Download References - Mines ParisTech CBIO

biogm
October 12, 2009
References
[1] 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.
[2] 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.
[3] 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.
[4] 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.
[5] 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.
[6] 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.
[7] 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.
[8] 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.
1
[9] 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.
[10] 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.
[11] 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.
[12] K. Murphy and S. Mian. Modelling gene expression data using dynamic
Bayesian networks. Technical report, Computer Science Division, University of California, Berkeley, CA., 1999.
[13] 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.
[14] 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.
[15] 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.
2