B Snel

Summary

Affiliation: European Molecular Biology Laboratory
Country: Germany

Publications

  1. pmc STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene
    B Snel
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Nucleic Acids Res 28:3442-4. 2000
  2. ncbi request reprint Genomes in flux: the evolution of archaeal and proteobacterial gene content
    Berend Snel
    European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Genome Res 12:17-25. 2002
  3. pmc The identification of functional modules from the genomic association of genes
    Berend Snel
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Proc Natl Acad Sci U S A 99:5890-5. 2002
  4. pmc Predicting protein function by genomic context: quantitative evaluation and qualitative inferences
    M Huynen
    European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Genome Res 10:1204-10. 2000
  5. ncbi request reprint Exploitation of gene context
    M Huynen
    European Molecular Biology Laboratory, Max Delbrück Centrum for Molecular Medicine, Heidelberg, Berlin Buch, 69117, 13122, Germany
    Curr Opin Struct Biol 10:366-70. 2000
  6. pmc Pathway alignment: application to the comparative analysis of glycolytic enzymes
    T Dandekar
    EMBL, P O Box 102209, D 69012 Heidelberg, Germany
    Biochem J 343:115-24. 1999
  7. ncbi request reprint Inversions and the dynamics of eukaryotic gene order
    M A Huynen
    EMBL, Biocomputing, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Trends Genet 17:304-6. 2001
  8. ncbi request reprint Phylogenomics reveal a robust fungal tree of life
    Eiko E Kuramae
    Yeast Research, Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands
    FEMS Yeast Res 6:1213-20. 2006
  9. pmc STRING: known and predicted protein-protein associations, integrated and transferred across organisms
    Christian von Mering
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 33:D433-7. 2005
  10. pmc STRING 7--recent developments in the integration and prediction of protein interactions
    Christian von Mering
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 35:D358-62. 2007

