Publications of Alisdair Fernie

Journal Article (1021)

1.
Journal Article
Liu, F.; Fernie, A. R.; Zhang, Y.: Plant gene co-expression defines the biosynthetic pathway of neuroactive alkaloids. Molecular Plant 17 (3), pp. 372 - 374 (2024)
2.
Journal Article
Bortlik, J.; Lühle, J.; Alseekh, S.; Weiste, C.; Fernie, A. R.; Dröge-Laser, W.; Börnke, F.: DOMAIN OF UNKNOWN FUNCTION581-9 negatively regulates SnRK1 kinase activity. Plant Physiology 194 (3), pp. 1853 - 1869 (2024)
3.
Journal Article
Gupta, S.; Petrov, V.; Garg, V.; Mueller-Roeber, B.; Fernie, A. R.; Nikoloski, Z.; Gechev, T.: The genome of Haberlea rhodopensis provides insights into the mechanisms for tolerance to multiple extreme environments. Cellular and Molecular Life Sciences 81 (1), 117 (2024)
4.
Journal Article
Martinez Rivas, F.J.; Fernie, A. R.; Aarabi, F.: Roles and Regulation of the RBOHD Enzyme in Initiating ROS-Mediated Systemic Signaling During Biotic and Abiotic Stress. Plant Stress 11, 100327 (2024)
5.
Journal Article
Naake, T.; Zhu, F.; Alseekh, S.; Scossa, F.; de Souza, L. P.; Borghi, M.; Brotman, Y.; Mori, T.; Nakabayashi, R.; Tohge, T. et al.; Fernie, A. R.: Genome-wide association studies identify loci controlling specialized seed metabolites in Arabidopsis. Plant Physiology 194 (3), pp. 1705 - 1721 (2024)
6.
Journal Article
Zhu, A.; Liu, M.; Tian, Z.; Liu, W.; Hu, X.; Ao, M.; Jia, J.; Shi, T.; Liu, H.; Li, D. et al.; Mao, H.; Su, H.; Yan, W.; Li, Q.; Lan, C.; Fernie, A. R.; Chen, W.: Chemical-tag-based semi-annotated metabolomics facilitates gene identification and specialized metabolic pathway elucidation in wheat. The Plant Cell 36 (3), pp. 540 - 558 (2024)
7.
Journal Article
He, Y.; Zhang, K.; Shi, Y.; Lin, H.; Huang, X.; Lu, X.; Wang, Z.; Li, W.; Feng, X.; Shi, T. et al.; Chen, Q.; Wang, J.; Tang, Y.; Chapman, M. A.; Germ, M.; Luthar, Z.; Kreft, I.; Janovská, D.; Meglič, V.; Woo, S.-H.; Quinet, M.; Fernie, A. R.; Liu, X.; Zhou, M.: Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat. Genome Biology: Biology for the Post-Genomic Era 25 (1), 61 (2024)
8.
Journal Article
Borghi, M.; Pacifico, D.; Crucitti, D.; Squartini, A.; Berger, M.M.J.; Gamboni, M.; Carimi, F.; Lehad, A.; Costa, A.; Gallusci, P. et al.; Fernie, A. R.; Zottini, M.: Smart selection of soil microbes for resilient and sustainable viticulture. The Plant Journal (2024)
9.
Journal Article
Boutoub, O.; Jadhav, S.; Zheng, X.; El Ghadraoui, L.; Al Babili, S.; Fernie, A. R.; Figueiredo, A.C.; Miguel, M.G.; Borghi, M.: Biochemical characterization of Euphorbia resinifera floral cyathia. Journal of Plant Physiology 293, 154184 (2024)
10.
Journal Article
Chen, J.; Zhang, Y.; Wei, J.; Hu, X.; Yin, H.; Liu, W.; Li, D.; Tian, W.; Hao, Y.; He, Z. et al.; Fernie, A. R.; Chen, W.: Beyond pathways: Accelerated flavonoids candidate identification and novel exploration of enzymatic properties using combined mapping populations of wheat. Plant Biotechnology Journal (2024)
11.
Journal Article
Dziubek, D.; Poeker, L.; Siemiatkowska, B.; Graf, A.; Marino, G.; Alseekh, S.; Arrivault, S.; Fernie, A. R.; Armbruster, U.; Geigenberger, P.: NTRC and thioredoxins m1/m2 underpin the light acclimation of plants on proteome and metabolome levels. Plant Physiology 194, pp. 982 - 1005 (2024)
12.
