Publications of Alisdair Fernie

851.

Journal Article

Saito, K.; Yonekura-Sakakibara, K.; Nakabayashi, R.; Higashi, Y.; Yamazaki, M.; Tohge, T.; Fernie, A. R.: The flavonoid biosynthetic pathway in Arabidopsis: Structural and genetic diversity. Plant Physiology and Biochemistry 72, pp. 21 - 34 (2013)

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852.

Journal Article

Spielbauer, G.; Li, L.; Romisch-Margl, L.; Do, P. T.; Fouquet, R.; Fernie, A. R.; Eisenreich, W.; Gierl, A.; Settles, A. M.: Chloroplast-localized 6-phosphogluconate dehydrogenase is critical for maize endosperm starch accumulation. Journal of Experimental Botany 64 (8), pp. 2231 - 2242 (2013)

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853.

Journal Article

Sulpice, R.; Nikoloski, Z.; Tschoep, H.; Antonio, C.; Kleeson, S.; Lahrlimi, A.; Selbig, J.; Hirofumi, I.; Gibon, Y.; Fernie, A. R. et al.; Stitt, M.: Impact of the carbon and nitrogen supply on relationships and connectivity between metabolism and biomass in a broad panel of Arabidopsis accessions. Plant Physiology 162 (1), pp. 347 - 363 (2013)

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854.

Journal Article

Sweetlove, L. J.; Fernie, A. R.: The Spatial Organization of Metabolism Within the Plant Cell. Annual Review of Plant Biology 64, pp. 723 - 746 (2013)

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855.

Journal Article

Szecowka, M.; Heise, R.; Tohge, T.; Nunes-Nesi, A.; Vosloh, D.; Huege, J.; Feil, R.; Lunn, J.; Nikoloski, Z.; Stitt, M. et al.; Fernie, A. R.; Arrivault, S.: Metabolic Fluxes in an Illuminated Arabidopsis Rosette. The Plant Cell 25 (2), pp. 694 - 714 (2013)

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856.

Journal Article

Tahir, J.; Watanabe, M.; Jing, H. C.; Hunter, D. A.; Tohge, T.; Nunes-Nesi, A.; Brotman, Y.; Fernie, A. R.; Hoefgen, R.; Dijkwel, P. P.: Activation of R-mediated innate immunity and disease susceptibility is affected by mutations in a cytosolic O-acetylserine (thiol) lyase in Arabidopsis. The Plant Journal 73 (1), pp. 118 - 130 (2013)

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857.

Journal Article

Timm, S.; Florian, A.; Wittmiss, M.; Jahnke, A.; Hagemann, M.; Fernie, A.; Bauwe, H.: Serine acts as metabolic signal for the transcriptional control of photorespiration-related genes in Arabidopsis thaliana. Plant Physiology 162 (1), pp. 379 - 389 (2013)

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858.

Journal Article

Tohge, T.; Watanabe, M.; Hoefgen, R.; Fernie, A. R.: Shikimate and phenylalanine biosynthesis in the green lineage. Frontiers in Plant Science 4, p. 62 (2013)

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859.

Journal Article

Watanabe, M.; Balazadeh, S.; Tohge, T.; Erban, A.; Giavalisco, P.; Kopka, J.; Mueller-Roeber, B.; Fernie, A. R.; Hoefgen, R.: Comprehensive dissection of spatio-temporal metabolic shifts in primary, secondary and lipid metabolism during developmental senescence in Arabidopsis thaliana. Plant Physiology 162 (3), pp. 1290 - 1310 (2013)

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860.

Journal Article

Tohge, T.; Fernie, A. R.: Co-expression and co-responses: within and beyond transcription. Frontiers in Plant Science 3, 248 (2012)

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861.

