Y Van de Peer

Summary

Affiliation: Ghent University
Country: Belgium

Publications

  1. ncbi Dealing with saturation at the amino acid level: a case study based on anciently duplicated zebrafish genes
    Yves Van de Peer
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Gent University, K L Ledeganckstraat 35, B 9000, Gent, Belgium
    Gene 295:205-11. 2002
  2. ncbi The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes
    Y Van de Peer
    Department of Biology, University of Konstanz, 78457 Konstanz, Germany
    J Mol Evol 53:436-46. 2001
  3. ncbi Wanda: a database of duplicated fish genes
    Yves Van de Peer
    Department of Biology, University of Konstanz, D 78457 Konstanz, Germany
    Nucleic Acids Res 30:109-12. 2002
  4. ncbi SpliceMachine: predicting splice sites from high-dimensional local context representations
    Sven Degroeve
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology VIB, Technologiepark 927, Gent 9052, Belgium
    Bioinformatics 21:1332-8. 2005
  5. ncbi Comparative genomics provides evidence for an ancient genome duplication event in fish
    J S Taylor
    Department of Biology, University of Konstanz, 78457, Konstanz, Germany
    Philos Trans R Soc Lond B Biol Sci 356:1661-79. 2001
  6. ncbi Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants
    Stefanie De Bodt
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, K.L Ledeganckstraat 35, Belgium
    J Mol Evol 56:573-86. 2003
  7. ncbi ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles
    Thomas Abeel
    Department of Plant Systems Biology, VIB, 9052 Gent, Belgium
    Bioinformatics 24:i24-31. 2008
  8. ncbi The hidden duplication past of Arabidopsis thaliana
    Cedric Simillion
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
    Proc Natl Acad Sci U S A 99:13627-32. 2002
  9. ncbi Building genomic profiles for uncovering segmental homology in the twilight zone
    Cedric Simillion
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB, Ghent University, B-9052 Ghent, Belgium
    Genome Res 14:1095-106. 2004
  10. ncbi Genome duplication, divergent resolution and speciation
    J S Taylor
    Department of Biology, University of Konstanz, 78457 Konstanz, Germany
    Trends Genet 17:299-301. 2001

Detail Information

Publications87

  1. ncbi Dealing with saturation at the amino acid level: a case study based on anciently duplicated zebrafish genes
    Yves Van de Peer
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Gent University, K L Ledeganckstraat 35, B 9000, Gent, Belgium
    Gene 295:205-11. 2002
    ..When trees are computed by omitting the saturated fraction of sites, most fish duplicates are sister sequences...
  2. ncbi The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes
    Y Van de Peer
    Department of Biology, University of Konstanz, 78457 Konstanz, Germany
    J Mol Evol 53:436-46. 2001
    ....
  3. ncbi Wanda: a database of duplicated fish genes
    Yves Van de Peer
    Department of Biology, University of Konstanz, D 78457 Konstanz, Germany
    Nucleic Acids Res 30:109-12. 2002
    ..Wanda is available at http://www.evolutionsbiologie.uni-konstanz.de/Wanda/...
  4. ncbi SpliceMachine: predicting splice sites from high-dimensional local context representations
    Sven Degroeve
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology VIB, Technologiepark 927, Gent 9052, Belgium
    Bioinformatics 21:1332-8. 2005
    ..Many tools for localizing these boundaries on DNA sequences have been developed and are available to researchers through the internet. Nevertheless, these tools still make many false positive predictions...
  5. ncbi Comparative genomics provides evidence for an ancient genome duplication event in fish
    J S Taylor
    Department of Biology, University of Konstanz, 78457, Konstanz, Germany
    Philos Trans R Soc Lond B Biol Sci 356:1661-79. 2001
    ..Alternatively, the loss of different duplicates in different populations (i.e. 'divergent resolution') may have promoted speciation in ancient teleost populations...
  6. ncbi Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants
    Stefanie De Bodt
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, K.L Ledeganckstraat 35, Belgium
    J Mol Evol 56:573-86. 2003
    ..It is therefore even more intriguing that, from an experimental point of view, almost nothing is known about the function of these MADS-box type I genes...
