Martijn A Huynen

Summary

Affiliation: Radboud University Nijmegen
Country: The Netherlands

Publications

  1. pmc The SYSCILIA gold standard (SCGSv1) of known ciliary components and its applications within a systems biology consortium
    Teunis Jp van Dam
    Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen 6500 HB, The Netherlands
    Cilia 2:7. 2013
  2. doi request reprint Loss, replacement and gain of proteins at the origin of the mitochondria
    Martijn A Huynen
    Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P O Box 9101, 6400 HB Nijmegen, The Netherlands
    Biochim Biophys Acta 1827:224-31. 2013
  3. pmc Structure based hypothesis of a mitochondrial ribosome rescue mechanism
    Martijn A Huynen
    Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P, O, Box 9101, 6400, HB Nijmegen, The Netherlands
    Biol Direct 7:14. 2012
  4. 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
  5. pmc The hydrogenosomes of Psalteriomonas lanterna
    Rob M de Graaf
    Department of Evolutionary Microbiology, IWWR, Radboud University Nijmegen, The Netherlands
    BMC Evol Biol 9:287. 2009
  6. 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
  7. 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
  8. pmc The organellar genome and metabolic potential of the hydrogen-producing mitochondrion of Nyctotherus ovalis
    Rob M de Graaf
    Department of Evolutionary Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
    Mol Biol Evol 28:2379-91. 2011
  9. doi request reprint A mutation in the FAM36A gene, the human ortholog of COX20, impairs cytochrome c oxidase assembly and is associated with ataxia and muscle hypotonia
    Radek Szklarczyk
    Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen 6500HB, The Netherlands
    Hum Mol Genet 22:656-67. 2013
  10. 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

