Urbanczyk-Wochniak, E.; Leisse, A.; Roessner-Tunali, U.; Lytovchenko, A.; Reismeier, J.; Willmitzer, L.; Fernie, A. R.: Expression of a bacterial xylose isomerase in potato tubers results in an altered hexose composition and a consequent induction of metabolism. Plant and Cell Physiology 44 (12), pp. 1359 - 1367 (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), pp. 989 - 993 (2003)

Fernie, A. R.; Roscher, A.; Ratcliffe, R. G.; Kruger, N. J.: Activation of pyrophosphate: fructose-6-phosphate 1-phosphotransferase by fructose 2,6-bisphosphate stimulates conversion of hexose phosphates to triose phosphates but does not influence accumulation of carbohydrates in phosphate-deficient tobacco cells. Physiologia Plantarum 114 (2), pp. 172 - 181 (2002)

Fernie, A. R.; Swiedrych, A.; Tauberger, E.; Lytovchenko, A.; Trethewey, R. N.; Willmitzer, L.: Potato plants exhibiting combined antisense repression of cytosolic and plastidial isoforms of phosphoglucomutase surprisingly approximate wild type with respect to the rate of starch synthesis. Plant Physiology and Biochemistry 40 (11), pp. 921 - 927 (2002)

Fernie, A. R.; Tauberger, E.; Lytovchenko, A.; Roessner, U.; Willmitzer, L.; Trethewey, R. N.: Antisense repression of cytosolic phosphoglucomutase in potato (Solanum tuberosum) results in severe growth retardation, reduction in tuber number and altered carbon metabolism. Planta 214 (4), pp. 510 - 520 (2002)

Fernie, A. R.; Tiessen, A.; Stitt, M.; Willmitzer, L.; Geigenberger, P.: Altered metabolic fluxes result from shifts in metabolite levels in sucrose phosphorylase-expressing potato tubers. Plant Cell and Environment 25 (10), pp. 1219 - 1232 (2002)

Fernie, A. R.; Willmitzer, L.; Trethewey, R. N.: Sucrose to starch: a transition in molecular plant physiology. Trends in Plant Science 7 (1), pp. 35 - 41 (2002)

Lytovchenko, A.; Bieberich, K.; Willmitzer, L.; Fernie, A. R.: Carbon assimilation and metabolism in potato leaves deficient in plastidial phosphoglucomutase. Planta 215 (5), pp. 802 - 811 (2002)

Lytovchenko, A.; Sweetlove, L.; Pauly, M.; Fernie, A. R.: The influence of cytosolic phosphoglucomutase on photosynthetic carbohydrate metabolism. Planta 215 (6), pp. 1013 - 1021 (2002)

Regierer, B.; Fernie, A. R.; Springer, F.; Perez-Melis, A.; Leisse, A.; Koehl, K. I.; Willmitzer, L.; Geigenberger, P.; Kossmann, J.: Starch content and yield increase as a result of altering adenylate pools in transgenic plants. Nature Biotechnology 20 (12), pp. 1256 - 1260 (2002)

Roessner, U.; Willmitzer, L.; Fernie, A. R.: Metabolic profiling and biochemical phenotyping of plant systems. Plant Cell Reports 21 (3), pp. 189 - 196 (2002)

Veramendi, J.; Fernie, A. R.; Leisse, A.; Willmitzer, L.; Trethewey, R. N.: Potato hexokinase 2 complements transgenic Arabidopsis plants deficient in hexokinase 1 but does not play a key role in tuber carbohydrate metabolism. Plant Molecular Biology 49 (5), pp. 491 - 501 (2002)

Fernie, A. R.; Roessner, U.; Geigenberger, P.: The sucrose analog palatinose leads to a stimulation of sucrose degradation and starch synthesis when supplied to discs of growing potato tubers. Plant Physiology 125 (4), pp. 1967 - 1977 (2001)

Fernie, A. R.; Roessner, U.; Leisse, A.; Lubeck, J.; Trethewey, R. N.; Willmitzer, L.: Simultaneous antagonistic modulation of enzyme activities in transgenic plants through the expression of a chimeric transcript. Plant Physiology and Biochemistry 39 (10), pp. 825 - 830 (2001)

Fernie, A. R.; Roessner, U.; Trethewey, R. N.; Willmitzer, L.: The contribution of plastidial phosphoglucomutase to the control of starch synthesis within the potato tuber. Planta 213 (3), pp. 418 - 426 (2001)

Fernie, A. R.; Roscher, A.; Ratcliffe, R. G.; Kruger, N. J.: Fructose 2,6-bisphosphate activates pyrophosphate: fructose-6-phosphate 1-phosphotransferase and increases triose phosphate to hexose phosphate cycling in heterotrophic cells. Planta 212 (2), pp. 250 - 263 (2001)

