M A Huynen

Summary

Affiliation: University of Nijmegen
Country: The Netherlands

Publications

  1. pmc The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
    Brigitte Boxma
    Department of Evolutionary Microbiology, Faculty of Science, Radboud University Nijmegen, Toernooiveld 1, NL 6525 ED Nijmegen, The Netherlands
    BMC Evol Biol 7:230. 2007
  2. doi request reprint Mitochondrial proteome evolution and genetic disease
    Martijn A Huynen
    CMBI 260, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Box 9101, 6500 HB Nijmegen, Netherlands
    Biochim Biophys Acta 1792:1122-9. 2009
  3. ncbi request reprint The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly
    M A Huynen
    Biocomputing, EMBL Max Delbrueck Center fur molecular medicin, Berlin Buch, Germany
    Hum Mol Genet 10:2463-8. 2001
  4. 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
  5. ncbi request reprint Assessment of phylogenomic and orthology approaches for phylogenetic inference
    B E Dutilh
    Center for Molecular and Biomolecular Informatics Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, P O Box 9101, 6500 HB, Nijmegen, The Netherlands
    Bioinformatics 23:815-24. 2007
  6. pmc Measuring genome evolution
    M A Huynen
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany, and Max Delbrück Centrum for Molecular Medicine, 13122 Berlin Buch, Germany
    Proc Natl Acad Sci U S A 95:5849-56. 1998
  7. ncbi request reprint Prediction of protein function and pathways in the genome era
    T Gabaldón
    NCMLS, CMBI, Center for Molecular and Biomolecular Informatics, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
    Cell Mol Life Sci 61:930-44. 2004
  8. 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
  9. 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
  10. ncbi request reprint Combinatorial gene regulation in Plasmodium falciparum
    Vera van Noort
    Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Toernooiveld 1, 3525 ED Nijmegen, The Netherlands
    Trends Genet 22:73-8. 2006

