Main Page
From BTRY4840/6840 Website
This is the course web page for BTRY 4840/6840, "Computational Genomics" (Fall 2009).
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. It is due Nov 6.
- Homework #4 has been posted. It is due Oct 23.
- Homework #3 has been posted. It is due Oct 9.
- Homework #2 has been posted. It is due Sep 25.
- Notes for recitation #1 (9/3) have been posted.
- The lecture schedule has been updated. It should be pretty well set through Fall Break, but there will likely be a few changes later in the semester.
- Homework #1 has been posted. It is due Sep 11.
- Welcome to the course! The first meeting will be on Thurs, Aug 28 in Plant Science 143 from 11:40-12:55
General Information
- Lectures: Tues/Thurs, 11:40-12:55, Plant Science 143
- Recitations: Tues, 1:25-2:15, Plant Science 143
- Credit Hours: 4 (S/U or letter)
- Instructor: Adam Siepel, 102E Weill
- TA: Abra Brisbin, 101 Biotech
- Office Hours: Tues, 4:30-5:30
Resources
- Syllabus
- Questionnaire
- Notes from recitation of 9/3: questions, solutions
- Project guidelines and ideas
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.
- DOE HGP Genomics Primers
- NCBI "What is a Genome" Primer
- Wikipedia on bioinformatics
Lecture Schedule
| Date | Readings | Topics | Slides |
|---|---|---|---|
| Aug 27 | MBG or similar as needed | Course introduction. Molecular biology background. | |
| Sep 1 | DEKM ch 1, pp 300-314; DTW ch 2&3; HC, CB or similar as needed | Probability and statistics background. | |
| Sep 3 | J&P ch 2 | Statistics. | |
| Sep 8 | DEKM ch 2; JP ch 5 or CLRS ch 15 | Finish statistics; Dynamic programming. | |
| Sep 10 | – | No lecture; ACS on travel | – |
| Sep 15 | DEKM pp 320-322 | Sequence alignment. | |
| Sep 17 | Wasserman & Sandelin review article | More on alignment; introduction to motif models. | |
| Sep 22 | – | Information theory; Markov models. | |
| Sep 24 | DEKM pp 46-58; Supplementary: Eddy Rabiner | Hidden Markov models. | |
| Sep 29 | DEKM pp 58-61, 68-79 | More on HMMs. | |
| Oct 1 | DEKM pp 160-165, 173-176, 192-202; F ch 1&2, pp 196-206, 248-255 | More on HMMs; phylogenetic models. | |
| Oct 6 | – | Phylogenetic models. | |
| Oct 8 | DEKM pp 202 | More on phylogenetic models. | |
| Oct 13 | – | Happy Fall Break! | – |
| Oct 15 | Jordan ch 2; See also this review | General graphical models. | |
| Oct 20 | Jordan ch 3,4,9 | More on graphical models. | |
| Oct 22 | DEKM pp 323-325, Jordan ch 9-10 | Expectation maximization (EM). | |
| Oct 27 | DEKM pp 63-66 | EM for HMMs and motif models. | |
| Oct 29 | DEKM pp 314-319, 154-159; Jordan ch 21 | Introduction to MCMC. | |
| Nov 3 | – | Gibbs sampling and use in motif finding. | |
| Nov 5 | – | Regulatory network inference (Ben Logsdon). | |
| Nov 10 | DEKM ch 4 | Statistical pairwise alignment. | |
| Nov 12 | DEKM pp 165-172,189-191; F ch 11 | Phylogeny reconstruction (Ilan Gronau). | |
| Nov 17 | – | Fast heuristic alignment and short-read sequence analysis. | |
| Nov 19 | DEKM ch 9 & 10 | Stochastic context-free grammars and RNA structure prediction. | |
| Nov 24 | DEKM ch 6 | Multiple alignment. | |
| Nov 26 | – | Happy Thanksgiving! | – |
| Dec 1 | – | Applied motif finding (Charles Danko). | |
| Dec 3 | Phylo-HMM review | Applied comparative genomics. |
Homework Schedule
| Homework | Date Assigned | Date Due | Topics | Data |
|---|---|---|---|---|
| HW#1 | Aug 28 | Sep 11 | Probability and statistics warm up | |
| HW#2 | Sep 11 | Sep 25 | Dynamic programming and sequence alignment | sequences.fa |
| HW#3 | Sep 25 | Oct 9 | Motif models, HMMs | sequence.fa |
| HW#4 | Oct 9 | Oct 23 | Phylogenetic models | apoe.fa |
| Proposal | Oct 26 | Nov 6 | Detailed project proposal | |
| HW#5 | Oct 25 | Nov 6 | EM and Gibbs sampling |
