Publications of Joachim Kopka

1.

Journal Article

Cheong, B.E.; Beine-Golovchuk, O.; Gorka, M.; Ho, W.W.H.; Martinez-Seidel, F.; Firmino, A.; Skirycz, A.; Roessner, U.; Kopka, J.: Arabidopsis REI-LIKE proteins activate ribosome biogenesis during cold acclimation. Scientific Reports 11 (1), 2410 (2021)

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2.

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Franzisky, B. L.; Geilfus, C.-M.; Romo-Perez, M. L.; Fehrle, I.; Erban, A.; Kopka, J.; Zorb, C.: Acclimatisation of guard cell metabolism to long-term salinity. Plant, Cell and Environment 44 (3), pp. 870 - 884 (2021)

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3.

Journal Article

Luzarowski, M.; Vicente, R.; Kiselev, A.; Wagner, M.; Schlossarek, D.; Erban, A.; de Souza, L. P.; Childs, D.; Wojciechowska, I.; Luzarowska, U. et al.; Gorka, M.; Sokolowska, E.; Kosmacz, M.; Moreno, J.C.; Brzezinska, A.; Vegesna, B.; Kopka, J.; Fernie, A. R.; Willmitzer, L.; Ewald, J. C.; Skirycz, A.: Global mapping of protein–metabolite interactions in Saccharomyces cerevisiae reveals that Ser-Leu dipeptide regulates phosphoglycerate kinase activity. Communications Biology 4 (1), 181 (2021)

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4.

Journal Article

Pries, C.; Razaghi-Moghadam, Z.; Kopka, J.; Nikoloski, Z.: Integration of relative metabolomics and transcriptomics time-course data in a metabolic model pinpoints effects of ribosome biogenesis defects on Arabidopsis thaliana metabolism. Scientific Reports 11 (1), 4787 (2021)

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5.

Journal Article

Samo, N.; Ebert, A.; Kopka, J.; Mozgová, I.: Plant chromatin, metabolism and development – an intricate crosstalk. Current Opinion in Plant Biology 61, 102002 (2021)

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6.

Journal Article

Schaarschmidt, S.; Lawas, L.M.F.; Kopka, J.; Jagadish, S. V. K.; Zuther, E.: Physiological and molecular attributes contribute to high night temperature tolerance in cereals. Plant, Cell and Environment (2021)

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7.

Journal Article

Schumacher, C.; Krannich, C. T.; Maletzki, L.; Koehl, K. I.; Kopka, J.; Sprenger, H.; Hincha, D. K.; Seddig, S.; Peters, R.; Hamera, S. et al.; Zuther, E.; Haas, M.; Horn, R.: Unravelling Differences in Candidate Genes for Drought Tolerance in Potato (Solanum tuberosum L.) by Use of New Functional Microsatellite Markers. Genes 12 (4), 494 (2021)

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8.

Journal Article

Takahashi, D.; Johnson, K.; Hao, P.; Tuong, T.; Erban, A.; Sampathkumar, A.; Bacic, A.; Livingston III, D. P.; Kopka, J.; Kuroha, T. et al.; Yokoyama, R.; Nishitani, K.; Zuther, E.; Hincha, D. K.: Cell wall modification by the xyloglucan endotransglucosylase/hydrolase XTH19 influences freezing tolerance after cold and sub-zero acclimation. Plant, Cell and Environment 44 (3), pp. 915 - 930 (2021)

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9.

Journal Article

Cotton, C. A. R.; Bernhardsgrütter, I.; He, H.; Burgener, S.; Schulz, L.; Paczia, N.; Dronsella, B.; Erban, A.; Toman, S.; Dempfle, M. et al.; de Maria, A.; Kopka, J.; Lindner, S. N.; Erb, T. J.; Bar-Even, A.: Underground isoleucine biosynthesis pathways in E. coli. eLife 9, e54207 (2020)

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10.

Journal Article

Firmino, A.; Gorka, M.; Graf, A.; Skirycz, A.; Martinez-Seidel, F.; Zander, K.; Kopka, J.; Beine-Golovchuk, O.: Separation and paired proteome profiling of plant chloroplast and cytoplasmic ribosomes. Plants 9 (7), 892 (2020)

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11.

