Publications
Your search yielded 69 results
Van Landeghem, S., De Bodt, S., Drebert, Z. J., Inzé, D., Van de Peer, Y. (2013) The potential of text mining in data integration and network biology for plant research: a case study on Arabidopsis. The Plant Cell 25, 794-807. De Wilde, K., De Buck, S., Vanneste, K., Depicker, A. (2013) Recombinant antibody production in Arabidopsis seeds triggers an unfolded protein response. Plant Physiololgy 161, 1021-33. Fawcett, J., Rouzé, P., Van de Peer, Y. (2012) Higher intron loss rate in Arabidopsis thaliana than A. lyrata is consistent with stronger selection for a smaller genome. Mol. Biol. Evol. 29,849-59. 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. 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 Heyndrickx, KS., Vandepoele, K. (2012) Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol. 159, 884-901. * Vandesteene, L., * Lopez-Galvis, L., Vanneste, K., Maere, S., Lammens, T., Rolland, F., Lunn, J., Avonce, N., Beeckman, T., Van Dijck, P. (2012) Expansive evolution of the Trehalose-6-phosphatase gene family in Arababidopsis thaliana. Plant Physiol. 160, 884-96. *contributed equally Movahedi, S., Masoudi-Nejad, A., Jauregui email, R. (2011) Genome-scale computational analysis of DNA curvature and repeats in Arabidopsis and rice uncovers plant-specific genomic properties. BMC Genomics 12,214. 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. * 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 Proost, S., Pattyn, P., Gerats, T., Van de Peer, Y. (2011) Journey through the past: 150 million years of plant genome evolution. Plant J. 66, 58-65. * Hu, T.T., * Pattyn, P., Bakker, E.G., Cao, J., Cheng, Y.-Y., Clarck, R.M., Fahlgren, N., Fawcette, J., Grimwood, J., Gundlach, H., Haberer, G., Hollister, J.D., Ossowski, S., Ottilar, R.P., Salamov, A., Schneeberger, K., Spannagl, M., Wang, X., Yang, L., Nasrallah, M.E., Bergelson, J., Carrington, J.C., Gaut, B.S., Schmutz, J., Mayer, K., Van de Peer, Y., Grigoriev, I., Nordborg, M., Weigel, D., Guo, Y-L. (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat. Genet. 4,476-81. *contributed equally De Bodt, S., Carvajal, D., Hollunder, J., Van den Cruyce, J., Movahedi, S., Inzé, D. (2010) CORNET: a user-friendly tool for data mining and integration. Plant Physiol. 152(3), 1167-79. 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. Rehrauer, H., Aquino, C., Gruissem, W., Henz, SR., Hilson, P., Laubinger, S., Naouar, N., Patrignani, A., Rombauts, S., Shu, C.-L., Van de Peer, Y., Vuylsteke, M., Weigel, D., Zeller, G., Hennig, L. (2010) AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. Plant Physiol. 152, 487-499. Van Leene, J., Hollunder, J., Eeckhout, D., Persiau, G., Van De Slijke, E., Stals, H., Van Isterdael, G., Verkest, A., Neirynck, S., Buffel, Y., Inzé, D., Witters, E., De Jaeger, G. (2010) Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Mol. Syst. Biol. 6, 397. Boyko, A., Blevins, T., Yao, Y., Golubov, A., Bilichak, A., Ilnytskyy, Y., Hollunder, J., Meins, F., Kovalchuk, I. (2010) Transgenerational Adaptation of Arabidopsis to Stress Requires DNA Methylation and the Function of Dicer-Like Proteins. PLOS One 5(3), e9514. Boruc, J., Van Den Daele, H., Hollunder, J., Rombauts, S., Mylle, E., Hilson, P., Inzé, D., De Veylder, L., Russinova, E. (2010) Functional modules in the Arabidopsis core cell cycle binary protein-protein interaction network. The Plant Cell 22(4), 1264-80. Boruc, J., Engler, G., Mylle, E., De Veylder, L., De Groodt, R., Duda, M., De Clercq, R., Rombauts, S., Boudolf, V., Duda, M., Geelen, D., Geelen, D., Hilson, P., Inzé, D., Ferreira, P.C.P., Van Damme, D., Beeckman, T., Russinova, E., Karimi, M., Hilson, P., Inzé, D., Engler, G. (2010) Systematic localization of the Arabidopsis core cell cycle proteins reveals novel cell division complexes. Plant Physiol. 