Zeitschriftenartikel (154)

51.
Zeitschriftenartikel
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)
52.
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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)
53.
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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)
54.
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Duan, G. Y.; Walther, D.: Computational phosphorylation network reconstruction: methods and resources. Methods in Molecular Biology 1306, S. 177 - 194 (2015)
55.
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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)
56.
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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)
57.
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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)
58.
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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), S. 655 - 667 (2015)
59.
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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), S. e0120533 - e0120533 (2015)
60.
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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), S. 181 - 200 (2014)
61.
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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)
62.
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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)
63.
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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)
64.
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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), S. 2367 - 2389 (2014)
65.
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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 65 (4), S. 1051 - 1068 (2014)
66.
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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 4, 540 (2013)
67.
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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)
68.
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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)
69.
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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)
70.
Zeitschriftenartikel
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)
71.
Zeitschriftenartikel
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)
72.
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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)
73.
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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), S. 948 - 957 (2012)
74.
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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)
75.
Zeitschriftenartikel
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)
76.
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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, S. 207 (2012)
77.
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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)
78.
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Girbig, D.; Grimbs, S.; Selbig, J.: Systematic Analysis of Stability Patterns in Plant Primary Metabolism. PLoS One 7 (4), S. e34686 (2012)
79.
Zeitschriftenartikel
Girbig, D.; Selbig, J.; Grimbs, S.: A MATLAB toolbox for structural kinetic modeling. Bioinformatics 28 (19), S. 2546 - 2547 (2012)
80.
Zeitschriftenartikel
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)
81.
Zeitschriftenartikel
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)
82.
Zeitschriftenartikel
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)
83.
Zeitschriftenartikel
Kleessen, S.; Nikoloski, Z.: Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations. BMC Systems Biology 6 (1), S. 16 (2012)
84.
Zeitschriftenartikel
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)
85.
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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)
86.
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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)
87.
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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)
88.
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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)
89.
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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), S. 1990 - 2010 (2011)
90.
Zeitschriftenartikel
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), S. 364 - 376 (2011)
91.
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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), S. 1395 - 1405 (2011)
92.
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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), S. 2979 - 2991 (2011)
93.
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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, S. 54 (2011)
94.
Zeitschriftenartikel
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), S. 429 (2011)
95.
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Kryvych, S.; Kleessen, S.; Ebert, B.; Kersten, B.; Fisahn, J.: Proteomics - The key to understanding systems biology of Arabidopsis trichomes. Phytochemistry 72 (10), S. 1061 - 1070 (2011)
96.
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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, S. 483 (2011)
97.
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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), S. 999 - 1013 (2011)
98.
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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, S. 43 (2011)
99.
Zeitschriftenartikel
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), S. e1002155 (2011)
100.
Zeitschriftenartikel
Schudoma, C.: It's a loop world – single strands in RNA as structural and functional elements. BioMolecular Concepts 2 (3), S. 171 - 181 (2011)
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