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Publications

Peer-reviewed articles acknowledging support by the AGRON-OMICS grant

 

2012

  • Grønlund JT, Eyres A, Kumar S, Buchanan-Wollaston V, Gifford ML.(2012) Cell specific analysis of Arabidopsis leaves using fluorescence activated cell sorting. J Vis Exp. Oct 4;(68) PMID: 23070217

  • Wolf S, Mravec J, Greiner S, Mouille G, Höfte H. (2012) Plant cell wall homeostasis is mediated by brassinosteroid feedback signaling. Curr Biol. Sep 25;22(18):1732-7. PMID: 22885061

  • Pantin F, Simonneau T, Muller B. (2012) Coming of leaf age: control of growth by hydraulics and metabolics during leaf ontogeny. New Phytol. Aug 24. PMID: 22924516

  • Danisman S, van der Wal F, Dhondt S, Waites R, de Folter S, Bimbo A, van Dijk AJ, Muino JM, Cutri L, Dornelas MC, Angenent GC, Immink RG. (2012) Arabidopsis Class I and Class II TCP Transcription Factors Regulate Jasmonic Acid Metabolism and Leaf Development Antagonistically. Plant Physiol. Aug;159(4):1511-23. PMID: 22718775

  • Baerenfaller K, Massonnet C, Walsh S, Baginsky S, Bühlmann P, Hennig L, Hirsch-Hoffmann M, Howell KA, Kahlau S, Radziejwoski A, Russenberger D, Rutishauser D, Small I, Stekhoven D, Sulpice R, Svozil J, Wuyts N, Stitt M, Hilson P, Granier C, Gruissem W. (2012) Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit. Mol Syst Biol. Aug 28;8:606. PMID: 22929616

  • Eloy NB, Gonzalez N, Van Leene J, Maleux K, Vanhaeren H, De Milde L, Dhondt S, Vercruysse L, Witters E, Mercier R, Cromer L, Beemster GT, Remaut H, Van Montagu MC, De Jaeger G, Ferreira PC, Inzé D. (2012) SAMBA, a plant-specific anaphase-promoting complex/cyclosome regulator is involved in early development and A-type cyclin stabilization. Proc Natl Acad Sci U S A. Aug 21;109(34):13853-8. PMID: 22869741

  • Müller M, Patrignani A, Rehrauer H, Gruissem W, Hennig L. (2012) Evaluation of alternative RNA labeling protocols for transcript profiling with Arabidopsis AGRONOMICS1 tiling arrays. Plant Methods. Jun 13;8(1):18. PMID: 22694760

  • Peaucelle A, Braybrook S, Höfte H.(2012) Cell wall mechanics and growth control in plants: the role of pectins revisited.Front Plant Sci. 3:121. PMID: 22685449

  • Hirsch-Hoffmann M, Gruissem W, Baerenfaller K. (2012) pep2pro: the high-throughput proteomics data processing, analysis, and visualization tool. Front Plant Sci. 2012;3:123. PMID: 22701464

  • Robaglia C, Thomas M, Meyer C. (2012) Sensing nutrient and energy status by SnRK1 and TOR kinases. Curr Opin Plant Biol. Jun;15(3):301-7. PMID: 22305521

  • Claeys H, Skirycz A, Maleux K, Inzé D. (2012) DELLA Signaling Mediates Stress-Induced Cell Differentiation in Arabidopsis Leaves through Modulation of Anaphase-Promoting Complex/Cyclosome Activity. Plant Physiol. Jun;159(2):739-47.PMID: 22535421

  • Rubio-Díaz S, Pérez-Pérez JM, González-Bayón R, Muñoz-Viana R, Borrega N, Mouille G, Hernández-Romero D, Robles P, Höfte H, Ponce MR, Micol JL. (2012) Cell Expansion-Mediated Organ Growth Is Affected by Mutations in Three EXIGUA Genes. PLoS One. 2012;7(5):e36500. PMID: 22586475

  • Meyer RC, Witucka-Wall H, Becher M, Blacha A, Boudichevskaia A, Dörmann P, Fiehn O, Friedel S, von Korff M, Lisec J, Melzer M, Repsilber D, Schmidt R, Scholz M, Selbig J, Willmitzer L, Altmann T.  (2012) Heterosis manifestation during early Arabidopsis seedling development is characterized by intermediate gene expression and enhanced metabolic activity in the hybrids. Plant J. 2012 Apr 9. PMID: 22487254

  • De Bodt S, Hollunder J, Nelissen H, Meulemeester N, Inzé D.(2012) CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations.New Phytol. May 31. doi: 10.1111/j.1469-8137.2012.04184.x. PMID: 22651224

