Publications of the Group

Journal Article (863)

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Zhu, F.; Luo, T.; Liu, C.; Wang, Y.; Zheng, L.; Xiao, X.; Zhang, M.; Yang, H.; Yang, W.; Xu, R. et al.; Zeng, Y.; Ye, J.; Xu, J.; Xu, J.; Larkin, R. M.; Wang, P.; Wen, W.; Deng, X.; Fernie, A. R.; Cheng, Y.: A NAC transcription factor and its interaction protein hinder abscisic acid biosynthesis by synergistically repressing NCED5 in Citrus reticulata. Journal of Experimental Botany 71 (12), pp. 3613 - 3625 (2020)
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Zhang, Y.; Fernie, A. R.: Stable and temporary enzyme complexes and metabolons involved in energy and redox metabolism. ANTIOXIDANTS & REDOX SIGNALING (2020)
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Brito, D. S.; Agrimi, G.; Charton, L.; Brilhaus, D.; Bitetto, M. G.; Lana-Costa, J.; Messina, E.; Nascimento, C. P.; Araújo, E. F.; Viana Pires, M. et al.; Pérez-Díaz, J. L.; Obata, T.; Porcelli, V.; Palmieri, L.; Araújo, W. L.; Weber, A. P. M.; Linka, N.; Fernie, A. R.; Palmieri, F.; Nunes-Nesi, A.: Biochemical and Functional Characterization of a Mitochondrial Citrate Carrier in Arabidopsis thaliana. Biochemical Journal 477 (9), pp. 1759 - 1777 (2020)
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Alseekh, S.; de Souza, L. P.; Benina, M.; Fernie, A. R.: The Style and Substance of Plant Flavonoid decoration; Towards Defining both Structure and Function. Phytochemistry 174, 112347 (2020)
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Artiukhov V, A.; Grabarska, A.; Gumbarewicz, E.; Aleshin, V. A.; Kaehne, T.; Obata, T.; Kazantsev V, A.; Lukashev V, N.; Stepulak, A.; Fernie, A. R. et al.; Bunik I, V.: Synthetic analogues of 2-oxo acids discriminate metabolic contribution of the 2-oxoglutarate and 2-oxoadipate dehydrogenases in mammalian cells and tissues. Scientific Reports 10 (1), 1886 (2020)
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Aucique-Pérez, C.E.; Resende, R.S.; Martins, A.O.; Silveira, P.R.; Cavalcanti, J.H.F.; Vieira, N.M.; Fernie, A. R.; Araújo, W.L.; DaMatta, F.M.; Rodrigues, F.Á.: How do wheat plants cope with Pyricularia oryzae infection? A physiological and metabolic approach. Planta 252 (2), 24 (2020)
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Bianchetti, R.; De Luca, B.; de Haro, L.A.; Rosado, D.; Demarco, D.; Conte, M.; Bermudez, L.; Freschi, L.; Fernie, A. R.; Michaelson, L.V. et al.; Haslam, R.P.; Rossi, M.; Carrari, F.: Phytochrome-Dependent Temperature Perception Modulates Isoprenoid Metabolism. Plant Physiology 183 (3), pp. 869 - 882 (2020)
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Chen, J.; Hu, X.; Shi, T.; Yin, H.; Sun, D.; Hao, Y.; Xia, X.; Luo, J.; Fernie, A. R.; He, Z. et al.; Chen, W.: Metabolite-based genome-wide association study enables dissection of the flavonoid decoration pathway of wheat kernels. Plant Biotechnology Journal 18 (8), pp. 1722 - 1735 (2020)
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Chen, M.-X.; Zhu, F.-Y.; Gao, B.; Ma, K.-L.; Zhang, Y.; Fernie, A. R.; Chen, X.; Dai, L.; Ye, N.-H.; Zhang, X. et al.; Tian, Y.; Zhang, D.; Xiao, S.; Zhang, J.; Liu, Y.-G.: Full-length transcript-based proteogenomics of rice improves its genome and proteome annotation. Plant Physiology 182 (3), pp. 1510 - 1526 (2020)
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Clemente-Moreno, M.; Omranian, N.; Sáez, P.; Figueroa, C.; Del-Saz, N.; Elso, M.; Poblete, L.; Orf, I.; Cuadros-Inostroza, A.; Cavieres, L.A. et al.; Bravo, L.; Fernie, A. R.; Ribas-Carbó, M.; Flexas, J.; Nikoloski, Z.; Brotman, Y.; Gago, J.: Low temperature tolerance of the Antarctic species Deschampsia antarctica: a complex metabolic response associated with nutrient remobilization. Plant, Cell and Environment 43 (6), pp. 1376 - 1393 (2020)
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da Fonseca-Pereira, P.; Souza, P. V.L.; Hou, L.-Y.; Schwab, S.; Geigenberger, P.; Nunes-Nesi, A.; Timm, S.; Fernie, A. R.; Thormählen, I.; Araújo, W. L. et al.; Daloso, D. M.: Thioredoxin h2 contributes to the redox regulation of mitochondrial photorespiratory metabolism. Plant, Cell and Environment 43 (1), pp. 188 - 208 (2020)
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de Souza, L. P.; Alseekh, S.; Brotman, Y.; Fernie, A. R.: Network based strategies in metabolomics data analysis and interpretation: from molecular networking to biological interpretation. Expert Review of Proteomics 17 (4), pp. 243 - 255 (2020)
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de Souza, L. P.; Garbowicz, K.; Brotman, Y.; Tohge, T.; Fernie, A. R.: The acetate pathway supports flavonoid and lipid biosynthesis in Arabidopsis. Plant Physiology 182 (2), pp. 857 - 869 (2020)
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Devkar, V.; Thirumalaikumar, V. P.; Xue, G.-P.; Vallarino, J. G.; Turečková, V.; Strnad, M.; Fernie, A. R.; Hoefgen, R.; Mueller-Roeber, B.; Balazadeh, S.: Multifaceted regulatory function of tomato SlTAF1 in the response to salinity stress. New Phytologist 225 (4), pp. 1681 - 1698 (2020)
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Diretto, G.; Frusciante, S.; Fabbri, C.; Schauer, N.; Busta, L.; Wang, Z.; Matas, A. J.; Fiore, A.; Rose, J. K.C.; Fernie, A. R. et al.; Jetter, R.; Mattei, B.; Giovannoni, J.; Giuliano, G.: Manipulation of β-carotene levels in tomato fruits results in increased ABA content and extended shelf-life. Plant Biotechnology Journal 18 (5), pp. 1185 - 1199 (2020)
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Feitosa-Araujo, E.; Chaves, I. d. S.; Florian, A.; da Fonseca-Pereira, P.; Apfata, J. A. C.; Heyneke, E.; Medeiros, D.B.; Pires, M. V.; Mettler-Altmann, T.; Neuhaus, H. E. et al.; Palmieri, F.; Araújo, W. L.; Obata, T.; Weber, A. P. M.; Linka, N.; Fernie, A. R.; Nunes-Nesi, A.: Down-regulation of a Mitochondrial NAD+ Transporter (NDT2) Alters Seed Production and Germination in Arabidopsis. Plant and Cell Physiology 61 (5), pp. 897 - 908 (2020)
17.

