biogm references

[Murphy1999Modelling] K. Murphy and S. Mian. Modelling gene expression data using dynamic Bayesian networks. Technical report, Computer Science Division, University of California, Berkeley, CA., 1999. [ bib | .pdf ]
[Heckerman1999tutorial] D. Heckerman. A tutorial on learning with Bayesian networks. In M. Jordan, editor, Learning in graphical models, pages 301-354. MIT Press, Cambridge, MA, USA, 1999. [ bib | .pdf ]
[Friedman2000Using] N. Friedman, M. Linial, I. Nachman, and D. Pe'er. Using Bayesian networks to analyze expression data. J. Comput. Biol., 7(3-4):601-620, 2000. [ bib | DOI | http | .pdf | Abstract ]
[Imoto2002Bayesian] S. Imoto, K. Sunyong, T. Goto, S. Aburatani, K. Tashiro, S. Kuhara, and S. Miyano. Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network. Proc. IEEE Comput. Soc. Bioinform. Conf., 1:219-227, 2002. [ bib | DOI | http | .pdf | Abstract ]
[Imoto2002Estimation] S. Imoto, T. Goto, and S. Miyano. Estimation of genetic networks and functional structures between genes by using Bayesian networks and nonparametric regression. Pac. Symp. Biocomput., pages 175-186, 2002. [ bib | .pdf | .pdf | Abstract ]
[Segal2003Module] E. Segal, M. Shapira, A. Regev, D. Pe'er, D. Botstein, D. Koller, and N. Friedman. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet., 34(2):166-176, Jun 2003. [ bib | DOI | http | .pdf | Abstract ]
[Jansen2003Bayesian] R. Jansen, H. Yu, D. Greenbaum, Y. Kluger, N.J. Krogan, S. Chung, A. Emili, M. Snyder, J.F. Greenblatt, and M. Gerstein. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science, 302(5644):449-453, 2003. [ bib | DOI | http | .pdf | Abstract ]
[Imoto2003Bayesian] S. Imoto, S. Kim, T. Goto, S. Miyano, S. Aburatani, K. Tashiro, and S. Kuhara. Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network. J. Bioinform. Comput. Biol., 1(2):231-252, Jul 2003. [ bib | DOI | http | .pdf | Abstract ]
[Alexandersson2003SLAM] M. Alexandersson, S. Cawley, and L. Pachter. SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Res., 13(3):496-502, Mar 2003. [ bib | DOI | http | .pdf | Abstract ]
[Xing2004LOGOS] E. P. Xing, W. Wu, M. I. Jordan, and R. M. Karp. LOGOS: A modular Bayesian model for de novo motif detection. J. Bioinform. Comput. Biol., 2:127-154, 2004. [ bib | DOI | http | .pdf | Abstract ]
[Segal2004module] E. Segal, N. Friedman, D. Koller, and A. Regev. A module map showing conditional activity of expression modules in cancer. Nat. Genet., 36(10):1090-1098, Oct 2004. [ bib | DOI | http | .pdf | Abstract ]
[McAuliffe2004Multiple-sequence] J. D. McAuliffe, L. Pachter, and M. I. Jordan. Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. Bioinformatics, 20(12):1850-1860, Aug 2004. [ bib | DOI | http | .pdf | Abstract ]
[Engelhardt2005Protein] B. E. Engelhardt, M. I. Jordan, K. E. Muratore, and S. E. Brenner. Protein Molecular Function Prediction by Bayesian Phylogenomics. PLoS Comput. Biol., 1(5):e45, Oct 2005. [ bib | DOI | http | .pdf | Abstract ]
[Beal2005Bayesian] M. J. Beal, F. Falciani, Z. Ghahramani, C. Rangel, and D. L. Wild. A Bayesian approach to reconstructing genetic regulatory networks with hidden factors. Bioinformatics, 21(3):349-356, Feb 2005. [ bib | DOI | http | .pdf | Abstract ]
[Majoros2005Efficient] W. H. Majoros, L. Pertea, and S. L. Salzberg. Efficient implementation of a generalized pair hidden Markov model for comparative gene finding. Bioinformatics, 21(9):1782-1788, May 2005. [ bib | DOI | http | .pdf | Abstract ]

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