  • Salomé PA, Bomblies K, Fitz J, Laitinen RA, Warthmann N, Yant L, Weigel D. (2012) The recombination landscape in Arabidopsis thaliana F2 populations. Heredity (Edinb). Apr;108(4):447-55. PMID: 22072068

  • Tóth R, Gerding-Reimers C, Deeks MJ, Menninger S, Gallegos RM, Tonaco IA, Hübel K, Hussey PJ, Waldmann H, Coupland G. (2012) Prieurianin/ endosidin1 is an actin stabilizing small molecule identified from a chemical genetic screen for circadian clock effectors in Arabidopsis thaliana. Plant J. Mar 12. PMID: 22409627

  • Wuyts N, Massonnet C, Dauzat M, Granier C. (2012) Structural assessment of the impact of environmental constraints on Arabidopsis thaliana leaf growth: a 3D approach. Plant Cell Environ.  Apr 3. PMID: 22471732

  • Whitford R, Fernandez A, Tejos R, Pérez AC, Kleine-Vehn J, Vanneste S, Drozdzecki A, Leitner J, Abas L, Aerts M, Hoogewijs K, Baster P, De Groodt R, Lin YC, Storme V, Van de Peer Y, Beeckman T, Madder A, Devreese B, Luschnig C, Friml J, Hilson P. (2012) GOLVEN Secretory Peptides Regulate Auxin Carrier Turnover during Plant Gravitropic Responses. Dev Cell. Mar 13;22(3):678-85. PMID: 22421050

  • Moreau M, Azzopardi M, Clement G, Dobrenel T, Marchive C, Renne C, Martin-Magniette L, Taconnat L, Renou JP, Robaglia C, Meyer C. (2012) Mutations in the Arabidopsis homolog of LST8/GβL, a partner of the target of Rapamycin kinase, impair plant growth, flowering, and metabolic adaptation to long days. Plant Cell. Feb;24(2):463-81. PMID: 22307851

  • Andriankaja M, Dhondt S, De Bodt S, Vanhaeren H, Coppens F, De Milde L, Mühlenbock P, Skirycz A, Gonzalez N, Beemster GT, Inzé D. (2012) Exit from Proliferation during Leaf Development in Arabidopsis thaliana: A Not-So-Gradual Process. Dev Cell. Jan 4 PMID: 2222731

2011

  • Todesco M, Balasubramanian S, Cao J, Ott F, Sureshkumar S, Schneeberger K, Meyer RC, Altmann T, Weigel D. (2011) Natural Variation in Biogenesis Efficiency of Individual Arabidopsis thaliana MicroRNAs. Curr Biol. Dec 28. PMID: 22206705

  • Massonnet C, Tisné S, Radziejwoski A, Vile D, De Veylder L, Dauzat M, Granier C. (2011) New insights into the control of endoreduplication: endoreduplication could be driven by organ growth in Arabidopsis leaves. Plant Physiol. Dec;157(4):2044-55. PMID: 22010109

  • Bischoff V, Desprez T, Mouille G, Vernhettes S, Gonneau M, and Hofte H. (2011) Phytochrome Regulation of Cellulose Synthesis in Arabidopsis. Curr Biol Nov 8;21(21):1822-7. PMID : 22036185

  • Peaucelle A, Braybrook SA, Le Guillou L, Bron E, Kuhlemeier C, and Hofte H. (2011) Pectin-Induced Changes in Cell Wall Mechanics Underlie Organ Initiation in Arabidopsis. Curr Biol Oct 25;21(20):1720-6 PMID : 21982593

  • Vile D, Pervent M, Belluau M, Vasseur F, Bresson J, Muller B, Granier C, Simonneau T. (2011) Arabidopsis growth under prolonged high temperature and water deficit: independent or interactive effects? Plant Cell Environ. Oct 11. doi: 10.1111/j.1365-3040.2011.02445.x. PMID: 21988660

  • Dhondt S, Van Haerenborgh D, Van Cauwenbergh C, Merks RM, Philips W, Beemster GT, Inzé D. (2011) Quantitative analysis of venation patterns of Arabidopsis leaves by supervised image analysis. Plant J. Sep 29. doi:10.1111/j.1365-313X.2011.04803.x. PMID: 21955023

  • Pérez-Pérez JM, Rubio-Díaz S, Dhondt S, Hernández-Romero D, Sánchez-Soriano J, Beemster GT, Ponce MR, Micol JL. (2011) Whole organ, venation and epidermal cell morphological variations are correlated in the leaves of Arabidopsis mutants. Plant Cell Environ.  Plant Cell Environ. Dec;34(12):2200-11. PMID: 21883289

