CSC

	Tehdyt toimenpiteet University of Helsinki Department of Computer Science Group leader: Esko Ukkonen Home page: http://www.cs.helsinki.fi/research/fdk/ The group of Professor Ukkonen has worked in the field of bioinformatics since the 1980s when they started to develop algorithms for DNA sequence assembly. These algorithms have influenced to the sequence assembly algorithms that were later on used, for example, in the genome projects. Later on, Ukkonens' group studied theory of string methods, in order to develop effective algorithms for string analysis tasks, like string comparison or similarity searches. The algorithms that resulted form these studies, have gained a significant status and they have, for example, been used in several computer science books (D. Gusfield: Algorithms on strings, trees, and sequences - Computer Science and Computational Biology. Cambridge University Press 1997; B. Smyth: Computing patterns in strings. Pearson/Addison-Wesley 2003). Collaboration with biological research groups strengthened again at the end of 1990 when the group started to study analysis of gene expression data. Both Alvis Brazma and Jaak Vilo have been working in Ukkonens' laboratory on this topic. One of the first computational methods to predict transcription factor binding sites in the DNA were developed in Ukkonens' group. Currently the group is studying the following bioinformatics related topics: Modeling metabolic networks and flux analysis Development of data management tools for VTT-TRAC gene expression measuring technology New algorithms for haplotype analysis Algorithms for detecting gene regulatory factor binding sites in mammalian genomes Reconstruction of macromolecular complexes based on electron microscopy images Back to the group list