Evaluating different methods of microarray data normalization. - André Fujita; João Ricardo Sato; Leonardo de Oliveira Rodrigues; Carlos Eduardo Ferreira; Mari Cleide Sogayar (BMC Bioinform., 2006)

DWT-CEM: an algorithm for scale-temporal clustering in fMRI. - João Ricardo Sato; André Fujita; Edson Amaro Jr.; Janaina Mourão Miranda; Pedro Alberto Morettin; Michael John Brammer (Biol. Cybern., 2007)

Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method. - André Fujita; João Ricardo Sato; Humberto Miguel Garay-Malpartida; Pedro Alberto Morettin; Mari Cleide Sogayar; Carlos Eduardo Ferreira (Bioinform., 2007)

GEDI: a user-friendly toolbox for analysis of large-scale gene expression data. - André Fujita; João Ricardo Sato; Carlos Eduardo Ferreira; Mari Cleide Sogayar (BMC Bioinform., 2007)

Modeling gene expression regulatory networks with the sparse vector autoregressive model. - André Fujita; João Ricardo Sato; Humberto Miguel Garay-Malpartida; Rui Yamaguchi; Satoru Miyano; Mari Cleide Sogayar; Carlos Eduardo Ferreira (BMC Syst. Biol., 2007)

Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates. - André Fujita; Luciana Rodrigues Gomes; João Ricardo Sato; Rui Yamaguchi; Carlos E. Thomaz; Mari Cleide Sogayar; Satoru Miyano (BMC Syst. Biol., 2008)

Modeling Nonlinear Gene Regulatory Networks from Time Series Gene Expression Data. - André Fujita; João Ricardo Sato; Humberto Miguel Garay-Malpartida; Mari Cleide Sogayar; Carlos Eduardo Ferreira; Satoru Miyano (J. Bioinform. Comput. Biol., 2008)

Hyperplane navigation: A method to set individual scores in fMRI group datasets. - João Ricardo Sato; Carlos Eduardo Thomaz; Ellison Fernando Cardoso; André Fujita; Maria da Graça Morais Martin; Edson Amaro Jr. (NeuroImage, 2008)

The impact of measurement errors in the identification of regulatory networks. - André Fujita; Alexandre Galvão Patriota; João Ricardo Sato; Satoru Miyano (BMC Bioinform., 2009)

Recursive regularization for inferring gene networks from time-course gene expression profiles. - Teppei Shimamura; Seiya Imoto; Rui Yamaguchi; André Fujita; Masao Nagasaki; Satoru Miyano (BMC Syst. Biol., 2009)

Comparing Pearson, Spearman and Hoeffding's d Measure for Gene Expression Association Analysis. - André Fujita; João Ricardo Sato; Marcos Angelo Almeida Demasi; Mari Cleide Sogayar; Carlos Eduardo Ferreira; Satoru Miyano (J. Bioinform. Comput. Biol., 2009)

Corrigendum to "Evaluating SVM and MLDA in the extraction of discriminant regions for mental state prediction": [NeuroImage 46 (2009) 105-114]. - João Ricardo Sato; André Fujita; Carlos Eduardo Thomaz; Maria da Graça Morais Martin; Janaina Mourão Miranda; Michael John Brammer; Edson Amaro Jr. (NeuroImage, 2009)

Evaluating SVM and MLDA in the extraction of discriminant regions for mental state prediction. - João Ricardo Sato; André Fujita; Carlos Eduardo Thomaz; Maria da Graça Morais Martin; Janaina Mourão Miranda; Michael John Brammer; Edson Amaro Júnior (NeuroImage, 2009)

Granger Causality in Systems Biology: Modeling Gene Networks in Time Series Microarray Data Using Vector Autoregressive Models. - André Fujita; Patricia Severino; João Ricardo Sato; Satoru Miyano (BSB, 2010)

A fast and robust statistical test based on likelihood ratio with Bartlett correction to identify Granger causality between gene sets. - André Fujita; Kaname Kojima; Alexandre Galvão Patriota; João Ricardo Sato; Patricia Severino; Satoru Miyano (Bioinform., 2010)

Model-free unsupervised gene set screening based on information enrichment in expression profiles. - Atsushi Niida; Seiya Imoto; Rui Yamaguchi; Masao Nagasaki; André Fujita; Teppei Shimamura; Satoru Miyano (Bioinform., 2010)

Identification of Granger Causality between Gene Sets. - André Fujita; João Ricardo Sato; Kaname Kojima; Luciana Rodrigues Gomes; Masao Nagasaki; Mari Cleide Sogayar; Satoru Miyano (J. Bioinform. Comput. Biol., 2010)

Analyzing the connectivity between regions of interest: An approach based on cluster Granger causality for fMRI data analysis. - João Ricardo Sato; André Fujita; Ellison Fernando Cardoso; Carlos E. Thomaz; Michael J. Brammer; Edson Amaro Jr. (NeuroImage, 2010)

Systems biology model repository for macrophage pathway simulation. - Masao Nagasaki; Ayumu Saito; André Fujita; Georg Tremmel; Kazuko Ueno; Emi Ikeda; Euna Jeong; Satoru Miyano (Bioinform., 2011)

