Publications of the institute

Journal Article (230)

1.
Journal Article
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)
2.
Journal Article
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)
3.
Journal Article
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)
4.
Journal Article
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)
5.
Journal Article
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)
6.
Journal Article
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)
7.
Journal Article
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)
8.
Journal Article
Qiu, Y.; Köhler, C.: Endosperm evolution by duplicated and neofunctionalized Type I MADS-box transcription factors. Molecular Biology and Evolution 39 (1), msab355 (2021)
9.
Journal Article
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)
10.
Journal Article
Hashemi, S.; Razaghi-Moghadam, Z.; Nikoloski, Z.: Identification of flux trade-offs in metabolic networks. Scientific Reports 11 (1), 23776 (2021)
11.
Journal Article
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)
12.
Journal Article
Fàbregas, N.; Fernie, A. R.: The reliance of phytohormone biosynthesis on primary metabolite precursors. Journal of Plant Physiology 268, 153589 (2021)
13.
Journal Article
Qin, K.; Fernie, A. R.; Zhang, Y.: The assembly of super-complexes in the plant chloroplast. Biomolecules 11 (12), 1839 (2021)
14.
Journal Article
Fàbregas, N.; Fernie, A. R.: The interface of central metabolism with hormone signaling in plants. Current Biology 31 (23), pp. R1535 - R1548 (2021)
15.
Journal Article
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)
16.
Journal Article
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)
17.
Journal Article
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)
18.
Journal Article
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)
19.
Journal Article
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)
20.
Journal Article
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)
21.
Journal Article
Zhou, Y.; Li, X.; Guo, Q.; Liu, P.; Li, Y.; Wu, C.; Yang, G.; Huang, J.; Zhang, S.; Zheng, C. et al.; Yan, K.: Salt responsive alternative splicing of a RING finger E3 ligase modulates the salt stress tolerance by fine-tuning the balance of COP9 signalosome subunit 5A. PLoS Genetics 17 (11), 1009898. (2021)
22.
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)
23.
Journal Article
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)
24.
Journal Article
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)
25.
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)
26.
Journal Article
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)
27.
Journal Article
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)
28.
Journal Article
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)
29.
Journal Article
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)
30.
Journal Article
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)
31.
Journal Article
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)
32.
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)
33.
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)
34.
Journal Article
Sun, S.; Feng, L.; Chung, K. P.; Lee, K.-M.; Cheung, H. H.-Y.; Luo, M.; Ren, K.; Law, K. C.; Jiang, L.; Wong, K.-B. et al.; Zhuang, X.: Mechanistic insights into an atypical interaction between ATG8 and SH3P2 in Arabidopsis thaliana. Autophagy (2021)
35.
Journal Article
Angeleska, A.; Omranian, N.; Nikoloski, Z.: Coherent network partitions: Characterizations with cographs and prime graphs. Theoretical computer science 894, pp. 3 - 11 (2021)
36.
Journal Article
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)
37.
Journal Article
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)
38.
Journal Article
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)
39.
Journal Article
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)
40.
Journal Article
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)
41.
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)
42.
Journal Article
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)
43.
Journal Article
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)
44.
Journal Article
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)
45.
Journal Article
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)
46.
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)
47.
Journal Article
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)
48.
Journal Article
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)
49.
Journal Article
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)
50.
Journal Article
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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