Publications of D. Walther

Lenz, D., May, P. & Walther, D. Comparative analysis of miRNAs and their targets across four plant species. BMC Research Notes 4, 483 (2011).

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, e1002155 (2011).

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, 1247–1257 (2011).

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, 188 (2010).

Hummel, J., Strehmel, N., Selbig, J., Walther, D. & Kopka, J. Decision tree supported substructure prediction of metabolites from GC-MS profiles. Metabolomics 6, 322–333 (2010).

Lohse, M., Nunes-Nesi, A., Krueger, P., Nagel, A., Hannemann, J., Giorgi, F. M., Childs, L., Osorio, S., Walther, D., Selbig, J., 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, 642–651 (2010).

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, 411 (2010).

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, 970–980 (2010).

Schudoma, C., May, P. & Walther, D. Modeling RNA loops using sequence homology and geometric constraints. Bioinformatics 26, 1671–1672 (2010).

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, 249–259 (2010).

Sun, X., Zou, Y., Nikiforova, V., Kurths, J. & Walther, D. The complexity of gene expression dynamics revealed by permutation entropy. BMC Bioinformatics 11, 607 (2010).

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, 261–274 (2010).

Childs, L., Nikoloski, Z., May, P. & Walther, D. Identification and classification of ncRNA molecules using graph properties. Nucleic Acids Research 37, e66 (2009).

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, 133–153 (2009).

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, 117 (2009).

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, 1916–1924 (2009).

Pant, B. D., Musialak-Lange, M., Nuc, P., May, P., Buhtz, A., Kehr, J., Walther, D. & Scheible, W.-R. Identification of Nutrient-Responsive Arabidopsis and Rapeseed MicroRNAs by Comprehensive Real-Time Polymerase Chain Reaction Profiling and Small RNA Sequencing. Plant Physiology 150, 1541–1555 (2009).

Durek, P. & Walther, D. The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles. BMC Systems Biology 2, 100 (2008).

Heazlewood, J. L., Durek, P., Hummel, J., Selbig, J., Weckwerth, W., Walther, D. & Schulze, W. X. PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor. Nucleic Acids Research 36, D1015–D1021 (2008).

Koehl, K. I., Basler, G., Lüdemann, A., Selbig, J. & Walther, D. A plant resource and experiment management system based on the Golm Plant Database as a basic tool for omics research. Plant Methods 4, 11 (2008).