152, 553-565. 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. Engler, G., De Veylder, L., De Groodt, R., Rombauts, S., Boudolf, V., De Meyer, B., Hemerly, A., Ferreira, P.C.P., Beeckman, T., Karimi, M., Hilson, P., Inzé, D., Engler, G. (2009) Systematic analysis of cell-cycle gene expression during Arabidopsis development. Plant J. 59(4), 645-60. 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. Van Bel, M., Saeys, Y., Van de Peer, Y. (2008) FunSiP : A Modular and Extensible Classifier for the Prediction of Functional Sites in DNA. Bioinformatics 24, 1532-3. Amoutzias, G., Van de Peer, Y. (2008) Together We Stand: Genes Cluster to Coordinate Regulation. Dev. Cell. 14, 640-2. 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. 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. Jakoby, M., Falkenhan, D., Mader, M., Brininstool, G., Wischnitzki, E., Platz, N., Hudson, A., Hulskamp, M., Larkin, J.C., Schnittger, A. (2008) Transcriptional profiling of mature Arabidopsis trichomes reveals that NOECK encodes the MIXTA-like transcriptional regulator MYB106. Plant Physiol. 148, 358-368. Benhamed, M., Martin-Magniette, ML., Taconnat, L., Bitton, F., Servet, C., De Clercq, R., De Meyer, B., Buysschaert, C., Rombauts, S., Villarroel, R., Aubourg, S., Beynon, J., Bhalerao, R.P., Coupland, G., Gruissem, W., Menke, FL., Weisshaar, B., Renou, JP., Zhou, K., Hilson, P. (2008) Genome-scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5. Plant J. 56(3), 493-504. Den Herder, G., De Keyser, A., De Rycke, R., Rombauts, S., Van De Velde, S., Clemente, MR., Verplancke, C., Mergaert, P., Kondorosi, E., Holsters, M. & Ver, Goormachtig, S. (2008) Seven in absentia proteins affect plant growth and nodulation in Medicago truncatula. Plant Physiol. 148(1), 369-82. Itoh, T., Tanaka, T., Barrero, R., Yamasaki, C., Fujii, Y., Hilton, P., Antonio, B., Aono, H., Apweiler, R., Bruskiewich, R., Bureau, T., Burr, F., Oliveira, A., Fuks, G., Habara, T., Haberer, G., Han, B., Harada, E., Hiraki, A., Hirochika, H., Hoen, D., Hokari, H., Hosokawa, S., Hsing, Y., Ikawa, H., Ikeo, K., Imanishi, T., Ito, Y., Jaiswal, P., Kanno, M., Kawahara, T., Kawamura, T., Kawashima, H., Khurana, J., Kikuchi, S., Komatsu, S., Koyanagi, K., Kubooka, H., Lieberherr, D., Lin, Y.-C., Lonsdale, D., Matsumoto, T., Matsuya, A., W. McCombie, R., Messing, J., Miyao, A., Mulder, N., Nagamura, Y., Putnam, N., Namiki, N., Numa, H., Nurimoto, S., O'Donovan, C., Ohyanagi, H., Okido, T., OOta, S., Osato, N., Palmer, L., Quetier, F., Raghuvanshi, S., Saichi, N., Sakai, H., Sakai, Y., Sakata, K., Sakurai, T., Sato, S., Sato, S., Schoof, H., Seki, M., Shibata, M., Shimizu, Y., Shinozaki, K., Shinso, Y., Singh, N., Smith-White, B., Takeda, J., Tanino, M., Tatusova, T., Thongjuea, S., Todokoro, F., Tsugane, M., Tyagi, A., Vanavichit, A., Wang, X., Wing, R., Yamaguchi, K., Yamamoto, M., Yamamoto, N., Feldblyum, T., Zhang, J., Zhao, Q., Higo, K., Burr, B., Gojobori, T., Sasaki, T. (2007) Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res. 17, 175-83. Fleury, D., Himanen, K., Cnops, G., Nelissen, B., Boccardi, T.M., Maere, S., Beemster, G.T.S., Neyt, P., Anami, S., Robles, P., Micol, J.S., Inzé, D., Van Lijsebettens, M. (2007) The Arabidopsis thaliana homolog of yeast BRE1 has a function in cell cycle regulation during early leaf and root growth. Plant Cell 19, 417-32. Van Leene, J., Stals, H., Eeckhout, D., Persiau, G., Van De Slijke, E., Van Isterdael, G., De Clercq, R., Bonnet, E., Laukens, K., Remmerie, N., Hendrickx, K., De Vijlder, T., Abdelkrim, A., Pharazyn, A., Van Onckelen, H., Witters, E., Inzé, D., De Jaeger, G. (2007) A Tandem Affinity Purification-based technology platform to study the cell cycle interactome in Arabidopsis thaliana. Mol. Cel. Prot. 