Research Team

We are aiming at biological discoveries and often develop tools and resources to make this happen. We usually work in new or emerging areas; for example we have projects that integrate drugs (and other small molecules) with cellular and phenotypic information to predict new uses for old drugs (e.g. Campillos et al., 2008, Science) or find biomolecules that cause disease or side effects. We study temporal and spatial aspects of protein networks to identify biological principles that determine function and evolution (e.g. de Lichtenberg et al., 2005, Science; Jensen et al., 2006, Nature; Kuehner et al., 2009, Nature).

We study environmental aspects via comparative metagenomics (Tringe et al., 2005, Science; von Mering et al., 2007, Science; Qin et al., 2010, Nature) and hope to find marker genes for various diseases like obesity and cancer, and also to understand microbial community interactions, with application potential for human health and well-being. For example, our recent discovery of enterotypes - three distinct community compositions in the human gut analogous to blood groups (Arumugam et al., 2011 Nature) – was considered as one of the breakthroughs of 2011 by Science because it might explain different responses of people to drug intake and diet. In Tara Oceans, we apply our know how in bioinformatics, networks and metabolomics to the analysis of Global Ocean Functional Biodiversity (Raes et al. MSB 2011, Gianoulis et al. PNAS 2009).

Relevant publications

  1. Iskar, M., Zeller, G., Zhao, X.M., van Noort, V. & Bork, P. Drug discovery in the age of systems biology: the rise of computational approaches for data integration. Curr Opin Biotechnol. 2011 Dec 5.
  2. Powell, S., Szklarczyk, D., Trachana, K., Roth, A., Kuhn, M., Muller, J., Arnold, R., Rattei, T., Letunic, I., Doerks, T., Jensen, L.J., von Mering, C. & Bork, P. eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res. 2012 Jan;40(Database issue):D284-9. Epub 2011 Nov 16.
  3. Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D.R., Fernandes, G.R., Tap, J., Bruls, T., Batto, J.M., Bertalan, M., Borruel, N., Casellas, F., Fernandez, L., Gautier, L., Hansen, T., Hattori, M., Hayashi, T., Kleerebezem, M., Kurokawa, K., Leclerc, M., Levenez, F., Manichanh, C., Nielsen, H.B., Nielsen, T., Pons, N., Poulain, J., Qin, J., Sicheritz-Ponten, T., Tims, S., Torrents, D., Ugarte, E., Zoetendal, E.G., Wang, J., Guarner, F., Pedersen, O., de Vos, W.M., Brunak, S., Dore, J., Antolin, M., Artiguenave, F., Blottiere, H.M., Almeida, M., Brechot, C., Cara, C., Chervaux, C., Cultrone, A., Delorme, C., Denariaz, G., Dervyn, R., Foerstner, K.U., Friss, C., van de Guchte, M., Guedon, E., Haimet, F., Huber, W., van Hylckama-Vlieg, J., Jamet, A., Juste, C., Kaci, G., Knol, J., Lakhdari, O., Layec, S., Le Roux, K., Maguin, E., Merieux, A., Melo Minardi, R., M'rini, C., Muller, J., Oozeer, R., Parkhill, J., Renault, P., Rescigno, M., Sanchez, N., Sunagawa, S., Torrejon, A., Turner, K., Vandemeulebrouck, G., Varela, E., Winogradsky, Y., Zeller, G., Weissenbach, J., Ehrlich, S.D. & Bork, P. Enterotypes of the human gut microbiome. Nature. 2011 May 12;473(7346):174-80. Epub 2011 Apr 20.
  4. Raes J, Letunic I, Yamada T, Jensen LJ, Bork P. Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Mol Syst Biol. 2011 Mar 15; 7: 473.
  5. Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB. Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci U S A. 2009 Feb 3; 106(5): 1374-9. Epub 2009 Jan 22.

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.