All Publications

1.

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Calderan-Rodrigues, M.J.; Luzarowski, M.; Monte Bello, C.C.; Minen, R.I.; Zühlke, B. M.; Nikoloski, Z.; Skirycz, A.; Caldana, C.: Proteogenic Dipeptides Are Characterized by Diel Fluctuations and Target of Rapamycin Complex-Signaling Dependency in the Model Plant Arabidopsis thaliana. Frontiers in Plant Science 12, 758933 (2021)

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Treves, H.; Küken, A.; Arrivault, S.; Ishihara, H.; Hoppe, I.; Erban, A.; Höhne, M.; Moraes, T. A.; Kopka, J.; Szymanski, J. et al.; Nikoloski, Z.; Stitt, M.: Carbon flux through photosynthesis and central carbon metabolism show distinct patterns between algae, C-3 and C-4 plants. Nature Plants 8, pp. 78 - 91 (2021)

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Martinez-Seidel, F.; Hsieh, Y.-C.; Walther, D.; Kopka, J.; Firmino, A.: COSNet(i): ComplexOme-Structural Network Interpreter used to study spatial enrichment in metazoan ribosomes. BMC Bioinformatics 22, 605 (2021)

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David, Z.; Swart, C.; Graf, A.; Arrivault, S.; Tillich, M.; Proost, S.; Nikoloski, Z.; Stitt, M.; Bock, R.; Mühlhaus, M. et al.; Boulouis, A.: Topology of the redox network during induction of photosynthesis as revealed by time-resolved proteomics in tobacco. Science Advances 7 (51), eabi8307 (2021)

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Frusciante, S.; Demurtas, O. C.; Sulli, M.; Mini, P.; Aprea, G.; Diretto, G.; Karcher, D.; Bock, R.; Giuliano, G.: Heterologous expression of Bixa orellana cleavage dioxygenase 4–3 drives crocin but not bixin biosynthesis. Plant Physiology 188 (3), pp. 1469 - 1482 (2021)

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Verbančič, J.; Huang, J.J.; McFarlane, H.E.: Analysis of cellulose synthase activity in Arabidopsis using spinning disk microscopy. STAR Protocols 2 (4), 100863 (2021)

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Shen, S.; Peng, M.; Fang, H.; Wang, Z.; Zhou, S.; Jing, X.; Zhang, M.; Yang, C.; Guo, H.; Li, Y. et al.; Lei, L.; Shi, Y.; Sun, Y.; Liu, X.; Xu, C.; Tohge, T.; Yuan, M.; Fernie, A. R.; Ning, Y.; Wang, G.; Luo, J.: An Oryza-specific hydroxycinnamoyl tyramine gene cluster contributes to enhanced disease resistance. Science Bulletin 66 (23), pp. 2369 - 2380 (2021)

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Qiu, Y.; Köhler, C.: Endosperm evolution by duplicated and neofunctionalized Type I MADS-box transcription factors. Molecular Biology and Evolution 39 (1), msab355 (2021)

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Fadoul, H.E.; Rivas, F.J.M.; Neumann, K.; Balazadeh, S.; Fernie, A. R.; Alseekh, S.: Comparative molecular and metabolic profiling of two contrasting wheat cultivars under drought stress. International Journal of Molecular Sciences 22 (24), 13287 (2021)

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Hashemi, S.; Razaghi-Moghadam, Z.; Nikoloski, Z.: Identification of flux trade-offs in metabolic networks. Scientific Reports 11 (1), 23776 (2021)

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Siani, R.; Stabl, G.; Gutjahr, C.; Schloter, M.; Radl, V.: Acidovorax pan-genome reveals specific functional traits for plant beneficial and pathogenic plant-associations. Microbial Genomics 7 (12), 000666 (2021)

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Zsögön, A.; Peres, L. E. P.; Xiao, Y.; Yan, J.; Fernie, A. R.: Enhancing crop diversity for food security in the face of climate uncertainty. The Plant Journal 109 (2), pp. 402 - 414 (2021)

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Fàbregas, N.; Fernie, A. R.: The reliance of phytohormone biosynthesis on primary metabolite precursors. Journal of Plant Physiology 268, 153589 (2021)

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Qin, K.; Fernie, A. R.; Zhang, Y.: The assembly of super-complexes in the plant chloroplast. Biomolecules 11 (12), 1839 (2021)

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Fàbregas, N.; Fernie, A. R.: The interface of central metabolism with hormone signaling in plants. Current Biology 31 (23), pp. R1535 - R1548 (2021)

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Tiozon, R.J.N.; Bonto, A.; Sreenivasulu, N.: Enhancing the functional properties of rice starch through biopolymer blending for industrial applications: A review. International Journal of Biological Macromolecules 192, pp. 100 - 117 (2021)

