioinformatics and Computational Biology. 7(4):663-684, 2009.
  14. Fujita A, Sato JR, Sogayar MC, Ferreira CE. Non parametric regression and canonical correlation analysis in tumor classification. Asia-Pacific Journal of Operational Research. 2009. (accepted).
  15. Sato JR, Martin MGM, Fujita A, Mourão-Miranda J, Brammer MJ, Amaro Jr E. An fMRI normative database for connectivity networks using one-class support vector machines. Human Brain Mapping. 30:1068-1076, 2009.
  16. Sato JR, Fujita A, Thomaz CE, Martin MG, Mourão-Miranda J, Brammer MJ, Amaro Jr E. Evaluating SVM and MLDA in the extraction of discriminant regions for mental state prediction. NeuroImage. 46:105-114, 2009.
  17. Fujita A, Gomes LR, Sato JR, Yamaguchi R, Thomaz CE, Sogayar MC, Miyano S. Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates. BMC Systems Biology 2:106, 2008.
  18. Hatanaka Y, Nagasaki M, Yamaguchi R, Obayashi T, Numata K, Fujita A, Shimamura T, Tamada Y, Imoto S, Kinoshita K, Nakai K, Miyano S. A novel strategy to search conserved transcriptional factor binding sites among coexpressing genes in human. Genome Informatics 20:212-221, 2008.
  19. Kojima K, Fujita A, Shimamura T, Imoto S, Miyano S. Estimation of nonlinear gene regulatory networks via L1 regularized NVAR from time series gene expression data. Genome Informatics 20:37-51, 2008.
  20. Sato JR, Thomaz CE, Cardoso EF, Fujita A, Morais-Martin MG, Amaro Jr E. Hyperplane Navigation: a method to set individual scores in fMRI group datasets. NeuroImage. 42:1473-1480, 2008.
  21. Fujita A, Sogayar MC, Ferreira CE. Análise de dados de expressão gênica: normalização de microarrays e modelagem de redes regulatórias. Annals of the Brazilian Society for Computer Science. 9-16, 2008.
  22. Fujita A, Sato JR, Garay-Malpartida HM, Sogayar MC, Ferreira CE, Miyano S. Modeling nonlinear gene regulatory networks from time-series gene expression data. Journal of Bioinformatics and Computational Biology 6:961-79, 2008.
  23. Fujita A, Sato JR, Festa F, Gomes LR, Oba-Shinjo SM, Marie SKN, Ferreira CE, Sogayar MC. Identification of COL6A1 as a differentially expressed gene in human astrocytomas. Genetics and Molecular Research 7:371-378, 2008.
  24. Takehara EC, Carvalho LS, Fujita A. Correlacao entre a maturidade das vertebras cervicais e o surto de crescimento puberal em populacao brasileira. Revista Dental Press de Ortodontia e Ortopedia Facial, 2008 (in press).
  25. Fujita A, Sato JR, Ferreira CE, Sogayar MC. GEDI: a user-friendly toolbox for analysis of large-scale gene expression data. BMC Bioinformatics 8:457, 2007.
  26. Fujita A, Sato JR, Garay-Malpartida HM, Yamaguchi R, Miyano S, Sogayar MC, Ferreira CE. Modeling gene expression regulatory networks with the sparse vector autoregressive model. BMC Systems Biology 1:39, 2007.
  27. Fujita A, Sato JR, Garay-Malpartida HM, Morettin PA, Sogayar MC, Ferreira CE. Time-varying modeling of gene expression regulatory networks using wavelet dynamic vector autoregressive method. Bioinformatics 23:1623-1630, 2007.
  28. Sato JR, Fujita A, Amaro Jr E, Miranda JM, Morettin PA, Brammer MJ. DWT-CEM: An algorithm for scale-temporal clustering in fMRI. Biological Cybernetics 97:33-45, 2007.
  29. Fujita A, Sato JR, Rodrigues LO, Ferreira MC, Sogayar MC. Evaluating different methods of microarray data normalization. BMC Bioinformatics 7:469, 2006.
  30. Fujita A, Massirer KB, Durham AM, Ferreira CE, Sogayar MC. The GATO gene annotation tool for research laboratories. Brazilian Journal of Medical and Biological Research 38:1571-1574, 2005.
publication_list.txt · Last modified: 2011/01/07 18:32 by mlabadm
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