CENTER FOR ALGORITHMIC SYSTEMS
MSc Programme ``Computing Science"
Seminar: Algorithmic Computational Biology (MACB)
- Prof.dr Jan van Leeuwen.
- Email: -- , tel. 030-2534001, BBL office 505. (The email adress was only
active at the time of the seminar.)
The Life Sciences are an exciting field for computer scientists. The field is heavily
reliant on algorithmic models and computational techniques, and is in great need of
efficient and highly scalable algorithms e.g. for the analysis and understanding of
biological systems. Many problems involve massive data sets and discrete algorithmic
questions of great complexity: sequence comparison, alignment of multiple sequences,
genome rearrangements, and so on, questions that are being studied by computer
scientists everywhere. The long-term goal is to develop realistic simulation models of
cells, organisms and the principles of their development. The insights would make it
possible to test new hypotheses, new developmental models, and even new drugs by
computer simulation. Before that goal is achieved, many fundamental computer science
problems must be solved. In this course we will study the typical algorithmic challenges
and complexities that must be overcome.
The concrete seminar contents will be specified below.
- Seminar hours:
- Monday 13.15-15.00, in: BBL 075.
- Thursday 09.00-10.45, in: BBL 075.
- First meeting: April 23rd, 2012 (in: BBL 075).
- Office hours: by appointment.
- Present: present;
some criteria: criteria.
- Final exam: The grade will be based on the course work (see below).
- Here is the weekly schedule.
The seminar is part of the MSc program `Computing Science' and is to be taken after
you have completed at least several of the regular courses in the program. If you have not, see
the MSc-program advisor: you may not be admissable to this seminar yet. (The seminar will be
mostly self-contained, but requires a good understanding of basic algorithm design and
Note. If there is considerable interest for the seminar, students may be grouped in two for the
presentations part of the seminar requirement. Due to the seminar format, the total number of
participants is limited to 20.
The seminar is based on the book
The book is required and should be at your disposal at the start of the seminar, to study the
weekly readings from the very beginning. We will treat a selection of chapters from this
book. Additional material will be listed in the weekschedule as the seminar develops.
The seminar meets twice a week. After a few introductory lectures by the lecturer, students
are expected to give presentations on (specific parts of) the book chapters and related
material. Students are expected to give at least two presentations each, each presentation
typically being a 45-minute part of one seminar session. (The course will be in
English unless all participating students are fluent in Dutch.)
- Term paper
Students are challenged to explore their topics in an active way. Towards the end of the
seminar every participant must write a term paper (in English) of a special topic from the
seminar domain and present an outline of it, typically based on new research material.
Students are expected to participate in an active way. Attendance is recorded. (The
participation grade is lost when the seminar is missed five times or more.)
The grade depends on the given presentations (50%), summary reports
(40%) and active participation (10%).
Recommended for further interest
Useful further references (books)
- R.C. Deonier, S. Tavaré, M.S. Waterman, Computational genome analysis
- An introduction,Springer, 2005.
- D. Gusfield, Algorithms on strings, trees, and sequences - Computer science and
computational biology, Cambridge University press, 1997.
- N.C. Jones, P.A. Pevzner, An introduction to bioinformatics algorithms,
The MIT Press, 2004.
- S. Kim, H. Tang, E.R. Mardis, Genome Sequencing Technology and Algorithms,
Artech House, 2007.
- P.A. Pevzner, Computational molecular biology - An algorithmic approach,
The MIT Press, 2000.
- C. Setubal, J. Meidanus, Introduction to computational molecular biology,
PWS Publishing, 1997.
- V. Sperschneider, Bioinformatics - Problem solving paradigms, Springer,
- W-K. Sung, Algorithms in bioinformatics - A practical introduction,
Chapman & Hall/CRC, 2009.
- C-W. Tseng (Ed.), Advances in Computers, vol 68: Computational biology and
bioinformatics, Academic Press, 2006.
- M.S. Waterman, Introduction to computational biology - Maps, sequences and
genomes, Chapman & Hall/CRC, 1995.
Useful further references (professional organizations, conferences)
Useful further references (groups, institutes)
Last modified: January 16, 2012