Journal Article
Elbanna, A. H.; Abdelghany, S.; Alseekh, S.; Fernie, A. R.; Farag, M. A.: Seasonal and taxa impact on edible sea cucumber metabolome as analyzed via a multiplex approach of mass spectroscopy-based metabolomics. Food Bioscience 57, 103456 (2024)
13.
Journal Article
Fuchs, P.; Feixes-Prats, E.; Arruda, P.; Feitosa-Araújo, E.; Fernie, A. R.; Grefen, C.; Lichtenauer, S.; Linka, N.; de Godoy Maia, I.; Meyer, A. J. et al.; Schilasky, S.; Sweetlove, L. J.; Wege, S.; Weber, A. P. M.; Millar, A. H.; Keech, O.; Florez-Sarasa, I.; Barreto, P.; Schwarzländer, M.: PLANT UNCOUPLING MITOCHONDRIAL PROTEIN 2 localizes to the Golgi. Plant Physiology 194 (2), pp. 623 - 628 (2024)
14.
Journal Article
Pereira, A.M.; Martins, A.O.; Batista-Silva, W.; Condori-Apfata, J.A.; Silva, V.F.; Oliveira, L.A.; Andrade, E.S.; Martins, S.C.V.; Medeiros, D.B.; Nascimento, V.L. et al.; Fernie, A. R.; Nunes-Nesi, A.; Araújo, W.L.: Differential content of leaf and fruit pigment in tomatoes culminate in a complex metabolic reprogramming without growth impacts. Journal of Plant Physiology 293, 154170 (2024)
15.
Journal Article
Rosa-Téllez, S.; Alcántara-Enguídanos, A.; Martinez-Seidel, F.; Casatejada-Anchel, R.; Saeheng, S.; Bailes, C. L.; Erban, A.; Medeiros, D.B.; Alepúz, P.; Matus, J. T. et al.; Kopka, J.; Muñoz-Bertomeu, J.; Krueger, S.; Roje, S.; Fernie, A. R.; Ros, R.: The serine-glycine-one carbon metabolic network orchestrates changes in nitrogen and sulfur metabolism and shapes plant development. The Plant Cell 36 (2), koad256, pp. 404 - 426 (2024)
16.
Journal Article
Sun, Y.; Zhou, Y.; Long, Q.; Xing, J.; Guo, P.; Liu, Y.; Zhang, C.; Zhang, Y.; Fernie, A. R.; Shi, Y. et al.; Luo, Y.; Luo, J.; Jin, C.: OsBCAT2, a gene responsible for the degradation of branched-chain amino acids, positively regulates salt tolerance by promoting the synthesis of vitamin B5. New Phytologist 241 (6), pp. 2558 - 2574 (2024)
17.
Journal Article
Carreno-Quintero, N.; Tohge, T.; Van Acker, R.; McKee, L.S.; Zhou, Q.; Bolze, A.; Xing, X.; Özparpucu, M.; Rüggeberg, M.; Piofczyk, T. et al.; Koram, Y.; Bulone, V.; Boerjan, W.; Fernie, A. R.; Fraser, P.D.: Non-targeted discovery of high-value bio-products in Nicotiana glauca L: a potential renewable plant feedstock. Bioresources and Bioprocessing 11, 12 (2024)
18.
Journal Article
Liu, N.; Du, Y.; Yan, S.; Chen, W.; Deng, M.; Xu, S.; Wang, H.; Zhan, W.; Huang, W.; Yin, Y. et al.; Yang, X.; Zhao, Q.; Fernie, A. R.; Yan, J.: The light and hypoxia induced gene ZmPORB1 determines tocopherol content in the maize kernel. Science China Life Sciences 67, pp. 435 - 448 (2024)
19.
Journal Article
Yin, B.; Jia, J.; Sun, X.; Hu, X.; Ao, M.; Liu, W.; Tian, Z.; Liu, H.; Li, D.; Tian, W. et al.; Hao, Y.; Xia, X.; Sade, N.; Brotman, Y.; Fernie, A. R.; Chen, J.; He, Z.; Chen, W.: Dynamic metabolite QTL analyses provide novel biochemical insights into kernel development and nutritional quality improvement in common wheat. Plant Communications (2024)
20.
