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)

Denby, K.; Treves, H.; Bohlmann, J.; Fernie, A. R.: Announcement of the 2024 TPJ fellows. The Plant Journal 120 (5), S. 1699 - 1699 (2024)

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)

Yu, Y.; Fotopoulos, V.; Zhou, K.; Fernie, A. R.: The role of gasotransmitter hydrogen sulfide in plant cadmium stress responses. Trends in Plant Science 30 (1), S. 35 - 53 (2025)

Lachica, M.K.E.; Watanabe, M.; Kanaya, S.; Fernie, A. R.; Tohge, T.: Prospects for functional genomics of genes involved in coffee-specialized metabolism through cross-species integrative omics. Current Opinion in Plant Biology 85, 102729 (2025)

Tiozon, R. J. N.; Lenaerts, B.; Kor, S.; Demont, M.; Fernie, A. R.; Sreenivasulu, N.: Low glycemic index rice: a healthier diet for countering diabetes epidemic in Asia. Trends in Plant Science 30 (6), S. 603 - 614 (2025)

Tiozon, R. J. N.; Zhang, C.; Kim, S.-R.; Liu, Q.; Fernie, A. R.; Sreenivasulu, N.: Unlocking the potential of wild rice to bring the missing nutrition to elite grains. Plant Communications 6 (6), 101344 (2025)

Barreto, P.; Feitosa-Araujo, E.; Fernie, A. R.; Schwarzländer, M.: How to turbo charge respiration – thermogenic metabolism in plants. Current Opinion in Plant Biology 85, 102730 (2025)

Liu, F.; Zhao, Z.; Fernie, A. R.; Zhang, Y.: Towards establishing functional nitrogenase activities within plants. Trends in Biotechnology (2025)

Cao, Y.; Chen, Q.; Xu, X.; Fernie, A. R.; Li, J.; Zhang, Y.: Insights from natural rubber biosynthesis evolution for pathway engineering. Trends in Plant Science (2025)

Fettke, J.; Fernie, A. R.: Do storage reserves contribute to plant phenotypic plasticity? Trends in Plant Science 30 (4), S. 364 - 372 (2025)

Qin, K.; Ye, X.; Luo, S.; Fernie, A. R.; Zhang, Y.: Engineering carbon assimilation in plants. Journal of Integrative Plant Biology 67 (4), S. 926 - 948 (2025)

Bulut, M.; Karakas, E.; Fernie, A. R.: Metabolic responses to multi-stress: An update. Plant Stress 15, 100729 (2025)

de Oliveira, H.O.; Siqueira, J.A.; Medeiros, D.B.; Fernie, A. R.; Nunes-Nesi, A.; Araújo, W.L.: Harnessing the dynamics of plant organic acids metabolism following abiotic stresses. Plant Physiology and Biochemistry 220, 109465 (2025)

Jahan, T.; Huda, M.N.; Zhang, K.; He, Y.; Lai, D.; Dhami, N.; Quinet, M.; Ali, M.A.; Kreft, I.; Woo, S.-H. et al.; Georgiev, M.I.; Fernie, A. R.; Zhou, M.: Plant secondary metabolites against biotic stresses for sustainable crop protection. Biotechnology Advances 79, 108520 (2025)

Zhao, Z.; Fernie, A. R.; Zhang, Y.: Engineering nitrogen and carbon fixation for next-generation plants. Current Opinion in Plant Biology 85, 102699 (2025)

Liu, H.-J.; Liu, J.; Zhai, Z.; Dai, M.; Tian, F.; Wu, Y.; Tang, J.; Lu, Y.; Wang, H.; Jackson, D. et al.; Yang, X.; Qin, F.; Xu, M.; Fernie, A. R.; Zhang, Z.; Yan, J.: Maize2035: A decadal vision for intelligent maize breeding. Molecular Plant 18 (2), S. 313 - 332 (2025)

Petersen, M.; Avin-Wittenberg, T.; Bassham, D. C.; Dagdas, Y.; Fan, C.; Fernie, A. R.; Jiang, L.; Mishra, D.; Otegui, M. S.; Rodriguez, E. et al.; Hofius, D.: Autophagy in plants. Autophagy Reports 3 (1), 2395731 (2024)

Ye, X.; Qin, K.; Fernie, A. R.; Zhang, Y.: Prospects for synthetic biology in 21st Century agriculture. International Journal of Genetics and Genomics (2024)

de Vries, J.; de Vries, S.; Fernie, A. R.: Current and future perspectives for enhancing our understanding of the evolution of plant metabolism. Philosophical Transactions B 379 (1914), 20240253 (2024)

Fernie, A. R.; de Vries, S.; de Vries, J.: Evolution of plant metabolism: the state-of-the-art. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 379 (1914), 20230347 (2024)

Fernie, A. R.; Liu, F.; Zhang, Y.: Post-genomic illumination of paclitaxel biosynthesis. Nature Plants 10, S. 1875 - 1885 (2024)

Sun, Y.; Yuan, H.; Fernie, A. R.: Harnessing plant-associated microorganism to alleviate the detrimental effects of environmental abiotic stresses on medicinal plants. Medicinal Plant Biology 3, e024 (2024)

Yu, Y.; Alseekh, S.; Zhu, Z.; Zhou , K.; Fernie, A. R.: Multiomics and biotechnologies for understanding and influencing cadmium accumulation and stress response in plants. Plant Biotechnology Journal 22 (10), S. 2641 - 2659 (2024)

Fischer, H.D.; Fernie, A.; Skirycz, A.: Using protein–metabolite interactions to identify novel plant metabolite receptors. Phytochemistry Reviews (2024)