Publications of Joachim Kopka

121.

Journal Article

Mettler, T.; Mühlhaus, T.; Hemme, D.; Schöttler, M. A.; Rupprecht, J.; Idoine, A.; Veyel, D.; Pal, S. K.; Yaneva-Roder, L.; Winck, F. V. et al.; Sommer, F.; Vosloh, D.; Seiwert, B.; Erban, A.; Burgos, A.; Arvidsson, S.; Schönfelder, S.; Arnold, A.; Günther, M.; Krause, U.; Lohse, M.; Kopka, J.; Nikoloski, Z.; Mueller-Roeber, B.; Willmitzer, L.; Bock, R.; Schroda, M.; Stitt, M.: Systems Analysis of the Response of Photosynthesis, Metabolism, and Growth to an Increase in Irradiance in the Photosynthetic Model Organism Chlamydomonas reinhardtii. The Plant Cell 26 (6), pp. 2310 - 2350 (2014)

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122.

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Schmidt, S.; Dethloff, F.; Beine-Golovchuk, O.; Kopka, J.: REIL proteins of Arabidopsis thaliana interact in yeast-2-hybrid assays with homologs of the yeast RLP24, RPl24a, RLP24b, ARX1, and jjj1 proteins. Plant Signaling & Behavior 9 (3), e28224 (2014)

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123.

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Schroeder, F.; Lisso, J.; Obata, T.; Erban, A.; Maximova, E.; Giavalisco, P.; Kopka, J.; Fernie, A. R.; Willmitzer, L.; Muessig, C.: Consequences of induced brassinosteroid deficiency in Arabidopsis leaves. BMC Plant Biology 14, 309 (2014)

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124.

Journal Article

Schwarz, D.; Orf, I.; Kopka, J.; Hagemann, M.: Effects of Inorganic Carbon Limitation on the Metabolome of the Synechocystis sp. PCC 6803 Mutant Defective in glnB Encoding the Central Regulator PII of Cyanobacterial C/N Acclimation. Metabolites 4 (2), pp. 232 - 247 (2014)

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125.

Journal Article

Agudelo-Romero, P.; Erban, A.; Sousa, L.; Pais, M. S.; Kopka, J.; Fortes, A. M.: Search for Transcriptional and Metabolic Markers of Grape Pre-Ripening and Ripening and Insights into Specific Aroma Development in Three Portuguese Cultivars. PLoS One 8 (4), e60422 (2013)

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126.

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Degenkolbe, T.; Do, P. T.; Kopka, J.; Zuther, E.; Hincha, D. K.; Koehl, K. I.: Identification of Drought Tolerance Markers in a Diverse Population of Rice Cultivars by Expression and Metabolite Profiling. PLoS One 8 (5), e63637 (2013)

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127.

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Do, P. T.; Degenkolbe, T.; Erban, A.; Heyer, A. G.; Kopka, J.; Koehl, K. I.; Hincha, D. K.; Zuther, E.: Dissecting Rice Polyamine Metabolism under Controlled Long-Term Drought Stress. PLoS One 8 (4), e60325 (2013)

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128.

Journal Article

Hauf, W.; Schlebusch, M.; Huege, J.; Kopka, J.; Hagemann, M.; Forchhammer, K.: Metabolic Changes in Synechocystis PCC6803 upon Nitrogen-Starvation: Excess NADPH Sustains Polyhydroxybutyrate Accumulation. Metabolites 3, pp. 101 - 118 (2013)

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129.

Journal Article

Perez-Delgado, C. M.; Garcia-Calderon, M.; Sanchez, D. H.; Udvardi, M. K.; Kopka, J.; Marquez, A. J.; Betti, M.: Transcriptomic and Metabolic Changes Associated with Photorespiratory Ammonium Accumulation in the Model Legume Lotus japonicus. Plant Physiology 162 (4), pp. 1834 - 1848 (2013)

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130.

