Fundamentals of Bioinformatics 2012-2013
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- Mondays & Tuesdays:
- Biology Classes (see below for times and rooms)
- Monday October 8, 9.00-11.00 we will have a question hour for the exam in room C1.21. Jaap, Sanne and me will all be there. This will be your opportunity to ask questions for the exam!
- Question Hour slides (on blackboard, so you will need to be logged to blackboard for the link to work)
- Monday October 15, 10.00-11.00 we will have the second question hour for the exam in room C1.21. Jaap, Sanne and me will all be there. This will be your final opportunity to ask questions for the exam!
- The written exam will be on Monday October 22 from 8.45-11.30 (room F619/F637/F647).
- Friday, October 28, 9.00-17.30 there will be the mini symposium 'Bioinformatics meets Systems Biology' where all students from the Fundamentals of Bioinformatics and the Introduction to Systems Biology courses will present their work.
- The symposium will take place in Artis Zoo, in the lecture room “De Volharding” (Artis - Building 42 highlighted in a yellow circle), which is at 10-15 min. walking distance from the main entrance.
The biology classes are given at the UvA Science Park. Pleas note that times and rooms are not always the same! Also, four hours are scheduled, but only about three hours should be needed for each session.
Schedule - times and rooms - changed Thu Sept 13
Recommended book: Molecular Biology of the Cell by Alberts et al.; Garland Science, 2008.
|week||date (Fridays)||time||room (UvA Science Park)||lecturer|
|2||14/9||9-13u||SP B0.203||Teixeira De Mattos|
|4||28/9||9-13h||SP B0.207||Teixeira De Mattos|
|6||12/10||9-13h||SP B0.207||Teixeira De Mattos|
|7||18/10 (Thursday)||13-16h||SP F1.02||Teixeira De Mattos|
|Lecture Topic||Slides||Reading before the lecture!|
|1a||General introduction / housekeeping||FoB_lec1_2012_part1.pdf|
|2||Genetics, evolution, alignment and homology searching||FoB_PoB_lec2_2012.pdf||hunter.pdf Chapter 1|
|3||Domains||FoB_PoB_lec3_2012.pdf||UB Ch. 2  / EB Ch. 12 Focus on primary, secondary, tertiary structure; hydrogen bonding; hydrophobic residues.|
|4||PSI-BLAST||FoB_PoB_lec4_2012.pdf|| Students with a Biology background, have a look at the Needleman-Wunsch Algorithm, see Essential Bioinformatics Chapter 3, focus on Figure 3.4 or Understanding Bioinformatics 5.2, focus on figures 5.9 and 5.10.
Students with a Computer Science Backrgound, have a look the HMM logo, the sequence alignment (in jalview) and the structure of protein family - PF14396 in pfam (). How may the information in the HMM logo help to find distant relatives of this protein family?
Note: the answers to the questions are in the slides, but not explicitly. If there are still questions about that, we can cover that during the next lecture (Monday Sept 24)
|Reid, Yeats & Orengo 2007 Methods of remote homology detection. Focus on Figure 3a; according to this figure, which of the methods performs best?|
(Note: the three papers are about Mycoplasma pneumoniae; only the two full-size images (slide 14 tissue and slide 15 electron microscopy) are of Mycobacterium Tuberculosis.)
|Kühner et al. Science 326, 1235 (2009) abstract, fig 1, fig 2 and fig 4|
Eva Yus et al. Science 326, 1263 (2009) abstract, fig 2 caption
|8||Massively Parallel Sequencing||FoB_PoB_lec8_2012.pdf|| Please watch the following video Next Generation Sequencing
and read the following (review) paper Compeau et al.
|9a||Crossing Schedule Optimization||FoB_PoB_lec9a_2012.pdf||(Mohammed El-Kebir 2009 optional reading)|
|9b||Genetic regulation of cellular differentiation||FoB_PoB_lec9b_2012.pdf||Bonzanni, Feenstra, Fokkink & Krepska. Lecture Notes in Computer Science 2009 please read the abstract and the first section Systems Biology.|
|9c||Domain prediction||FoB_PoB_lec9c_2012.pdf||George & Heringa, Proteins 2002 please read the abstract and Fig 3.|
|10||Open Challenges in Bioinformatics||FoB_PoB_lec10_2012.pdf||The economist: Welcome to the yotta world A good read that you should not miss!|