Publications

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2009
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, Kempa, S.; Hummel, J.; Schwemmer, T.; Pietzke, M.; Strehmel, N.; Wienkoop, S.; Kopka, J.; Weckwerth, W. , Journal of Basic Microbiolgy, Volume 49(1), p.82-91, (2009)
Characterization of leaf apoplastic peroxidases and metabolites in Vigna unguiculata in response to toxic manganese supply and silicon, Führs, H.; Götze, S.; Specht, A.; Erban, A.; Gallien, S.; Heintz, D.; Van Dorsselaer, A.; Kopka, J.; Braun, H.P.; Horst, W.J. , Journal of Experimental Botany, Volume 60(6), p.1663-1678, (2009)
Composite Medicago truncatula plants harbouring Agrobacterium rhizogenes-transformed roots reveal normal mycorrhization by Glomus intraradices, Mrosk, C.; Forner, S.; Hause, G.; Küster, H.; Kopka, J.; Hause, B. , Journal of Experimental Botany, Volume 60(13), p.3797-3807, (2009)
Global changes in the transcript and metabolic profiles during symbiotic nitrogen fixation in phosphorus-stressed common bean plants, Hernandez, G.; Valdes-Lopez, O.; Ramirez, M.; Goffard, N.; Weiller, G.; Aparicio-Fabre, R.; Fuentes, S. I; Erban, A.; Kopka, J.; Udvardi, M.K.; Vance, C.P. , Plant Physiology, Volume 151(3), p.1221-1238, (2009)
Inter-laboratory reproducibility of fast gas chromatography–electron impact–time of flight mass spectrometry (GC–EI–TOF/MS) based plant metabolomics, Allwood, J.W.; Erban, A.; de Koning, S.; Dunn, W.B.; Luedemann, A.; Lommen, A.; Kay, L.; Löscher, R.; Kopka, J.; Goodacre, R. , Metabolomics, Volume 5(4), p.479-496, (2009)
Metabolome and water status phenotyping of Arabidopsis under abiotic stress cues reveals new insight into ESK1 function, Lugan, R.; Niogret, M.F.; Kervazo, L.; Larher, F.R.; Kopka, J.; Bouchereau, A. , Plant Cell and Environment, Volume 32(2), p.95-108, (2009)
Metabolic profiling of Conference pears under low oxygen stress, Pedreschi, R.; Franck, C.; Lammertyn, J.; Erban, A.; Kopka, J.; Hertog, M.; Verlinden, B.; Nicolai, B. , Postharvest Biology and Technology, Volume 51(2), p.123-130, (2009)
Transcript and metabolite profiling of the adaptive response to mild decreases in oxygen concentration in the roots of Arabidopsis plants, Van Dongen, J.T.; Fröhlich, A.; Ramírez-Aguilar, S.J.; Schauer, N.; Fernie, A.R.; Erban, A.; Kopka, J.; Clark, J.; Langer, A.; Geigenberger, P. , Annals of Botany, Volume 103(2), p.269-280, (2009)
2008
A rapid approach for phenotype-screening and database independent detection of cSNP/protein polymorphism using mass accuracy precursor alignment, Hoehenwarter, W.; van Dongen, J.T.; Wienkoop, S.; Steinfath, M.; Hummel, J.; Erban, A.; Sulpice, R.; Regierer, B.; Kopka, J.; Geigenberger, P.; Weckwerth, W. , Proteomics, Volume 8(20), p.4214-4225, (2008)
A central role of abscisic acid in stress-regulated carbohydrate metabolism, Kempa, S.; Krasensky, J.; Dal Santo, S.; Kopka, J.; Jonak, C. , PLoS One, Volume 3(12), p.e3935, (2008)
Estimation of retention index thresholds for compound matching using routine gas chromatography-mass spectrometry based metabolite profiling experiments, Strehmel, N.; Hummel, J.; Erban, A.; Strassburg, K.; Kopka, J. , Journal of Chromatography B, Volume 871, p.182-190, (2008)
