Complete publication list

Publications of Joachim Kopka

Journal Article (150)

  1. 1.
    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)
  2. 2.
    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)
  3. 3.
    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)
  4. 4.
    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)
  5. 5.
    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)
  6. 6.
    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)
  7. 7.
    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)
  8. 8.
    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)
  9. 9.
    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)
  10. 10.
    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)
  11. 11.
    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)
  12. 12.
    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)
  13. 13.
    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)
  14. 14.
    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)
  15. 15.
    Pade, N.; Erdmann, S.; Enke, H.; Dethloff, F.; Duehring, U.; Georg, J.; Wambutt, J.; Kopka, J.; Hess, W. R.; Zimmermann, R. et al.; Kramer, D.; Hagemann, M.: Insights into isoprene production using the cyanobacterium Synechocystis sp PCC 6803. Biotechnology for Biofuels 9, 89 (2016)
  16. 16.
    Sequera-Mutiozabal, M.I.; Erban, A.; Kopka, J.; Atanasov, K.E.; Bastida, J.; Fotopoulos, V.; Alcázar, R.; Tiburcio, A.F.: Global metabolic profiling of arabidopsis polyamine oxidase 4 (AtPAO4) loss-of-function mutants exhibiting delayed dark-induced senescence. Frontiers in Plant Science 7 (FEB2016), 173 (2016)
  17. 17.
    Sprenger, H.; Kurowsky, C.; Horn, R.; Erban, A.; Seddig, S.; Rudack, K.; Fischer, A.; Walther, D.; Zuther, E.; Koehl, K. I. et al.; Hincha, D. K.; Kopka, J.: The drought response of potato reference cultivars with contrasting tolerance. Plant Cell Environment 39 (11), pp. 2370 - 2389 (2016)
  18. 18.
    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)
  19. 19.
    Agudelo-Romero, P.; Erban, A.; Rego, C.; Carbonell-Bejerano, P.; Nascimento, T.; Sousa, L.; Martinez-Zapater, J. M.; Kopka, J.; Fortes, A. M.: Transcriptome and metabolome reprogramming in Vitis vinifera cv. Trincadeira berries upon infection with Botrytis cinerea. Journal of Experimental Botany 66 (7), pp. 1769 - 1785 (2015)
  20. 20.
    Dobritzsch, S.; Weyhe, M.; Schubert, R.; Dindas, J.; Hause, G.; Kopka, J.; Hause, B.: Dissection of jasmonate functions in tomato stamen development by transcriptome and metabolome analyses. BMC Biology 13, 28 (2015)
  21. 21.
    Gaude, N.; Bortfeld, S.; Erban, A.; Kopka, J.; Krajinski, F.: Symbiosis dependent accumulation of primary metabolites in arbuscule-containing cells. BMC Plant Biology 15 (1), 234 (2015)
  22. 22.
    Glaubitz, U.; Erban, A.; Kopka, J.; Hincha, D. K.; Zuther, E.: High night temperature strongly impacts TCA cycle, amino acid and polyamine biosynthetic pathways in rice in a sensitivity-dependent manner. Journal of Experimental Botany 66 (20), pp. 6385 - 6397 (2015)
  23. 23.
    Klahn, S.; Orf, I.; Schwarz, D.; Matthiessen, J. K. F.; Kopka, J.; Hess, W. R.; Hagemann, M.: Integrated Transcriptomic and Metabolomic Characterization of the Low-Carbon Response Using an ndhR Mutant of Synechocystis sp. PCC 6803. Plant physiology 169 (3), pp. 1540 - 156 (2015)
  24. 24.
    Koehler, G.; Rohloff, J.; Wilson, R. C.; Kopka, J.; Erban, A.; Winge, P.; Bones, A. M.; Davik, J.; Alsheikh, M. K.; Randall, S. K.: Integrative "omic" analysis reveals distinctive cold responses in leaves and roots of strawberry, Fragaria x ananassa 'Korona'. Frontiers in Plant Science 6, 826 (2015)
  25. 25.
    Kohl, S.; Hollmann, J.; Erban, A.; Kopka, J.; Riewe, D.; Weschke, W.; Weber, H.: Metabolic and transcriptional transitions in barley glumes reveal a role as transitory resource buffers during endosperm filling. Journal of Experimental Botany 66 (5), pp. 1397 - 1411 (2015)
  26. 26.
    Li, X.; Lawas, L. M. F.; Malo, R.; Glaubitz, U.; Erban, A.; Mauleon, R.; Heuer, S.; Zuther, E.; Kopka, J.; Hincha, D. K. et al.; Jagadish, K. S. V.: Metabolic and transcriptomic signatures of rice floral organs reveal sugar starvation as a factor in reproductive failure under heat and drought stress. Plant, Cell and Environment 38 (10), pp. 2171 - 2192 (2015)
  27. 27.
    Orf, I.; Klahn, S.; Schwarz, D.; Frank, M.; Hess, W. R.; Hagemann, M.; Kopka, J.: Integrated Analysis of Engineered Carbon Limitation in a Quadruple CO2/HCO3- Uptake Mutant of Synechocystis sp. PCC 6803. Plant Cell Physiology 169 (3), pp. 1787 - 1806 (2015)
  28. 28.
