Detection of viruses via statistical gene expression analysis

IEEE Transactions on Biomedical Engineering

Volumn 58, Issue 3 PART 1, 2011, Pages 468-479

  Chen, Minhua ^a   Carlson, David ^a   Zaas, Aimee ^b   Woods, Christopher W ^b   Ginsburg, Geoffrey S ^b   Hero III, Alfred ^c   Lucas, Joseph ^b   Carin, Lawrence ^a  

^a Duke University   (United States)

^b DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Bayesian Lasso; elastic net (ENet); grouping effect; multitask learning; variable selection

Indexed keywords

BAYESIAN; ELASTIC NET; GROUPING EFFECT; MULTITASK LEARNING; VARIABLE SELECTION;

BAYESIAN NETWORKS; GENE EXPRESSION; VIRUSES;

COMPUTER VIRUSES;

ARTICLE; BAYES THEOREM; ELASTIC TISSUE; GENE EXPRESSION REGULATION; INFLUENZA VIRUS A H1N1; INFLUENZA VIRUS A H3N2; NONHUMAN; RESPIRATORY SYNCYTIAL PNEUMOVIRUS; RHINOVIRUS; VIRUS DETECTION;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; BAYES THEOREM; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; HOST-PATHOGEN INTERACTIONS; HUMANS; INFLUENZA A VIRUS, H1N1 SUBTYPE; INFLUENZA A VIRUS, H3N2 SUBTYPE; RESPIRATORY SYNCYTIAL VIRUSES; RHINOVIRUS; VIRUS DISEASES;

EID: 79952129490     PISSN: 00189294     EISSN: None     Source Type: Journal    
DOI: 10.1109/TBME.2010.2059702     Document Type: Article

References (31)

