Publications

545. Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species

MARTENS, C, VANDEPOELE, K, VAN DE PEER, Y

(2008) - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DOI
544. i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles

SIMILLION, C, JANSSENS, K, STERCK, L, VAN DE PEER, Y

(2008) - BIOINFORMATICS

DOI
543. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants

RENSING, SA, LANG, D, ZIMMER, AD, TERRY, A, SALAMOV, A, SHAPIRO, H, NISHIYAMA, T, PERROUD, PF, LINDQUIST, EA, KAMISUGI, Y, TANAHASHI, T, SAKAKIBARA, K, FUJITA, T, OISHI, K, SHIN-I, T, KUROKI, Y, TOYODA, A, SUZUKI, Y, HASHIMOTO, S, YAMAGUCHI, K, SUGANO, S, KOHARA, Y, FUJIYAMA, A, ANTEROLA, A, AOKI, S, ASHTON, N, BARBAZUK, WB, BARKER, E, BENNETZEN, JL, BLANKENSHIP, R, CHO, SH, DUTCHER, SK, ESTELLE, M, FAWCETT, JA, GUNDLACH, H, HANADA, K, HEYL, A, HICKS, KA, HUGHES, J, LOHR, M, MAYER, K, MELKOZERNOV, A, MURATA, T, NELSON, DR, PILS, B, PRIGGE, M, REISS, B, RENNER, T, ROMBAUTS, S, RUSHTON, PJ, SANDERFOOT, A, SCHWEEN, G, SHIU, SH, STUEBER, K, THEODOULOU, FL, TU, H, VAN DE PEER, Y, VERRIER, PJ, WATERS, E, WOOD, A, YANG, LX, COVE, D, CUMING, AC, HASEBE, M, LUCAS, S, MISHLER, BD, RESKI, R, GRIGORIEV, IV, QUATRANO, RS, BOORE, JL

(2008) - SCIENCE

DOI
542. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

MARTIN, F, AERTS, A, AHREN, D, BRUN, A, DANCHIN, EGJ, DUCHAUSSOY, F, GIBON, J, KOHLER, A, LINDQUIST, E, PEREDA, V, SALAMOV, A, SHAPIRO, HJ, WUYTS, J, BLAUDEZ, D, BUEE, M, BROKSTEIN, P, CANBACK, B, COHEN, D, COURTY, PE, COUTINHO, PM, DELARUELLE, C, DETTER, JC, DEVEAU, A, DIFAZIO, S, DUPLESSIS, S, FRAISSINET-TACHET, L, LUCIC, E, FREY-KLETT, P, FOURREY, C, FEUSSNER, I, GAY, G, GRIMWOOD, J, HOEGGER, PJ, JAIN, P, KILARU, S, LABBE, J, LIN, YC, LEGUE, V, LE TACON, F, MARMEISSE, R, MELAYAH, D, MONTANINI, B, MURATET, M, NEHLS, U, NICULITA-HIRZEL, H, OUDOT-LE SECQ, MP, PETER, M, QUESNEVILLE, H, RAJASHEKAR, B, REICH, M, ROUHIER, N, SCHMUTZ, J, YIN, T, CHALOT, M, HENRISSAT, B, KUES, U, LUCAS, S, VAN DE PEER, Y, PODILA, GK, POLLE, A, PUKKILA, PJ, RICHARDSON, PM, ROUZE, P, SANDERS, IR, STAJICH, JE, TUNLID, A, TUSKAN, G, GRIGORIEV, IV

(2008) - NATURE

DOI
541. Together we stand: Genes cluster to coordinate regulation

AMOUTZIAS, G, VAN DE PEER, Y

(2008) - DEVELOPMENTAL CELL

DOI
540. A Model-Based Approach to Study Nearest-Neighbor Influences Reveals Complex Substitution Patterns in Non-coding Sequences

BAELE, G, VAN DE PEER, Y, VANSTEELANDT, S

(2008) - SYSTEMATIC BIOLOGY

DOI
539. ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles

ABEEL, T, SAEYS, Y, ROUZE, P, VAN DE PEER, Y

(2008) - BIOINFORMATICS

DOI
538. FunSiP: A modular and extensible classifier for the prediction of functional sites in DNA

Van Bel, M., Saeys, Y., Van de Peer, Y.

