Max Planck Institute of Molecular Plant Physiology

Publications of the Group

Journal Article (163)

1.

Journal Article

Rindfleisch, T.; Nencini, R.; Ollila, O. H. S.; Walther, D.; Miettinen, M. S.; Thalhammer, A.: Molecular Dynamics of the Intrinsically Disordered Protein COR15A─A Force Field Validation on Structure and Dynamics. Journal of Chemical Theory and Computation 21, pp. 9147 - 9163 (2025)

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2.

Journal Article

Kullmann, S.; Singh, A.; Sehgal, R.; Eichelmann, F.; Sandforth, L.; Wilms, B.; Jähnert, M.; Peter, A.; Meyhöfer, S.; Walther, D. et al.; Preissl, H.; Häring, H.-U.; Schulze, M. B.; Heni, M.; Birkenfeld, A. L.; Schürmann, A.; Ouni, M.: Circulating epigenetic signatures classifying brain insulin resistance in humans. Science translational medicine 17 (810), eadv7834 (2025)

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3.

Journal Article

Zillmer, H.; Walther, D.: Towards a comprehensive view of the pocketome universe—biological implications and algorithmic challenges. PLOS Computational Biology 21 (7), e1013298 (2025)

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4.

Journal Article

Wagner, M.; Kang, J.; Mercado, C.; Thirumlaikumar, V. P.; Gorka, M.; Zillmer, H.; Guo, J.; Minen, R. I.; Plecki, C. F.; Dehesh, K. et al.; Schroeder, F. C.; Walther, D.; Skirycz, A.: Mapping protein-metabolite interactions in E. coli by integrating chromatographic techniques and co-fractionation mass spectrometry. iScience 28 (6), 112611 (2025)

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5.

Journal Article

Leer, M.; Soultoukis, G. A.; Jähnert, M.; Oveisi, M.; Walther, D.; Schulz, T. J.: pubCounteR: an R package for interrogating published literature for experimentally-derived gene lists within a user-defined biological context. Frontiers in Bioinformatics Volume 5, 1523184 (2025)

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6.

Journal Article

Paajanen, P.; Tomkins, M.; Hoerbst, F.; Veevers, R.; Heeney, M.; Thomas, H. R.; Apelt, F.; Saplaoura, E.; Gupta, S.; Frank, M. et al.; Walther, D.; Faulkner, C.; Kehr, J.; Kragler, F.; Morris, R. J.: Re-analysis of mobile mRNA datasets raises questions about the extent of long-distance mRNA communication. Nature Plants 11, pp. 977 - 984 (2025)

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7.

Journal Article

Hernández-Sánchez, I.E.; Rindfleisch, T.; Alpers, J.; Dulle, M.; Garvey, C. J.; Knox-Brown, P.; Miettinen, M. S.; Nagy, G.; Pusterla, J. M.; Rekas, A. et al.; Shou, K.; Stadler, A. M.; Walther, D.; Wolff, M.; Zuther, E.; Thalhammer, A.: Functional in vitro diversity of an intrinsically disordered plant protein during freeze–thawing is encoded by its structural plasticity. Protein Science 33 (5), e4989 (2024)

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8.

Journal Article

Uflewski, M.; Rindfleisch, T.; Korkmaz, K.; Tietz, E.; Mielke, S.; Correa Galvis, V.; Dünschede, B.; Luzarowski, M.; Skirycz, A.; Schwarzländer, M. et al.; Strand, D.; Hertle, A. P.; Schünemann, D.; Walther, D.; Thalhammer, A.; Wolff, M.; Armbruster, U.: The thylakoid proton antiporter KEA3 regulates photosynthesis in response to the chloroplast energy status. Nature Communications 15, 2792 (2024)

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9.

Journal Article

Murik, O.; Geffen, O.; Shotland, Y.; Fernandez-Pozo, N.; Ullrich, K. K.; Walther, D.; Rensing, S. A.; Treves, H.: Genomic imprints of unparalleled growth. New Phytologist 241 (3), pp. 1144 - 1160 (2023)

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10.

Journal Article

Back, G.; Walther, D.: Predictions of DNA mechanical properties at a genomic scale reveal potentially new functional roles of DNA flexibility. NAR: genomics and bioinformatics 5 (4), lqad097 (2023)

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11.