Inferring Contagion in Regulatory Networks. - André Fujita; João Ricardo Sato; Marcos Angelo Almeida Demasi; Rui Yamaguchi; Teppei Shimamura; Carlos Eduardo Ferreira; Mari Cleide Sogayar; Satoru Miyano (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing. - Kaname Kojima; Seiya Imoto; Rui Yamaguchi; André Fujita; Mai Yamauchi; Noriko Gotoh; Satoru Miyano (BMC Genom., 2012)

Functional clustering of time series gene expression data by Granger causality. - André Fujita; Patricia Severino; Kaname Kojima; João Ricardo Sato; Alexandre Galvão Patriota; Satoru Miyano (BMC Syst. Biol., 2012)

Discriminating different classes of biological networks by analyzing the graphs spectra distribution - Daniel Yasumasa Takahashi; João Ricardo Sato; Carlos Eduardo Ferreira; André Fujita (CoRR, 2012)

XiP: a computational environment to create, extend and share workflows. - Masao Nagasaki; André Fujita; Yayoi Sekiya; Ayumu Saito; Emi Ikeda; Chen Li 007; Satoru Miyano (Bioinform., 2013)

Measuring network's entropy in ADHD: A new approach to investigate neuropsychiatric disorders. - João Ricardo Sato; Daniel Yasumasa Takahashi; Marcelo Queiroz Hoexter; Katlin Brauer Massirer; André Fujita (NeuroImage, 2013)

A comparative study of statistical methods used to identify dependencies between gene expression signals. - Suzana de Siqueira Santos; Daniel Yasumasa Takahashi; Asuka Nakata; André Fujita (Briefings Bioinform., 2014)

A non-parametric method to estimate the number of clusters. - André Fujita; Daniel Yasumasa Takahashi; Alexandre Galvão Patriota (Comput. Stat. Data Anal., 2014)

Source and sink nodes in absence seizures. - Abner Cardoso Rodrigues; Birajara S. Machado; Luis Otavio S. F. Caboclo; André Fujita; Luiz A. Baccalá; Koichi Sameshima (EMBC, 2016)

Correlation between graphs with an application to brain network analysis. - André Fujita; Daniel Yasumasa Takahashi; Joana Bisol Balardin; Maciel Calebe Vidal; João Ricardo Sato (Comput. Stat. Data Anal., 2017)

Complex Network Measures in Autism Spectrum Disorders. - João Ricardo Sato; Maciel Calebe Vidal; Suzana de Siqueira Santos; Katlin Brauer Massirer; André Fujita (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

A semi-parametric statistical test to compare complex networks. - André Fujita; Eduardo Silva Lira; Suzana de Siqueira Santos; Silvia Yumi Bando; Gabriela Eleutério Soares; Daniel Yasumasa Takahashi (J. Complex Networks, 2020)

Stage I non-small cell lung cancer stratification by using a model-based clustering algorithm with covariates. - Carlos E. M. Relvas; André Fujita (CoRR, 2020)

Predicting soft robot's locomotion fitness. - Renata B. Biazzi; André Fujita; Daniel Y. Takahashi (GECCO Companion, 2021)

Spectral density of random graphs: convergence properties and application in model fitting. - Suzana de Siqueira Santos; André Fujita; Catherine Matias (J. Complex Networks, 2021)

Granger Causality among Graphs and Application to Functional Brain Connectivity in Autism Spectrum Disorder. - Adèle Helena Ribeiro; Maciel Calebe Vidal; João Ricardo Sato; André Fujita (Entropy, 2021)

Convolution-based linear discriminant analysis for functional data classification. - Grover E. C. Guzman; André Fujita (Inf. Sci., 2021)

Efficient Laplacian spectral density computations for networks with arbitrary degree distributions. - Grover E. C. Guzman; Peter F. Stadler; André Fujita (Netw. Sci., 2021)

Efficient eigenvalue counts for tree-like networks. - Grover E. C. Guzman; Peter F. Stadler; André Fujita (J. Complex Networks, 2022)

A fast parameter estimator for large complex networks. - Grover E. C. Guzman; Daniel Yasumasa Takahashi; André Fujita (J. Complex Networks, 2022)

Applications of graph theory to the analysis of fNIRS data in hyperscanning paradigms. - Amanda Yumi Ambriola Oku; Candida Barreto; Guilherme Bruneri; Guilherme Brockington; André Fujita; João Ricardo Sato (Frontiers Comput. Neurosci., 2022)

Spectrum-Based Statistical Methods for Directed Graphs with Applications in Biological Data. - Victor Chavauty Villela; Eduardo Silva Lira; André Fujita (BSB, 2023)

A fast algorithm to approximate the spectral density of locally tree-like networks with assortativity. - Grover E. C. Guzman; André Fujita (J. Complex Networks, 2023)

A model-based clustering algorithm with covariates adjustment and its application to lung cancer stratification. - Carlos E. M. Relvas; Asuka Nakata; Guoan Chen; David G. Beer; Noriko Gotoh; André Fujita (J. Bioinform. Comput. Biol., 2023)

Primitive, edge-short, isometric, and pantochordal cycles. - Gover E. C. Guzman; Marcos E. González Laffitte; André Fujita; Peter F. Stadler (Art Discret. Appl. Math., 2025)

Statistical methods for hypergraphs: a parameter estimator, a model selection, and a comparative test. - Grover E. C. Guzman; André Fujita (J. Complex Networks, 2025)

Vertex-wise graph's spectral density decomposition and its applications. - Grover E. C. Guzman; Daniel Yasumasa Takahashi; André Fujita (J. Complex Networks, 2025)