All Publications

1.

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)

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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)

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Porto, N.P.; Bret, R.S.C.; Souza, P.V.L.; Cândido-Sobrinho, S.A.; Medeiros, D.B.; Fernie, A. R.; Daloso, D. M.: Thioredoxins regulate the metabolic fluxes throughout the tricarboxylic acid cycle and associated pathways in a light-independent manner. Plant Physiology and Biochemistry 193, pp. 36 - 49 (2022)

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Aleman, J.; H., G.; Thirumalaikumar, V. P.; Jander, G.; Fernie, A. R.; Skirycz, A.: OPDA, more than just a jasmonate precursor. Phytochemistry 204, 113432 (2022)

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Omranian, N.; Nikoloski, Z.: CUBCO+: prediction of protein complexes based on min-cut network partitioning into biclique spanned subgraphs. Applied Network Science 7, 71 (2022)

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Ostendorp, A.; Ostendorp, S.; Zhou, Y.; Chaudron, Z.; Wolffram, L.; Rombi, K.; von Pein, L.; Falke, S.; Jeffries, C. M.; Svergun, D. I. et al.; Betzel, C.; Morris, R. J.; Kragler, F.; Kehr, J.: Intrinsically disordered plant protein PARCL co-localizes with RNA in phase-separated condensates whose formation can be regulated by mutating the PLD. The Journal of Biological Chemistry 298 (12), 102631 (2022)

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Shi, Z.; Li, H.; Zhang, W.; Chen, Y.; Zeng, C.; Kang, X.; Xu, X.; Xia, Z.; Qing, B.; Yuan, Y. et al.; Song, G.; Caldana, C.; Hu, J.; Willmitzer, L.; Li, Y.: A Comprehensive Mass Spectrometry-Based Workflow for Clinical Metabolomics Cohort Studies. Metabolites 12 (12), 1168 (2022)

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Caldana, C.; Fernie, A. R.: Plant biology: Identification of the connecTOR linking metabolism, epigenetics and development. Current Biology 32 (22), pp. R1272 - R1274 (2022)

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Wiszniewski, A.A.G.; Uberegui, E.; Messer, M.; Sultanova, G.; Borghi, M.; Duarte, G. T.; Vicente, R.; Sageman-Furnas, K.; Fernie, A. R.; Nikoloski, Z. et al.; Laitinen, R. A.E.: Temperature-mediated flower size plasticity in Arabidopsis. iScience 25 (11), 105411 (2022)

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Urrea-Castellanos, R.; Caldana, C.; Henriques, R.: Growing at the right time: interconnecting the TOR pathway with photoperiod and circadian regulation. Journal of Experimental Botany 73 (20), pp. 7006 - 7015 (2022)

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Kishor, P. B. K.; Tiozon, R. J. N.; Fernie, A. R.; Sreenivasulu, N.: Abscisic acid and its role in the modulation of plant growth, development, and yield stability. Trends in Plant Science 27 (12), pp. 1283 - 1295 (2022)

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Apriyanto, A.; Compart, J.; Zimmermann, V.; Alseekh, S.; Fernie, A. R.; Fettke, J.: Indication that starch and sucrose are biomarkers for oil yield in oil palm (Elaeis guineensis Jacq.). FOOD CHEMISTRY 393, 133361 (2022)

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Balparda, M.; Schmitz, J.; Duemmel, M.; Wuthenow, I. C.; Schmidt, M.; Alseekh, S.; Fernie, A. R.; Lercher, M. J.; Maurino, V. G.: Two plant glyoxalase systems with different evolutionary origins detoxify diverse reactive carbonyl species. Plant Physiology, kiac526 (2022)

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Bohra, A.; Tiwari, A.; Kaur, P.; Ganie, S. A.; Raza, A.; Roorkiwal, M.; Mir, R. R.; Fernie, A. R.; Smýkal, P.; Varshney, R. K.: The Key to the Future Lies in the Past: Insights from Grain Legume Domestication and Improvement Should Inform Future Breeding Strategies. Plant and Cell Physiology 63 (11), pcac086, pp. 1554 - 1572 (2022)

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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 (2022)

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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 (2022)

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Chen, L.; Zhao, H.; Chen, Y.; Jiang, F.; Zhou, F.; Liu, Q.; Fan, Y.; Liu, T.; Tu, W.; Walther, D. et al.; Song, B.: Comparative transcriptomics analysis reveals a calcineurin B-like gene to positively regulate constitutive and acclimated freezing tolerance in potato. Plant, Cell and Environment 45 (11), pp. 3305 - 3321 (2022)

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Laitinen, R. A. E.; Nikoloski, Z.: Strategies to identify and dissect trade-offs in plants. Molecular Ecology (2022)

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Li, X.; Deng, D.; Cataltepe, G.; Román, Á.; Buckley, C.R.; Monte Bello, C.C.; Skirycz, A.; Caldana, C.; Haydon, M.J.: A reactive oxygen species Ca2+ signalling pathway identified from a chemical screen for modifiers of sugar-activated circadian gene expression. New Phytologist 236 (3), pp. 1027 - 1041 (2022)