  7. ncbi ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles
    Thomas Abeel
    Department of Plant Systems Biology, VIB, 9052 Gent, Belgium
    Bioinformatics 24:i24-31. 2008
    ..Nevertheless, better core promoter prediction can improve genome annotation and can be used to guide experimental work...
  8. ncbi The hidden duplication past of Arabidopsis thaliana
    Cedric Simillion
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
    Proc Natl Acad Sci U S A 99:13627-32. 2002
    ..Therefore, adding such hidden blocks to the duplication landscape of Arabidopsis sheds light on the number of polyploidy events that this model plant genome has undergone in its evolutionary past...
  9. ncbi Building genomic profiles for uncovering segmental homology in the twilight zone
    Cedric Simillion
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB, Ghent University, B-9052 Ghent, Belgium
    Genome Res 14:1095-106. 2004
    ..When applying this new method to the combined genomes of Arabidopsis and rice, we find additional evidence for ancient duplication events in the rice genome...
  10. ncbi Genome duplication, divergent resolution and speciation
    J S Taylor
    Department of Biology, University of Konstanz, 78457 Konstanz, Germany
    Trends Genet 17:299-301. 2001
    ..Genome duplication events produce thousands of duplicated genes. Therefore, lineages with a history of genome duplication might have been especially prone to speciation via divergent resolution...
  11. ncbi Modeling gene and genome duplications in eukaryotes
    Steven Maere
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
    Proc Natl Acad Sci U S A 102:5454-9. 2005
    ..Our evolutionary model is widely applicable and can be used to evaluate different assumptions regarding small- or large-scale gene duplication events in eukaryotic genomes...
  12. ncbi Genome duplication, a trait shared by 22000 species of ray-finned fish
    John S Taylor
    Department of Biology, University of Konstanz, D-78457, Konstanz, Germany
    Genome Res 13:382-90. 2003
    ....
  13. ncbi Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting
    Stefanie De Bodt
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Ghent, Belgium
    Mol Biol Evol 23:1293-303. 2006
    ..Furthermore, using phylogenetic footprinting, a distinction can be made between redundancy, neo/nonfunctionalization, and subfunctionalization...
  14. ncbi The flowering world: a tale of duplications
    Yves Van de Peer
    Department of Plant Systems Biology, Flanders Institute for Biotechnology VIB, 9052 Gent, Belgium
    Trends Plant Sci 14:680-8. 2009
    ..This is important if we want to demonstrate the significance of genome duplications for the evolution and radiation of (different groups of) flowering plants...
  15. ncbi The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice
    Klaas Vandepoele
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, B-9000 Gent, Belgium
    Genome Res 12:1792-801. 2002
    ..These regions comprise from 4 up to 11 conserved homologous gene pairs. We predict the number of homologous regions and the extent of microcolinearity to increase significantly once better annotations of the rice genome become available...
  16. ncbi FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA
    Michiel Van Bel
    Department of Plant Systems Biology, VIB, 9052 Gent, Belgium
    Bioinformatics 24:1532-3. 2008
    ..Most of the software currently in use is written for a very specific problem, thereby limiting the possibilities for reuse...
  17. ncbi Pelistega europaea gen. nov., sp. nov., a bacterium associated with respiratory disease in pigeons: taxonomic structure and phylogenetic allocation
    P Vandamme
    Laboratorium voor Microbiologie, Universiteit Gent, Belgium
    Int J Syst Bacteriol 48:431-40. 1998
    ..It is not unlikely that the name P. europaea will be restricted in the future to organisms belonging to fatty acid cluster I, or even to protein electrophoretic sub-group 1, upon discovery of differential diagnostic features...
  18. ncbi Feature selection for splice site prediction: a new method using EDA-based feature ranking
    Yvan Saeys
    Department of Plant Systems Biology, Ghent University, Flanders Interuniversity Institute for Biotechnology VIB, Technologiepark 927, B 9052 Ghent, Belgium
    BMC Bioinformatics 5:64. 2004
    ..Thus, robust methods for fast feature selection are of key importance in extracting knowledge from complex biological data...
  19. ncbi And then there were many: MADS goes genomic
    Stefanie De Bodt
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
    Trends Plant Sci 8:475-83. 2003
    ....
  20. ncbi Fast feature selection using a simple estimation of distribution algorithm: a case study on splice site prediction
    Yvan Saeys
    Department of Plant Systems Biology, Ghent University, Flanders Interuniversity Institute for Biotechnology VIB, Ghent, Belgium
    Bioinformatics 19:ii179-88. 2003
    ....
