Journal Article (155)

51.
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)
52.
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)
53.
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)
54.
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)
55.
Journal Article
Duan, G. Y.; Walther, D.: Computational phosphorylation network reconstruction: methods and resources. Methods in Molecular Biology 1306, pp. 177 - 194 (2015)
56.
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)
57.
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)
58.
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)
59.
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)
60.
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)
61.
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)
62.
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)
63.
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)
64.
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)
65.
Journal Article
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)
66.
Journal Article
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 65 (4), pp. 1051 - 1068 (2014)
67.
Journal Article
Duan, G. Y.; Walther, D.; Schulze, W. X.: Reconstruction and analysis of nutrient-induced phosphorylation networks in Arabidopsis thaliana. Frontiers in Plant Science 4, 540 (2013)
68.
Journal Article
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), pp. 4209 - 4226 (2013)
69.
Journal Article
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), pp. 717 - 733 (2013)
70.
Journal Article
Kleessen, S.; Klie, S.; Nikoloski, Z.: Data Integration through Proximity-Based Networks Provides Biological Principles of Organization across Scales. The Plant Cell 25 (6), pp. 1917 - 1927 (2013)
71.
Journal Article
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)
72.
Journal Article
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 8 (11), e79909 (2013)
73.
Journal Article
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 3, 154 (2012)
74.
Journal Article
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)
75.
Journal Article
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), pp. 666 - 674 (2012)
76.
Journal Article
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)
77.
Journal Article
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)
78.
Journal Article
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), pp. 2143 - 2154 (2012)
79.
Journal Article
Girbig, D.; Grimbs, S.; Selbig, J.: Systematic Analysis of Stability Patterns in Plant Primary Metabolism. PLoS One 7 (4), p. e34686 (2012)
80.
Journal Article
Girbig, D.; Selbig, J.; Grimbs, S.: A MATLAB toolbox for structural kinetic modeling. Bioinformatics 28 (19), pp. 2546 - 2547 (2012)
81.
Journal Article
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, p. 1319 (2012)
82.
Journal Article
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), pp. 11122 - 11131 (2012)
83.
Journal Article
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, p. 217 (2012)
84.
Journal Article
Kleessen, S.; Nikoloski, Z.: Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations. BMC Systems Biology 6 (1), p. 16 (2012)
85.
Journal Article
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)
86.
Journal Article
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), pp. 115 - 128 (2012)
87.
Journal Article
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), pp. 1860 - 1878 (2012)
88.
Journal Article
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), pp. 895 - 907 (2011)
89.
Journal Article
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), pp. 1609 - 1611 (2011)
90.
Journal Article
Devers, E. A.; Branscheid, A.; May, P.; Krajinski, F.: Stars and Symbiosis: MicroRNA- and MicroRNA*-Mediated Transcript Cleavage Involved in Arbuscular Mycorrhizal Symbiosis. Plant Physiology 156 (4), pp. 1990 - 2010 (2011)
91.
Journal Article
Giavalisco, P.; Li, Y.; Matthes, A.; Eckhardt, A.; Hubberten, H.-M.; Hesse, H.; Segu, S.; Hummel, J.; Koehl, K. I.; Willmitzer, L.: Elemental formula annotation of polar and lipophilic metabolites using 13C, 15N and 34S isotope labelling, in combination with high-resolution mass spectrometry. The Plant Journal 68 (2), pp. 364 - 376 (2011)
92.
Journal Article
Haedrich, N.; Gibon, Y.; Schudoma, C.; Altmann, T.; Lunn, J. E.; Stitt, M.: Use of TILLING and robotised enzyme assays to generate an allelic series of Arabidopsis thaliana mutants with altered ADP-glucose pyrophosphorylase activity. Journal of Plant Physiology 168 (12), pp. 1395 - 1405 (2011)
93.
Journal Article
Hoehenwarter, W.; Larhlimi, A.; Hummel, J.; Egelhofer, V.; Selbig, J.; van Dongen, J. T.; Wienkoop, S.; Weckwerth, W.: MAPA Distinguishes Genotype-Specific Variability of Highly Similar Regulatory Protein Isoforms in Potato Tuber. Journal of Proteome Research 10 (7), pp. 2979 - 2991 (2011)
94.
Journal Article
Hummel, J.; Segu, S.; Li, Y.; Irgang, S.; Jueppner, J.; Giavalisco, P.: Ultra performance liquid chromatography and high resolution mass spectrometry for the analysis of plant lipids. Frontiers in Plant Science 2, p. 54 (2011)
95.
Journal Article
Janssen, S.; Schudoma, C.; Steger, G.; Giegerich, R.: Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction. BMC Bioinformatics 12 (1), p. 429 (2011)
96.
Journal Article
Kryvych, S.; Kleessen, S.; Ebert, B.; Kersten, B.; Fisahn, J.: Proteomics - The key to understanding systems biology of Arabidopsis trichomes. Phytochemistry 72 (10), pp. 1061 - 1070 (2011)
97.
Journal Article
Lenz, D.; May, P.; Walther, D.: Comparative analysis of miRNAs and their targets across four plant species. BMC Research Notes 4, p. 483 (2011)
98.
Journal Article
Rohrmann, J.; Tohge, T.; Alba, R.; Osorio, S.; Caldana, C.; McQuinn, R.; Arvidsson, S.; van der Merwe, M. J.; Riano-Pachon, D. M.; Mueller-Roeber, B. et al.; Fei, Z.; Nunes-Nesi, A.; Giovannoni, J. J.; Fernie, A. R.: Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development. The Plant Journal 68 (6), pp. 999 - 1013 (2011)
99.
Journal Article
Ryngajllo, M.; Childs, L.; Lohse, M.; Giorgi, F. M.; Lude, A.; Selbig, J.; Usadel, B.: SLocX: predicting subcellular localization of Arabidopsis proteins leveraging gene expression data. Frontiers in Plant Science 2, p. 43 (2011)
100.
Journal Article
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)
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