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Mehring, A.; Zayed, A.; Salem, M.A.; Alseekh, S.; Fernie, A.; Ulber, R.: Time-dependent behaviour of methyl jasmonate elicited cell suspension cultures of Ocimum species via untargeted mass spectrometry-based metabolomics. Industrial Crops and Products 187 (Part A), 115414 (2022)

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Siqueira, J. A.; da Fonseca-Pereira, P.; Fernie, A. R.; Nunes-Nesi, A.; Araújo, W. L.: Recycling amino acids ensures meiosis and seed development. Trends in Plant Science 27 (11), pp. 1084 - 1086 (2022)

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Sun, Y.; Guo, J.; Ruan, Y.; Zhang, T.; Fernie, A. R.; Yuan, H.: The recruitment of specific rhizospheric bacteria facilitates Stevia rebaudiana salvation under nitrogen and/or water deficit stresses. Industrial Crops and Products 187 (B), 115434 (2022)

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Tan, J.; Forner, J.; Karcher, D.; Bock, R.: DNA base editing in nuclear and organellar genomes. Trends in Genetics 38 (11), pp. 1147 - 1169 (2022)

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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 (2022)

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von Bismarck, T.; Korkmaz, K.; Ruß, J.; Skurk, K.; Kaiser, E.; Correa Galvis, V.; Cruz, J. A.; Strand, D.; Koehl, K. I.; Eirich, J. et al.; Finkemeier, I.; Jahns, P.; Kramer, D. M.; Armbruster, U.: Light acclimation interacts with thylakoid ion transport to govern the dynamics of photosynthesis in Arabidopsis. New Phytologist (2022)

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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 (2022)

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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, koac337 (2022)

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Yang, M.-K.; Zhu, X.-J.; Chen, C.-M.; Guo, X.; Xu, S.-X.; Xu, Y.-R.; Du, S.-X.; Xiao, S.; Mueller-Roeber, B.; Huang, W. et al.; Chen, L.: The plant circadian clock regulates autophagy rhythm through transcription factor LUX ARRHYTHMO. Journal of Integrative Plant Biology 64 (11), pp. 2135 - 2149 (2022)

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Li, Y.; Yang, Z.; Yang, C.; Liu, Z.; Shen, S.; Zhan, C.; Lyu, Y.; Zhang, F.; Li, K.; Shi, Y. et al.; Zhou, J.; Liu, X.; Fang, C.; Fernie, A. R.; Li, J.; Luo, J.: The NET locus determines the food taste, cooking and nutrition quality of rice. Science Bulletin 67, pp. 2045 - 2049 (2022)

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Yin, Z.; Dong, T.; Huang, W.; Du, M.; Chen, D.; Fernie, A. R.; Yi, G.; Yan, S.: Spatially resolved metabolomics reveals variety-specific metabolic changes in banana pulp during postharvest senescence. FOOD CHEMISTRY: X 15, 100371 (2022)

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Sedaghatmehr, M.; Stüwe, B.; Mueller-Roeber, B.; Balazadeh, S.: Heat shock factor HSFA2 fine-tunes resetting of thermomemory via plastidic metalloprotease FtsH6. Journal of Experimental Botany 73 (18), pp. 6394 - 6404 (2022)

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Lucius, S.; Theune, M.; Arrivault, S.; Hildebrandt, S.; Mullineaux, C. W.; Gutekunst, K.; Hagemann, M.: CP12 fine-tunes the Calvin-Benson cycle and carbohydrate metabolism in cyanobacteria. Frontiers in Plant Science 13, 1028794 (2022)

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Zhang, Y.; Fernie, A. R.: Metabolite profiling of Arabidopsis mutants of lower glycolysis. Scientific Data 9 (1), 614 (2022)

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Sayed, S.M.A.; Alseekh, S.; Siems, K.; Fernie, A. R.; Luyten, W.; Schmitz-Linneweber, C.; Saul, N.: Identification of a Hydroxygallic Acid Derivative, Zingibroside R1 and a Sterol Lipid as Potential Active Ingredients of Cuscuta chinensis Extract That Has Neuroprotective and Antioxidant Effects in Aged Caenorhabditis elegans. Nutrients 14 (19), 4199 (2022)

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Hölscher, M.; Forner, J.; Calderone, S.; Krämer, C.; Taylor, Z.; Loiacono, F.V.; Agrawal, S.; Karcher, D.; Moratti, F. G.; Kroop, X. et al.; Bock, R.: Expression strategies for the efficient synthesis of antimicrobial peptides in plastids. Nature Communications 13, 5856 (2022)

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Ahouvi, Y.; Haber, Z.; Zach, Y. Y.; Rosental, L.; Toubiana, D.; Sharma, D.; Alseekh, S.; Tajima, H.; Fernie, A. R.; Brotman, Y. et al.; Blumwald, E.; Sade, N.: The Alteration Of Tomato CHLOROPLAST VESICULATION Positively Affects Whole-Plant Source–Sink Relations And Fruit Metabolism Under Stress Conditions. Plant and Cell Physiology (2022)

