Publications

479. The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: Organelle genomes of the smallest eukaryote are examples of compaction

Robbens, S., Derelle, E., Ferraz, C., Wuyts, J., Moreau, H., Van De Peer, Y.

(2007) - Molecular Biology and Evolution

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478. An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens

Rensing, S.A., Ick, J., Fawcett, J.A., Lang, D., Zimmer, A., Van De Peer, Y., Reski, R.

(2007) - BMC Evolutionary Biology

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477. In search of the small ones: Improved prediction of short exons in vertebrates, plants, fungi and protists

Saeys, Y., Rouzé, P., Van de Peer, Y.

(2007) - Bioinformatics

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476. In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation

Casneuf, T., Van de Peer, Y., Huber, W.

(2007) - BMC Bioinformatics

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475. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation

Palenik, B., Grimwood, J., Aerts, A., Rouzé, P., Salamov, A., Putnam, N., Dupont, C., Jorgensen, R., Derelle, E., Rombauts, S., Zhou, K., Otillar, R., Merchant, S.S., Podell, S., Gaasterland, T., Napoli, C., Gendler, K., Manuell, A., Tai, V., Vallon, O., Piganeau, G., Jancek, S., Heijde, M., Jabbari, K., Bowler, C., Lohr, M., Robbens, S., Werner, G., Dubchak, I., Pazour, G.J., Ren, Q., Paulsen, I., Delwiche, C., Schmutz, J., Rokhsar, D., Van De Peer, Y., Moreau, H., Grigoriev, I.V.

(2007) - Proceedings of the National Academy of Sciences of the United States of America

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474. A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety

VELASCO, R, ZHARKIKH, A, TROGGIO, M, CARTWRIGHT, DA, CESTARO, A, PRUSS, D, PINDO, M, FITZGERALD, LM, VEZZULLI, S, REID, J, MALACARNE, G, ILIEV, D, COPPOLA, G, WARDELL, B, MICHELETTI, D, MACALMA, T, FACCI, M, MITCHELL, JT, PERAZZOLLI, M, ELDREDGE, G, GATTO, P, OYZERSKI, R, MORETTO, M, GUTIN, N, STEFANINI, M, CHEN, Y, SEGALA, C, DAVENPORT, C, DEMATTE, L, MRAZ, A, BATTILANA, J, STORMO, K, COSTA, F, TAO, QZ, SI-AMMOUR, A, HARKINS, T, LACKEY, A, PERBOST, C, TAILLON, B, STELLA, A, SOLOVYEV, V, FAWCETT, JA, STERCK, L, VANDEPOELE, K, GRANDO, SM, TOPPO, S, MOSER, C, LANCHBURY, J, BOGDEN, R, SKOLNICK, M, SGARAMELLA, V, BHATNAGAR, SK, FONTANA, P, GUTIN, A, VAN DE PEER, Y, SALAMINI, F, VIOLA, R

(2007) - PLOS ONE

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473. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis

Carlton, J.M., Hirt, R.P., Silva, J.C., Delcher, A.L., Schatz, M., Zhao, Q., Wortman, J.R., Bidwell, S.L., Alsmark, U.C.M., Besteiro, S., Sicheritz-Ponten, T., Noel, C.J., Dacks, J.B., Foster, P.G., Simillion, C., Van De Peer, Y., Miranda-Saavedra, D., Barton, G.J., Westrop, G.D., Müller, S., Dessi, D., Fiori, P.L., Ren, Q., Paulsen, I., Zhang, H., Bastida-Corcuera, F.D., Simoes-Barbosa, A., Brown, M.T., Hayes, R.D., Mukherjee, M., Okumura, C.Y., Schneider, R., Smith, A.J., Vanacova, S., Villalvazo, M., Haas, B.J., Pertea, M., Feldblyum, T.V., Utterback, T.R., Shu, C.-L., Osoegawa, K., De Jong, P.J., Hrdy, I., Horvathova, L., Zubacova, Z., Dolezal, P., Malik, S.-B., Logsdon Jr., J.M., Henze, K., Gupta, A., Wang, C.C., Dunne, R.L., Upcroft, J.A., Upcroft, P., White, O., Salzberg, S.L., Tang, P., Chiu, C.-H., Lee, Y.-S., Embley, T.M., Coombs, G.H., Mottram, J.C., Tachezy, J., Fraser-Liggett, C.M., Johnson, P.J.

(2007) - Science

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472. Unique regulation of the Calvin cycle in the ultrasmall green alga Ostreococcus

Robbens, S., Petersen, J., Brinkmann, H., Rouzé, P., Van De Peer, Y.