Detail Information

Publications83

  1. pmc The SYSCILIA gold standard (SCGSv1) of known ciliary components and its applications within a systems biology consortium
    Teunis Jp van Dam
    Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen 6500 HB, The Netherlands
    Cilia 2:7. 2013
    ..Here, we present the inaugural SYSCILIA gold standard of known ciliary components as a public resource...
  2. doi request reprint Loss, replacement and gain of proteins at the origin of the mitochondria
    Martijn A Huynen
    Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P O Box 9101, 6400 HB Nijmegen, The Netherlands
    Biochim Biophys Acta 1827:224-31. 2013
    ..This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems...
  3. pmc Structure based hypothesis of a mitochondrial ribosome rescue mechanism
    Martijn A Huynen
    Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P, O, Box 9101, 6400, HB Nijmegen, The Netherlands
    Biol Direct 7:14. 2012
    ..We subsequently modeled the 3D structure of mtRF1a and mtRF1 bound to the ribosome, highlighting the structural implications of these differences to derive a hypothesis for the function of mtRF1...
  4. 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...
  5. pmc The hydrogenosomes of Psalteriomonas lanterna
    Rob M de Graaf
    Department of Evolutionary Microbiology, IWWR, Radboud University Nijmegen, The Netherlands
    BMC Evol Biol 9:287. 2009
    ..This taxon is rather unrelated to taxa with hitherto studied hydrogenosomes...
  6. 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...
  7. 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...
  8. pmc The organellar genome and metabolic potential of the hydrogen-producing mitochondrion of Nyctotherus ovalis
    Rob M de Graaf
    Department of Evolutionary Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
    Mol Biol Evol 28:2379-91. 2011
    ..Thus, our data show that the hydrogenosomes of N. ovalis are highly specialized hydrogen-producing mitochondria...
  9. doi request reprint A mutation in the FAM36A gene, the human ortholog of COX20, impairs cytochrome c oxidase assembly and is associated with ataxia and muscle hypotonia
    Radek Szklarczyk
    Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen 6500HB, The Netherlands
    Hum Mol Genet 22:656-67. 2013
    ..These results establish the function of the human gene FAM36A/COX20 in complex IV assembly and support a causal role of the gene in complex IV deficiency...
  10. 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...
  11. pmc Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase
    Radek Szklarczyk
    Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, Nijmegen, 6500 HB, The Netherlands
    Genome Biol 13:R12. 2012
    ..Major advances have been made to determine orthology relations among a set of homologous proteins. However, they depend on the comparison of individual sequences and do not take into account divergent orthologs...
  12. 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...
  13. 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...
  14. 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...
  15. 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...
  16. pmc C7orf30 specifically associates with the large subunit of the mitochondrial ribosome and is involved in translation
    Bas F J Wanschers
    Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, The Netherlands
    Nucleic Acids Res 40:4040-51. 2012
    ..Based on our data we propose that C7orf30 is involved in ribosomal large subunit function. Sequencing the gene in 35 patients with impaired mitochondrial translation did not reveal disease-causing mutations in C7orf30...
  17. pmc The biological coherence of human phenome databases
    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
    Am J Hum Genet 85:801-8. 2009
    ..More generally, we propose that curation and more systematic annotation of human phenome databases can greatly improve the power of the phenotype for genetic disease analysis...
  18. pmc Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication
    Radek Szklarczyk
    Centre for Molecular and Biomolecular Informatics, NCMLS, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands
    Genome Biol 10:R135. 2009
    ..The experimental elucidation of organellar proteomes combined with the sequencing of complete genomes allows us to trace the evolution of the mitochondrial proteome...
  19. pmc Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns
    Guenola Ricard
    Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Nijmegen, The Netherlands
    BMC Genomics 9:587. 2008
    ..N. ovalis generates its macronuclear chromosomes by forming polytene chromosomes that subsequently develop into macronuclear chromosomes by DNA elimination and rearrangement...
  20. pmc The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus
    Rob M de Graaf
    Department of Evolutionary Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands
    BMC Genomics 10:514. 2009
    ..These ciliates are only distantly related to Tetrahymena spp. and Paramecium aurelia, but more closely related to Nyctotherus ovalis, which possesses a hydrogenosomal (mitochondrial) genome...
  21. 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...
  22. 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...
  23. 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...
  24. 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...
  25. 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...
  26. pmc Complex fate of paralogs
    Radek Szklarczyk
    Centre for Molecular and Biomolecular Informatics, NCMLS, Radboud University Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands
    BMC Evol Biol 8:337. 2008
    ..Gene duplications, known to be a major source of innovation in evolution, can now be readily examined in the context of protein complexes...
  27. pmc Asymmetric relationships between proteins shape genome evolution
    Richard A Notebaart
    Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert Grooteplein 26 28, 6525 GA, Nijmegen, The Netherlands
    Genome Biol 10:R19. 2009
    ..Asymmetric relations are analogous to the "if->then" logical relation where A implies B, but B does not imply A (A->B)...
