Publications

Your search yielded 95 results
Novikova, P.Y., Tsuchimatsu, T., Simon, S., Nizhynska, V., Voronin, V., Burns, R., Fedorenko, O.M., Holm, S., Säll, T., Prat, E., Marande, W., Castric, V., Nordborg, M. (2017) Genome sequencing reveals the origin of the allotetraploid Arabidopsis suecica. Mol. Biol. Evol. pii: msw299.

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Rabanal, F.A., Nizhynska, V., Mandáková, T., Novikova, P.Y., Lysak, M., Mott, R., Nordborg, M. (2017) Unstable inheritance of 45S rRNA genes in Arabidopsis thaliana. G3 (Bethesda) pii: g3.117.040204.

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Lee, C.R., Svardal, H., Farlow, A., Exposito-Alonso, M., Ding, D.J., Novikova, P.Y., Alonso-Blanco, C., Weigel, D., Nordborg, M. (2017) On the post-glacial spread of human commensal Arabidopsis thaliana. Nature Comm. 8:14458.

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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.

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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.

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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.

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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.

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Fernandez-Moreno, JP., Tzfadia, O., Forment, J., Presa, S., Rogachev, I., Meir, S., Orzaez, D., Aharoni, A., Granell, A. (2016) Characterization of a New Pink-Fruited Tomato Mutant Results in the Identification of a Null Allele of the SlMYB12 Transcription Factor. Plant Physiol. 171(3):1821-1836.

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Lashbrooke, J., Cohen, H., Levy-Samocha, D., Tzfadia, O., Panizel, I., Zeisler, V., Massalha, H., Stern, A., Trainotti, L., Schreiber, F., Costa, F., Aharoni, A. (2016) MYB107 and MYB9 Homologs Regulate Suberin Deposition in Angiosperms. The Plant Cell (In press).

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He, F., Arce, AL., Schmitz, G., Koornneef, M., Novikova, P.Y., Beyer, A., de Meaux, J. (2016) The Footprint of Polygenic Adaptation on Stress-Responsive Cis-Regulatory Divergence in the Arabidopsis Genus. Mol. Biol. Evol. 33(8):2088-101.

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Alonso-Blanco, C., Andrade, J., Becker, C., Bemm, F., Bergelson, J., Borgwardt, K.M., Cao, J., Chae, E., Dezwaan, T.M., Ding, D.J., Ecker, J.R., Exposito-Alonso, M., Farlow, A., Fitz, J., Gan, X., Grimm, D.G., Hancock, A.M., Henz, SR., Holm, S., Horton, M., Jarsulic, M., Kerstetter, R.A., Korte, A., Korte, P., Lanz, C., Lee, C.R., Meng, D., Michael, T.P., Mott, R., Muliyati, N.W., Nägele, T., Nagler, M., Nizhynska, V., Nordborg, M., Novikova, P.Y., Pico, A.R., Platzer, U., Rabanal, F.A., Rodríguez, A., Rowan, B.A., Salomé, P.A., Schmid, M., Schmitz, G., Seren, U., Sperone, F.G., Sudkamp, M., Svardal, H., Tanzer, M.M., Todd, J.A., Volchenboum, S.L., Wang, X., Wang, X., Wang, X., Weckwerth, W., Weigel, D., Zhou, X. (2016) 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell 166(2):481-91.

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Novikova, P.Y., Hohmann, N., Nizhynska, V., Tsuchimatsu, T., Ali, J., Muir, G., Guggisberg, A., Paape, T., Schmid, M., Fedorenko, O.M., Holm, S., Säll, T., Schlötterer, C., Marhold, K., Widmer, A., Sese, J., Shimizu, Y., Weigel, D., Krämer, U., Koch, M.A., Nordborg, M. (2016) Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. Nat. Genet. 48(9):1077-82.

