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. et al.; 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 (3), S. 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, S. 14 (2006)

Kopka, J.: Current challenges and developments in GC-MS based metabolite profiling technology. Journal of Biotechnology 124 (1), S. 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 (1), S. 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 (6), S. 593 - 604 (2006)

Schauer, N.; Semel, Y.; Roessner, U.; Gur, A.; Balbo, I.; Carrari, F.; Pleban, T.; Perez-Melis, A.; Bruedigam, C.; Kopka, J. et al.; Willmitzer, L.; Zamir, D.; Fernie, A. R.: Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nature Biotechnology 24 (4), S. 447 - 454 (2006)

Skirycz, A.; Reichelt, M.; Burow, M.; Birkemeyer, C.; Rolcik, J.; Kopka, J.; Zanor, M. I.; Gershenzon, J.; Strnad, M.; Szopa, J. et al.; 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 (1), S. 10 - 24 (2006)

Damiani, I.; Morreel, K.; Danoun, S.; Goeminne, G.; Yahiaoui, N.; Marque, C.; Kopka, J.; Messens, E.; Goffner, D.; Boerjan, W. et al.; 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 (5), S. 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 (4), S. 1302 - 1318 (2005)

Kopka, J.; Schauer, N.; Krueger, S.; Birkemeyer, C.; Usadel, B.; Bergmueller, E.; Doermann, P.; Weckwerth, W.; Gibon, Y.; Stitt, M. et al.; Willmitzer, L.; Fernie, A. R.; Steinhauser, D.: GMD@CSB.DB: the Golm Metabolome Database. Bioinformatics 21 (8), S. 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 (8), S. 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 (1), S. 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 (1), S. 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 (4), S. e40 (2005)

Schauer, N.; Steinhauser, D.; Strelkov, S.; Schomburg, D.; Allison, G.; Moritz, T.; Lundgren, K.; Roessner-Tunali, U.; Forbes, M. G.; Willmitzer, L. et al.; Fernie, A. R.; Kopka, J.: GC-MS libraries for the rapid identification of metabolites in complex biological samples. FEBS Letters 579 (6), S. 1332 - 1337 (2005)

Scholz, M.; Kaplan, F.; Guy, C. L.; Kopka, J.; Selbig, J.: Non-linear PCA: a missing data approach. Bioinformatics 21 (20), S. 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 (6), S. 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. et al.; 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 (9), S. 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. et al.; 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 (12), S. 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 (4), S. 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 (11), S. 1395 - 1404 (2004)

Luedemann, A.; Weicht, D.; Selbig, J.; Kopka, J.: PaVESy: Pathway visualization and editing system. Bioinformatics 20 (16), S. 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 (12), S. 1928 - 1939 (2004)

Steinhauser, D.; Usadel, B.; Luedemann, A.; Thimm, O.; Kopka, J.: CSB.DB: a comprehensive systems-biology database. Bioinformatics 20 (18), S. 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 (1-2), S. 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 (1), S. 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 (10), S. 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 (6), S. 887 - 900 (2003)

Bohmert, K.; Balbo, I.; Kopka, J.; Mittendorf, V.; Nawrath, C.; Poirier, Y.; Tischendorf, G.; Trethewey, R. N.; Willmitzer, L.: Transgenic Arabidopsis plants can accumulate polyhydroxybutyrate to up to 4% of their fresh weight. Planta 211 (6), S. 841 - 845 (2000)

Fiehn, O.; Kopka, J.; Doermann, P.; Altmann, T.; Trethewey, R. N.; Willmitzer, L.: Metabolite profiling for plant functional genomics. Nature Biotechnology 18 (11), S. 1157 - 1161 (2000)

Fiehn, O.; Kopka, J.; Trethewey, R. N.; Willmitzer, L.: Identification of uncommon plant metabolites based on calculation of elemental compositions using gas chromatography and quadrupole mass spectrometry. Analytical Chemistry 72 (15), S. 3573 - 3580 (2000)

Roessner, U.; Wagner, C.; Kopka, J.; Trethewey, R. N.; Willmitzer, L.: Simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry. Plant Journal 23 (1), S. 131 - 142 (2000)

Aitken, F. L.; Pical, C.; Mueller-Roeber, B.; Kopka, J.; Gray, J. E.: Phosphoinositide signal transduction in guard cells. Biochemical Society Transactions 26 (4), S. S397 (1998)

Kopka, J.; Pical, C.; Gray, J. E.; Mueller-Roeber, B.: Molecular and enzymatic characterization of three phosphoinositide-specific phospholipase C isoforms from potato. Plant Physiology 116 (1), S. 239 - 250 (1998)

Kopka, J.; Ludewig, M.; Mueller-Roeber, B.: Complementary DNAs encoding eukaryotic-type cytidine-5'-diphosphate-diacylglycerol synthases of two plant species. Plant Physiology 113 (3), S. 997 - 1002 (1997)

