1. Introduction BNFO 602 Usman Roshan

2. Course grade Project: –Find a bioinformatics topic by Feb 5th. This can be a paper or a research question you wish to answer. Your project topic must be approved by me in person or via email. –Present 10 minute project proposal on Feb 12th. This deadline is strict and NO EXCEPTIONS will be made under ANY circumstances. –No project proposal = no grade –45 minute final presentations begin in March/April. Final report due on last class day.

3. Suggested project topics Genome-wide association studies: SNP selection, disease risk prediction Sequence alignment: sequence, structure, hidden Markov models Phylogenetics: distance-based, parsimony, and likelihood reconstruction Protein function prediction: conserved motif detection methods, classification methods Protein networks: network alignment Classification methods applied to bioinformatics problems

4. Journals Bioinformatics (Oxford Press) BMC Bioinformatics (Biomed Central) Genome Research (CSHL) PLoS Computational Biology (ISCB)

5. Conferences Intelligent Systems in Molecular Biology (ISMB) Research in Computational Biology (RECOMB) Computational Systems Bioinformatics (CSB) Workshop on Algorithms in Bioinformatics (WABI) International Conference on Bioinformatics and Bioengineering (BIBE)

6. Course schedule Intro and background today More background on bioinformatics problems Proposal presentations Machine learning algorithms in bioinformatics: –Dimensionality reduction (principal component analysis) –Support vector machines Final project presentations