  21. ncbi Validating module network learning algorithms using simulated data
    Tom Michoel
    Bioinformatics and Evolutionary Genomics, Department of Plant Systems Biology, VIB Ghent University, Ghent, Belgium
    BMC Bioinformatics 8:S5. 2007
    ..Additionally, we assess the effect of various parameters, such as the size of the data set and the amount of noise, on the inference performance...
  22. ncbi Structural diversification and neo-functionalization during floral MADS-box gene evolution by C-terminal frameshift mutations
    Michiel Vandenbussche
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology VIB, Ghent University, K L Ledeganckstraat 35, B 9000 Gent, Belgium
    Nucleic Acids Res 31:4401-9. 2003
    ..3' terminal frameshift mutations might provide an important but so far unrecognized mechanism to generate novel functional C-terminal motifs instrumental to the functional diversification of transcription factor families...
  23. ncbi Investigating ancient duplication events in the Arabidopsis genome
    Jeroen Raes
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
    J Struct Funct Genomics 3:117-29. 2003
    ..However, for now it is impossible to conclude whether these old duplicates are the result of one or more large-scale gene duplication events...
  24. ncbi Feature subset selection for splice site prediction
    Sven Degroeve
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology VIB, Gent, Belgium
    Bioinformatics 18:S75-83. 2002
    ..Using fewer features will of course also improve the prediction speed of the system...
  25. ncbi In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists
    Yvan Saeys
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology VIB, Technologiepark 927, B 9052 Ghent, Belgium
    Bioinformatics 23:414-20. 2007
    ..SUPPLEMENTARY DATA: http://bioinformatics.psb.ugent.be/...
  26. ncbi AFLPinSilico, simulating AFLP fingerprints
    Stephane Rombauts
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology VIB, K L Ledeganckstraat 35, Gent 9000, Belgium
    Bioinformatics 19:776-7. 2003
    ..AFLPinSilico is available through the www or as a stand-alone version, through a command line executable (available upon request, for any platform running PERL)...
  27. ncbi Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event
    Jeffrey A Fawcett
    Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium
    Proc Natl Acad Sci U S A 106:5737-42. 2009
    ....
  28. ncbi Are all fishes ancient polyploids?
    Yves Van de Peer
    Department of Plant Systems Biology, Vlaams Interuniversitair Instituut voor Biotechnologie VIB, Ghent University, K L Ledeganckstraat 35, B 9000 Gent, Belgium
    J Struct Funct Genomics 3:65-73. 2003
    ..We also comment here on the evolutionary consequences of this ancient genome duplication...
  29. ncbi Translation initiation site prediction on a genomic scale: beauty in simplicity
    Yvan Saeys
    Department of Plant Systems Biology, VIB, Technologiepark 927, B 9052 Ghent, Belgium
    Bioinformatics 23:i418-23. 2007
    ....
  30. ncbi An updated and comprehensive rRNA phylogeny of (crown) eukaryotes based on rate-calibrated evolutionary distances
    Y Van de Peer
    Department of Biology, University of Konstanz, D 78457 Konstanz, Germany
    J Mol Evol 51:565-76. 2000
    ....
  31. ncbi Microsporidia: accumulating molecular evidence that a group of amitochondriate and suspectedly primitive eukaryotes are just curious fungi
    Y Van de Peer
    Department of Biology, University of Konstanz, D 78457, Konstanz, Germany
    Gene 246:1-8. 2000
    ..In this respect, the importance of incorporating detailed knowledge of the substitution pattern of sequences into phylogenetic methods is discussed...
  32. ncbi The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction
    Steven Robbens
    Department of Plant Systems Biology, Flanders Institute for Biotechnology VIB, Ghent University, Ghent, Belgium
    Mol Biol Evol 24:956-68. 2007
    ..Phylogenetic analyses based on a concatenated alignment of cp, mt, and nuclear genes confirm the position of O. tauri within the Prasinophyceae, an early branch of the Chlorophyta...
  33. ncbi Exploring the plant transcriptome through phylogenetic profiling
    Klaas Vandepoele
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, B-9052 Ghent, Belgium
    Plant Physiol 137:31-42. 2005
    ..In addition, a majority of large gene families, typically containing more than 50 genes, are bigger in rice than Arabidopsis, whereas the opposite seems true for small gene families...
