Pensum/syllabus INF380 Spring 2006

Eidhammer, Jonassen, Taylor: Protein Bioinformatics - An Algorithmic Approach to Sequence and Structure Analysis. Wiley 2004. Chapters 4-9, 14-15, except the following sections: 4.3.6-4.3.7, 4.4.3, 4.5, 5.5, 7.7-7.8, 8.7-8.8, 9.3.3, 14.7-14.9, 15.6-15.8. Book website with errata and supplementary information. Some more errata not mentioned on the website.

• Ewens and Grant: Statistical Methods in Bioinformatics: An Introduction. Springer, 2002.
  Ch. 4.4-4.9, Ch. 11 (Markov Chains and Hidden Markov Models).
• Selected articles on gene prediction (see the lecture slides):
  • Uberbacher, E.C. and Mural, R.J. (1991). Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. Proc. Natl. Acad. Sci. USA, 88, 11261-11265
  • Pedersen, A.G., and Nielsen, H. (1997). Neural network prediction of translation initiation sites in eukaryotes: Perspectives for EST and Genome analysis. In Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, ISMB97, AAAI Press, 226-233.
  • Hatzigeorgiou, A.G. (2002). Translation initiation start prediction in human cDNAs with high accuracy. Bioinformatics, 18, 343-350.
  • Burset, M. and Guigo, R. (1996). Evaluation of gene structure prediction programs. Genomics, 34, 353-367.
  • Claverie, J.-M. (1997). Computational methods for the identification of genes in vertebrate genome sequences. Hum. Mol. Genet., 6, 1735-1744.
  • Krogh, A., Saira Mian, I., and Haussler, D. (1994). A Hidden Markov Model that finds genes in E. coli DNA. Nucleic Acids Res., 22, 4768-4778.
  • Burge, C. and Karlin, S. (1997). Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
• Gene Ontology (see the lecture slides):
  • The Gene Ontology Consortium (2000). Gene Ontology: tool for the unification of biology. Nat. Genet. 25, 25-29.
  • The Gene Ontology Consortium (2004). The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res., 32, D258-D261.
• The assignments and exercises.

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