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Blankenagel, S.; Eggels, S.; Frey, M.; Grill, E.; Bauer, E.; Dawid, C.; Fernie, A. R.; Haberer, G.; Hammerl, R.; Medeiros, D.B. et al.; Ouzunova, M.; Presterl, T.; Ruß, V.; Schäufele, R.; Schlüter, U.; Tardieu, F.; Urbany, C.; Urzinger, S.; Weber, A. P. M.; Schön, C.-C.; Avramova, V.: Natural alleles of the abscisic acid catabolism gene ZmAbh4 modulate water use efficiency and carbon isotope discrimination in maize. The Plant Cell 34 (10), pp. 3860 - 3872 (2022)

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Brigante, F. I.; Lucini Mas, A.; Erban, A.; Fehrle, I.; Martinez-Seidel, F.; Kopka, J.; Wunderlin, D. A.; Baroni, M. V.: Authenticity assessment of commercial bakery products with chia, flax and sesame seeds: Application of targeted and untargeted metabolomics results from seeds and lab-scale cookies. Food control 140, 109114 (2022)

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Chen, L.; Luo, J.; Jin, M.; Yang, N.; Liu, X.; Peng, Y.; Li, W.; Phillips, A.; Cameron, B.; Bernal, J. S. et al.; Rellán-Álvarez, R.; Sawers, R. J. H.; Liu, Q.; Yin, Y.; Ye, X.; Yan, J.; Zhang, Q.; Zhang, X.; Wu, S.; Gui, S.; Wei, W.; Wang, Y.; Luo, Y.; Jiang, C.; Deng, M.; Jin, M.; Jian, L.; Yu, Y.; Zhang, M.; Yang, X.; Hufford, M. B.; Fernie, A. R.; Warburton, M. L.; Ross-Ibarra, J.; Yan, J.: Genome sequencing reveals evidence of adaptive variation in the genus Zea. Nature Genetics 54, pp. 1736 - 1745 (2022)

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de Souza, L. P.; Naake, T.; Fernie, A. R.: Computational approaches that aid annotation in metabolomics. Trends in Plant Science 27 (10), pp. 1077 - 1078 (2022)

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Loiacono, F.V.; Walther, D.; Seeger, S.; Thiele, W.; Gerlach, I.; Karcher, D.; Schöttler, M. A.; Zoschke, R.; Bock, R.: Emergence of novel RNA editing sites by changes in the binding affinity of a conserved PPR protein. Molecular Biology and Evolution (2022)

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Orf, I.; Tenenboim, H.; Omranian, N.; Nikoloski, Z.; Fernie, A. R.; Lisec, J.; Brotman, Y.; Bromke, M.A.: Transcriptomic and Metabolomic Analysis of a Pseudomonas-Resistant versus a Susceptible Arabidopsis Accession. International Journal of Molecular Sciences 23 (20), 12087 (2022)

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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 (2022)

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Sato, H.; Köhler, C.: Genomic imprinting regulates establishment and release of seed dormancy. Current Opinion in Plant Biology 69, 102264 (2022)

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Schulten, A.; Pietzenuk, B.; Quintana, J.; Scholle, M.; Feil, R.; Krause, M.; Romera-Branchat, M.; Wahl, V.; Severing, E.; Coupland, G. et al.; Krämer, U.: Energy status-promoted growth and development of Arabidopsis require copper deficiency response transcriptional regulator SPL7. The Plant Cell 34 (10), pp. 3873 - 3898 (2022)

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Sun, Y.; Alseekh, S.; Fernie, A. R.: Plant secondary metabolic responses to global climate change: A meta-analysis in medicinal and aromatic plants. GCB Bioenergy (2022)

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Wang, S.; Qiang, Q.; Xiang, L.; Fernie, A. R.; Yang, J.: Targeted approaches to improve tomato fruit taste. Horticulture Research (2022)

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Yang, Z.; Liu, Z.; Xu, H.; Yufei, L.; Huang, S.; Cao, G.; Shi, M.; Zhu, J.; Zhou, J.; Li, R. et al.; Ding, Y.; Xiao, Y.; Liu, X.; Fernie, A. R.; Luo, J.: ArecaceaeMDB: A comprehensive multi-omics database for Arecaceae breeding and functional genomics studies. Plant Biotechnology Journal (2022)

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Zhan, C.; Shen, S.; Yang, C.; Liu, Z.; Fernie, A. R.; Graham, I. A.; Luo, J.: Plant metabolic gene clusters in the multi-omics era. Trends in Plant Science 27 (10), pp. 981 - 1001 (2022)

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Ciuffa, R.; Uliana, F.; Mannion, J.; Mehnert, M.; Tenev, T.; Marulli, C.; Satanowski, A.; Keller, L.M.L.; Rodilla Ramírez, P.N.; Ori, A. et al.; Gstaiger, M.; Meier, P.; Aebersold, R.: Novel biochemical, structural, and systems insights into inflammatory signaling revealed by contextual interaction proteomics. Proceedings of the National Academy of Sciences of the United States of America 119 (40), e21171751 (2022)

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