
This Article  
 
Share  
Bibliographic References  
Add to:  
Digg Furl Spurl Blink Simpy Del.icio.us Y!MyWeb  
Search  
 
ASCII Text  x  
Yoshinori Tamada, Seiya Imoto, Hiromitsu Araki, Masao Nagasaki, Cristin Print, D. Stephen CharnockJones, Satoru Miyano, "Estimating GenomeWide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 3, pp. 683697, May/June, 2011.  
BibTex  x  
@article{ 10.1109/TCBB.2010.68, author = {Yoshinori Tamada and Seiya Imoto and Hiromitsu Araki and Masao Nagasaki and Cristin Print and D. Stephen CharnockJones and Satoru Miyano}, title = {Estimating GenomeWide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {8}, number = {3}, issn = {15455963}, year = {2011}, pages = {683697}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.68}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }  
RefWorks Procite/RefMan/Endnote  x  
TY  JOUR JO  IEEE/ACM Transactions on Computational Biology and Bioinformatics TI  Estimating GenomeWide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers IS  3 SN  15455963 SP683 EP697 EPD  683697 A1  Yoshinori Tamada, A1  Seiya Imoto, A1  Hiromitsu Araki, A1  Masao Nagasaki, A1  Cristin Print, A1  D. Stephen CharnockJones, A1  Satoru Miyano, PY  2011 KW  Biology and genetics KW  gene networks KW  Bayesian network structure learning KW  gene expression data analysis. VL  8 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
[1] A.L. Barabási and Z.N. Oltvai, "Network Biology: Understanding the Cell's Functional Organization," Nature Rev. Genetics, vol. 5, no. 10, pp. 101113, 2004.
[2] E.P. van Someren, L.F.A. Wesssels, E. Backer, and M.J.T. Reinders, "Genetic Network Modeling," Pharmacogenomics, vol. 3, pp. 507525, 2002.
[3] X. Zhu, M. Gerstein, and M. Snyder, "Getting Connected: Analysis and Principles of Biological Networks," Genes & Development, vol. 21, pp. 10101024, 2007.
[4] N. Friedman, M. Linial, I. Nachman, and D. Péer, "Using Bayesian Networks to Analyze Expression Data," J. Computational Biology, vol. 7, pp. 601620, 2000.
[5] S. Imoto, T. Goto, and S. Miyano, "Estimation of Genetic Networks and Functional Structures between Genes by Using Bayesian Networks and Nonparametric Regression," Proc. Pacific Symp. Biocomputing, vol. 7, pp. 175186, 2002.
[6] J.M. Peña, J. Björkegren, and J. Tegnér, "Growing Bayesian Network Models of Gene Networks from Seed Genes," Bioinformatics, vol. 21, pp. ii224ii229, 2005.
[7] J. Yu, V.A. Smith, P.P. Wang, A.J. Hartemink, and E.D. Jarvis, "Advances to Bayesian Network Inference for Generating Causal Networks from Observational Biological Data," Bioinformatics, vol. 20, no. 18, pp. 35943603, 2004.
[8] X.W. Chen, G. Anantha, and X. Wang, "An Effective Structure Learning Method for Constructing Gene Networks," Bioinformatics, vol. 22, no. 11, pp. 13671374, 2006.
[9] D.M. Chickering, "Learning Bayesian Network is NP Complete," Learning from Data: Artificial Intelligence and Statisitcs V, D. Fisher and H.J. Lenz, eds., pp. 121130, SpringerVerlag, 1996.
[10] S. Ott, S. Imoto, and S. Miyano, "Finding Optimal Models for Small Gene Networks," Proc. Pacific Symp. Biocomputing, vol. 9, pp. 557567, 2004.
[11] E. Perrier, S. Imoto, and S. Miyano, "Finding Optimal Bayesian Network Given a SuperStructure," J. Machine Learning Research, vol. 9, pp. 22512286, 2008.
[12] N. Friedman, I. Nachman, and D. Péer, "Learning Bayesian Network Structure from Massive Datasets: The 'Sparse Candidate' Algorithm," Proc. 15th Ann. Conf. Uncertainty in Artificial Intelligence, pp. 206215, 1999.
