Publikationen von Joachim Kopka | Max-Planck-Institut für Molekulare Pflanzenphysiologie

Max-Planck-Institut für Molekulare Pflanzenphysiologie

Zeitschriftenartikel (189)

121.

Zeitschriftenartikel

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), S. 1221 - 1238 (2009)

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122.

Zeitschriftenartikel

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), S. 82 - 91 (2009)

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123.

Zeitschriftenartikel

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), S. 95 - 108 (2009)

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124.

Zeitschriftenartikel

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), S. 3797 - 3807 (2009)

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125.

Zeitschriftenartikel

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), S. 123 - 130 (2009)

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126.

Zeitschriftenartikel

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), S. 269 - 280 (2009)

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127.

Zeitschriftenartikel

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), S. 136 - 149 (2008)

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128.

Zeitschriftenartikel

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), S. 244 - 259 (2008)

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129.

Zeitschriftenartikel

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), S. 2109 - 2120 (2008)

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130.

Zeitschriftenartikel

Guy, C.; Kaplan, F.; Kopka, J.; Selbig, J.; Hincha, D. K.: Metabolomics of temperature stress. Physiologia Plantarum 132 (2), S. 220 - 235 (2008)

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131.

Zeitschriftenartikel

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), S. 4214 - 4225 (2008)

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132.

Zeitschriftenartikel

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), S. e3935 (2008)

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133.

Zeitschriftenartikel

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), S. 1917 - 1928 (2008)

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134.

Zeitschriftenartikel

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), S. 732 - 737 (2008)

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135.

Zeitschriftenartikel

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), S. 973 - 987 (2008)

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136.

Zeitschriftenartikel

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), S. 598 - 600 (2008)

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137.

Zeitschriftenartikel

Sanchez, D. H.; Siahpoosh, M. R.; Roessner, U.; Udvardi, M. K.; Kopka, J.: Plant metabolomics reveals conserved and divergent metabolic responses to salinity. Physiologia Plantarum 132 (2), S. 209 - 219 (2008)

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138.

Zeitschriftenartikel

Strehmel, N.; Hummel, J.; Erban, A.; Strassburg, K.; Kopka, J.: Retention index thresholds for compound matching in GC-MS metabolite profiling. Journal of Chromatography B-Analytical Technologies in the Biomedical and Life Sciences 871 (2), S. 182 - 190 (2008)

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139.

Zeitschriftenartikel

Dauwe, R.; Morreel, K.; Goeminne, G.; Gielen, B.; Rohde, A.; van Beeumen, J.; Ralph, J.; Boudet, A. M.; Kopka, J.; Rochange, S. F. et al.; Halpin, C.; Messens, E.; Boerjan, W.: Molecular phenotyping of lignin-modified tobacco reveals associated changes in cell-wall metabolism, primary metabolism, stress metabolism and photorespiration. Plant Journal 52 (2), S. 263 - 285 (2007)

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140.

Zeitschriftenartikel

Hannah, M. A.; Kraemer, K. M.; Geffroy, V.; Kopka, J.; Blair, M. W.; Erban, A.; Vallejos, C. E.; Heyer, A. G.; Sanders, F. E.; Millner, P. A. et al.; Pilbeam, D. J.: Hybrid weakness controlled by the dosage-dependent lethal (DL) gene system in common bean (Phaseolus vulgaris) is caused by a shoot-derived inhibitory signal leading to salicylic acid-associated root death. New Phytologist 176 (3), S. 537 - 549 (2007)

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141.

Zeitschriftenartikel

Hernandez, G.; Ramirez, M.; Valdes-Lopez, O.; Tesfaye, M.; Graham, M. A.; Czechowski, T.; Schlereth, A.; Wandrey, M.; Erban, A.; Cheung, F. et al.; Wu, H. C.; Lara, M.; Town, C. D.; Kopka, J.; Udvardi, M. K.; Vance, C. P.: Phosphorus stress in common bean: Root transcript and metabolic responses. Plant Physiology 144 (2), S. 752 - 767 (2007)

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142.