(2008) - Bioinformatics

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537. Evolution and taxonomic distribution of nonribosomal peptide and polyketide synthases

AMOUTZIAS, GD, VAN DE PEER, Y, MOSSIALOS, D

(2008) - FUTURE MICROBIOLOGY

DOI
536. Analysis of a Gibbs sampler method for model-based clustering of gene expression data

JOSHI, A, VAN DE PEER, Y, MICHOEL, T

(2008) - BIOINFORMATICS

DOI
535. Generic eukaryotic core promoter prediction using structural features of DNA

ABEEL, T, SAEYS, Y, BONNET, E, ROUZE, P, VAN DE PEER, Y

(2008) - GENOME RESEARCH

DOI
534. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

BOWLER, C, ALLEN, AE, BADGER, JH, GRIMWOOD, J, JABBARI, K, KUO, A, MAHESWARI, U, MARTENS, C, MAUMUS, F, OTILLAR, RP, RAYKO, E, SALAMOV, A, VANDEPOELE, K, BESZTERI, B, GRUBER, A, HEIJDE, M, KATINKA, M, MOCK, T, VALENTIN, K, VERRET, F, BERGES, JA, BROWNLEE, C, CADORET, JP, CHIOVITTI, A, CHOI, CJ, COESEL, S, DE MARTINO, A, DETTER, JC, DURKIN, C, FALCIATORE, A, FOURNET, J, HARUTA, M, HUYSMAN, MJJ, JENKINS, BD, JIROUTOVA, K, JORGENSEN, RE, JOUBERT, Y, KAPLAN, A, KROGER, N, KROTH, PG, LA ROCHE, J, LINDQUIST, E, LOMMER, M, MARTIN-JEZEQUEL, V, LOPEZ, PJ, LUCAS, S, MANGOGNA, M, MCGINNIS, K, MEDLIN, LK, MONTSANT, A, OUDOT-LE SECQ, MP, NAPOLI, C, OBORNIK, M, PARKER, MS, PETIT, JL, PORCEL, BM, POULSEN, N, ROBISON, M, RYCHLEWSKI, L, RYNEARSON, TA, SCHMUTZ, J, SHAPIRO, H, SIAUT, M, STANLEY, M, SUSSMAN, MR, TAYLOR, AR, VARDI, A, VON DASSOW, P, VYVERMAN, W, WILLIS, A, WYRWICZ, LS, ROKHSAR, DS, WEISSENBACH, J, ARMBRUST, EV, GREEN, BR, VAN DE PEER, Y, GRIGORIEV, IV

(2008) - NATURE

DOI
533. MANTIS: a phylogenetic framework for multi-species genome comparisons

TZIKA, AC, HELAERS, R, VAN DE PEER, Y, MILINKOVITCH, MC

(2008) - BIOINFORMATICS

DOI
532. Genome annotation in plants and fungi: EuGène as a model platform

Foissac, S., Gouzy, J., Rombauts, S., Mathé, C., Amselem, J., Sterck, L., Van De Peer, Y., Rouzé, P., Schiex, T.

(2008) - Current Bioinformatics

DOI
531. Meta analysis of gene expression data within and across species

Fierro, A.C., Vandenbussche, F., Engelen, K., Van de Peer, Y., Marchal, K.

(2008) - Current Genomics

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530. Extracting expression modules from perturbational gene expression compendia

Maere, Steven, Van Dijck, Patrick, Kuiper, Martin

(2008) - Bmc Systems Biology

DOI
529. The auxin influx carrier LAX3 promotes lateral root emergence

Swarup, K., Benkova, E., Swarup, R., Casimiro, I., Peret, B., Yang, Y., Parry, G., Nielsen, E., De Smet, I., Vanneste, S., Levesque, M. P., Carrier, D., James, N., Calvo, V., Ljung, K., Kramer, E., Roberts, R., Graham, N., Marillonnet, S., Patel, K., Jones, J. D. G., Taylor, C. G., Schachtman, D. P., May, S., Sandberg, G., Benfey, P., Friml, J., Kerr, I., Beeckman, T., Laplaze, L., Bennett, M. J.