Journal Article

Alejandro, S.; Lee, Y.; Tohge, T.; Sudre, D.; Osorio, S.; Park, J.; Bovet, L.; Lee, Y.; Geldner, N.; Fernie, A. R. et al.; Martinoia, E.: AtABCG29 Is a Monolignol Transporter Involved in Lignin Biosynthesis. Current Biology 22 (13), pp. 1207 - 1212 (2012)

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862.

Journal Article

Amid, A.; Lytovchenko, A.; Fernie, A. R.; Warren, G.; Thorlby, G. J.: The sensitive to freezing3 mutation of Arabidopsis thaliana is a cold-sensitive allele of homomeric acetyl-CoA carboxylase that results in cold-induced cuticle deficiencies. Journal of Experimental Botany 63 (14), pp. 5289 - 5299 (2012)

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863.

Journal Article

Araujo, W. L.; Fernie, A. R.: Systems biology of gibberellin induced plant cell growth. Frontiers in Plant Science 3, p. 173 (2012)

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864.

Journal Article

Araujo, W. L.; Nunes-Nesi, A.; Nikoloski, Z.; Sweetlove, L. J.; Fernie, A. R.: Metabolic control and regulation of the tricarboxylic acid cycle in photosynthetic and heterotrophic plant tissues. Plant, Cell and Environment 35 (1), pp. 1 - 21 (2012)

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865.

Journal Article

Araujo, W. L.; Tohge, T.; Nunes-Nesi, A.; Daloso, D. M.; Nimick, M.; Krahnert, I.; Bunik, V. I.; Moorhead, G. B.; Fernie, A. R.: Phosphonate analogs of 2-oxoglutarate perturb metabolism and gene expression in illuminated Arabidopsis leaves. Frontiers in plant science 3, p. 114 (2012)

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866.

Journal Article

Araujo, W. L.; Tohge, T.; Osorio, S.; Lohse, M.; Balbo, I.; Krahnert, I.; Sienkiewicz-Porzucek, A.; Usadel, B.; Nunes-Nesi, A.; Fernie, A. R.: Antisense Inhibition of the 2-Oxoglutarate Dehydrogenase Complex in Tomato Demonstrates Its Importance for Plant Respiration and during Leaf Senescence and Fruit Maturation. The Plant Cell 24 (6), pp. 2328 - 2351 (2012)

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867.

Journal Article

Caldana, C.; Fernie, A. R.; Willmitzer, L.; Steinhauser, D.: Unraveling retrograde signaling pathways: finding candidate signaling molecules via metabolomics and systems biology driven approaches. Frontiers in Plant Science 3, p. 267 (2012)

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868.

Journal Article

Chen, L. Q.; Qu, X. Q.; Hou, B. H.; Sosso, D.; Osorio, S.; Fernie, A. R.; Frommer, W. B.: Sucrose Efflux Mediated by SWEET Proteins as a Key Step for Phloem Transport. Science 335 (6065), pp. 207 - 211 (2012)

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869.

Journal Article

Colmsee, C.; Mascher, M.; Czauderna, T.; Hartmann, A.; Schluter, U.; Zellerhoff, N.; Schmitz, J.; Brautigam, A.; Pick, T. R.; Alter, P. et al.; Gahrtz, M.; Witt, S.; Fernie, A. R.; Bornke, F.; Fahnenstich, H.; Bucher, M.; Dresselhaus, T.; Weber, A. P.; Schreiber, F.; Scholz, U.; Sonnewald, U.: OPTIMAS-DW: A comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize. BMC plant biology 12 (1), p. 245 (2012)

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870.

Journal Article

Cronje, C.; George, G. M.; Fernie, A. R.; Bekker, J.; Kossmann, J.; Bauer, R.: Manipulation of L: -ascorbic acid biosynthesis pathways in Solanum lycopersicum: elevated GDP-mannose pyrophosphorylase activity enhances L: -ascorbate levels in red fruit. Planta 235 (3), pp. 553 - 564 (2012)

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871.