1. G. J. McLachlan, K.-A. Do, and C. Ambroise, Analyzing Microarray Gene Expression Data. New York: Wiley, 2004.
2. H. Zou and T. Hastie, "Regularization and variable selection via the elastic net," J. R. Statist. Soc. Series B, vol. 67, pp. 301-320, 2005.
3. R. Tibshirani, "Regression shrinkage and selection via the lasso," J. R. Statist. Soc. Series B, vol. 58, pp. 267-288, 1996.
4. M. Figueiredo, R. Nowak, and S. Wright, "Gradient projection for sparse reconstruction: Application to compressed sensing and other inverse problems," IEEE J. Sel. Topics Signal Process., vol. 1, no. 4, pp. 586-597, Dec. 2007.
5. S. Chen, D. Donoho, and M. Saunders, "Atomic decomposition by basis pursuit," SIAM J. Sci. Comput., vol. 20, pp. 33-61, 1998.
6. T. Park and G. Casella, "The bayesian lasso," J. Amer. Statist. Assoc., vol. 103, pp. 681-686, 2008.
7. L. Bornn, R. Gottardo, and A. Doucet, "Grouping priors and the Bayesian elastic net," arXiv: 1001.4083v1[stat.ME], Jan. 2010.
8. J. Albert and S. Chib, "Bayesian analysis of binary and polychotomous response data," J. Amer. Statist. Assoc., vol. 88, pp. 669-679, 1993.
9. J. Ashford and R. Sowden, "Multi-variate probit analysis," Biometrics, vol. 26, pp. 535-546, 1970.
10. S. Ji, D. Dunson, and L. Carin, "Multitask compressive sensing," IEEE Trans. Signal Process., vol. 57, no. 1, pp. 92-106, Jan. 2009.
11. H. Liu, J. Lafferty, and L. Wasserman, "Nonparametric regression and classification with joint sparsity constraints," in Advances in Neural Information Processing Systems (NIPS), MIT Press, vol. 21, 2008, pp. 969-976. [Online]. Available: http://books.nips.cc/papers/files/nips21/NIPS2008-0329.pdf
12. A. Kaban, "On bayesian classificationwith laplace priors," Pattern Recognit. Lett., vol. 28, pp. 1271-1282, 2007.
13. M. Figueiredo, "Adaptive sparseness for supervised learning," IEEE Trans. Pattern Anal. Mach. Intell., vol. 25, no. 9, pp. 1150-1159, Sep. 2003.
14. J. Griffin and P. Brown, "Bayesian adaptive lassos with non-convex penalization," Centre for Research in Statistical Methodology, University of Warwick, Tech. Rep. 07-2, 2007.
15. H. Zou, "The adaptive lasso and its oracle properties," J. Amer. Statist. Assoc., vol. 101, pp. 1418-1429, 2006.
16. M. Kyung, J. Gill, M. Ghosh, and G. Casella, "Penalized regression, standard errors, and Bayesian lassos," Bayesian Anal., vol. 5, pp. 369-412, 2010.
17. H. Zou and H. Zhang, "On the adaptive elastic-netwith a diverging number of parameters," Ann. Statist., vol. 37, pp. 1733-1751, 2009.
18. T. Ferguson, "A Bayesian analysis of some nonparametric problems," Ann. Statist., vol. 1, pp. 209-230, 1973.
19. J. Sethuraman, "A constructive definition of the dirichlet prior," Statistica Sinica, vol. 2, pp. 639-650, 1994.
20. M. Beal, "Variational algorithms for approximate Bayesian inference," Ph.D. dissertation, Gatsby Computational Neuroscience Unit, Univ. College London, London, U.K., 2003.
21. M. Woodbury, "Inverting modified matrices," Statistical Research Group, Princeton University, Princeton, NJ, Tech. Rep. 42, 1950.
22. B. Efron, T. Hastie, I. Johnstone, and R. Tibshirani, "Least angle regression annals of statistics," Ann. Statist., vol. 32, pp. 460-465, 2004.
23. T. Golub, D. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek, J. Mesirov, H. Coller, M. Loh, J. Downing, M. Caligiuri, C. Bloomfield, and E. Lander, "Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring," Science, vol. 286, pp. 531-537, 1999.
24. A. Rakotomamonjy, "Variable selection using SVM-based criteria," J. Mach. Learning Res., vol. 3, pp. 1357-1370, 2003.
25. J. Khan, J. Wei, M. Ringner, L. Saal, M. Ladanyi, F. Westermann, F. Berthold, M. Schwab, C. Antonescu, C. Peterson, and P. Meltzer, "Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks," Nature Med., vol. 7, pp. 673-679, 2001.
26. A. K. Zaas, M. Chen, J. Lucas, T. Veldman, A. O. Hero, J. Varkey, R. Turner, C. Oien, S. Kingsmore, L. Carin, C. W. Woods, and G. S. Ginsburg, "Peripheral blood gene expression signatures characterize symptomatic respiratory viral infection," Cell Host Microbe, vol. 6, pp. 207-217, 2009.
27. M. Tipping, "Sparse bayesian learning and the relevance vector machine," J. Mach. Learning Res., vol. 1, pp. 211-244, 2001.
28. S. Der, A. Zhou, B. G. Williams, and R. Silverman, "Identification of genes differentially regulated by interferon α, β, or γ using oligonucleotide arrays," Proc. Nat. Ac. Sci., vol. 95, pp. 15 623-15 628, 1998.
29. A. Garcia-Sastre, "Antiviral response in pandemic influenza viruses," Emerg. Infect. Dis., vol. 12, pp. 43-47, 2006.
30. C. Zhao, G. Sun, S. Li, M.-F. Lang, S. Yang, W. Li, and Y. Shi, "MicroRNA let-7b regulates neural stem cell proliferation and differentiation by targeting nuclear receptor TLX signaling," Proc. Nat. Ac. Sci., vol. 107, pp. 1876-1881, 2010.
31. G. Versteeg, B. Hale, S. van Boheemen, T. Wolff, D. Lenschow, and A. GarcÃ-a-Sastre, "Species-specific antagonism of host ISGylation by the influenza B virus NS1 protein," J. Virol., vol. 10, pp. 5423-5430, 2010.