An introduction to Bioinformatics Algorithms

1. An introduction to Bioinformatics Algorithms Qi Liu email: qi.liu@vanderbilt.edu Presented by Liu Qi

2. Description of the Course • introduce the basic computational issues and methods used in molecular biology • Topics will include basic algorithms for alignment of biological sequences and structures. These include, for example, dynamic programming algorithms for alignment, motif definition and computation, Hidden Markov Models, neural networks etc. Presented By Liu Qi

3. Related Courses • University of Washington （Computational Biology) • http://www.cs.washington.edu/education/courses/527/09au/ • Tel Aviv University School of Computer Science (Algorithms in Molecular Biology ) • http://www.cs.tau.ac.il/~rshamir/algmb/algmb-archive.htm • Stanford(Representations and Algorithms for Computational Molecular Biology  ) • http://www-helix.stanford.edu/courses/bmi214/ • MIT(Foundations of Computational and Systems Biology) • http://ocw.mit.edu/courses/biology/7-91j-foundations-of-computational-and-systems-biology-spring-2004/ • Imperial College (Introduction to Bioinformatics) • http://www.doc.ic.ac.uk/~sgc/teaching/341/ Presented By Liu Qi

4. Reference Books • An Introduction to Bioinformatics AlgorithmsNeil C. Jones and Pavel A. Pevzner • Bioinformatics: The Machine Learning Approachby Baldi, Pierre. Brunak, Søren. • Bioinformatics: Sequence and genome analysis (cold spring harbor laboratory press) Mount, David W. • Biological sequence analysis: Probabilistic models of proteins and nucleic acids (Cambridge university press) R. Durbin et al. Presented By Liu Qi

5. Content • Pairwise Sequence Alignment • Multiple sequence alignment • Motif discovery • Protein secondary structure prediction • Microarrays, Clustering and Classification •  Topics for Discussion Presented By Liu Qi

6. Pairwise Sequence alignment • Dot matrix (intuitive) • Dynamic programming (exact) • Global Needleman-Wunsch • Local Smith-Waterman • Word or k-tuple (heuristic) • FASTA • BLAST Presented By Liu Qi

7. Multiple sequence alignment • Dynamic Programming • Heuristic Alignment Methods • Progressive alignment • clustalw • Iterative refinement • Hidden Markov Model Presented By Liu Qi

8. Motif discovery • Greedy Search • Expectation Maximization • Gibbs sampler • … Presented By Liu Qi

9. Protein secondary structure prediction • Chou-Fasman predictions • Garnier, Osguthorpe and Robson • Neural networks • Nearest neighbor methods • Consensus prediction approaches Presented By Liu Qi

10. Microarrays, Clustering and Classification  • Normalization • Differential Expression Genes Detection • Clustering • – Hierarchical • – K-means • – SOM • Class Prediction • Integrating other Biological Knowledge Presented By Liu Qi

11. Topics for Discussion • Proteomics data analysis • NGS Data Analysis • Integrative analysis of various omics data • ….. Presented By Liu Qi