Gaining Insight into the Uncultured Microbial World by Computational Metagenome Analysis

This keynote lecture was given during the ECCB'14 conference, Monday, September 8, 2014, Palais de la Musique et des Congrès, Strasbourg, France. Professor Alice McHardy was introduced by Yves Moreau, University of Leuven, Belgium.

Next generation sequencing allows to extensively survey the genome-wide genetic diversity of microbial communities, as well as populations from all domains of life. A major challenge is the development of computational methods for hypothesis generation and basic computational analysis of these large-scale data sets.  I will present our work on computational methods for metagenome analysis.  We have developed fast and accurate methods for the taxonomic assignment of sequence fragments obtained by DNA shotgun sequencing of microbial communities to the species or higher-ranking taxa from which they originate. Furthermore, we are working on techniques for predicting and characterizing microbial phenotypes, as well as identifying the relevant protein repertoire for a given phenotype, focusing hereby on microbial plant biomass degradation and plant-associated microbial communities.

 Alice Carolyn McHardy

HHU D√ľsseldorf and¬†Helmholtz Center¬†for Infection Biology in Braunschweig, Germany¬†
Chair of the Department for Algorithmic Bioinformatics at HHU, Head of the Computational Biology for Infection Research Group at the Helmholtz Center 

Bio: Alice Carolyn McHardy research interest is the design of computational methods to solve problems from the medical and biotechnological domains using next generation sequence data. A particular focus is the study of the evolution of influenza A viruses and characterizing the taxonomic composition, functions and evolution of microbial communities using metagenome sequence samples. She has a PhD in bioinformatics and a master’s degree in biochemistry, both from Bielefeld University. From 2005 to 2007 she worked as a postdoctoral researcher, then as a permanent staff member in the Bioinformatics & Pattern Discovery Group at the IBM T.J. Watson Research Center in Yorktown Heights, NY. From 2007 to 2012 she led the Max-Planck research group for Computational Genomics & Epidemiology at the Max-Planck institute for Informatics in Saarbruecken, Germany.

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