INF 389 (autumn 2003): Statistical methods in bioinformatics

The course consists of lectures and two minicourses organized by CBU. Both the lectures and the minicourses will be given in English.

The lectures are given by Eivind Coward (coward@ii.uib.no) every Tuesday at 14:15-16:00 in Room 2103 (first lecture Oct 7).
In addition, there will be a regular exercise session every Monday 13:15-14:00 in the CBU room (5th floor).

The minicourses are organized by David Liberles (liberles@cbu.uib.no). They are called "Statistical Analysis of Protein Structure" and "Statistics in Phylogeny and Genome Analysis". More information is found here.

Textbook

Warren J. Ewens and Gregory R. Grant
Statistical Methods in Bioinformatics
Springer, 2001.

Topics

The main topic of the lectures is Markov chain theory, with application to hidden Markov models and evolutionary models. This gives a relevant background for the second minicourse on phylogeny.

Students should take both minicourses if possible! If not possible, at least half of the first course and the second course is required.

Tentative plan for the lectures: Chapters 4, 10 (excerpt), 11, 13.
Possibly smaller parts of 5, 8, 12.

Prerequisites for the lectures: Mainly elementary probability and statistics. In the textbook, this corresponds roughly to Sections 1.1-1.6, 1.8-1.13, 2.1-2.10, and 3.1-3.4. If this is not familiar, you might need to repeat some of this. The most important thing is to understand the basic concepts, especially in Ch. 1.

In addition, a little linear algebra will be useful. Some background in bioinformatics; the contents of I181 will be (more than) sufficient.

Plan for the course

weekdatetimeroomwhatabout
41Tue, Oct 714-162103 Information meeting plan for course, repetition of basic statistics
42Mon, Oct 1312-14CBU room Lecture Poisson processes (Ch. 4.1-4.3)
Tue, Oct 1414-162103 Lecture Markov chains (Ch. 4.4-4.9)
43Mon, Oct 2013-14CBU room Exercises Exercise 1
Tue, Oct 2114-162103 Lecture Markov chains (from Ch. 10)
44Mon, Oct 2713-14CBU room Exercises Exercise 2
Tue, Oct 2814-162103 Lecture Higher order Markov chains, evolutionary models (from Ch. 10, 13)
45Mon, Nov 313-14CBU room Exercises Exercise 3
Tue, Nov 414-162103 Lecture Continuous time Markov chains, evolutionary models (from Ch. 10, 13)
46Mon, Nov 1013-14CBU room Lecture Evolutionary models (Ch. 13)
Tue, Nov 1114-162103 Lecture Hidden Markov models (Ch. 11)
Fri, Nov 1414-15 CBU room Midterm test Lectures until Nov 10 (Ch. 4, 10.1-10.3, 10.7, 13)
47Nov 17-22 Minicourse Statistical Analysis of Protein Structure
48Nov 24-25 Minicourse Statistics in Phylogeny and Genome Analysis
49 Wed, Dec 3 Final exam Oral examination

Exam

A written one-hour midterm test will be given on Friday Nov 14, 14:15 in the CBU room. The topics are the contents of the lectures until and including Monday Nov 10, preparing for the minicourses (especially the phylogeny course). The midterm test will count 25% on the final mark, but only if the result is better than the oral exam. Thus, it can only improve your result!

The final oral examination is scheduled to Wednesday, Dec 3.

Exercises

Regular exercises will be published here.

Exercise 1 (ps,pdf) Recapitulation of basic probability theory.
Exercise 2 (ps,pdf) Poisson processes.
Exercise 3 (html) Markov chains.
Exercise 4 (html) Evolutionary models.
Exercise 5 (html) Hidden Markov models.


Eivind Coward
Last modified: Tue Nov 11 18:19:41 CET 2003