Publications of Alisdair Fernie

Journal Article (1079)

1.
Journal Article
Novello, M.; Bustamante, C.; Svetaz, L.; Goldy, C.; Valentini, G.; Drincovich, M.; Brotman, Y.; Fernie, A. R.; Lara, M.: Integrated Metabolomic, Lipidomic and Proteomic Analysis Define the Metabolic Changes Occurring in Curled Areas in Leaves With Leaf Peach Curl Disease. Plant, Cell and Environment 48 (2), pp. 1179 - 1200 (2025)
2.
Journal Article
Siqueira, J.; Martins, A.; Wakin, T.; Silva, M.; Batista-Silva, W.; Brito, F.; Zsögön, A.; Fernie, A. R.; Nunes-Nesi, A.; Araújo, W.: The Modulation of Growth and Metabolism in Solanum lycopersicum Contrast With the Leaf-Specific Regulation of Wild Tomato Species. Plant, Cell and Environment 48 (2), pp. 1201 - 1214 (2025)
3.
Journal Article
Alseekh, S.; Klemmer, A.; Yan, J.; Guo, T.; Fernie, A. R.: Embracing plant plasticity or robustness as a means of ensuring food security. Nature Communications 16 (1), 461 (2025)
4.
Journal Article
Casatejada-Anchel, R.; Torres-Moncho, A.; Anoman, A. D.; Budhagatapalli, N.; Pérez-Lorences, E.; Alcántara-Enguídanos, A.; Rosa-Téllez, S.; de Souza, L. P.; Kumlehn, J.; Fernie, A. R. et al.; Muñoz-Bertomeu, J.; Ros, R.: Metabolic engineering of the serine/glycine network as a means to improve the nitrogen content of crops. Plant Biotechnology Journal 23 (1), pp. 268 - 280 (2025)
5.
Journal Article
Fernie, A. R.; Martinez-Rivas, F.: Br(e)aking the tomato fruit size-sweetness trade-off. Trends in Plant Science (2025)
6.
Journal Article
Liu, M.-Y.; Jiao, Z.; Lou, H.; Tang, D.; Tian, X.; Zhou, B.-W.; Ruan, J.; Fernie, A. R.; Zhang, Q.: A glutamine synthetase-DOF transcription factor module regulates N remobilization from source to sink tissues in tea plants. Plant Physiology 197 (1), kiae644 (2025)
7.
Journal Article
López, C.; Alseekh, S.; Rivas, F.; Fernie, A. R.; Prieto, P.; Alamillo, J.: CRISPR/Cas9 editing of two adenine phosphoribosyl transferase coding genes reveals the functional specialization of adenine salvage proteins in common bean. Journal of Experimental Botany 76 (2), pp. 346 - 362 (2025)
8.
Journal Article
López-Tubau, J.; Laibach, N.; Burciaga-Monge, A.; Alseekh, S.; Deng, C.; Fernie, A. R.; Altabella, T.; Ferrer, A.: Differential impact of impaired steryl ester biosynthesis on the metabolome of tomato fruits and seeds. Physiologia Plantarum 177 (1), e70022 (2025)
9.
Journal Article
Nascimento, C.P.; da Fonseca-Pereira, P.; Ferreira-Silva, M.; Rosado-Souza, L.; Linka, N.; Fernie, A. R.; Araújo, W.L.; Nunes-Nesi, A.: Functional analysis of the extraplastidial TRX system in germination and early stages of development of Arabidopsis thaliana. Plant Science 350, 112310 (2025)
10.
Journal Article
Qin, K.; Ye, X.; Luo, S.; Fernie, A. R.; Zhang, Y.: Engineering carbon assimilation in plants. Journal of Integrative Plant Biology (2025)
11.
Journal Article
Tiozon, R. J. N.; Pasion-Uy, E.; Alseekh, S.; Sartagoda, K. J. D.; Gempesaw, S.; Tolentino, J. H. G.; Fernie, A. R.; Sreenivasulu, N.: Lipidomics-based association study reveals genomic signatures of anti-cancer qualities of pigmented rice sprouts. Frontiers in Plant Science 16, 1533442 (2025)
12.
