Publikationen der Gruppe

Zeitschriftenartikel (154)

1.
Zeitschriftenartikel
Fischer, A.; Dotzek, J.; Walther, D.; Greiner, S.: Graph-based models of the Oenothera mitochondrial genome capture the enormous complexity of higher plant mitochondrial DNA organization. NAR: genomics and bioinformatics 4 (2), lqac027 (2022)
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Hoang, Y.; Gryzik, S.; Hoppe, I.; Rybak, A.; Schädlich, M.; Kadner, I.; Walther, D.; Vera, J.; Radbruch, A.; Groth, D. et al.; Baumgart, S.; Baumgrass, R.: PRI: Re-analysis of a public mass cytometry dataset reveals patterns of effective tumor treatments. Frontiers in immunology 13, 849329 (2022)
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3.
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Thieme, S.; Walther, D.: Biclique extension as an effective approach to identify missing links in metabolic compound-protein interaction networks. Bioinformatics advances 2 (1), vbac001 (2022)
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Vyse, K.; Fischer, A.; Zajancauskaite, G.; Erban, A.; Kopka, J.; Balazadeh, S.; Zuther, E.: Co-expression networks of deacclimation-impaired transcription factor mutants identified complex regulation of the cold stress release response. Physiologia Plantarum, e13746 (2022)
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5.
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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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6.
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Moreno, J.C.; Rojas, B.E.; Vicente, R.; Gorka, M.; Matz, T.; Kosmacz, M.; Peralta-Ariza, J.S.; Zhang, Y.; Alseekh, S.; Childs, D. et al.; Luzarowski, M.; Nikoloski, Z.; Zarivach, R.; Walther, D.; Hartman, M.D.; Figueroa, C.M.; Iglesias, A.A.; Fernie, A. R.; Skirycz, A.: Tyr-Asp inhibition of glyceraldehyde 3-phosphate dehydrogenase affects plant redox metabolism. EMBO Journal, e106800 (2021)
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7.
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Back, G.; Walther, D.: Identification of cis-regulatory motifs in first introns and the prediction of intron-mediated enhancement of gene expression in Arabidopsis thaliana. BMC Genomics 22 (1), 390 (2021)
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8.
Zeitschriftenartikel
Gefen‐treves, S.; Bartholomäus, A.; Horn, F.; Zaborowski, A.B.; Tchernov, D.; Wagner, D.; Oren, A.; Kaplan, A.: The microbiome associated with the reef builder neogoniolithon sp. In the eastern mediterranean. Microorganisms 9 (7), 1374 (2021)
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9.
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Kuang, J.-F.; Wu, C.-J.; Guo, Y.-F.; Walther, D.; Shan, W.; Chen, J.-Y.; Chen, L.; Lu, W.-J.: Deciphering Transcriptional Regulators of Banana Fruit Ripening by Regulatory Network Analysis. Plant Biotechnology Journal 19 (3), S. 477 - 489 (2021)
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10.
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Martinez-Seidel, F.; Beine-Golovchuk, O.; Hsieh, Y.-C.; El Eshraky, K.; Gorka, M.; Cheong, B.-E.; Jimenez‐posada, E.V.; Walther, D.; Skirycz, A.; Roessner, U. et al.; Kopka, J.; Firmino, A.: Spatially enriched paralog rearrangements argue functionally diverse ribosomes arise during cold acclimation in arabidopsis. International Journal of Molecular Sciences 22 (11), 6160 (2021)
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11.
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Schumacher, C.; Thümecke, S.; Schilling, F.; Koehl, K. I.; Kopka, J.; Sprenger, H.; Hincha, D. K.; Walther, D.; Seddig, S.; Peters, R. et al.; Zuther, E.; Haas, M.; Horn, R.: Genome-wide approach to identify quantitative trait loci for drought tolerance in tetraploid potato (Solanum tuberosum L.). International Journal of Molecular Sciences 22 (11), 6123 (2021)
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12.
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Zaborowski, A. B.; Walther, D.: Determinants of correlated expression of transcription factors and their target genes. Nucleic Acids Research 48 (20), S. 11347 - 11369 (2020)
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13.
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Claassens, N. J.; Scarinci, G.; Fischer, A.; Flamholz, A.I.; Newell, W.; Frielingsdorf, S.; Lenz, O.; Bar-Even, A.: Phosphoglycolate salvage in a chemolithoautotroph using the Calvin cycle. Proceedings of the National Academy of Sciences of the United States of America 117 (36), S. 22452 - 22461 (2020)
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14.
