Klaas Vandepoele
CVBirthdate: 21 May 1978, Oostende, Belgium. April 2005 - now: Postdoc: Evolutionary analysis of transcriptional regulation in plants and other eukaryotic organisms, Bioinformatics & Evolutionary Genomics, Ghent University/VIB, Belgium (F.W.O.- Vlaanderen). October 2000 - March 2005: Ph.D. studies Mode and tempo of gene and genome evolution in plants, Promoter Prof. Dr. Yves Van de Peer, Bioinformatics & Evolutionary Genomics, Ghent University/VIB, Belgium (IWT-Vlaanderen). October 1998 - September 2000: Licentiate Biotechnology (M. Sc.), Ghent University, Belgium October 1996 - September 1998: Candidate Chemistry (B. Sc.), Ghent University, Belgium Service as reviewer: Bioinformatics, BMC Bioinformatics/Evolutionary Biology/Genomics/Plant Biology, 'Development, Genes and Evolution', Journal of Experimental botany, Journal of Molecular Evolution, Molecular Genetics and Genomics, Plant Cell, Plant Physiology, Tree Genetics and Genomes. Lecturer course "Comparative Genome Analysis" (Master I Biochemistry and Biotechnology, Ghent University) ResearchPlant evolutionary genomicsPlants come in a wide range of forms and colors and their genomes exhibit a large degree of variation, even between different species from the same gene family. Apart from the diversity present in the construction and organization of DNA sequences in different species, molecular and evolutionary processes are continuously shaping nuclear genome structures. Although it has become clear that major genome size differences can be explained by differences in ploidy levels and dissimilar amounts of mobile and tandem repetitive elements, the mechanisms driving gene and genome evolution in higher plants, together with their implications on gene function and regulation, are largely unknown. Despite the fact that it is easy to understand that changes in the place or time of gene expression can create new or alternative molecular interactions, little information about the evolution of transcriptional regulation in plants is known. This knowledge however, is essential, because each gene is flanked by regulatory sequences which, together with the expression and activity of other proteins, determine the amount, place, and timing of expression. Therefore, characterizing these motifs is required in order to understand the regulatory interactions between trans-acting proteins and the promoters of thousands of genes within a eukaryotic genome. This information is also essential when studying biological processes from a holistic point of view by incorporating and combining complementary functional data sets (systems biology). Papers(54) De Smet, R., Adams, K., Vandepoele, K., Van Montagu, M., Maere, S., Van de Peer, Y. (2013) Convergent gene loss following gene and genome duplications createssingle-copy families in flowering plants. PNAS 110, 2898-2903.