Publications of S. Klie

Cookson, S. J., Yadav, U. P., Klie, S., Morcuende, R., Usadel, B., Lunn, J. E. & Stitt, M. Temporal kinetics of the transcriptional response to carbon depletion and sucrose readdition in Arabidopsis seedlings. Plant, Cell and Environment 39, 768–786 (2016).

Ruprecht, C., Mendrinna, A., Tohge, T., Sampathkumar, A., Klie, S., Fernie, A. R., Nikoloski, Z., Persson, S. & Mutwil, M. FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants. Plant Physiology 170, 1878–1894 (2016).

Bordag, N., Klie, S., Juerchott, K., Vierheller, J., Schiewe, H., Albrecht, V., Tonn, J.-C., Schwartz, C., Schichor, C. & Selbig, J. Glucocorticoid (dexamethasone)-induced metabolome changes in healthy males suggest prediction of response and side effects. Scientific Reports 5, (2015).

Bellucci, E., Bitocchi, E., Ferrarini, A., Benazzo, A., Biagetti, E., Klie, S., Minio, A., Rau, D., Rodriguez, M., Panziera, A., Venturini, L., Attene, G., Albertini, E., Jackson, S. A., Nanni, L., Fernie, A. R., Nikoloski, Z., Bertorelle, G., Delledonne, M. & Papa, R. Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean. The Plant Cell 26, 1901–1912 (2014).

Guo, K., Zou, W., Feng, Y., Zhang, M., Zhang, J., Tu, F., Xie, G., Wang, L., Wang, Y., Klie, S., Persson, S. & Peng, L. An integrated genomic and metabolomic framework for cell wall biology in rice. BMC Genomics 15, (2014).

Kleessen, S., Klie, S. & Nikoloski, Z. Concurrent Conditional Clustering of Multiple Networks: COCONETS. PLoS One 9, (2014).

Klie, S., Nikoloski, Z. & Selbig, J. Biological Cluster Evaluation for Gene Function Prediction. Journal of Computational Biology 21, 428–445 (2014).

Klie, S., Osorio, S., Tohge, T., Drincovich, M. F., Fait, A., Giovannoni, J. J., Fernie, A. R. & Nikoloski, Z. Conserved Changes in the Dynamics of Metabolic Processes during Fruit Development and Ripening across Species. Plant Physiology 164, 55–68 (2014).

Rajasundaram, D., Selbig, J., Persson, S. & Klie, S. Co-ordination and divergence of cell-specific transcription and translation of genes in arabidopsis root cells. Annals of Botany 114, 1109–23 (2014).

Kleessen, S., Klie, S. & Nikoloski, Z. Data Integration through Proximity-Based Networks Provides Biological Principles of Organization across Scales. The Plant Cell 25, 1917–1927 (2013).

Omranian, N., Klie, S., Mueller-Roeber, B. & Nikoloski, Z. Network-Based Segmentation of Biological Multivariate Time Series. PLoS One 8, e62974 (2013).

Hubberten, H.-M., Klie, S., Caldana, C., Degenkolbe, T., Willmitzer, L. & Hoefgen, R. An additional role of O-acetylserine as a sulphur status independent regulator during plant growth. Plant Journal 70, 666–677 (2012).

Klie, S., Caldana, C. & Nikoloski, Z. Compromise of multiple time-resolved transcriptomics experiments identifies tightly regulated functions. Frontiers in Plant Science 3, 249 (2012).

Klie, S. & Nikoloski, Z. The Choice between MapMan and Gene Ontology for Automated Gene Function Prediction in Plant Science. Frontiers in Genetics 3, 115 (2012).

Caldana, C., Degenkolbe, T., Cuadros-Inostroza, A., Klie, S., Sulpice, R., Leisse, A., Steinhauser, D., Fernie, A. R., Willmitzer, L. & Hannah, M. A. High-density kinetic analysis of the metabolomic and transcriptomic response of Arabidopsis to eight environmental conditions. The Plant Journal 67, 869–884 (2011).

Klie, S., Krueger, S., Krall, L., Giavalisco, P., Fluegge, U.-I., Willmitzer, L. & Steinhauser, D. Analysis of the compartmentalized metabolome – a validation of the non-aqueous fractionation technique. Frontiers in Plant Science 2, 55 (2011).

Mutwil, M., Klie, S., Tohge, T., Giorgi, F. M., Wilkins, O., Campbell, M. M., Fernie, A. R., Usadel, B., Nikoloski, Z. & Persson, S. PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species. The Plant Cell 23, 895–910 (2011).

Nikoloski, Z., Grimbs, S., Klie, S. & Selbig, J. Complexity of automated gene annotation. Biosystems 104, 1–8 (2011).

Jozefczuk, S., Klie, S., Catchpole, G., Szymanski, J., Cuadros-Inostroza, A., Steinhauser, D., Selbig, J. & Willmitzer, L. Metabolomic and transcriptomic stress response of Escherichia coli. Molecular Systems Biology 6, 364 (2010).

Klie, S., Nikoloski, Z. & Selbig, J. Biological Cluster Evaluation for Gene Function Prediction. Journal of Computational Biology 17, 1–18 (2010).