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Gottmann, P.; Ouni, M.; Zellner, L.; Jähnert, M.; Rittig, K.; Walther, D.; Schürmann, A.: Polymorphisms in miRNA binding sites involved in metabolic diseases in mice and humans. Scientific Reports 10 (1), 7202 (2020)
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15.
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Guan, D.; Yan, B.; Thieme, C. J.; Hua, J.; Zhu, H.; Boheler, K.R.; Zhao, Z.; Kragler, F.; Xia, Y.; Zhang, S.: PlaMoM: a comprehensive database compiles plant mobile macromolecules. Nucleic acids research 48 (13), S. 7607 - 7607 (2020)
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16.
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Haas, M.; Sprenger, H.; Zuther, E.; Peters, R.; Seddig, S.; Walther, D.; Kopka, J.; Hincha, D. K.; Koehl, K. I.: Can Metabolite- and Transcript-Based Selection for Drought Tolerance in Solanum tuberosum Replace Selection on Yield in Arid Environments? Frontiers in Plant Science 11, 1071 (2020)
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17.
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Kaiser, E.; Walther, D.; Armbruster, U.: Growth under fluctuating light reveals large trait variation in a panel of arabidopsis accessions. Plants 9 (3), 319 (2020)
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18.
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Knox-Brown, P.; Rindfleisch, T.; Günther, A.; Balow, K.; Bremer, A.; Walther, D.; Miettinen, M.S.; Hincha, D. K.; Thalhammer, A.: Similar yet different–structural and functional diversity among arabidopsis thaliana LEA_4 proteins. International Journal of Molecular Sciences 21 (8), 2794 (2020)
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19.
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Schaarschmidt, S.; Fischer, A.; Lawas, L.M.F.; Alam, R.; Septiningsih, E. M.; Bailey-Serres, J.; Jagadish, S. V. K.; Huettel, B.; Hincha, D. K.; Zuther, E.: Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L. International Journal of Molecular Sciences 21 (21), 8148 (2020)
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20.
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Schaarschmidt, S.; Fischer, A.; Zuther, E.; Hincha, D. K.: Evaluation of seven different rna-seq alignment tools based on experimental data from the model plant arabidopsis thaliana. International Journal of Molecular Sciences 21 (5), 1720 (2020)
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21.
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Sujeeth, N.; Mehterov, N.; Gupta, S.; Qureshi, M. K.; Fischer, A.; Proost, S.; Omidbakhshfard, M. A.; Obata, T.; Benina, M.; Staykov, N. et al.; Balazadeh, S.; Walther, D.; Fernie, A. R.; Mueller-Roeber, B.; Hille, J.; Gechev, T. S.: A novel seed plants gene regulates oxidative stress tolerance in Arabidopsis thaliana. Cellular and Molecular Life Sciences 77, S. 705 - 718 (2020)
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22.
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Watanabe, M.; Ueda, Y.; Kondo, K.; Ishikawa, S.; Tohge, T.; Burgos, A.; Brotman, Y.; Fernie, A. R.; Walther, D.; Hoefgen, R. et al.; Wissuwa, M.: Metabolomic markers and physiological adaptations for high phosphate utilization efficiency in rice. Plant, Cell and Environment 43 (9), S. 2066 - 2079 (2020)
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23.
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Whitcomb, S. J.; Rakpenthai, A.; Brückner, F.; Fischer, A.; Parmar, S.; Erban, A.; Kopka, J.; Hawkesford, M.J.; Hoefgen, R.: Cysteine and Methionine Biosynthetic Enzymes Have Distinct Effects on Seed Nutritional Quality and on Molecular Phenotypes Associated With Accumulation of a Methionine-Rich Seed Storage Protein in Rice. Frontiers in Plant Science 11, 1118 (2020)
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24.
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Zwaag, J.; Horst, R.; Blaženovic, I.; Stoessel, D.; Ratter, J.; Worseck, J.M.; Schauer, N.; Stienstra, R.; Netea, M.G.; Jahn, D. et al.; Pickkers, P.; Kox, M.: Involvement of lactate and pyruvate in the anti-inflammatory effects exerted by voluntary activation of the sympathetic nervous system. Metabolites 10 (4), 148 (2020)
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25.
Zeitschriftenartikel
Armarego-Marriott, T.; Kowalewska, L.; Burgos, A.; Fischer, A.; Thiele, W.; Erban, A.; Strand, D.; Kahlau, S.; Hertle, A. P.; Kopka, J. et al.; Walther, D.; Reich, Z.; Schöttler, M. A.; Bock, R.: Highly Resolved Systems Biology to Dissect the Etioplast-to-Chloroplast Transition in Tobacco Leaves. Plant Physiology 180 (1), S. 654 - 681 (2019)
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26.
