Research Topics
| B E DutilhSummaryAffiliation: Radboud University Nijmegen Country: The Netherlands Publications
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Detail Information
Publications
Asymmetric relationships between proteins shape genome evolutionRichard 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)...- Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny intronsGuenola 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... - The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassusRob 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... - 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... - 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.... - FACIL: Fast and Accurate Genetic Code Inference and LogoBas 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..Results are intuitively visualized in a Genetic Code Logo. Availability and implementation: FACIL is available as a web-based service at http://www.cmbi.ru.nl/FACIL/ and as a stand-alone program... - 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... - Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assemblyBas 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... - 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... - 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... - 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... - 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... - 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... - 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... - 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... - 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...