Journal Article
Wu, S.; Zhang, S.; Liu, C.-M.; Fernie, A. R.; Yan, S.: Recent Advances in Mass Spectrometry-based Protein Interactome Studies. Molecular & Cellular Proteomics 24 (1), 100887 (2025)
13.
Journal Article
Yu, Y.; Li, W.; Liu, Y.; Liu, Y.; Zhang, Q.; Ouyang, Y.; Ding, W.; Xue, Y.; Zou, Y.; Yan, J. et al.; Jia, A.; Yan, J.; Hao, X.; Gou, Y.; Zhai, Z.; Liu, L.; Zheng, Y.; Zhang, B.; Xu, J.; Yang, N.; Xiao, Y.; Zhuo, L.; Lai, Z.; Yin, P.; Liu, H.-J.; Fernie, A. R.; Jackson, D.; Yan, J.: A Zea genus-specific micropeptide controls kernel dehydration in maize. Cell 188, pp. 44 - 59 (2025)
14.
Journal Article
D'Auria, J.C.; Fernie, A. R.: The BAHD and the bold: the mitochondria's role in alkaloid artistry. Trends in Plant Science 29 (12), pp. 1290 - 1291 (2024)
15.
Journal Article
Domer, A.; Jasinska, W.; Rosental, L.; Shochat, E.; Alseekh, S.; Fernie, A. R.; Brotman, Y.; Ovadia, O.: Comparative analysis of the plasma metabolome of migrating passerines: novel insights into stopover metabolism. Journal of Avian Biology (2024)
16.
Journal Article
Fontanet-Manzaneque, J. B.; Laibach, N.; Herrero-García, I.; Coleto-Alcudia, V.; Blasco-Escámez, D.; Zhang, C.; Orduña, L.; Alseekh, S.; Miller, S.; Bjarnholt, N. et al.; Fernie, A. R.; Matus, J. T.; Caño-Delgado, A. I.: Untargeted mutagenesis of brassinosteroid receptor SbBRI1 confers drought tolerance by altering phenylpropanoid metabolism in Sorghum bicolor. Plant Biotechnology Journal 22 (12), pp. 3406 - 3423 (2024)
17.
Journal Article
He, J.; Hao, Y.; He, Y.; Li, W.; Shi, Y.; Khurshid, M.; Lai, D.; Ma, C.; Wang, X.; Li, J. et al.; Cheng, J.; Fernie, A. R.; Ruan, J.; Zhang, K.; Zhou, M.: Genome-wide associated study identifies FtPMEI13 gene conferring drought resistance in Tartary buckwheat. The Plant Journal 120 (6), pp. 2398 - 2419 (2024)
18.
Journal Article
Kanojia, A.; Lyall, R.; Sujeeth, N.; Alseekh, S.; Martinez Rivas, F.J.; Fernie, A. R.; Gechev, T.S.; Petrov, V.: Physiological and molecular insights into the effect of a seaweed biostimulant on enhancing fruit yield and drought tolerance in tomato. Plant Stress 14, 100692 (2024)
19.
Journal Article
Luo, J.; He, C.; Yan, S.; Jiang, C.; Chen, A.; Li, K.; Zhu, Y.; Gui, S.; Yang, N.; Xiao, Y. et al.; Wu, S.; Zhang, F.; Liu, T.; Wang, J.; Huang, W.; Yang, Y.; Wang, H.; Yang, W.; Li, W.; Zhuo, L.; Fernie, A. R.; Zhan, J.; Wang, L.; Yan, J.: A metabolic roadmap of waxy corn flavor. Molecular Plant 17 (12), pp. 1883 - 1898 (2024)
20.
Journal Article
Mazzarella, T.; Chialva, M.; de Souza, L. P.; Wang, J.Y.; Votta, C.; Tiozon, R.; Vaccino, P.; Salvioli di Fossalunga, A.; Sreenivasulu, N.; Asami, T. et al.; Fernie, A. R.; Al-Babili, S.; Lanfranco, L.; Fiorilli, V.: Effect of exogenous treatment with zaxinone and its mimics on rice root microbiota across different growth stages. Scientific Reports 14, 31374 (2024)
21.