Journal Article
Daubermann, A. G.; Lima, V. F.; Erban, A.; Kopka, J.; Fernie, A. R.; Schwarzländer, M.; dos Anjos, L.; Daloso, D. M.: Novel guard cell sink characteristics revealed by a multi-species/cell-types meta-analysis of 13C-labelling experiments. Theoretical and Experimental Plant Physiology (2024)
21.
Journal Article
John, A.; Krämer, M.; Lehmann, M.; Kunz, H.-H.; Aarabi, F.; Alseekh, S.; Fernie, A. R.; Sommer, F.; Schroda, M.; Zimmer, D. et al.; Mühlhaus, T.; Peisker, H.; Gutbrod, K.; Dörmann, P.; Neunzig, J.; Philippar, K.; Neuhaus, H. E.: Degradation of FATTY ACID EXPORT PROTEIN1 by RHOMBOID-LIKE PROTEASE11 contributes to cold tolerance in Arabidopsis. The Plant Cell, koae011 (2024)
22.
Journal Article
Li, J.; Martin, C.; Fernie, A. R.: Biofortification’s contribution to mitigating micronutrient deficiencies. Nature Food 5, pp. 19 - 27 (2024)
23.
Journal Article
Lv, Y.; Zhu, J.; Huang, S.; Xing, X.; Zhou, S.; Yao, H.; Yang, Z.; Liu, L.; Huang, S.; Miao, Y. et al.; Liu, X.; Fernie, A. R.; Ding, Y.; Luo, J.: Metabolome profiling and transcriptome analysis filling the early crucial missing steps of piperine biosynthesis in Piper nigrum L. The Plant Journal 117 (1), pp. 107 - 120 (2024)
24.
Journal Article
Karakas, E.; Ferrante, P.; Schafleitner, R.; Giuliano, G.; Fernie, A. R.; Alseekh, S.: Plant Sample Collection and Shipment for Multi-omic Analyses and Phytosanitary Evaluation. Current Protocols 3 (12), e952 (2023)
25.
Journal Article
Lai, D.; Zhang, K.; He, Y.; Fan, Y.; Li, W.; Shi, Y.; Gao, Y.; Huang, X.; He, J.; Zhao, H. et al.; Lu, X.; Xiao, Y.; Cheng, J.; Ruan, J.; Georgiev, M. I.; Fernie, A. R.; Zhou, M.: Multi-omics identification of a key glycosyl hydrolase gene FtGH1 involved in rutin hydrolysis in Tartary buckwheat (Fagopyrum tataricum). Plant Biotechnology Journal (2023)
26.
Journal Article
Zhang, Y.; Wiese, L.; Fang, H.; Alseekh, S.; de Souza, L. P.; Scossa, F.; Molloy, J.; Christmann, M.; Fernie, A. R.: Synthetic biology identifies the minimal gene set required for Paclitaxel biosynthesis in a plant chassis. Molecular Plant 16 (12), pp. 1951 - 1961 (2023)
27.
Journal Article
Artins, A.; Fernie, A. R.: FCS-like zinc finger proteins maintain energy homeostasis during stresses. Trends in Plant Science 28 (12), pp. 1347 - 1349 (2023)
28.
Journal Article
Barros, J.A.S.; Cavalcanti, J.H.F.; Pimentel, K.G.; Magen, S.; Soroka, Y.; Weiss, S.; Medeiros, D.B.; Nunes-Nesi, A.; Fernie, A. R.; Avin-Wittenberg, T. et al.; Araújo, W.L.: The interplay between autophagy and chloroplast vesiculation pathways under dark-induced senescence. Plant, Cell and Environment 46 (12), pp. 3721 - 3736 (2023)
29.
Journal Article
Bulut, M.; Nunes-Nesi, A.; Fernie, A. R.; Alseekh, S.: Characterization of PetM cytochrome b6f subunit 7 domain-containing protein in tomato. Horticulture Research 10 (12), uhad224 (2023)
30.
Journal Article
Duque-Jaramillo, A.; Ulmer, N.; Alseekh, S.; Bezrukov, I.; Fernie, A. R.; Skirycz, A.; Karasov, T.L.; Weigel, D.: The genetic and physiological basis of Arabidopsis thaliana tolerance to Pseudomonas viridiflava. New Phytologist 240 (5), pp. 1961 - 1975 (2023)
31.