  • Arabidopsis Interactome Mapping Consortium. (2011) Science. Jul 29;333(6042):601-7. Evidence for network evolution in an Arabidopsis interactome map. PMID: 21798944

  • Mukhtar MS, Carvunis AR, Dreze M, Epple P, Steinbrenner J, Moore J, Tasan M, Galli M, Hao T, Nishimura MT, Pevzner SJ, Donovan SE, Ghamsari L, Santhanam B, Romero V, Poulin MM, Gebreab F, Gutierrez BJ, Tam S, Monachello D, Boxem M, Harbort CJ, McDonald N, Gai L, Chen H, He Y; European Union Effectoromics Consortium, Vandenhaute J, Roth FP, Hill DE, Ecker JR, Vidal M, Beynon J, Braun P, Dangl JL. (2011) Independently evolved virulence effectors converge onto hubs in a plant immune system network. Science. Jul 29;333(6042):596-601. PMID: 21798943

  • Smith LM, Bomblies K, Weigel D. (2011) Complex evolutionary events at a tandem cluster of Arabidopsis thaliana genes resulting in a single-locus genetic incompatibility. PLoS Genet. 2011 Jul;7(7):e1002164. PMID: 21779175

  • Crowell EF, Timpano H, Desprez T, Franssen-Verheijen T, Emons AM, Hofte H, and Vernhettes S. (2011) Differential regulation of cellulose orientation at the inner and outer face of epidermal cells in the Arabidopsis hypocotyl. Plant Cell Jul;23(7):2592-605. PMID : 21742992

  • Salomé PA, Bomblies K, Laitinen RA, Yant L, Mott R, Weigel D. (2011) Genetic architecture of flowering-time variation in Arabidopsis thaliana. Genetics. 2011 Jun;188(2):421-33. PMID: 21406681

  • Pantin F, Simonneau T, Rolland G, Dauzat M, Muller B. (2011) Control of leaf expansion: a developmental switch from metabolics to hydraulics. Plant Physiol. 2011 Jun;156(2):803-15. PMID: 21474437

  • Vain P, Thole V, Worland B, Opanowicz M, Bush MS, Doonan JH. (2011) A T-DNA mutation in the RNA helicase eIF4A confers a dose-dependent dwarfing phenotype in Brachypodium distachyon. Plant J. Jun;66(6):929-40. doi: 10.1111/j.1365-313X.2011.04555.x. Epub 2011 Apr 4. PMID: 21457366

  • Schneeberger K, Weigel D. (2011) Fast-forward genetics enabled by new sequencing technologies. Trends Plant Sci. May;16(5):282-8. Epub 2011 Mar 24. PMID: 21439889

  • Skirycz A, Claeys H, De Bodt S, Oikawa A, Shinoda S, Andriankaja M, Maleux K, Eloy NB, Coppens F, Yoo SD, Saito K, Inzé D. (2011) Pause-and-stop: the effects of osmotic stress on cell proliferation during early leaf development in Arabidopsis and a role for ethylene signaling in cell cycle arrest. Plant Cell. May;23(5):1876-88. Epub 2011 May 10. PMID: 21558544

  • Fabre J, Dauzat M, Nègre V, Wuyts N, Tireau A, Gennari E, Neveu P, Tisné S, Massonnet C, Hummel I, Granier C. (2011) PHENOPSIS DB: an information system for Arabidopsis thaliana phenotypic data in an environmental context. BMC Plant Biol. 2011 May 9;11:77 PMID: 21554668

  • Gou JY, Felippes FF, Liu CJ, Weigel D, Wang JW (2011) Plant Cell. Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor. Apr;23(4):1512-22. Epub 2011 Apr 12. PMID: 21487097

  • Candela H, Pérez-Pérez JM, Micol JL. ( 2011) Uncovering the post-embryonic functions of gametophytic- and embryonic-lethal genes. Trends Plant Sci. Jun;16(6):336-45. Epub 2011 Mar 17. PMID: 21420345

  • Hruz T, Wyss M, Docquier M, Pfaffl MW, Masanetz S, Borghi L, Verbrugghe P, Kalaydjieva L, Bleuler S, Laule O, Descombes P, Gruissem W, Zimmermann P. (2011) RefGenes: identification of reliable and condition specific reference genes for RT-qPCR data normalization. BMC Genomics. Mar 21;12(1):156. PMID: 21418615

  • Skirycz A, Vandenbroucke K, Clauw P, Maleux K, De Meyer B, Dhondt S, Pucci A, Gonzalez N, Hoeberichts F, Tognetti VB, Galbiati M, Tonelli C, Van Breusegem F, Vuylsteke M, Inzé D. (2011) Survival and growth of Arabidopsis plants given limited water are not equal. Nat Biotechnol. Mar;29(3):212-4. PMID: 21390020