(53) Verelst, W., Bertolini, E., De Bodt, S., Vandepoele, K., Demeulenaere, M., Enrico Pe, M., Inzé, D. (2012) Molecular and physiological analysis of growth-limiting drought stress in Brachypodium distachyon leaves. Molecular Plant (In Press). (52) Moreau, H., Verhelst, B., Couloux, A., Derelle, E., Rombauts, S., Grimsley, N., Van Bel, M., Poulain, J., Katinka, M., Hohmann-Marriott, M., Piganeau, G., Rouzé, P., Da Silva, C., Wincker, P., Van de Peer, Y., Vandepoele, K. (2012) Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage . Genome Biology 13, R74. (51) Vaulot, D., Lepere, C., Toulza, E., De la Iglesia, R., Poulain, J., Gaboyer, F., Moreau, H., Vandepoele, K., Ulloa, O., Gavory, F., Piganeau, G. (2012) Metagenomes of the Picoalga Bathycoccus from the Chile Coastal Upwelling . PLOS One 7, e39648. (50) Heyndrickx, KS., Vandepoele, K. (2012) Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol. 159, 884-901. (49) Movahedi, S., Van Bel, M., Heyndrickx, KS., Vandepoele, K. (2012) Comparative co-expression analysis in plant biology. Plant, Cell & Environment 35, 1787-98. (48) Wang, X., Vandepoele, K., Van Lijsebettens, M. (2012) Tetraspanin genes in plants. Plant Sci. 190, 9-15. (47) Dessimoz, C., Gabaldon, T., Roos, D. S., Sonnhammer, E., Herrero, J., Altenhoff, A., Apweiler, R., Blake, J., Boeckmann, B., Bridge, A., Bruford, E., Cherry, M., Conte, M., Dannie, D., Datta, R., Entfellner, J., Ebersberger, I., Galperin, M., Joseph, J., Koestler, T., Kriventseva, E., Lecompte, O., Leunissen, J., Lewis, S., Linard, B., Livstone, M., Lu, H., Martin, F., Mazumder, R., Miele, V., Muffato, M., Perriere, G., Punta, M., Rouard, M., Schmitt, T., Schreiber, F., Silva, E.P., Sjolander, K., Skunca, N., Stanley, M., Szklarczyk, R., Thomas, E., Uchiyama, I., Van Bel, M., Vandepoele, K., Vilella, A., Yates, J.R., Zdobnov, E. (2012) Toward Community Standards in the Quest for Orthologs. Bioinformatics 28, 900-4. (46) Petrov, V., Vermeirssen, V., De Clercq, R., Van Breusegem, F., Minkov, I., * Vandepoele, K., * Gechev, T. (2012) Identification of cis-regulatory elements specific for different types of reactive oxygen species in Arabidopsis thaliana. Gene 499, 52-60. *contributed equally (45) * Van Bel, M., * Proost, S., Wischnitzki, E., Movahedi, S., Scheerlinck, C., Van de Peer, Y., Vandepoele, K. (2012) Dissecting plant genomes with the PLAZA comparative genomics platform. Plant Physiol. 158,590-600. *contributed equally (44) * Proost, S., * Fostier, J., De Witte, D., Dhoedt, B., Demeester, P., Van de Peer, Y., Vandepoele, K. (2012) i-ADHoRe 3.0 - Fast and Sensitive Detection of Genomic Homology in Extremely Large Data Sets. Nucleic Acids Res. 40,e11. *contributed equally (43) Quimbaya, M., Vandepoele, K., Raspe, E., Matthijs, M., Dhondt, S., Beemster, G.T.S., Berx, G., De Veylder, L. (2012) Identification of putative cancer genes through data integration and comparative genomics between plants and humans. Cell Mol Life Sci. (42) Mittler, R., Vanderauwera, S., Suzuki, Y., Miller, G., Tognetti, VB., Vandepoele, K., Gollery, M., Shulaev, V., Van Breusegem, F. (2011) ROS signaling: the new wave?. Trends Plant Sci. 16,300-9. (41) Movahedi, S., Van de Peer, Y., Vandepoele, K. (2011) Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice. Plant Physiology 156,1316-1330. (40) Babiychuk, E., Vandepoele, K., Wissing, J., Garcia-Diaz, M., De Rycke, R., Akbari, H., Joubes, J., Beeckman, T., Jansch, L., Frentzen, M., Van Montagu, M., Kushnir, S. (2011) Plastid gene expression and plant development require a plastidic protein of the mitochondrial transcription termination factor family. Proc. Natl. Acad. Sci. USA 