(2008) - Nature Cell Biology

DOI
528. The evolving complexity of the auxin pathway

Lau, S., Jurgens, G., De Smet, I.

(2008) - Plant Cell

DOI
527. Diarch symmetry of the vascular bundle in Arabidopsis root encompasses the pericycle and is reflected in distich lateral root initiation

Parizot, B., Laplaze, L., Ricaud, L., Boucheron-Dubuisson, E., Bayle, V., Bonke, M., De Smet, I., Poethig, S. R., Helariutta, Y., Haseloff, J., Chriqui, D., Beeckman, T., Nussaume, L.

(2008) - Plant Physiology

DOI
526. Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root

De Smet, I., Vassileva, V., De Rybel, B., Levesque, M. P., Grunewald, W., Van Damme, D., Van Noorden, G., Naudts, M., Van Isterdael, G., De Clercq, R., Wang, J. Y., Meuli, N., Vanneste, S., Friml, J., Hilson, P., Jurgens, G., Ingram, G. C., Inze, D., Benfey, P. N., Beeckman, T.

(2008) - Science

DOI
525. A review of estimation of distribution algorithms in bioinformatics

Rubén Armañanzas, Iñaki Inza, Roberto Santana, Yvan Saeys, Jose Luis Flores, Jose Antonio Lozano, Yves Van de Peer, Rosa Blanco, Víctor Robles, Concha Bielza, Pedro Larrañaga

(2008) - BioData Mining

DOI
524. The DOF transcription factor OBP1 is involved in cell cycle regulation in Arabidopsis thaliana.

Skirycz A, Radziejwoski A, Busch W, Hannah MA, Czeszejko J, Kwaśniewski M, Zanor MI, Lohmann JU, De Veylder L, Witt I, Mueller-Roeber B

(2008) -

DOI
523. Flowering-time genes modulate meristem determinacy and growth form in Arabidopsis thaliana

Siegbert Melzer, Frederic Lens, Jerôme Gennen, Steffen Vanneste, Antje Rohde, Tom Beeckman

(2008) - Nature Genetics

DOI
522. Physiological and transcriptomic evidence for a close coupling between chloroplast ontogeny and cell cycle progression in the pennate diatom Seminavis robusta.

Gillard J, Devos V, Huysman MJ, De Veylder L, D'Hondt S, Martens C, Vanormelingen P, Vannerum K, Sabbe K, Chepurnov VA, Inzé D, Vuylsteke M, Vyverman W

(2008) -

DOI
521. Functional Specialization of the TRANSPARENT TESTA GLABRA1 Network Allows Differential Hormonal Control of Laminal and Marginal Trichome Initiation in Arabidopsis Rosette Leaves

Lies Maes, Dirk Inzé, Alain Goossens

(2008) - Plant Physiology

DOI
520. ABAP1 is a novel plant Armadillo BTB protein involved in DNA replication and transcription.

Masuda HP, Cabral LM, De Veylder L, Tanurdzic M, de Almeida Engler J, Geelen D, Inzé D, Martienssen RA, Ferreira PC, Hemerly AS

(2008) -

DOI
519. Singlet oxygen is the major reactive oxygen species involved in photooxidative damage to plants.

Triantaphylidès C, Krischke M, Hoeberichts FA, Ksas B, Gresser G, Havaux M, Van Breusegem F, Mueller MJ

(2008) -

DOI
518. Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root.

De Smet I, Vassileva V, De Rybel B, Levesque MP, Grunewald W, Van Damme D, Van Noorden G, Naudts M, Van Isterdael G, De Clercq R, Wang JY, Meuli N, Vanneste S, Friml J, Hilson P, Jürgens G, Ingram GC, Inzé D, Benfey PN, Beeckman T

(2008) -

DOI
517. Fine-tuning of early events in the jasmonate response.

Pauwels L, Goossens A

(2008) -

DOI
516. Fine-tuning of early events in the jasmonate response

Laurens Pauwels, Alain Goossens

(2008) - Plant Signaling & Behavior

DOI
515. Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root.