Integrative functional genomics of salt acclimation in the model legume Lotus japonicus, Sanchez, D.H.; Lippold, F.; Redestig, H.; Hannah, M.; Erban, A.K.U.K.J.; Udvardi, M.K. , Plant Journal, Volume 53 (6), p.973-987, (2008)
Metabolomics of temperature stress, Guy, C.L.; Kaplan, F.; Kopka, J.; Selbig, J.; Hincha, D. , Physiologia Plantarum, Volume 132(2), p.220-235, (2008)
Metabolome phenotyping of inorganic carbon limitation in cells of the wild type and photorespiratory mutants of the cyanobacterium Synechocystis sp strain PCC 6803, Eisenhut, M.; Huege, J.; Schwarz, D.; Bauwe, H.; Kopka, J.; Hagemann, M. , Plant Physiology, Volume 148(4), p.2109-2120, (2008)
Metabolome-ionome-biomass interactions: What can we learn about salt stress by multiparallel phenotyping?, Sanchez, D.H.; Redestig, H.; Kraemer, U.; Udvardi, M.K.; Kopka, J. , Plant Signaling & Behavior, Volume 3(8), p.598-600, (2008)
Plant metabolomics coming of age, Guy, C.L.; Kopka, J.; Moritz, T. , Physiologia Plantarum, Volume 132(2), p.113-116, (2008)
Physiologic and metabolic responses of wheat seedlings to elevated and super-elevated carbon dioxide, Levine, L.H.; Kasahara, H.; Kopka, J.; Erban, A.; Fehrle, I; Kaplan, F.; Zhao, W.; Littell, R.C.; Guy, C.; Wheeler, R.; Sager, J.; Mills, A.; Levine, H.G. , Advances in Space Research, Volume 42, p.1917–1928, (2008)
Plant metabolomics reveals conserved and divergent metabolic responses to salinity, Sanchez, D.H.; Siahpoosh, M.R.; Roessner, U.; Udvardi, M.K.; Kopka, J. , Physiologia Plantarum, Volume 132 (2), p.209-219, (2008)
Simultaneous interaction of Arabidopsis thaliana with Bradyrhizobium sp strain ORS278 and Pseudomonas syringae pv tomato DC3000 leads to complex transcriptome changes, Cartieaux, F.; Contesto, C.; Gallou, A.; Desbrosses, G.; Kopka, J.; Taconnat, L.; Renou, J.P.; Touraine, B. , Molecular Plant Microbe Interactions, Volume 21(2), p.244-259, (2008)
The Golm metabolome database: a database for GC-MS based metabolite profiling, Hummel, J.; Selbig, J.; Walther, D.; Kopka, J. , Metabolomics a powerful tool in systems biology. Topics in Current Genetics Vol. 18, Berlin, Heidelberg, New York, p.75-96, (2008)
Teaching (and learning from) metabolomics - The 2006 PlantMetaNet ETNA metabolomics research school, Böttcher, C.; Centeno, D.; Freitag, J.; Hoefgen, R.; Koehl, K.; Kopka, J.; Kroymann, J.; Matros, A.; Mock, H.P.; Neumann, S.; Pfalz, M.; von Roepenack-Lahaye, E.; Schauer, N.; Trenkamp, S.; Zubriggen, M.; Fernie, A.R. , Physiologia Plantarum, Volume 132 (2), p.136-149, (2008)
TagFinder for the quantitative analysis of gas chromatography - mass spectrometry (GC-MS) based metabolite profiling experiments, Luedemann, A.; Strassburg, K.; Erban, A.; Kopka, J. , Bioinformatics, Volume 24 (5), p.732 -737, (2008)
2007
A plastid-localized glycogen synthase kinase 3 modulates stress tolerance and carbohydrate metabolism, Kempa, S.; Rozhon, W.; Samaj, J.; Erban, A.; Baluska, F.; Becker, T.; Haselmayer, J.; Schleiff, E.; Kopka, J.; Hirt, H.; Jonak, C. , Plant Journal, Volume 49 (6), p.1076-1090, (2007)
Application of gas chromatography-mass spectrometry metabolite profiling techniques to the analysis of heathland plant diets of sheep, Parveen, I; Moorby, J.M.; Fraser, M.D.; Allison, G.G.; Kopka, J. , Journal of Agricultural and Food Chemistry, Volume 55 (4), p.1129-1138, (2007)
