Algorithms in Bioinformatics - Trees and Structures
Announcements
- 06/12/11: Description of mandatory project 3 (due Dec 13) is available.
- 21/11/11: Schedule for week 5, 6, and 7 is available.
- 21/11/11: Description of mandatory project 2 (due Dec 6) is available.
- 15/11/11: Schedule for week 4 is available.
- 03/11/11: Description of mandatory project 1 (due Nov 22) is available.
- 03/11/11: Schedule for week 2 and 3 is available.
- 27/09/11: Schedule for week 1 is available.
- 27/09/11: Initial www-pages ready.
About
Bioinformatics is an interdisciplinary area focusing on developing and utilizing algorithms and computer programs for analyzing biological data. Due to extremely efficient biotechnological methods for gathering biological data, the amount of available data grows much faster than the growth in available computational power. Making sense of the collected data thus requires efficient algorithmic and computational techniques.
This class covers central algorithmic problems and computational techniques in phylogenetics and molecular structure prediction. The class introduces the underlying biological questions and models, but concentrates on algorithmic problems and computational techniques in relation to reconstruction and comparison of phylogenetic trees; RNA secondary structure prediction; protein structure prediction.
Schedule
Lectures take place:
- Tuesday 11.15-14.00 in the lecture room DI-Nygaard-184.
First lecture is on Tuesday, November 1.
The tentative plan is:
- Week 1: Evolutionary trees. Comparison of trees.
- Week 2: Tree reconstruction methods, part 1. Handout project 1.
- Week 3: Tree reconstruction methods, part 2.
- Week 4: Prediction of RNA 2nd structures, part 1 (Paula Tataru). Handin project 1, handout project 2.
- Week 5: Prediction of RNA 2nd structures, part 2 (Paula Tataru).
- Week 6: Protein folding, part 1. Handin project 2, handout project 3.
- Week 7: Protein folding, part 2. Handin project 3.
Check the weekly schedule for information about each lecture.
Literature
We will use research papers (that can be downloaded) and excerpts from text books (that will be handed out in class).
Exam and Projects
To participate in the final oral exam each student must complete all mandatory projects.
The final exam is an individual oral exam (20 min) which includes a presentation based on an exam question followed by a general discussion of related topics and mandatory projects.
List of exam question and curriculum.
The exam takes place on Friday, January 13 and Friday, January 20 in Lecture Room 1111-100 at the BiRC building. Both days starting at 09:00 according to this exam schedule.
Lecturer
If you have any comments or questions related to the course, do not hesitate to contact one of the lectures:
Christian Nørgaard Storm Pedersen
Office: 1110.325
Phone: +45 8942 3121
E-mail: cstorm [at] birc.au.dk
Office: 1110.427
Phone: +45 8942 3187
E-mail: paula [at] birc.au.dk