Journal Article
Giese, J.; Eirich, J.; Walther, D.; Zhang, Y.; Lassowskat, I.; Fernie, A. R.; Elsässer, M.; Maurino, V. G.; Schwarzländer, M.; Finkemeier, I.: The interplay of post-translational protein modifications in Arabidopsis leaves during photosynthesis induction. The Plant Journal 116 (4), pp. 1172 - 1193 (2023)
32.
Journal Article
Qian, D.; Xi, J.; Nie, Y.; Zou, M.; Zhang, J.; Alseekh, S.; Fernie, A. R.; Chen, J.; Huang, L.: Chemical characterization of dicaffeoyl polyamine derivatives to understand specific secondary metabolites in goji berry. Journal of Food Composition and Analysis 122, 105434 (2023)
33.
Journal Article
Qiu, H.; Zhang, X.; Zhang, Y.; Jiang, X.; Ren, Y.; Gao, D.; Zhu, X.; Usadel, B.; Fernie, A. R.; Wen, W.: Depicting the genetic and metabolic panorama of chemical diversity in the tea plant. Plant Biotechnology Journal (2023)
34.
Journal Article
Vicente, M. H.; MacLeod, K.; Zhu, F.; Rafael, D. D.; Figueira, A.; Fernie, A. R.; Mohareb, F.; Kevei, Z.; Thompson, A. J.; Zsögön, A. et al.; Peres, L. E. P.: The ORGAN SIZE (ORG) locus modulates both vegetative and reproductive gigantism in domesticated tomato. Annals of Botany 132 (7), pp. 1233 - 1248 (2023)
35.
Journal Article
Bao, Y.-J.; Chen, J.-X.; Zhang, Y.; Fernie, A. R.; Zhang, J.; Huang, B.-X.; Zhu, F.-Y.; Cao, F.-L.: Emerging role of jasmonic acid in woody plant development. Advanced Agrochem (2023)
36.
Journal Article
Aarabi, F.; Ghigi, A.; Wijesingha Ahchige, M.; Bulut, M.; Geigenberger, P.; Neuhaus, H. E.; Sampathkumar, A.; Alseekh, S.; Fernie, A. R.: Genome-Wide Association Study unveils ascorbate regulation by PAS/LOV PROTEIN during high light acclimation. Plant Physiology 193 (3), pp. 2037 - 2054 (2023)
37.
Journal Article
Bulut, M.; Wendenburg, R.; Bitocchi, E.; Bellucci, E.; Kroc, M.; Gioia, T.; Susek, K.; Papa, R.; Fernie, A. R.; Alseekh, S.: A Comprehensive Metabolomics and Lipidomics Atlas for the Legumes Common Bean, Chickpea, Lentil and Lupin. The Plant Journal 116 (4), pp. 1152 - 1171 (2023)
38.
Journal Article
Fernie, A. R.; Yan, J.; Aharoni, A.; Ma, J.: Editorial: The past, present and future of The Plant Journal Resource Articles. The Plant Journal 116 (4), pp. 967 - 973 (2023)
39.
Journal Article
Li, C.; Huang, W.; Han, X.; Zhao, G.; Zhang, W.; He, W.; Nie, B.; Chen, X.; Zhang, T.; Bai, W. et al.; Zhang, X.; He, J.; Zhao, C.; Fernie, A. R.; Tschaplinski, T.J.; Yang, X.; Yan, S.; Wang, L.: Diel dynamics of multi-omics in elkhorn fern provide new insights into weak CAM photosynthesis. Plant Communications 4 (5), 100594 (2023)
40.
Journal Article
Shen, S.; Wang, S.; Yang, C.; Wang, C.; Zhou, Q.; Zhou, S.; Zhang, R.; Li, Y.; Wang, Z.; Dai, L. et al.; Peng, W.; Hao, Y.; Guo, H.; Cao, G.; Liu, X.; Yao, F.; Xu, Q.; Fernie, A. R.; Luo, J.: Elucidation of the melitidin biosynthesis pathway in pummelo. Journal of Integrative Plant Biology 65 (11), pp. 2505 - 2518 (2023)
41.
