Publications of Z. Nikoloski

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

Sulpice, R., Nikoloski, Z., Tschoep, H., Antonio, C., Kleeson, S., Lahrlimi, A., Selbig, J., Hirofumi, I., Gibon, Y., Fernie, A. R. & Stitt, M. Impact of the carbon and nitrogen supply on relationships and connectivity between metabolism and biomass in a broad panel of Arabidopsis accessions. Plant Physiology 162, 347–363 (2013).

Szecowka, M., Heise, R., Tohge, T., Nunes-Nesi, A., Vosloh, D., Huege, J., Feil, R., Lunn, J., Nikoloski, Z., Stitt, M., Fernie, A. R. & Arrivault, S. Metabolic Fluxes in an Illuminated Arabidopsis Rosette. The Plant Cell 25, 694–714 (2013).

Toubiana, D., Fernie, A. R., Nikoloski, Z. & Fait, A. Network analysis: tackling complex data to study plant metabolism. Trends in Biotechnology 31, 29–36 (2013).

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, (2013).

Xue, W., Batushansky, A., Toubiana, D., Botnick, I., Szymanski, J., Khozin-Goldberg, I., Nikoloski, Z., Lewinsohn, E. & Fait, A. The Investment in Scent: Time-Resolved Metabolic Processes in Developing Volatile-Producing Nigella sativa L. Seeds. PLoS One 8, (2013).

Zakharova, A., Nikoloski, Z. & Koseska, A. Dimensionality reduction of multistable biological systems. Bulletin of Mathematical Biology 75, 373–392 (2013).

Araujo, W. L., Nunes-Nesi, A., Nikoloski, Z., Sweetlove, L. J. & Fernie, A. R. Metabolic control and regulation of the tricarboxylic acid cycle in photosynthetic and heterotrophic plant tissues. Plant, Cell and Environment 35, 1–21 (2012).

Basler, G., Grimbs, S. & Nikoloski, Z. Optimizing metabolic pathways by screening for feasible synthetic reactions. Biosystems 109, 186–191 (2012).

Güell, O., Sagués, F., Basler, G., Nikoloski, Z. & Serrano, M. S. Assessing the significance of knockout cascades in metabolic networks. Journal of Computational Interdisciplinary Sciences 3, 45–53 (2012).

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, 1319 (2012).

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, 11122–11131 (2012).

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, 217 (2012).

Kleessen, S. & Nikoloski, Z. Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations. BMC Systems Biology 6, 16 (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., Mutwil, M., Persson, S. & Nikoloski, Z. Inferring gene functions through dissection of relevance networks: interleaving the intra- and inter-species views. Molecular BioSystems 8, 2233–2241 (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).