Interdisciplinary Seminar on Biological Networks - Feb-June 2012

Networks are becoming increasingly important in core areas of biology and their study has important applications, for example, in personalized medicine and biotechnology. Mathematical and computational techniques play a key role in understanding these networks. This seminar covers some of the most relevant topics in this area. 

Interdisciplinary seminar Tuesdays, 7 Feb 2012 - 11 June 2012, 15:15 - 16:45
Lecturer: Dr. Gunnar W. Klau Mathematical Institute Utrecht University, Minnaert building, Room 016
vakcode: WISM531 Internal web site (access-restricted) 


  • 10 April. Rough project descriptions (on internal webpage). Fine-tune until 17 April!  
  • 1 March. There is a vakcode. It is: WISM531.
  • 26 February. Internal web site up. 
  • 8 February. Slides of the first meeting. Choose or propose a topic until 14 February. 


Meetings take place Tuesdays, 15:15 - 16:45, in the Minnaert building, room 016, Utrecht (Uithof location). The following meetings are already scheduled.

7 February 2012 Introduction, organizational issues [slides] Gunnar Klau
14 February 2012 no seminar  
21 February 2012 Introduction to cell biology and biological networks Oleksandr Ivanov
28 February 2012 Network properties and network models Martin van Meerkerk
6 March 2012 Network alignment with natalie (Integer linear program + Lagrangian relaxation) Mohammed El-Kebir 
13 March 2012 Network motifs and food webs Floor Soudijn
20 March 2012 Dense modules (MCODE and Newman) Willem van Valenberg
27 March 2012 Networks in disease Nela Lekic
3 April 2012 Perturbed modules in PPI networks Gunnar Klau
10 April 2012 Bayesian network inference (chromatin) Ricky Lim
17 April 2012 Reconstructing signaling pathways Emiel Suilen
24 April 2012 no seminar  
1 May 2012 Inferring functional connectivity of neurons Philip Klop
8 May 2012 Network modules via bi-clustering  Viktorian Miok
15 May 2012 Network alignment with IsoRank Hasse Boven
22 May 2012 Networks in classification Christine Staiger
29 May 2012 no seminar (pentecoste)  
26 June 2012 project presentations Martin, Willem, Ricky, Emiel
24 July 2012 project presentations Philip, Hasse, Bas, Gunnar 

Target group

This seminar is intended for master students and beginning PhD students. It will be truly interdisciplinary, and students from mathematics, biology, bioinformatics, and computer science as well as other disciplines are welcome. The seminar covers aspects of graph theory, network analysis, algorithmics, combinatorial optimization, computational complexity, statistics, probability theory, and cell biology, and knowledge in at least one of these fields as well as interest in the others is a hard requirement for participation. The number of ECTS points is 7.5. The seminar will take place on Tuesdays at Utrecht University, 15:15 - 16:45, in room 016 of the Minnaert building

Motivation and Topics

It has turned out that the complexity of life is rather due to complex interactions between molecules than to the complexity of single entities. Consequently, research in the life sciences has focused on studying systems of interactions such as regulatory, metabolic, signaling, and interaction networks. Mathematical and computational techniques play a key role in understanding these networks and this seminar focuses on some of their core contributions to network biology:

  • Introduction to cell biology and biological networks, basic graph theory
  • Network analysis. (Random) network models and their properties. Network motifs and modules.
  • Networks in inference: Protein function, disease genes, drug targets
  • Network modules. Clustering and bi-clustering.
  • Network mining: Active/dysfunctional subnetworks. Classification. 
  • Network evolution and comparison. Alignment and queries.
  • Late-breaking results (from the top conferences RECOMB and ISMB)


We will discuss original work on one topic in each class, which is presented by one or two students. Assignment of topics will take place at the first meeting on 7 February. In addition, participants will carry out an additional small project on an appropriate topic of choice. Grades will be given based on the presentation, active participation in interdisciplinary discussions, and the project.