  • Vercruyssen L, Gonzalez N, Werner T, Schmülling T, Inzé D. (2011) Combining Enhanced Root and Shoot Growth Reveals Cross Talk between Pathways That Control Plant Organ Size in Arabidopsis.Plant Physiol. Mar;155(3):1339-52. PMID: 21205622

  • Baerenfaller K, Hirsch-Hoffmann M, Svozil J, Hull R, Russenberger D, Bischof S, Lu Q, Gruissem W, Baginsky (2011)  pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana.S. Integr Biol (Camb). Mar 8;3(3):225-37. PMID: 21264403

  • Mollá-Morales A, Sarmiento-Mañús R, Robles P, Quesada V, Pérez-Pérez JM, González-Bayón R, Hannah MA, Willmitzer L, Ponce MR, Micol JL. (2011) Analysis of ven3 and ven6 reticulate mutants reveals the importance of arginine biosynthesis in Arabidopsis leaf development. Plant J. Feb;65(3):335-45. PMID: 21265888

  • Horiguchi G, Mollá-Morales A, Pérez-Pérez JM, Kojima K, Robles P, Ponce MR, Micol JL, Tsukaya H. (2011) Differential contributions of ribosomal protein genes to Arabidopsis thaliana leaf development. Plant J. Mar;65(5):724-36. PMID: 21251100

2010

  • Joshi HJ, Hirsch-Hoffmann M, Baerenfaller K, Gruissem W, Baginsky S, Schmidt R, Schulze WX, Sun Q, van Wijk KJ, Egelhofer V, Wienkoop S, Weckwerth W, Bruley C, Rolland N, Toyoda T, Nakagami H, Jones AM, Briggs SP, Castleden I, Tanz SK, Millar AH, Heazlewood JL. (2010) MASCP Gator: An aggregation portal for the visualization of Arabidopsis proteomics data.  Plant Physiol. 2010 Nov 22. PMID: 21075962

  • Bechtold U, Lawson T, Mejia-Carranza J, Meyer RC, Brown IR, Altmann T, Ton J, Mullineaux PM. (2010) Constitutive salicylic acid defences do not compromise seed yield, drought tolerance and water productivity in the Arabidopsis accession C24. Plant Cell Environ. 2010 Nov;33(11):1959-73. PMID: 20573051

  • Cookson SJ, Turc O, Massonnet C, Granier C. (2010) Phenotyping the development of leaf area in Arabidopsis thaliana.  Methods Mol Biol. 2010;655:89-103. PMID: 20734256

  • Chan J, Crowell E, Eder M, Calder G, Bunnewell S, Findlay K, Vernhettes S, Hofte H, Lloyd C. (2010) The rotation of cellulose synthase trajectories is microtubule dependent and influences the texture of epidermal cell walls in Arabidopsis hypocotyls. J Cell Sci 2010 Oct 15;123(Pt 20):3490-5. PMID : 20876662

  • Pérez-Pérez JM, Candela H, Robles P, López-Torrejón G, del Pozo JC, Micol JL. (2010) A role for AUXIN RESISTANT3 in the coordination of leaf growth. Plant Cell Physiol. 2010 Oct;51(10):1661-73. PMID: 20739302

  • Pelletier S, Van Orden J, Wolf S, Vissenberg K, Delacourt J, Assoumou Ndong Y, Pelloux J, Bischoff V, Urbain A, Mouille G, Lemonnier G, Renou JP, Hofte H. (2010)  A role for pectin de-methylesterification in a developmentally-regulated growth acceleration in dark-grown arabidopsis hypocotyls.  New Phytologist 2010 Sep 3. PMID: 20819179

  • Dhondt S, Coppens F, De Winter F, Swarup K, Merks RM, Inze D, Bennett MJ, Beemster GT.  (2010) SHORT-ROOT and SCARECROW regulate leaf growth in Arabidopsis by stimulating S-phase progression of the cell cycle. Plant Physiol. 2010 Aug 25. PMID: 20739610

  • Sulpice R, Trenkamp S, Steinfath M, Usadel B, Gibon Y, Witucka-Wall H, Pyl ET, Tschoep H, Steinhauser MC, Guenther M, Hoehne M, Rohwer JM, Altmann T, Fernie AR, Stitt M. Network analysis of enzyme activities and metabolite levels and their relationship to biomass in a large panel of Arabidopsis accessions.  Plant Cell. 2010 Aug;22(8):2872-93. Epub 2010 Aug 10. PMID: 20699391

