Fundamentals of Bioinformatics 2012-2013

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Question Hour

  • 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!

Written Exam

  • The written exam will be on Monday October 22 from 8.45-11.30 (room F619/F637/F647).

Final Presentation

  • 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.


Biology class

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
1 7/9 9-13u SP B0.203 Hellingwerf
2 14/9 9-13u SP B0.203 Teixeira De Mattos
3 21/9 9-13u SP B0.203 Hellingwerf
4 28/9 9-13h SP B0.207 Teixeira De Mattos
5 5/10 11-13h SP D1.162 Hellingwerf
5 5/10 13-15h SP G4.15 Hellingwerf
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
1b FoB/PoB Introduction FoB_PoB_lec1_2012_part2.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 [21] / 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 ([1]). How may the information in the HMM logo help to find distant relatives of this protein family?

5 Benchmarking FoB_PoB_lec5_2012.pdf

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?
6 Sematic Web FoB_PoB_lec6_2012.pdf
7 Multi-omics FoB_PoB_lec7_2012.pdf

(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
Marc Güell et al. Science 326, 1268 (2009) Abstract, fig 2
Note: these are complex, highly condensed papers! If you want to try and understand all of what they describe, you need much more than a few days to prepare (and look up many other papers in the process). Focus only on the abstracts and figures listed above!

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.

9 Research Highlights:
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!

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