Journal Article

Detmann, K. C.; Araujo, W. L.; Martins, S. C. V.; Sanglard, L. M. V. P.; Reis, J. V.; Detmann, E.; Rodrigues, F. A.; Nunes-Nesi, A.; Fernie, A. R.; DaMatta, F. M.: Silicon nutrition increases grain yield, which, in turn, exerts a feed-forward stimulation of photosynthetic rates via enhanced mesophyll conductance and alters primary metabolism in rice. New Phytologist 196 (3), pp. 752 - 762 (2012)

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872.

Journal Article

Draffehn, A. M.; Durek, P.; Nunes-Nesi, A.; Stich, B.; Fernie, A. R.; Gebhardt, C.: Tapping natural variation at functional level reveals allele specific molecular characteristics of potato invertase Pain-1. Plant, Cell and Environment 35 (12), pp. 2143 - 2154 (2012)

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873.

Journal Article

Fernie, A. R.; Stitt, M.: On the discordance of metabolomics with proteomics and transcriptomics: coping with increasing complexity in logic, chemistry, and network interactions scientific correspondence. Plant Physiology 158 (3), pp. 1139 - 1145 (2012)

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874.

Journal Article

Florez-Sarasa, I.; Araujo, W. L.; Wallstrom, S. V.; Rasmusson, A. G.; Fernie, A. R.; Ribas-Carbo, M.: Light-responsive metabolite and transcript levels are maintained following a dark-adaptation period in leaves of Arabidopsis thaliana. New Phytologist 195 (1), pp. 136 - 148 (2012)

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875.

Journal Article

Gechev, T. S.; Benina, M.; Obata, T.; Tohge, T.; Sujeeth, N.; Minkov, I.; Hille, J.; Temanni, M. R.; Marriott, A. S.; Bergstrom, E. et al.; Thomas-Oates, J.; Antonio, C.; Mueller-Roeber, B.; Schippers, J. H.; Fernie, A. R.; Toneva, V.: Molecular mechanisms of desiccation tolerance in the resurrection glacial relic Haberlea rhodopensis. Cellular and Molecular Life Sciences 70 (4), pp. 689 - 709 (2012)

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876.

Journal Article

Geisler, D. A.; Päpke, C.; Obata, T.; Nunes-Nesi, A.; Matthes, A.; Schneitz, K.; Maximova, E.; Araujo, W. L.; Fernie, A. R.; Persson, S.: Downregulation of the delta-Subunit Reduces Mitochondrial ATP Synthase Levels, Alters Respiration, and Restricts Growth and Gametophyte Development in Arabidopsis. The Plant Cell 24 (7), pp. 2792 - 2811 (2012)

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877.

Journal Article

Gomez, S.; Steinbrenner, A. D.; Osorio, S.; Schueller, M.; Ferrieri, R. A.; Fernie, A. R.; Orians, C. M.: From shoots to roots: transport and metabolic changes in tomato after simulated feeding by a specialist lepidopteran. Entomologia Experimentalis et Applicata 144 (1), pp. 101 - 111 (2012)

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878.

Journal Article

Gouws, L. M.; Botes, E.; Wiese, A. J.; Trenkamp, S.; Torres-Jerez, I.; Tang, Y.; Hills, P. N.; Usadel, B.; Lloyd, J. R.; Fernie, A. R. et al.; Kossmann, J.; van der Merwe, M. J.: The plant growth promoting substance, lumichrome, mimics starch, and ethylene-associated symbiotic responses in lotus and tomato roots. Frontiers in Plant Science 3, p. 120 (2012)

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879.

Journal Article

Hampp, C.; Richter, A.; Osorio, S.; Zellnig, G.; Sinha, A. K.; Jammer, A.; Fernie, A. R.; Grimm, B.; Roitsch, T.: Establishment of a Photoautotrophic Cell Suspension Culture of Arabidopsis thaliana for Photosynthetic, Metabolic, and Signaling Studies. Molecular Plant 5 (2), pp. 524 - 527 (2012)

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880.

