582606 Introduction to bioinformatics (4 cr)
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.
News
| 11.6.2007 | Results from the separate exam 5.6.2007 are available. |
| 5.4.2007 | Results from the separate exam 23.3.2007 are available. Next exam is held on Tuesday 5 June 16-20 (auditorium A111). |
| 22.11.2006 | Results from the separate exam 9.1.2007 are available. Next exam is held on Friday 23 March 2007 16-20 (auditorium A111). |
| 9.11.2006 | Results from the course exam 16.10.2006 are now available. Next exam is held on Tuesday 9 January 2007 16-20 (auditorium A111). Please remember to register 10 days in advance. |
| 16.10.2006 | Note that the exam will be held only in auditorium CK112! (course exam list is ambiguous) |
| 15.10.2006 | Please give feedback on the course! |
| 3.10.2006 | Course exam will be held on Monday 16.10.2006 16.00-18.30 in auditorium CK112. |
| 31.8.2006 | Please note: both the first lecture and exercise session have been postponed. First lecture on 8.9.2006 14.15-16.00 in Exactum C222, first exercise session on 22.9. 12.15-14.00 in Exactum C222. |
Lecture schedule
- Fri 8.9.
- What is bioinformatics? (pages 1-21 of lecture slides)
- Chapter 1: Molecular biology primer (slides available in C127 for copying)
- Tue 12.9.
- Chapter 1: Molecular biology primer (continued)
- Chapter 2: Words (up to section 2.5)
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Fri 15.9.
- Chapter 2: Words (finished)
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Tue 19.9.
- Chapter 3: Word Distributions and Occurences
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Fri 22.9.
- Chapter 3: Word Distributions and Occurences (finished)
- Chapter 6: Sequence Alignment (6.1. and 6.2., pages 22-39 of lecture slides)
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Tue 26.9.
- Chapter 6: Sequence Alignment (finished, pages 40-65 of lecture slides)
- Chapter 12: Phylogenetic Trees (12.1., pages 66-69 of lecture slides)
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Fri 29.9.
- Chapter 12: Phylogenetic Trees (12.2. & 12.3., pages 70-107 of lecture slides)
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Tue 3.10.
- Chapter 12: Phylogenetic Trees (12.4., 12.5., 12.6., pages 108-137 of lecture slides)
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Fri 6.10.
- Chapter 11: Measuring Expression of Genome Information
Lecture slides
Esa's slides (pages 1-137): slides, handouts
- Pages 1-21, "What is bioinformatics?": slides, handouts
- Pages 22-65, "Sequence alignment": slides, handouts
- Pages 66-117, "Phylogenetic trees": slides, handouts
- Pages 117-137, "Phylogenetic trees": slides, handouts
- Measuring Expression of Genome Information (pages 1-72, updated 13.10.): slides (in CS intranet; if you do not have an account, copy the slides in C127)
- Clustering (pages 1-40): slides
Slides for the molecular biology primer available for copying in room C127.
Exercises
- Fri 22.9. Exercise 1 [ps] [pdf]
- Fri 29.9. Exercise 2 [ps] [pdf]
- Fri 6.10. Exercise 3 [ps] [pdf]
- Fri 13.10. Exercise 4 [ps] [pdf]
Time and place
- Lectures: 8.9.-13.10.2006 Tue, Fri 14.15-16.00 Exactum C222
- Exercises: 22.9.-13.10.2006 Fri 12.15-14.00 Exactum C222
Enrolling for the course
Please use the registration system of the Department of Computer Science to enroll for the course.Contents
- Biological background (course book chapter 1)
- Probability calculus (chapter 2)
- Word distributions and occurrences (chapter 3)
- Sequence alignment (chapter 6)
- Phylogenetic trees (chapter 12)
- Expression data analysis (chapter 11)
Course organizers
- Esa Pitkänen (main organizer, exercises), Department of Computer Science, University of Helsinki
- Professor Elja Arjas, Department of Mathematics and Statistics, University of Helsinki
- Professor Samuel Kaski, Laboratory of Computer and Information Science, Helsinki University of Technology
Grading
To successfully pass the course, you have to get 30 out of 60 points from the course exam and exercises.
- Course exam: max. 50 points
- Exercises: max. 10 points
Exam
- Course exam: Monday 16.10.2006 16.00-18.30, auditorium CK112 (course exam list)
- Separate exams in Spring 2007
Course book
Lectures will be based on Richard C. Deonier, Simon Tavaré and Michael S. Waterman: Computational Genome Analysis: An Introduction, Springer, 2005.
Additional material
- Molecular biology for computer scientists [pdf]
- Lodish et al. (ed.) 1999: Molecular and Cell Biology, 4th ed., Freeman & Co.
- Griffiths et al. (ed.) 1999: Introduction to Genetic Analysis, 7th ed., New York, Freeman & Co.
- Griffiths et al. (ed.) 1999: Modern Genetic Analysis, York, Freeman & Co.
Previous update: 11.06.2007 16:00 - Esa Pitkänen