  34. ncbi Computational approaches to unveiling ancient genome duplications
    Yves Van de Peer
    Department of Plant Systems Biology, Flanders Interuniversity, Institute for Biotechnology, Ghent, Belgium
    Nat Rev Genet 5:752-63. 2004
    ..Several new approaches have been used to show that large-scale gene duplications are more common than previously thought...
  35. ncbi From 2R to 3R: evidence for a fish-specific genome duplication (FSGD)
    Axel Meyer
    Lehrstuhl fur Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Germany
    Bioessays 27:937-45. 2005
    ..Most duplicated genes were secondarily lost, yet some evolved new functions. The genomic complexity of the teleosts might be the reason for their evolutionary success and astounding biological diversity...
  36. ncbi Reverse-engineering transcriptional modules from gene expression data
    Tom Michoel
    Department of Plant Systems Biology, VIB, Gent, Belgium
    Ann N Y Acad Sci 1158:36-43. 2009
    ..We show that the inferred probabilistic models extend beyond the dataset used to learn the models...
  37. ncbi PLAZA: a comparative genomics resource to study gene and genome evolution in plants
    Sebastian Proost
    Department of Plant Systems Biology, Flanders Institute for Biotechnology, B 9052 Ghent, Belgium
    Plant Cell 21:3718-31. 2009
    ..In conclusion, PLAZA provides a comprehensible and up-to-date research environment to aid researchers in the exploration of genome information within the green plant lineage...
  38. ncbi Evidence that rice and other cereals are ancient aneuploids
    Klaas Vandepoele
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
    Plant Cell 15:2192-202. 2003
    ..This date predates the divergence of most of the cereals, and relative dating by phylogenetic analysis shows that this duplication event is shared by most if not all of them...
  39. ncbi Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species
    Cindy Martens
    Department of Plant Systems Biology, VIB, and Department of Molecular Genetics, Ghent University, Technologiepark 927, B 9052 Ghent, Belgium
    Proc Natl Acad Sci U S A 105:3427-32. 2008
    ..In general, chromalveolates show a tremendous difference in genome structure and evolution and in the number of genes they have lost or gained either through duplication or horizontal gene transfer...
  40. ncbi Gene duplication, the evolution of novel gene functions, and detecting functional divergence of duplicates in silico
    Jeroen Raes
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB, Ghent University, Ghent, Belgium
    Appl Bioinformatics 2:91-101. 2003
    ..In this review, we discuss the strengths and limitations of both older and novel approaches to investigate the evolution of duplicated genes in silico...
  41. ncbi Evolutionary genetics: when duplicated genes don't stick to the rules
    Y Van de Peer
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
    Heredity 96:204-5. 2006
  42. ncbi Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana
    Tineke Casneuf
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology VIB, Ghent University, Technologiepark 927, B 9052 Ghent, Belgium
    Genome Biol 7:R13. 2006
    ....
  43. ncbi Posttranslational regulation impacts the fate of duplicated genes
    Grigoris D Amoutzias
    Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium
    Proc Natl Acad Sci U S A 107:2967-71. 2010
    ..This way, small changes in the sequences of unstructured regions in proteins can contribute to the rapid rewiring and adaptation of regulatory networks...
  44. ncbi The gain and loss of genes during 600 million years of vertebrate evolution
    Tine Blomme
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB, Ghent University, Technologiepark, B-9052 Ghent, Belgium
    Genome Biol 7:R43. 2006
    ....
  45. ncbi Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics
    Klaas Vandepoele
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB, Ghent University, Technologiepark, B-9052 Ghent, Belgium
    Genome Biol 7:R103. 2006
    ..CONCLUSION: These results create a starting point to unravel regulatory networks in plants and to study the regulation of biological processes from a systems biology point of view...
  46. ncbi In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation
    Tineke Casneuf
    Department of Plant Systems Biology, VIB, B 9052 Ghent, Belgium
    BMC Bioinformatics 8:461. 2007
    ..An approach that is able to distinguish these factors permits the detection of more biologically relevant co-expression signatures...