Collaborators

Detail Information

Publications36

  1. pmc STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene
    B Snel
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Nucleic Acids Res 28:3442-4. 2000
    ..The usefulness of STRING is illustrated with an example that suggests a functional context for an RNA methylase with unknown specificity...
  2. ncbi request reprint Genomes in flux: the evolution of archaeal and proteobacterial gene content
    Berend Snel
    European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Genome Res 12:17-25. 2002
    ..Gene loss, unlike the other processes, correlates fairly well with time. This clock-like behavior suggests that gene loss is under negative selection, while the processes that add genes are under positive selection...
  3. pmc The identification of functional modules from the genomic association of genes
    Berend Snel
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Proc Natl Acad Sci U S A 99:5890-5. 2002
    ..Comparative genome analysis, thus, allows identification of a level of functional interaction between that of pairwise interactions, and of the complete genome...
  4. pmc Predicting protein function by genomic context: quantitative evaluation and qualitative inferences
    M Huynen
    European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Genome Res 10:1204-10. 2000
    ..Using a combination of genomic context and homology searches, new functional features can be predicted for 10% of M. genitalium genes...
  5. ncbi request reprint Exploitation of gene context
    M Huynen
    European Molecular Biology Laboratory, Max Delbrück Centrum for Molecular Medicine, Heidelberg, Berlin Buch, 69117, 13122, Germany
    Curr Opin Struct Biol 10:366-70. 2000
    ..This type of information complements functional features that are predicted by classical homology-based search techniques...
  6. pmc Pathway alignment: application to the comparative analysis of glycolytic enzymes
    T Dandekar
    EMBL, P O Box 102209, D 69012 Heidelberg, Germany
    Biochem J 343:115-24. 1999
    ..Archaean, bacterial and parasite specific adaptations are identified and described...
  7. ncbi request reprint Inversions and the dynamics of eukaryotic gene order
    M A Huynen
    EMBL, Biocomputing, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Trends Genet 17:304-6. 2001
    ..Nevertheless, qualitatively interesting examples of conservation of gene order in eukaryotes can be observed...
  8. ncbi request reprint Phylogenomics reveal a robust fungal tree of life
    Eiko E Kuramae
    Yeast Research, Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands
    FEMS Yeast Res 6:1213-20. 2006
    ..The single tree that we inferred from our dataset showed excellent nodal support for each branch, suggesting that it reflects the true phylogenetic relationships of the species involved...
  9. pmc STRING: known and predicted protein-protein associations, integrated and transferred across organisms
    Christian von Mering
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 33:D433-7. 2005
    ..STRING currently holds 730,000 proteins in 180 fully sequenced organisms, and is available at http://string.embl.de/...
  10. pmc STRING 7--recent developments in the integration and prediction of protein interactions
    Christian von Mering
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 35:D358-62. 2007
    ..Novel features include AJAX-based web-navigation, inclusion of additional resources such as BioGRID, and detailed protein domain annotation. STRING is available at http://string.embl.de/..
  11. ncbi request reprint Variation and evolution of biomolecular systems: searching for functional relevance
    Martijn A Huynen
    Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, P O Box 9010, 6500 GL Nijmegen, The Netherlands
    FEBS Lett 579:1839-45. 2005
    ..Mapping the inter-species variation of complex biomolecular systems on a phylogenetic species tree allows one to reconstruct their evolution...
  12. ncbi request reprint Genome trees and the nature of genome evolution
    Berend Snel
    Center for Molecular and Biomolecular Informatics, Nijmegen, The Netherlands
    Annu Rev Microbiol 59:191-209. 2005
    ..We expect such sophisticated methods to help us resolve the branching order between the main bacterial phyla...
  13. pmc Correlation between sequence conservation and the genomic context after gene duplication
    Richard A Notebaart
    Center for Molecular and Biomolecular Informatics, Radboud University, Nijmegen, The Netherlands
    Nucleic Acids Res 33:6164-71. 2005
    ..e. gene-neighborhood in prokaryotes and co-expression in eukaryotes) with protein sequence information to predict the most probable functional equivalent ortholog in the presence of inparalogs...
  14. pmc A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation
    Bas E Dutilh
    Center for Molecular and Biomolecular Informatics Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands
    BMC Genomics 7:10. 2006
    ..Thus far, comparative studies of gene expression between species have been based on the level of expression of the gene across corresponding tissues, or on the co-expression of the gene with another gene...
  15. ncbi request reprint Toward automatic reconstruction of a highly resolved tree of life
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Science 311:1283-7. 2006
    ..For example, we place the phylum Acidobacteria as a sister group of delta-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor...
  16. pmc Orthology prediction at scalable resolution by phylogenetic tree analysis
    Rene T J M van der Heijden
    Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
    BMC Bioinformatics 8:83. 2007
    ..Published procedures to extract orthologous groups from phylogenetic trees do not allow identification of orthology at various levels of resolution, nor do they document the relations between the orthologous groups...
  17. ncbi request reprint The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise
    Bas E Dutilh
    Center for Molecular and Biomolecular Informatics Nijmegen Center for Molecular Life Sciences, University of Nijmegen, Nijmegen, The Netherlands
    J Mol Evol 58:527-39. 2004
    ..Horizontal gene transfer or parallel gene loss does not cause systematic biases in the gene content tree...
  18. pmc Quantifying modularity in the evolution of biomolecular systems
    Berend Snel
    Nijmegen Center for Molecular Life Sciences, p a Centre for Molecular and Biomolecular Informatics, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
    Genome Res 14:391-7. 2004
    ..Analysis within one collection does not suffer from such differences, and we show that within the EcoCyc metabolic pathway database, biosynthetic pathways are evolutionarily more modular than catabolic pathways...