Journal Article

Haas, M.; Sprenger, H.; Zuther, E.; Peters, R.; Seddig, S.; Walther, D.; Kopka, J.; Hincha, D. K.; Koehl, K. I.: Can Metabolite- and Transcript-Based Selection for Drought Tolerance in Solanum tuberosum Replace Selection on Yield in Arid Environments? Frontiers in Plant Science 11, 1071 (2020)

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12.

Journal Article

Kalampokis, I.F.; Erban, A.; Amillis, S.; Diallinas, G.; Kopka, J.; Aliferis, K.A.: Untargeted metabolomics as a hypothesis-generation tool in plant protection product discovery: Highlighting the potential of trehalose and glycerol metabolism of fungal conidiospores as novel targets. Metabolomics 16 (7), 79 (2020)

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13.

Journal Article

Martinez-Seidel, F.; Beine-Golovchuk, O.; Hsieh, Y.-C.; Kopka, J.: Systematic review of plant ribosome heterogeneity and specialization. Frontiers in Plant Science 11, 948 (2020)

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14.

Journal Article

Moing, A.; Allwood, J. W.; Aharoni, A.; Baker, J.; Beale, M. H.; Ben-Dor, S.; Biais, B.; Brigante, F.; Burger, Y.; Deborde, C. et al.; Erban, A.; Faigenboim, A.; Gur, A.; Goodacre, R.; Hansen, T. H.; Jacob, D.; Katzir, N.; Kopka, J.; Lewinsohn, E.; Maucourt, M.; Meir, S.; Miller, S.; Mumm, R.; Oren, E.; Paris, H. S.; Rogachev, I.; Rolin, D.; Saar, U.; Schjoerring, J. K.; Tadmor, Y.; Tzuri, G.; de Vos, R. C.H.; Ward, J. L.; Yeselson, E.; Hall, R. D.; Schaffer, A. A.: Comparative Metabolomics and Molecular Phylogenetics of Melon (Cucumis melo, Cucurbitaceae) Biodiversity. Metabolites 10 (3), 121 (2020)

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15.

Journal Article

Schaarschmidt, S.; Lawas, L.M.F.; Glaubitz, U.; Li, X.; Erban, A.; Kopka, J.; Krishna Jagadish, S.V.; Hincha, D. K.; Zuther, E.: Season affects yield and metabolic profiles of rice (Oryza sativa) under high night temperature stress in the field. International Journal of Molecular Sciences 21 (9), 3187 (2020)

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16.

Journal Article

Treves, H.; Siemiatkowska, B.; Luzarowska, U.; Murik, O.; Fernandez-Pozo, N.; Moraes, T. A.; Erban, A.; Armbruster, U.; Brotman, Y.; Kopka, J. et al.; Rensing, S. A.; Szymanski, J.; Stitt, M.: Multi-omics reveals mechanisms of total resistance to extreme illumination of a desert alga. Nature Plants 6, pp. 1031 - 1043 (2020)

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17.

Journal Article

Whitcomb, S. J.; Rakpenthai, A.; Brückner, F.; Fischer, A.; Parmar, S.; Erban, A.; Kopka, J.; Hawkesford, M.J.; Hoefgen, R.: Cysteine and Methionine Biosynthetic Enzymes Have Distinct Effects on Seed Nutritional Quality and on Molecular Phenotypes Associated With Accumulation of a Methionine-Rich Seed Storage Protein in Rice. Frontiers in Plant Science 11, 1118 (2020)

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18.

Journal Article

Lawas, L.M.F.; Erban, A.; Kopka, J.; Jagadish, S. V. K.; Zuther, E.; Hincha, D. K.: Metabolic responses of rice source and sink organs during recovery from combined drought and heat stress in the field. GigaScience 8 (8), giz102 (2019)

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19.

Journal Article

Lawas, L.M.F.; Li, X.; Erban, A.; Kopka, J.; Jagadish, S. V. K.; Zuther, E.; Hincha, D. K.: Metabolic responses of rice cultivars with different tolerance to combined drought and heat stress under field conditions. GigaScience 8 (5), giz050 (2019)

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20.

