Research Team

Jeroen Raes

Bioinformatics and (eco-)systems biology lab

Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium

The focus of the Bioinformatics and (eco-)Systems Biology (BSB) research group (VIB, Brussels) is on the computational analysis and integration of high-throughput omics data at the ecosystem level and the application of these techniques in both collaborative and in-house community profiling projects. Prof. Raes has been involved early in the development of computational techniques to analyze large-scale metagenomic sequence data (Gianoulis et al., 2009; Raes et al., 2007).

The BSB lab focuses on using meta-omics and computational techniques to elucidate on the one hand the functioning of microbial communities in various environments and on the other hand to study the variability and alteration of human microbial communities in healthy and diseased states (Arumugam et al., 2011; Qin et al., 2010). Notably the research group is involved in several large international consortia for metagenomic characterization of diverse environments (e.g. MetaHIT, Tara Oceans). Within Tara Oceans, the group is performing global data integration and cross-platform ecological studies, using multiple data sources such as environmental data (physico-chemical and oceanographic data), metagenomic and metatranscriptomics data as well as high-throughput imaging protocol measurements.

The analysis and integration of meta-omics data (metagenomics, metatranscriptomincs, metaproteomics, meta-metabolomics) with environmental and imaging data enable the research group to reconstruct global ecosystem networks at the molecular level (eco-systems biology; Raes & Bork Nat Rev Microbiol 2008).

Relevant publications

  1. Gianoulis, T.A., Raes, J., Patel, P.V., Bjornson, R., Korbel, J.O., Letunic, I., Yamada, T., Paccanaro, A., Jensen, L.J., Snyder, M., et al. (2009). Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci U S A 106, 1374-1379.
  2. Raes, J., Korbel, J.O., Lercher, M.J., von Mering, C., and Bork, P. (2007). Prediction of effective genome size in metagenomic samples. Genome Biol 8, R10. Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D.R., Fernandes, G.R., Tap, J., Bruls, T., Batto, J.M., et al. (2011). Enterotypes of the human gut microbiome. Nature 473, 174-180.
  3. Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K.S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., et al. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65.
  4. Raes, J. and Bork, P. (2008). Molecular eco-systems biology: towards an understanding of community function. Nature Rev Microbiol 6, 693-699.

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The scientific activities of the Tara Oceans expedition, led by EMBL senior scientist Eric Karsenti, present an unprecedented effort that resulted in 35,000 samples containing millions of small organism collected in more than 210 ocean stations, chosen for their climatic significance or biodiversity.