Journal Article

Schmidt, S.; Dethloff, F.; Beine-Golovchuk, O.; Kopka, J.: The REIL1 and REIL2 proteins of Arabidopsis thaliana are required for leaf growth in the cold. Plant Physiology 163 (4), pp. 1623 - 1639 (2013)

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131.

Journal Article

Schwarz, D.; Orf, I.; Kopka, J.; Hagemann, M.: Recent Applications of Metabolomics Toward Cyanobacteria. Metabolites 3, pp. 72 - 100 (2013)

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132.

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Strehmel, N.; Kopka, J.; Scheel, D.; Böttcher, C.: Annotating unknown components from GC/EI-MS-based metabolite profiling experiments using GC/APCI(+)-QTOFMS. Metabolics 10 (2), pp. 324 - 336 (2013)

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133.

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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134.

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Anetzberger, C.; Reiger, M.; Fekete, A.; Schell, U.; Stambrau, N.; Plener, L.; Kopka, J.; Schmitt-Kopplin, P.; Hilbi, H.; Jung, K.: Autoinducers act as biological timers in Vibrio harveyi. PLoS One 7 (10), p. e48310 (2012)

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135.

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Beisser, D.; Grohme, M. A.; Kopka, J.; Frohme, M.; Schill, R. O.; Hengherr, S.; Dandekar, T.; Klau, G. W.; Dittrich, M.; Muller, T.: Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum. BMC Systems Biology 6, p. 72 (2012)

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136.

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Calingacion, M. N.; Boualaphanh, C.; Daygon, V. D.; Anacleto, R.; Sackville Hamilton, R.; Biais, B.; Deborde, C.; Maucourt, M.; Moing, A.; Mumm, R. et al.; de Vos, R. C. H.; Erban, A.; Kopka, J.; Hansen, T. H.; Laursen, K. H.; Schjoerring, J. K.; Hall, R. D.; Fitzgerald, M. A.: A genomics and multi-platform metabolomics approach to identify new traits of rice quality in traditional and improved varieties. Metabolomics 8 (5), pp. 771 - 783 (2012)

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137.

Journal Article

Dunn, W. B.; Erban, A.; Weber, R. J. M.; Creek, D. J.; Brown, M.; Breitling, R.; Hankemeier, T.; Goodacre, R.; Neumann, S.; Kopka, J. et al.; Viant, M. R.: Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics. Metabolomics 9 (S1), pp. 44 - 66 (2012)

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138.

Journal Article

Fuehrs, H.; Specht, A.; Erban, A.; Kopka, J.; Horst, W. J.: Functional associations between the metabolome and manganese tolerance in Vigna unguiculata. Journal of Experimental Botany 63 (1), pp. 329 - 340 (2012)

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139.

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Hackenberg, C.; Huege, J.; Engelhardt, A.; Wittink, F.; Laue, M.; Matthijs, H. C.; Kopka, J.; Bauwe, H.; Hagemann, M.: Low-carbon acclimation in carboxysome-less and photorespiratory mutants of the cyanobacterium Synechocystis sp. strain PCC 6803. Microbiology 158 (Pt 2), pp. 398 - 413 (2012)

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140.

Journal Article

Rohloff, J.; Kopka, J.; Erban, A.; Winge, P.; Wilson, R. C.; Bones, A. M.; Davik, J.; Randall, S. K.; Alsheikh, M. K.: Metabolite profiling reveals novel multi-level cold responses in the diploid model Fragaria vesca (woodland strawberry). Phytochemistry 77, pp. 99 - 109 (2012)

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141.

Journal Article

Sanchez, D. H.; Schwabe, F.; Erban, A.; Udvardi, M. K.; Kopka, J.: Comparative metabolomics of drought acclimation in model and forage legumes. Plant Cell and Environment 35 (1), pp. 136 - 149 (2012)

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142.

