BIOINF4110 - Bioinformatics I
| Lecturers | Prof. Dr. Daniel Huson, Ania Gorska and Caner Bagci |
| Lectures | Mondays, 10:15-12:00, A104, Sand 14 Wednesdays, 10:15-12:00, A 104, Sand 14 |
| Problem sessions | A) Mo, 8:30-10:00, A104, Sand 14 (starts 24.10., no session on 31.10) B) Wed, 12:15-14h:00, A104, Sand 14, starts 2.11) |
| Target audience | MSc and diploma students in bioinformatics and computer science |
| Language | English |
| Links | Campus Ilias |
Contents
Bioinformatics I focuses on concepts, data-structures and algorithms for sequence analysis. Our goal is to teach you to understand, to be able to implement and to apply some of the most fundamental algorithms used in bioinformatics. Programming assignments are to be solved in Python. Students will be assigned projects in which the goal will be to address a biological problem using methods discussed in the lectures.
Some contents of this lecture were already taught in "Grundlagen der Bioinformatik". While we try avoid overlap with that bachelor level course, some content is so fundamental that we cannot completely avoid some repetition of earlier material. This is for the benefit of students that do not have a BSc in bioinformatics.
Script and assignments
The script and assignment sheets will be available here: Ilias
Also, please upload your solutions to the assignment sheets there.
Schedule
The following schedule is subject to change:
| Date | Topic | Assignments |
|---|---|---|
| 17.10. | 1. Introduction | Assign. 01 |
| 19.10. | 2. Pairwise sequence alignment | |
| 24.10. | continued | |
| 26.10. | continued | Assign. 02 |
| 31.10.. | Introduction to Python | |
| 2.11. | 3. Multiple sequence alignment | Assign. 03 |
| 7.11. | continued | |
| 9.11. | continued Examples of ILPs in Operations Research. | Assign. 04 data04 |
| 14.11. | 4. Read mapping | |
| 16.11. | 5. RNA-seq | Assign. 05 data05 |
| 21.11. | 6. RNA secondary structure | |
| 23.11. | continued | Assign. 06 data06 |
| 28.11. | 7. Phylogeny | |
| 30.11. | continued | Assign. 07 data07 |
| 5.12. | continued | |
| 7.12. | continued | Practice exam (Ilias) |
| 12.12. | First part of exam (covering chapters 1-7) Takes place in Hörsaal 1, Sand 6/7 | |
| 14.12. | 8. Suffix trees | Assign. 08 |
| 19.12. | continued | |
| 21.12. | continued | Assign. 09 |
| 9.1. | 9. Sequence assembly | Assign. 10 |
| 11.1. | 10. Genome comparison | |
| 16.1. | 11. Classic exact string matching | |
| 18.1. | continued | Assign. 11 |
| 23.1. | 12. SVMs | |
| 25.1. | 13. BLAST and beyond | Assign. 12 |
| 30.1. | continued | |
| 1.2. | Synthesis | Practice exam |
| 6.2. | Free for exam preparation (If you have questions, please arrange to meet with your tutor between 10 and 12 o'clock) | |
| 8.2. | Second part of exam (covering chapters 8-13) Takes place in Hörsaal 2, Sand 6/7 | |
Make up exams:
Part I: Wednesday, 18. Jan 2017, 8:15-10:00, A104
Part II: Wednesday, 29. March 2017, 10:15-12:00, A104
Recommended textbooks (but none covers the whole course)
- Hodgeman, Frence and Westhead, Instant Notes- Bioinformatics, Taylor and Francis, second edition, 2010.
- Neil C. Jones, Pavel A. Pevzner: An Introduction to Bioinformatics Algorithms. MIT Press, 2004.
- Richard Durbin, Sean R. Eddy, Anders Krogh, and Graeme Mitchison: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge UP, 1998.
- Pierre Baldi, Soren Brunak: Bioinformatics: The Machine Learning Approach. MIT Press, 1998.
- Dan Gusfield: Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge UP, 1997.
How to get credit for this course
- Always participate in the weekly problem sessions and actively present your results.
- Obtain 50% of all assignment points in the first part of the course to participate in part 1 of the exam
- Obtain 50% of all assignment points in the second part of the course to participate in part 2 of the exam
- Assignments are set every Wednesday and are due on the following Wednesday, 8 am.
- Your final grade is determined by the two parts of the exam.