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)

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)

Zhang, Y.; Qin, K.; Fernie, A. R.: Plant Tissue Culture and Metabolite Profiling for High-Value Natural Product Synthesis. In: Methods in Modern Biology, Vol. 2827, pp. 405 - 416 (Eds. Loyola-Vargas, V.; Ochoa-Alejo, N.) (2024)

de Souza, L. P.; Fernie, A. R.: Databases and Tools to Investigate Protein-Metabolite Interactions. In: Methods in Molecular Biology (Ed. Walker, J. M.) (2023)

Zhu, F.; Bulut, M.; Cheng, Y.; Alseekh, S.; Fernie, A. R.: Metabolite-Based Genome-Wide Association Studies of Large-Scale Metabolome Analysis to Illustrate Alterations in the Metabolite Landscape of Plants upon Responses to Stresses. In: Methods in Molecular Biology, Vol. 2642, pp. 241 - 255 (2023)

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.: 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)

Wu, S.; Alseekh, S.; Brotman, Y.; Fernie, A. R.: Metabolomic Analysis of Natural Variation in Arabidopsis. In: ARABIDOPSIS PROTOCOLS, 4 EDITION, Vol. 2200, pp. 393 - 411 (Eds. Sanchez-Serrano, J.; Salinas, J.) (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)

Geigenberger, P.; Fernie, A. R.: Starch biosynthesis in the potato tuber. In: Food Biochemistry and Food Processing, pp. 253 - 270 (Eds. Hui, Y. H.; Corke, H.; DeLeyn, I.; Nip, W.-K.; Cross, N.). Blackwell Publ., Ames, IA, USA (2006)

Lytovchenko, A.; Geigenberger, P.; Willmitzer, L.; Fernie, A. R.: Starch content in plant tissues. In: Plant Genetic Engineering: Improving the Nutritional & Therapeutic Qualities of Plants, pp. 1 - 29 (Ed. Jaiwal, P. K.). Studium Press LLC, Houston, TX, USA (2006)

Fernie, A. R.; Sweetlove, L. J.: Broad range metabolite analysis: integration into genomics programs. In: Experimental standardization of classification of enzyme characteristics (Eds. Ketner, C.; Hicks, M. G.) (2004)

Fernie, A. R.; Willmitzer, L.: Carbohydrate metabolism. In: The handbook of Plant Biotechnology (Eds. Christou, P.; Klee, H. K.). Wiley, Chichester, UK (2004)

Urbanczyk-Wochniak, E.; Fernie, A. R.; Willmitzer, L.: The utility of transcriptomics and metabolomics in systems based analysis of plant metabolism. In: Understanding the Plant Genome. (Ed. Sadowski, J.). Institute of Plant Genetics, PAS, Poznan, POL (2004)

Fernie, A. R.; Roessner, U.; Willmitzer, L.: Metabolic Profiling of Plant Cells. In: Plant Physiology 3rd Edition (Eds. Taiz, L.; Zeiger, E.). Sinauer Associates, Inc., Sunderland, MA, USA (2001)

Pick, T. R.; Brautigam, A.; Schulz, M. A.; Obata, T.; Fernie, A. R.; Weber, A. P.: PLGG1, a plastidic glycolate glycerate transporter, is required for photorespiration and defines a unique class of metabolite transporters. Proceedings of the National Academy of Sciences of the United States of America 110, pp. 3185 - 3190 (2013)

Araujo, W. L.; Trofimova, L.; Yu, K.; Steinhauser, D.; Krall, L.; Fernie, A. R.; Bunik, V. I.: On the role of the mitochondrial 2-oxoglutarate dehydrogenase complex in the amino acid metabolism. Amino Acids 41, p. S39 - S39 (2011)

Urbanczyk-Wochniak, E.; Baxter, C.; Sweetlove, L. J.; Fernie, A. R.: Profiling diurnal changes in metabolite and transcript levels in potato leaves. In: 3rd International Congress on Plant Metabolomics, pp. 183 - 192. 3rd International Congress on Plant Metabolomics, Iowa State Univ, Ames, IA. (2007)

Willmitzer, L.; Caldana, C.; Fernie, A. R.; Giavalisco, P.; MA, H.; Redestig, H.; Steinhauser, D.: Integrative Analysis of Transcriptome and Metabolome Data. In: Proceedings of the German Conference on Bioinformatics, Vol. 01. Proceedings of the German Conference on Bioinformatics, GCB 2007, Potsdam, Germany, September 26, 2007 - September 28, 2007. (2007)

Nunes-Nesi, A.; Carrari, F.; Lytovchenko, A.; Fernie, A. R.: Enhancing crop yield in Solanaceous species through the genetic manipulation of energy metabolism. In: BioScience 2005 Conference, pp. 1430 - 1434. BioScience 2005 Conference, Glasgow, SCOTLAND. (2005)

Fernie, A. R.; Riesmeire, J. W.; Martiny, A.; Ramalingam, S.; Willmitzer, L.; Trethewey, R. N.: Consequences of the expression of a bacterial glucokinase in potato tubers, both in combination with and independently of a yeast-derived invertase. In: Australian Journal of Plant Physiology, pp. 827 - 833. Australian Journal of Plant Physiology. (2000)

Hincha, D. K.; Schulz, E.; Thalhammer, A.; Tohge, T.; Sulpice, R.; Fernie, A. R.; Zuther, E.: The Role of Secondary Metabolites and COR Proteins in Plant Freezing Tolerance. In In Vitro Cellular & Developmental Biology-Animal, 50, p. S13 - S13. Tissue Culture Association, Columbia, MD (2014)

van der Merwe, M. J.; Osorio, S.; Moritz, T.; Nunes-Nesi, A.; Fernie, A. R.: The role and regulation of the tricarboxylic acid cycle in Solanum lycopersicum roots. In South African Journal of Botany, 75 (2), p. 424 - 424. (2009)

Carrari, F.; Fernie, A. R.: Characterizing the metabolic regulation that underlies tomato fruit development. In Comparative Biochemistry and Physiology a-Molecular & Integrative Physiology, 141 (3), p. S297 - S297. (2005)

Ishizaki, K.; Larson, T. A.; Schauer, N.; Fernie, A. R.; Graham, I. A.; Leaver, C. J.: The critical role of Arabidopsis electron-transfer flavoprotein:ubiquinone oxidoreductase during dark-induced starvation. In Plant Cell, 17 (9), pp. 2587 - 2600. (2005)

Urbanczyk-Wochniak, E.; Willmitzer, L.; Fernie, A. R.: mRNA Analysis of Plant Metabolic Regulation: Comparison of Transcript and Metabolic Complements of Developing Plant Tissues. In Acta Physiologiae Plantarum, 26 (3), p. 55 - 55. (2004)