Kopka, J.; Provart, N. J.; Mueller-Roeber, B.: Potato guard cells respond to drying soil by a complex change in the expression of genes related to carbon metabolism and turgor regulation. Plant Journal 11 (4), S. 871 - 882 (1997)

Kopka, J.; Ohlrogge, J. B.; Jaworski, J. G.: Analysis of in-Vivo Levels of Acyl-Thioesters with Gas-Chromatography Mass-Spectrometry of the Butylamide Derivative. Analytical Biochemistry 224 (1), S. 51 - 60 (1995)

Kopka, J.; Robers, M.; Schuch, R.; Spener, F.: Acyl Carrier Proteins from Developing Seeds of Cuphea-Lanceolata Ait. Planta 191 (1), S. 102 - 111 (1993)

Erban, A.; Martinez-Seidel, F.; Rajarathinam, Y.; Dethloff, F.; Orf, I.; Fehrle, I.; Alpers, J.; Beine-Golovchuk, O.; Kopka, J.: Multiplexed Profiling and Data Processing Methods to Identify Temperature-Regulated Primary Metabolites Using Gas Chromatography Coupled to Mass Spectrometry. In: Plant Cold Acclimation: Methods in molecular biology, Bd. 2156, S. 203 - 239 (Hg. Hincha, D. K.; Zuther, E.) (2020)

Vallarino, J. G.; Erban, A.; Fehrle, I.; Fernie, A. R.; Kopka, J.; Osorio, S.: Acquisition of Volatile Compounds by Gas Chromatography–Mass Spectrometry (GC-MS). In: Methods in Molecular Biology, Bd. 1778, S. 225 - 240 (Hg. António, C.). Humana Press, Clifton, N.J. (2018)

Watanabe, M.; Tohge, T.; Balazadeh, S.; Erban, A.; Giavalisco, P.; Kopka, J.; Mueller-Roeber, B.; Fernie, A. R.; Hoefgen, R.: Comprehensive Metabolomics Studies of Plant Developmental Senescence. In: Plant Senescence: Methods and Protocols, S. 339 - 358 (Hg. Guo, Y.). Springer New York, New York, NY (2018)

Zuther, E.; Lee, Y. P.; Erban, A.; Kopka, J.; Hincha, D. K.: Natural Variation in Freezing Tolerance and Cold Acclimation Response in Arabidopsis thaliana and Related Species. In: Survival Strategies in Extreme Cold and Desiccation: Adaptation Mechanisms and Their Applications, S. 81 - 98 (Hg. Iwaya-Inoue, M.; Sakurai, M.; Uemura, M.). Springer Singapore, Singapore (2018)

Dethloff, F.; Erban, A.; Orf, I.; Alpers, J.; Fehrle, I.; Beine-Golovchuk, O.; Schmidt, S.; Schwachtje, J.; Kopka, J.: Profiling Methods to Identify Cold-Regulated Primary Metabolites Using Gas Chromatography Coupled to Mass Spectrometry. In: Plant Cold Acclimation: Methods and Protocols, S. 171 - 197. HUMANA PRESS INC, 999 RIVERVIEW DR, STE 208, TOTOWA, NJ 07512-1165 USA, 999 RIVERVIEW DR, STE 208, TOTOWA, NJ 07512-1165 USA (2014)

Huege, J.; Goetze, J.; Dethloff, F.; Junker, B.; Kopka, J.: Quantification of Stable Isotope Label in Metabolites via Mass Spectrometry. In: Plant Chemical Genomics: Methods and Protocols, S. 213 - 223. HUMANA PRESS INC, 999 RIVERVIEW DR, STE 208, TOTOWA, NJ 07512-1165 USA (2014)

Huege, J.; Goetze, J.; Dethloff, F.; Junker, B.; Kopka, J.: Quantification of stable isotope label in metabolites via mass spectrometry. In: Methods in Molecular Biology, Bd. 1056, S. 213 - 223. Humana Press Inc., Totowa, NJ, USA (2012)

Hummel, J.; Strehmel, N.; Boelling, C.; Schmidt, S.; Walther, D.; Kopka, J.: Mass spectral search and analysis using the Golm Metabolome Database. In: The Handbook of Plant Metabolomics, S. 321 - 343 (Hg. Weckwerth, W.) (2012)

Lüdemann, A.; von Malotky, L.; Erban, A.; Kopka, J.: TagFinder: Preprocessing software for the fingerprinting and the profiling of gas chromatography-mass spectrometry based metabolome analyses. In: Methods in Molecular Biology, Bd. 860, S. 255 - 286 (Hg. Hardy, N. W.; Hall, R. D.). Springer, Berlin (2012)

Luedemann, A.; von Malotky, L.; Erban, A.; Kopka, J.: TagFinder-preprocessing software for the fingerprinting and the profiling of gas chromatography-mass spectrometry (GC-MS) based metabolome analyses. In: Plant Metabolomics: Methods and Protocols, 2012/02/29 Aufl., S. 255 - 286 (Hg. Hardy, N. W.; Hall, R. D.). Humana Press Inc., Totowa, NJ, USA (2012)