Journal Article
Tiozon, R. J. N.; Alseekh, S.; Fernie, A. R.; Bonto, A. P.; Yu, J.; Buenafe, R. J. Q.; Sreenivasulu, N.: Comprehensive lipidomic insights of differentially accumulating lipids in large pigmented rice sprout collection and the changes in the starch composition upon germination. Food Chemistry 460 (Part 2), 140677 (2024)
22.
Journal Article
Wijesingha Ahchige, M.; Fisher, J.; Sokolowska, E.; Lyall, R.; Illing, N.; Skirycz, A.; Zamir, D.; Alseekh, S.; Fernie, A. R.: The variegated canalized-1 tomato mutant is linked to photosystem assembly. Computational and Structural Biotechnology Journal 23, pp. 3967 - 3988 (2024)
23.
Journal Article
Farag, M.; Baky, M.; Kuehnhold, H.; Kriege, E.; Kunzmann, A.; Alseekh, S.; Al-Hammady, M.; Ezz, S.; Fernie, A. R.; Westphal, H. et al.; Stuhr, M.: Effects of thermal and UV stress on the polar and non-polar metabolome of photosymbiotic jellyfish and sea anemones. Marine Pollution Bulletin 208, 116983 (2024)
24.
Journal Article
Huang, X.; He, Y.; Zhang, K.; Shi, Y.; Zhao, H.; Lai, D.; Lin, H.; Wang, X.; Yang, Z.; Xiao, Y. et al.; Li, W.; Ouyang, Y.; Woo, S.H.; Quinet, M.; Georgiev, M.I.; Fernie, A. R.; Liu, X.; Zhou, M.: Evolution and Domestication of a Novel Biosynthetic Gene Cluster Contributing to the Flavonoid Metabolism and High-Altitude Adaptability of Plants in the Fagopyrum Genus. Advanced Science 11 (43), 2403603 (2024)
25.
Journal Article
Li, Y.; Yang, Z.; Li, K.; Yang, C.; Lei, L.; Li, J.; Zhou, J.; Hou, H.; Liu, H.; Xiong, X. et al.; Zhan, C.; Shen, S.; Liu, X.; Maher, M.; Ahmad, H.; Fernie, A. R.; Luo, J.: Two major rice loci determine rice-staple food populations differences in vitamin B1 deficiency levels. Science Bulletin (2024)
26.
Journal Article
Liu, F.; Fernie, A. R.; Zhang, Y.: Can a nitrogen-fixing organelle be engineered within plants? Trends in Plant Science 29 (11), pp. 1168 - 1171 (2024)
27.
Journal Article
Che, Y.; Ding, Z.; Shen, C.; Fernie, A. R.; Tang, X.; Yao, Y.; Liu, J.; Wang, Y.; Li, R.; Guo, J.: Physiological and Microstructure Analysis Reveals the Mechanism by Which Formic Acid Delays Postharvest Physiological Deterioration of Cassava. Antioxidants: open access journal 13 (10), 1245 (2024)
28.
Journal Article
El-Shiekh, R. A.; Elshimy, R.; Mandour, A. A.; Kassem, H. A. H.; Khaleel, A. E.; Alseekh, S.; Fernie, A. R.; Salem, M. A.: Phytochemical characterisation of leaves and stems of Murraya koenigii (L.) Sprengel and Murraya paniculata (L.) Jack and their antibacterial activity against multidrug-resistant Acinetobacter baumannii bacterial infection. International journal of food science & technology 59 (10), pp. 7998 - 8010 (2024)
29.
Journal Article
Figueiredo, Y.G.; Gasparini, K.; Bulut, M.; Fernie, A. R.; Zsögön, A.: The genetic basis of prickle loss in the Solanaceae. Trends in Plant Science (2024)
30.
Journal Article
Naake, T.; D'Auria, J.; Fernie, A. R.; Scossa, F.: Phylogenomic and synteny analysis of BAHD and SCP/SCPL gene families reveal their evolutionary histories in plant specialized metabolism. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 379 (1914), 20230349 (2024)
31.