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. Smykal, P., Gennen, J., De Bodt, S., Ranganath, V., Melzer, S. (2007) Flowering of strict photoperiodic Nicotiana variaties in non-inductive conditions by transgenic approaches. Plant Mol. Biol. (in press). Ruttink, T., Arend, M., Morreel, K., Storme, V., Rombauts, S., Fromm, J., Bhalerao, R.P., Boerjan, W., Rohde, A. (2007) A molecular timetable for apical bud formation and dormancy induction in poplar. Plant Cell 19,2370-90. Casneuf, T., De Bodt, S., Raes, J., Maere, S., Van de Peer, Y. (2006) Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biol. 7, R13. 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. Degroeve, S., Saeys, Y., De Baets, B., Rouzé, P., Van de Peer, Y. (2005) Predicting splice sites from high-dimensional local context representations. Bioinformatics 21, 1332-8. Vandepoele, K., Van de Peer, Y. (2005) Exploring the plant transcriptome through phylogenetic profiling. Plant Physiol. 137, 31-42. * De Bodt, S., * Maere, S., Van de Peer, Y. (2005) Genome duplication and the origin of angiosperms. Trends Ecol. Evol. 20, 591-7. *contributed equally 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. Ren, X.Y., Fiers, M., Stiekema, W., Nap, J.P. (2005) Local coexpression domains of two to four genes in the genome of Arabidopsis. Plant Physiology 138, 923-934. Vanderauwera, S., Zimmermann, P. ., Rombauts, S., Vandenabeele, S., Langebartels, C., Gruissem, W., Inzé, D., Van Breusegem, F. (2005) Genome-wide analysis of hydrogen peroxide-regulated gene expression in Arabidopsis reveals a high light-induced transcriptional cluster involved in anthocyanin biosynthesis. Plant Physiol. 139,806-21. Torres Acosta, J.A., de Almeida Engler, J., Raes, J., Magyar, Z., De Groodt, R., Inzé, D., De Veylder, L. (2004) Molecular characterization of Arabidopsis PHO80-like proteins, a novelclass of CDKA;1-interacting cyclins. Cell Mol. Life Sci. 61, 1485-97. Bonnet, E., Wuyts, J., Rouzé, P., Van de Peer, Y. (2004) Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important new target genes. Proc. Natl. Acad. Sci. USA 101, 11511-6. Vandenabeele, S., Vuylsteke, M., Vanderauwera, S., Rombauts, S., Langebartels, C., Zabeau, M., Van Montagu, M., Inzé, D., Van Breusegem, F. (2004) Catalase deficiency drastically affects gene expression induced byhigh light in Arabidopsis thaliana. Plant J. 39, 45-58. 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. 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. Saeys, Y., Degroeve, S., Aeyels, D., Van de Peer, Y. (2003) Fast feature selection using a simple Estimation of Distribution Algorithm: A case study on splice site prediction. Bioinformatics 19 Suppl 2, II179-II188. Vlieghe, K., Florquin, K., Vuylsteke, M., Rombauts, S., Van Hummelen, P., Van de Peer, Y., Inzé, D., De Veylder, L. (2003) Microarray analysis of E2Fa-DPa-overexpressingplants uncovers a cross-talking genetic networkbetween DNA replication and nitrogen assimilation. J. Cell Science 116, 4249-59. 