  28. 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...
  29. 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
    ....
  30. doi request reprint Restoration of complex V deficiency caused by a novel deletion in the human TMEM70 gene normalizes mitochondrial morphology
    An I Jonckheere
    Department of Pediatrics, Nijmegen Center for Mitochondrial Disorders, Laboratory for Genetic, Endocrine, and Metabolic Disorders, Radboud University Nijmegen Medical Center, 6500 HB Nijmegen, The Netherlands
    Mitochondrion 11:954-63. 2011
    ..This study demonstrates that the role of complex V in mitochondrial cristae morphology applies to human mitochondrial disease pathology...
  31. 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
    ....
  32. pmc Evolution of modular intraflagellar transport from a coatomer-like progenitor
    Teunis J P van Dam
    Radboud University Medical Centre, 6500 HB, Nijmegen, The Netherlands
    Proc Natl Acad Sci U S A 110:6943-8. 2013
    ..Expansion of IFT subunits by duplication and their subsequent independent loss supports the idea of modularity and structural independence of the IFT subcomplexes...
  33. 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...
  34. doi request reprint Analysis of genes regulated by the transcription factor LUMAN identifies ApoA4 as a target gene in dendritic cells
    Anna Sanecka
    Department of Tumor Immunology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    Mol Immunol 50:66-73. 2012
    ..Subsequent validation experiments, bioinformatics-based promoter analysis, and silencing studies confirmed that ApoA4 is a true target gene of LUMAN in bone marrow-derived DCs (BMDCs)...
  35. pmc A mutation in C2orf64 causes impaired cytochrome c oxidase assembly and mitochondrial cardiomyopathy
    Merei Huigsloot
    Nijmegen Center for Mitochondrial Disorders, Department of Pediatrics, Radboud University Nijmegen Medical Centre, PO Box 9101, NL 6500HB, Nijmegen, The Netherlands
    Am J Hum Genet 88:488-93. 2011
    ....
  36. pmc FACIL: Fast and Accurate Genetic Code Inference and Logo
    Bas E Dutilh
    Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, Germany
    Bioinformatics 27:1929-33. 2011
    ..A total of 0.65% of the DNA sequences currently in Genbank encode their proteins with a variant genetic code, and these exceptions occur in many unrelated taxa...
  37. pmc A three-dimensional topology of complex I inferred from evolutionary correlations
    Philip R Kensche
    Center for Molecular and Biomolecular Informatics Nijmegen Center for Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, Nijmegen, HB, 6500, The Netherlands
    BMC Struct Biol 12:19. 2012
    ..We approached these questions by correlating the evolutionary rates of eukaryotic complex I subunits using the mirror-tree method and mapping the results into a 3D representation by multidimensional scaling...
  38. pmc BOLA1 is an aerobic protein that prevents mitochondrial morphology changes induced by glutathione depletion
    Peter Willems
    Department of Biochemistry, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    Antioxid Redox Signal 18:129-38. 2013
    ..In Escherichia coli, BolA causes a spherical cell shape and is overexpressed during oxidative stress. Here we aim to elucidate the possible role of its human homolog BOLA1 in mitochondrial morphology and thiol redox potential regulation...
  39. 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
    ....
  40. pmc Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly
    Bas E Dutilh
    Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands, Germany
    Bioinformatics 25:2878-81. 2009
    ..This diversity can confound existing strict assembly programs and lead to a fragmented assembly, which is unnecessary if we have a related reference genome available that can function as a scaffold...
  41. pmc Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity
    Edwin Lasonder
    Department of Molecular Biology, NCMLS, Radboud University Nijmegen, Nijmegen, The Netherlands
    PLoS Pathog 4:e1000195. 2008
    ..This study sheds light on the development and maturation of the malaria parasite in an Anopheles mosquito and also identifies proteins that may be essential for sporozoite infectivity to humans...
  42. 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...
  43. 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...
  44. 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
    ....
  45. 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...
  46. 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...
  47. doi request reprint A complex V ATP5A1 defect causes fatal neonatal mitochondrial encephalopathy
    An I Jonckheere
    Department of Paediatrics, Nijmegen Centre for Mitochondrial Disorders, Laboratory for Genetic, Endocrine, and Metabolic Disorders, Radboud University Medical Centre, Nijmegen, The Netherlands
    Brain 136:1544-54. 2013
    ..This study demonstrates the important value of functional studies in the diagnostic work-up of mitochondrial patients, in order to guide genetic variant prioritization, and to validate gene defects...
  48. 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
  49. doi request reprint NDUFB7 and NDUFA8 are located at the intermembrane surface of complex I
    Radek Szklarczyk
    Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, 6500 HB, Nijmegen, The Netherlands
    FEBS Lett 585:737-43. 2011
    ..We experimentally confirm the localization of the latter two, while our data are consistent with disulfide bridges in NDUFA8. We propose these subunits stabilize the membrane domain of complex I...
  50. 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...
  51. pmc Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus
    Evelyn N Kouwenhoven
    Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    PLoS Genet 6:e1001065. 2010
    ..These data provide a proof-of-concept that the catalogue of p63 binding sites identified in this study may be of relevance to the studies of SHFM and other congenital malformations that resemble the p63-associated phenotypes...
  52. pmc MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters
    Bastiaan J H Jansen
    Department of Tumor Immunology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    BMC Genomics 12:330. 2011
