Fernie, A. R.; Tohge, T.: The Genetics of Plant Metabolism. In: Annual Review of Genetics, Bd. 51, S. 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, Bd. 1670, S. 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, Bd. 1670, S. 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 Aufl., S. 101 - 110 (Hg. Hardy, N. W.; Hall, R. D.). Humana Press Inc., Totowa, NJ, USA (2012)

Osorio, S.; Fernie, A. R.: Plant Systems Biology. In: Systems Biology (Hg. 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 Aufl., S. 219 - 260 (Hg. 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, S. 249 - 268 (Hg. 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, S. 19 - 38 (Hg. 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, S. 77 - 85 (Hg. 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, S. 185 - 198 (Hg. 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, S. 253 - 270 (Hg. 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, S. 1 - 29 (Hg. 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 (Hg. Ketner, C.; Hicks, M. G.) (2004)

Fernie, A. R.; Willmitzer, L.: Carbohydrate metabolism. In: The handbook of Plant Biotechnology (Hg. 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. (Hg. 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 (Hg. 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, S. 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, S. 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, S. 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, Bd. 01. Proceedings of the German Conference on Bioinformatics, GCB 2007, Potsdam, Germany, 26. September 2007 - 28. September 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, S. 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, S. 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, S. 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), S. 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), S. 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), S. 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), S. 55 - 55. (2004)

Fernie, A. R.: Interview with Alisdair R. Fernie. (2014)

Fernie, A. R.; Aharoni, A.; Willmitzer, L.; Stitt, M.; Tohge, T.; Kopka, J.; Carroll, A. J.; Saito, K.; Fraser, P. D.; DeLuca, V.: Recommendations for Reporting Metabolite Data, The Plant Cell 23, S. 2477 - 2482 (2011)

Yan, J.; Fernie, A. R.: Editorial overview: 21st Century solutions for crop improvement. Current Opinion in Biotechnology 83, 102982 (2023)

Fernie, A. R.; Hashida, S.-N.; Yoshimura, K.; Gakière, B.; Mou, Z.; Pétriacq, P.: Editorial: NAD Metabolism and Signaling in Plants. Frontiers in Plant Science 11, 146 (2020)

Fernie, A. R.; Wen, W.: Editorial overview: Evolution of metabolic diversity. Current Opinion in Plant Biology 55, S. A1 - A4 (2020)

Fernie, A. R.: Seeing is believing: the three-way division of labor in the photosynthetic thylakoid membrane. The Plant Journal 97 (3), S. 410 - 411 (2019)

Fernie, A. R.: Making sense of the complex role of the mitochondria in mediating the plant touch response. The Plant Journal 97 (4), S. 621 - 622 (2019)

Fernie, A. R.; Sweetlove, L.: The Plant Journal actively supports Open Science and data transparency. The Plant Journal 97 (3), S. 409 - 409 (2019)

Sweetlove, L. J.; Aharoni, A.; Fernie, A. R.: Introducing TPJ Fellowships for early stage Principal Investigators. The Plant Journal 100 (3), S. 435 - 435 (2019)

Kopka, J.; Fernie, A. R.: Editorial overview: Plant synthetic and systems biology. Current Opinion in Biotechnology 49, S. viii - xi (2018)

Fernie, A. R.; Pichersky, E.: Focus Issue on Metabolism: Metabolites, Metabolites Everywhere. Plant Physiology 169 (3), S. 1421 - 1423 (2015)

Batushansky, A.; Kirma, M.; Grillich, N.; Toubiana, D.; Pham, P. A.; Balbo, I.; Fromm, H.; Galili, G.; Fernie, A. R.; Fait, A.: Combined Transcriptomics and Metabolomics of Arabidopsis thaliana Seedlings Exposed to Exogenous GABA Suggest Its Role in Plants Is Predominantly Metabolic. Molecular Plant 7 (6), S. 1065 - 1068 (2014)

Fernie, A. R.: Editorial overview - the Computational approaches in aid of advancing understanding in Plant Physiology. Frontiers in Plant Science 2, S. 78 (2011)

Kopka, J.; Fernie, A. R.; Weckwerth, W.; Gibon, Y.; Stitt, M.: Metabolite profiling in plant biology: platforms and destinations. Genome Biology 5 (6), S. 109 (2004)

Martinez Rivas, F.J.; Fernie, A. R.: Metabolomics to understand metabolic regulation underpinning fruit ripening, development, and quality. (2024)

Yoshida, T.; Fernie, A. R.: Hormonal regulation of plant primary metabolism under drought. (2024)

Artins, A.; Martins, M. C. M.; Meyer, C.; Fernie, A. R.; Caldana, C.: Sensing and regulation of C and N metabolism – novel features and mechanisms of the TOR and SnRK1 signaling pathways. (2024)

Li, H.; Che, R.; Zhu, J.; Yang, X.; Li, J.; Fernie, A. R.; Yan, J.: Multi-omics-driven advances in the understanding of triacylglycerol biosynthesis in oil seeds. (2024)

Sun, Y.; Fernie, A. R.: Plant secondary metabolism in a fluctuating world: climate change perspectives. (2023)

Song, Y.-C.; Das, D.; Zhang, Y.; Chen, M.-X.; Fernie, A. R.; Zhu, F.-Y.; Han, J.: Proteogenomics-based functional genome research: approaches, applications, and perspectives in plants. (2023)

Xie, J.-Q.; Zhou, X.; Jia, Z.-C.; Su, C.-F.; Zhang, Y.; Fernie, A. R.; Zhang, J.; Du, Z.-Y.; Chen, M.-X.: Alternative Splicing, An Overlooked Defense Frontier of Plants with Respect to Bacterial Infection. (2023)

Siqueira, J.A.; Zsögön, A.; Fernie, A. R.; Nunes-Nesi, A.; Araújo, W.L.: Does day length matter for nutrient responsiveness? (2023)

Fernie, A. R.; Sampathkumar, A.: SPOTLIGHT: Chemical imaging reveals diverse functions of TCA cycle intermediates in root growth and development. (2023)