Research Topics
Genomes and Genes | M A HuynenSummaryAffiliation: University of Nijmegen Country: The Netherlands Publications
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Publications
The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric originBrigitte 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...
Mitochondrial proteome evolution and genetic diseaseMartijn 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...
The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assemblyM 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...- Function prediction and protein networksMartijn 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'... - Assessment of phylogenomic and orthology approaches for phylogenetic inferenceB 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... - Measuring genome evolutionM 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... - Prediction of protein function and pathways in the genome eraT 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... - Inversions and the dynamics of eukaryotic gene orderM 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... - Correlation between sequence conservation and the genomic context after gene duplicationRichard 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... - Combinatorial gene regulation in Plasmodium falciparumVera 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... - A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservationBas 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... - Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environmentGuenola 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.... - Deciphering the evolution and metabolism of an anammox bacterium from a community genomeMarc 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... - Benchmarking ortholog identification methods using functional genomics dataTim 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... - Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primateNicole 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... - Orthology prediction at scalable resolution by phylogenetic tree analysisRene 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... - Practical and theoretical advances in predicting the function of a protein by its phylogenetic distributionPhilip 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... - Molecular and biochemical analysis of the plastidic ADP-glucose transporter (ZmBT1) from Zea maysSimon 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... - Signature genes as a phylogenomic toolBas 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... - Reconstructing the evolution of the mitochondrial ribosomal proteomePaulien 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... - Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactionsVera 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... - Conserved co-expression for candidate disease gene prioritizationMartin 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... - Genome trees and the nature of genome evolutionBerend 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... - 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... - Variation and evolution of biomolecular systems: searching for functional relevanceMartijn 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... - Genomes in flux: the evolution of archaeal and proteobacterial gene contentBerend 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... - SHOT: a web server for the construction of genome phylogeniesJan 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... - Predicting gene function by conserved co-expressionVera 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... - Quantifying modularity in the evolution of biomolecular systemsBerend 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... - The consistent phylogenetic signal in genome trees revealed by reducing the impact of noiseBas 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... - Comparative genomics for reliable protein-function prediction from genomic dataMartijn 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.... - Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotesBerend 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.... - Identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolismThijs 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... - Evolutionary diversity of vertebrate small heat shock proteinsErik 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... - Evolution of closely linked gene pairs in vertebrate genomesErik Franck
Biomolecular Chemistry, 271 Nijmegen Center of Molecular Life Science, Radboud University Nijmegen, Nijmegen, The Netherlands
Mol Biol Evol 25:1909-21. 2008.... - The iron-sulphur protein Ind1 is required for effective complex I assemblyKatrine 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... - Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotesToni 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... - Signature, a web server for taxonomic characterization of sequence samples using signature genesBas 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... - An anaerobic mitochondrion that produces hydrogenBrigitte 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... - The identification of functional modules from the genomic association of genesBerend 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... - Phenome connectionsMartin 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... - Combining data from genomes, Y2H and 3D structure indicates that BolA is a reductase interacting with a glutaredoxinMartijn 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... - From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolismToni 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... - Reconstruction of the proto-mitochondrial metabolismToni Gabaldón
Nijmegen Center for Molecular Life Sciences, CMBI, Toernooiveld 1, 6525 ED Nijmegen, Netherlands
Science 301:609. 2003 - The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple modelVera 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.... - STRING: known and predicted protein-protein associations, integrated and transferred across organismsChristian 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/... - Molecular characterization of phosphoglycerate mutase in archaeaJohn 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... - Shaping the mitochondrial proteomeToni 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... - Conservation of divergent transcription in fungiPhilip 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...