Jeroen Raes

Summary

Affiliation: European Molecular Biology Laboratory
Country: Germany

Publications

  1. ncbi Molecular eco-systems biology: towards an understanding of community function
    Jeroen Raes
    European Molecular Biology Laboratory, Heidelberg, Germany
    Nat Rev Microbiol 6:693-9. 2008
  2. ncbi Prediction of effective genome size in metagenomic samples
    Jeroen Raes
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Genome Biol 8:R10. 2007
  3. ncbi Discovering functional novelty in metagenomes: examples from light-mediated processes
    Amoolya H Singh
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    J Bacteriol 191:32-41. 2009
  4. ncbi Assessment of metagenomic assembly using simulated next generation sequencing data
    Daniel R Mende
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS ONE 7:e31386. 2012
  5. ncbi Enterotypes of the human gut microbiome
    Manimozhiyan Arumugam
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 473:174-80. 2011
  6. ncbi Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours
    Takuji Yamada
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 8:581. 2012
  7. ncbi Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data
    Jeroen Raes
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 7:473. 2011
  8. ncbi SmashCommunity: a metagenomic annotation and analysis tool
    Manimozhiyan Arumugam
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Bioinformatics 26:2977-8. 2010
  9. ncbi A holistic approach to marine eco-systems biology
    Eric Karsenti
    European Molecular Biology Laboratory EMBL, Heidelberg, Germany
    PLoS Biol 9:e1001177. 2011
  10. ncbi A nitrile hydratase in the eukaryote Monosiga brevicollis
    Konrad U Foerstner
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS ONE 3:e3976. 2008

Collaborators

Detail Information

Publications18

  1. ncbi Molecular eco-systems biology: towards an understanding of community function
    Jeroen Raes
    European Molecular Biology Laboratory, Heidelberg, Germany
    Nat Rev Microbiol 6:693-9. 2008
    ..Here, we discuss the necessary data types that are required to unite molecular microbiology and ecology to develop an understanding of community function and discuss the potential shortcomings of these approaches...
  2. ncbi Prediction of effective genome size in metagenomic samples
    Jeroen Raes
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Genome Biol 8:R10. 2007
    ..7 Mb; for bacteria in a nutrient-poor, organism-sparse ocean surface water sample, EGS is as low as 1.6 Mb. The method also permits evaluation of completion status and assembly bias in single-genome sequencing projects...
  3. ncbi Discovering functional novelty in metagenomes: examples from light-mediated processes
    Amoolya H Singh
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    J Bacteriol 191:32-41. 2009
    ..While the discoveries illustrate the opportunities in function discovery, we also discuss the immense conceptual and practical challenges that come along with this new type of data...
  4. ncbi Assessment of metagenomic assembly using simulated next generation sequencing data
    Daniel R Mende
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS ONE 7:e31386. 2012
    ..The metagenomic simulators developed for this research are freely available...
  5. ncbi Enterotypes of the human gut microbiome
    Manimozhiyan Arumugam
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 473:174-80. 2011
    ..For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers...
  6. ncbi Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours
    Takuji Yamada
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 8:581. 2012
    ....
  7. ncbi Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data
    Jeroen Raes
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 7:473. 2011
    ..Together, our results show that the functional community composition derived from metagenomes is an important quantitative readout for molecular trait-based biogeography and ecology...
  8. ncbi SmashCommunity: a metagenomic annotation and analysis tool
    Manimozhiyan Arumugam
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Bioinformatics 26:2977-8. 2010
    ..It provides tools to estimate the quantitative phylogenetic and functional compositions of metagenomes, to compare compositions of multiple metagenomes and to produce intuitive visual representations of such analyses...
  9. ncbi A holistic approach to marine eco-systems biology
    Eric Karsenti
    European Molecular Biology Laboratory EMBL, Heidelberg, Germany
    PLoS Biol 9:e1001177. 2011
    ..The Tara Oceans consortium organizes expeditions to help fill this gap at the global level...
  10. ncbi A nitrile hydratase in the eukaryote Monosiga brevicollis
    Konrad U Foerstner
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS ONE 3:e3976. 2008
    ..The newly discovered NHase might open biotechnological routes due to its unconventional structure, its new type of host and its apparent integration into eukaryotic protein networks...
  11. ncbi Get the most out of your metagenome: computational analysis of environmental sequence data
    Jeroen Raes
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Curr Opin Microbiol 10:490-8. 2007
    ....
  12. ncbi A molecular study of microbe transfer between distant environments
    Sean D Hooper
    Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
    PLoS ONE 3:e2607. 2008
    ..In this study, we compare two environmental sequencing projects to find molecular evidence of transfer of microbes over vast geographical distances...
  13. ncbi An improved statistical method for detecting heterotachy in nucleotide sequences
    Guy Baele
    Department of Applied Mathematics and Computer Science, Ghent University, Ghent, Belgium
    Mol Biol Evol 23:1397-405. 2006
    ..Using extensive testing, we show that this may not be due to heterotachy itself but merely due to the increased substitution rate at the detected heterotachous sites...
  14. ncbi Modeling gene and genome duplications in eukaryotes
    Steven Maere
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
    Proc Natl Acad Sci U S A 102:5454-9. 2005
    ..Our evolutionary model is widely applicable and can be used to evaluate different assumptions regarding small- or large-scale gene duplication events in eukaryotic genomes...
  15. ncbi Duplication and divergence: the evolution of new genes and old ideas
    John S Taylor
    Department of Biology, University of Victoria, British Columbia V8W 3N5, Canada
    Annu Rev Genet 38:615-43. 2004
    ..We document conceptual and technological advances in gene duplication research from this early research in comparative cytology up to recent research on whole genomes, "transcriptomes," and "interactomes."..
  16. ncbi Gene duplication, the evolution of novel gene functions, and detecting functional divergence of duplicates in silico
    Jeroen Raes
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB, Ghent University, Ghent, Belgium
    Appl Bioinformatics 2:91-101. 2003
    ..In this review, we discuss the strengths and limitations of both older and novel approaches to investigate the evolution of duplicated genes in silico...
  17. ncbi And then there were many: MADS goes genomic
    Stefanie De Bodt
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
    Trends Plant Sci 8:475-83. 2003
    ....
  18. ncbi The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice
    Klaas Vandepoele
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, B-9000 Gent, Belgium
    Genome Res 12:1792-801. 2002
    ..These regions comprise from 4 up to 11 conserved homologous gene pairs. We predict the number of homologous regions and the extent of microcolinearity to increase significantly once better annotations of the rice genome become available...