De Smet I, Vassileva V, De Rybel B, Levesque MP, Grunewald W, Van Damme D, Van Noorden G, Naudts M, Van Isterdael G, De Clercq R, Wang JY, Meuli N, Beeckman T

(2008) - Science (New York, N.Y.)

DOI
514. Receptor-Like Kinase ACR4 Restricts Formative Cell Divisions in the Arabidopsis Root

Ive De Smet, Valya Vassileva, Bert De Rybel, Mitchell P. Levesque, Wim Grunewald, Daniël Van Damme, Giel Van Noorden, Mirande Naudts, Gert Van Isterdael, Rebecca De Clercq, Jean Y. Wang, Nicholas Meuli, Steffen Vanneste, Jiří Friml, Pierre Hilson, Gerd Jürgens, Gwyneth C. Ingram, Dirk Inzé, Philip N. Benfey, Tom Beeckman

(2008) - Science

DOI
513. Atypical E2F activity restrains APC/CCCS52A2 function obligatory for endocycle onset.

Lammens T, Boudolf V, Kheibarshekan L, Zalmas LP, Gaamouche T, Maes S, Vanstraelen M, Kondorosi E, La Thangue NB, Govaerts W, Inzé D, De Veylder L

(2008) -

DOI
512. Seven in absentia proteins affect plant growth and nodulation in Medicago truncatula.

Den Herder G, De Keyser A, De Rycke R, Rombauts S, Van de Velde W, Clemente MR, Verplancke C, Mergaert P, Kondorosi E, Holsters M, Goormachtig S

(2008) -

DOI
511. Arabidopsis SOMATIC EMBRYOGENESIS RECEPTOR KINASE proteins serve brassinosteroid-dependent and -independent signaling pathways.

Albrecht C, Russinova E, Kemmerling B, Kwaaitaal M, de Vries SC

(2008) -

DOI
510. Morph-ratio variation, population size and female reproductive success in distylous Pulmonaria officinalis (Boraginaceae).

Brys R, Hans Jacquemyn, Tom Beeckman

(2008) - Journal of Evolutionary Biology

DOI
509. A Role for AtWRKY23 in Feeding Site Establishment of Plant-Parasitic Nematodes

Wim Grunewald, Mansour Karimi, Krzysztof Wieczorek, Elke Van de Cappelle, Elisabeth Wischnitzki, Florian Grundler, Dirk Inzé, Tom Beeckman, Godelieve Gheysen

(2008) - Plant Physiology

DOI
508. LC-MS metabolic profiling of Arabidopsis thaliana plant leaves and cell cultures: optimization of pre-LC-MS procedure parameters.

t'Kindt R, De Veylder L, Storme M, Deforce D, Van Bocxlaer J

(2008) -

DOI
507. The PRA1 gene family in Arabidopsis.

Alvim Kamei CL, Boruc J, Vandepoele K, Van den Daele H, Maes S, Russinova E, Inzé D, De Veylder L

(2008) -

DOI
506. Vesicle trafficking during somatic cytokinesis.

Van Damme D, Inzé D, Russinova E

(2008) -

DOI
505. The PRA1 gene family in Arabidopsis.

Alvim Kamei CL, Boruc J, Vandepoele K, Van den Daele H, Maes S, Russinova E, Inzé D, De Veylder L

(2008) -

DOI
504. The Molecular Cloning of Artemisinic Aldehyde Δ11(13) Reductase and Its Role in Glandular Trichome-dependent Biosynthesis of Artemisinin in Artemisia annua

Yansheng Zhang, Keat H. Teoh, Darwin W. Reed, Lies Maes, Alain Goossens, Douglas J.H. Olson, Andrew R.S. Ross, Patrick S. Covello

(2008) - Journal of Biological Chemistry

DOI
503. Vesicle trafficking during somatic cytokinesis.