Journal Article

Siahpoosh, M. R.; Sanchez, D. H.; Schlereth, A.; Scofield, G. N.; Furbank, R. T.; van Dongen, J. T.; Kopka, J.: Modification of OsSUT1 gene expression modulates the salt response of rice Oryza sativa cv. Taipei 309. Plant Science 182, pp. 101 - 111 (2012)

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143.

Journal Article

Clauss, K.; von Roepenack-Lahaye, E.; Boettcher, C.; Roth, M. R.; Welti, R.; Erban, A.; Kopka, J.; Scheel, D.; Milkowski, C.; Strack, D.: Overexpression of Sinapine Esterase BnSCE3 in Oilseed Rape Seeds Triggers Global Changes in Seed Metabolism. Plant Physiology 155 (3), pp. 1127 - 1145 (2011)

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144.

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Hackenberg, C.; Kern, R.; Huege, J.; Stal, L. J.; Tsuji, Y.; Kopka, J.; Shiraiwa, Y.; Bauwe, H.; Hagemann, M.: Cyanobacterial lactate oxidases serve as essential partners in N2 fixation and evolved into photorespiratory glycolate oxidases in plants. The Plant Cell 23 (8), pp. 2978 - 2990 (2011)

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145.

Journal Article

Huege, J.; Goetze, J.; Schwarz, D.; Bauwe, H.; Hagemann, M.; Kopka, J.: Modulation of the Major Paths of Carbon in Photorespiratory Mutants of Synechocystis. PLoS One 6 (1), p. e16278 (2011)

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146.

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Moing, A.; Aharoni, A.; Biais, B.; Rogachev, I.; Meir, S.; Brodsky, L.; Allwood, J. W.; Erban, A.; Dunn, W. B.; Kay, L. et al.; de Koning, S.; de Vos, R. C. H.; Jonker, H.; Mumm, R.; Deborde, C.; Maucourt, M.; Bernillon, S.; Gibon, Y.; Hansen, T. H.; Husted, S.; Goodacre, R.; Kopka, J.; Schjoerring, J. K.; Rolin, D.; Hall, R. D.: Extensive metabolic cross-talk in melon fruit revealed by spatial and developmental combinatorial metabolomics. New Phytologist 190 (3), pp. 683 - 696 (2011)

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147.

Journal Article

Sanchez, D. H.; Pieckenstain, F. L.; Escaray, F.; Erban, A.; Kraemer, U.; Udvardi, M. K.; Kopka, J.: Comparative ionomics and metabolomics in extremophile and glycophytic Lotus species under salt stress challenge the metabolic pre-adaptation hypothesis. Plant Cell and Environment 34 (4), pp. 605 - 617 (2011)

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148.

Journal Article

Sanchez, D. H.; Pieckenstain, F. L.; Szymanski, J.; Erban, A.; Bromke, M.; Hannah, M. A.; Kraemer, U.; Kopka, J.; Udvardi, M. K.: Comparative Functional Genomics of Salt Stress in Related Model and Cultivated Plants Identifies and Overcomes Limitations to Translational Genomics. PLoS One 6 (2), p. e17094 (2011)

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149.

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Schwarz, D.; Nodop, A.; Huege, J.; Purfurst, S.; Forchhammer, K.; Michel, K. P.; Bauwe, H.; Kopka, J.; Hagemann, M.: Metabolic and Transcriptomic Phenotyping of Inorganic Carbon Acclimation in the Cyanobacterium Synechococcus elongatus PCC 7942. Plant Physiology 155 (4), pp. 1640 - 1655 (2011)

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150.

Journal Article

Ebert, B.; Zoller, D.; Erban, A.; Fehrle, I.; Hartmann, J.; Niehl, A.; Kopka, J.; Fisahn, J.: Metabolic profiling of Arabidopsis thaliana epidermal cells. Journal of Experimental Botany 61 (5), pp. 1321 - 1335 (2010)

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151.

