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From Computational Genomics Course

This is the course web page for BTRY 484/684, "Computational Genomics" (Fall 2007).

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 1 Announcements 2 General Information 3 Resources 4 Books 5 Online tutorials 6 Lecture Schedule 7 Homework Schedule

Announcements

• Homework #5 has been posted (10/30)
• Homework #4 has been posted (10/15)
• Guidelines and ideas for the class project have been posted (10/14)
• The lecture schedule for the remainder of the class has been revised (10/14)
• The midterms have been graded and will be returned on Tues 10/16. Still working on homework #3. (10/14)

General Information

• Lectures: Tues/Thurs, 11:40-12:55, Bradfield 105
• Recitations: Thurs, 1:25-2:15, Plant Science 143
• Credit Hours: 4 (S/U or letter)
• Professor: Adam Siepel, 101 Biotech
• Office Hours: Tues, 4:30-5:30

Resources

• Syllabus
• Questionnaire
• 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

• CBCB Sequence Assembly Primer

• Wikipedia on bioinformatics

Lecture Schedule

Date	Readings	Topics	Slides
Aug 23	MBG or similar as needed	Course introduction. Molecular biology background.	PDF
Aug 28	DEKM ch 1, pp 300-314; DTW ch 2&3; HC, CB or similar as needed	Probability and statistics background.	PDF
Aug 30	–	More on statistics.	PDF
Sep 4	J&P ch 2	Intro to algorithms.	PDF
Sep 6	DEKM ch 2; JP ch 5 or CLRS ch 15	Dynamic programming and sequence alignment.	PDF
Sep 11	DEKM pp 320-322; Wasserman & Sandelin review article	More on alignment; motif models.	PDF
Sep 13	–	Information theory and motif models	PDF
Sep 18	DEKM pp 46-58; Supplementary: Eddy Rabiner	Hidden Markov models.	PDF
Sep 20	DEKM pp 58-61, 68-79	More on HMMs.	PDF
Sep 25	DEKM pp 160-165, 173-176, 192-202; F ch 1&2, pp 196-206, 248-255	Phylogenetic models.	PDF
Sep 27	DEKM pp 202	More on phylogenetic models.	PDF
Oct 2	Jordan ch 2; See also this review	General graphical models.	PDF
Oct 4	Jordan ch 3&4	More on graphical models.	PDF
Oct 9	–	Happy Fall Break!	–
Oct 11	–	midterm	–
Oct 16	Jordan ch 4&9	More on graphical models	PDF
Oct 18	DEKM pp 323-325, Jordan ch 9-10	Expectation maximization (EM).	PDF
Oct 23	DEKM pp 63-66	EM for HMMs and motif models	PDF
Oct 25	–	Guest lecture by Tomas Vinar. Applied gene finding.	PDF
Oct 30	DEKM pp 314-319, 154-159	Introduction to MCMC.	PDF
Nov 1	Jordan ch 21	Gibbs sampling and use in motif finding.	PDF
Nov 6	DEKM section 2.5; Brown et al. review	Guest lecture by Brona Brejova. Hash-based alignment.	PDF
Nov 8	DEKM ch 4	Statistical pairwise alignment	PDF
Nov 13	–	Guest lecture by Carolin Kosiol. Codon models and tests for positive selection	PDF
Nov 15	DEKM ch 9 & 10	Stochastic context-free grammars and RNA structure prediction.	PDF
Nov 20	DEKM ch 6	Multiple alignment.	PDF
Nov 22	–	Happy Thanksgiving!	–
Nov 27	DEKM pp 165-172,189-191; F ch 11	Phylogeny reconstruction.	PDF
Nov 29	Phylo-HMM review	Applied comparative genomics.	PDF

Homework Schedule

Homework	Date Assigned	Date Due	Topics	Data
HW#1	Aug 24	Sep 7	Probability and statistics warm up
HW#2	Sep 7	Sep 21	Dynamic programming and sequence alignment	sequences.fa
HW#3	Sep 21	Oct 5	Motif models, HMMs	sequence.fa
HW#4	Oct 15	Oct 29	Phylogenetic models	apoe.fa
HW#5	Oct 30	Nov 12	EM and Gibbs sampling