Journal Article

Hebbelmann, I.; Selinski, J.; Wehmeyer, C.; Goss, T.; Voss, I.; Mulo, P.; Kangasjarvi, S.; Aro, E.-M.; Oelze, M. L.; Dietz, K. J. et al.; Nunes-Nesi, A.; Do, P. T.; Fernie, A. R.; Talla, S. K.; Raghavendra, A. S.; Linke, V.; Scheibe, R.: Multiple strategies to prevent oxidative stress in Arabidopsis plants lacking the malate valve enzyme NADP-malate dehydrogenase. Journal of Experimental Botany 63 (3), pp. 1445 - 1459 (2012)

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881.

Journal Article

Keren, I.; Tal, L.; des Francs-Small, C. C.; Araujo, W. L.; Shevtsov, S.; Shaya, F.; Fernie, A. R.; Small, I.; Ostersetzer-Biran, O.: nMAT1, a nuclear-encoded maturase involved in the trans-splicing of nad1 intron 1, is essential for mitochondrial complex I assembly and function. The Plant Journal 71 (3), pp. 413 - 426 (2012)

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882.

Journal Article

Kleessen, S.; Antonio, C.; Sulpice, R.; Laitinen, R.; Fernie, A. R.; Stitt, M.; Nikoloski, Z.: Structured patterns in geographic variability of metabolic phenotypes in Arabidopsis thaliana. Nature Communications 3, p. 1319 (2012)

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883.

Journal Article

Kleessen, S.; Araujo, W. L.; Fernie, A. R.; Nikoloski, Z.: Model-based Confirmation of Alternative Substrates of Mitochondrial Electron Transport Chain. Journal of Biological Chemistry 287 (14), pp. 11122 - 11131 (2012)

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884.

Journal Article

Kleessen, S.; Fernie, A. R.; Nikoloski, Z.: A computational framework for evaluating the efficiency of Arabidopsis accessions in response to nitrogen stress reveals important metabolic mechanisms. Frontiers in Plant Science 3, p. 217 (2012)

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885.

Journal Article

Kochevenko, A.; Araujo, W. L.; Maloney, G. S.; Tieman, D. M.; Do, P. T.; Taylor, M. G.; Klee, H. J.; Fernie, A. R.: Catabolism of Branched Chain Amino Acids Supports Respiration but Not Volatile Synthesis in Tomato Fruits. Molecular Plant 5 (2), pp. 366 - 375 (2012)

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886.

Journal Article

Kochevenko, A.; Klee, H. J.; Fernie, A. R.; Araújo, W. L.: Molecular identification of a further branched-chain aminotransferase 7 (BCAT7) in tomato plants. Journal of Plant Physiology 169 (5), pp. 437 - 443 (2012)

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887.

Journal Article

Lehmann, M.; Laxa, M.; Sweetlove, L. J.; Fernie, A. R.; Obata, T.: Metabolic recovery of Arabidopsis thaliana roots following cessation of oxidative stress. Metabolomics 8 (1), pp. 143 - 153 (2012)

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888.

Journal Article

Lohse, M.; Bolger, A. M.; Nagel, A.; Fernie, A. R.; Lunn, J. E.; Stitt, M.; Usadel, B.: RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Research 40 (W1), pp. W622 - W627 (2012)

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889.

Journal Article

Mounet, F.; Moing, A.; Kowalczyk, M.; Rohrmann, J.; Petit, J.; Garcia, V.; Maucourt, M.; Yano, K.; Deborde, C.; Aoki, K. et al.; Berges, H.; Granell, A.; Fernie, A. R.; Bellini, C.; Rothan, C.; Lemaire-Chamley, M.: Down-regulation of a single auxin efflux transport protein in tomato induces precocious fruit development. Journal of Experimental Botany 63 (13), pp. 4901 - 4917 (2012)

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890.