  • Dhondt S, Vanhaeren H, Van Loo D, Cnudde V, Inzé D.  Plant structure visualization by high-resolution X-ray computed tomography. Trends Plant Sci. 2010 Aug;15(8):419-22. PMID: 20542721

  • Van Leene J, Hollunder J, Eeckhout D, Persiau G, Van De Slijke E, Stals H, Van Isterdael G, Verkest A, Neirynck S, Buffel Y, De Bodt S, Maere S, Laukens K, Pharazyn A, Ferreira PC, Eloy N, Renne C, Meyer C, Faure JD, Steinbrenner J, Beynon J, Larkin JC, Van de Peer Y, Hilson P, Kuiper M, De Veylder L, Van Onckelen H, Inzé D, Witters E, De Jaeger G. Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana.  Mol Syst Biol. 2010 Aug 10;6:397. PMID: 20706207

  • Grossmann J, Roschitzki B, Panse C, Fortes C, Barkow-Oesterreicher S, Rutishauser D, Schlapbach R. (2010) Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods.J Proteomics. Aug 5;73(9):1740-6. PMID: 20576481

  • de Longevialle AF, Small ID, Lurin C.  (2010) Nuclearly encoded splicing factors implicated in RNA splicing in higher plant organelles.  Mol Plant. Jul;3(4):691-705. Epub 2010 Jul 5. PMID: 20603383

  • de Montaigu A, Tóth R, Coupland G.(2010) Plant development goes like clockwork. Trends Genet. 2010 Jul;26(7):296-306. PMID: 20483501

  • Gonzalez N, De Bodt S, Sulpice R, Jikumaru Y, Chae E, Dhondt S, Van Daele T, De Milde L, Weigel D, Kamiya Y, Stitt M, Beemster GT, Inzé D. Increased leaf size: different means to an end.  Plant Physiol. 2010 Jul;153(3):1261-79. PMID: 20460583

  • Todesco M, Balasubramanian S, Hu TT, Traw MB, Horton M, Epple P, Kuhns C, Sureshkumar S, Schwartz C, Lanz C, Laitinen RA, Huang Y, Chory J, Lipka V, Borevitz JO, Dangl JL, Bergelson J, Nordborg M, Weigel D. Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana.Nature. 2010 Jun 3;465(7298):632-6. PMID: 20520716

  • Vanhaeren H, Gonzalez N, Inzé D. (2010) Hide and seek: Uncloaking the vegetative shoot apex of Arabidopsis thaliana. Plant J. 2010 May 22. PMID: 20497383

  • Wuyts N, Palauqui JC, Conejero G, Verdeil JL, Granier C, Massonnet C. High-contrast three-dimensional imaging of the Arabidopsis leaf enables the analysis of cell dimensions in the epidermis and mesophyll.  Plant Methods 2010, 6:17doi:10.1186/1746-4811-6-17 PMID: 20598116

  • Bomblies K, Yant L, Laitinen RA, Kim ST, Hollister JD, Warthmann N, Fitz J, Weigel D. Local-scale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana.  PLoS Genet. 2010 Mar 26;6(3):e1000890. PMID: 20361058

  • De Bodt S, Carvajal D, Hollunder J, Van den Cruyce J, Movahedi S, Inzé D. CORNET: a user-friendly tool for data mining and integration. Plant Physiol. 2010 Mar;152(3):1167-79. PMID: 20053712

  • Robles P, Fleury D, Candela H, Cnops G, Alonso-Peral MM, Anami S, Falcone A, Caldana C, Willmitzer L, Ponce MR, Van Lijsebettens M, Micol JL. (2010) The RON1/FRY1/SAL1 gene is required for leaf morphogenesis and venation patterning in Arabidopsis. Plant Physiol. 2010 Mar;152(3):1357-72. PMID: 20044451

  • Baginsky S, Hennig L, Zimmermann P, Gruissem W. Gene expression analysis, proteomics, and network discovery.  Plant Physiol. 2010 Feb;152(2):402-10.  PMID: 20018595

  • Rehrauer H, Aquino C, Gruissem W, Henz SR, Hilson P, Laubinger S, Naouar N, Patrignani A, Rombauts S, Shu H, Van de Peer Y, Vuylsteke M, Weigel D, Zeller G, Hennig L. AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling.  Plant Physiol. 2010 Feb;152(2):487-99. PMID: 20032078

  • Massonnet C, Vile D, Fabre J, Hannah MA, Caldana C, Lisec J, Beemster GT, Meyer RC, Messerli G, Gronlund JT, Perkovic J, Wigmore E, May S, Bevan MW, Meyer C, Rubio-Díaz S, Weigel D, Micol JL, Buchanan-Wollaston V, Fiorani F, Walsh S, Rinn B, Gruissem W, Hilson P, Hennig L, Willmitzer L, Granier C. Probing the reproducibility of leaf growth and molecular phenotypes: a comparison of three Arabidopsis accessions cultivated in ten laboratories.  Plant Physiol. 2010 Apr;152(4):2142-57. PMID : 20200072