Zeitschriftenartikel

Huege, J.; Sulpice, R.; Gibon, Y.; Lisec, J.; Koehl, K. I.; Kopka, J.: GC-EI-TOF-MS analysis of in vivo carbon-partitioning into soluble metabolite pools of higher plants by monitoring isotope dilution after 13CO2 labelling. Phytochemistry 68 (16-18), S. 2258 - 2272 (2007)

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143.

Zeitschriftenartikel

Kaplan, F.; Kopka, J.; Sung, D. Y.; Zhao, W.; Popp, M.; Porat, R.; Guy, C. L.: Transcript and metabolite profiling during cold acclimation of Arabidopsis reveals an intricate relationship of cold-regulated gene expression with modifications in metabolite content. Plant Journal 50 (6), S. 967 - 981 (2007)

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144.

Zeitschriftenartikel

Kempa, S.; Rozhon, W.; Samaj, J.; Erban, A.; Baluska, F.; Becker, T.; Haselmayer, J.; Schleiff, E.; Kopka, J.; Hirt, H. et al.; Jonak, C.: A plastid-localized glycogen synthase kinase 3 modulates stress tolerance and carbohydrate metabolism. Plant Journal 49 (6), S. 1076 - 1090 (2007)

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145.

Zeitschriftenartikel

Leple, J. C.; Dauwe, R.; Morreel, K.; Storme, V.; Lapierre, C.; Pollet, B.; Naumann, A.; Kang, K. Y.; Kim, H.; Ruel, K. et al.; Lefebvre, A.; Joseleau, J. P.; Grima-Pettenati, J.; De Rycke, R.; Andersson-Gunneras, S.; Erban, A.; Fehrle, I.; Petit-Conil, M.; Kopka, J.; Polle, A.; Messens, E.; Sundberg, B.; Mansfield, S. D.; Ralph, J.; Pilate, G.; Boerjan, W.: Downregulation of cinnamoyl-coenzyme a reductase in poplar: multiple-level phenotyping reveals effects on cell wall polymer metabolism and structure. Plant Cell 19 (11), S. 3669 - 3691 (2007)

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146.

Zeitschriftenartikel

Parveen, I.; Moorby, J. M.; Fraser, M. D.; Allison, G. G.; Kopka, J.: Application of gas chromatography-mass spectrometry metabolite profiling techniques to the analysis of heathland plant diets of sheep. Journal of Agricultural and Food Chemistry 55 (4), S. 1129 - 1138 (2007)

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147.

Zeitschriftenartikel

Schaarschmidt, S.; Kopka, J.; Ludwig-Mueller, J.; Hause, B.: Regulation of arbuscular mycorrhization by apoplastic invertases: enhanced invertase activity in the leaf apoplast affects the symbiotic interaction. Plant Journal 51 (3), S. 390 - 405 (2007)

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148.

Zeitschriftenartikel

Sumner, L. W.; Amberg, A.; Barrett, D.; Beale, M. H.; Beger, R.; Daykin, C. A.; Fan, T. W. M.; Fiehn, O.; Goodacre, R.; Griffin, J. L. et al.; Hankemeier, T.; Hardy, N.; Harnly, J.; Higashi, R.; Kopka, J.; Lane, A. N.; Lindon, J. C.; Marriott, P.; Nicholls, A. W.; Reily, M. D.; Thaden, J. J.; Viant, M. R.: Proposed minimum reporting standards for chemical analysis. Metabolomics 3 (3), S. 211 - 221 (2007)

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149.

Zeitschriftenartikel

Domoney, C.; Duc, G.; Ellis, T. H. N.; Ferrandiz, C.; Firnhaber, C.; Gallardo, K.; Hofer, J.; Kopka, J.; Kuester, H.; Madueno, F. et al.; Munier-Jolain, N. G.; Mayer, K.; Thompson, R.; Udvardi, M. K.; Salon, C.: Genetic and genomic analysis of legume flowers and seeds. Current Opinion in Plant Biology 9 (2), S. 133 - 141 (2006)

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150.

