Syllabus for Roster(s):

  • 17Sp BME 6550-003 (ENGR)
  • 17Sp ECE 6502-003 (ENGR)
In the UVaCollab course site:   17SP Inference Methods

Topics

  1. Review of probability
    1. Random variables & processes
    2. Markov chains and Perron-Frobenius theory
    3. Hidden Markov models 
  2. Inference, estimation, and phylogenetics
    1. Maximum likelihood
    2. Hypothesis testing
    3. Bayesian inference
    4. Monte-Carlo Markov chains
    5. Applications to phylogenetics
  3. Hidden Markov models in computational biology
    1. Three problems: evaluation, decoding, and inference
    2. Gapped sequence alignment
    3. Gene finding
    4. Protein classification
  4. Information theory and computational biology:
    1. Introduction to Information theory
    2. Source coding and compression of biological sequences
    3. Stochastic approximation and sequence evolution
    4. Communication channels and sequence reconstruction
    5. Constrained codes and models of DNA as language