Journal Article

Giese, J.; Eirich, J.; Walther, D.; Zhang, Y.; Lassowskat, I.; Fernie, A. R.; Elsässer, M.; Maurino, V. G.; Schwarzländer, M.; Finkemeier, I.: The interplay of post-translational protein modifications in Arabidopsis leaves during photosynthesis induction. The Plant Journal 116 (4), pp. 1172 - 1193 (2023)

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12.

Journal Article

Forner, J.; Kleinschmidt, D.; Meyer, E. H.; Gremmels, J.; Morbitzer, R.; Lahaye, T.; Schöttler, M. A.; Bock, R.: Targeted knockout of a conserved plant mitochondrial gene by genome editing. Nature Plants 9, pp. 1818 - 1831 (2023)

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13.

Journal Article

Weiszmann, J.; Walther, D.; Clauw, P.; Back, G.; Gunis, J.; Reichardt, I.; Koemeda, S.; Jez, J.; Nordborg, M.; Schwarzerova, J. et al.; Pierides, I.; Nägele, T.; Weckwerth, W.: Metabolome plasticity in 241 Arabidopsis thaliana accessions reveals evolutionary cold adaptation processes. Plant Physiology 193 (2), pp. 980 - 1000 (2023)

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14.

Journal Article

Qiu, Y.; Li, Z.; Walther, D.; Köhler, C.: Updated phylogeny and protein structure predictions revise the hypothesis on the origin of MADS-box transcription factors in land plants. Molecular Biology and Evolution 40 (9), msad194 (2023)

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15.

Journal Article

Skeffington, A. W.; Fischer, A.; Sviben, S.; Brzezinka , M.; Gorka, M.; Bertinetti, L.; Woehle, C.; Huettel, B.; Graf, A.; Scheffel, A.: A joint proteomic and genomic investigation provides insights into the mechanism of calcification in coccolithophores. Nature Communications 14, 3749 (2023)

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16.

Journal Article

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 39 (12), msac222 (2022)

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17.

Journal Article

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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18.

Journal Article

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 174 (4), e13746 (2022)

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19.

Journal Article

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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20.

Journal Article

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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21.

Journal Article

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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22.

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)

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23.

Journal Article

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 40 (15), e106800 (2021)

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24.

Journal Article

Moreno, J.C.; Martinez-Jaime, S.; Kosmacz, M.; Sokolowska, E.; Schulz, P.; Fischer, A.; Luzarowska, U.; Havaux, M.; Skirycz, A.: A Multi-OMICs Approach Sheds Light on the Higher Yield Phenotype and Enhanced Abiotic Stress Tolerance in Tobacco Lines Expressing the Carrot lycopene β-cyclase1 Gene. Frontiers in Plant Science 12, 624365 (2021)

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25.

Journal Article

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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26.

Journal Article

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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27.

Journal Article

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), pp. 477 - 489 (2021)

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28.

Journal Article

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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29.

Journal Article

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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30.

Journal Article

Zaborowski, A. B.; Walther, D.: Determinants of correlated expression of transcription factors and their target genes. Nucleic Acids Research 48 (20), pp. 11347 - 11369 (2020)

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31.

Journal Article

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), pp. 22452 - 22461 (2020)

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32.

Journal Article

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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33.

Journal Article

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), p. 7607 - 7607 (2020)

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34.

Journal Article

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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35.

Journal Article

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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36.

Journal Article

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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37.

Journal Article

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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38.

Journal Article

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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39.

Journal Article

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, pp. 705 - 718 (2020)

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40.

Journal Article

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), pp. 2066 - 2079 (2020)

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41.

Journal Article

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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42.

Journal Article

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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43.

Journal Article

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), pp. 654 - 681 (2019)

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44.

Journal Article

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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45.

Journal Article

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), pp. 5665 - 5674 (2019)

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46.

Journal Article

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), pp. 525 - 538 (2019)

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47.

Journal Article

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), pp. 854 - 873 (2019)

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48.

Journal Article

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), pp. 2251 - 2276 (2018)

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49.

Journal Article

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), pp. 8114 - 8132 (2018)

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50.

Journal Article

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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