Articles

microbial ME[GT]Agenomics: computational methods for big data from small cells

Thomas Rattei, Computational Systems Biology, University of Vienna

Microbial life is populating many different habitats (including ourselves – the human body) on earth. Many of these habitats exhibit an unseen diversity of microorganisms, of which most cannot be grown in the lab using cultivation techniques. By applying high-throughput sequencing of DNA and RNA to environmental samples, metagenomic and metatranscriptomic sequences have revolutionized microbiology and microbial ecology during the last years and allow for an understanding of environmental communities on the molecular level.

This talk surveys the major computational methods necessary to process, analyse and interpret these sequences. The talk will discuss how to estimate taxonomic diversity in metagenomic and metatranscriptomic samples and how to predict the function and taxonomy of environmental sequences. Finally, the perspectives of upcoming new sequencing and single-cell techniques not only on environmental genomics, but also to studying microbial populations will be discussed.

 

Short CV

Thomas Rattei is chemist by training and did his PhD in Dresden, Germany, in analytical and computational biochemistry. He joined the MIPS team (Institute of Bioinformatics and Systems Biology, Helmholtz-Center Munich) and the Department of Genome Oriented Bioinformatics at the Technical University Munich. Since 2010 he is full professor of “In silico genomics” and head of the Department of Computational Systems Biology (CUBE) at the Faculty of Life Sciences of the University of Vienna.

The research of CUBE is focused on the analysis and annotation of microbial genomes, evolution of genomes and comparative genomics, bioinformatics for metagenomics and metatranskriptomics, molecular pathogen-host interactions, molecular networks and functional modules, but also large-scale sequence analysis, grid computing, bioinformatics infrastructure and databases.