Schudoma, C.; Steinfath, M.; Sprenger, H.; van Dongen, J.; Hincha, D. K.; Zuther, E.; Geigenberger, P.; Kopka, J.; Koehl, K. I.; Walther, D.: Conducting molecular biomarker discovery studies in plants. In: High Throughput Phenotyping in Plants, 10 (Hg. Normanly, J.). Humana Press Inc., Totowa, NJ, USA (2012)

Allwood, J. W.; De Vos, R. C.H.; Moing, A.; Deborde, C.; Erban, A.; Kopka, J.; Goodacre, R.; Hall, R. D.: Plant metabolomics and its potential for systems biology research: background concepts, technology and methodology. In: Methods in Enzymology, Bd. 500, S. 299 - 336 (Hg. Jameson, D.; Verma, M.; Westerhoff, H.V.). Elsevier - Academic Press, Amsterdam, NED (2011)

Kopka, J.; Walther, D.; Allwood, J. W.; Goodacre, R.: Progress in chemometrics and biostatistics for plant applications: Or a good red wine is a bad white wine. In: The biology of plant metabolomics, 10, 2011/05/03 Aufl., S. 317 - 342 (Hg. Hall, R. D.). Blackwell-Wiley, London, UK (2011)

Erban, A.; Schauer, N.; Fernie, A. R.; Kopka, J.: Nonsupervised construction and application of mass spectral and retention time index libraries from time-of-flight gas chromatography-mass spectrometry metabolite profiles. In: Metabolomics: Methods and Protocols, S. 19 - 38 (Hg. Weckwerth, W.). Humana Press Inc., Totowa, NJ, USA (2007)

Hummel, J.; Selbig, J.; Walther, D.; Kopka, J.: The Golm Metabolome Database: a database for GC-MS based metabolite profiling. In: Metabolomics: A Powerful Tool in Systems Biology, S. 75 - 95 (Hg. Nielsen, J.; Jewett, M.). Springer-Verlag, Berlin, Heidelberg, New York (2007)

Steinhauser, D.; Kopka, J.: Methods, applications and concepts of metabolite profiling: primary metabolism. In: Plant Systems Biology, S. 171 - 194 (Hg. Baginsky, S.; Fernie, A. R.). Verlag Birkhäuser, Basel, SUI (2007)

Zuther, E.; Koehl, K. I.; Kopka, J.: Comparative metabolome analysis of the salt response in breeding cultivars of rice. In: Advances in molecular breeding toward drought and salt tolerant crops., S. 285 - 315 (Hg. Jenks, M. A.; Hasegawa, P. M.; Jain, S. M.). Springer-Verlag, Berlin, Heidelberg, New York (2007)

Kopka, J.: Metabolomics: Comprehensive analysis of metabolism. In: Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine (Hg. Ganten, D.; Ruckpaul, K.). Springer-Verlag, Berlin, Heidelberg (2006)

Kopka, J.: Gas chromatography mass spectrometry. In: Biotechnology in Agriculture and Forestry, S. 3 - 20 (Hg. Nagata, T.; Lörz, H.; Widholm, J. M.; Dixon, R. A.; Willmitzer, L.). Springer-Verlag, Berlin, Heidelberg, New York (2006)

Udvardi, M. K.; Ott, T.; Krusell, L.; Desbrosses, G.; Voroshilova, V.; Colebatch, G.; Wandrey, M.; Montanari, O.; Kakar, K.; Krause, K. et al.; Guenther, C.; van Dongen, J. T.; Vigeolas, H.; Geigenberger, P.; Kraemer, U.; Kloska, S.; Kopka, J.; Sato, S.; Nakamura, Y.; Tabata, S.; James, E. K.; Kawaguchi, M.; Miyamoto, A.; Suganuma, N.; Sandal, N.; Stougaard, J.: Insights into nodule physiology and metabolism from transcriptomics, metabolomics, bioinformatics, and genetics. In: Biology of plant-microbe interactions, Bd. 5, S. 96 - 102 (Hg. Sánchez, F.; Quinto, C.; López-Lara, I. M.; Geiger, O.). ISMPMI, St. Paul, MN, USA (2006)

Desbrosses, G.; Steinhauser, D.; Kopka, J.; Udvardi, M. K.: Lotus metabolome analysis using GC-MS. In: Lotus japonicus handbook, S. 165 - 174 (Hg. Marquez, A. J.; Stougaard, J.; Udvardi, M.; Parniske, M.; Spaink, H. P. et al.). Kluwer, Dordrecht (2005)

Metabolic, Transcriptional and Proteomic Profiling of Cold Response in Fragaria vesca. 6th International Strawberry Symposium, Huelva, SPAIN, 2009-08. (2009)