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Wagner, M.; Zhang, B.; Tauffenberger, A.; Schroeder, F.C.; Skirycz, A.: Experimental methods for dissecting the terraincognita of protein-metabolite interactomes. Current Opinion in Systems Biology 28, 100403 (2021)

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Kasote, D.; Tiozon, R.J.N.; Sartagoda, K. J. D.; Itagi, H.; Roy, P.; Kohli, A.; Regina, A.; Sreenivasulu, N.: Food Processing Technologies to Develop Functional Foods With Enriched Bioactive Phenolic Compounds in Cereals. Frontiers in Plant Science 12, 771276 (2021)

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19.

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Curtin, S.; Qi, Y.; Peres, L. E. P.; Fernie, A. R.; Zsögön, A.: Pathways to de novo domestication of crop wild relatives. Plant Physiology 188 (4), pp. 1746 - 1756 (2021)

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Ginsawaeng, O.; Heise, C.; Sangwan, R.; Karcher, D.; Hernández-Sánchez, I.E.; Sampathkumar, A.; Zuther, E.: Subcellular Localization of Seed-Expressed LEA_4 Proteins Reveals Liquid-Liquid Phase Separation for LEA9 and for LEA48 Homo- and LEA42-LEA48 Heterodimers. Biomolecules 11 (12), 1770 (2021)

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Joshi, J.; Hasnain, G.; Logue, T.; Lynch, M.; Wu, S.; Guan, J.; Alseekh, S.; Fernie, A. R.; Hanson, A.; McCarty, D.: A Core Metabolome Response of Maize Leaves Subjected to Long-Duration Abiotic Stresses. Metabolites 11 (11), 797 (2021)

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Candido-Sobrinho, S.; Lima, V.; Freire, F.; de Souza, L. P.; Gago, J.; Fernie, A. R.; Daloso, D.: Metabolism-mediated mechanisms underpin the differential stomatal speediness regulation among ferns and angiosperms. Plant, Cell and Environment 45 (2), pp. 296 - 311 (2021)

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Journal Article

Zhu, F.; Alseekh, S.; Wen, W.; Cheng, Y.; Fernie, A. R.: Genome-wide association studies of Arabidopsis dark-induced senescence reveals signatures of autophagy in metabolic reprogramming. Autophagy 18 (2), pp. 457 - 458 (2021)

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24.

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Oliver, C.; Annacondia, M. L.; Wang, Z.; Jullien, P. E.; Slotkin, R. K.; Köhler, C.; Martinez, G.: The miRNome function transitions from regulating developmental genes to transposable elements during pollen maturation. The Plant Cell 34 (2), pp. 784 - 801 (2021)

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25.

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Machado, M.; Vaz, M. G. M. V.; Bromke, M. A.; Rosa, R. M.; Covell, L.; de Souza, L. P.; Rocha, D. I.; Martins, M. A.; Araújo, W. L.; Szymański, J. et al.; Nunes-Nesi, A.: Metabolic stability of freshwater Nitzschia palea strains under silicon stress associated with triacylglycerol accumulation. Algal Research 60, 102554 (2021)

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26.

Journal Article

Gabriel, C.; Fernhout, J.-J.; Fichtner, F.; Feil, R.; Lunn, J. E.; Kossmann, J.; Lloyd, J. R.; van der Vyver, C.: Genetic manipulation of trehalose-6-phosphate synthase results in changes in the soluble sugar profile in transgenic sugarcane stems. Plant Direct 5 (11), e358 (2021)

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da Fonseca-Pereira, P.; Pham, P. A.; Cavalcanti, J. H. F.; Omena-Garcia, R. P.; Barros, J. A. S.; Rosado-Souza, L.; Vallarino, J. G.; Mutwil, M.; Avin-Wittenberg, T.; Nunes-Nesi, A. et al.; Fernie, A. R.; Araújo, W. L.: The Arabidopsis electron-transfer flavoprotein:ubiquinone oxidoreductase is required during normal seed development and germination. The Plant Journal 109 (1), pp. 196 - 214 (2021)

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Del-Saz, N. F.; Douthe, C.; Carriquí, M.; Ortíz, J.; Sanhueza, C.; Rivas-Medina, A.; McDonald, A.; Fernie, A. R.; Ribas-Carbo, M.; Gago, J. et al.; Florez-Sarasa, I.; Flexas, J.: Different Metabolic Roles for Alternative Oxidase in Leaves of Palustrine and Terrestrial Species. Frontiers in Plant Science 12, 752795 (2021)

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29.