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Szakonyi, D., Van Landeghem, S., Baerenfaller, K., Baeyens, L., Blomme, J., Casanova-Sáez, R., De Bodt, S., Esteve-Bruna, D., Fiorani, F., Gonzalez, A., Grønlund, J., G.H. Immink, R., Jover-Gil, S., Kuwabara, A., Muñoz-Nortes, T., D.J. van Dijk, A., Wilson-Sánchez, D., Buchanan-Wollaston, V., C. Angenent, G., Van de Peer, Y., Inzé, D., Luis Micol, J., Gruissem, W., Walsh, S., Hilson, P. (2015) The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining. Current Plant Biology 2:1-11.

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Ghorbani, S., Lin, Y.-C., Parizot, B., Fernandez, A., Fransiska Njo, M., Van de Peer, Y., Beeckman, T., Hilson, P. (2015) Expanding the Repertoire of Secretory Peptides Controlling Root Development with Comparative Genome Analysis and Functional Assays. Journal of Experimental Botany 66(17):5257-69.

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Olvera-Carrillo, Y., Van Bel, M., Van Hautegem, T., Fendrych, M., Huysmans, M., Simaskova, M., van Durme, M., Buscaill, P., Rivas, S., Coll, N.S., Coppens, F., Maere, S., Nowack, M.K. (2015) A conserved core of PCD indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiol. 169(4):2684-99.

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Walton, A., Stes, E., Cybulski, N., Van Bel, M., Iñigo, S., Nagels Durand, A., Timmerman, D., Heyman, J., Pauwels, L., De Veylder, L., Goossens, A., De Smet, I., Coppens, F., Goormachtig, S., Gevaert, O. (2015) It's time for some "site"-seeing: novel tools to monitor the ubiquitin landscape in Arabidopsis thaliana. The Plant Cell 28(1):6-16.

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Zhurov, V., Navarro, M., Bruinsma, K.A., Arbona, V., Santamaria, M.E., Wybouw, M.C.N., Osborne, E.J., Ens, C., Rioja, C., Vermeirssen, V., Rubio-Somoza, I., Krishna, P., Diaz, I., Schmid, M., Gómez-Cadenas, A., Van de Peer, Y., Grbic, M., Clark, R.M., Van Leeuwen, T., Grbic, V. (2014) Reciprocal responses in the interaction between Arabidopsis and the cell-content feeding chelicerate herbivore Tetranychus urticae. Plant Physiol. 164(1):384-399.

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Morreel, K., Saeys, Y., Dima, O., Lu, F., Van de Peer, Y., Vanholme, R., Ralph, S., Vanholme, B., Boerjan, W. (2014) Systematic Structural Characterization of Metabolites in Arabidopsis via Candidate Substrate-Product Pair Networks. The Plant Cell 26(3):929-945.

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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 .

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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.

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* Pajoro, A., * Biewers, S., * Dougali, E., * Leal Valentim, F., * Adelina Mendes, M., * Porri, A., Coupland, G., Van de Peer, Y., van Dijk, A.D.J., Colombo, L., Davies, B., Angenent, G.C. (2014) The (r)evolution of gene regulatory networks controlling Arabidopsis plant reproduction, a two decades history. Journal of Experimental Botany 65(17):4731-4745. *contributed equally

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Claeys, M., Van Landeghem, S., Dubois, M., Maleux, K., Inzé, D. (2014) What Is Stress? Dose-Response Effects in Commonly Used in Vitro Stress Assays. Plant Physiol. 165(2):519-527.

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* 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

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* 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

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Vermeirssen, V., De Clercq, I., Van Parys, T., Van Breusegem, F., Van de Peer, Y. (2014) Arabidopsis ensemble reverse-engineered gene regulatory network discloses interconnected transcription factors in oxidative stress. The Plant Cell 26(12):4656-4679.

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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(3):794-807.

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De Wilde, K., De Buck, S., Vanneste, K., Depicker, A. (2013) Recombinant antibody production in Arabidopsis seeds triggers an unfolded protein response. Plant Physiol. 161(2):1021-33.