Zeitschriftenartikel

Engelsberger, W. R.; Erban, A.; Kopka, J.; Schulze, W. X.: Metabolic labeling of plant cell cultures with K(15)NO3 as a tool for quantitative analysis of proteins and metabolites. Plant Methods 2, S. 14 (2006)

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151.

Zeitschriftenartikel

Kopka, J.: Current challenges and developments in GC-MS based metabolite profiling technology. Journal of Biotechnology 124 (1), S. 312 - 322 (2006)

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152.

Zeitschriftenartikel

Lisec, J.; Schauer, N.; Kopka, J.; Willmitzer, L.; Fernie, A. R.: Gas chromatography mass spectrometry-based metabolite profiling in plants. Nature Protocols 1 (1), S. 387 - 396 (2006)

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153.

Zeitschriftenartikel

Niehl, A.; Lacomme, C.; Erban, A.; Kopka, J.; Kraemer, U.; Fisahn, J.: Systemic Potato virus X infection induces defence gene expression and accumulation of beta-phenylethylamine-alkaloids in potato. Functional Plant Biology 33 (6), S. 593 - 604 (2006)

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154.

Zeitschriftenartikel

Schauer, N.; Semel, Y.; Roessner, U.; Gur, A.; Balbo, I.; Carrari, F.; Pleban, T.; Perez-Melis, A.; Bruedigam, C.; Kopka, J. et al.; Willmitzer, L.; Zamir, D.; Fernie, A. R.: Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nature Biotechnology 24 (4), S. 447 - 454 (2006)

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155.

Zeitschriftenartikel

Skirycz, A.; Reichelt, M.; Burow, M.; Birkemeyer, C.; Rolcik, J.; Kopka, J.; Zanor, M. I.; Gershenzon, J.; Strnad, M.; Szopa, J. et al.; Mueller-Roeber, B.; Witt, I.: DOF transcription factor AtDof1.1 (OBP2) is part of a regulatory network controlling glucosinolate biosynthesis in Arabidopsis. Plant Journal 47 (1), S. 10 - 24 (2006)

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156.

Zeitschriftenartikel

Birkemeyer, C.; Luedemann, A.; Wagner, C.; Erban, A.; Kopka, J.: Metabolome analysis: the potential of in vivo labeling with stable isotopes for metabolite profiling. Trends in Biotechnology 23 (1), S. 28 - 33 (2005)

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157.

Zeitschriftenartikel

Damiani, I.; Morreel, K.; Danoun, S.; Goeminne, G.; Yahiaoui, N.; Marque, C.; Kopka, J.; Messens, E.; Goffner, D.; Boerjan, W. et al.; Boudet, A. M.; Rochange, S.: Metabolite profiling reveals a role for atypical cinnamyl alcohol dehydrogenase CAD1 in the synthesis of coniferyl alcohol in tobacco xylem. Plant Molecular Biology 59 (5), S. 753 - 769 (2005)

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158.

Zeitschriftenartikel

Desbrosses, G. G.; Kopka, J.; Udvardi, M. K.: Lotus japonicus metabolic profiling. Development of gas chromatography-mass spectrometry resources for the study of plant-microbe interactions. Plant Physiology 137 (4), S. 1302 - 1318 (2005)

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159.

Zeitschriftenartikel

Kopka, J.; Schauer, N.; Krueger, S.; Birkemeyer, C.; Usadel, B.; Bergmueller, E.; Doermann, P.; Weckwerth, W.; Gibon, Y.; Stitt, M. et al.; Willmitzer, L.; Fernie, A. R.; Steinhauser, D.: GMD@CSB.DB: the Golm Metabolome Database. Bioinformatics 21 (8), S. 1635 - 1638 (2005)

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160.

