Elements of Bioinformatics
Lectures
Time | Room | Lecturer | Date |
---|---|---|---|
Mon 12-14 | B222 | Veli Mäkinen | 01.11.2010-10.12.2010 |
Thu 10-12 | B222 | Veli Mäkinen | 01.11.2010-10.12.2010 |
Tue 14-16 | B221 | Veli Mäkinen | 02.11.2010-02.11.2010 |
Thu 10-12 | B221 | Veli Mäkinen | 11.11.2010-11.11.2010 |
Mon 12-14 | B221 | Ilari Scheinin | 15.11.2010-15.11.2010 |
Tue 16-18 | B222 | Veli Mäkinen | 07.12.2010-07.12.2010 |
Exercise groups
Time | Room | Instructor | Date | Observe |
---|---|---|---|---|
Tue 14-16 | BK107 | Markus Heinonen | 09.11.2010—09.11.2010 |
Time | Room | Instructor | Date | Observe |
---|---|---|---|---|
Thu 8-10 | B222 | Esa Pitkänen | 11.11.2010—11.11.2010 | |
Tue 16-18 | C222 | Esa Pitkänen | 15.11.2010—10.12.2010 |
Registration for this course starts on Tuesday 12th of October at 9.00.
Information for international students
Course will be given in English.
General
This course gives an introduction to the central topics in bioinformatics, and gives a foundation for further courses in the Master"s Degree Programme in Bioinformatics (MBI).
First period course Molecules for Bioinformatics is strongly recommended to be taken before this course (unless with earlier biology & practical bioinformatics background). Also first period courses Markovian modeling and Bayesian learning, and Algorithms for Bioinformatics are recommended (unless with strong statistics or computer science background before, respectively).
Completing the course
Active participation to lectures and exercises is recommended.
There will be an exam giving 60 points at the maximum. Active participation to exercises gives maximum 6 extra points (25%->1p,37.5%->2p,50%->3p,62.5%->4p,75%->5p,87.5%->6p). The grading is then based on the total points achieved.
Literature and material
Course book: Richard C. Deonier, Simon Tavare & Michael S. Waterman: Computational Genome Analysis - An Introduction (Springer, 2005).
Some material will also follow the books: Neil C. Jones & Pavel A. Pevzner: An Introduction to Bioinformatics Algorithms (MIT Press, 2004), and
R. Durbin, S. Eddy, A. Krogh, and G. Mitchison: Biological sequence analysis - probabilistic models of proteins and nucleid acids (Cambridge University Press, 1998).
Course content:
- Mon 1.11. 12-14 B222: Global and local alignment, gap open and extension (Chapter 6, Veli Mäkinen)
- Tue 2.11. 14-16 B221: SQL basics (Ilari Scheinin)
- Thu 4.11. 10-12 B222: Scoring matrices for amino acids and multiple alignment (Chapter 6 + multiple alignment from Durbin et al. Chapter 6, Veli Mäkinen)
- Exercise 1 Tue 9.11. 14-16 BK107 (group 1) and Thu 11.11. 8-10 B222 (group 2): Exercise sheet, solutions
- Mon 8.11. 12-14 B222: Rapid alignment methods and tools for genome-wide comparison (Chapter 7, Veli Mäkinen)
- Thu 11.11. 10-12 B221: SQL and biodatabases I (Ilari Scheinin)
- Mon 15.11. 12-14 B222: SQL and biodatabases II (Ilari Scheinin)
- Exercise 2 Tue 16.11. 16-18 C222: Exercise sheet, template for 2.7, solutions
- Thu 18.11. 10-12 B221: Signals in DNA (Chapter 9, Veli Mäkinen)
- Mon 22.11. 12-14 B222: Gene prediction (Chapters 2,3 and similarity-based approach from Chapter 6 in J & P, Veli Mäkinen)
- Exercise 3 Tue 23.11. 16-18 C222: Exercise sheet, solutions
- Thu 26.11. 10-12 B222: Gene prediction continued + completing the pipelines: clustering, UPGMA, neighbor joining (HMMs from Durbin et al., Section 3.2,and Chapters 10, 11, Veli Mäkinen)
- Mon 29.11. 12-14 B222: Proof of correctness for neigbor joining and overview of sequence assembly methods (Durbin et al. pp. 190-191, and Chapter 8, Veli Mäkinen)
- Exercise 4 Tue 30.11. 16-18 C222: Exercise sheet, solutions
- Canceled: Wed 1.12. 16-17 B222: Guest lecture by Richard Durbin: "Assembling and analysing terabases of DNA sequence"
- Thu 2.12. 10-12 B222: High-throughput sequencing technologies (invited talk by Lars Paulin)
- Tue 7.12. 16-18 B222: Introduction to systems biology (Esa Pitkänen)
- Exercise 5 Thu 9.12. 10-12 B222: Exercise sheet, solutions
- Exam graded