[13] S. Imoto, Y. Tamada, H. Araki, K. Yasuda, C.G. Print, D.S. CharnockJones, D. Sanders, C.J. Savoie, K. Tashiro, S. Kuhara, and S. Miyano, "Computational Strategy for Discovering Druggable Gene Networks from GenomeWide RNA Expression Profiles," Proc. Pacific Symp. Biocomputing, vol. 11, pp. 559571, 2006.
[14] Y. Tamada, H. Araki, S. Imoto, M. Nagasaki, A. Doi, Y. Nakanishi, Y. Tomiyasu, K. Yasuda, B. Dunmore, D. Sanders, S. Humphreys, C. Print, D.S. CharnockJones, K. Tashiro, S. Kuhara, and S. Miyano, "Unraveling Dynamic Activities of Autocrine Pathways that Control DrugResponse Transcriptome Networks," Proc. Pacific Symp. Biocomputing, vol. 14, pp. 251263, 2009.
[15] J. Pearl, Causality. Springer, 2000.
[16] G. Maldonado and S. Greenland, "Estimating Causal Effects," Int'l J. Epidemiology, vol. 31, no. 2, pp. 422429, 2002.
[17] V.G. Tusher, R. Tibshirani, and G. Chu, "Significance Analysis of Microarrays Applied to the Ionizing Radiation Response," Proc. Nat'l Academy of Sciences USA, vol. 98, no. 9, pp. 51165121, 2001.
[18] C. de Boor, A Practical Guide to Splines. SpringerVerlag, 1978.
[19] R. OpgenRhein and K. Strimmer, "Learning Causal Networks from Systems Biology Time Course Data: An Effective Model Selection Procedure for the Vector Autoregressive Process," BMC Bioinformatics, vol. 8, p. S3, 2007.
[20] D.J. Pearce and P.H. Kelly, "A Dynamic Topological Sort Algorithm for Directed Acyclic Graphs," ACM J. Experimental Algorithmics, vol. 11, no. 1.7, pp. 124, 2006.
[21] D. Ajwani, T. Friedrich, and U. Meyer, "An $o(n^{2.75})$ Algorithm for Online Topological Ordering," Proc. 10th Scandinavian Workshop Algorithm Theory (SWAT '06), pp. 5364, 2006.
[22] I. Tsamardinos, L.E. Brown, and C.F. Aliferis, "The MaxMin HillClimbing Bayesian Network Structure Learning Algorithm," Machine Learning, vol. 65, pp. 3178, 2006.
[23] I.A. Beinlich, H.J. Suermondt, R.M. Chavez, and G.F. Cooper, "The ALARM Monitoring System: A Case Study with Two Probabilistic Inference Techniques for Belief Networks," Proc. Second European Conf. Artificial Intelligence in Medicine, vol. 38, pp. 247256, 1989.
[24] Y. Tamada, S. Imoto, K. Tashiro, S. Kuhara, and S. Miyano, "Identifying Drug Active Pathways from Gene Networks Estimated by Gene Expression Data," Genome Informatics, vol. 16, no. 1, pp. 182191, 2005.
[25] http://www.hgc.jp/~tamada/suppl/GWGNindex.html , 2009.
[26] P.H.C. Eilers and B.D. Marx, "Flexible Smoothing with $B$ Splines and Penalties," Statistical Science, vol. 11, no. 2, pp. 89121, 1996.
[27] T.H. Bø, B. Dysvik, and I. Jonassen, "LSimpute: Accurate Estimation of Missing Values in Microarray Data with Least Squares Methods," Nucleic Acids Research, vol. 32, no. 3, p. e34, 2004.
[28] http://www.geneontology.orgGO.slims.shtml , 2010.
[29] M. Karin and Y. BenNeriah, "Phosphorylation Meets Ubiquitination: The Control of NF$\kappa$ B Activity," Ann. Rev. Immunology, vol. 18, pp. 621663, 2000.