Journal Article
Rüscher, D.; Vasina, V. V.; Knoblauch, J.; Bellin, L.; Pommerrenig, B.; Alseekh, S.; Fernie, A. R.; Neuhaus, H. E.; Knoblauch, M.; Sonnewald, U. et al.; Zierer, W.: Symplasmic phloem loading and subcellular transport in storage roots are key factors for carbon allocation in cassava. Plant Physiology 196 (2), pp. 1322 - 1339 (2024)
32.
Journal Article
Tóth, D.; Tengölics, R.; Aarabi, F.; Karlsson, A.; Vidal-Meireles, A.; Kovács, L.; Kuntam, S.; Körmöczi, T.; Fernie, A. R.; Hudson, E. P. et al.; Papp, B.; Tóth, S. Z.: Chloroplastic ascorbate modifies plant metabolism and may act as a metabolite signal regardless of oxidative stress. Plant Physiology 196 (2), pp. 1691 - 1711 (2024)
33.
Journal Article
Dorrell, R. G.; Zhang, Y.; Liang, Y.; Gueguen, N.; Nonoyama, T.; Croteau, D.; Penot, M.; Adiba, S.; Bailleul, B.; Gros, V. et al.; Karlusich, P.; José, J.; Zweig, N.; Fernie, A. R.; Jouhet, J.; Maréchal, E.; Bowler, C.: Complementary environmental analysis and functional characterization of lower glycolysis-gluconeogenesis in the diatom plastid. The Plant Cell 36 (9), pp. 3584 - 3610 (2024)
34.
Journal Article
Fu, C.-C.; Huang, B.-X.; Wang, S.-S.; Song, Y.-C.; Metok, D.; Tan, Y.-X.; Fan, T.-P.; Fernie, A. R.; Zargar, M.; Wang, Y. et al.; Chen, M.-X.; Yu, L.-W.; Zhu, F.-Y.: Deciphering the roles of bacterial and fungal communities in the formation and quality of agarwood. Stress Biology 4, 40 (2024)
35.
Journal Article
von Steimker, J.; Tripodi, P.; Wendenburg, R.; Tringovska, I.; Nankar, A. N.; Stoeva, V.; Pasev, G.; Klemmer, A.; Todorova, V.; Bulut, M. et al.; Tikunov, Y.; Bovy, A.; Gechev, T.; Kostova, D.; Fernie, A. R.; Alseekh, S.: The genetic architecture of the pepper metabolome and the biosynthesis of its signature capsianoside metabolites. Current Biology 34 (18), pp. 4209 - 4223 (2024)
36.
Journal Article
Badoni, S.; Pasion-Uy, E. A.; Kor, S.; Kim, S.-R.; Tiozon, R. J. N.; Misra, G.; Buenafe, R. J. Q.; Labarga, L. M.; Ramos-Castrosanto, A. R.; Pratap, V. et al.; Slamet-Loedin, I.; von Steimker, J.; Alseekh, S.; Fernie, A. R.; Kohli, A.; Khush, G. S.; Sreenivasulu, N.: Multiomics of a rice population identifies genes and genomic regions that bestow low glycemic index and high protein content. Proceedings of the National Academy of Sciences of the United States of America 121 (36), e2410598121 (2024)
37.
Journal Article
Gutschker, S.; Ruescher, D.; Rabbi, I.Y.; Rosado-Souza, L.; Pommerrenig, B.; Pauly, M.; Robertz, S.; van Doorn, A.M.; Schlereth, A.; Neuhaus, H.E. et al.; Fernie, A. R.; Reinert, S.; Sonnewald, U.; Zierer, W.: Carbon usage in yellow-fleshed Manihot esculenta storage roots shifts from starch biosynthesis to cell wall and raffinose biosynthesis via the myo-inositol pathway. The Plant Journal 119 (4), pp. 2045 - 2062 (2024)
38.
Journal Article
Hayashi, K.; Fernie, A. R.: A neat wheat trick to hide genes from selection. Trends in Plant Science 29 (8), pp. 837 - 838 (2024)
39.
