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First name: Renzo
Last name: Kottmann
Country: Germany
Thesis Subject:
Data integration for marine ecological genomics
Education:
1999-2006 Diplom Computer Science, University Bremen
2003-2005 MSc. in Marine Microbiology, IMPRS for Marine Microbiology Bremen
Scientific Interests and Goals:
Metagenomics defined as “the functional and sequence-based analysis of the collective microbial genomes contained in an environmental sample” (Riesenfeld et al. 2004) enables studies on the basic question to which extend the environment influences the genome and to which extend the
genome influences the capacity of a microorganism to interact with the environment. Moreover, metagenomics allows to test the hypothesis that a substantial portion of the unknown genes shows habitat specific patterns from which functions can be deduced. The goal of the EU-Project MetaFunctions “Environmental And Meta-Genomics: A Bioinformatics System to Detect and Assign Functions to Habitat Specific Gene Patterns” (http://www.metafunctions.org) is to correlate metagenome sequence data with geographic and ecological data to find such habitat specific gene patterns to predict functions of genes. Currently, no methodology or database integrates these kinds of information in a single concept which is a prerequisite for systematic
tests of the habitat specificity of genes. Therefore the aims of this thesis are first the development and implementation of a database concept to integrate geographic, environmental and molecular sequence data. Secondly, finding new ways of acquisition and integration of such kind
of data and third to do research on existing and new statistical models
for the correlation of environmental- and molecular sequence data.
Selected Publications: