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This is the course web page for BTRY 4840/6840, "Computational Genomics" (Fall 2011).

Please check this page frequently throughout the semester. It will continually be updated with information you will need. Keep in mind that the schedules for lectures and homeworks are provisional.

Contents

Announcements

  • Homework #5 has been posted.
  • Homework #4 has been posted
  • Homework #3 has been posted.
  • Homework #2 has been posted.
  • Class is cancelled for Sep. 8. This will be true even if the University opens at 11AM.
  • The due date for homework #1 has been moved to Sep 12.
  • We now have a room for the discussion section: Comstock B108 (4:00-4:50PM Tues). Unfortunately, this room does not support videoconferencing.
  • Homework #1 has been posted. It is due Sep 9. Note that you will need a password to access PDFs from this site. If you need it before Tues you can email me.
  • The course mailing list is now in place (btry4840-l@cornell.edu). To join, follow these instructions
  • We have tentatively rescheduled the discussion section for Tues 4-5PM. We are still working on finding a room. We plan to hold the first meeting on Tues 8/30.
  • Office hours have been rescheduled to Thurs 4-5PM, to avoid a conflict with the discussion section.
  • The room for the course has been changed to Weill 224, to permit videoconferencing with NYC. We will meet in Weill 224 every day except October 20, when we will be in Weill 321.

General Information

  • Lectures: Tues/Thurs, 11:40-12:55, Weill 224
  • Recitations: Tues, 4:00-5:00 [room TBD]
  • Credit Hours: 4 (S/U or letter)
  • Instructor: Adam Siepel, 102E Weill
  • TA: Brad Gulko, 102 Weill
  • Instructor Office Hours: Thurs, 4:00-5:00
  • Mailing list: btry4840-l@cornell.edu

Resources

Books

  • Primary textbook:
    • Durbin R, Eddy SR, Krogh A, and Mitchison G [DEKM], Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, 1998 (10th printing, 2006).
  • Auxiliary bioinformatics books:
    • Felsenstein J [F], Inferring Phylogenies, Sinauer Associates, Inc., 2004.
    • Jones NC, Pevzner PA [JP], An Introduction to Bioinformatics Algorithms, MIT Press, 2004.
    • Deonier RC, Tavare S, Waterman MS [DTW], Computational Genome Analysis: An Introduction, Springer, 2005.
    • Ewens WJ, Grant G [EG], Statistical Methods in Bioinformatics: An Introduction, Springer, 2005.
  • Recommended reference books:
    • Hogg RV, Craig AT [HC], Introduction to Mathematical Statistics. Prentice Hall, 1995.
    • Casella G, Berger RL [CB], Statistical Inference. Duxbury Press, 2001.
    • Cormen TH, Leiserson CE, Rivest RL, Stein C [CLRS], Introduction to Algorithms. MIT Press, 2001.
    • Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R [MBG], Molecular Biology of the Gene. CSHL Press, 2004.

Online tutorials

Here is a small collection of possibly useful online tutorials on genomics and bioinformatics. Please email me if you find others that are particularly useful.

Lecture Schedule

Date Readings Topics Slides
Aug 25 MBG or similar as needed Course introduction. PDF
Aug 30 DEKM ch 1, pp 300-314; DTW ch 2&3; HC, CB or similar as needed Molecular biology background. Probability and statistics intro. PDF
Sep 1 J&P ch 2 More statistics background. PDF
Sep 6 More statistics background. PDF
Sep 8 DEKM ch 2; JP ch 5 or CLRS ch 15 Finish statistics. Dynamic programming. PDF
Sep 13 DEKM pp 320-322 Sequence alignment. PDF
Sep 15 Wasserman & Sandelin review article More on alignment; introduction to motif models. PDF
Sep 20 Information theory; Markov models. PDF
Sep 22 DEKM pp 46-58; Supplementary: Eddy Rabiner Hidden Markov models. PDF
Sep 27 DEKM pp 58-61, 68-79 More on HMMs. PDF
Sep 29 DEKM pp 160-165, 173-176, 192-202; F ch 1&2, pp 196-206, 248-255 More on HMMs; phylogenetic models. PDF
Oct 4 Phylogenetic models. PDF
Oct 6 DEKM pp 202 More on phylogenetic models. PDF
Oct 11 Happy Fall Break!
Oct 13 DEKM pp 165-172,189-191; F ch 11 Phylogeny reconstruction (Ilan Gronau). PDF
Oct 18 Jordan ch 2; See also this review General graphical models. PDF
Oct 20 Jordan ch 3,4,9 More on graphical models. PDF
Oct 25 DEKM pp 323-325, Jordan ch 9-10 Expectation maximization (EM). PDF
Oct 27 DEKM pp 63-66 EM for HMMs and motif models. PDF
Nov 1 DEKM pp 314-319, 154-159; Jordan ch 21 Introduction to MCMC. PDF
Nov 3 Gibbs sampling and use in motif finding. PDF
Nov 8 Positive selection (Leo Arbiza). PDF
Nov 10 DEKM ch 4 Statistical pairwise alignment. PDF
Nov 15 Fast heuristic alignment and short-read sequence analysis. PDF
Nov 17 DEKM ch 9 & 10 Stochastic context-free grammars and RNA structure prediction. PDF
Nov 22 DEKM ch 6 Multiple alignment. PDF
Nov 24 Happy Thanksgiving!
Nov 29 Gene duplication and loss (Matt Rasmussen) PDF
Dec 1 Phylo-HMM review Applied comparative genomics. PDF

Homework Schedule

Homework Date Assigned Date Due Topics Data
HW#1 Aug 26 Sep 12 Probability and statistics warm up
HW#2 Sep 10 Sep 23 Dynamic programming and sequence alignment sequences.fa
HW#3 Sep 24 Oct 7 Motif models, HMMs sequence.fa
HW#4 Oct 11 Oct 24 Phylogenetic models apoe.fa
Proposal Oct 25 Nov 11 Detailed project proposal
HW#5 Oct 24 Nov 7 EM and Gibbs sampling