Fundamentals of Bioinformatics 2011-2012

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Course Manual and Schedule.pdf

  • Rooms for the lectures have been updated. You can also check the schedule at
  • Times for the programming class and the project have been updated, as communicated earlier.
  • The planning of the programming classes has changed, we now continue into week seven (Mon 17/10 and Tue 18/10) because of that - please adjust your agenda's accordingly.
  • The ordering and days of the last three lectures has changed. We now have one lecture in week 6, on Mon 10/10.
  • Last assignment in programming class is canceled, and updated Project schedule.


  • Friday, October 28, 9.00-16.30 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.
  • We will be in Artis - Building 42 (highlighted in a yellow circle).
    • Artis will open at 9.00, and it will take you another 10-15 minutes to get to the right building. With the busy schedule, please be in time!

Question Hour

  • Monday October 24, 9.00-11.00 we will have a question hour for the exam (location to be announced - please come to P1.36 if you do not hear otherwise)


Additional Lectures

  • Prof Alan Mark (Queensland University, Brisbane, Australia):
    "Atomistic models of biomolecular systems: the search for certainty in an uncertain world"
    • Time: Tuesday 13th of September, 13.00 h
    • Location: M-639
    • if you are interested in protein modeling, you simply cannot miss this!


N.b.: these classes are a part of the courses Fundamentals of Bioinformatics and Introduction to Systems Biology. You do not need to register for these classes (also not at the UvA).

Programming classes

Programming Classes

Biology classes

  • organized and given by Prof Joost Teixeira De Mattos
Day Time Room Lecturer
Friday Sept 9 9.15-13.00 F1.24C Klaas Hellingwerf
Friday Sept 16 9.15-13.00 F3.21 Joost Teixeira De Mattos
Friday Sept 23 9.15-13.00 F3.21 Joost Teixeira De Mattos
Friday Sept 30 9.15-13.00 F3.21 Joost Teixeira De Mattos
Friday Oct 7 9.00-13.00 F2.19 Klaas Hellingwerf
Friday Oct 14 9.00-13.00 F2.19 Klaas Hellingwerf
  • Test/exam:
    • date: Friday October 21
    • time: 10.00
    • place: F3.21 in the NIKHEF building (see below)

(all in Nikhef building, Science Park 105, ask one of our UvA students!)

  • Recommended book: Molecular Biology of the Cell by Alberts et al.; Garland Science, 2008.
  • If, after approval by one of us (Jaap, Bas, Sanne, Douwe or Anton), you do this in self-study, you may consider signing up for the NCSB course Module I: Basic biology for non-biologists. The site mentions a fee of €50, which you should not need to pay -- please contact us if you hear otherwise.


Mathemathics classes



Practical Project 2011-2012

Reading materials

The course book is: Marketa Zvelebil and Jeremy O. Baum Understanding Bioinformatics, Garland Science 2008 ISBN-10: 0-8153-4024-9

Recommended reading: Larry Hunter's "Molecular biology for computer scientists". This is a nice and concise description of the most important concepts in molecular biology, explained with the non-biologist in mind. It is a useful document for revising your knowledge.

Jin Xiong's Essential Bioinformatics is a nice read providing a good overview of a number of important aspects of bioinformatics. Written to serve as bedside reading! Parts of this book are to be found here.

Paper discussion

Papers to read for Monday October 17, 11.00-12.00 in P3.37:

The papers are on homology detection and benchmarking - you'll recognize that topic. Within each Project Group, please assign two (or three) people to each paper. So each of you only needs to read and prepare for discussion for one paper.

For further reading on this topic, please refer to:

  • Reid AJ, Yeats C, Orengo CA. Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone. Bioinformatics. 2007 23:2353-60.
  • Rapp M, Granseth E, Seppälä S, von Heijne G. Identification and evolution of dual-topology membrane proteins. Nat Struct Mol Biol. 2006 13:112-6.



Lecture Topic Slides Handouts Reading
General FoB_lec1.pdf FoB_lec1_handout.pdf
Genomics 1 FoB_lec2.pdf FoB_lec2_handout.pdf
Genomics 2 FoB_lec3.pdf FoB_lec3_handout.pdf
Ontologies and GO FoB_lec4.pdf
Protein Bioinformatics 1 FoB_lec5.pdf FoB_lec5_handout.pdf Chapter 12 Essential Bioinformatics OR Chapter 2 Understanding Bioinformatics
Protein Bioinformatics 2. FoB_lec6.pdf Viral protein structure solved by FoldIt game and X-ray crystallography Nature 2011, September 18
Petri-net modeling FoB_lec7.pdf
Secondary Structure prediction FoB_lec8.pdf
Repeat and Domain prediction. FoB_lec9.pdf FoB_lec9_handout.pdf
Next Generation Sequencing FoB_lec10.pdf FoB_lec10_handout.pdf Flicek & Birney, see Blackboard

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