    ..Regulatory elements in miRNA promoters are less well studied, but may reveal a link between their expression and a specific cell type...
  53. 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
    ....
  54. 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...
  55. 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...
  56. doi request reprint CEP89 is required for mitochondrial metabolism and neuronal function in man and fly
    Bregje W M van Bon
    Department of Human Genetics, Radboud University Medical Centre, 6500 HB, Nijmegen, The Netherlands
    Hum Mol Genet 22:3138-51. 2013
    ..We conclude that CEP89 proteins play an important role in mitochondrial metabolism, especially complex IV activity, and are required for neuronal and cognitive function across evolution. ..
  57. 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...
  58. doi request reprint Identification of Nipsnap1 as a novel auxiliary protein inhibiting TRPV6 activity
    Joost P H Schoeber
    Department of Physiology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    Pflugers Arch 457:91-101. 2008
    ..In conclusion, this study presents the first physiological function of Nipsnap1 as an associated protein inhibiting TRPV6 activity that possibly exerts its effect directly at the plasma membrane...
  59. 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...
  60. doi request reprint Mosaic origin of the mitochondrial proteome
    Radek Szklarczyk
    Radboud University Nijmegen Medical Centre, CMBI NCMLS, Nijmegen, The Netherlands
    Proteomics 10:4012-24. 2010
    ..We observe that they neither change their subcellular compartments in the course of evolution, even when their genes do...
  61. pmc Human intellectual disability genes form conserved functional modules in Drosophila
    Merel A W Oortveld
    Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
    PLoS Genet 9:e1003911. 2013
    ..The combined data indicate that ID disorders, despite their extreme genetic diversity, are caused by disruption of a limited number of highly connected functional modules. ..
  62. pmc Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation
    Joanna L Parmley
    Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    PLoS Genet 5:e1000548. 2009
    ..As genes that regulate transcription in lower eukaryotes are known to be involved in translation on demand, this suggests that the mechanism of translation level expression regulation also exists within the human genome...
  63. 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'...
  64. 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...
  65. doi request reprint Dominant processes during human dendritic cell maturation revealed by integration of proteome and transcriptome at the pathway level
    Sonja I Buschow
    Department of Tumor Immunology and CMBI at the Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    J Proteome Res 9:1727-37. 2010
    ..We conclude that integration of different but related data sets at the pathway level can significantly increase the predictive power of multi "omics" analyses...
  66. pmc Measuring the physical cohesiveness of proteins using physical interaction enrichment
    Iziah Edwin Sama
    Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    Bioinformatics 26:2737-43. 2010
    ..These biases skew quantitative results from comparing PPI networks with genomics data. Here, we introduce an approach named physical interaction enrichment (PIE) to eliminate these biases...
  67. pmc Discovery of a HapE mutation that causes azole resistance in Aspergillus fumigatus through whole genome sequencing and sexual crossing
    Simone M T Camps
    Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    PLoS ONE 7:e50034. 2012
    ..fumigatus. The discovery may help understand alternate pathways for azole resistance in A. fumigatus with implications for the molecular diagnosis of resistance and drug discovery...
  68. pmc The alpha-kinase family: an exceptional branch on the protein kinase tree
    Jeroen Middelbeek
    Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, The Netherlands
    Cell Mol Life Sci 67:875-90. 2010
    ..Here, we review the current state of knowledge on different members of this kinase family and discuss the potential use of alpha-kinases as drug targets in diseases such as cancer...
  69. 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...
  70. 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...
  71. 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...
  72. 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...
  73. 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...
  74. 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...
  75. ncbi request reprint TRASH: a novel metal-binding domain predicted to be involved in heavy-metal sensing, trafficking and resistance
    Thijs J G Ettema
    Laboratory of Microbiology, Wageningen University and Research Center Hesselink van Suchtelenweg 4, NL 6703CT, Wageningen, The Netherlands
    Trends Biochem Sci 28:170-3. 2003
    ..The role of the multiple copies of TRASH that are present in vertebrate proteins remains to be elucidated...
  76. 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...
  77. 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...
  78. 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/...
  79. 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...
  80. ncbi request reprint The properties of protein family space depend on experimental design
    Victor Kunin
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Bioinformatics 21:2618-22. 2005
    ..Databases of protein families often exhibit drastically different properties of the protein family space...
  81. 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...
  82. ncbi request reprint Optimized design and assessment of whole genome tiling arrays
    Stefan Graf
    EMBL European Bioinformatics Institute, Hinxton, Cambridge, UK
    Bioinformatics 23:i195-204. 2007
    ..We have identified a number of design parameters to be optimized including uniqueness of the probe sequences within the whole genome, melting temperature and self-hybridization potential...
  83. 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...