Journal Article
Su, C.; Kokosza, A.; Xie, X.; Pěnčík, A.; Zhang, Y.; Raumonen, P.; Shi, X.; Muranen, S.; Topcu, M. K.; Immanen, J. et al.; Hagqvist, R.; Safronov, O.; Alonso-Serra, J.; Eswaran, G.; Venegas, M. P.; Ljung, K.; Ward, S.; Mähönen, A. P.; Himanen, K.; Salojärvi, J.; Fernie, A. R.; Novák, O.; Leyser, O.; Pałubicki, W.; Helariutta, Y.; Nieminen, K.: Tree architecture: A strigolactone-deficient mutant reveals a connection between branching order and auxin gradient along the tree stem. Proceedings of the National Academy of Sciences of the United States of America 120 (48), e2308587120 (2023)
42.
Journal Article
von Bismarck, T.; Wendering, P.; de Souza, L. P.; Ruß, J.; Strandberg, L.; Heyneke, E.; Walker, B. J.; Schöttler, M. A.; Fernie, A. R.; Nikoloski, Z. et al.; Armbruster, U.: Growth in fluctuating light buffers plants against photorespiratory perturbations. Nature Communications 14 (1), 7052 (2023)
43.
Journal Article
Zemach, I.; Alseekh, S.; Tadmor-Levi, R.; Fisher, J.; Torgeman, S.; Trigerman, S.; Nauen, J.; Hayut, S. F.; Mann, V.; Rochsar, E. et al.; Finkers, R.; Wendenburg, R.; Osorio, S.; Bergmann, S.; Lunn, J. E.; Semel, Y.; Hirschberg, J.; Fernie, A. R.; Zamir, D.: Multi-year field trials provide a massive repository of trait data on a highly diverse population of tomato and uncover novel determinants of tomato productivity. The Plant Journal 116 (4), pp. 1136 - 1151 (2023)
44.
Journal Article
Zhang, Y.; Martinez-Jaime, S.; Bulut, M.; Graf, A.; Fernie, A. R.: The conditional mitochondrial protein complexome in Arabidopsis thaliana root and shoot. Plant Communications 4 (5), 100635 (2023)
45.
Journal Article
Fernie, A. R.; Zhang, Y.: Observations and implication of thermal tolerance in the Arabidopsis proteome. Cell Systems 14 (10), pp. 819 - 821 (2023)
46.
Journal Article
Lamm, C. E.; Rabbi, I. Y.; Medeiros, D.B.; Rosado-Souza, L.; Pommerrenig, B.; Dahmani, I.; Rüscher, D.; Hofmann, J.; van Doorn; M., A. et al.; Schlereth, A.; Neuhaus, H. E.; Fernie, A. R.; Sonnewald, U.; Zierer, W.: Efficient sugar utilization and transition from oxidative to substrate-level phosphorylation in high starch storage roots of African cassava genotypes. The Plant Journal 116 (1), pp. 38 - 57 (2023)
47.
Journal Article
Nicolas, P.; Pattison, R. J.; Zheng, Y.; Lapidot-Cohen, T.; Brotman, Y.; Osorio, S.; Fernie, A. R.; Fei, Z.; Catalá, C.: Starch deficiency in tomato causes transcriptional reprogramming that modulates fruit development, metabolism, and stress responses. Journal of Experimental Botany 74 (20), pp. 6331 - 6348 (2023)
48.
Journal Article
Pereira-Lima, Í.A.; Batista-Silva, W.; Siqueira, J.A.; Silva, M.F.; Medeiros, D.B.; Cavalcanti, J.H.; Gonçalves, J.F.D.C.; Ribeiro, D.M.; Fernie, A. R.; Nunes-Nesi, A. et al.; Araújo, W.L.: Differential Aluminum tolerance in Arabidopsis thaliana ecotypes is seemingly related to metabolite changes. Environmental and Experimental Botany 214, 105472 (2023)
49.
Journal Article
Segarra-Medina, C.; Alseekh, S.; Fernie, A. R.; Rambla, J. L.; Pérez-Clemente, R. M.; Gómez-Cádenas, A.; Zandalinas, S. I.: Abscisic acid promotes plant acclimation to the combination of salinity and high light stress. Plant Physiology and Biochemistry 203, 108008 (2023)
50.
Journal Article
Shan, N.; Zhang, Y.; Guo, Y.; Zhang, W.; Nie, J.; Fernie, A. R.; Sui, X.: Cucumber malate decarboxylase, CsNADP-ME2, functions in the balance of carbon and amino acid metabolism in fruit. Horticulture Research 10 (12), uhad216 (2023)
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