Journal Article

Armarego-Marriott, T.; Kowalewska, L.; Burgos, A.; Fischer, A.; Thiele, W.; Erban, A.; Strand, D.; Kahlau, S.; Hertle, A. P.; Kopka, J. et al.; Walther, D.; Reich, Z.; Schöttler, M. A.; Bock, R.: Highly Resolved Systems Biology to Dissect the Etioplast-to-Chloroplast Transition in Tobacco Leaves. Plant Physiology 180 (1), pp. 654 - 681 (2019)

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21.

Journal Article

Awada, R.; Campa, C.; Gibault, E.; Dechamp, E.; Georget, F.; Lepelley, M.; Abdallah, C.; Erban, A.; Martinez-Seidel, F.; Kopka, J. et al.; Legendre, L.; Leran, S.; Conejero, G.; Verdeil, J.-L.; Crouzillat, D.; Breton, D.; Bertrand, B.; Etienne, H.: Unravelling the Metabolic and Hormonal Machinery During Key Steps of Somatic Embryogenesis: A Case Study in Coffee. International Journal of Molecular Sciences 20 (19), 4665 (2019)

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22.

Journal Article

Calabrese, S.; Cusant, L.; Sarazin, A.; Niehl, A.; Erban, A.; Brulé, D.; Recorbet, G.; Wipf, D.; Roux, C.; Kopka, J. et al.; Boller, T.; Courty, P.-E.: Imbalanced regulation of fungal nutrient transports according to phosphate availability in a symbiocosm formed by poplar, sorghum and Rhizophagus irregularis. Frontiers in Plant Science 10, 1617 (2019)

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23.

Journal Article

Erban, A.; Fehrle, I.; Martinez-Seidel, F.; Brigante, F.; Más, A. L.; Baroni, V.; Wunderlin, D.; Kopka, J.: Discovery of food identity markers by metabolomics and machine learning technology. Scientific Reports 9 (1), 9697 (2019)

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24.

Journal Article

Heyneke, E.; Watanabe, M.; Erban, A.; Duan, G.; Buchner, P.; Walther, D.; Kopka, J.; Hawkesford, M. J.; Hoefgen, R.: Effect of Senescence Phenotypes and Nitrate Availability on Wheat Leaf Metabolome during Grain Filling. Agronomy 9 (6), 305 (2019)

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25.

Journal Article

Li, L.; Krznar, P.; Erban, A.; Agazzi, A.; Martin-Levilain, J.; Supale, S.; Kopka, J.; Zamboni, N.; Maechler, P.: Metabolomics identifies a biomarker revealing in vivo loss of functional β-cell mass before diabetes onset. Diabetes 68 (12), pp. 2272 - 2286 (2019)

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26.

Journal Article

Madhavan, S.; Paranidharan, V.; Erban, A.; Al-Sadi, A.M.; Kopka, J.; Velazhahan, R.: The metabolic response of suspension-cultured cells from blast-resistant and -susceptible rice (Oryza sativa L.) genotypes to a Pyricularia oryzae elicitor. Indian Phytopathology 72 (2), pp. 195 - 202 (2019)

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27.

Journal Article

Nieva, A.S.; Vilas, J.M.; Gárriz, A.; Maiale, S.J.; Menéndez, A.B.; Erban, A.; Kopka, J.; Ruiz, O.A.: The fungal endophyte Fusarium solani provokes differential effects on the fitness of two Lotus species. Plant Physiology and Biochemistry 144, pp. 100 - 109 (2019)

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28.

Journal Article

Richter, J. A.; Behr, J. H.; Erban, A.; Kopka, J.; Zoerb, C.: Ion-dependent metabolic responses of Vicia faba L. to salt stress. Plant, Cell and Environment 42 (1-SI), pp. 295 - 309 (2019)

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29.

Journal Article

Schwachtje, J.; Whitcomb, S. J.; Firmino, A.; Zuther, E.; Hincha, D. K.; Kopka, J.: Induced, Imprinted, and Primed Responses to Changing Environments: Does Metabolism Store and Process Information? Frontiers in Plant Science 10, 106 (2019)

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30.

Journal Article

Takahashi, D.; Gorka, M.; Erban, A.; Graf, A.; Kopka, J.; Zuther, E.; Hincha, D. K.: Both cold and sub-zero acclimation induce cell wall modification and changes in the extracellular proteome in Arabidopsis thaliana. Scientific Reports 9 (1), 2289 (2019)

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31.