    Pant, B.-D.; Pant, P.; Erban, A.; Huhman, D.; Kopka, J.; Scheible, W.-R.: Identification of primary and secondary metabolites with phosphorus status-dependent abundance in Arabidopsis, and of the transcription factor PHR1 as a major regulator of metabolic changes during phosphorus limitation. Plant, Cell and Environment 38 (1), pp. 172 - 187 (2015)
  29. 29.
    Richter, J. A.; Erban, A.; Kopka, J.; Zoerb, C.: Metabolic contribution to salt stress in two maize hybrids with contrasting resistance. Plant Science 233, pp. 107 - 115 (2015)
  30. 30.
    Salek, R. M.; Neumann, S.; Schober, D.; Hummel, J.; Billiau, K.; Kopka, J.; Correa, E.; Reijmers, T.; Rosato, A.; Tenori, L. et al.; Turano, P.; Marin, S.; Deborde, C.; Jacob, D.; Rolin, D.; Dartigues, B.; Conesa, P.; Haug, K.; Rocca-Serra, P.; O'Hagan, S.; Hao, J.; Vliet, M. v.; Sysi-Aho, M.; Ludwig, C.; Bouwman, J.; Cascante, M.; Ebbels, T.; Griffin, J. L.; Moing, A.; Nikolski, M.; Oresic, M.; Sansone, S.-A.; Viant, M. R.; Goodacre, R.; Guenther, U. L.; Hankemeier, T.; Luchinat, C.; Walther, D.; Steinbeck, C.: COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access. Metabolomics 11 (6), pp. 1587 - 1597 (2015)
  31. 31.
    Sprenger, H.; Rudack, K.; Schudoma, C.; Neumann, A.; Seddig, S.; Peters, R.; Zuther, E.; Kopka, J.; Hincha, D. K.; Walther, D. et al.; Koehl, K. I.: Assessment of drought tolerance and its potential yield penalty in potato. Functional Plant Biology 42 (7), pp. 655 - 667 (2015)
  32. 32.
    Devanathan, S.; Erban, A.; Perez-Torres Jr., R.; Kopka, J.; Makaroff, C. A.: Arabidopsis thaliana Glyoxalase 2-1 Is Required during Abiotic Stress but Is Not Essential under Normal Plant Growth. PLOS ONE 9 (4), e95971 (2014)
  33. 33.
    Gao, J.; van Kleeff, P. J. M.; Oecking, C.; Li, K. W.; Erban, A.; Kopka, J.; Hincha, D. K.; de Boer, A. H.: Light modulated activity of root alkaline/neutral invertase involves the interaction with 14-3-3 proteins. The Plant Journal 80 (5), pp. 785 - 796 (2014)
  34. 34.
    Hooks, M. A.; Allwood, J. W.; Harrison, J. K. D.; Kopka, J.; Erban, A.; Goodacre, R.; Balk, J.: Selective induction and subcellular distribution of ACONITASE 3 reveal the importance of cytosolic citrate metabolism during lipid mobilization in Arabidopsis. Biochemical Journal 463, pp. 309 - 317 (2014)
  35. 35.
    Meret, M.; Kopetzki, D.; Degenkolbe, T.; Kleessen, S.; Nikoloski, Z.; Tellstroem, V.; Barsch, A.; Kopka, J.; Antonietti, M.; Willmitzer, L.: From systems biology to systems chemistry: metabolomic procedures enable insight into complex chemical reaction networks in water. RSC Advances 4 (32), pp. 16777 - 16781 (2014)
  36. 36.
    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)
  37. 37.
    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 (MAR), e28224 (2014)
  38. 38.
    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)
  39. 39.
    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)
  40. 40.
    Veyel, D.; Erban, A.; Fehrle, I.; Kopka, J.; Schroda, M.: Rationales and Approaches for Studying Metabolism in Eukaryotic Microalgae. Metabolites 4 (2), pp. 184 - 217 (2014)
  41. 41.
    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 (2013)
  42. 42.
    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 (2013)
  43. 43.
    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)
  44. 44.
    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 (2013)
  45. 45.
    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)
  46. 46.
    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 (2013)
  47. 47.
    Schwarz, D.; Orf, I.; Kopka, J.; Hagemann, M.: Recent Applications of Metabolomics Toward Cyanobacteria. Metabolites (2013)
  48. 48.
    Strehmel, N.; Kopka, J.; Scheel, D.; Böttcher, C.: Annotating unknown components from GC/EI-MS-based metabolite profiling experiments using GC/APCI(+)-QTOFMS. Metabolics (2013)
  49. 49.
    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)
  50. 50.
    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)
  51. 51.
    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)
  52. 52.
    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)
  53. 53.
    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)
  54. 54.
    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)
  55. 55.
    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)
  56. 56.
    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)
  57. 57.
    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)
  58. 58.
    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)
  59. 59.
    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)
  60. 60.
    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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