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Fernández-Marín, B.; Gulías, J.; Figueroa, C. M.; Iñiguez, C.; Clemente-Moreno, M. J.; Nunes-Nesi, A.; Fernie, A. R.; Cavieres, L. A.; Bravo, L. A.; García-Plazaola, J. I. et al.; Gago, J.: How do vascular plants perform photosynthesis in extreme environments? An integrative ecophysiological and biochemical story. The Plant Journal (accepted)
18.

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Fernandez-Marin, B.; Nadal, M.; Gago, J.; Fernie, A. R.; Lopez-Pozo, M.; Artetxe, U.; Garcia-Plazaola, J. I.; Verhoeven, A.: Born to revive: molecular and physiological mechanisms of double tolerance in a paleotropical and resurrection plant. New Phytologist 226 (3), pp. 741 - 759 (2020)
19.

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Fernie, A. R.: Degrading to inhibit: a role for Phytochrome Initiation Factors in determining hypocotyl growth under UV-B. The Plant Journal 101 (3), pp. 505 - 506 (2020)
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Fernie, A. R.; Bachem, C.W.B.; Helariutta, Y.; Neuhaus, H.E.; Prat, S.; Ruan, Y.-L.; Stitt, M.; Sweetlove, L.J.; Tegeder, M.; Wahl, V. et al.; Sonnewald, S.; Sonnewald, U.: Synchronization of developmental, molecular and metabolic aspects of source–sink interactions. Nature Plants 6, pp. 55 - 66 (2020)
21.

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Fernie, A. R.; Bauwe, H.: Wasteful, essential, evolutionary stepping stone? The multiple personalities of the photorespiratory pathway. The Plant Journal (accepted)
22.