Journal Article

Girin, T.; El-Kafafi, E. S.; Widiez, T.; Erban, A.; Hubberten, H.-M.; Kopka, J.; Hoefgen, R.; Gojon, A.; Lepetit, M.: Identification of Arabidopsis Mutants Impaired in the Systemic Regulation of Root Nitrate Uptake by the Nitrogen Status of the Plant. Plant Physiology 153 (3), pp. 1250 - 1260 (2010)

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152.

Journal Article

Hofmann, J.; El Ashry, A.; Anwar, S.; Erban, A.; Kopka, J.; Grundler, F.: Metabolic profiling reveals local and systemic responses of host plants to nematode parasitism. Plant Journal 62 (6), pp. 1058 - 1071 (2010)

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153.

Journal Article

Hummel, J.; Strehmel, N.; Selbig, J.; Walther, D.; Kopka, J.: Decision tree supported substructure prediction of metabolites from GC-MS profiles. Metabolomics 6 (2), pp. 322 - 333 (2010)

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154.

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Korn, M.; Gärtner, T.; Erban, A.; Kopka, J.; Selbig, J.; Hincha, D. K.: Predicting Arabidopsis Freezing Tolerance and Heterosis in Freezing Tolerance from Metabolite Composition. Molecular Plant 3 (1), pp. 224 - 235 (2010)

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155.

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Lugan, R.; Niogret, M. F.; Leport, L.; Guegan, J. P.; Larher, F. R.; Savoure, A.; Kopka, J.; Bouchereau, A.: Metabolome and water homeostasis analysis of Thellungiella salsuginea suggests that dehydration tolerance is a key response to osmotic stress in this halophyte. Plant Journal 64 (2), pp. 215 - 229 (2010)

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156.

Journal Article

Parveen, I.; Moorby, J. M.; Fraser, M. D.; Erban, A.; Kopka, J.: Relationship between Grazing Lamb Growth Rate and Blood Plasma Analytes as Profiled by Gas Chromatography with Time-of-Flight Mass Spectrometry (GC-TOF/MS). Journal of Agricultural and Food Chemistry 58 (2), pp. 913 - 917 (2010)

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157.

Journal Article

Sanchez, D. H.; Szymanski, J.; Erban, A.; Udvardi, M. K.; Kopka, J.: Mining for robust transcriptional and metabolic responses to long-term salt stress: a case study on the model legume Lotus japonicus. Plant Cell and Environment 33 (4), pp. 468 - 480 (2010)

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158.

Journal Article

Steinfath, M.; Strehmel, N.; Peters, R.; Schauer, N.; Groth, D.; Hummel, J.; Steup, M.; Selbig, J.; Kopka, J.; Geigenberger, P. et al.; van Dongen, J. T.: Discovering plant metabolic biomarkers for phenotype prediction using an untargeted approach. Plant Biotechnology Journal 8 (8), pp. 900 - 911 (2010)

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159.

Journal Article

Strassburg, K.; Walther, D.; Takahashi, H.; Kanaya, S.; Kopka, J.: Dynamic Transcriptional and Metabolic Responses in Yeast Adapting to Temperature Stress. Omics-a Journal of Integrative Biology 14 (3), pp. 249 - 259 (2010)

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160.

Journal Article

Strehmel, N.; Praeger, U.; Koenig, C.; Fehrle, I.; Erban, A.; Geyer, M.; Kopka, J.; van Dongen, J. T.: Time course effects on primary metabolism of potato (Solanum tuberosum) tuber tissue after mechanical impact. Postharvest Biology and Technology 56 (2), pp. 109 - 116 (2010)

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161.

Journal Article

Walther, D.; Strassburg, K.; Durek, P.; Kopka, J.: Metabolic Pathway Relationships Revealed by an Integrative Analysis of the Transcriptional and Metabolic Temperature Stress-Response Dynamics in Yeast. OMICS: A Journal of Integrative Biology 14 (3), pp. 261 - 274 (2010)

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162.

