Algorithmic computational biology

CENTER FOR ALGORITHMIC SYSTEMS

MSc Programme ``Computing Science" 2011-2012

Seminar: Algorithmic Computational Biology (MACB)

Lecturer:

Prof.dr Jan van Leeuwen.
Email: -- , tel. 030-2534001, BBL office 505. (The email adress was only active at the time of the seminar.)

Seminar overview

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.

Class schedule

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.

Prerequisites

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 complexity theory.)
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.

Text

The seminar is based on the book

H-J. Böckenhauer, D. Bongartz, Algorithmic Aspects of Bioinformatics, Springer-Verlag, Berlin, 2007.
(See e.g. here for the details of 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.

Course Work

Presentations 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.
Participation 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.)

Grading

The grade depends on the given presentations (50%), summary reports (40%) and active participation (10%).

Recommended for further interest

Interdisciplinary Seminar on Biological Networks (Klau, Spring 2012, Utrecht - Math Dept).
Bio-informatics track (Leiden/Delft).
Computational Molecular Biology (Bakker, 2011).
Algorithms in Biology (Batzoglou, 2010).
Bio-computing (Cardelli, Microsoft).
Algorithmic Foundations of Computational Biology (Istrail, 2011)
Algorithms in Computational Biology (Pedersen, 2000)
Algorithms in molecular biology (computational genomics) (Shamir).
Skiena's Computational Biology Lectures (Skiena)
Introduction to Computational Biology (Skiena, 2011)
(more to follow)

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, 2008.
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)

Bioinformatics and Systems Biology - Bridging the Divide (Lorentz Center, Leiden, 2012).
Workshop on Algorithms in Biology (WABI)
Algorithms for Molecular Biology (BioMed Central Journal)
Bioinformatics (OUP Journal)
International Society for Computational Biology (ISCB)

Useful further references (groups, institutes)

Algorithmic computational biology (CWI, Amsterdam).
Algorithmic Bioinformatics (Frohlich, Bonn)
European Bio-informatics Institute (EMBL-EBI).
Pole Bioinformatique Lyonnais (Lyon).
Computational Biology and Applied Algorithmics (Max Planck Institut fuer Informatik, Saarbruecken)
Microsoft Biology Initiative (Microsoft Research).
National Center for Biotechnology Information (NCBI).
Swiss Institute of Bio-informatics (SIB).
Bio-informatics Group (UCL London)
Bio-informatics (Wikipedia)

Search tools

For searching documentation: use the scientific information links of the Center for Algorithmic Systems.