Publications of Dirk Walther

Journal Article (65)

1. 1.
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   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)
2. 2.
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   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)
3. 3.
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   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), pp. 939 - 950 (2018)
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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)
5. 5.
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   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)
6. 6.
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   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 (2017)
7. 7.
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   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), pp. 78 - 92 (2017)
8. 8.
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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), pp. 251 - 262 (2017)
9. 9.
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   Weissenborn, S.; Walther, D.: Metabolic Pathway Assignment of Plant Genes based on Phylogenetic Profiling-A Feasibility Study. Frontiers in Plant Science (2017)
10. 10.
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    Korkuc, P.; Walther, D.: Spatial proximity statistics suggest a regulatory role of protein phosphorylation on compound binding. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 84 (5), pp. 565 - 579 (2016)
11. 11.
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    Walther, D.; Kragler, F.: Mobile RNAs convey the message. Nature Plants 2 (4), 16040 (2016)
12. 12.
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    Korkuc, P.; Walther, D.: The Identification of Cis-Regulatory Sequence Motifs in Gene Promoters Based on SNP Information. PLANT SYNTHETIC PROMOTERS: METHODS AND PROTOCOLS, pp. 31 - 47 (2016)
13. 13.
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    Lis, M.; Walther, D.: The orientation of transcription factor binding site motifs in gene promoter regions: does it matter? BMC Genomics 17, 185 (2016)
14. 14.
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    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), pp. 2370 - 2389 (2016)
15. 15.
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    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), pp. 1237 - 1249 (2016)
16. 16.
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    Salek, R. M.; Neumann, S.; Schober, D.; Hummel, J.; Billiau, K.; Kopka, J.; Correa, E.; Reijmers, T.; Rosato, A.; Tenori, L. et al.; Turano, P.; Marin, S.; Deborde, C.; Jacob, D.; Rolin, D.; Dartigues, B.; Conesa, P.; Haug, K.; Rocca-Serra, P.; O'Hagan, S.; Hao, J.; Vliet, M. v.; Sysi-Aho, M.; Ludwig, C.; Bouwman, J.; Cascante, M.; Ebbels, T.; Griffin, J. L.; Moing, A.; Nikolski, M.; Oresic, M.; Sansone, S.-A.; Viant, M. R.; Goodacre, R.; Guenther, U. L.; Hankemeier, T.; Luchinat, C.; Walther, D.; Steinbeck, C.: COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access. Metabolomics 11 (6), pp. 1587 - 1597 (2015)
17. 17.
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    Thieme, C. J.; Rojas-Triana, M.; Stecyk, E.; Schudoma, C.; Zhang, W.; Yang, L.; Minambres, M.; Walther, D.; Schulze, W. X.; Paz-Ares, J. et al.; Scheible, W.-R.; Kragler, F.: Endogenous Arabidopsis messenger RNAs transported to distant tissues. Nature Plants 1, 15025 (2015)
18. 18.
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    Duan, G. Y.; Walther, D.: The Roles of Post-translational Modifications in the Context of Protein Interaction Networks. PLoS Computational Biology 11 (2), e1004049 (2015)
19. 19.
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    Duan, G. Y.; Walther, D.: Computational phosphorylation network reconstruction: methods and resources. Methods in Molecular Biology 1306, pp. 177 - 194 (2015)
20. 20.
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    Korkuc, P.; Walther, D.: Physicochemical characteristics of structurally determined metabolite-protein and drug-protein binding events with respect to binding specificity. Frontiers in molecular biosciences 2, 51 (2015)
21. 21.
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    Mucha, S.; Walther, D.; Mueller, T. M.; Hincha, D. K.; Glawischnig, E.: Substantial reprogramming of the Eutrema salsugineum (Thellungiella salsuginea) transcriptome in response to UV and silver nitrate challenge. BMC Plant Biology 15, 137 (2015)
22. 22.