Zeitschriftenartikel
Heyneke, E.; Watanabe, M.; Erban, A.; Duan, G.; Buchner, P.; Walther, D.; Kopka, J.; Hawkesford, M. J.; Hoefgen, R.: Effect of Senescence Phenotypes and Nitrate Availability on Wheat Leaf Metabolome during Grain Filling. Agronomy 9 (6), 305 (2019)
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27.
Zeitschriftenartikel
Sobanski, J.; Giavalisco, P.; Fischer, A.; Kreiner, J.M.; Walther, D.; Schöttler, M. A.; Pellizzer, T.; Golczyk, H.; Obata, T.; Bock, R. et al.; Sears, B.B.; Greiner, S.: Chloroplast competition is controlled by lipid biosynthesis in evening primroses. Proceedings of the National Academy of Sciences of the United States of America 116 (12), S. 5665 - 5674 (2019)
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28.
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Wu, G.; Meyer, E. H.; Richter, A. S.; Schuster, M.; Ling, Q.; Schöttler, M. A.; Walther, D.; Zoschke, R.; Grimm, B.; Jarvis, R. P. et al.; Bock, R.: Control of retrograde signalling by protein import and cytosolic folding stress. Nature Plants 5 (5), S. 525 - 538 (2019)
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29.
Zeitschriftenartikel
Zuther, E.; Schaarschmidt, S.; Fischer, A.; Erban, A.; Pagter, M.; Mubeen, U.; Giavalisco, P.; Kopka, J.; Sprenger, H.; Hincha, D. K.: Molecular signatures associated with increased freezing tolerance due to low temperature memory in Arabidopsis. Plant, Cell and Environment 42 (3- SI), S. 854 - 873 (2019)
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30.
Zeitschriftenartikel
Beine-Golovchuk, O.; Firmino, A.; Dabrowska, A.; Schmidt, S.; Erban, A.; Walther, D.; Zuther, E.; Hincha, D. K.; Kopka, J.: Plant Temperature Acclimation and Growth Rely on Cytosolic Ribosome Biogenesis Factor Homologs. Plant Physiology 176 (3), S. 2251 - 2276 (2018)
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31.
Zeitschriftenartikel
Perlaza-Jiménez, L.; Walther, D.: A genome-wide scan for correlated mutations detects macromolecular and chromatin interactions in Arabidopsis thaliana. Nucleic Acids Research 46 (16), S. 8114 - 8132 (2018)
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32.
Zeitschriftenartikel
Schwachtje, J.; Fischer, A.; Erban, A.; Kopka, J.: Primed primary metabolism in systemic leaves: a functional systems analysis. Scientific Reports 8, 216 (2018)
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33.
Zeitschriftenartikel
Sprenger, H.; Erban, A.; Seddig, S.; Rudack, K.; Thalhammer, A.; Le, M. Q.; Walther, D.; Zuther, E.; Koehl, K. I.; Kopka, J. et al.; Hincha, D. K.: Metabolite and transcript markers for the prediction of potato drought tolerance. Plant Biotechnology Journal 16 (4), S. 939 - 950 (2018)
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34.
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Stoessel, D.; Schulte, C.; Teixeira dos Santos, M. C.; Scheller, D.; Rebollo-Mesa, I.; Deuschle, C.; Walther, D.; Schauer, N.; Berg, D.; Nogueira da Costa, A. et al.; Maetzler, W.: Promising Metabolite Profiles in the Plasma and CSF of Early Clinical Parkinson's Disease. Frontiers in Aging Neuroscience 10, 51 (2018)
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35.
Zeitschriftenartikel
Stoessel, D.; Stellmann, J.-P.; Willing, A.; Behrens, B.; Rosenkranz, S. C.; Hodecker, S. C.; Stuerner, K. H.; Reinhardt, S.; Fleischer, S.; Deuschle, C. et al.; Maetzler, W.; Berg, D.; Heesen, C.; Walther, D.; Schauer, N.; Friese, M. A.; Pless, O.: Metabolomic Profiles for Primary Progressive Multiple Sclerosis Stratification and Disease Course Monitoring. Frontiers in Human Neuroscience 12, 226 (2018)
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36.
Zeitschriftenartikel
Guan, D.; Yan, B.; Thieme, C. J.; Hua, J.; Zhu, H.; Boheler, K. R.; Zhao, Z.; Kragler, F.; Xia, Y.; Zhang, S.: PlaMoM: a comprehensive database compiles plant mobile macromolecules. Nucleic Acids Research 4 (45 (D1)), S. D1021 - D1028 (2017)
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37.