  • Higgins JA, Bailey PC, Laurie DA (2010) Comparative Genomics of Flowering Time Pathways Using Brachypodium distachyon as a Model for the Temperate Grasses. PLoS ONE 5(4): e10065. PMID : 20419097

  • Vlad D, Rappaport F, Simon M, Loudet O (2010) Gene Transposition Causing Natural Variation for Growth in Arabidopsis thaliana. PLoS Genet 6(5): e1000945.

  • Stitt, M, Usadel, B. and Lunn, J. (2010) Arabidopsis and primary photosynthetic metabolism - more than the icing on the cake- Plant J. Arabidopsis special issue. Plant J. Mar;61(6):1067-91 PMID: 20409279

  • Dreze M., Monachello D., Lurin C., Cusick M.E., Hill D.E., Vidal M. and Braun P.  High quality binary interactome mapping. 2010. Meth. Enzymol. 470: 281- 315. DOI: 10.1016/S0076-6879(10)70012-4

  • Pérez-Pérez JM, Esteve-Bruna D, Micol JL. QTL analysis of leaf architecture. J Plant Res. 2010 Jan;123(1):15-23. Epub 2009 Nov 3. PMID: 19885640

  • Meyer RC, Kusterer B, Lisec J, Steinfath M, Becher M, Scharr H, Melchinger AE, Selbig J, Schurr U, Willmitzer L, Altmann T. (2010) QTL analysis of early stage heterosis for biomass in Arabidopsis. Theor Appl Genet. Jan;120(2):227-37. PMID: 19504257

  • Steinfath M, Gärtner T, Lisec J, Meyer RC, Altmann T, Willmitzer L, Selbig J. (2010) Prediction of hybrid biomass in Arabidopsis thaliana by selected parental SNP and metabolic markers. Theor Appl Genet. Jan;120(2):239-47. PMID: 19911163

2009

  • Naouar N, Vandepole K, Lammens T, Casneuf T, Zeller G, van Hummelen P, Weigel D, Ratsch G, Inze' D, Kuiper M, De Veylder L, Vuylsteke M (2009). Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. Plant J. Jan;57(1):184-94. PMID: 18764924

  • Pignocchi C, Minns GE, Nesi N, Koumproglou R, Kitsios G, Benning C, Lloyd CW, Doonan JH, Hills MJ. (2009). ENDOSPERM DEFECTIVE1 Is a Novel Microtubule-Associated Protein Essential for Seed Development in Arabidopsis. Plant Cell. Jan;21(1):90-105. PMID:19151224

  • Hannemann J, Poorter H, Usadel B, Bläsing OE, Finck A, Tardieu F, Atkin OK, Pons T, Stitt M, Gibon Y. (2009). Xeml Lab: a tool that supports the design of experiments at a graphical interface and generates computer-readable meta-data files, which capture information about genotypes, growth conditions, environmental perturbations and sampling strateg. Plant Cell Environ. Sep;32(9):1185-200. PMID:19236607

  • Micol, J.L. (2009). Leaf development: Time to turn over a new leaf? Current Opinion in Plant Biology Feb;12(1):9-16. PMID:19109050

  • Sureshkumar, S., Todesco, M., Schneeberger, K., Harilal, R., Balasubramanian, S., and Weigel, D. (2009). A genetic defect caused by a triplet repeat expansion in Arabidopsis thaliana. Science. Feb 20;323 (5917):1060-3. PMID: 19150812

  • Lisec J, Steinfath M, Meyer RC, Selbig J, Melchinger AE, Willmitzer L, Altmann T. (2009) Identification of heterotic metabolite QTL in Arabidopsis thaliana RIL and IL populations. Plant J. Sep;59(5):777-88. Epub 2009 May 4. PMID: 19453458

  • Pérez-Pérez JM, Candela H, Micol JL. (2009) Understanding synergy in genetic interactions. Trends Genet. Aug;25(8):368-76. Epub 2009 Aug 6. PMID: 19665253

  • Granier C, Tardieu F. (2009). Multi-scale phenotyping of leaf expansion in response to environmental changes: the whole is more than the sum of parts.Plant Cell Environ. Sep;32(9):1175-84. PMID: 19210637

  • Bleys A, Karimi M, Hilson P. (2009) Methods Mol Biol. Clone-based functional genomics. 553:141-77. PMID: 19588105