Journal Article
Liu, Y.; Li, H.; Liu, J.; Wang, Y.; Jiang, C.; Zhou, Z.; Zhuo, L.; Li, W.; Fernie, A. R.; Jackson, D. et al.; Yan, J.; Luo, Y.: The additive function of YIGE2 and YIGE1 in regulating maize ear length. The Plant Journal 119 (3), pp. 1327 - 1335 (2024)
40.
Journal Article
Singh, P.; Kumari, A.; Khaladhar, V.C.; Singh, N.; Pathak, P.K.; Kumar, V.; Kumar, R.J.; Jain, P.; Thakur, J.K.; Fernie, A. R. et al.; Bauwe, H.; Raghavendra, A.S.; Gupta, K.J.: Serine hydroxymethyltransferase6 is involved in growth and resistance against pathogens via ethylene and lignin production in Arabidopsis. The Plant Journal 119 (4), pp. 1920 - 1936 (2024)
41.
Journal Article
Tariq, A.; Meng, M.; Jiang, X.; Bolger, A.; Beier, S.; Buchmann, J.P.; Fernie, A. R.; Wen, W.; Usadel, B.: In-depth exploration of the genomic diversity in tea varieties based on a newly constructed pangenome of Camellia sinensis. The Plant Journal 119 (4), pp. 2096 - 2115 (2024)
42.
Journal Article
Yang, C.; Shen, S.; Zhan, C.; Li, Y.; Zhang, R.; Lv, Y.; Yang, Z.; Zhou, J.; Shi, Y.; Liu, X. et al.; Shi, J.; Zhang, D.; Fernie, A. R.; Luo, J.: Variation in a Poaceae-conserved fatty acid metabolic gene cluster controls rice yield by regulating male fertility. Nature Communications 15 (1), 6663 (2024)
43.
Journal Article
Zhu, F.; Wijesingha Ahchige, M.; Wen, W.; Cheng, Y.; Alseekh, S.; Fernie, A. R.: The natural variance of Arabidopsis secondary metabolism on extended darkness. Scientific Data 11 (1), 841 (2024)
44.
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 22 (7), pp. 2033 - 2050 (2024)
45.
Journal Article
Pérez-Alfocea, F.; Borghi, M.; Guerrero, J. J.; Jiménez, A. R.; Jiménez-Gómez, J. M.; Fernie, A. R.; Bartomeus, I.: Pollinator-assisted plant phenotyping, selection, and breeding for crop resilience to abiotic stresses. The Plant Journal 119 (1), pp. 56 - 64 (2024)
46.
Journal Article
Tripathi, D.; Bhat, J.; Antoniou, C.; Kandhol, N.; Singh, V.; Fernie, A. R.; Fotopoulos, V.: Redox Regulation by Priming Agents Toward a Sustainable Agriculture. Plant and Cell Physiology 65 (7), pp. 1087 - 1102 (2024)
47.
Journal Article
Yin, Z.; Huang, W.; Li, K.; Fernie, A. R.; Yan, S.: Advances in mass spectrometry imaging for plant metabolomics—Expanding the analytical toolbox. The Plant Journal 119 (5), pp. 2168 - 2180 (2024)
48.
Journal Article
Yoshida, T.; Mergner, J.; Yang, Z.; Liu, J.; Kuster, B.; Fernie, A. R.; Grill, E.: Integrating multi-omics data reveals energy and stress signaling activated by abscisic acid in Arabidopsis. The Plant Journal 119 (2), pp. 1112 - 1133 (2024)
49.
Journal Article
Pei, L.; Gao, X.; Tian, X.; Liu, N.; Chen, M.; Fernie, A. R.; Li, H.: A microRNA528-ZmLac3 module regulates low phosphate tolerance in maize. The Plant Journal 118 (6), pp. 2233 - 2248 (2024)
50.
Journal Article
Yuan, H.; Jiangfang, Y.; Liu, Z.; Su, R.; Li, Q.; Fang, C.; Huang, S.; Liu, X.; Fernie, A. R.; Luo, J.: WTV2.0: A high-coverage plant volatilomics method with a comprehensive selective ion monitoring acquisition mode. Molecular Plant 17 (6), pp. 972 - 985 (2024)
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