Publications of J. Kopka

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).

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, 1395–1404 (2004).

Luedemann, A., Weicht, D., Selbig, J. & Kopka, J. PaVESy: Pathway visualization and editing system. Bioinformatics 20, 2841–2844 (2004).

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

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

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, 89–102 (2003).

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, 47–55 (2003).

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, 989–993 (2003).

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, 887–900 (2003).