All Publications

Journal Article (4185)

1.
Journal Article
Tan, Q.W.; Lim, P.K.; Chen, Z.; Pasha, A.; Provart, N.; Arend, M.; Nikoloski, Z.; Mutwil, M.: Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses. Nature Communications 14 (1), 986 (2023)
2.
Journal Article
Alseekh, S.; Fernie, A. R.: Expanding our coverage: Strategies to detect a greater range of metabolites. Current Opinion in Plant Biology 73, 102335 (2023)
3.
Journal Article
Moghe, G.; Kruse, L. H.; Petersen, M.; Scossa, F.; Fernie, A. R.; Gaquerel, E.; D'Auria, J. C.: BAHD Company: The Ever-Expanding Roles of the BAHD Acyltransferase Gene Family in Plants. Annual Review of Plant Biology 74 (2023)
4.
Journal Article
Mutwil, M.; Fernie, A. R.: Ancestral Genome Reconstruction for Studies of the Green Lineage. Molecular Plant (2023)
5.
Journal Article
Bruinsma, L.; Wenk, S.; Claassens, N.J.; Martins dos Santos, V.A.P.: Paving the way for synthetic C1. Metabolic Engineering 76, pp. 215 - 224 (2023)
6.
Journal Article
Campana, P.; Nikoloski, Z.: Self- and cross-attention accurately predicts metabolite–protein interactions. NAR: genomics and bioinformatics 5 (1), lqad008 (2023)
7.
Journal Article
Chen, J.; Zhang, Y.; Yin, H.; Liu, W.; Hu, X.; Li, D.; Lan, C.; Gao, L.; He, Z.; Cui, F. et al.; Fernie, A. R.; Chen, W.: The pathway of melatonin biosynthesis in common wheat (Triticum aestivum). Journal of Pineal Research 74 (2), e12841 (2023)
8.
Journal Article
Fan, R.; Zhu, C.; Qiu, D.; Mao, G.; Mueller-Roeber, B.; Zeng, J.: Integrated transcriptomic and metabolomic analyses reveal key genes controlling flavonoid biosynthesis in Citrus grandis ‘Tomentosa’ fruits. Plant Physiology and Biochemistry 196, pp. 210 - 221 (2023)
9.
Journal Article
Gago, J.; Nadal, M.; Clemente-Moreno, M. J.; Figueroa, C. M.; Medeiros, D.B.; Cubo-Ribas, N.; Cavieres, L. A.; Gulías, J.; Fernie, A. R.; Flexas, J. et al.; Bravo, L. A.: Nutrient availability regulates Deschampsia antarctica photosynthetic and stress tolerance performance in Antarctica. Journal of Experimental Botany, erad043 (2023)
10.
Journal Article
Luzarowska, U.; Ruß, A.-K.; Joubès, J.; Batsale, M.; Szymański, J.; Thirumalaikumar, V. P.; Luzarowski, M.; Wu, S.; Zhu, F.; Endres, N. et al.; Khedhayir, S.; Schumacher, J.; Jasinska, W.; Xu, K.; Cordoba, S. M. C.; Weil, S.; Skirycz, A.; Fernie, A. R.; Li-Beisson, Y.; Fusari, C. M.; Brotman, Y.: Hello darkness, my old friend: 3-KETOACYL-COENZYME A SYNTHASE4 is a branch point in the regulation of triacylglycerol synthesis in Arabidopsis thaliana. The Plant Cell, koad059 (2023)
11.
Journal Article
Schada von Borzyskowski, L.; Schulz-Mirbach, H.; Troncoso Castellanos, M.; Severi, F.; Gomez Coronado, P. A.; Paczia, N.; Glatter, T.; Bar-Even, A.; Lindner, S. N.; Erb, T.J.: Implementation of the β-hydroxyaspartate cycle increases growth performance of Pseudomonas putida on the PET monomer ethylene glycol. Metabolic Engineering 76, pp. 97 - 109 (2023)
12.
Journal Article
Sheng, O.; Yin, Z.; Huang, W.; Chen, M.; Du, M.; Kong, Q.; Fernie, A. R.; Yi, G.; Yan, S.: Metabolic profiling reveals genotype-associated alterations in carotenoid content during banana postharvest ripening. Food Chemistry 403, 134380 (2023)
13.
Journal Article
Xue, J.-Y.; Li, Z.; Hu, S.-Y.; Kao, S.-M.; Zhao, T.; Wang, J.-Y.; Wang, Y.; Chen, M.; Qiu, Y.; Fan, H.-Y. et al.; Liu, Y.; Shao, Z.-Q.; Van de Peer, Y.: The Saururus chinensis genome provides insights into the evolution of pollination strategies and herbaceousness in magnoliids. The Plant Journal 113 (5), pp. 1021 - 1034 (2023)
14.