Fernie, A. R.; Willmitzer, L.: Molecular and biochemical triggers of potato tuber development. Plant Physiology 127 (4), pp. 1459 - 1465 (2001)

Fernie, A. R.; Willmitzer, L.: Update on tuber formation, dormancy and sprouting. Molecular and biochemical triggers of potato tuber development. Plant Physiology 127 (4), pp. 1459 - 1465 (2001)

Roessner, U.; Luedemann, A.; Brust, D.; Fiehn, O.; Linke, T.; Willmitzer, L.; Fernie, A. R.: Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. Plant Cell 13 (1), pp. 11 - 29 (2001)

Roessner, U.; Willmitzer, L.; Fernie, A. R.: High-resolution metabolic phenotyping of genetically and environmentally diverse potato tuber systems. Identification of phenocopies. Plant Physiology 127 (3), pp. 749 - 764 (2001)

Trethewey, R. N.; Fernie, A. R.; Bachmann, A.; Fleischer-Notter, H.; Geigenberger, P.; Willmitzer, L.: Expression of a bacterial sucrose phosphorylase in potato tubers results in a glucose-independent induction of glycolysis. Plant, Cell & Environment 24 (3), pp. 357 - 365 (2001)

Geigenberger, P.; Fernie, A. R.; Gibon, Y.; Christ, M.; Stitt, M.: Metabolic activity decreases as an adaptive response to low internal oxygen in growing potato tubers. Journal of Biological Chemistry 381 (8), pp. 723 - 740 (2000)

Tauberger, E.; Fernie, A. R.; Emmermann, M.; Renz, A.; Kossmann, J.; Willmitzer, L.; Trethewey, R. N.: Antisense inhibition of plastidial phosphoglucomutase provides compelling evidence that potato tuber amyloplasts import carbon from the cytosol in the form of glucose-6-phosphate. Plant Journal 23 (1), pp. 43 - 53 (2000)

Hempstead, P. D.; Yewdall, S. J.; Fernie, A. R.; Lawson, D. M.; Artymiuk, P. J.; Rice, D. W.; Ford, G. C.; Harrison, P. M.: Comparison of the three-dimensional structures of recombinant human H and horse L ferritins at high resolution. Journal of Molecular Biology 268 (2), pp. 424 - 448 (1997)

Fernie, A. R.; Bauwe, H.; Weber, A. P.M. (Eds.): Photorespiration: Methods and Protocols. Humanapress, New York (2017), 274 pp.

Baginsky, S.; Fernie, A. R.: Plant Systems Biology. Birkhäuser Verlag, Basel, SUI (2007)

Wen, W.; Jia, X.; Zhang, W.; Jiang, X.; Fernie, A. R.: Understanding carotenoid biosynthetic pathway control points using metabolomic analysis and natural genetic variation. In: Methods in Enzymology, Vol. 671, pp. 127 - 151 (2022)

Zhu, F.; Fernie, A. R.; Scossa, F. (Central Metabolism, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society), F.: Preparation and Curation of Omics Data for Genome-Wide Association Studies. In: Methods in Molecular Biology, Vol. 2481 (Eds. Torkamabeh, D.; Belzile, F.). Humana, New York, NY (2022)

Borghi, M.; de Souza, L. P.; Fernie, A. R.: Measurement of Flower Metabolite Concentrations Using Gas Chromatography–Mass Spectrometry and High-Performance Liquid Chromatography–Mass Spectrometry. In: Methods in Molecular Biology, Vol. 2484 (Ed. Lambing, C.) (2022)

Alseekh, S.; Fernie, A. R.: Using Metabolomics to Assist Plant Breeding. In: Crop Breeding: Genetic Improvement Methods, Vol. 2264, pp. 33 - 46 (Ed. Tripodi, P.). Springer US, New York, NY (2021)

Bauwe, H.; Fernie, A. R.: With a Little Help from My Friends: The Central Role of Photorespiration and Related Metabolic Processes in the Acclimation and Adaptation of Plants to Oxygen and to Low-CO2 Stress. In: Photosynthesis, Respiration, and Climate Change, Vol. 48, pp. 355 - 385 (Eds. Becklin, K. M.; Ward, J. K.; Way, D. A.). Springer, Cham (2021)

Naake, T.; Gaquerel, E.; Fernie, A. R.: Annotation of Specialized Metabolites from High-Throughput and High Resolution Mass Spectrometry Metabolomics. In: Computational Methods and Data Analysis for Metabolomics, pp. 209 - 225 (Ed. Li, S.). Springer US, New York, NY (2020)

Llorente, C.; Jimenez, R.; Brotman, Y.; Fernie, A. R.; Sreenivasulu, N.; Jackie: Rice Grain Quality Benchmarking Through Profiling of Volatiles and Metabolites in Grains Using Gas Chromatography Mass Spectrometry. In: Rice Grain Quality: Methods and Protocols, Vol. 1892, pp. 187 - 199 (Ed. Sreenivasulu, N.). Springer New York, New York, NY (2019)