Journal Article

Ulaszewska, M. M.; Weinert, C. H.; Trimigno, A.; Portmann, R.; Andres Lacueva, C.; Badertscher, R.; Brennan, L.; Brunius, C.; Bub, A.; Capozzi, F. et al.; Rosso, M. C.; Cordero, C. E.; Daniel, H.; Durand, S.; Egert, B.; Ferrario, P. G.; Feskens, E. J. M.; Franceschi, P.; Garcia-Aloy, M.; Giacomoni, F.; Giesbertz, P.; Gonzalez-Dominguez, R.; Hanhineva, K.; Hemeryck, L. Y.; Kopka, J.; Kulling, S. E.; Llorach, R.; Manach, C.; Mattivi, F.; Migne, C.; Munger, L. H.; Ott, B.; Picone, G.; Pimentel, G.; Pujos-Guillot, E.; Riccadonna, S.; Rist, M. J.; Rombouts, C.; Rubert, J.; Skurk, T.; Harsha, P. S. C. S.; Van Meulebroek, L.; Vanhaecke, L.; Vazquez-Fresno, R.; Wishart, D.; Vergeres, G.: Nutrimetabolomics: An Integrative Action for Metabolomic Analyses in Human Nutritional Studies. Molecular Nutriton & Food Research 63 (1-SI), 1800384 (2019)

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32.

Journal Article

Wenke, K.; Kopka, J.; Schwachtje, J.; van Dongen, J. T.; Piechulla, B.: Volatiles of rhizobacteria Serratia and Stenotrophomonas alter growth and metabolite composition of Arabidopsis thaliana. Plant Biology 21 (SI suppl.), pp. 109 - 119 (2019)

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33.

Journal Article

Zuther, E.; Schaarschmidt, S.; Fischer, A.; Erban, A.; Pagter, M.; Mubeen, U.; Giavalisco, P.; Kopka, J.; Sprenger, H.; Hincha, D. K.: Molecular signatures associated with increased freezing tolerance due to low temperature memory in Arabidopsis. Plant, Cell and Environment 42 (3- SI), pp. 854 - 873 (2019)

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34.

Journal Article

Atanasov, K. E.; Liu, C.; Erban, A.; Kopka, J.; Parker, J. E.; Alcázar, R.: NLR Mutations Suppressing Immune Hybrid Incompatibility and Their Effects on Disease Resistance. Plant Physiology 177 (3), pp. 1152 - 1169 (2018)

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35.

Journal Article

Beine-Golovchuk, O.; Firmino, A.; Dabrowska, A.; Schmidt, S.; Erban, A.; Walther, D.; Zuther, E.; Hincha, D. K.; Kopka, J.: Plant Temperature Acclimation and Growth Rely on Cytosolic Ribosome Biogenesis Factor Homologs. Plant Physiology 176 (3), pp. 2251 - 2276 (2018)

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36.

Journal Article

Geuss, D.; Lortzing, T.; Schwachtje, J.; Kopka, J.; Steppuhn, A.: Oviposition by Spodoptera exigua on Solanum dulcamara Alters the Plant’s Response to Herbivory and Impairs Larval Performance. International Journal of Molecular Sciences 19 (12), 4008 (2018)

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37.

Journal Article

Rai, S.; Lucius, S.; Kern, R.; Bauwe, H.; Kaplan, A.; Kopka, J.; Hagemann, M.: The Synechocystis sp PCC 6803 Genome Encodes Up to Four 2-Phosphoglycolate Phosphatases. Frontiers in Plant Science 9, 1718 (2018)

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38.

Journal Article

Ruebsam, H.; Kirsch, F.; Reimann, V.; Erban, A.; Kopka, J.; Hagemann, M.; Hess, W. R.; Klaehn, S.: The iron-stress activated RNA 1 (IsaR1) coordinates osmotic acclimation and iron starvation responses in the cyanobacterium Synechocystis sp PCC 6803. Environmental Microbiology Reports 20 (8-SI), pp. 2757 - 2768 (2018)

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39.

Journal Article

Schwachtje, J.; Fischer, A.; Erban, A.; Kopka, J.: Primed primary metabolism in systemic leaves: a functional systems analysis. Scientific Reports 8, 216 (2018)

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40.

