Reading list of the first half of STAT 598T, Spring 2002

1. Background references
   • Page, R. D. M and Holmes, E. C., "Molecular Evolution: A phylogenetic approach", Blackwell Science.
   • Durbin, R., Eddy, S., Krogh, A., and Mitchison, G. (1998) "Biological sequence analysis: Probabilistic models of proteins and nucleic acids", Cambridge University Press.
2. Protein motif alignment
   • Gribskov, M., McLachlan, A.D. and Eisenberg, D. (1987) "Profile analysis: detection of distantly related proteins." Proc. Natl. Acad. Sci. USAR 84:4355-4358.
   • Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J. (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.
   • Henikoff, S., Henikoff, J.G, Alford, W.J, and Pietrokovski, S. (1995), "Automated construction and graphical presentation of protein blocks from unaligned sequences", Gene 163:GC17-26.
   • Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.
   • S.R. Eddy. Profile hidden Markov models. Bioinformatics 14:755-763, 1998.
   • Liu, J. S., Neuwald, A. F., and Lawrence, C. E. (1995), "Bayesian models for multiple local sequence alignment and Gibbs sampling strategies", JASA 90, no.432, p.1156-1170.
   • Bucher, P., Karplus, K., Moeri, N., & Hofmann, K. (1996). "A flexible motif search technique based on generalized profiles". Comput Chem, 20(1), 3-23.

3. Probabilistic model for phylogenetic trees
   • Felsenstein, J. 1981, "Evolutionary trees from DNA sequences: a maximum likelihood approach", Journal of Molecular Evolution 17:368-376.
   • Kishino, H., Miyata, T. and Hasegawa, M. 1990, "Maximum likelihood inference of protein phylogeny and the origin of chloroplasts", Journal of Molecular Evolution 31:151-160.
   • Mitchison, G. and Durbin, R. 1995, "Tree-based maximal likelihood substitution matrices and hidden Markov models", Journal of Molecular Evolution 41:1139-1151.
   • Rannala, B. and Yang, Z. 1996, "Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference", Journal of Molecular Evolution 43:304-311.