Seminar: Pattern Discovery in Bioinformatics

Main themes and learning objectives »
58311311
3
Bioinformatics
Advanced studies
Year Semester Date Period Language In charge
2011 autumn 05.09-05.12. English

Lectures

Time Room Lecturer Date
Mon 14-16 B119 Veli Mäkinen 05.09.2011-10.10.2011
Mon 14-16 B119 Veli Mäkinen 31.10.2011-05.12.2011

General

We will cover selected parts of the book:

Laxmi Parida. Pattern Discovery in Bioinformatics - Theory and Algorithms, Chapman & Hall, 2008.

In addition, own topics can be suggested around the theme.

 

Completing the course

We will study the book in study group fashion. Each week everybody studies the same part and we gather for presenting the material. The main presenter is chosen by random, so everybody needs to be prepared.

Literature and material

 Laxmi Parida. Pattern Discovery in Bioinformatics - Theory and Algorithms, Chapman & Hall, 2008.

Schedule:

  • Monday 12.9: Study the book upto page 20 before coming to the meeting.
  • Monday 19.9: Pages 21-46, especially Minimum Mutation Labeling and Prüfer sequences. Exercises 6,8, and 10.
  • Monday 26.9: Pages 47-69. Exercises 13, 14, 16, and 20.
  • Monday 3.10: Pages 70-82. Exercises 17, 18, 19, 21, and 22.
  • Monday 10.10: Chapter 4. Especially concepts irredundancy, maximality, and basis. Exercise 29, and from previous week 17 (part 3), 19 (part 2), 21 (part 1 b), 22.
  • Period break
  • Monday 31.10: Chapter 5. Exercises: 40, 41, 42, 43, 44, 45
  • Monday 7.11: no meeting!
  • Monday 17.11: Chapter 6, pp. 139-160. Exercises: 46, 49, 52, 53, 54
  • Monday 21.11: rest of Chapter 6. Exercises: 60, 61, 62, 67
  • Friday 25.11 at 14-16 A219: half of Chapter 7. Exercises: 69, 70, 71, 72, 73
  • Monday 5.12: rest of Chapter 7. Exercises 74, 75, 78, 82. Lecture by JK on Chapters 8 & 9.