(2007) - Journal of Molecular Evolution

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471. Translation initiation site prediction on a genomic scale: Beauty in simplicity

Saeys, Y., Abeel, T., Degroeve, S., Van de Peer, Y.

(2007) - Bioinformatics

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470. Validating module network learning algorithms using simulated data

Michoel, T., Maere, S., Bonnet, E., Joshi, A., Saeys, Y., Van den Bulcke, T., Van Leemput, K., Van Remortel, P., Kuiper, M., Marchal, K., Van de Peer, Y.

(2007) - BMC Bioinformatics

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469. How many genes are there in plants (... and why are they there)?

Sterck, L., Rombauts, S., Vandepoele, K., Rouzé, P., Van de Peer, Y.

(2007) - Current Opinion in Plant Biology

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468. Canalization without flux sensors: a traveling-wave hypothesis

MERKS, RMH, VAN DE PEER, Y, INZE, D, BEEMSTER, GTS

(2007) - TRENDS IN PLANT SCIENCE

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467. Divergence of regulatory sequences in duplicated fish genes

Van Hellemont, R., Blomme, T., Van De Peer, Y., Marchal, K.

(2007) - Genome Dynamics

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466. The future for plants and plants for the future

Yves Van de Peer

(2007) - Genome Biology

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465. The interplay between salicylic acid and reactive oxygen species during cell death in plants

Dat, J.F., Capelli, N., Van Breusegem, F.

(2007) - Salicylic Acid: A Plant Hormone

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464. The Interplay Between Salicylic Acid and Reactive Oxygen Species During Cell Death in Plants

J. F. Dat, N. Capelli, F. Van Breusegem

(2007) - Salicylic Acid: A Plant Hormone

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463. The Arabidopsis thaliana homolog of yeast BRE1 has a function in cell cycle regulation during early leaf and root growth

Fleury, Delphine, Himanen, Kristiina, Cnops, Gerda, Nelissen, Hilde, Boccardi, Tommaso Matteo, Maere, Steven, Beemster, Gerrit T. S., Neyt, Pia, Anami, Sylvester, Robles, Pedro, Micol, Jose Luis, Inze, Dirk, Van Lijsebettens, Mieke

(2007) - Plant Cell

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462. Integration of biological networks and gene expression data using Cytoscape

Cline, Melissa S., Smoot, Michael, Cerami, Ethan, Kuchinsky, Allan, Landys, Nerius, Workman, Chris, Christmas, Rowan, Avila-Campilo, Iliana, Creech, Michael, Gross, Benjamin, Hanspers, Kristina, Isserlin, Ruth, Kelley, Ryan, Killcoyne, Sarah, Lotia, Samad, Maere, Steven, Morris, John, Ono, Keiichiro, Pavlovic, Vuk, Pico, Alexander R., Vailaya, Aditya, Wang, Peng-Liang, Adler, Annette, Conklin, Bruce R., Hood, Leroy, Kuiper, Martin, Sander, Chris, Schmulevich, Ilya, Schwikowski, Benno, Warner, Guy J., Ideker, Trey, Bader, Gary D.

(2007) - Nature Protocols

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461. Validating module network learning algorithms using simulated data

Michoel, Tom, Maere, Steven, Bonnet, Eric, Joshi, Anagha, Saeys, Yvan, Van den Bulcke, Tim, Van Leemput, Koenraad, van Remortel, Piet, Kuiper, Martin, Marchal, Kathleen, de Peer, Yves Van

(2007) - Bmc Bioinformatics

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460. Patterning the axis in plants-auxin in control

De Smet, I., Jurgens, G.

(2007) - Current Opinion in Genetics & Development

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459. Auxin-dependent regulation of lateral root positioning in the basal meristem of Arabidopsis

De Smet, I., Tetsumura, T., De Rybel, B., Frey, N. F. D., Laplaze, L., Casimiro, I., Swarup, R., Naudts, M., Vanneste, S., Audenaert, D., Inze, D., Bennett, M. J., Beeckman, T.

(2007) - Development

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458. Mitochondrial type-I prohibitins of Arabidopsis thaliana are required for supporting proficient meristem development.

