Class activities will be recorded here.

This page has the entire plan for the semester. For weeks in the future, consider it a plan subject to change. For weeks in the past consider it a record of what we have done. As for the current week, keep a watch for updates and changes.

Week 1 : August 27,29

• Tuesday

  Course introduction (pdf)

  Thursday

  Some more biology (pdf)

Week 2 : Sept 3,5

• Tuesday

  Motif finding (sections 4.4-4.6 in Jones and Pevzner) (pdf)
  Assignment 1 is available

  Thursday

  Motif finding: Gibbs sampling (section 12.2 in Jones and Pevzner) (pdf)

Week 3 : Sept 10,12

• Tuesday

  Sequence alignment (chapter 6 in Jones and Pevzner) (pdf)

  Thursday

  Sequence alignment (cont)

Week 4 : Sept 17,19

• Tuesday

  Phylogeny (sections 10.5-10.7 in Jones and Pevzner) (pdf)
  Assignment 2 is available

  Thursday

  Guest lecture by Rachel Mueller from the Biology Department

Week 5 : Sept 24,26

• Tuesday

  Phylogeny (sections 10.5-10.7 in Jones and Pevzner) (pdf)

  Thursday

  Review of probability theory (pdf)

Week 6 : Oct 1,3

• Tuesday

  Hidden Markov models (pdf)
  Assignment 3 is available

  Thursday

  More HMMs

Week 7 : Oct 8,10

• Tuesday

  Review for midterm

  Thursday

  Midterm