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Jeroen Raes
Bioinformatics and (eco)systems biology
VIB Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel
PhD: Univ. of Ghent, Ghent, Belgium, '03
Postdoc: VIB-dept of Plant Systems Biology, VIB, Ghent, Belgium, '03-'05
Postdoc: EMBL, Heidelberg, Germany, '05-'07
Scientist at EMBL, Heidelberg, Germany, '07-'09
VIB Group leader since 2009 |
e-mail |
Current team members
Group leader: Jeroen Raes
Postdoctoral scientists: Gipsi Lima Mendez, Gwen Falony, Karoline Faust
Ph.D. Students: Falk Hildebrand, Youssef El Darzi
Keywords
bioinformatics - next-generation sequencing - metagenomics - human microbiome - eco-systems biology
Science
The functioning of the human body constitutes a complex interplay of human processes and ‘services’ rendered to us by the 1000 trillion microbial cells we carry. Disruption of this natural microbial flora is linked to infection, autoimmune diseases and cancer, but detailed knowledge about our microbial component remains scarce. Recent technological advances such as metagenomics and next-generation sequencing permit, for the first time, to study the various microbiota of the human body at a previously unseen scale. These advances have allowed the initiation of the International Human Microbiome Project, aiming at genomically characterizing the totality of human-associated microorganisms (the “microbiome”).
However, the complexity of metagenomic datasets makes their analysis a major bottleneck. This allowed the birth of a new, exciting subfield in computational biology which will eventually permit classical, cellular level systems biology progress towards modeling of entire communities (“eco-systems biology”), and untangling interspecies networks of competition, collaboration and communication at the molecular level.
The Raes lab combines large-scale, next-generation sequencing with novel computational approaches to investigate the functioning and variability of the healthy human microbiome at the systems level and study its alteration in disease. In addition, we focus on development of computational methods for the analysis of (next-generation) sequence data and the investigation of community properties from metagenomics, metatranscriptomics and meta-metabolomics data, which are applied in a wide range of environments (ocean, soil, ...).
Press Releases
See also press release (03/03/2010): The largest meta-genomic study ever: We’re more microbe than human in Nature (Qin et al.)
Selected Publications
Qin J, Li R, Raes J, Arumugam M, Burgdorf K, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende D, Li J, Xu J, Li E, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto J, Hansen T, Le Paslier D, Linneberg A, Nielsen H, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu h, Yu c, Li S, Jian M, Zhou Y, Li y, Zhang X, Qin N, Yang h, Wang J, Brunak S, Dore J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Antolin M, Artiguenave F, Blottiere H, Borruel N, Bruls T, Casellas F, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Forte M, Friss C, Van De Guchte M, Guedon E, Haimet F, Jamet A, Juste C, Kaci G, Kleerebezem M, Knol J, Kristensen M, Layec S, Le Roux K, Leclerc M, Maguin E, Melo Minardi R, Oozeer R, Rescigno M, Sanchez N, Tims S, Torrejon T, Varela E, De Vos W, Winogradsky Y, Zoetendal E, Bork P, Ehrlich S
A human gut microbial gene catalogue established by metagenomic sequencing
NATURE 464, 59-65, 2010
Gianoulis T, Raes J, Patel P, Bjornson R, Korbel J, Letunic I, Yamada T, Paccanaro A, Jensen L, Snyder M, Bork P, Gerstein M
Quantifying environmental adaptation of metabolic pathways in metagenomics
P NATL ACAD SCI USA 106, 1374-9, 2009
Raes J, Bork P
Molecular eco-systems biology: towards an understanding of community function
NAT REV MICROBIOL 6, 693-9, 2008
Raes J, Foerstner K, Bork P
Get the most out of your metagenome: computational analysis of environmental sequence data
CURR OPIN MICROBIOL 10, 490-8, 2007
Von Mering C, Hugenholtz P, Raes J, Tringe S, Doerks T, Jensen L, Ward N, Bork P
Quantitative phylogenetic assessment of microbial communities in diverse environments
SCIENCE 315, 1126-30, 2007
Search Publications
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