Journal Article

Sprenger, H.; Erban, A.; Seddig, S.; Rudack, K.; Thalhammer, A.; Le, M. Q.; Walther, D.; Zuther, E.; Koehl, K. I.; Kopka, J. et al.; Hincha, D. K.: Metabolite and transcript markers for the prediction of potato drought tolerance. Plant Biotechnology Journal 16 (4), pp. 939 - 950 (2018)

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41.

Journal Article

Dethloff, F.; Orf, I.; Kopka, J.: Rapid in situ 13C tracing of sucrose utilization in Arabidopsis sink and source leaves. Plant Methods 13 (1), 87 (2017)

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42.

Journal Article

Pagter, M.; Alpers, J.; Erban, A.; Kopka, J.; Zuther, E.; Hincha, D. K.: Rapid transcriptional and metabolic regulation of the deacclimation process in cold acclimated Arabidopsis thaliana. BMC Genomics 18 (1), 731 (2017)

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43.

Journal Article

Andersen, U. B.; Kjaer, K. H.; Erban, A.; Alpers, J.; Hincha, D. K.; Kopka, J.; Zuther, E.; Pagter, M.: Impact of seasonal warming on overwintering and spring phenology of blackcurrant. Environmental and Experimental Botany 140, pp. 96 - 109 (2017)

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44.

Journal Article

Glaubitz, U.; Li, X.; Schaedel, S.; Erban, A.; Sulpice, R.; Kopka, J.; Hincha, D. K.; Zuther, E.: Integrated analysis of rice transcriptomic and metabolomic responses to elevated night temperatures identifies sensitivity- and tolerance-related profiles. Plant, Cell and Environment 40 (1), pp. 121 - 137 (2017)

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45.

Journal Article

Heyneke, E.; Watanabe, M.; Erban, A.; Duan, G. Y.; Buchner, P.; Walther, D.; Kopka, J.; Hawkesford, M. J.; Hoefgen, R.: Characterization of the Wheat Leaf Metabolome during Grain Filling and under Varied N-Supply. Frontiers in Plant Science 8, 2048 (2017)

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46.

Journal Article

Kopka, J.; Schmidt, S.; Dethloff, F.; Pade, N.; Berendt, S.; Schottkowski, M.; Martin, N.; Dühring, U.; Kuchmina, E.; Enke, H. et al.; Kramer, D.; Wilde, A.; Hagemann, M.; Friedrich, A.: Systems analysis of ethanol production in the genetically engineered cyanobacterium Synechococcus sp. PCC 7002. Biotechnology for Biofuels 10 (1), 56 (2017)

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47.

Journal Article

Rahmoune, B.; Morsli, A.; Khelifi-Slaoui, M.; Khelifi, L.; Strueh, A.; Erban, A.; Kopka, J.; Prell, J.; van Dongen, J. T.: Isolation and characterization of three new PGPR and their effects on the growth of Arabidopsis and Datura plants. Journal of Plant Interaction 12 (1), pp. 1 - 6 (2017)

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48.

Journal Article

Rotsch, A.H.; Kopka, J.; Feussner, I.; Ischebeck, T.: Central metabolite and sterol profiling divides tobacco male gametophyte development and pollen tube growth into eight metabolic phases. The Plant Journal 92 (1), pp. 129 - 146 (2017)

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49.

Journal Article

Treves, H.; Murik, O.; Kedem, I.; Eisenstadt, D.; Meir, S.; Rogachev, I.; Szymanski, J.; Keren, N.; Orf, I.; Tiburcio, A. F. et al.; Alcazar, R.; Aharoni, A.; Kopka, J.; Kaplan, A.: Metabolic Flexibility Underpins Growth Capabilities of the Fastest Growing Alga. Current Biology 27 (16), pp. 2559 - 2567 (2017)

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50.

Journal Article

Zarza, X.; Atanasov, K. E.; Marco, F.; Arbona, V.; Carrasco, P.; Kopka, J.; Fotopoulos, V.; Munnik, T.; Gomez-Cadenas, A.; Tiburcio, A. F. et al.; Alcazar, R.: Polyamine oxidase 5 loss-of-function mutations in Arabidopsis thaliana trigger metabolic and transcriptional reprogramming and promote salt stress tolerance. Plant, Cell and Environment 40 (4), pp. 527 - 542 (2017)

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51.