[30] S.A. Marsters, J.P. Sheridan, C.J. Donahue, R.M. Pitti, C.L. Gray, A.D. Goddard, K.D. Bauer, and A. Ashkenazi, "Apo3, A New Member of the Tumor Necrosis Factor Receptor Family, Contains a Death Domain and Activates Apoptosis and NF$\kappa$ B," Current Biology, vol. 6, no. 12, pp. 16691676, 1996.
[31] T. Okayasu, A. Tomizawa, K. Suzuki, K. Manaka, and Y. Hattori, "PPAR$\alpha$ Activators Upregulate eNOS Activity and Inhibit CytokineInduced NF$\kappa$ B Activation through AMPActivated Protein Kinase Activation," Life Sciences, vol. 82, pp. 884891, 2008.
[32] C.J. Savoie, S. Aburatan, S. Watanabe, Y. Eguch, S. Muta, S. Imoto, S. Miyano, S. Kuhara, and K. Tashiro, "Use of Gene Networks from Full Genome Microarray Libraries to Identify Functionally Relevant DrugAffected Genes and Gene Regulation Cascades," DNA Research, vol. 10, pp. 1925, 2003.
[33] M. Affara, B. Dunmore, C. Savoie, S. Imoto, Y. Tamada, H. Araki, D.S. CharnockJones, S. Miyano, and C. Print, "Understanding Endothelial Cell Apoptosis: What Can the Transcriptome, Glycome and Proteome Reveal?" Philosophical Trans. Royal Soc. B, vol. 362, pp. 14691487, 2007.
[34] H. Araki, Y. Tamada, S. Imoto, B. Dunmore, D. Sanders, S. Humphrey, M. Nagasaki, A. Doi, Y. Nakanishi, K. Yasuda, Y. Tomiyasu, K. Tashiro, C. Print, D.S. CharnockJones, S. Kuhara, and S. Miyano, "Analysis of PPAR$\alpha$ Dependent and PPAR$\alpha$ Independent Transcript Regulation Following Fenofibrate Treatment of Human Endothelial Cells," Angiogenesis, vol. 12, no. 3, pp. 221229, 2009.
[35] D. Heckerman, D.M. Chickering, C. Meek, R. Rounthwaite, and C. Kadie, "Dependency Networks for Inference, Collaborative Filtering, and Data Visualization," J. Machine Learning Research, vol. 1, pp. 4975, 2001.
[36] O. Hirose, R. Yoshida, S. Imoto, R. Yamaguchi, T. Higuchi, D.S. CharnockJones, C. Print, and S. Miyano, "Statistical Inference of Transcriptional ModuleBased Gene Networks from Time Course Gene Expression Profiles by Using State Space Models," Bioinformatics, vol. 24, no. 7, pp. 932942, 2008.
[37] M.J.L. de Hoon, S. Imoto, K. Kobayashi, N. Ogasawara, and S. Miyano, "Inferring Gene Regulatory Networks from TimeOrdered Gene Expression Data of Bacillus Subtilis Using Differential Equations," Proc. Pacific Symp. Biocomputing, vol. 8, pp. 1728, 2003.
[38] K. Basso, A.A. Margolin, G. Stolovitzky, U. Klein, R. DallaFavera, and A. Califano, "Reverse Engineering of Regulatory Networks in Human B Cells," Nature Genetics, vol. 37, pp. 382390, 2005.
[39] T. Shimamura, R. Yamaguchi, S. Imoto, and S. Miyano, "Weighted Lasso in Graphical Gaussian Modeling for Large Gene Network Estimation Based on Microarray Data," Genome Informatics, vol. 19, pp. 142153, 2007.
[40] A. Dobra, B. Jones, C. Hans, J. Nevis, and M. West, "Sparse Graphical Models for Exploring Gene Expression Data," J. Multivariate Analysis, vol. 90, pp. 196212, 2004.
[41] H. Toh and K. Horimoto, "Inference of a Genetic Network by a Combined Approach of Cluster Analysis and Graphical Gaussian Modeling," Bioinformatics, vol. 18, no. 2, pp. 287297, 2002.
[42] H. Zou, "Adaptive Lasso and Its Oracle Properties," J. Am. Statistical Assoc., vol. 101, pp. 14181429, 2006.