Final Projects
Project presentations will be given on May 14 and 17 at 10am.Components
Final Projects for Graduate Credit will have two components:- One final project from this list – the choice should be made by discussing with Sorin. It will entitle a final presentation and a paper.
- One program piece of the GENOMATHICA package an enhanced version of one of the class homeworks. A list of such to be posted soon.
Suggested Projects
- ASSEMBLY – metagenomics, assembly simulations, percolation models.
- MULTIPLE ALIGNMENT – approaches of integrating pairwise alignments into a multiple alignment, Fiedler vector algorithm, progressive alignment.
- PROTEIN FOLDING – application of voting theory to the problem of preference of interaction of amino acids in protein folds, and the inference of energy functions or statistical potentials for folding models.
- HIDDEN MARKOV MODELS – generalization of the HMM to probabilistic context-free and context-sensitive grammars.
- PROGRAMMING LANGUAGES FOR GENOMICS – two components: CELLARIUM and GENOMATHICA – programming frameworks for integrative genomics workflows.
- GENETIC VARIATION AND GENETIC BASIS OF DISEASE – SNPs, Haplotypes and Disease Associations – Population Stratification.
- REGULATORY GENOMICS – regulatory modules and motifs, CRM LEXICON, automatic literature extraction of regulatory genomics information.
- ALTERNATIVE SPLICING – project for Biologist
- VIRUS GENOME – project for Biologist
- BACTERIA GENOME – project for Biologist
- MEDICAL BIOINFORMATICS OF CANCER