Zeitschriftenartikel
Heyneke, E.; Watanabe, M.; Erban, A.; Duan, G. Y.; Buchner, P.; Walther, D.; Kopka, J.; Hawkesford, M. J.; Hoefgen, R.: Characterization of the Wheat Leaf Metabolome during Grain Filling and under Varied N-Supply. Frontiers in Plant Science 8, 2048 (2017)
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38.
Zeitschriftenartikel
Hochrein, L.; Machens, F.; Gremmels, J.; Schulz, K.; Messerschmidt, K.; Mueller-Roeber, B.: AssemblX: a user-friendly toolkit for rapid and reliable multi-gene assemblies. Nucleic Acids Research 45 (10), e80 (2017)
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39.
Zeitschriftenartikel
Korkuc, P.; Walther, D.: Towards understanding the crosstalk between protein post-translational modifications: Homo- and heterotypic PTM pair distances on protein surfaces are not random. Proteins: Structure, Function, and Bioinformatics 85 (1), S. 78 - 92 (2017)
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40.
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Ploetner, B.; Nurmi, M.; Fischer, A.; Watanabe, M.; Schneeberger, K.; Holm, S.; Vaid, N.; Schöttler, M. A.; Walther, D.; Hoefgen, R. et al.; Weigel, D.; Laitinen, R.: Chlorosis caused by two recessively interacting genes reveals a role of RNA helicase in hybrid breakdown in Arabidopsis thaliana. The Plant Journal 91 (2), S. 251 - 262 (2017)
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41.
Zeitschriftenartikel
Scharff, L. B.; Ehrnthaler, M.; Janowski, M.; Childs, L. H.; Hasse, C.; Gremmels, J.; Ruf, S.; Zoschke, R.; Bock, R.: Shine-Dalgarno Sequences Play an Essential Role in the Translation of Plastid mRNAs in Tobacco. Plant Cell 29 (12), S. 3085 - 3101 (2017)
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42.
Zeitschriftenartikel
Swiadek, M.; Proost, S.; Sieh, D.; Yu, J.; Todesco, M.; Jorzig, C.; Cubillos, A.; Plötner, B.; Nikoloski, Z.; Chae, E. et al.; Giavalisco, P.; Fischer, A.; Schröder, F.; Kim, S.-T.; Weigel, D.; Laitinen, R.: Novel allelic variants in ACD6 cause hybrid necrosis in local collection of Arabidopsis thaliana. New Phytologist 213 (2), S. 900 - 915 (2017)
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Tillich, M.; Lehwark, P.; Pellizzer, T.; Ulbricht-Jones, E. S.; Fischer, A.; Bock, R.; Greiner, S.: GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Research 45 (W1), S. W6 - W11 (2017)
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44.
Zeitschriftenartikel
Weissenborn, S.; Walther, D.: Metabolic Pathway Assignment of Plant Genes based on Phylogenetic Profiling-A Feasibility Study. Frontiers in Plant Science 8, 1831 (2017)
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45.
Zeitschriftenartikel
Korkuc, P.; Walther, D.: Spatial proximity statistics suggest a regulatory role of protein phosphorylation on compound binding. Proteins-Structure Function and Bioinformatics 84 (5), S. 565 - 579 (2016)
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46.
Zeitschriftenartikel
Walther, D.; Kragler, F.: Mobile RNAs convey the message. Nature Plants 2 (4), 16040 (2016)
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47.
Zeitschriftenartikel
Korkuc, P.; Walther, D.: The Identification of Cis-Regulatory Sequence Motifs in Gene Promoters Based on SNP Information. PLANT SYNTHETIC PROMOTERS: METHODS AND PROTOCOLS, S. 31 - 47 (2016)
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48.
Zeitschriftenartikel
Lis, M.; Walther, D.: The orientation of transcription factor binding site motifs in gene promoter regions: does it matter? BMC Genomics 17, 185 (2016)
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49.
Zeitschriftenartikel
Sprenger, H.; Kurowsky, C.; Horn, R.; Erban, A.; Seddig, S.; Rudack, K.; Fischer, A.; Walther, D.; Zuther, E.; Koehl, K. I. et al.; Hincha, D. K.; Kopka, J.: The drought response of potato reference cultivars with contrasting tolerance. Plant Cell Environment 39 (11), S. 2370 - 2389 (2016)
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50.
Zeitschriftenartikel
Zhang, W.; Thieme, C. J.; Kollwig, G.; Apelt, F.; Yang, L.; Winter, N.; Andresen, N.; Walther, D.; Kragler, F.: tRNA-Related Sequences Trigger Systemic mRNA Transport in Plants. Plant Cell 28 (6), S. 1237 - 1249 (2016)
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