Klaas Vandepoele
Research
More info on the web page of the
Comparative & Integrative Genomics
lab.
Papers(89) Kreft, L., Botzki, A., Coppens, F., Vandepoele, K., Van Bel, M. (2017) PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization. Bioinformatics (In Press).(88) Ritter, A., Iñigo, S., Fernández-Calvo, P., Heyndrickx, KS., Dhondt, S., Shi, J., De Milde, L., Vanden Bossche, R., De Clercq, R., Eeckhout, D., Ron, Shamir., Somers, DE., Inzé, D., Gevaert, O., De Jaeger, G., Vandepoele, K., Pauwels, L., Goossens, A. (2017) The transcriptional repressor complex FRS7-FRS12 regulates flowering time and growth in Arabidopsis. Nat Commun. 8:15235. (87) Ruprecht, C., Proost, S., Hernandez-Coronado, M., Ortiz-Ramirez, C., Lang, D., Rensing, S.A., Becker, C., Vandepoele, K., Mutwil, M. (2017) Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules. Plant J. 90(3):447-465. (86) Babiychuk, E., Hoang, KT., Vandepoele, K., Van De Slijke, E., Geelen, D., De Jaeger, G., Obokata, J., Kushnir, S. (2017) The mutation nrpb1-A325V in the largest subunit of RNA polymerase II suppresses compromised growth of Arabidopsis plants deficient in a function of the general transcription factor IIF. Plant J. 89(4):730-745. (85) Zhang, X., Ivanova, A., Vandepoele, K., Radomiljac, J., Van de Velde, J., Berkowitz, O., Willems, A., Xu, SX., Ng, S., Van Aken, O., Duncan, O., Zhang, B., Storme, V., Chan, KX., Vaneechoutte, D., Pogson, BJ., Van Breusegem, F., Whelan, J., De Clercq, I. (2017) The Transcription Factor MYB29 Is a Regulator of ALTERNATIVE OXIDASE1a. Plant Physiol. 173(3):1824-1843. (84) Vandepoele, K. (2017) A Guide to the PLAZA 3.0 Plant Comparative Genomic Database. Methods Mol Biol. 1533:183-200. (83) Van Leene, J., Blomme, J., Kulkarni, SR., Cannoot, B., De Winne, N., Eeckhout, D., Persiau, G., Van De Slijke, E., Vercruysse, L., Vanden Bossche, R., Heyndrickx, KS., Vanneste, S., Goossens, A., Gevaert, O., Vandepoele, K., Gonzalez, A., Inzé, D., De Jaeger, G. (2016) Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development. J Exp Bot. pii: erw347. [Epub ahead of print]. (82) Veeckman, E., Ruttink, T., Vandepoele, K. (2016) Are We There Yet? Reliably Estimating the Completeness of Plant Genome Sequences. The Plant Cell 28(8):1759-68. (81) Veeckman, E., Vandepoele, K., Asp, T., Roldán-Ruiz, I., Ruttink, T. (2016) Genomic Variation in the FT Gene Family of Perennial Ryegrass (Lolium perenne). Breeding in a World of Scarcity pp 121-126. (80) Van de Velde, J., Van Bel, M., Van Eechoutte, D., Vandepoele, K. (2016) A Collection of Conserved Non-Coding Sequences to Study Gene Regulation in Flowering Plants. Plant Physiol. pp.00821.2016. [Epub ahead of print]. (79) Tzfadia, O., Diels, T., De Meyer, S., Vandepoele, K., Aharoni, A., Van de Peer, Y. (2016) CoExpNetViz: the Construction and Vizualisation of Co-expression Networks. Frontiers in Plant Science 6:1194. (78) Wang, X., Muto, A., Van de Velde, J., Neyt, P., Himanen, K., Vandepoele, K., Van Lijsebettens, M. (2015) Functional Analysis of Arabidopsis TETRASPANIN Gene Family in Plant Growth and Development. Plant Physiol. 169(3):2200-14. (77) Glover, N., Daron, J., Pingault, L., Vandepoele, K., Paux, E., Feuillet, C., Choulet, F. (2015) Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B. Genome Biol. 16(1):188. (76) * De Witte, D., * Van de Velde, J., Decap, D., Van Bel, M., Audenaert, P., Demeester, P., Dhoedt, B., * Vandepoele, K., * Fostier, J. (2015) BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements. Bioinformatics 31(23):3758-66. *contributed equally (75) Gonzalez, A., Pauwels, L., Baekelandt, A., De Milde, L., Van Leene, J., Besbrugge, N., Heyndrickx, KS., Pérez, A.C., Durand, C., De Clercq, R., Van De Slijke, E., Vanden Bossche, R., Eeckhout, D., Gevaert, O., Vandepoele, K., De Jaeger, G., Goossens, A., Inzé, D. (2015) A Repressor Protein Complex Regulates Leaf Growth in Arabidopsis. The Plant Cell 27(8):2273-87. (74) Verkest, A., Byzova, M., Martens, C., Willems, A., Verwulgen, T., Slabbinck, B., Rombaut, D., Van de Velde, J., Vandepoele, K., Standaert, E., Peeters, M., Van Lijsebettens, M., Van Breusegem, F., De Block, J. (2015) Selection for Improved Energy Use Efficiency and Drought Tolerance in Canola Results in Distinct Transcriptome and Epigenome Changes. Plant Physiol. 