108,6674-9. (39) * Fostier, J., * Proost, S., Dhoedt, B., Saeys, Y., Demeester, P., Van de Peer, Y., Vandepoele, K. (2011) A Greedy, Graph-Based Algorithm for the Alignment of Multiple Homologous Gene Lists. Bioinformatics 27, 749-56. *contributed equally (38) Huysman, M., Martens, C., Vandepoele, K., Gillard, J., Rayko, E., Heijde, M., Bowler, C., Inzé, D., Van de Peer, Y., De Veylder, L., Vyverman, W. (2010) Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signalling. Genome Biol. 11, R17. (37) Takahashi, N., Quimbaya, M., Schubert, V., Lammens, T., Vandepoele, K., Schubert, I., Matsui, M., Inzé, D., Berx, G., De Veylder, L. (2010) The MCM-binding protein ETG1 aids sister chromatid cohesion required for postreplicative homologous recombination repair. PLoS Genet. 6, e1000817. (36) * Proost, S., * Van Bel, M., Sterck, L., Billiau, K., Van Parys, T., Van de Peer, Y., Vandepoele, K. (2009) PLAZA: a comparative genomics resource to study gene and genome evolution in plants. The Plant Cell 21, 3718-3731. *contributed equally (35) Van de Peer, Y., Fawcett, J., Proost, S., Sterck, L., Vandepoele, K. (2009) The flowering world: a tale of duplications. Trends Plant Science 14, 680-688 . (34) * Piganeau, G., * Vandepoele, K., Gourbiere, S., Van de Peer, Y., Moreau, H. (2009) Unravelling cis-Regulatory Elements in the Genome of the Smallest Photosynthetic Eukaryote: Phylogenetic Footprinting in Ostreococcus. J. Mol. Evol. 69, 249-59. *contributed equally (33) De Bodt, S., Proost, S., Vandepoele, K., Rouzé, P., Van de Peer, Y. (2009) Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. BMC Genomics 10, 288. (32) Dhaese, S., Vandepoele, K., Waterschoot, D., Vanloo, B., Vandekerckhove, J., Ampe, C., Van Troys, M. (2009) The mouse thymosin beta15 gene family displays unique complexity and encodes a functional thymosin repeat. J. Mol. Biol. 387, 809-25. (31) Vandepoele, K., Quimbaya, M., Casneuf, T., De Veylder, L., Van de Peer, Y. (2009) Unravelling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks. Plant Physiol. 150, 535-46. (30) Bowler, C., * Allen, A., * Badger, J., * Grimwood, J., * Jabbari, K., * Kuo, Y.-C., * Maheswari, U., * Martens, C., * Maumus, F., * Otillar, R., * Rayko, E., * Salamov, A., * Vandepoele, K., Beszteri, B., Gruber, A., Heijde, M., Katinka, M., Mock, T., Valentin, K., Vérret, F., Berges, J., Brownlee, C., Cadoret, J., Chiovitti, A., Jae Choi, C., Coesel, S., Martino, A., Detter, J., Durkin, C., Falciatore, A., Fournet, J., Haruta, M., Huysman, M., Jenkins, B., Jiroutova, K., Jorgensen, R., Joubert, Y., Kaplan, A., Kroeger, N., Kroth, P., Roche, J., Lindquist, E., Lommer, M., Martin-Jézéquel, V., Lopez, P., Lucas, S., Mangogna, M., McGinnis, K., Medlin, L., Montsant, A., Oudot-Secq, M., Napoli, C., Obornik, M., Petit, J., Porcel, B., Poulsen, N., Robison, M., Rychlewski, L., Rynearson, T., Schmutz, J., Schnitzler Parker, M., Shapiro, H.J., Siaut, M., Stanley, M., J.Sussman, M., Taylor, J.S., Vardi, A., von Dassow, P., Vyverman, W., Willis, A., Wyrwicz, L., Rokhsar, D., Weissenbach, J., Armbrust, V., Green, P.J., Van de Peer, Y., Grigoriev, I. (2008) The Phaeodactylum genome reveals the dynamic nature and multi-lineage evolutionary history of diatom genomes. Nature 456, 239-44. *contributed equally (29) Naouar, N., Vandepoele, K., Lammens, T., Casneuf, T., Zeller, G., van, Hummelen, Weigel, D., Rätsch, G., Inzé, D., Kuiper, M., De Veylder, L., Vuylsteke, M. (2008) Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. Plant J. 57(1), 184-194. (28) Alvim, CL., Boruc, J., Vandepoele, K., Van Den Daele, H., Maes, W., Russinova, E., Inzé, D., De Veylder, L. (2008) The PRA1 gene family in Arabidopsis. Plant Physiol. 