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    Sprenger, H.; Rudack, K.; Schudoma, C.; Neumann, A.; Seddig, S.; Peters, R.; Zuther, E.; Kopka, J.; Hincha, D. K.; Walther, D. et al.; Koehl, K. I.: Assessment of drought tolerance and its potential yield penalty in potato. Functional Plant Biology 42 (7), pp. 655 - 667 (2015)
23. 23.
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    Zhou, W. B.; Karcher, D.; Fischer, A.; Maximova, E.; Walther, D.; Bock, R.: Multiple RNA Processing Defects and Impaired Chloroplast Function in Plants Deficient in the Organellar Protein-Only RNase P Enzyme. PLoS One 10 (3), p. e0120533 - e0120533 (2015)
24. 24.
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    Korkuc, P.; Schippers, J. H. M.; Walther, D.: Characterization and Identification of cis-Regulatory Elements in Arabidopsis Based on Single-Nucleotide Polymorphism Information. Plant Physiology 164 (1), pp. 181 - 200 (2014)
25. 25.
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    van Wijk, K. J.; Friso, G.; Walther, D.; Schulze, W. X.: Meta-Analysis of Arabidopsis thaliana Phospho-Proteomics Data Reveals Compartmentalization of Phosphorylation Motifs. Plant Cell 26 (6), pp. 2367 - 2389 (2014)
26. 26.
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    Yadav, U. P.; Yadav, U. P.; Ivakov, A.; Feil, R.; Duan, G. Y.; Walther, D.; Giavalisco, P.; Piques, M.; Carillo , P.; Hubberten, H. M. et al.; Stitt, M.; Lunn, J. E.: The sucrose–trehalose 6-phosphate (Tre6P) nexus: specificity and mechanisms of sucrose signalling by Tre6P. Journal of Experimental Botany (2014)
27. 27.
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    Duan, G. Y.; Walther, D.; Schulze, W. X.: Reconstruction and analysis of nutrient-induced phosphorylation networks in Arabidopsis thaliana. Frontiers in Plant Science (2013)
28. 28.
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    Duan, G. Y.; Christian, N.; Schwachtje, J.; Walther, D.; Ebenhoeh, O.: The Metabolic Interplay between Plants and Phytopathogens. Metabolites 3 (1), pp. 1 - 23 (2013)
29. 29.
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    Billiau, K.; Sprenger, H.; Schudoma, C.; Walther, D.; Koehl, K. I.: Data management pipeline for plant phenotyping in a multisite project. Functional Plant Biology 39 (10-11), pp. 948 - 957 (2012)
30. 30.
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    Childs, L. H.; Lisec, J.; Walther, D.: Matapax: An Online High-Throughput Genome-Wide Association Study Pipeline. Plant Physiology 158 (4), pp. 1534 - 1541 (2012)
31. 31.
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    Christian, J. O.; Braginets, R.; Schulze, W. X.; Walther, D.: Characterization and Prediction of Protein Phosphorylation Hotspots in Arabidopsis thaliana. Frontiers in Plant Science 3, p. 207 (2012)
32. 32.
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    Thieme, C. J.; Schudoma, C.; May, P.; Walther, D.: Give It AGO: The Search for miRNA-Argonaute Sorting Signals in Arabidopsis thaliana Indicates a Relevance of Sequence Positions Other than the 5'-Position Alone. Frontiers in plant science 3, p. 272 (2012)
33. 33.
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    Lenz, D.; May, P.; Walther, D.: Comparative analysis of miRNAs and their targets across four plant species. BMC Research Notes 4, p. 483 (2011)
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    Scharff, L. B.; Childs, L.; Walther, D.; Bock, R.: Local Absence of Secondary Structure Permits Translation of mRNAs that Lack Ribosome-Binding Sites. PLoS Genetics 7 (6), p. e1002155 (2011)
35. 35.
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    Schudoma, C.; Larhlimi, A.; Walther, D.: The influence of the local sequence environment on RNA loop structures. Rna-a Publication of the Rna Society 17 (7), pp. 1247 - 1257 (2011)
36. 36.