Zeitschriftenartikel

Lisso, J.; Steinhauser, D.; Altmann, T.; Kopka, J.; Muessig, C.: Identification of brassinosteroid-related genes by means of transcript co-response analyses. Nucleic Acids Research 33 (8), S. 2685 - 2696 (2005)

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161.

Zeitschriftenartikel

Lohse, S.; Schliemann, W.; Ammer, C.; Kopka, J.; Strack, D.; Fester, T.: Organization and metabolism of plastids and mitochondria in arbuscular mycorrhizal roots of Medicago truncatula. Plant Physiology 139 (1), S. 329 - 340 (2005)

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162.

Zeitschriftenartikel

Nikiforova, V. J.; Kopka, J.; Tolstikov, V.; Fiehn, O.; Hopkins, L.; Hawkesford, M. J.; Hesse, H.; Hoefgen, R.: Systems rebalancing of metabolism in response to sulfur deprivation, as revealed by metabolome analysis of arabidopsis plants. Plant Physiology 138 (1), S. 304 - 318 (2005)

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163.

Zeitschriftenartikel

Rautengarten, C.; Steinhauser, D.; Buessis, D.; Stintzi, A.; Schaller, A.; Kopka, J.; Altmann, T.: Inferring Hypotheses on Functional Relationships of Genes: Analysis of the Arabidopsis thaliana Subtilase Gene Family. PLoS Computational Biology 1 (4), S. e40 (2005)

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164.

Zeitschriftenartikel

Schauer, N.; Steinhauser, D.; Strelkov, S.; Schomburg, D.; Allison, G.; Moritz, T.; Lundgren, K.; Roessner-Tunali, U.; Forbes, M. G.; Willmitzer, L. et al.; Fernie, A. R.; Kopka, J.: GC-MS libraries for the rapid identification of metabolites in complex biological samples. FEBS Letters 579 (6), S. 1332 - 1337 (2005)

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165.

Zeitschriftenartikel

Scholz, M.; Kaplan, F.; Guy, C. L.; Kopka, J.; Selbig, J.: Non-linear PCA: a missing data approach. Bioinformatics 21 (20), S. 3887 - 3895 (2005)

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166.

Zeitschriftenartikel

Urbanczyk-Wochniak, E.; Baxter, C.; Kolbe, A.; Kopka, J.; Sweetlove, L. J.; Fernie, A. R.: Profiling of diurnal patterns of metabolite and transcript abundance in potato (Solanum tuberosum) leaves. Planta 221 (6), S. 891 - 903 (2005)

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167.

Zeitschriftenartikel

Bino, R. J.; Hall, R. D.; Fiehn, O.; Kopka, J.; Saito, K.; Draper, J.; Nikolau, B. J.; Mendes, P.; Roessner-Tunali, U.; Beale, M. H. et al.; Trethewey, R. N.; Lange, B. M.; Wurtele, E. S.; Sumner, L. W.: Potential of metabolomics as a functional genomics tool. Trends in Plant Science 9 (9), S. 418 - 425 (2004)

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168.

Zeitschriftenartikel

Colebatch, G.; Desbrosses, G.; Ott, T.; Krusell, L.; Montanari, O.; Kloska, S.; Kopka, J.; Udvardi, M. K.: Global changes in transcription orchestrate metabolic differentiation during symbiotic nitrogen fixation in Lotus japonicus. Plant Journal 39 (4), S. 487 - 512 (2004)

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169.

Zeitschriftenartikel

Jenkins, H.; Hardy, N.; Beckmann, M.; Draper, J.; Smith, A. R.; Taylor, J.; Fiehn, O.; Goodacre, R.; Bino, R. J.; Hall, R. et al.; Kopka, J.; Lane, G. A.; Lange, B. M.; Liu, J. R.; Mendes, P.; Nikolau, B. J.; Oliver, S. G.; Paton, N. W.; Rhee, S.; Roessner-Tunali, U.; Saito, K.; Smedsgaard, J.; Sumner, L. W.; Wang, T.; Walsh, S.; Wurtele, E. S.; Kell, D. B.: A proposed framework for the description of plant metabolomics experiments and their results. Nature Biotechnology 22 (12), S. 1601 - 1606 (2004)

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170.