  19. ncbi request reprint SHOT: a web server for the construction of genome phylogenies
    Jan O Korbel
    EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
    Trends Genet 18:158-62. 2002
    ..SHOT is a useful tool for analysing the tree of life from a genomic point of view. It is available at http://www.Bork.EMBL-Heidelberg.de/SHOT...
  20. pmc Coevolution of gene families in prokaryotes
    Otto X Cordero
    Theoretical Biology and Bioinformatics, University of Utrecht, 3584 CH Utrecht, The Netherlands
    Genome Res 18:462-8. 2008
    ..3) "Long-range" coevolutionary relationships, caused mostly by large family expansions or contractions, reveal high-level evolutionary organization of cellular processes in prokaryotes...
  21. pmc STRING: a database of predicted functional associations between proteins
    Christian von Mering
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 31:258-61. 2003
    ..The database predicts functional interactions at an expected level of accuracy of at least 80% for more than half of the genes; it is online at http://www.bork.embl-heidelberg.de/STRING/...
  22. ncbi request reprint Function prediction and protein networks
    Martijn A Huynen
    Nijmegen Center for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands
    Curr Opin Cell Biol 15:191-8. 2003
    ..Finally, the interaction networks that can be obtained by combining the predicted pair-wise interactions have enough internal structure to detect higher levels of organization, such as 'functional modules'...
  23. pmc Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties
    Jos Boekhorst
    Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, The Netherlands
    BMC Bioinformatics 8:356. 2007
    ..However additional improvement could be made by exploiting sources of genomic information other than the primary sequence or tertiary structure...
  24. ncbi request reprint Deciphering the evolution and metabolism of an anammox bacterium from a community genome
    Marc Strous
    Department of Microbiology, IWWR, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
    Nature 440:790-4. 2006
    ..Most significantly, we identified candidate genes responsible for ladderane biosynthesis and biological hydrazine metabolism, and discovered unexpected metabolic versatility...
  25. pmc The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model
    Vera van Noort
    Nijmegen Center for Molecular Life Sciences, P A Center for Molecular and Biomolecular Informatics, Nijmegen, The Netherlands
    EMBO Rep 5:280-4. 2004
    ....
  26. pmc Signature genes as a phylogenomic tool
    Bas E Dutilh
    Center for Molecular and Biomolecular Informatics Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    Mol Biol Evol 25:1659-67. 2008
    ..Summarizing, signature genes can complement traditional sequence-based methods in addressing taxonomic questions...
  27. pmc Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions
    Vera van Noort
    Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Toernooiveld, 6525 ED Nijmegen, The Netherlands
    Genome Biol 8:R197. 2007
    ..While some of these techniques are specific for a certain type of interaction, most predict a mixture of interactions. Qualitative labels are essential for the molecular biologist to experimentally verify predicted interactions...
  28. ncbi request reprint Conflicting phylogenetic position of Schizosaccharomyces pombe
    Eiko E Kuramae
    Centraalbureau voor Schimmelcultures, Comparative Genomics and Bioinformatics, Uppsalalaan 8, 3584 Utrecht, The Netherlands
    Genomics 88:387-93. 2006
    ..This apparent paradox may point to a heterogeneous nuclear genome of the fungi. Importantly, this needs to be taken in consideration for a correct understanding of the fungal Tree of Life...
  29. ncbi request reprint Combining data from genomes, Y2H and 3D structure indicates that BolA is a reductase interacting with a glutaredoxin
    Martijn A Huynen
    CMBI, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Toernooiveld 1, 6525ED Nijmegen, The Netherlands
    FEBS Lett 579:591-6. 2005
    ..We propose that BolA uses the mono-thiol glutaredoxin as the source for these...
  30. pmc Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes
    Berend Snel
    Nijmegen Center for Molecular Life Sciences, University Medical Center St Radboud, p a CMBI, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
    Nucleic Acids Res 32:4725-31. 2004
    ....
  31. ncbi request reprint Comparative genomics for reliable protein-function prediction from genomic data
    Martijn A Huynen
    Nijmegen Center for Molecular Life Sciences, University Medical Center St Radboud and Center for Molecular and Biomolecular Informatics, PO Box 9010, 6500 GL Nijmegen, The Netherlands
    Trends Genet 20:340-4. 2004
    ....
  32. ncbi request reprint Systematic discovery of analogous enzymes in thiamin biosynthesis
    Enrique Morett
    Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Av Universidad 2001, Cuernavaca, Morelos, 62210, Mexico
    Nat Biotechnol 21:790-5. 2003
    ..The results demonstrate the ability of our computational approach to predict specific functions without taking into account sequence similarity...
  33. ncbi request reprint Predicting gene function by conserved co-expression
    Vera van Noort
    Nijmegen Center for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, PO Box 9010, 6500 GL Nijmegen, The Netherlands
    Trends Genet 19:238-42. 2003
    ..The use of conservation between parallel duplicated gene pairs to predict function is especially promising given that gene duplication is common in eukaryotes, and that data from only a single organism can be used...
  34. pmc The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract
    Mark A Schell
    Nestle Research Center, Vers chez les Blanc, Lausanne 1000, Switzerland
    Proc Natl Acad Sci U S A 99:14422-7. 2002
    ..We also found a eukaryotic-type serine protease inhibitor (serpin) possibly involved in the reported immunomodulatory activity of bifidobacteria...
  35. ncbi request reprint Comparative assessment of large-scale data sets of protein-protein interactions
    Christian von Mering
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nature 417:399-403. 2002
    ..To measure their accuracy and potential as well as to identify biases, strengths and weaknesses, we compare the methods with each other and with a reference set of previously reported protein interactions...
  36. pmc Protein complex evolution does not involve extensive network rewiring
    Teunis J P van Dam
    Theoretical Biology and Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
    PLoS Comput Biol 4:e1000132. 2008
    ..e. acquisition or loss of co-complex memberships), but mainly due to genomic acquisition or loss of genes coding for subunits. We thus reveal evidence for the tight interrelation of genomic and network evolution...