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    Childs, L. H.; Witucka-Wall, H.; Gunther, T.; Sulpice, R.; Korff, M. V.; Stitt, M.; Walther, D.; Schmid, K. J.; Altmann, T.: Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth-related metabolic traits in Arabidopsis thaliana. BMC Genomics 11, p. 188 (2010)
37. 37.
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    Hummel, J.; Strehmel, N.; Selbig, J.; Walther, D.; Kopka, J.: Decision tree supported substructure prediction of metabolites from GC-MS profiles. Metabolomics 6 (2), pp. 322 - 333 (2010)
38. 38.
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    Lohse, M.; Nunes-Nesi, A.; Krueger, P.; Nagel, A.; Hannemann, J.; Giorgi, F. M.; Childs, L.; Osorio, S.; Walther, D.; Selbig, J. et al.; Sreenivasulu, N.; Stitt, M.; Fernie, A. R.; Usadel, B.: Robin: An Intuitive Wizard Application for R-Based Expression Microarray Quality Assessment and Analysis. Plant Physiology 153 (2), pp. 642 - 651 (2010)
39. 39.
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    Riano-Pachon, D. M.; Kleessen, S.; Neigenfind; Durek, P.; Weber, E.; Engelsberger, W. R.; Walther, D.; Selbig, J.; Schulze, W. X.; Kersten, B.: Proteome-wide survey of phosphorylation patterns affected by nuclear DNA polymorphisms in Arabidopsis thaliana. BMC Genomics 11, p. 411 (2010)
40. 40.
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    Schudoma, C.; May, P.; Walther, D.: Modeling RNA loops using sequence homology and geometric constraints. Bioinformatics 26 (13), pp. 1671 - 1672 (2010)
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    Schudoma, C.; May, P.; Nikiforova, V.; Walther, D.: Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling. Nucleic Acids Research 38 (3), pp. 970 - 980 (2010)
42. 42.
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    Strassburg, K.; Walther, D.; Takahashi, H.; Kanaya, S.; Kopka, J.: Dynamic Transcriptional and Metabolic Responses in Yeast Adapting to Temperature Stress. Omics-a Journal of Integrative Biology 14 (3), pp. 249 - 259 (2010)
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    Sun, X.; Zou, Y.; Nikiforova, V.; Kurths, J.; Walther, D.: The complexity of gene expression dynamics revealed by permutation entropy. BMC Bioinformatics 11, p. 607 (2010)
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    Walther, D.; Strassburg, K.; Durek, P.; Kopka, J.: Metabolic Pathway Relationships Revealed by an Integrative Analysis of the Transcriptional and Metabolic Temperature Stress-Response Dynamics in Yeast. OMICS: A Journal of Integrative Biology 14 (3), pp. 261 - 274 (2010)
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    Childs, L.; Nikoloski, Z.; May, P.; Walther, D.: Identification and classification of ncRNA molecules using graph properties. Nucleic Acids Research 37 (9), p. e66 (2009)
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    Degenkolbe, T.; Do, P. T.; Zuther, E.; Repsilber, D.; Walther, D.; Hincha, D. K.; Koehl, K. I.: Expression profiling of rice cultivars differing in their tolerance to long-term drought stress. Plant Molecular Biology 69 (1-2), pp. 133 - 153 (2009)
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    Durek, P.; Schudoma, C.; Weckwerth, W.; Selbig, J.; Walther, D.: Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins. BMC Bioinformatics 10, p. 117 (2009)
48. 48.
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    Kersten, B.; Agrawal, G. K.; Durek, P.; Neigenfind, J.; Schulze, W. X.; Walther, D.; Rakwal, R.: Plant phosphoproteomics: An update. Proteomics 9 (4), pp. 964 - 988 (2009)
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    Kierszniowska, S.; Walther, D.; Schulze, W. X.: Ratio-dependent significance thresholds in reciprocal N-15-labeling experiments as a robust tool in detection of candidate proteins responding to biological treatment. Proteomics 9 (7), pp. 1916 - 1924 (2009)
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    May, P.; Christian, J. O.; Kempa, S.; Walther, D.: ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii. BMC Genomics 10, p. 209 (2009)