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Fernie, A. R.; Yan, J.: Targeting Key Genes to Tailor Old and New Crops for a Greener Agriculture. Molecular Plant 13 (3), pp. 354 - 356 (2020)
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Fernie, A. R.; Zhang, Y.; Sampathkumar, A.: Cytoskeleton Architecture Regulates Glycolysis Coupling Cellular Metabolism to Mechanical Cues. Trends in biochemical sciences 45 (8), pp. 637 - 638 (2020)
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Ferrari, C.; Shivhare, D.; Hansen, B. O.; Pasha, A.; Esteban, E.; Provart, N. J.; Kragler, F.; Fernie, A. R.; Tohge, T.; Mutwil, M.: Expression Atlas of Selaginella moellendorffii Provides Insights into the Evolution of Vasculature, Secondary Metabolism, and Roots. The Plant Cell 32, pp. 853 - 870 (2020)
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Florez-Sarasa, I.; Fernie, A. R.; Gupta, K.J.: Does the alternative respiratory pathway offer protection against the adverse effects resulting from climate change? Journal of Experimental Botany 71 (2), pp. 465 - 469 (2020)
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Fraser, P. D.; Aharoni, A.; Hall, R. D.; Huang, S.; Giovannoni, J. J.; Sonnewald, U.; Fernie, A. R.: Metabolomics should be deployed in identification and characterization of gene-edited crops. The Plant Journal (accepted)
27.