Van Damme D, Inzé D, Russinova E

(2008) - Plant physiology

DOI
502. The auxin influx carrier LAX3 promotes lateral root emergence

Kamal Swarup, Eva Benková, Ranjan Swarup, Ilda Casimiro, Benjamin Péret, Yaodong Yang, Geraint Parry, Erik Nielsen, Ive De Smet, Steffen Vanneste, Mitch P. Levesque, David Carrier, Nicholas James, Vanessa Calvo, Karin Ljung, Eric Kramer, Rebecca Roberts, Neil Graham, Sylvestre Marillonnet, Kanu Patel, Jonathan D.G. Jones, Christopher G. Taylor, Daniel P. Schachtman, Sean May, Goran Sandberg, Philip Benfey, Jiri Friml, Ian Kerr, Tom Beeckman, Laurent Laplaze, Malcolm J. Bennett

(2008) - Nature Cell Biology

DOI
501. The DNA replication checkpoint aids survival of plants deficient in the novel replisome factor ETG1.

Takahashi N, Lammens T, Boudolf V, Maes S, Yoshizumi T, De Jaeger G, Witters E, Inzé D, De Veylder L

(2008) -

DOI
500. Unraveling the tapestry of networks involving reactive oxygen species in plants.

Van Breusegem F, Bailey-Serres J, Mittler R

(2008) -

DOI
499. Two microtubule-associated proteins of Arabidopsis MAP65s promote antiparallel microtubule bundling.

Gaillard J, Neumann E, Van Damme D, Stoppin-Mellet V, Ebel C, Barbier E, Geelen D, Vantard M

(2008) - Molecular biology of the cell

DOI
498. The Arabidopsis COP9 signalosome is essential for G2 phase progression and genomic stability.

Dohmann EM, Levesque MP, De Veylder L, Reichardt I, Jürgens G, Schmid M, Schwechheimer C

(2008) -

DOI
497. Natural variation in the degree of autonomous endosperm formation reveals independence and constraints of embryo growth during seed development in Arabidopsis thaliana.

Ungru A, Nowack MK, Reymond M, Shirzadi R, Kumar M, Biewers S, Grini PE, Schnittger A

(2008) -

DOI
496. Mitochondrial respiratory pathways modulate nitrate sensing and nitrogen-dependent regulation of plant architecture in Nicotiana sylvestris.

Pellny TK, Van Aken O, Dutilleul C, Wolff T, Groten K, Bor M, De Paepe R, Reyss A, Van Breusegem F, Noctor G, Foyer CH

(2008) -

DOI
495. Lignin engineering

R VANHOLME, K MORREEL, J RALPH, W BOERJAN

(2008) - Current Opinion in Plant Biology

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494. Pollen deposition rates and the functioning of distyly in the perennial Pulmonaria officinalis (Boraginaceae)

Rein Brys, Hans Jacquemyn, Martin Hermy, Tom Beeckman

(2008) - Plant Systematics and Evolution

DOI
493. Choose your partners: dimerization in eukaryotic transcription factors

Grigoris D. Amoutzias, David L. Robertson, Yves Van de Peer, Stephen G. Oliver

(2008) - Trends in Biochemical Sciences

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492. Structure of the genetic diversity in black poplar (Populus nigra L.) populations across European river systems: Consequences for conservation and restoration

M.J.M. Smulders, J.E. Cottrell, F. Lefèvre, J. van der Schoot, P. Arens, B. Vosman, H.E. Tabbener, F. Grassi, T. Fossati, S. Castiglione, V. Krystufek, S. Fluch, K. Burg, B. Vornam, A. Pohl, K. Gebhardt, N. Alba, D. Agúndez, C. Maestro, E. Notivol, R. Volosyanchuk, M. Pospíšková, S. Bordács, J. Bovenschen, B.C. van Dam, H.P. Koelewijn, D. Halfmaerten, B. Ivens, J. van Slycken, A. Vanden Broeck, V. Storme, W. Boerjan

(2008) - Forest Ecology and Management

DOI
491. Genome-wide identification of NBS resistance genes in Populus trichocarpa

Annegret Kohler, Cécile Rinaldi, Sébastien Duplessis, Marie Baucher, Danny Geelen, Frédéric Duchaussoy, Blake C. Meyers, Wout Boerjan, Francis Martin

(2008) - Plant Molecular Biology

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490. Hydrogen peroxide-induced gene expression across kingdoms: a comparative analysis.