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Wang, S.; Xiao, Y.; Zhou, Z.-W.; Yuan, J.; Guo, H.; Yang, Z.; Yang, J.; Sun, P.; Sun, L.; Deng, Y. et al.; Xie, W.-Z.; Song, J.-M.; Qamar, M. T. u.; Xia, W.; Liu, R.; Gong, S.; Wang, Y.; Wang, F.; Liu, X.; Fernie, A. R.; Wang, X.; Fan, H.; Chen, L.-L.; Luo, J.: High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height. Genome Biology: Biology for the Post-Genomic Era 22 (1), 304 (2021)

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Garg, V.; Dudchenko, O.; Wang, J.; Khan, A.W.; Gupta, S.; Kaur, P.; Han, K.; Saxena, R.K.; Kale, S.M.; Pham, M. et al.; Yu, J.; Chitikineni, A.; Zhang, Z.; Fan, G.; Lui, C.; Valluri, V.; Meng, F.; Bhandari, A.; Liu, X.; Yang, T.; Chen, H.; Valliyodan, B.; Roorkiwal, M.; Shi, C.; Yang, H.B.; Durand, N.C.; Pandey, M.K.; Li, G.; Barmukh, R.; Wang, X.; Chen, X.; Lam, H.-M.; Jiang, H.; Zong, X.; Liang, X.; Liu, X.; Liao, B.; Guo, B.; Jackson, S.; Nguyen, H.T.; Zhuang, W.; Shubo, W.; Wang, X.; Aiden, E.L.; Bennetzen, J.L.; Varshney, R.K.: Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement. Journal of Advanced Research (2021)

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31.

Journal Article

Schmid, C.; Mittermeier-Klessinger, V.; Peters, V.; Berger, F.; Kramler, M.; Heuberger, H.; Rinder, R.; Hofmann, T.; Gutjahr, C.; Dawid, C.: Quantitative Mapping of Flavor and Pharmacologically Active Compounds in European Licorice Roots (Glycyrrhiza glabra L.) in Response to Growth Conditions and Arbuscular Mycorrhiza Symbiosis. Journal of Agricultural and Food Chemistry 69 (44), pp. 13173 - 13189 (2021)

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Jiang, X.; Zhang, W.; Fernie, A. R.; Wen, W.: Combining novel technologies with interdisciplinary basic research to enhance horticultural crops. The Plant Journal 109 (1), pp. 35 - 46 (2021)

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33.

Journal Article

Wang, J. Y.; Alseekh, S.; Xiao, T.; Ablazov, A.; de Souza, L. P.; Fiorilli, V.; Anggarani, M.; Lin, P.-Y.; Votta, C.; Novero, M. et al.; Jamil, M.; Lanfranco, L.; Hsing, Y.-I. C.; Blilou, I.; Fernie, A.; Al-Babili, S.: Multi-omics approaches explain the growth-promoting effect of the apocarotenoid growth regulator zaxinone in rice. Communications Biology 4, 1222 (2021)

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34.

Journal Article

Borràs, D.; Barchi, L.; Schulz, K.; Moglia, A.; Acquadro, A.; Kamranfar, I.; Balazadeh, S.; Lanteri, S.: Transcriptome-Based Identification and Functional Characterization of NAC Transcription Factors Responsive to Drought Stress in Capsicum annuum L. Frontiers in Genetics 12, 743902 (2021)

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35.

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Angeleska, A.; Omranian, N.; Nikoloski, Z.: Coherent network partitions: Characterizations with cographs and prime graphs. Theoretical computer science 894, pp. 3 - 11 (2021)

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Zhu, F.; Alseekh, S.; Koper, K.; Tong, H.; Nikoloski, Z.; Naake, T.; Liu, H.; Yan, J.; Brotman, Y.; Wen, W. et al.; Maeda, H.; Cheng, Y.; Fernie, A. R.: Genome-wide association of the metabolic shifts underpinning dark-induced senescence in Arabidopsis. The Plant Cell 34 (1), pp. 557 - 578 (2021)

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37.

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Schaarschmidt, S.; Glaubitz, U.; Erban, A.; Kopka, J.; Zuther, E.: Differentiation of the high night temperature response in leaf segments of rice cultivars with contrasting tolerance. International Journal of Molecular Sciences 22 (19), 10451 (2021)

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38.

