Computer Science Colloquium
Susanne Fischer
Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology
Spatial clustering of rabies virus genomes using affinity propagation clustering
Tue 10.05.2016, 16:30, 60 minutesRoom JKU S2-120 in Science Park 2
Abstract
Rabies is one of the oldest known zoonosis caused by rabies virus, which is an important species of the genus Lyssavirus. So far, the spread of rabies virus is analyzed on regional levels since a global phylogenetic clustering and classification system is not yet available. Phylogenetic trees of rabies genome sequences calculated by the Maximum Likelihood method suggest a space-dependent clustering. However, these analyses revealed two limitations: (i) The analysis of large datasets results in highly complex dendrograms. (ii) The clustering of phylogenetic trees by visual inspection leads to different results since criteria for cluster definition are still lacking.My presentation aims at showing how these limitations can be solved by means of affinity propagation clustering. This is a mathematical method that is able to uses the phylogenetic distance matrix to allocate sequences to generic clusters. I will present you how affinity propagation clustering was applied to the distance matrices derived from the RABV full genome sample sets, resulting in a cluster structure which strongly corresponds to the structure of the Maximum Likelihood-based phylogenetic tree. At the end of my presentation I would like to discuss on strategies to implement a workflow based on this method to validate evidence for space-dependent clustering of rabies virus sequences.
Bio
Susanne Fischer holds a master´s degree in biosystems technologies and bioinformatics from the Technical University of Applied Sciences in Wildau-Germany. In 2013, she worked at BIOCOM AG Berlin as an assistant for database curation. Since 2014, she has been working on her doctoral theses on spatial and temporal distributions of rabies viruses at the Friedrich-Loeffler-Institute in Greifswald-Isle of Riems. This work is part of the Lyssavirus Research Network and a cooperation with the biomathematical institute of the Ernst-Moritz Arndt University of Greifswald.Invited by Univ.-Prof. Dr. Sepp Hochreiter, Institute of Bioinformatics
The Computer Science Colloquium is organized by the Department of Coputer Science at JKU, the Österreichische Gesellschaft für Informatik (ÖGI) and the Österreichische Computergesellschaft (OCG).