Publications of J. Kopka

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., Reily, M. D., Thaden, J. J. & Viant, M. R. Proposed minimum reporting standards for chemical analysis. Metabolomics 3, 211–221 (2007).

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, 14 (2006).

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

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

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, 593–604 (2006).

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

Skirycz, A., Reichelt, M., Burow, M., Birkemeyer, C., Rolcik, J., Kopka, J., Zanor, M. I., Gershenzon, J., Strnad, M., Szopa, J., 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, 10–24 (2006).

Damiani, I., Morreel, K., Danoun, S., Goeminne, G., Yahiaoui, N., Marque, C., Kopka, J., Messens, E., Goffner, D., Boerjan, W., 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, 753–769 (2005).

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, 1302–1318 (2005).

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

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, 2685–2696 (2005).

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, 329–340 (2005).

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, 304–318 (2005).

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, e40 (2005).

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

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

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, 891–903 (2005).

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., 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, 418–425 (2004).

Jenkins, H., Hardy, N., Beckmann, M., Draper, J., Smith, A. R., Taylor, J., Fiehn, O., Goodacre, R., Bino, R. J., Hall, R., 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, 1601–1606 (2004).

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, 4159–4168 (2004).