Journal Article
Yang, L.; Zhou, Y.; Wang, S.; Xu, Y.; Ostendorp, S.; Tomkins, M.; Kehr, J.; Morris, R. J.; Kragler, F.: Non-cell-autonomous HSC70.1 chaperone displays homeostatic feed-back regulation by binding its own mRNA. New Phytologist 237 (6), pp. 2404 - 2421 (2023)
15.
Journal Article
Zhang, Q.; Shi, Y.; Hu, H.; Shi, Y.; Tang, D.; Ruan, J.; Fernie, A. R.; Liu, M.-Y.: Magnesium promotes tea plant growth via enhanced glutamine synthetase-mediated nitrogen assimilation. Plant Physiology, kiad143 (2023)
16.
Journal Article
Kleinschmidt, D.; Forner, J.: Plant genetic engineering makes treasure from trash. The Science Breaker 9 (1) (2023)
17.
Journal Article
Shi, Y.; Zhang, Y.; Sun, Y.; Xie, Z.; Luo, Y.; Long, Q.; Feng, J.; Liu, X.; Wang, B.; He, D. et al.; Ren, J.; Guo, P.; Xing, J.; He, L.; Fernie, A. R.; Chen, W.; Liu, X.; Luo, Y.; Jin, C.; Luo, J.: Natural variations of OsAUX5, a target gene of OsWRKY78, control the neutral essential amino acid content in rice grains. Molecular Plant 16 (2), pp. 322 - 336 (2023)
18.
Journal Article
Almeida, O.A.C.; de Araujo, N.O.; Mulato, A.T.N.; Persinoti, G.F.; Sforça, M.L.; Calderan-Rodrigues, M.J.; Oliveira, J.V.D.C.: Bacterial volatile organic compounds (VOCs) promote growth and induce metabolic changes in rice. Frontiers in Plant Science 13, 1056082 (2023)
19.
Journal Article
Avidan, O.; Moraes, T. A.; Mengin, V.; Feil, R.; Rolland, F.; Stitt, M.; Lunn, J. E.: In vivo protein kinase activity of SnRK1 fluctuates in Arabidopsis rosettes during light-dark cycles. Plant Physiology (2023)
20.
Journal Article
Cerqueira, J. V. A.; Zhu, F.; Mendes, K.; Nunes-Nesi, A.; Martins, S. C. V.; Benedito, V.; Fernie, A. R.; Zsögön, A.: Promoter replacement of ANTHOCYANIN1 induces anthocyanin accumulation and triggers shade avoidance response through developmental, physiological and metabolic reprogramming in tomato. Horticulture Research 10 (2), uhac254 (2023)
21.
Journal Article
Chen, Y.; Chao, Z.-F.; Jin, M.; Wang, Y.-L.; Li, Y.; Wu, J.-C.; Xiao, Y.; Peng, Y.; Lv, Q.-Y.; Gui, S. et al.; Wang, X.; Han, M.-L.; Fernie, A. R.; Chao, D.-Y.; Yan, J.: A heavy metal transporter gene ZmHMA3a promises safe agricultural production on cadmium-polluted arable land. Journal of Genetics and Genomics 50 (2), p. 130-134 (2023)
22.
Journal Article
Durand, M.; Brehaut, V.; Clement, G.; Kelemen, Z.; Macé, J.; Feil, R.; Duville, G.; Launay-Avon, A.; Paysant-Le Roux, C.; Lunn, J. E. et al.; Roudier, F.; Krapp, A.: The Arabidopsis transcription factor NLP2 regulates early nitrate responses and integrates nitrate assimilation with energy and carbon skeleton supply. The Plant Cell, koad025 (2023)
23.
Journal Article
Gui, S.; Martinez Rivas, F.J.; Wen, W.; Meng, M.; Yan, J.; Usadel, B.; Fernie, A. R.: Going broad and deep: sequencing driven insights into plant physiology, evolution and crop domestication. The Plant Journal 113 (3), pp. 446 - 459 (2023)
24.
Journal Article
Hu, X.; Fernie, A. R.; Yan, J.: Deep learning in regulatory genomics: from identification to design. Current Opinion in Biotechnology 79, 102887 (2023)
25.