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Nystedt, B., Street, N. R., Zuccolo, A., Lin, Y.-C., Wetterbom, A., Vezzi, A., Scofield, D. G., Delhomme, N., Alexeyenko, A., Giacomello, S., Vicedomini, R., Sahlin, K., Sherwood, E., Elfstand, M., Gramzow, L., Holmberg, K., Hällman, J., Keech, O., Klasson, L., Koriabine, M., Kucukoglu, M., Käller, M., Luthman, J., Lysholm, F., Olson, A., Niittylä, T., Ritland, K., Rilakovic, N., Rosselló, J. A., Sena, J., Svensson, T., Talavera-López, C., Theißen, G., Vanneste, K., Tuominen, H., Zhang, J., Wu, Z., Zerbe, P., Bhalerao, R.P., Bohlmann, J., Arvestad, L., Bousquet, J., Garcia Gil, R., de Jong, P.J., Hvidsten, T. R., MacKay, J., Ritland, K., Morgante, M., Sundberg, B., Van de Peer, Y., Lee Thompson, S., Nilsson, O., Andersson, B., Lundeberg, J., Jansson, S. (2013) The Norway spruce genome sequence and conifer genome evolution. Nature 497(7451):579-84.

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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.

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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(2):849-59.

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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.

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Wang, X., Vandepoele, K., Van Lijsebettens, M. (2012) Tetraspanin genes in plants. Plant Sci. 190, 9-15.

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Heyndrickx, KS., Vandepoele, K. (2012) Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol. 159(3):884-901.

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* 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(2):884-96. *contributed equally

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Tzfadia, O., Amar, M., Bradbury, LMT., Wurtzel, ET., Shamir, R. (2012) The MORPH algorithm: ranking candidate genes for membership in Arabidopsis thaliana pathways. The Plant Cell 24,4389-406.

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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.

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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.

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* 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

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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(1):58-65.

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* 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. 43(5):476-81. *contributed equally

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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.

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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.

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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(2):487-99.

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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.

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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.

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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.

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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(2):553-65.

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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.

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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.

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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.

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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(13):1532-3.

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Amoutzias, G., Van de Peer, Y. (2008) Together We Stand: Genes Cluster to Coordinate Regulation. Dev. Cell 14(5):640-2.

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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.

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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.

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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(3):1583-602.

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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.

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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.

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Keywords
Authors	Abeel, T. Adams, K. Alekseyev, Amoutzias, G. Aydoǧdu, E. Baele, G. Bafort, Q. Billiau, K. Blomme, T. Bonnet, E. Botelho, S. Casneuf, T. De Bodt, S. de Jonge, R. De Smet, R. Defoort, J. Degroeve, S. Diels, T. Dierick, F. Dougali, E. Fawcett, J. Florquin, K. Gevers, D. Gordon, J. Harikrishnan, S. He, Y. Heyndrickx, KS. Himelblau, E. Hollunder, J. Joshi, A. Kao, S.-M. Le, P. Lee, H.-F. Li, B. Li, Z. Lin, Y.-C. Lohaus, R. Maere, S. Mahy, B. Martens, C. Merks, R.M.H. Michoel, T. Movahedi, S. Novikova, P.Y. Pattyn, P. Pochet, N. Potenza, E. Proost, S. Raes, J. Ren, X.Y. Robbens, S. Rombauts, S. Rouzé, P. Sabaghian, E. Saeys, Y. Simillion, C. Slabbinck, B. Sterck, L. Tasdighian, S. Taylor, J.S. Thi Ngoc Cao, P. Timmermans, S. Tzfadia, O. Van Bel, M. Van de Peer, Y. Van den Ackerveken, G. Van Landeghem, S. Van Parys, T. Vandepoele, K. Vandevoorde, M. Vanneste, K. Verhelst, B. Vermeirssen, V. Wischnitzki, E. Wuyts, J. Yao, Y. Yu, X. Zhang, Z. Zwaenepoel, A.
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