  • Reiland S, Messerli G, Baerenfaller K, Gerrits B, Endler A, Grossmann J, Gruissem W, Baginsky S. (2009). Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks. Plant Physiol. Jun;150(2):889-903. PMID: 19376835

  • Gonzalez N, Beemster GT, Inzé D. (2009). David and Goliath: what can the tiny weed Arabidopsis teach us to improve biomass production in crops? Curr Opin Plant Biol. Apr;12(2):157-64. PMID: 19119056

  • Exner V, Aichinger E, Shu H, Wildhaber T, Alfarano P, Caflisch A, Gruissem W, Köhler C, Hennig L. (2009) The chromodomain of LIKE HETEROCHROMATIN PROTEIN 1 is essential for H3K27me3 binding and function during Arabidopsis development. PLoS One. 2009;4(4):e5335. PMID: 19399177

  • Crowell, E.F, Bischoff, V, Desprez, T, Rolland, A, Stierhof, Y-D, Schumacher, K, Gonneau, M, Höfte, H, and Vernhettes, S. (2009). Pausing of Golgi bodies on Microtubules Regulates Secretion of Cellulose Synthase Complexes in Arabidopsis. Plant Cell. Apr;21(4):1141-54. PMID: 19376932

  • Wargent JJ, Gegas VC, Jenkins GI, Doonan JH, Paul ND. (2009) UVR8 in Arabidopsis thaliana regulates multiple aspects of cellular differentiation during leaf development in response to ultraviolet B radiation. New Phytol. 2009;183(2):315-26. PMID: 19402876

  • Sulpice R, Pyl ET, Ishihara H, Trenkamp S, Steinfath M, Witucka-Wall H, Gibon Y, Usadel B, Poree F, Conceição Piques M, Von Korff M, Steinhauser MC, Keurentjes JJB, Guenther M, Hoehne M, Selbig J, Fernie AR, Altmann T, and Stitt M. (2009). Starch as a major integrator in the regulation of plant growth. PNAS. Jun 23;106(25):10348-53. PMID:19506259

  • Schneeberger K, Ossowski S, Lanz C, Juul T, Petersen AH, Nielsen KL, Jørgensen JE, Weigel D, Andersen SU. Nat Methods. (2009) SHOREmap: simultaneous mapping and mutation identification by deep sequencing. Aug;6(8):550-1. PMID: 19644454

  • Bush, M., Hutchins, A., Jones, A., Naldrett, M., Jarmolowski, A., Lloyd, C., and Doonan, J. (2009). Selective recruitment of proteins  to 5' CAP complexes during the growth cycle in Arabidopsis. Plant J Aug;59(3):400-12. PMID: 19453450

  • Piques M, Schulze W, Hoehne M, Usadel B, Gibon Y, Rohwer J, and Stitt M. (2009) Ribosome and Transcript Copy Numbers, Polysome Occupancy and Enzyme Dynamics in Arabidopsis. Molecular Systems Biology 2009;5:314. PMID:19888209

  • Horiguchi G, Gonzalez N, Beemster GT, Inzé D, Tsukaya H. (2009) Impact of segmental chromosomal duplications on leaf size in the grandifolia-D mutants of Arabidopsis thaliana. Plant J. 2009 Oct;60(1):122-33. Epub 2009 Jun 5. PMID: 19508432

  • Rehrauer H, Aquino C, Gruissem W, Henz S, Hilson P, Laubinger S, Naouar N, Patrignani A, Rombautsn S, Shu H, Van de Peer Y, Vuylsteke M, Weigel D, Zeller G, Hennig L. (2009) AGRONOMICS1 - A new resource for Arabidopsis transcriptome profiling. Plant Physiology. Dec 23. [Epub ahead of print] PMID: 20032078

  • Cuadros-Inostroza A, Caldana C, Redestig H, Kusano M, Lisec J, Peña-Cortés H, Willmitzer L, Hannah MA. (2009) TargetSearch--a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data. BMC Bioinformatics. 2009 Dec 16;10:428. PMID: 20015393

2008

  • Peaucelle A, Louvet R, Johansen JN, Höfte H, Laufs P, Pelloux J, Mouille G.Arabidopsis phyllotaxis is controlled by the methyl-esterification status of cell-wall pectins. Curr Biol. 2008 Dec 23;18(24):1943-8. PMID: 19097903

  • Perez-Perez JM, Candela H, Robles P, Quesada V, Ponce MR, Micol JL. Lessons from a search for leaf mutants in Arabidopsis thaliana. Int J Dev Biol. Dec 23;18(24):1943-8. PMID: 19247929