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Gago, J.; Estrany, J.; Estes, L.; Fernie, A. R.; Alorda, B.; Brotman, Y.; Flexas, J.; Escalona, J. M.; Medrano, H.: Nano and Micro Unmanned Aerial Vehicles (UAVs): A New Grand Challenge for Precision Agriculture? Current Protocols in Plant Biology 5 (1), e20103 (2020)
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Gechev, T.; Georgiev, M. I.; Fernie, A. R.: PlantaSyst: Teaming up for Systems Biology and Biotechnology. Trends in Plant Science 25 (7), pp. 621 - 624 (2020)
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Gupta, K. J.; Mur, L. A. J.; Wany, A.; Kumari, A.; Fernie, A. R.; Ratcliffe, R. G.: The role of nitrite and nitric oxide under low oxygen conditions in plants. New Phytologist 225 (SI-3), pp. 1143 - 1151 (2020)
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Hu, C.; Rao, J.; Song, Y.; Chan, S.-A.; Tohge, T.; Cui, B.; Lin, H.; Fernie, A. R.; Zhang, D.; Shi, J.: Dissection of flag leaf metabolic shifts and their relationship with those occurring simultaneously in developing seed by application of non-targeted metabolomics. PLoS One 15 (1), e0227577 (2020)
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Jiao, C.; Sørensen, I.; Sun, X.; Sun, H.; Behar, H.; Alseekh, S.; Philippe, G.; Palacio Lopez, K.; Sun, L.; Reed, R. et al.; Jeon, S.; Kiyonami, R.; Zhang, S.; Fernie, A. R.; Brumer, H.; Domozych, D. S.; Fei, Z.; Rose, J. K.C.: The Penium margaritaceum Genome: Hallmarks of the Origins of Land Plants. Cell 181 (5), pp. 1097 - 1111.e12 (2020)
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Karagiannis, E.; Tanou, G.; Scossa, F.; Samiotaki, M.; Michailidis, M.; Manioudaki, M.; Laurens, F.; Job, D.; Fernie, A. R.; Orsel, M. et al.; Molassiotis, A.: Systems-Based Approaches to Unravel Networks and Individual Elements Involved in Apple Superficial Scald. Frontiers in Plant Science 11, 8 (2020)
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Kuhalskaya, A.; Wijesingha Ahchige, M.; de Souza, L. P.; Vallarino, J. G.; Brotman, Y.; Alseekh, S.: Network analysis provides insight into tomato lipid metabolism. Metabolites 10 (4), 152 (2020)
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Liu, H.; Jian, L.; Xu, J.; Zhang, Q.; Zhang, M.; Jin, M.; Peng, Y.; Yan, J.; Han, B.; Liu, J. et al.; Gao, F.; Liu, X.; Huang, L.; Wei, W.; Ding, Y.; Yang, X.; Li, Z.; Zhang, M.; Sun, J.; Bai, M.; Song, W.; Chen, H.; Sun, X.; Li, W.; Lu, Y.; Liu, Y.; Zhao, J.; Qian, Y.; Jackson, D.; Fernie, A. R.; Yan, J.: High-Throughput CRISPR/Cas9 Mutagenesis Streamlines Trait Gene Identification in Maize. The Plant Cell 32 (5), pp. 1397 - 1413 (2020)
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Liu, J.; Fernie, A. R.; Yan, J.: The past, present and future of maize improvement – domestication, genomics and functional genomic routes towards crop enhancement. Plant Communications 1, 100010 (2020)
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Medeiros, D.B.; Barros, J. A.S.; Fernie, A. R.; Araújo, W. L.: Eating Away at ROS to Regulate Stomatal Opening. Trends in Plant Science 25 (3), pp. 220 - 223 (2020)
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Obata, T.; Klemens, P.A.W.; Rosado-Souza, L.; Schlereth, A.; Gisel, A.; Stavolone, L.; Zierer, W.; Morales, N.; Mueller, L.A.; Zeeman, S.C. et al.; Ludewig, F.; Stitt, M.; Sonnewald, U.; Neuhaus, H.E.; Fernie, A. R.: Metabolic profiles of six African cultivars of cassava (Manihot esculenta Crantz) highlight bottlenecks of root yield. The Plant Journal 102 (6), pp. 1202 - 1219 (2020)
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Omidbakhshfard, M. A.; Sujeeth, N.; Gupta, S.; Omranian, N.; Guinan, K.J.; Brotman, Y.; Nikoloski, Z.; Fernie, A. R.; Mueller-Roeber, B.; Gechev, T.S.: A Biostimulant Obtained from the Seaweed Ascophyllum nodosum Protects Arabidopsis thaliana from Severe Oxidative Stress. International Journal of Molecular Sciences 21 (2), 474 (2020)
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Osorio, S.; Carneiro, R. T.; Lytovchenko, A.; McQuinn, R.; Sorensen, I.; Vallarino, J. G.; Giovannoni, J. J.; Fernie, A. R.; Rose, J. K. C.: Genetic and metabolic effects of ripening mutations and vine detachment on tomato fruit quality. Plant Biotechnology Journal 18 (1), pp. 106 - 118 (2020)
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Parween, S.; Anonuevo, J.J.; Butardo, V.M.; Misra, G.; Anacleto, R.; Llorente, C.; Kosik, O.; Romero, M.V.; Bandonill, E.H.; Mendioro, M.S. et al.; Lovegrove, A.; Fernie, A. R.; Brotman, Y.; Sreenivasulu, N.: Balancing the double-edged sword effect of increased resistant starch content and its impact on rice texture: its genetics and molecular physiological mechanisms. Plant Biotechnology Journal 18 (8), pp. 1763 - 1777 (2020)
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Pott, D. M.; de Abreu e Lima, F.; Soria, C.; Willmitzer, L.; Fernie, A. R.; Nikoloski, Z.; Osorio, S.; Vallarino, J. G.: Metabolic reconfiguration of strawberry physiology in response to postharvest practices. Food Chemistry 321, 126747 (2020)
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Pott, D. M.; Vallarino, J. G.; Osorio, S.: Metabolite Changes during Postharvest Storage: Effects on Fruit Quality Traits. Metabolites (accepted)
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Qiu, H.; Zhu, X.; Wan, H.; Xu, L.; Zhang, Q.; Hou, P.; Fan, Z.; Lyu, Y.; Ni, D.; Usadel, B. et al.; Fernie, A. R.; Wen, W.: Parallel Metabolomic and Transcriptomic Analysis Reveals Key Factors for Quality Improvement of Tea Plants. Journal of Agricultural and Food Chemistry 68 (19), pp. 5483 - 5495 (2020)
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Richter, A. S.; Tohge, T.; Fernie, A. R.; Grimm, B.: The genomes uncoupled -dependent signalling pathway coordinates plastid biogenesis with the synthesis of anthocyanins. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 375 (1801), 20190403 (2020)
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Rosa-Téllez, S.; Anoman, A.D.; Alcántara-Enguídanos, A.; Garza-Aguirre, R.A.; Alseekh, S.; Ros, R.: PGDH family genes differentially affect Arabidopsis tolerance to salt stress. Plant Science 290, 110284 (2020)
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Rosado-Souza, L.; Fernie, A. R.; Aarabi, F.: Ascorbate and Thiamin: Metabolic Modulators in Plant Acclimation Responses. Plants 9 (SI-1), 101 (2020)
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Salem, M. A.; de Souza, L. P.; Serag, A.; Fernie, A. R.; Farag, M. A.; Ezzat, S. M.; Alseekh, S.: Metabolomics in the Context of Plant Natural Products Research: From Sample Preparation to Metabolite Analysis. Metabolites 10 (1), 37 (2020)
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Scossa, F.; Fernie, A. R.: The evolution of metabolism: How to test evolutionary hypotheses at the genomic level. Computational and Structural Biotechnology Journal 18, pp. 482 - 500 (2020)
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Shameer, S.; Vallarino, J. G.; Fernie, A. R.; Ratcliffe, R. G.; Sweetlove, L. J.: Flux balance analysis of metabolism during growth by osmotic cell expansion and its application to tomato fruits. The Plant Journal 103 (1), pp. 68 - 82 (2020)
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Shapiguzov, A.; Nikkanen, L.; Fitzpatrick, D.; Vainonen, J. P.; Gossens, R.; Alseekh, S.; Aarabi, F.; Tiwari, A.; Blokhina, O.; Panzarová, K. et al.; Benedikty, Z.; Tyystjärvi, E.; Fernie, A. R.; Trtílek, M.; Aro, E.-M.; Rintamäki, E.; Kangasjärvi, J.: Dissecting the interaction of photosynthetic electron transfer with mitochondrial signalling and hypoxic response in the Arabidopsis rcd1 mutant. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 375 (1801), 20190413 (2020)