Journal Article

Niessen, M.; Krause, K.; Horst, I.; Staebler, N.; Klaus, S.; Gaertner, S.; Kebeish, R.; Araujo, W. L.; Fernie, A. R.; Peterhansel, C.: Two alanine aminotranferases link mitochondrial glycolate oxidation to the major photorespiratory pathway in Arabidopsis and rice. Journal of Experimental Botany 63 (7), pp. 2705 - 2716 (2012)

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891.

Journal Article

Osorio, S.; Alba, R.; Nikoloski, Z.; Kochevenko, A.; Fernie, A. R.; Giovannoni, J. J.: Integrative Comparative Analyses of Transcript and Metabolite Profiles from Pepper and Tomato Ripening and Development Stages Uncovers Species-Specific Patterns of Network Regulatory Behavior. Plant Physiology 159 (4), pp. 1713 - 1729 (2012)

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892.

Journal Article

Ribeiro, D. M.; Araujo, W. L.; Fernie, A. R.; Schippers, J. H. M.; Mueller-Roeber, B.: Action of Gibberellins on Growth and Metabolism of Arabidopsis Plants Associated with High Concentration of Carbon Dioxide. Plant Physiology 160 (4), pp. 1781 - 1794 (2012)

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893.

Journal Article

Ribeiro, D. M.; Araujo, W. L.; Fernie, A. R.; Schippers, J. H.; Mueller-Roeber, B.: Translatome and metabolome effects triggered by gibberellins during rosette growth in Arabidopsis. Journal of Experimental Botany 63 (7), pp. 2769 - 2786 (2012)

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894.

Journal Article

Rohrmann, J.; McQuinn, R.; Giovannoni, J.; Fernie, A. R.; Tohge, T.: Tissue specificity and differential expression of transcription factors in tomato provide hints of unique regulatory networks during fruit ripening. Plant Signaling & Behavior 7 (12), pp. 1639 - 1647 (2012)

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895.

Journal Article

Steinhauser, D.; Fernie, A. R.; Araujo, W. L.: Unusual cyanobacterial TCA cycles: not broken just different. Trends in Plant Science 17 (9), pp. 503 - 509 (2012)

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896.

Journal Article

Szecowka, M.; Osorio, S.; Obata, T.; Araujo, W. L.; Rohrmann, J.; Nunes-Nesi, A.; Fernie, A. R.: Decreasing the Mitochondrial Synthesis of Malate in Potato Tubers Does Not Affect Plastidial Starch Synthesis, Suggesting That the Physiological Regulation of ADPglucose Pyrophosphorylase Is Context Dependent. Plant Physiology 160 (4), pp. 2227 - 2238 (2012)

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897.

Journal Article

Timm, S.; Florian, A.; Arrivault, S.; Stitt, M.; Fernie, A. R.; Bauwe, H.: Glycine decarboxylase controls photosynthesis and plant growth. FEBS Letters 586 (20), pp. 3692 - 3697 (2012)

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898.

Journal Article

Timm, S.; Mielewczik, M.; Florian, A.; Frankenbach, S.; Dreissen, A.; Hocken, N.; Fernie, A. R.; Walter, A.; Bauwe, H.: High-to-Low CO2 Acclimation Reveals Plasticity of the Photorespiratory Pathway and Indicates Regulatory Links to Cellular Metabolism of Arabidopsis. PLoS One 7 (8), p. e42809 (2012)

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899.

Journal Article

Tohge, T.; Fernie, A. R.: Annotation of plant gene function via combined genomics, metabolomics and informatics. Journal of visualized experiments (64), e3487, p. e3487 (2012)

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900.

Journal Article

Toubiana, D.; Semel, Y.; Tohge, T.; Beleggia, R.; Cattivelli, L.; Rosental, L.; Nikoloski, Z.; Zamir, D.; Fernie, A. R.; Fait, A.: Metabolic Profiling of a Mapping Population Exposes New Insights in the Regulation of Seed Metabolism and Seed, Fruit, and Plant Relations. PLoS Genetics 8 (3), p. e1002612 (2012)

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Journal Article (1112)