Vandenbroucke K, Robbens S, Vandepoele K, Inzé D, Van de Peer Y, Van Breusegem F

(2008) -

DOI
489. A Temperature-sensitive mutation in the Arabidopsis thaliana phosphomannomutase gene disrupts protein glycosylation and triggers cell death.

Hoeberichts FA, Vaeck E, Kiddle G, Coppens E, van de Cotte B, Adamantidis A, Ormenese S, Foyer CH, Zabeau M, Inzé D, Périlleux C, Van Breusegem F, Vuylsteke M

(2008) -

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488. Fluorescence fluctuation analysis of Arabidopsis thaliana somatic embryogenesis receptor-like kinase and brassinosteroid insensitive 1 receptor oligomerization.

Hink MA, Shah K, Russinova E, de Vries SC, Visser AJ

(2008) -

DOI
487. Novel Insights into Evolution of Protistan Polyketide Synthases through Phylogenomic Analysis

Uwe John, Bánk Beszteri, Evelyne Derelle, Yves Van de Peer, Betsy Read, Hervé Moreau, Allan Cembella

(2008) - Protist

DOI
486. The FTO Gene, Implicated in Human Obesity, Is Found Only in Vertebrates and Marine Algae

Steven Robbens, Pierre Rouzé, J. Mark Cock, Jürg Spring, Alexandra Z. Worden, Yves Van de Peer

(2008) - Journal of Molecular Evolution

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485. Hydrogen Peroxide-Induced Gene Expression across Kingdoms: A Comparative Analysis

K. Vandenbroucke, S. Robbens, K. Vandepoele, D. Inze, Y. Van de Peer, F. Van Breusegem

(2008) - Molecular Biology and Evolution

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484. Identification of the structure and origin of a thioacidolysis marker compound for ferulic acid incorporation into angiosperm lignins (and an indicator for cinnamoyl CoA reductase deficiency)

John Ralph, Hoon Kim, Fachuang Lu, John H. Grabber, Jean‐Charles Leplé, Jimmy Berrio‐Sierra, Mohammad Mir Derikvand, Lise Jouanin, Wout Boerjan, Catherine Lapierre

(2008) - The Plant Journal

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483. Mapping methyl jasmonate-mediated transcriptional reprogramming of metabolism and cell cycle progression in cultured Arabidopsis cells

Laurens Pauwels, Kris Morreel, Emilie De Witte, Freya Lammertyn, Marc Van Montagu, Wout Boerjan, Dirk Inzé, Alain Goossens

(2008) - Proceedings of the National Academy of Sciences

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482. Mapping methyl jasmonate-mediated transcriptional reprogramming of metabolism and cell cycle progression in cultured Arabidopsis cells

Laurens Pauwels, Kris Morreel, Emilie De Witte, Freya Lammertyn, Marc Van Montagu, Wout Boerjan, Dirk Inzé, Alain Goossens

(2008) - Proceedings of the National Academy of Sciences

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481. Diarch Symmetry of the Vascular Bundle in Arabidopsis Root Encompasses the Pericycle and Is Reflected in Distich Lateral Root Initiation

Boris Parizot, Laurent Laplaze, Lilian Ricaud, Elodie Boucheron-Dubuisson, Vincent Bayle, Martin Bonke, Ive De Smet, Scott R. Poethig, Yka Helariutta, Jim Haseloff, Dominique Chriqui, Tom Beeckman, Laurent Nussaume

(2008) - Plant Physiology

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480. Cytokinins Act Directly on Lateral Root Founder Cells to Inhibit Root Initiation

Laurent Laplaze, Eva Benkova, Ilda Casimiro, Lies Maes, Steffen Vanneste, Ranjan Swarup, Dolf Weijers, Vanessa Calvo, Boris Parizot, Maria Begoña Herrera-Rodriguez, Remko Offringa, Neil Graham, Patrick Doumas, Jiri Friml, Didier Bogusz, Tom Beeckman, Malcolm Bennett

(2008) - The Plant Cell

DOI