Journal Article

Weichert, N.; Saalbach, I.; Weichert, H.; Kohl, S.; Erban, A.; Kopka, J.; Hause, B.; Varshney, A.; Sreenivasulu, N.; Strickert, M. et al.; Kumlehn, J.; Weschke, W.; Weber, H.: Increasing Sucrose Uptake Capacity of Wheat Grains Stimulates Storage Protein Synthesis. Plant Physiology 152 (2), pp. 698 - 710 (2010)

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163.

Journal Article

Wulff-Zottele, C.; Gatzke, N.; Kopka, J.; Orellana, A.; Hoefgen, R.; Fisahn, J.; Hesse, H.: Photosynthesis and metabolism interact during acclimation of Arabidopsis thaliana to high irradiance and sulphur depletion. Plant Cell and Environment 33 (11), pp. 1974 - 1988 (2010)

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164.

Journal Article

Allwood, J. W.; Erban, A.; de Koning, S.; Dunn, W. B.; Lüdemann, A.; Lommen, A.; Kay, L.; Loscher, R.; Kopka, J.; Goodacre, R.: Inter-laboratory reproducibility of fast gas chromatography-electron impact-time of flight mass spectrometry (GC-EI-TOF/MS) based plant metabolomics. Metabolomics 5 (4), pp. 479 - 496 (2009)

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165.

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Fuehrs, H.; Goetze, S.; Specht, A.; Erban, A.; Gallien, S.; Heintz, D.; van Dorsselaer, A.; Kopka, J.; Braun, H. P.; Horst, W. J.: Characterization of leaf apoplastic peroxidases and metabolites in Vigna unguiculata in response to toxic manganese supply and silicon. Journal of Experimental Botany 60 (6), pp. 1663 - 1678 (2009)

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166.

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Hernandez, G.; Valdes-Lopez, O.; Ramirez, M.; Goffard, N.; Weiller, G.; Aparicio-Fabre, R.; Fuentes, S. I.; Erban, A.; Kopka, J.; Udvardi, M. K. et al.; Vance, C. P.: Global Changes in the Transcript and Metabolic Profiles during Symbiotic Nitrogen Fixation in Phosphorus-Stressed Common Bean Plants. Plant Physiology 151 (3), pp. 1221 - 1238 (2009)

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167.

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Kempa, S.; Hummel, J.; Schwemmer, T.; Pietzke, M.; Strehmel, N.; Wienkoop, S.; Kopka, J.; Weckwerth, W.: An automated GCxGC-TOF-MS protocol for batch-wise extraction and alignment of mass isotopomer matrixes from differential C-13-labelling experiments: a case study for photoautotrophic-mixotrophic grown Chlamydomonas reinhardtii cells. Journal of Basic Microbiology 49 (1), pp. 82 - 91 (2009)

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168.

Journal Article

Lugan, R.; Niogret, M. F.; Kervazo, L.; Larher, F. R.; Kopka, J.; Bouchereau, A.: Metabolome and water status phenotyping of Arabidopsis under abiotic stress cues reveals new insight into ESK1 function. Plant Cell and Environment 32 (2), pp. 95 - 108 (2009)

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169.

Journal Article

Mrosk, C.; Forner, S.; Hause, G.; Kuester, H.; Kopka, J.; Hause, B.: Composite Medicago truncatula plants harbouring Agrobacterium rhizogenes-transformed roots reveal normal mycorrhization by Glomus intraradices. Journal of Experimental Botany 60 (13), pp. 3797 - 3807 (2009)

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170.

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Pedreschi, R.; Franck, C.; Lammertyn, J.; Erban, A.; Kopka, J.; Hertog, M.; Verlinden, B.; Nicolai, B.: Metabolic profiling of 'Conference' pears under low oxygen stress. Postharvest Biology and Technology 51 (2), pp. 123 - 130 (2009)

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171.