Collaborators

Detail Information

Publications49

  1. pmc The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
    Brigitte Boxma
    Department of Evolutionary Microbiology, Faculty of Science, Radboud University Nijmegen, Toernooiveld 1, NL 6525 ED Nijmegen, The Netherlands
    BMC Evol Biol 7:230. 2007
    ..The hydrogenase permits direct reoxidation of NADH because it consists of a [FeFe] hydrogenase module that is fused to two modules, which are homologous to the 24 kDa and the 51 kDa subunits of a mitochondrial complex I...
  2. doi request reprint Mitochondrial proteome evolution and genetic disease
    Martijn A Huynen
    CMBI 260, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Box 9101, 6500 HB Nijmegen, Netherlands
    Biochim Biophys Acta 1792:1122-9. 2009
    ..For the latter we review and reanalyze the eukaryotic evolution of the NADH:ubiquinone oxidoreductase (complex I) and the proteins involved in its assembly...
  3. ncbi request reprint The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly
    M A Huynen
    Biocomputing, EMBL Max Delbrueck Center fur molecular medicin, Berlin Buch, Germany
    Hum Mol Genet 10:2463-8. 2001
    ..They indicate that frataxin is specifically involved in the same sub-process as HSP20/Jac1p...
  4. 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'...
  5. ncbi request reprint Assessment of phylogenomic and orthology approaches for phylogenetic inference
    B E Dutilh
    Center for Molecular and Biomolecular Informatics Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, P O Box 9101, 6500 HB, Nijmegen, The Netherlands
    Bioinformatics 23:815-24. 2007
    ..Here, we systematically compare these four phylogenomic approaches, in parallel with three approaches for large-scale orthology determination: pairwise orthology, cluster orthology and tree-based orthology...
  6. pmc Measuring genome evolution
    M A Huynen
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany, and Max Delbrück Centrum for Molecular Medicine, 13122 Berlin Buch, Germany
    Proc Natl Acad Sci U S A 95:5849-56. 1998
    ..Finally, we show that some genomes are more highly organized than others: they show a higher degree of the clustering of genes that have orthologs in other genomes...
  7. ncbi request reprint Prediction of protein function and pathways in the genome era
    T Gabaldón
    NCMLS, CMBI, Center for Molecular and Biomolecular Informatics, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
    Cell Mol Life Sci 61:930-44. 2004
    ..Techniques are highlighted with examples, including an analysis that combines information from genomic-context with homology to predict a role of the RNase L inhibitor in the maturation of ribosomal RNA...
  8. 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...
  9. 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...
  10. ncbi request reprint Combinatorial gene regulation in Plasmodium falciparum
    Vera van Noort
    Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Toernooiveld 1, 3525 ED Nijmegen, The Netherlands
    Trends Genet 22:73-8. 2006
    ..falciparum than in other eukaryotes, such as yeast. We propose that Plasmodium uses the few regulatory proteins it has in a combinatorial approach for gene regulation, explaining the relative paucity in regulatory proteins...
  11. 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...
  12. pmc Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment
    Guenola Ricard
    Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
    BMC Genomics 7:22. 2006
    ....
  13. 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...
  14. pmc Benchmarking ortholog identification methods using functional genomics data
    Tim Hulsen
    Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen, Toernooiveld 1, Nijmegen, 6500 GL, The Netherlands
    Genome Biol 7:R31. 2006
    ..To identify protein pairs with the highest possible functional similarity, it is important to qualify ortholog identification methods...
  15. pmc Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate
    Nicole A Datson
    Division of Medical Pharmacology, Leiden Amsterdam Center for Drug Research and Leiden University Medical Center, The Netherlands
    BMC Genomics 8:190. 2007
    ..In contrast to the growing interest for the marmoset as an animal model, the molecular tools for genetic analysis are extremely limited...
  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. pmc Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution
    Philip R Kensche
    Centre for Molecular and Biomolecular Informatics Nijmegen, Centre for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands
    J R Soc Interface 5:151-70. 2008
    ..Both practical examples and theoretical considerations suggest that in order to get a reliable and specific picture of a protein's function, results from phylogenetic profiling have to be combined with other sources of evidence...
  18. ncbi request reprint Molecular and biochemical analysis of the plastidic ADP-glucose transporter (ZmBT1) from Zea mays
    Simon Kirchberger
    Abteilung Pflanzenphysiologie, Fachbereich Biologie, Technische Universitat Kaiserslautern, P O Box 3049, D 67653 Kaiserslautern, Germany
    J Biol Chem 282:22481-91. 2007
    ..The second group occurs in mono- and dicotyledonous plants and is most probably involved in the export of adenine nucleotides synthesized inside plastids...
  19. 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...
  20. pmc Reconstructing the evolution of the mitochondrial ribosomal proteome
    Paulien Smits
    Nijmegen Center for Mitochondrial Disorders, Radboud University Nijmegen Medical Center, Geert Grooteplein zuid 10, Nijmegen, The Netherlands
    Nucleic Acids Res 35:4686-703. 2007
    ..These newly detected MRPs constitute, along with evolutionary conserved MRPs, excellent new screening targets for human patients with unresolved mitochondrial oxidative phosphorylation disorders...
  21. 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...
  22. pmc Conserved co-expression for candidate disease gene prioritization
    Martin Oti
    Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26 28, 6525 GA, Nijmegen, The Netherlands