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. Crowe, M.L., Serizet, C., Thareau, V., Aubourg, S., Rouzé, P., Hilson, P., Beynon, J., Weisbeek, P., Van Hummelen, P., Reymond, P., Paz-Ares, J., Nietfeld, W., Trick, M. (2003) CATMA: a complete Arabidopsis GST database. Nucleic Acids Res. 31, 156-8. De Bodt, S., Raes, J., Florquin, K., Rombauts, S., Rouzé, P., Theissen, G., Van de Peer, Y. (2003) Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants. J. Mol. Evol. 56, 573-86. Degroeve, S., De Baets, B., Van de Peer, Y., Rouzé, P. (2002) Feature subset selection for splice site prediction. Bioinformatics 18 Suppl 2, S75-83. Thijs, G., Marchal, K., Lescot, M., Rombauts, S., De Moor, B., Rouzé, P., Moreau, Y. (2002) A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J. Comput Biol. 9, 447-64. 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. Thijs, G., Lescot, M., Rombauts, S., Marchal, K., De Moor, B., Moreau, Y., Rouzé, P. (2001) A higher order background model improves the detection by Gibbs sampling of potential promoter regulatory elements in DNA sequences. Bioinformatics 17, 1113-22. Boudolf, V., Rombauts, S., Naudts, M., Inzé, D., De Veylder, L. (2001) Identification of novel cyclin-dependent kinases interacting with the CKS1protein of Arabidopsis. J. Exp. Bot. 52, 1381-2. Magyar, Z., Atanassova, A., De Veylder, L., Rombauts, S., Inzé, D. (2000) Characterization of two distinct DP-related genes from Arabidopsis thaliana. FEBS Lett. 486, 79-87. Mathé, C., Dehais, P., Pavy, N., Rombauts, S., Van Montagu, M., Rouzé, P. (2000) Gene prediction and gene classes in Arabidopsis thaliana. J. Biotechnol. 78, 293-9. Pavy, N., Rombauts, S., D?hais, P., Mathé, C., Ramana, D.V., Leroy, P., Rouzé, P. (1999) Evaluation of gene prediction software using a genomic data set: application of Arabidopsis thaliana sequences. Bioinformatics 15, 887-99. Terryn, N., Heijnen, L., De Keyser, A., Van Asseldonck, M., De Clercq, R., Verbakel, H., Gielen, J., Zabeau, M., Villarroel, R., Jesse, T., Neyt, P., Hogers, R., Van Den Daele, H., Ardiles, W., Schueller, C., Mayer, K., Dehais, P., Rombauts, S., Van Montagu, M., Rouzé, P., De Vos, P. (1999) Evidence for an ancient chromosomal duplication in Arabidopsis thaliana bysequencing and analyzing a 400-kb contig at the APETALA2 locus on chromosome 4. FEBS Lett. 445, 237-45. Mathé, C., Peresetsky, A., Dehais, P., Van Montagu, M., Rouzé, P. (1999) Classification of Arabidopsis thaliana gene sequences: clustering of coding sequences into two groups according to codon usage improves gene prediction. J. Mol. Biol. 285, 1977-91. Terryn, N., Gielen, J., De Keyser, A., Van Den Daele, H., Ardiles, W., Neyt, P., De Clercq, R., Coppieters, J., Dehais, P., Villarroel, R., Rouzé, P., Van Montagu, M. (1998) Sequence analysis of a 40-kb Arabidopsis thaliana genomic region located at the top of chromosome 1. Gene 215, 11-7. Santoni, V., Rouquié, D., Doumas, P., Mansion, M., Boutry, M., Degand, H., Dupree, P., Packman, L., Sherrier, J., Prime, T., Bauw, G., Posada, E., Rouzé, P., Dehais, P., Sahnoun, I., Barlier, I., Rossignol, M. (1998) Use of a proteome strategy for tagging proteins present at the plasma membrane. Plant J. 16, 633-41. Tolstrup, N., Rouzé, P., Brunak, S. (1997) A branch-point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites. Nucleic Acids Res. 25, 3159-63. Terryn, N., Neyt, P., De Clercq, R., De Keyser, A., Van Den Daele, H., Ardiles, W., Dehais, P., Rouzé, P., Gielen, J., Villarroel, R., Van Montagu, M. (1997) Sequence analysis of a 24-kb continuous genomic region at the Arabidopsis thaliana PFL locus on chromosome 1. FEBS Lett. 416,156-160. Korning, PG., Hebsgaard, S., Rouzé, P., Brunak, S. (1996) Cleaning the GenBank Arabidopsis thaliana data set. Nucleic Acids Res. 24, 316-20. Hebsgaard, S., Korning, PG., Tolstrup, N., Engelbrecht, J., Rouzé, P., Brunak, S. (1996) Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local & global sequence information. Nucleic Acids Res. 24, 3439-52. |
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