Alseekh, S.; Wu, S.; Brotman, Y.; Fernie, A. R.: Guidelines for Sample Normalization to Minimize Batch Variation for Large-Scale Metabolic Profiling of Plant Natural Genetic Variance. In: Methods in Molecular Biology, Vol. 1778, pp. 33 - 46 (Ed. António, C.). Humana Press, Clifton, N.J. (2018)

de Souza, L. P.; Fernie, A. R.; Tohge, T.: Carbon Atomic Survey for Identification of Selected Metabolic Fluxes. In: Methods in Molecular Biology, Vol. 1778, pp. 59 - 70 (Ed. António, C.). Humana Press, Clifton, N.J. (2018)

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, Vol. 1778, pp. 225 - 240 (Ed. 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, pp. 339 - 358 (Ed. Guo, Y.). Springer New York, New York, NY (2018)

de Souza, L. P.; Szecowka, M.; Fernie, A. R.; Tohge, T.: 13CO2 labeling and mass spectral analysis of photorespiration. In: Methods in Molecular Biology, Vol. 1653, pp. 157 - 166. Humana Press, Clifton, N.J. (2017)

Del-Saz, N.F.; Ribas-Carbo, M.; Martorell, G.; Fernie, A. R.; Florez-Sarasa, I. D.: Measurements of electron partitioning between cytochrome and alternative oxidase pathways in plant tissues. In: Methods in Molecular Biology, Vol. 1670, pp. 203 - 217. Humana Press, Clifton, N.J. (2017)

Fernie, A. R.; Bauwe, H.; Sweetlove, L.J.: Investigating the role of the photorespiratory pathway in non-photosynthetic tissues. In: Methods in Molecular Biology, Vol. 1653, pp. 217 - 225. Humana Press, Clifton, N.J. (2017)

Fernie, A. R.; Tohge, T.: The Genetics of Plant Metabolism. In: Annual Review of Genetics, Vol. 51, pp. 287 - 310. Annual Reviews, Palo Alto (2017)

Obata, T.; Rosado-Souza, L.; Fernie, A. R.: Coupling radiotracer experiments with chemical fractionation for the estimation of respiratory fluxes. In: Methods in Molecular Biology, Vol. 1670, pp. 17 - 30. Humana Press, Clifton, N.J. (2017)

Omena-Garcia, R.P.; Araújo, W.L.; Gibon, Y.; Fernie, A. R.; Nunes-Nesi, A.: Measurement of tricarboxylic acid cycle enzyme activities in plants. In: Methods in Molecular Biology, Vol. 1670, pp. 167 - 182. Springer, New York, NY (2017)

Osorio, S.; Do, P. T.; Fernie, A. R.: Profiling Primary Metabolites of Tomato Fruit with Gas Chromatography/Mass Spectrometry. In: Plant Metabolomics: Methods and Protocols, 2012/02/29 Ed., pp. 101 - 110 (Eds. Hardy, N. W.; Hall, R. D.). Humana Press Inc., Totowa, NJ, USA (2012)

Osorio, S.; Fernie, A. R.: Plant Systems Biology. In: Systems Biology (Ed. Meyers, R. A.). Wiley-Blackwell (2012)

Fernie, A. R.; Keurentjes, J. J. B.: Genetics, genomics and metabolomics. In: The biology of plant metabolomics, 8, 2011/05/03 Ed., pp. 219 - 260 (Ed. Hall, R. D.). Blackwell-Wiley, London, UK (2011)

Fait, A.; Sienkiewicz-Porzucek, A.; Fernie, A. R.: Metabolomics approaches to advance understanding of nitrogen assimilation and carbon nitrogen interactions. In: Nitrogen Metabolism in Plants in the Post-Genomic Era, 10, pp. 249 - 268 (Eds. Foyer, C. H.; Zhang, H.). Wiley-Blackwell, Oxford, UK (2010)

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, pp. 19 - 38 (Ed. Weckwerth, W.). Humana Press Inc., Totowa, NJ, USA (2007)

Urbanczyk-Wochniak, E.; Willmitzer, L.; Fernie, A. R.: Integrating profiling data: using linear correlation to reveal coregulation of transcript and metabolites. In: Metabolomics: Methods and Protocols, pp. 77 - 85 (Ed. Weckwerth, W.). Humana Press Inc., Totowa, NJ, USA (2007)

Carrari, F.; Schauer, N.; Willmitzer, L.; Fernie, A. R.: Systems biology: A renaissance of the Top-down approach for plant analysis. In: Plant Metabolomics, pp. 185 - 198 (Eds. Nagata, T.; Lörz, H.; Widholm, J. M.). Springer-Verlag, Heidelberg, GER (2006)