Ämnesdisposition
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Teaching
Teacher Marc HellmuthCourse literature (the following books cover a broad range of topics covered in this course)- Algorithmic Aspects of Bioinformatics, Böckenhauer and Bongartz, Springer, 2007
- An Introduction to Bioinformatics Algorithms, Jones and Pevzner, MIT Press, 2004
- Introduction to Computational Biology, Waterman, Chapman & Hali, 1995
- Algorithms on Strings, Trees, and Sequences, Gusfield, Cambridge University Press, 1997
- Phylogenetics, Semple and Steel, Oxford University Press. 2003
Further interesing paper:- Deciphering the Genetic Code: The Most Beautiful False Theory in Biochemistry – Part 1-3
[https://www.chemistryviews.org/details/ezine/11312121/Deciphering_the_Genetic_Code_The_Most_Beautiful_False_Theory_in_Biochemistry__Pa/] - What do Eulerian and Hamiltonian cycles have to do with genome assembly?
[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008928] - The many faces of sequence alignment
[https://academic.oup.com/bib/article/6/1/6/288918]
Schedule
The full course schedule is onlineALL lectures will be offline (check schedule - rooms change from time to time)
The lectures in the week 11 Feb - 16 Feb 2024 will be replaced by video-lectures (more detail will be announced)
Videos can be found under resources and here https://video.su.se/channel/DA7065+Computational+Biology+VT22/494275/subscribe- Video "Lesson 8 - Phylogenetics(Part1)" starting at 47min
- Video "Lesson 9 - Phylogenetics(Part2)"
- Video "Lesson 10 - Phylogenetics(Part3)" the first ~42min
[if you download the videos, then you may use the VLC player]
Content (Main topics that will be covered and Aim)
Computational problems in molecular biology
Formalization of biological problems (i.e.: how to turn a fuzzily described problem to a mathematical/computational problem)
Algorithmic techniques for solving common problem in molecular biology
Function and implementation of important bioinformatics softwareExamination
There will be three home assignments worth 6 credits and one oral/written exam worth 1.5 creditsPhD-students that take this course as part of their PhD-credits, will get additional exercises (that is, you must complete all three home assignments + exam + some extra tasks)
oral EXAM / March 21 / Room B1371 (Office Marc)time / student (1st letter first name 1st letter last name)12:00 / SV12:40 / FA13:20 / GR14:00 / JA14:40 / S?
Here you can find the teaching material (e.g. Slides, Script and Videos)..Resources
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