    BMC Bioinformatics 9:208. 2008
    ..Here we examine whether co-expression across multiple species is also a better prioritizer of disease genes than is co-expression between human genes alone...
  23. 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...
  24. ncbi request reprint Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I)
    Toni Gabaldón
    Center for Molecular and Biomolecular Informatics and Nijmegen Center for Molecular Life Sciences, University Medical Center St Radboud, Toernoooiveld 1, 6525 ED Nijmegen, The Netherlands
    J Mol Biol 348:857-70. 2005
    ..This evolutionary scenario is in contrast to that for Complex I in the prokaryotes, for which the combination of several separate, and previously independently functioning modules into a single complex has been proposed...
  25. 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...
  26. 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...
  27. 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...
  28. 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...
  29. 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...
  30. 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...
  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. 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
    ....
  33. pmc Identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolism
    Thijs J G Ettema
    Laboratory of Microbiology, Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
    J Bacteriol 186:7754-62. 2004
    ..The newly identified atPEPC, with its distinct properties, constitutes yet another example of the versatility of the enzymes of the central carbon metabolic pathways in the archaeal domain...
  34. ncbi request reprint Evolutionary diversity of vertebrate small heat shock proteins
    Erik Franck
    Department of Biochemistry, University of Nijmegen, 161 NCMLS, 9101, 6500 HB Nijmegen, The Netherlands
    J Mol Evol 59:792-805. 2004
    ..Interesting is the occurrence of several head-to-head located pairs of chordate sHsp genes...
  35. doi request reprint Evolution of closely linked gene pairs in vertebrate genomes
    Erik Franck
    Biomolecular Chemistry, 271 Nijmegen Center of Molecular Life Science, Radboud University Nijmegen, Nijmegen, The Netherlands
    Mol Biol Evol 25:1909-21. 2008
    ....
  36. pmc The iron-sulphur protein Ind1 is required for effective complex I assembly
    Katrine Bych
    Department of Plant Sciences, University of Cambridge, Cambridge, UK
    EMBO J 27:1736-46. 2008
    ..Our data suggest that Ind1 facilitates the assembly of Fe-S cofactors and subunits of complex I...
  37. ncbi request reprint Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes
    Toni Gabaldón
    Center for Molecular and Biomolecular Informatics and Nijmegen Center for Molecular Life Sciences, Radboud University of Nijmegen Medical Center, Nijmegen, The Netherlands
    Bioinformatics 21:ii144-50. 2005
    ..Proteins functioning in the same biochemical pathway tend to have a similar history of gene loss events, and we use this property to predict functional interactions among proteins in our set...
  38. pmc Signature, a web server for taxonomic characterization of sequence samples using signature genes
    Bas E Dutilh
    Center for Molecular and Biomolecular Informatics Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
    Nucleic Acids Res 36:W470-4. 2008
    ..This allows the user to quickly see from which part(s) of the taxonomy the query sequences likely originate...
  39. ncbi request reprint An anaerobic mitochondrion that produces hydrogen
    Brigitte Boxma
    Department of Evolutionary Microbiology, Faculty of Science, Radboud University Nijmegen, Toernooiveld 1, NL 6525 ED Nijmegen, The Netherlands
    Nature 434:74-9. 2005
    ..ovalis organelle as a missing link between mitochondria and hydrogenosomes...
  40. 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...
  41. doi request reprint Phenome connections
    Martin Oti
    Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands
    Trends Genet 24:103-6. 2008
    ..Their results imply that the human phenome can be viewed as a landscape of interrelated diseases, reflecting overlapping molecular causation...
  42. 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...
  43. pmc From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism
    Toni Gabaldón
    Nijmegen Center for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, University of Nijmegen, Nijmegen, The Netherlands
    PLoS Comput Biol 3:e219. 2007
    ..Altogether, the results indicate that the eukaryotic host has hijacked the proto-mitochondrion, taking control of its protein synthesis and metabolism...
  44. ncbi request reprint Reconstruction of the proto-mitochondrial metabolism
    Toni Gabaldón
    Nijmegen Center for Molecular Life Sciences, CMBI, Toernooiveld 1, 6525 ED Nijmegen, Netherlands
    Science 301:609. 2003
  45. 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
    ....
  46. 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/...
  47. ncbi request reprint Molecular characterization of phosphoglycerate mutase in archaea
    John van der Oost
    Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands
    FEMS Microbiol Lett 212:111-20. 2002
    ..In addition, as has been demonstrated in certain bacteria, some archaea appear to possess an alternative, cofactor-dependent PGM...
  48. ncbi request reprint Shaping the mitochondrial proteome
    Toni Gabaldón
    NCMLS, Nijmegen Center for Molecular Life Sciences, P O CMBI, Center for Molecular and Biomolecular Informatics, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
    Biochim Biophys Acta 1659:212-20. 2004
    ..Here we review recent advances in the fields of comparative genomics and proteomics that are throwing light on the origin and evolution of the mitochondrial proteome...
  49. doi request reprint Conservation of divergent transcription in fungi
    Philip R Kensche
    Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
    Trends Genet 24:207-11. 2008
    ..The functional interactions of the proteins encoded by the conserved divergent gene pairs indicate a potential for protein function prediction in eukaryotes...