The lectures are given by Eivind Coward
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 (firstname.lastname@example.org). They are called "Statistical Analysis of Protein Structure" and "Statistics in Phylogeny and Genome Analysis". More information is found here.
Warren J. Ewens and Gregory R. Grant
Statistical Methods in Bioinformatics
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.
|41||Tue, Oct 7||14-16||2103||Information meeting||plan for course, repetition of basic statistics|
|42||Mon, Oct 13||12-14||CBU room||Lecture||Poisson processes (Ch. 4.1-4.3)|
|Tue, Oct 14||14-16||2103||Lecture||Markov chains (Ch. 4.4-4.9)|
|43||Mon, Oct 20||13-14||CBU room||Exercises||Exercise 1|
|Tue, Oct 21||14-16||2103||Lecture||Markov chains (from Ch. 10)|
|44||Mon, Oct 27||13-14||CBU room||Exercises||Exercise 2||Tue, Oct 28||14-16||2103||Lecture||Higher order Markov chains, evolutionary models (from Ch. 10, 13)|
|45||Mon, Nov 3||13-14||CBU room||Exercises||Exercise 3||Tue, Nov 4||14-16||2103||Lecture||Continuous time Markov chains, evolutionary models (from Ch. 10, 13)|
|46||Mon, Nov 10||13-14||CBU room||Lecture||Evolutionary models (Ch. 13)||Tue, Nov 11||14-16||2103||Lecture||Hidden Markov models (Ch. 11)|
|Fri, Nov 14||14-15||CBU room||Midterm test||Lectures until Nov 10 (Ch. 4, 10.1-10.3, 10.7, 13)|
|47||Nov 17-22||Minicourse||Statistical Analysis of Protein Structure|
|48||Nov 24-25||Minicourse||Statistics in Phylogeny and Genome Analysis|
|49||Wed, Dec 3||Final exam||Oral examination|
The final oral examination is scheduled to Wednesday, Dec 3.
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.