  47. ncbi Module networks revisited: computational assessment and prioritization of model predictions
    Anagha Joshi
    Department of Plant Systems Biology, VIB, Ghent University, Technologiepark 927, B 9052 Gent, Belgium
    Bioinformatics 25:490-6. 2009
    ..As time progresses, computational power increases but well-established inference methods often remain locked in their initial suboptimal solution...
  48. ncbi Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences
    Guy Baele
    Department of Plant Systems Biology, VIB, B 9052 Ghent, Belgium
    BMC Evol Biol 10:244. 2010
    ....
  49. ncbi Genome-wide identification of potential plant E2F target genes
    Klaas Vandepoele
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Belgium
    Plant Physiol 139:316-28. 2005
    ..These genes encode proteins involved in cell cycle regulation, DNA replication, and chromatin dynamics. In addition, we identified several genes for potentially novel S phase regulatory proteins...
  50. ncbi 'Horizontal' plant biology on the rise
    Yves Van de Peer
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology VIB, Ghent University, Technologiepark 927, B 9052 Ghent, Belgium
    Genome Biol 6:302. 2005
    ..A report on the Plant Genomics European Meeting (Plant-GEMS2004), Lyon, France, 22-25 September 2004...
  51. ncbi Genome-wide characterization of the lignification toolbox in Arabidopsis
    Jeroen Raes
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
    Plant Physiol 133:1051-71. 2003
    ..Together, these data describe the full complement of monolignol biosynthesis genes in Arabidopsis, provide a unified nomenclature, and serve as a basis for further functional studies...
  52. ncbi Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates
    Klaas Vandepoele
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
    Proc Natl Acad Sci U S A 101:1638-43. 2004
    ....
  53. ncbi Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences
    Eric Bonnet
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
    Bioinformatics 20:2911-7. 2004
    ..A possible usage of this statistical test in the framework of the detection of genuine miRNA sequences is discussed...
  54. ncbi EST data suggest that poplar is an ancient polyploid
    Lieven Sterck
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
    New Phytol 167:165-70. 2005
    ....
  55. ncbi Functional divergence of proteins through frameshift mutations
    Jeroen Raes
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
    Trends Genet 21:428-31. 2005
    ....
  56. ncbi Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes
    Eric Bonnet
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
    Proc Natl Acad Sci U S A 101:11511-6. 2004
    ..These findings considerably broaden the scope of miRNA functions in plants...
  57. ncbi 'Natural selection merely modified while redundancy created'--Susumu Ohno's idea of the evolutionary importance of gene and genome duplications
    Axel Meyer
    Department of Biology, University of Konstanz, 78457 Konstanz, Germany
    J Struct Funct Genomics 3:vii-ix. 2003
    ....
  58. ncbi Generic eukaryotic core promoter prediction using structural features of DNA
    Thomas Abeel
    Department of Plant Systems Biology, Flanders Institute for Biotechnology VIB, 9052 Gent, Belgium
    Genome Res 18:310-23. 2008
    ..We also validated our method on 12 additional eukaryotic genomes, including vertebrates, invertebrates, plants, fungi, and protists...
  59. ncbi The European ribosomal RNA database
    Jan Wuyts
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
    Nucleic Acids Res 32:D101-3. 2004
    ..As of 2003, the European ribosomal RNA database is maintained at Ghent University (Belgium). The database can be consulted at http://www.psb.ugent.be/rRNA/...
  60. ncbi Together we stand: genes cluster to coordinate regulation
    Grigoris Amoutzias
    Department of Plant Systems Biology, VIB, Technologiepark 927, B 9052 Ghent, Belgium
    Dev Cell 14:640-2. 2008
    ..Now, a metabolic operon-like gene cluster has been described in Arabidopsis thaliana, that is needed for triterpene synthesis...
  61. ncbi Microarray analysis of E2Fa-DPa-overexpressing plants uncovers a cross-talking genetic network between DNA replication and nitrogen assimilation
    Kobe Vlieghe
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, B-9052 Gent, Belgium
    J Cell Sci 116:4249-59. 2003
    ....
  62. ncbi Large-scale structural analysis of the core promoter in mammalian and plant genomes
    Kobe Florquin
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB, Ghent University Technologiepark 927, B-9052 Ghent, Belgium
    Nucleic Acids Res 33:4255-64. 2005
    ..Using the structural profiles as discriminatory elements to separate promoter regions from non-promoter regions, reliable models can be built to identify core-promoter regions using a strictly computational approach...