Comparative metabolome analysis of the salt response in breeding cultivars of rice, Zuther, E.; Koehl, K.; Kopka, J. , Advances in molecular breeding toward drought and salt tolerant crops, Berlin, Heidelberg, New York, p.285-315, (2007)
Design of metabolite recovery by variations of the metabolite profiling protocol, Birkemeyer, C.; Kopka, J. , Concepts in plant metabolomics, Dordrecht, Netherlands, p.45-69, (2007)
GC-EI-TOF-MS analysis of in vivo-carbon-partitioning into soluble metabolite pools of higher plants by monitoring isotope dilution after (13CO2)-labelling, Huege, J.; Sulpice, R.; Gibon, Y.; Lisec, J.; Koehl, K.; Kopka, J. , Phytochemistry, Volume 68 (16-18), p.2258-2272, (2007)
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, Hannah, M.A.; Kraemer, K.M.; Geffroy, V.; Kopka, J.; Blair, M.W.; Erban, A.; Vallejos, C.E.; Heyer, A.G.; Sanders, F.E.T.; Millner, P.A.; Pilbeam, D.J. , New Phytologist, Volume 176 (3), p.537-549, (2007)
Methods, applications and concepts of metabolite profiling: primary metabolism, Steinhauser, D.; Kopka, J. , Plant systems biology. Experimentia Supplementum Vol. 97, Basel, p. 171-194, (2007)
Molecular phenotyping of lignin-modified tobacco reveals associated changes in cell-wall metabolism, primary metabolism, stress metabolism and photorespiration, Dauwe, R.; Morreel, K.; Goeminne, G.; Gielen, B.; Rohde, A.; Van Beeumen, J.; Ralph, J.; Boudet, A.M.; Kopka, J.; Rochange, S.F.; Halpin, C.; Messens, E.; Boerjan, W. , Plant Journal, Volume 52 (2), p.263-285, (2007)
Non-supervised construction and application of mass spectral and retention time index libraries from time-of-flight GC-MS metabolite profiles. , Erban, A.; Schauer, N.; Fernie, A.R.; Kopka, J. , Metabolomics: methods and protocols, Totowa, p.19-38, (2007)
Phosphorus stress in common bean: Root transcript and metabolic responses, Hernandez, G.; Ramirez, M.; Valdes-Lopez, O.; Tesfaye, M.; Graham, M.A.; Czechowski, T.; Schlereth, A.; Wandrey, M.; Erban, A.; Cheung, F.; Wu, H.C.; Lara, M.; Town, C.D.; Kopka, J.; Udvardi, M.K.; Vance, C.P. , Plant Physiology, Volume 144 (2), p.752-767, (2007)
Proposed minimum reporting standards for chemical analysis, 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.; Hankemeier, T.; Hardy, N.; Harnly, J.; Higashi, R.; Kopka, J.; Lane, A.N.; Lindon, J.C.; Marriott, P.; Nicholls, A.W. , Metabolomics, Volume 3(3), p.211-221, (2007)
Regulation of arbuscular mycorrhization by apoplastic invertases: enhanced invertase activity in the leaf apoplast affects the symbiotic interaction, Schaarschmidt, S.; Kopka, J.; Ludwig-Mueller, J.; Hause, B. , Plant Journal, Volume 51(3), p.390-405, (2007)
Transcript and metabolite profiling during cold acclimation of Arabidopsis reveals an intricate relationship of cold-regulated gene expression with modifications in metabolite content, Kaplan, F.; Kopka, J.; Sung, D.Y.; Zhao, W.; Popp, M.; Porat, R.; Guy, C.L. , Plant Journal, Volume 50 (6), p.967-981, (2007)
2004
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, Klotke, J.; Kopka, J.; Gatzke, N.; Heyer, AG. , Plant Cell Environment, Volume 27, p.1395-1404, (2004)