168(4):1338-50. (73) Nelissen, B., Eeckhout, D., Demuynck, K., Persiau, G., Walton, A., Van Bel, M., Vervoort, M., Candaele, J., De Block, J., Aesaert, S., Van Lijsebettens, M., Goormachtig, S., Vandepoele, K., Van Leene, J., Muszynski, M., Gevaert, O., Inzé, D., De Jaeger, G. (2015) Dynamic Changes in ANGUSTIFOLIA3 Complex Composition Reveal a Growth Regulatory Mechanism in the Maize Leaf. The Plant Cell 27(6):1605-19. (72) Vriet, C., Lemmens, K., Vandepoele, K., Reuzeau, C., Russinova, E. (2015) Evolutionary trails of plant steroid genes. Trends Plant Science 20(5):301-8. (71) Van Leene, J., Eeckhout, D., Cannoot, B., De Winne, N., Persiau, G., Van De Slijke, E., Vercruysse, L., Dedecker, M., Verkest, A., Vandepoele, K., Martens, L., Witters, E., Gevaert, O., De Jaeger, G. (2015) An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes. Nature Protocols 10(1):169-87. (70) Volders, P., Verheggen, K., Menschaert, G., Vandepoele, K., Martens, L., Vandesompele, J., Mestdagh, P. (2015) An update on LNCipedia: a database for annotated human lncRNA sequences. Nucleic Acids Research 43(Database issue):D174-80. (69) Proost, S., Van Bel, M., Vaneechoutte, D., Van de Peer, Y., Inzé, D., Mueller-Roeber, B., Vandepoele, K. (2015) PLAZA 3.0: an access point for plant comparative genomics. Nucleic Acids Research 43(Database issue):D974-81. (68) Vargas, L., Santa Brígida, A. B., Mota Filho, J.P., de Carvalho, T. G., Rojas, C. A., Vaneechoutte, D., Van Bel, M., Farrinelli, L., Ferreira, P. C.G., Vandepoele, K., Hemerly, A. S. (2014) Drought tolerance conferred to sugarcane by association with Gluconacetobacter diazotrophicus: a transcriptomic view of hormone pathways. PLoS One 9(12):e114744. (67) * Heyndrickx, KS., * Van de Velde, J., Wang, X., Weigel, D., Vandepoele, K. (2014) A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana. The Plant Cell 26(10):3894-910. *contributed equally (66) Sonnhammer, E., Gabaldon, T., Sousa da Silva, A.W., Martin, F., Robinson-Rechavi, M., Boeckmann, B., Thomas, E., Dessimoz, C., Vandepoele, K., Van Bel, M., Quest for Orthologs consortium, (2014) Big Data and Other Challenges in the Quest for Orthologs. Bioinformatics 30(21):2993-8. (65) Choulet, F., Alberti, A., Theil, S., Glover, N., Barbe, V., Daron, J., Pingault, L., Sourdille, P., Couloux, A., Paux, E., Leroy, P., Mangenot, S., Guilhot, N., Le Gouis, J., Balfourier, F., Alaux, M., Jamilloux, V., Poulain, J., Durand, C., Bellec, A., Gaspin, C., Safar, J., Dolezel, J., Rogers, J., Vandepoele, K., Aury, J., Mayer, K., Berges, J., Quesneville, H., Wincker, P., Feuillet, C. (2014) Structural and functional partitioning of bread wheat chromosome 3B. Science 345(6194):1249721. (64) * Van de Velde, J., * Heyndrickx, KS., Vandepoele, K. (2014) Inference of Transcriptional Networks in Arabidopsis through Conserved Noncoding Sequence Analysis. The Plant Cell 26(7):2729-45. *contributed equally (63) * Lindemose, S., * Jensen, M.K., * Van de Velde, J., O'Shea, C., Heyndrickx, KS., Workman, C.T., Vandepoele, K., Skriver, K., De Masi, F. (2014) A DNA binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana. Nucleic Acids Research 42(12):7681-93. *contributed equally (62) Fu, Q., Fierro, A.C., Meysman, P., Sanchez-Rodriguez, A., Vandepoele, K., Marchal, K., Engelen, K. (2014) MAGIC: access portal to a cross-platform gene expression compendium for maize. Bioinformatics 30(9):1316-8. (61) Verkest, A., Abeel, T., Heyndrickx, KS., Van Leene, J., Lanz, C., Van De Slijke, E., De Winne, N., Eeckhout, D., Persiau, G., Van Breusegem, F., Inzé, D., Vandepoele, K., De Jaeger, G. (2014) A Generic Tool for Transcription Factor Target Gene Discovery in Arabidopsis Cell Suspension Cultures Based on Tandem Chromatin Affinity Purification. Plant Physiol. 164(3):1122-33. (60) Zamariola, L., De Storme, N., Vannerum, K., Vandepoele, K., Armstrong, SJ., Franklin, FC., Geelen, D. (2014) SHUGOSHINs and PATRONUS protect meiotic centromere cohesion in Arabidopsis thaliana. Plant J. 77(5):782-94 . (59) Vercruyssen, L., Verkest, A., Gonzalez, A., Heyndrickx, KS., Eeckhout, D., Han, B., Jégu, T., Archacki, R., Van Leene, J., Andriankaja, M., De Bodt, S., Abeel, T., Coppens, F., Dhondt, S., De Milde, L., Vermeersch, M., Maleux, K., Gevaert, O., Jerzmanowski, A., Benhamed, M., Wagner, D., Vandepoele, K., De Jaeger, G., Inzé, D. (2014) ANGUSTIFOLIA3 Binds to SWI/SNF Chromatin Remodeling Complexes to Regulate Transcription during Arabidopsis Leaf Development. The Plant Cell 26(1):210-29 . (58) Van Bel, M., Proost, S., Van Neste, C., Deforce, D., Van de Peer, Y., Vandepoele, K. (2013) TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes. Genome Biol. 14(12):R134. (57) Heyman, J., Cools, T., Vandenbussche, M., Heyndrickx, KS., Van Leene, J., Vercauteren, I., Vanderauwera, S., Vandepoele, K., De Jaeger, G., Van Der Straeten, D., De Veylder, L. (2013) ERF115 Controls Root Quiescent Center Cell Division and Stem Cell Replenishment. Science 342(6160):860-3. (56) De Clercq, I., Vermeirssen, V., Van Aken, O., Vandepoele, K., Murcha, M., Law, S., Inzé, A., Ng, S., Ivanova, A., Rombaut, D., Van de Cotte, B., Jaspers, P., Van de Peer, Y., Kangasjarvi, J., Whelan, J., Van Breusegem, F. (2013) The membrane-bound NAC transcription factor ANAC013 is a regulator of mitochondrial retrograde regulation of the oxidative stress response in Arabidopsis. The Plant Cell 25(9):3472-90. (55) Vandepoele, K., Van Bel, M., Richard, G., Van Landeghem, S., Verhelst, B., Moreau, H., Van de Peer, Y., Grimsley, N., Piganeau, G. (2013) pico-PLAZA, a genome database of microbial photosynthetic eukaryotes. Environ. Microbiol. 