147, 1735-49. (27) Martens, C., Vandepoele, K., Van de Peer, Y. (2008) Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species. Proc. Natl. Acad. Sci. USA 105, 3427-32. (26) Vandenbroucke, K., Robbens, S., Vandepoele, K., Inzé, D., Van de Peer, Y., Van Breusegem, F. (2008) Hydrogen Peroxide-Induced Gene Expression across Kingdoms: A Comparative Analysis. Mol. Biol. Evol. 25, 507-16. (25) Velasco, R., Zharkikh, A., Troggio, M., Cartwright, D.A., Cestaro, A., Pruss, D., Pindo, M., FitzGerald, L.M., Vezzulli, S., Reid, J., Malacarne, G., Iliev, D., Coppola, G., Wardell, B., Micheletti, D., Macalma, T., Facci, M., Mitchell, J.T., Perazzolli, M., Eldredge, G., Gatto, P., Oyzerski, R., Moretto, M., Gutin, N., Stefanini, M., Chen, Y., Segala, C., Davenport, C., Demattè, L., Mraz, A., Battilana, J., Stormo, K., Costa, F., Tao, Q., Si-Ammour, A., Harkins, T., Lackey, A., Perbost, C., Taillon, B., Stella, A., Solovyev, V., Fawcett, J., Sterck, L., Vandepoele, K., Grando, M.S., Toppo, S., Moser, C., Lanchbury, J., Bogden, R., Skolnick, M., Sgaramella, V., Bhatnagar, S.K., Fontana, P., Gutin, A., Van de Peer, Y., Salamini, F., Viola, R. (2007) A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety. PLOS One 2, e1326. (24) Peresetsky, A., Churchman, M.L., Hariharan, S., Himanen, K., Verkest, A., Vandepoele, K., Magyar, Z., Hatzfeld, Y., Van Der Schueren, E., Beemster, G.T.S., Frankard, V., Larkin, J.C., Inzé, D., De Veylder, L. (2007) Novel plant-specific cyclin-dependent kinase inhibitors induced by biotic and abiotic stresses. J. Biol. Chem. (23) Polet, D., Lambrechts, A., Vandepoele, K., Vandekerckhove, J., Ampe, C. (2007) On the origin and evolution of vertebrate and viral profilins. . FEBS Lett. 581, 211-7. (22) Sterck, L., Rombauts, S., Vandepoele, K., Rouzé, P., Van de Peer, Y. (2007) How many genes are there in plants (... and why are they there)?. Curr Opin Plant Biol 10, 199-203. (21) Rymen, B., Fiorani, F., Kartal, F., Vandepoele, K., Inzé, D., Beemster, G.T.S. (2007) Cold Nights Impair Leaf Growth and Cell Cycle Progression in Maize Through Transcriptional Changes of Cell Cycle Genes. Plant Physiol. 143, 1429-38. (20) Vandepoele, K., Casneuf, T., Van de Peer, Y. (2006) Identification of novel regulatory modules in dicot plants using expression data and comparative genomics. Genome Biol. 7,R103. (19) Blomme, T., Vandepoele, K., De Bodt, S., Simillion, C., Maere, S., Van de Peer, Y. (2006) The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol. 7, R43. (18) Vandepoele, K., Van de Peer, Y. (2005) Exploring the plant transcriptome through phylogenetic profiling. Plant Physiol. 137, 31-42. (17) Paterson, A.H., Bowers, J. E., Van de Peer, Y., Vandepoele, K. (2005) Ancient duplication of cereal genomes. . New Phytol. 165, 658-61. (16) Vandepoele, K., Vlieghe, K., Florquin, K., Hennig, L., Beemster, G.T.S., Gruissem, W., Van de Peer, Y., Inzé, D., De Veylder, L. (2005) Genome-wide identification of potential plant E2F target genes. Plant Physiol. 