  63. ncbi Toward a gold standard for promoter prediction evaluation
    Thomas Abeel
    Department of Plant Systems Biology, VIB, Ghent University, Gent, Belgium
    Bioinformatics 25:i313-20. 2009
    ..In most cases, only a small portion of the genome is used to evaluate the program, which is not a realistic setting for whole genome annotation projects. In addition, a common evaluation design to properly compare PPPs is still lacking...
  64. ncbi The evolutionary significance of ancient genome duplications
    Yves Van de Peer
    Department of Plant Systems Biology, VIB Flanders Institute of Biotechnology, Ghent, Belgium
    Nat Rev Genet 10:725-32. 2009
    ....
  65. ncbi Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development
    Vanessa Vermeirssen
    Department of Plant Systems Biology, VIB, B 9052 Ghent, Belgium
    Mol Biosyst 5:1817-30. 2009
    ..In conclusion, through reverse-engineering of C. elegans expression data, we obtained transcription regulatory networks that can provide further insight into metazoan development...
  66. ncbi TAPIR, a web server for the prediction of plant microRNA targets, including target mimics
    Eric Bonnet
    Department of Plant Systems Biology, VIB, B 9052 Gent, Belgium
    Bioinformatics 26:1566-8. 2010
    ..AVAILABILITY: The TAPIR web server can be accessed at: http://bioinformatics.psb.ugent.be/webtools/tapir. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online...
  67. ncbi The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection
    Cindy Martens
    Department of Plant Systems Biology, VIB, Ghent, Belgium
    BMC Genomics 11:353. 2010
    ..Previous analyses of Phytophthora genomes uncovered many genes, large gene families and large genome sizes that can partially be explained by significant repeat expansion patterns...
  68. ncbi Discriminative and informative features for biomolecular text mining with ensemble feature selection
    Sofie Van Landeghem
    Department of Plant Systems Biology, VIB, Ghent University, Gent, Belgium
    Bioinformatics 26:i554-60. 2010
    ..This allows us to build more accurate classifiers while at the same time bridging the gap between the black box behavior and the end-user who has to interpret the results...
  69. ncbi Recent developments in computational approaches for uncovering genomic homology
    Cedric Simillion
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Belgium
    Bioessays 26:1225-35. 2004
    ..Recently, more advanced approaches have been developed that can combine gene order and content information of multiple genomic segments...
  70. ncbi Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features
    Evelyne Derelle
    , Laboratoire Arago, , , BP44, 66651 Banyuls sur Mer Cedex, France
    Proc Natl Acad Sci U S A 103:11647-52. 2006
    ..Taken together, the complete genome sequence, unusual features, and downsized gene families, make O. tauri an ideal model system for research on eukaryotic genome evolution, including chromosome specialization and green lineage ancestry...
  71. ncbi Detecting the undetectable: uncovering duplicated segments in Arabidopsis by comparison with rice
    Klaas Vandepoele
    Dept of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB, Ghent University, K.L. Ledeganckstraat 35, B-9000, Ghent, Belgium
    Trends Genet 18:606-8. 2002
    ..Here, we show that by comparison with an appropriate second genome, such paralogous regions can still be identified...
  72. ncbi Evolutionary relationships among heterokont algae (the autotrophic stramenopiles) based on combined analyses of small and large subunit ribosomal RNA
    Abdelghani Ben Ali
    Department of Biochemistry, University of Antwerp, Wilrijk, Belgium
    Protist 153:123-32. 2002
    ..However, apart from these sister group relationships, very few other internodes are well resolved and most groups of heterokont algae seem to have diverged within a relatively short time frame...
  73. ncbi The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants
    Stefan A Rensing
    Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, D 79104 Freiburg, Germany
    Science 319:64-9. 2008
    ..The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics...
  74. ncbi PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences
    Magali Lescot
    Vakgroep Moleculaire Genetica, Departement Plantengenetica, Vlaams Interuniversitair Instituut voor Biotechnologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
    Nucleic Acids Res 30:325-7. 2002
    ..New regulatory elements can be sent automatically and will be added to the database after curation. The PlantCARE relational database is available via the World Wide Web at http://sphinx.rug.ac.be:8080/PlantCARE/...