15(8):2147-53. (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 creates single-copy families in flowering plants. PNAS 110(8):2898-903. (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 6(2):311-22. (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 Biol. 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(6):e39648. (50) Heyndrickx, KS., Vandepoele, K. (2012) Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol. 159(3):884-901. (49) Movahedi, S., Van Bel, M., Heyndrickx, KS., Vandepoele, K. (2012) Comparative co-expression analysis in plant biology. Plant, Cell & Environment 35(10):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(1):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(2):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(2):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. 69(12):2041-55. (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 Science 16(6):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 Physiol. 156(3):1316-30. (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(16):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(6):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(2):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(1):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(12):3718-31. *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(12):680-8. (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(3):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(4):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(2):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(7219):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):184-94. (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(4):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(9):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(3):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(12):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. 282(35):25588-96. (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(2):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(2):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(3):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(11):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(5):R43. (18) Vandepoele, K., Van de Peer, Y. (2005) Exploring the plant transcriptome through phylogenetic profiling. Plant Physiol. 137(1):31-42. (17) Paterson, A.H., Bowers, J. E., Van de Peer, Y., Vandepoele, K. (2005) Ancient duplication of cereal genomes. . New Phytol. 165(3):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(1):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(44):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(36):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(6):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(4):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(6):1095-106. (10) Vandepoele, K., Simillion, C., Van de Peer, Y. (2004) The quest for genomic homology. Curr. Genomics 5(4):299-308. (9) Simillion, C., Vandepoele, K., Van de Peer, Y. (2004) Recent developments in computational approaches for uncovering genomic homology. BioEssays 26(11):1225-35. (8) Vandepoele, K., Simillion, C., Van de Peer, Y. (2003) Evidence that rice, and other cereals, are ancient aneuploids. The Plant Cell 15(9):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(1-4):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(2):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(23):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(21):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(12):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(11):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. The Plant Cell 14(4):903-16. |
Software   Contributor Genome Evolution |
||
|
Contact:
VIB / UGent Bioinformatics & Evolutionary Genomics Technologiepark 927 B-9052 Gent BELGIUM +32 (0) 9 33 13807 (phone) +32 (0) 9 33 13809 (fax) |
You are visiting an outdated page of the BEG/Van de Peer Lab site.
Not all pages have been ported, so these archived pages are still available.
Redirect to the new website?