Journal Article
Julca, I.; Mutwil-Anderwald, D.; Manoj, V.; Khan, Z.; Lai, S. K.; Yang, L. K.; Beh, I. T.; Dziekan, J.; Lim, Y. P.; Lim, S. K. et al.; Low, Y. W.; Lam, Y. I.; Tjia, S.; Mu, Y.; Tan, Q. W.; Nuc, P.; Choo, L. M.; Khew, G.; Shining, L.; Kam, A.; Tam, J. P.; Bozdech, Z.; Schmidt, M.; Usadel, B.; Kanagasundaram, Y. s.; Alseekh, S.; Fernie, A. R.; Li, H. Y.; Mutwil, M.: Genomic, transcriptomic, and metabolomic analysis of Oldenlandia corymbosa reveals the biosynthesis and mode of action of anti-cancer metabolites. Journal of Integrative Plant Biology (2023)
26.
Journal Article
Li, H.; Fernie, A. R.; Yang, X.: Using systems metabolic engineering strategies for high-oil maize breeding. Current Opinion in Biotechnology 79, 102847 (2023)
27.
Journal Article
Liu, Y.; Nour-Eldin, H.H.; Zhang, L.; Li, Z.; Fernie, A. R.; Ren, M.: Biotechnological detoxification: an unchanging source–sink balance strategy for crop improvement. Trends in Plant Science 28 (2), pp. 135 - 138 (2023)
28.
Journal Article
Lohmann, J.; de Luxán-Hernández, C.; Gao, Y.; Zoschke, R.; Weingartner, M.: Arabidopsis Translation factor eEF1Bγ impacts plant development and associates with heat-induced cytoplasmic foci. Journal of Experimental Botany, erad050 (2023)
29.
Journal Article
Martinez Rivas, F.J.; Blanco-Portales, R.; Pérez-Serratosa, M.; Ric-Varas, P.; Sánchez, V. G.; Puche, L. M.; Moyano, L.; Mercado, J. Á.; Alseekh, S.; Caballero, J. L. et al.; Fernie, A. R.; Muñoz-Blanco, J.; Molina-Hidalgo, F. J.: FaMYB123 interacts with FabHLH3 to regulate the late steps of anthocyanin and flavonol accumulation during ripening. The Plant Journal (2023)
30.
Journal Article
Silva, S.F.; Miranda, M.T.; Cunha, C.P.; Domingues-Jr, A.P.; Aricetti, J.A.; Caldana, C.; Machado, E.C.; Ribeiro, R.V.: Metabolic profiling of drought tolerance: Revealing how citrus rootstocks modulate plant metabolism under varying water availability. Environmental and Experimental Botany 206, 105169 (2023)
31.
Journal Article
Vidal-Meireles, A.; Kuntam, S.; Széles, E.; Tóth, D.; Neupert, J.; Bock, R.; Tóth, S. Z.: The lifetime of the oxygen-evolving complex subunit PSBO depends on light intensity and carbon availability in Chlamydomonas. Plant, Cell and Environment 46 (2), pp. 422 - 439 (2023)
32.
Journal Article
Wijesingha Ahchige, M.; Fernie, A. R.; Alseekh, S.: PANTOTHENATE KINASE4, LOSS OF GDU2, and TRANSPOSON PROTEIN1 affect the canalization of tomato fruit metabolism. Plant Physiology, kiad093 (2023)
33.
Journal Article
Wu, M.; Zhang, Q.; Dong, Y.; Wang, Z.; Zhan, W.; Ke, Z.; Li, S.; He, L.; Ruf, S.; Bock, R. et al.; Zhang, J.: Transplastomic tomatoes expressing double-stranded RNA against a conserved gene are efficiently protected from multiple spider mites. New Phytologist 237 (4), pp. 1363 - 1373 (2023)
34.
Journal Article
Xu, W.; Sato, H.; Bente, H.; Santos-González, J.; Köhler, C.: Endosperm cellularization failure induces a dehydration stress response leading to embryo arrest. The Plant Cell 35 (2), pp. 874 - 888 (2023)
35.
Journal Article
Yi, J.; Kradolfer, D.; Brownfield, L.; Ma, Y.; Piskorz, E.; Köhler, C.; Jiang, H.: Meiocyte size is a determining factor for unreduced gamete formation in Arabidopsis thaliana. New Phytologist 237 (4), pp. 1179 - 1187 (2023)
36.
Journal Article
Yin, Z.; Huang, W.; Fernie, A. R.; Yan, S.: Mass spectrometry imaging techniques: a versatile toolbox for plant metabolomics. Trends in Plant Science 28 (2), pp. 250 - 251 (2023)
37.
Journal Article
Awada, R.; Lepelley, M.; Breton, D.; Charpagne, A.; Campa, C.; Berry, V.; Georget, F.; Breitler, J.-C.; Léran, S.; Djerrab, D. et al.; Martinez-Seidel, F.; Descombes, P.; Crouzillat, D.; Bertrand, B.; Etienne, H.: Global transcriptome profiling reveals differential regulatory, metabolic and hormonal networks during somatic embryogenesis in Coffea arabica. BMC Genomics 24, 41 (2023)
38.