  • Bach L, Michaelson LV, Haslam R, Bellec Y, Gissot L, Marion J, Da Costa M, Boutin JP, Miquel M, Tellier F, Domergue F, Markham JE, Beaudoin F, Napier JA, Faure JD (2008) The very-long-chain hydroxy fatty acyl-CoA dehydratase PASTICCINO2 is essential and limiting for plant development. Proc Natl Acad Sci U S A. Sep 23;105(38):14727-31. PMID: 18799749

  • Van Leene J, Witters E, Inzé D, De Jaeger G. (2008) Boosting tandem affinity purification of plant protein complexes. Trends Plant Sci. Oct;13(10):517-20. PMID: 18771946

  • Hématy K, Höfte H. (2008) Novel receptor kinases involved in growth regulation. Curr Opin Plant Biol. 2008 Jun;11(3):321-8. PMID:18395489

  • Tisne S, Reymond M, Vile D, Fabre J, Dauzat M, Koornneef M, Granier C (2008) Combined genetic and modelling approaches reveal that epidermal cell area and number in leaves are controlled by leaf and plant developmental processes in A. thaliana Plant Physiol. Oct;148(2):1117-27. PMID: 18701672

  • Marion J, Bach L, Bellec Y, Meyer C, Gissot L, Faure JD (2008) Systematic analysis of protein subcellular localization and interaction using high-throughput transient transformation of Arabidopsis seedlings. Plant J. Oct;56(1):169-79. PMID: 18643979

  • Laubinger S, Zeller G, Henz SR, Sachsenberg T, Widmer CK, Naouar N, Vuylsteke M, Scholkopf B, Ratsch G, Weigel D (2008) At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Genome Biology, 9(7):R112. PMID: 18613972

  • Tsesmetzis N, Couchman M, Higgins J, Smith A, Doonan JH, Seifert GJ, Schmidt EE, Vastrik I, Birney E, Guanming Wu, D'Eustachio P, Stein LD, Morris RJ, Bevan MW, Walsh SV (2008) Arabidopsis Reactome: A Foundation Knowledgebase for Plant Systems Biology. Plant Cell Jun;20(6):1426-36. PMID: 18591350

  • Laubinger S, Sachsenberg T, Zeller G, Busch W, Lohmann JU, Ratsch G, Weigel D (2008) Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana. Jun 24;105(25):8795-800. PMID: 18550839

  • Jia-Wei Wang, Schwab R, Czech B, Mica E, Weigel D (2008) Dual Effects of miR156-Targeted SPL Genes and CYP78A5/KLUH on Plastochron Length and Organ Size in Arabidopsis thaliana. Plant Cell. May;  20(5):1231-43. PMID: 18492871

  • Yunhai Li, Leiying Zheng, Fiona Corke, Caroline Smith, and Michael W. Bevan (2008) Control of final seed and organ size by the DA1 gene family in Arabidopsis thaliana Genes Dev. May 15;22(10):1331-6. PMID: 18483219

  • Baerenfaller K, Grossmann J, Grobei MA, Hull R, Hirsch-Hoffmann M, Yalovsky S, Zimmermann P, Grossniklaus U, Gruissem W, Baginsky S. (2008) Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics. Science. May 16;320(5878):938-41. PMID: 18436743

  • Ossowsky S., Schwab R, Weigel D (2008) Gene silencing in plants using artificial microRNAs and other small RNAs. The Plant J. Feb;53(4):674-90. PMID: 1826957

 

2007

  • Karimi, M., Bleys, A., Vanderhaeghen, R. and Hilson, P. (2007) Building blocks for plant gene assembly. Plant Physiology 145:1183-1191  PMID: 17965171

  • Kitsios, G  Alexiou, KG, Bush, M, Shaw P, and Doonan JH. (2007)  A Cyclin dependent protein kinase, CDKC2, co-localizes with and modulates the distribution of spliceosomal components in Arabidopsis.  The Plant J PMID: 18208522

  • Lisec, J., Meyer, R.C., Steinfath, M., Redestig, H., Becher, M., Witucka-Wall, H., Fiehn, O., Törjék, O, Selbig, J., Altmann, T., and Willmitzer, L. (2007) Identification of metabolic and biomass QTL in Arabidopsis thaliana in a parallel analysis of RIL and IL populations. The Plant J  PMID: 18047556

  • Stitt M. Patent Application 07118640: System and method for producing weighed portions of powder from at least one biological material at cryotemperatures (Cryogenic Grinde). 2007

 

Other publications featuring AGRON-OMICS

  • Marcus, F (2008) Bioinformatics and Systems Biology Collaborative Research and Resources. Springer Verlag, ISBN: 978-3-540-78352-7

  • MASC Report 2007 Multinational Coordinated Arabidopsis thaliana functional genomics project

 

 

 

 

 

 

 



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