Publikationen der Gruppe

Zeitschriftenartikel (116)

  1. 1.
    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 (2017)
  2. 2.
    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 (2017)
  3. 3.
    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)
  4. 4.
    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)
  5. 5.
    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)
  6. 6.
    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)
  7. 7.
    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)
  8. 8.
    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)
  9. 9.
    Lis, M.; Walther, D.: The orientation of transcription factor binding site motifs in gene promoter regions: does it matter? BMC Genomics 17, 185 (2016)
  10. 10.
    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)
  11. 11.
    Walther, D.; Kragler, F.: Mobile RNAs convey the message. Nature Plants 2 (4), 16040 (2016)
  12. 12.
    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)
  13. 13.
    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)
  14. 14.
    Duan, G. Y.; Walther, D.: Computational phosphorylation network reconstruction: methods and resources. Methods in Molecular Biology 1306, S. 177 - 194 (2015)
  15. 15.
    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)
  16. 16.
    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)
  17. 17.
    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)
  18. 18.
    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), S. 1587 - 1597 (2015)
  19. 19.
    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), S. 655 - 667 (2015)
  20. 20.
    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)
  21. 21.
    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), S. e0120533 - e0120533 (2015)
  22. 22.
    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), S. 181 - 200 (2014)
  23. 23.
    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), S. 1891 - 911 (2014)
  24. 24.
    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), S. 1250 - 1258 (2014)
  25. 25.
    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), S. 2310 - 2350 (2014)
  26. 26.
    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.
    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), S. 2367 - 2389 (2014)
  28. 28.
    Duan, G. Y.; Christian, N.; Schwachtje, J.; Walther, D.; Ebenhoeh, O.: The Metabolic Interplay between Plants and Phytopathogens. Metabolites 3 (1), S. 1 - 23 (2013)
  29. 29.
    Duan, G. Y.; Walther, D.; Schulze, W. X.: Reconstruction and analysis of nutrient-induced phosphorylation networks in Arabidopsis thaliana. Frontiers in Plant Science (2013)
  30. 30.
    Kleessen, S.; Klie, S.; Nikoloski, Z.: Data Integration through Proximity-Based Networks Provides Biological Principles of Organization across Scales. The Plant Cell 25 (6), S. 1917 - 1927 (2013)
  31. 31.
    Shao, N.; Duan, G. Y.; Bock, R.: A Mediator of Singlet Oxygen Responses in Chlamydomonas reinhardtii and Arabidopsis Identified by a Luciferase-Based Genetic Screen in Algal Cells. The Plant Cell 25 (10), S. 4209 - 4226 (2013)
  32. 32.
    Toepel, J.; Illmer-Kephalides, M.; Jaenicke, S.; Straube, J.; May, P.; Goesmann, A.; Kruse, O.: New insights into Chlamydomonas reinhardtii hydrogen production processes by combined microarray/RNA-seq transcriptomics. PLANT BIOTECHNOLOGY JOURNAL 11 (6), S. 717 - 733 (2013)
  33. 33.
    Winck, F. V.; Arvidsson, S.; Mauricio Riano-Pachon, D.; Hempel, S.; Koseska, A.; Nikoloski, Z.; Urbina Gomez, D. A.; Rupprecht, J.; Mueller-Roeber, B.: Genome-Wide Identification of Regulatory Elements and Reconstruction of Gene Regulatory Networks of the Green Alga Chlamydomonas reinhardtii under Carbon Deprivation. PLoS One (2013)
  34. 34.
    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), S. 948 - 957 (2012)
  35. 35.
    Bringmann, M.; Landrein, B.; Schudoma, C.; Hamant, O.; Hauser, M. T.; Persson, S.: Cracking the elusive alignment hypothesis: the microtubule-cellulose synthase nexus unraveled. Trends in Plant Science 17 (11), S. 666 - 674 (2012)
  36. 36.
    Childs, L. H.; Lisec, J.; Walther, D.: Matapax: An Online High-Throughput Genome-Wide Association Study Pipeline. Plant Physiology 158 (4), S. 1534 - 1541 (2012)
  37. 37.
    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, S. 207 (2012)
  38. 38.
    Draffehn, A. M.; Durek, P.; Nunes-Nesi, A.; Stich, B.; Fernie, A. R.; Gebhardt, C.: Tapping natural variation at functional level reveals allele specific molecular characteristics of potato invertase Pain-1. Plant, Cell and Environment 35 (12), S. 2143 - 2154 (2012)
  39. 39.
    Girbig, D.; Selbig, J.; Grimbs, S.: A MATLAB toolbox for structural kinetic modeling. Bioinformatics 28 (19), S. 2546 - 2547 (2012)
  40. 40.
    Girbig, D.; Grimbs, S.; Selbig, J.: Systematic Analysis of Stability Patterns in Plant Primary Metabolism. PLoS One 7 (4), S. e34686 (2012)
  41. 41.
    Kleessen, S.; Nikoloski, Z.: Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations. BMC Systems Biology 6 (1), S. 16 (2012)
  42. 42.
    Kleessen, S.; Fernie, A. R.; Nikoloski, Z.: A computational framework for evaluating the efficiency of Arabidopsis accessions in response to nitrogen stress reveals important metabolic mechanisms. Frontiers in Plant Science 3, S. 217 (2012)
  43. 43.
    Kleessen, S.; Araujo, W. L.; Fernie, A. R.; Nikoloski, Z.: Model-based Confirmation of Alternative Substrates of Mitochondrial Electron Transport Chain. Journal of Biological Chemistry 287 (14), S. 11122 - 11131 (2012)
  44. 44.
    Kleessen, S.; Antonio, C.; Sulpice, R.; Laitinen, R.; Fernie, A. R.; Stitt, M.; Nikoloski, Z.: Structured patterns in geographic variability of metabolic phenotypes in Arabidopsis thaliana. Nature Communications 3, S. 1319 (2012)
  45. 45.
    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, S. 272 (2012)
  46. 46.
    Usadel, B.; Schwacke, R.; Nagel, A.; Kersten, B.: GabiPD – The GABI Primary Database integrates plant proteomic data with gene-centric information. Frontiers in Plant Science (2012)
  47. 47.
    Zhang, J.; Ruf, S.; Hasse, C.; Childs, L.; Scharff, L. B.; Bock, R.: Identification of cis-elements conferring high levels of gene expression in non-green plastids. Plant Journal 72 (1), S. 115 - 128 (2012)
  48. 48.
    Zuther, E.; Schulz, E.; Childs, L. H.; Hincha, D. K.: Clinal variation in the non-acclimated and cold-acclimated freezing tolerance of Arabidopsis thaliana accessions. Plant Cell and Environment 35 (10), S. 1860 - 1878 (2012)
  49. 49.
    Arvidsson, S.; Perez-Rodriguez, P.; Mueller-Roeber, B.: A growth phenotyping pipeline for Arabidopsis thaliana integrating image analysis and rosette area modeling for robust quantification of genotype effects. New Phytologist 191 (3), S. 895 - 907 (2011)
  50. 50.
    Branscheid, A.; Devers, E. A.; May, P.; Krajinski, F.: Distribution pattern of small RNA and degradome reads provides information on miRNA gene structure and regulation. Plant Signaling & Behavior 6 (10), S. 1609 - 1611 (2011)
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