Zeitschriftenartikel

Kaplan, F.; Kopka, J.; Haskell, D. W.; Zhao, W.; Schiller, K. C.; Gatzke, N.; Sung, D. Y.; Guy, C. L.: Exploring the temperature-stress metabolome of Arabidopsis. Plant Physiology 136 (4), S. 4159 - 4168 (2004)

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171.

Zeitschriftenartikel

Klotke, J.; Kopka, J.; Gatzke, N.; Heyer, A. G.: Impact of soluble sugar concentrations on the acquisition of freezing tolerance in accessions of Arabidopsis thaliana with contrasting cold adaptation - evidence for a role of raffinose in cold acclimation. Plant Cell and Environment 27 (11), S. 1395 - 1404 (2004)

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172.

Zeitschriftenartikel

Luedemann, A.; Weicht, D.; Selbig, J.; Kopka, J.: PaVESy: Pathway visualization and editing system. Bioinformatics 20 (16), S. 2841 - 2844 (2004)

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173.

Zeitschriftenartikel

Steinhauser, D.; Junker, B. H.; Luedemann, A.; Selbig, J.; Kopka, J.: Hypothesis-driven approach to predict transcriptional units from gene expression data. Bioinformatics 20 (12), S. 1928 - 1939 (2004)

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174.

Zeitschriftenartikel

Steinhauser, D.; Usadel, B.; Luedemann, A.; Thimm, O.; Kopka, J.: CSB.DB: a comprehensive systems-biology database. Bioinformatics 20 (18), S. 3647 - 3651 (2004)

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175.

Zeitschriftenartikel

Birkemeyer, C.; Kolasa, A.; Kopka, J.: Comprehensive chemical derivatization for gas chromatography-mass spectrometry-based multi-targeted profiling of the major phytohormones. Journal of Chromatography A 993 (1-2), S. 89 - 102 (2003)

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176.

Zeitschriftenartikel

Hunt, L.; Mills, L. N.; Pical, C.; Leckie, C. P.; Aitken, F. L.; Kopka, J.; Mueller-Roeber, B.; McAinsh, M. R.; Hetherington, A. M.; Gray, J. E.: Phospholipase C is required for the control of stomatal aperture by ABA. Plant Journal 34 (1), S. 47 - 55 (2003)

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177.

Zeitschriftenartikel

Urbanczyk-Wochniak, E.; Luedemann, A.; Kopka, J.; Selbig, J.; Roessner-Tunali, U.; Willmitzer, L.; Fernie, A. R.: Parallel analysis of transcript and metabolic profiles: a new approach in systems biology. EMBO Reports 4 (10), S. 989 - 993 (2003)

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178.

Zeitschriftenartikel

Wagner, C.; Sefkow, M.; Kopka, J.: Construction and application of a mass spectral and retention time index database generated from plant GC/EI-TOF-MS metabolite profiles. Phytochemistry 62 (6), S. 887 - 900 (2003)

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179.

Zeitschriftenartikel

Bohmert, K.; Balbo, I.; Kopka, J.; Mittendorf, V.; Nawrath, C.; Poirier, Y.; Tischendorf, G.; Trethewey, R. N.; Willmitzer, L.: Transgenic Arabidopsis plants can accumulate polyhydroxybutyrate to up to 4% of their fresh weight. Planta 211 (6), S. 841 - 845 (2000)

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180.

Zeitschriftenartikel

Fiehn, O.; Kopka, J.; Doermann, P.; Altmann, T.; Trethewey, R. N.; Willmitzer, L.: Metabolite profiling for plant functional genomics. Nature Biotechnology 18 (11), S. 1157 - 1161 (2000)

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