139, 316-28. (15) Vercammen, D., Van de Cotte, B., De Jaeger, G., Eeckhout, D., Casteels, P., Vandepoele, K., Vandenberghe, A., Van Beeumen, J., Inzé, D., Van Breusegem, F. (2004) Type II metacaspases Atmc4 and Atmc9 of Arabidopsis thaliana cleave substrates after arginine and lysine. J. Biol. Chem. 279, 45329-36. (14) Landrieu, I., da Costa, M., De Veylder, L., Dewitte, F., Vandepoele, K., Hassan, S., Wieruszeski, J.-M., Faure, J.-D., Van Montagu, M., Inzé, D., Lippens, G. (2004) A small CDC25 dual-specificity tyrosine phosphatase isoform in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 101, 13380-5. (13) Vandepoele, K., De Vos, W., Taylor, J.S., Meyer, A., Van de Peer, Y. (2004) Major events in the genome evolution of vertebrates: paranome age and size differs considerably between fishes and land vertebrates. Proc. Natl. Acad. Sci. USA 101, 1638-43. (12) Gevers, D., Vandepoele, K., Simillion, C., Van de Peer, Y. (2004) Gene duplication and biased functional retention of paralogs in bacterial genomes. Trends Microbiol. 12, 148-54. (11) Simillion, C., Vandepoele, K., Saeys, Y., Van de Peer, Y. (2004) Building genomic profiles for uncovering segmental homology in the twilight zone. Genome Res. 14, 1095-106. (10) Vandepoele, K., Simillion, C., Van de Peer, Y. (2004) The quest for genomic homology. Curr. Genomics 5, 299-308. (9) Simillion, C., Vandepoele, K., Van de Peer, Y. (2004) Recent developments in computational approaches for uncovering genomic homology. BioEssays 26, 1225-35. (8) Vandepoele, K., Simillion, C., Van de Peer, Y. (2003) Evidence that rice, and other cereals, are ancient aneuploids. Plant Cell 15, 2192-202. (7) Raes, J., Vandepoele, K., Saeys, Y., Simillion, C., Van de Peer, Y. (2003) Investigating ancient duplication events in the Arabidopsis genome. J. Struct. Func. Genomics. 3, 117-29. (6) Breyne, P., Dreesen, R., Cannoot, B., Rombaut, D., Vandepoele, K., Rombauts, S., Vanderhaeghen, R., Inzé, D., Zabeau, M. (2003) Quantitative cDNA-AFLP analysis for genome-wide expression studies. Mol. Genet. Genom. 269, 173-9. (5) Breyne, P., Dreesen, R., Vandepoele, K., De Veylder, L., Van Breusegem, F., Callewaert, L., Rombauts, S., Raes, J., Cannoot, B., Engler, G., Inzé, D., Zabeau, M. (2002) Analysis of the transcriptome during cell division in plants. Proc. Natl. Acad. Sci. USA 99, 14825-30. (4) Simillion, C., Vandepoele, K., Van Montagu, M., Zabeau, M., Van de Peer, Y. (2002) The hidden duplication past of Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 99, 13627-32. (3) Vandepoele, K., Simillion, C., Van de Peer, Y. (2002) Detecting the undetectable: Uncovering duplicated segments in Arabidopsis through rice. Trends Genet. 18, 606-8. (2) Vandepoele, K., Saeys, Y., Simillion, C., Raes, J., Van de Peer, Y. (2002) The Automatic Detection of Homologous Regions (ADHoRe) and its application to microcolinearity between Arabidopsis and Rice. Genome Res. 12, 1792-801. (1) Vandepoele, K., Raes, J., De Veylder, L., Rouzé, P., Rombauts, S., Inzé, D. (2002) Genome-wide analysis of core cell cycle genes in Arabidopsis. Plant Cell 14, 903-16. |
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