  75. ncbi An improved statistical method for detecting heterotachy in nucleotide sequences
    Guy Baele
    Department of Applied Mathematics and Computer Science, Ghent University, Ghent, Belgium
    Mol Biol Evol 23:1397-405. 2006
    ..Using extensive testing, we show that this may not be due to heterotachy itself but merely due to the increased substitution rate at the detected heterotachous sites...
  76. ncbi A novel approach to identifying regulatory motifs in distantly related genomes
    Ruth Van Hellemont
    ESAT SCD, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven Heverlee, Belgium
    Genome Biol 6:R113. 2005
    ..The results on well-studied benchmark datasets indicate that the presented method outperforms other methods when the sequences become either too long or too heterogeneous in size...
  77. ncbi The European database on small subunit ribosomal RNA
    Jan Wuyts
    Departement Biochemie, Universiteit Antwerpen (UIA, Universiteitsplein 1, B-2610 Antwerpen, Belgium
    Nucleic Acids Res 30:183-5. 2002
    ..Additional information such as literature references, taxonomy, secondary structure models and nucleotide variability maps, is also available...
  78. ncbi Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes
    Steven B Cannon
    Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
    Proc Natl Acad Sci U S A 103:14959-64. 2006
    ..Phylogenetic comparisons place this duplication within the Rosid I clade, clearly after the split between legumes and Salicaceae (poplar)...
  79. ncbi Ancient duplication of cereal genomes
    Andrew H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    New Phytol 165:658-61. 2005
  80. ncbi Moss transcriptome and beyond
    Stefan A Rensing
    Plant Biotechnology, Freiburg University, Germany
    Trends Plant Sci 7:535-8. 2002
    ..However, for careful comparison with other plant model systems, the complete genomic sequence is needed as well as the transcriptome...
  81. ncbi Tetraodon genome confirms Takifugu findings: most fish are ancient polyploids
    Yves Van de Peer
    Bioinformatics and Evolutionary Genomics, Vlaams Interuniversitair Instituut voor Biotechnologie, Ghent University, Technologiepark 927, B 9052 Ghent, Belgium
    Genome Biol 5:250. 2004
    ..Ray-finned fish underwent a whole-genome duplication some 350 million years ago that might explain their evolutionary success...
  82. ncbi Genome-wide analysis of core cell cycle genes in the unicellular green alga Ostreococcus tauri
    Steven Robbens
    , Laboratoire Arago, , Banyuls sur Mer, France
    Mol Biol Evol 22:589-97. 2005
    ..We discuss the potential of genome-wide analysis in the identification of divergent orthologs of cell cycle genes in different lineages by mining the genomes of evolutionarily important and strategic organisms...
  83. ncbi An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens
    Stefan A Rensing
    Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
    BMC Evol Biol 7:130. 2007
    ..Analyses of complete genomes and large collections of gene transcripts have shown that most, if not all seed plants have undergone one or more genome duplications in their evolutionary past...
  84. ncbi i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles
    Cedric Simillion
    Institute for Cell and Molecular Biosciences ICaMB, Newcastle University, Newcastle upon Tyne, UK
    Bioinformatics 24:127-8. 2008
    ..The software runs on any Linux- or -UNIX based platform. The package is freely available for academic users and can be downloaded from http://bioinformatics.psb.ugent.be/..
  85. ncbi MANTIS: a phylogenetic framework for multi-species genome comparisons
    Athanasia C Tzika
    Laboratory of Evolutionary Genetics, Institute for Molecular Biology and Medicine, Universite Libre de Bruxelles, Belgium
    Bioinformatics 24:151-7. 2008
    ..Furthermore, the field would greatly benefit from a better integration of this wealth of data with evolutionary concepts...
  86. ncbi A high quality draft consensus sequence of the genome of a heterozygous grapevine variety
    Riccardo Velasco
    IASMA Research Center, San Michele all Adige, Trento, Italy
    PLoS ONE 2:e1326. 2007
    ..In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented...
  87. ncbi Novel insights into evolution of protistan polyketide synthases through phylogenomic analysis
    Uwe John
    Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
    Protist 159:21-30. 2008
    ..In any case, we show that environmental genome sequencing projects are likely to be a valuable resource when mining for genes resembling protistan PKS I genes...