Journal Article

Staroske, N.; Conrad, U.; Kumlehn, J.; Hensel, G.; Radchuk, R.; Erban, A.; Kopka, J.; Weschke, W.; Weber, H.: Increasing abscisic acid levels by immunomodulation in barley grains induces precocious maturation without changing grain composition. Journal of Experimental Botany 67 (9), pp. 2675 - 2687 (2016)

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52.

Journal Article

Coleto, I.; Trenas, A. T.; Erban, A.; Kopka, J.; Pineda, M.; Alamillo, J. M.: Functional specialization of one copy of glutamine phosphoribosyl pyrophosphate amidotransferase in ureide production from symbiotically fixed nitrogen in Phaseolus vulgaris. Plant, Cell and Environment 39 (8), pp. 1767 - 1779 (2016)

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53.

Journal Article

Fuentes, P.; Zhou, F.; Erban, A.; Karcher, D.; Kopka, J.; Bock, R.: A new synthetic biology approach allows transfer of an entire metabolic pathway from a medicinal plant to a biomass crop. eLife 5, e13664 (2016)

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54.

Journal Article

Gal, A.; Wirth, R.; Kopka, J.; Fratzl, P.; Faivre, D.; Scheffel, A.: Macromolecular recognition directs calcium ions to coccolith mineralization sites. Science 353 (6299), pp. 590 - 593 (2016)

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55.

Journal Article

Hilker, M.; Schwachtje, J.; Baier, M.; Balazadeh, S.; Bäurle, I.; Geiselhardt, S.; Hincha, D. K.; Kunze, R.; Mueller-Roeber, B.; Rillig, M. C. et al.; Rolff, J.; Romeis, T.; Schmülling, T.; Steppuhn, A.; van Dongen, J.; Whitcomb, S. J.; Wurst, S.; Zuther, E.; Kopka, J.: Priming and memory of stress responses in organisms lacking a nervous system. Biological Reviews 91 (4), pp. 1118 - 1133 (2016)

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56.

Journal Article

Lee, Y. P.; Funk, C.; Erban, A.; Kopka, J.; Koehl, K. I.; Zuther, E.; Hincha, D. K.: Salt stress responses in a geographically diverse collection of Eutrema/Thellungiella spp. accessions. Functional Plant Biology 43, pp. 590 - 606 (2016)

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57.

Journal Article

Lortzing, T.; Calf, O. W.; Boehlke, M.; Schwachtje, J.; Kopka, J.; Geuss, D.; Kosanke, S.; van Dam, N. M.; Steppuhn, A.: Extrafloral nectar secretion from wounds of Solanum dulcamara. Nature Plants 2 (5), 16056 (2016)

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58.

Journal Article

Mumm, R.; Hageman, J. A.; Calingacion, M. N.; de Vos, R. C. H.; Jonker, H. H.; Erban, A.; Kopka, J.; Hansen, T. H.; Laursen, K. H.; Schjoerring, J. K. et al.; Ward, J. L.; Beale, M. H.; Jongee, S.; Rauf, A.; Habibi, F.; Indrasari, S. D.; Sakhan, S.; Ramli, A.; Romero, M.; Reinke, R. F.; Ohtsubo, K.; Boualaphanh, C.; Fitzgerald, M. A.; Hall, R. D.: Multi-platform metabolomics analyses of a broad collection of fragrant and non-fragrant rice varieties reveals the high complexity of grain quality characteristics. Metabolomics 12 (2), 38 (2016)

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59.

Journal Article

Orf, I.; Timm, S.; Bauwe, H.; Fernie, A. R.; Hagemann, M.; Kopka, J.; Nikoloski, Z.: Can cyanobacteria serve as a model of plant photorespiration? - a comparative meta-analysis of metabolite profiles. Journal of Experimental Botany 67 (10), pp. 2941 - 2952 (2016)

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60.

Journal Article

Orf, I.; Schwarz, D.; Kaplan, A.; Kopka, J.; Hess, W.R.; Hagemann, M.; Klähn, S.: CyAbrB2 contributes to the transcriptional regulation of low CO2 acclimation in synechocystis sp. PCC 6803. Plant and Cell Physiology 57 (10), pp. 2232 - 2243 (2016)

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Publications of Joachim Kopka

Journal Article (197)