Publications of Z. Nikoloski

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).

Omidbakhshfard, M. A., Omranian, N., Ahmadi, F. S., Nikoloski, Z. & Mueller-Roeber, B. Effect of salt stress on genes encoding translation-associated proteins in Arabidopsis thaliana. Plant Signaling & Behavior 7, 1095–1102 (2012).

Omranian, N., Mueller-Roeber, B. & Nikoloski, Z. PageRank-based identification of signaling crosstalk from transcriptomics data: the case of Arabidopsis thaliana. Molecular BioSystems 8, 1121–1127 (2012).

Osorio, S., Alba, R., Nikoloski, Z., Kochevenko, A., Fernie, A. R. & Giovannoni, J. J. Integrative Comparative Analyses of Transcript and Metabolite Profiles from Pepper and Tomato Ripening and Development Stages Uncovers Species-Specific Patterns of Network Regulatory Behavior. Plant Physiology 159, 1713–1729 (2012).

Sajitz-Hermstein, M. & Nikoloski, Z. Restricted cooperative games on metabolic networks reveal functionally important reactions. Journal of Theoretical Biology 314, 192–203 (2012).

Toepfer, N., Jozefczuk, S. & Nikoloski, Z. Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli. BMC Systems Biology 6, 148 (2012).

Toubiana, D., Semel, Y., Tohge, T., Beleggia, R., Cattivelli, L., Rosental, L., Nikoloski, Z., Zamir, D., Fernie, A. R. & Fait, A. Metabolic Profiling of a Mapping Population Exposes New Insights in the Regulation of Seed Metabolism and Seed, Fruit, and Plant Relations. PLoS Genetics 8, e1002612 (2012).

Basler, G., Ebenhoeh, O., Selbig, J. & Nikoloski, Z. Mass-balanced randomization of metabolic networks. Bioinformatics 27, 1397–1403 (2011).

Basler, G., Grimbs, S., Ebenhoeh, O., Selbig, J. & Nikoloski, Z. Evolutionary significance of metabolic network properties. Journal of the Royal Society Interface 9, 1168–1176 (2011).

Basler, G. & Nikoloski, Z. JMassBalance: mass-balanced randomization and analysis of metabolic networks. Bioinformatics 27, 2761–2762 (2011).

Grimbs, S., Arnold, A., Koseka, A., Kurths, J., Selbig, J. & Nikoloski, Z. Spatiotemporal dynamics of the Calvin cycle: Multistationarity and symmetry breaking instabilities. Biosystems 103, 212–223 (2011).

Hempel, S., Koseska, A., Nikoloski, Z. & Kurths, J. Unraveling gene regulatory networks from time-resolved gene expression data - a measures comparison study. BMC Bioinformatics 12, 292 (2011).

Hempel, S., Kurths, J., Koseska, A. & Nikoloski, Z. Inner Composition Alignment for Inferring Directed Networks from Short Time Series. Physical Review Letters 107, 054101 (2011).

Lisec, J., Romisch-Margl, L., Nikoloski, Z., Piepho, H. P., Giavalisco, P., Selbig, J., Gierl, A. & Willmitzer, L. Corn hybrids display lower metabolite variability and complex metabolite inheritance patterns. The Plant Journal 68, 326–336 (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).

Ruprecht, C., Mutwil, M., Saxe, F., Eder, M., Nikoloski, Z. & Persson, S. Large-scale co-expression approach to dissect secondary cell wall formation across plant species. Frontiers in Plant Science 2, 23 (2011).

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

Nikoloski, Z., May, P. & Selbig, J. Algebraic connectivity may explain the evolution of gene regulatory networks. Journal of Theoretical Biology 267, 7–14 (2010).