Journal Article
Chung, K. P.; Gonzalez-Duran, E.; Ruf, S.; Endries, P.; Bock, R.: Control of plastid inheritance by environmental and genetic factors. Nature Plants 9, pp. 68 - 80 (2023)
39.
Journal Article
Hashemi, S.; Laitinen, R.; Nikoloski, Z.: Models and molecular mechanisms for trade-offs in the context of metabolism. Molecular Ecology (2023)
40.
Journal Article
Kim, S.; Giraldo, N.; Rainaldi, V.; Machens, F.; Collas, F.; Kubis, A.; Kensy, F.; Bar-Even, A.; Lindner, S. N.: Optimizing E. coli as a formatotrophic platform for bioproduction via the reductive glycine pathway. Frontiers in Bioengineering and Biotechnology 11, 1091899 (2023)
41.
Journal Article
Lima, L.G.A.D.; Ferreira, S.S.; Simões, M.S.; Cunha, L.X.D.; Fernie, A. R.; Cesarino, I.: Comprehensive expression analyses of the ABCG subfamily reveal SvABCG17 as a potential transporter of lignin monomers in the model C4 grass Setaria viridis. Journal of Plant Physiology 280, 153900 (2023)
42.
Journal Article
Natale, R.; Coppola, M.; D'Agostino, N.; Zhang, Y.; Fernie, A. R.; Castaldi, V.; Rao, R.: In silico and in vitro approaches allow the identification of the Prosystemin molecular network. Computational and Structural Biotechnology Journal 21, pp. 212 - 223 (2023)
43.
Journal Article
Perlikowski, D.; Skirycz, A.; Marczak, Ł.; Lechowicz, K.; Augustyniak, A.; Michaelis, Ä.; Arkadiusz, K.; Kosmala, A.: Metabolism of crown tissue is crucial for drought tolerance and recovery after stress cessation in Lolium/Festuca forage grasses. Journal of Experimental Botany 74 (1), pp. 396 - 414 (2023)
44.
Journal Article
Poplawski, P.; Alseekh, S.; Jankowska, U.; Skupien-Rabian, B.; Iwanicka-Nowicka, R.; Kossowska, H.; Fogtman, A.; Rybicka, B.; Bogusławska, J.; Adamiok-Ostrowska, A. et al.; Hanusek, K.; Hanusek, J.; Koblowska, M.; Fernie, A. R.; Piekiełko-Witkowska, A.: Coordinated reprogramming of renal cancer transcriptome, metabolome and secretome associates with immune tumor infiltration. Cancer Cell International 23 (1), 2 (2023)
45.
Journal Article
Reginaldo, F.P.S.; Bueno, P.C.P.; Lourenço, E.M.G.; de Matos Costa, I.C.; Moreira, L.G.L.; de Araújo Roque, A.; Barbosa, E.G.; Fett-Neto, A.G.; Cavalheiro, A.J.; Giordani, R.B.: Methyl jasmonate induces selaginellin accumulation in Selaginella convoluta. Metabolomics 19, 2 (2023)
46.
Journal Article
Röhricht, H.; Przybyla-Toscano, J.; Forner, J.; Boussardon, C.; Keech, O.; Rouhier, N.; Meyer, E. H.: Mitochondrial ferredoxin-like is essential for forming complex I-containing supercomplexes in Arabidopsis. Plant Physiology (2023)
47.
Journal Article
Salem, M.; El-Shiekh, R.; Aborehab, N.; Al-Karmalawy, A.; Ezzat, S.; Alseekh, S.; Fernie, A. R.: Metabolomics driven analysis of Nigella sativa seeds identifies the impact of roasting on the chemical composition and immunomodulatory activity. Food Chemistry 398, 133906 (2023)
48.
Journal Article
Siqueira, J.A.; Batista-Silva, W.; Zsögön, A.; Fernie, A. R.; Araújo, W.L.; Nunes-Nesi, A.: Plant domestication: setting biological clocks. Trends in Plant Science (2023)
49.
Journal Article
Sreenivasulu, N.; Alseekh, S.; Tiozon, R. N.; Graner, A.; Martin, C.; Fernie, A. R.: Metabolic Signatures from Genebank Collections: An Underexploited Resource for Human Health? Annual Review of Food Science and Technology 14 (2023)
50.
Journal Article
Strand, D.; Karcher, D.; Ruf, S.; Schadach, A.; Schöttler, M. A.; Sandoval-Ibanez, O.; Hall, D.; Kramer, D. M.; Bock, R.: Characterization of mutants deficient in N-terminal phosphorylation of the chloroplast ATP synthase subunit β. Plant Physiology (2023)
Go to Editor View