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Pimentel, D.; Amaro, R.; Erban, A.; Mauri, N.; Soares, F.; Rego, C.; Martínez-Zapater, J.M.; Mithöfer, A.; Kopka, J.; Fortes, A.M.: Transcriptional, hormonal, and metabolic changes in susceptible grape berries under powdery mildew infection. Journal of Experimental Botany 72 (18), pp. 6544 - 6569 (2021)

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Wang, Q.; Bao, X.; Chen, S.; Zhong, H.; Liu, Y.; Zhang, L.; Xia, Y.; Kragler, F.; Luo, M.; Li, X. et al.; Lam, H.-M.; Zhang, S.: AtHDA6 functions as an H3K18ac eraser to maintain pericentromeric CHG methylation in Arabidopsis thaliana. Nucleic Acids Research 49 (17), pp. 9755 - 9767 (2021)

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Omini, J.; Wojciechowska, I.; Skirycz, A.; Moriyama, H.; Obata, T.: Association of the malate dehydrogenase-citrate synthase metabolon is modulated by intermediates of the Krebs tricarboxylic acid cycle. Scientific Reports 11 (1), 18770 (2021)

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Journal Article

Omranian, N.; Angeleska, A.; Nikoloski, Z.: Efficient and accurate identification of protein complexes from protein-protein interaction networks based on the clustering coefficient. Computational and Structural Biotechnology Journal 19, pp. 5255 - 5263 (2021)

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DeTar, R.A.; Barahimipour, R.; Manavski, N.; Schwenkert, S.; Höhner, R.; Bölter, B.; Inaba, T.; Meurer, J.; Zoschke, R.; Kunz, H.-H.: Erratum: Loss of inner-envelope K +/H + exchangers impairs plastid rRNA maturation and gene expression. The Plant Cell 33 (12), p. 3746 - 3746 (2021)

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43.

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Nieva, A.S.; Romero, F. M.; Erban, A.; Carrasco, P.; Ruiz, O. A.; Kopka, J.: Metabolic Profiling and Metabolite Correlation Network Analysis Reveal That Fusarium solani Induces Differential Metabolic Responses in Lotus japonicus and Lotus tenuis against Severe Phosphate Starvation. Journal of Fungi 7 (9), 765 (2021)

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Muralidhara, P.; Weiste, C.; Collani, S.; Krischke, M.; Kreisz, P.; Draken, J.; Feil, R.; Mair, A.; Teige, M.; Müller, M. J. et al.; Schmid, M.; Becker, D.; Lunn, J. E.; Rolland, F.; Hanson, J.; Dröge-Laser, W.: Perturbations in plant energy homeostasis prime lateral root initiation via SnRK1-bZIP63-ARF19 signaling. Proceedings of the National Academy of Sciences of the United States of America 118 (37), e2106961118 (2021)

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Gao, J.; van Kleeff, P.J.M.; de Boer, M.H.; Erban, A.; Kopka, J.; Hincha, D. K.; de Boer, A.H.: Ion Homeostasis and Metabolome Analysis of Arabidopsis 14-3-3 Quadruple Mutants to Salt Stress. Frontiers in Plant Science 12, 697324 (2021)

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Journal Article

Zhang, Y.; Fernie, A. R.: Stable and temporary enzyme complexes and metabolons involved in energy and redox metabolism. ANTIOXIDANTS & REDOX SIGNALING 35 (10), pp. 788 - 807 (2021)

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Medeiros, D.B.; Aarabi, F.; Rivas f; Fernie, A. R.: The knowns and unknowns of intracellular partitioning of carbon and nitrogen, with focus on the organic acid-mediated interplay between mitochondrion and chloroplast. Journal of Plant Physiology 266, 153521 (2021)

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Tuvia, N.; Pivovarova-Ramich, O.; Murahovschi, V.; Lück, S.; Grudziecki, A.; Ost, A.-C.; Kruse, M.; Nikiforova, V.; Osterhoff, M.; Gottmann, P. et al.; GÖgebakan, {.; Sticht, C.; Gretz, N.; Schupp, M.; Schürmann, A.; Rudovich, N.; Pfeiffer, A. F.H.; Kramer, A.: Insulin directly regulates the circadian clock in adipose tissue. Diabetes 70 (6), pp. 1985 - 1999 (2021)

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Yuan, H.; Cao, G.; Hou, X.; Huang, M.; Du, P.; Tan, T.; Zhang, Y.; Zhou, H.; Liu, X.; Liu, L. et al.; Jiangfang, Y.; Li, Y.; Liu, Z.; Fang, C.; Zhao, L.; Fernie, A. R.; Luo, J.: Development of a widely targeted volatilomics method for profiling volatilomes in plants. Molecular Plant 15 (1), pp. 189 - 202 (2021)

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Jin, C.; Fang, C.; Zhang, Y.; Fernie, A. R.; Luo, J.: Plant metabolism paves the way for breeding crops with high nutritional value and stable yield. Science China Life Sciences 64, pp. 2202 - 2205 (2021)

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