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van Dongen, J. T.; Frohlich, A.; Ramirez-Aguilar, S. J.; Schauer, N.; Fernie, A. R.; Erban, A.; Kopka, J.; Clark, J.; Langer, A.; Geigenberger, P.: Transcript and metabolite profiling of the adaptive response to mild decreases in oxygen concentration in the roots of arabidopsis plants. Annals of Botany 103 (2), pp. 269 - 280 (2009)

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172.

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Boettcher, C.; Centeno, D.; Freitag, J.; Hoefgen, R.; Koehl, K. I.; Kopka, J.; Kroymann, J.; Matros, A.; Mock, H.-P.; Neumann, S. et al.; Pfalz, M.; von Roepenack-Lahaye, E.; Schauer, N.; Trenkamp, S.; Zurbriggen, M.; Fernie, A. R.: Teaching (and learning from) metabolomics: The 2006 PlantMetaNet ETNA Metabolomics Research School. Physiologia Plantarum 132 (2), pp. 136 - 149 (2008)

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173.

Journal Article

Cartieaux, F.; Contesto, C.; Gallou, A.; Desbrosses, G.; Kopka, J.; Taconnat, L.; Renou, J. P.; Touraine, B.: Simultaneous interaction of Arabidopsis thaliana with Bradyrhizobium sp strain ORS278 and Pseudomonas syriugae pv. tomato DC3000 leads to complex transcriptome changes. Molecular Plant-Microbe Interactions 21 (2), pp. 244 - 259 (2008)

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174.

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Eisenhut, M.; Huege, J.; Schwarz, D.; Bauwe, H.; Kopka, J.; Hagemann, M.: Metabolome Phenotyping of Inorganic Carbon Limitation in Cells of the Wild Type and Photorespiratory Mutants of the Cyanobacterium Synechocystis sp Strain PCC 6803. Plant Physiology 148 (4), pp. 2109 - 2120 (2008)

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175.

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Hoehenwarter, W.; van Dongen, J. T.; Wienkoop, S.; Steinfath, M.; Hummel, J.; Erban, A.; Sulpice, R.; Regierer, B.; Kopka, J.; Geigenberger, P. et al.; Weckwerth, W.: A rapid approach for phenotype-screening and database independent detection of cSNP/protein polymorphism using mass accuracy precursor alignment. Proteomics 8 (20), pp. 4214 - 4225 (2008)

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176.

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Kempa, S.; Krasensky, J.; Dal Santo, S.; Kopka, J.; Jonak, C.: A Central Role of Abscisic Acid in Stress-Regulated Carbohydrate Metabolism. PLoS One 3 (12), p. e3935 (2008)

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177.

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Levine, L. H.; Kasahara, H.; Kopka, J.; Erban, A.; Fehrle, I.; Kaplan, F.; Zhao, W.; Littell, R. C.; Guy, C.; Wheeler, R. et al.; Sager, J.; Mills, A.; Levine, H. G.: Physiologic and metabolic responses of wheat seedlings to elevated and super-elevated carbon dioxide. Advances in Space Research 42 (12), pp. 1917 - 1928 (2008)

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178.

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Lüdemann, A.; Strassburg, K.; Erban, A.; Kopka, J.: TagFinder for the quantitative analysis of gas chromatography - mass spectrometry (GC-MS)-based metabolite profiling experiments. Bioinformatics 24 (5), pp. 732 - 737 (2008)

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179.

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Sanchez, D. H.; Lippold, F.; Redestig, H.; Hannah, M. A.; Erban, A.; Kraemer, U.; Kopka, J.; Udvardi, M. K.: Integrative functional genomics of salt acclimatization in the model legume Lotus japonicus. Plant Journal 53 (6), pp. 973 - 987 (2008)

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180.

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Sanchez, D. H.; Redestig, H.; Kraemer, U.; Udvardi, M. K.; Kopka, J.: Metabolome-ionome-biomass interactions: What can we learn about salt stress by multiparallel phenotyping? Plant Signaling & Behavior 3 (8), pp. 598 - 600 (2008)

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Journal Article (228)