Van Aken O, Pecenková T, van de Cotte B, De Rycke R, Eeckhout D, Fromm H, De Jaeger G, Witters E, Beemster GT, Inzé D, Van Breusegem F

(2007) -

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457. Downregulation of Cinnamoyl-Coenzyme A Reductase in Poplar: Multiple-Level Phenotyping Reveals Effects on Cell Wall Polymer Metabolism and Structure

Jean-Charles Leplé, Rebecca Dauwe, Kris Morreel, Véronique Storme, Catherine Lapierre, Brigitte Pollet, Annette Naumann, Kyu-Young Kang, Hoon Kim, Katia Ruel, Andrée Lefèbvre, Jean-Paul Joseleau, Jacqueline Grima-Pettenati, Riet De Rycke, Sara Andersson-Gunnerås, Alexander Erban, Ines Fehrle, Michel Petit-Conil, Joachim Kopka, Andrea Polle, Eric Messens, Björn Sundberg, Shawn D. Mansfield, John Ralph, Gilles Pilate, Wout Boerjan

(2007) - The Plant Cell

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456. Gene expression during the induction, maintenance, and release of dormancy in apical buds of poplar

Antje Rohde, Tom Ruttink, Vanessa Hostyn, Lieven Sterck, Klara Van Driessche, Wout Boerjan

(2007) - Journal of Experimental Botany

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455. Are metacaspases caspases?

Vercammen D, Declercq W, Vandenabeele P, Van Breusegem F

(2007) -

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454. Conditional oxidative stress responses in the Arabidopsis photorespiratory mutant cat2 demonstrate that redox state is a key modulator of daylength-dependent gene expression, and define photoperiod as

Queval G, Issakidis-Bourguet E, Hoeberichts FA, Vandorpe M, Gakière B, Vanacker H, Miginiac-Maslow M, Van Breusegem F, Noctor G

(2007) -

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453. Functional characterisation of genes involved in pyridine alkaloid biosynthesis in tobacco

Suvi T. Häkkinen, Sofie Tilleman, Agnieszka Šwiątek, Valerie De Sutter, Heiko Rischer, Isabelle Vanhoutte, Harry Van Onckelen, Pierre Hilson, Dirk Inzé, Kirsi-Marja Oksman-Caldentey

(2007) - Phytochemistry

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452. Determination of saponins in Maesa lanceolata by LC-UV: Development and validation

Mart H.B.L. Theunis, Kenn Foubert, Jacob Pollier, Miguel Gonzalez-Guzman, Alain Goossens, Arnold J. Vlietinck, Luc A.C. Pieters, Sandra Apers

(2007) - Phytochemistry

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451. Demarcation of the cortical division zone in dividing plant cells.

Van Damme D, Geelen D

(2007) - Cell biology international

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450. Molecular phenotyping of lignin‐modified tobacco reveals associated changes in cell‐wall metabolism, primary metabolism, stress metabolism and photorespiration

Rebecca Dauwe, Kris Morreel, Geert Goeminne, Birgit Gielen, Antje Rohde, Jos Van Beeumen, John Ralph, Alain‐Michel Boudet, Joachim Kopka, Soizic F. Rochange, Claire Halpin, Eric Messens, Wout Boerjan

(2007) - The Plant Journal

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449. A Molecular Timetable for Apical Bud Formation and Dormancy Induction in Poplar

Tom Ruttink, Matthias Arend, Kris Morreel, Véronique Storme, Stephane Rombauts, Jörg Fromm, Rishikesh P. Bhalerao, Wout Boerjan, Antje Rohde

(2007) - The Plant Cell

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448. Impact of Core Histone Modifications on Transcriptional Regulation and Plant Growth

Hilde Nelissen, Tommaso Matteo Boccardi, Kristiina Himanen, Mieke Van Lijsebettens

(2007) - Critical Reviews in Plant Sciences

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447. Silencing of poly(ADP-ribose) polymerase in plants alters abiotic stress signal transduction.

Vanderauwera S, De Block M, Van de Steene N, van de Cotte B, Metzlaff M, Van Breusegem F

(2007) -

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446. Lignins

John Ralph, Gösta Brunow, Wout Boerjan

(2007) - Encyclopedia of Life Sciences

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445. Novel plant-specific cyclin-dependent kinase inhibitors induced by biotic and abiotic stresses.

Peres A, Churchman ML, Hariharan S, Himanen K, Verkest A, Vandepoele K, Magyar Z, Hatzfeld Y, Van Der Schueren E, Beemster GT, Frankard V, Larkin JC, Inzé D, De Veylder L

(2007) -

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444. The ins and outs of the plant cell cycle.

De Veylder L, Beeckman T, Inzé D

(2007) -

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443. Resistance to Botrytis cinerea in sitiens, an abscisic acid-deficient tomato mutant, involves timely production of hydrogen peroxide and cell wall modifications in the epidermis.

Asselbergh B, Curvers K, Franca SC, Audenaert K, Vuylsteke M, Van Breusegem F, Höfte M

(2007) -

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442. Comparative transcriptome analysis reveals common and specific tags for root hair and crack-entry invasion in Sesbania rostrata.

