Publications of the Group

Journal Article (141)

1.
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)
2.
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)
3.
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), 7607 (2020)
4.
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)
5.
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)
6.
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)
7.
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)
8.
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)
9.
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)
10.
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)
11.
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)
12.
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)
13.
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)
14.
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)
15.
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)
16.
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)
17.
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)
18.
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)
19.
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)
20.
Journal Article
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)
21.
Journal Article
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)
22.
Journal Article
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)
23.
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 4 (45 (D1)), pp. D1021 - D1028 (2017)
24.
Journal Article
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)
25.
Journal Article
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)
26.
Journal Article
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)
27.
Journal Article
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)
28.
Journal Article
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), pp. 3085 - 3101 (2017)
29.
Journal Article
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), pp. 900 - 915 (2017)
30.
Journal Article
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), pp. W6 - W11 (2017)
31.
Journal Article
Weissenborn, S.; Walther, D.: Metabolic Pathway Assignment of Plant Genes based on Phylogenetic Profiling-A Feasibility Study. Frontiers in Plant Science 8, 1831 (2017)
32.
Journal Article
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)
33.
Journal Article
Walther, D.; Kragler, F.: Mobile RNAs convey the message. Nature Plants 2 (4), 16040 (2016)
34.
Journal Article
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)
35.
Journal Article
Lis, M.; Walther, D.: The orientation of transcription factor binding site motifs in gene promoter regions: does it matter? BMC Genomics 17, 185 (2016)
36.
Journal Article
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)
37.
Journal Article
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)
38.
Journal Article
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)
39.
Journal Article
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)
40.
Journal Article
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)
41.
Journal Article
Duan, G. Y.; Walther, D.: Computational phosphorylation network reconstruction: methods and resources. Methods in Molecular Biology 1306, pp. 177 - 194 (2015)
42.
Journal Article
Ikeue, D.; Schudoma, C.; Zhang, W.; Ogata, Y.; Sakamoto, T.; Kurata, T.; Furuhashi, T.; Kragler, F.; Aoki, K.: A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads. Plant Methods 11, 34 (2015)
43.
Journal Article
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)
44.
Journal Article
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)
45.
Journal Article
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)
46.
Journal Article
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)
47.
Journal Article
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)
48.
Journal Article
Kuppusamy, T.; Giavalisco, P.; Arvidsson, S.; Sulpice, R.; Stitt, M.; Finnegan, P. M.; Scheible, W.-R.; Lambers, H.; Jost, R.: Lipid Biosynthesis and Protein Concentration Respond Uniquely to Phosphate Supply during Leaf Development in Highly Phosphorus-Efficient Hakea prostrata. Plant Physiology 166 (4), pp. 1891 - 911 (2014)
49.
Journal Article
Lohse, M.; Nagel, A.; Herter, T.; May, P.; Schroda, M.; Zrenner, R.; Tohge, T.; Fernie, A. R.; Stitt, M.; Usadel, B.: Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. Plant Cell Environment 37 (5), pp. 1250 - 1258 (2014)
50.
Journal Article
Mettler, T.; Mühlhaus, T.; Hemme, D.; Schöttler, M. A.; Rupprecht, J.; Idoine, A.; Veyel, D.; Pal, S. K.; Yaneva-Roder, L.; Winck, F. V. et al.; Sommer, F.; Vosloh, D.; Seiwert, B.; Erban, A.; Burgos, A.; Arvidsson, S.; Schönfelder, S.; Arnold, A.; Günther, M.; Krause, U.; Lohse, M.; Kopka, J.; Nikoloski, Z.; Mueller-Roeber, B.; Willmitzer, L.; Bock, R.; Schroda, M.; Stitt, M.: Systems Analysis of the Response of Photosynthesis, Metabolism, and Growth to an Increase in Irradiance in the Photosynthetic Model Organism Chlamydomonas reinhardtii. The Plant Cell 26 (6), pp. 2310 - 2350 (2014)
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