Capoen W, Den Herder J, Rombauts S, De Gussem J, De Keyser A, Holsters M, Goormachtig S

(2007) -

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441. Cortical division zone establishment in plant cells.

Van Damme D, Vanstraelen M, Geelen D

(2007) - Trends in plant science

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440. Cytological investigations of the Arabidopsis thaliana elo1 mutant give new insights into leaf lateral growth and Elongator function.

Falcone A, Nelissen H, Fleury D, Van Lijsebettens M, Bitonti MB

(2007) -

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439. The ins and outs of the plant cell cycle

Lieven De Veylder, Tom Beeckman, Dirk Inzé

(2007) - Nature Reviews Molecular Cell Biology

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438. Ethylene Regulates Root Growth through Effects on Auxin Biosynthesis and Transport-Dependent Auxin Distribution

Kamil Růžička, Karin Ljung, Steffen Vanneste, Radka Podhorská, Tom Beeckman, Jiří Friml, Eva Benková

(2007) - The Plant Cell

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437. A symbiotic plant peroxidase involved in bacterial invasion of the tropical legume Sesbania rostrata.

Den Herder J, Lievens S, Rombauts S, Holsters M, Goormachtig S

(2007) -

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436. Classical anticytokinins do not interact with cytokinin receptors but inhibit cyclin-dependent kinases.

Spíchal L, Krystof V, Paprskárová M, Lenobel R, Styskala J, Binarová P, Cenklová V, De Veylder L, Inzé D, Kontopidis G, Fischer PM, Schmülling T, Strnad M

(2007) -

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435. Bypassing genomic imprinting allows seed development.

Nowack MK, Shirzadi R, Dissmeyer N, Dolf A, Endl E, Grini PE, Schnittger A

(2007) -

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434. T-loop phosphorylation of Arabidopsis CDKA;1 is required for its function and can be partially substituted by an aspartate residue.

Dissmeyer N, Nowack MK, Pusch S, Stals H, Inzé D, Grini PE, Schnittger A

(2007) -

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433. Implementation of functional genomics for gene discovery in alkaloid producing plants

Alain Goossens, Heiko Rischer

(2007) - Phytochemistry Reviews

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432. Auxin-dependent regulation of lateral root positioning in the basal meristem of Arabidopsis.

De Smet I, Tetsumura T, De Rybel B, Frei dit Frey N, Laplaze L, Casimiro I, Swarup R, Naudts M, Vanneste S, Audenaert D, Inzé D, Bennett MJ, Beeckman T

(2007) -

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431. Genetically modified lignin below ground

David W. Hopkins, Elizabeth A. Webster, Wout Boerjan, Gilles Pilate, Claire Halpin

(2007) - Nature Biotechnology

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430. Nod factor perception during infection thread growth fine-tunes nodulation.

Den Herder J, Vanhee C, De Rycke R, Corich V, Holsters M, Goormachtig S

(2007) -

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429. The Arabidopsis thaliana homolog of yeast BRE1 has a function in cell cycle regulation during early leaf and root growth.

Fleury D, Himanen K, Cnops G, Nelissen H, Boccardi TM, Maere S, Beemster GT, Neyt P, Anami S, Robles P, Micol JL, Inzé D, Van Lijsebettens M

(2007) -

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428. Auxin-dependent regulation of lateral root positioning in the basal meristem ofArabidopsis

Ive De Smet, Takuya Tetsumura, Bert De Rybel, Nicolas Frei dit Frey, Laurent Laplaze, Ilda Casimiro, Ranjan Swarup, Mirande Naudts, Steffen Vanneste, Dominique Audenaert, Dirk Inzé, Malcolm J. Bennett, Tom Beeckman

(2007) - Development

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427. Arabidopsis WEE1 kinase controls cell cycle arrest in response to activation of the DNA integrity checkpoint.

De Schutter K, Joubès J, Cools T, Verkest A, Corellou F, Babiychuk E, Van Der Schueren E, Beeckman T, Kushnir S, Inzé D, De Veylder L

(2007) -

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426. Metacaspase activity of Arabidopsis thaliana is regulated by S-nitrosylation of a critical cysteine residue.

Belenghi B, Romero-Puertas MC, Vercammen D, Brackenier A, Inzé D, Delledonne M, Van Breusegem F

(2007) -

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425. Arabidopsis WEE1 kinase controls cell cycle arrest in response to activation of the DNA integrity checkpoint.

Kristof De Schutter, Jérôme Joubès, Cools T, Verkest A, Florence Corellou, Babiychuk E, Van Der Schueren E, Tom Beeckman, Sergei Kushnir, Dirk Inzé, Lieven De Veylder

(2007) - The Plant Cell

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