Publications of Z. Nikoloski

Meret, M., Kopetzki, D., Degenkolbe, T., Kleessen, S., Nikoloski, Z., Tellstroem, V., Barsch, A., Kopka, J., Antonietti, M. & Willmitzer, L. From systems biology to systems chemistry: metabolomic procedures enable insight into complex chemical reaction networks in water. RSC Advances 4, 16777–16781 (2014).

Mettler, T., Mühlhaus, T., Hemme, D., Schöttler, M. A., Rupprecht, J., Idoine, A., Veyel, D., Pal, S. K., Yaneva-Roder, L., Winck, F. V., 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, 2310–2350 (2014).

Recht, L., Toepfer, N., Batushansky, A., Sikron, N., Gibon, Y., Fait, A., Nikoloski, Z., Boussiba, S. & Zarka, A. Metabolite Profiling and Integrative Modeling Reveal Metabolic Constraints for Carbon Partitioning under Nitrogen Starvation in the Green Algae Haematococcus pluvialis. The Journal of Biological Chemistry 289, 30387–30403 (2014).

Toepfer, N., Scossa, F., Fernie, A. R. & Nikoloski, Z. Variability of Metabolite Levels Is Linked to Differential Metabolic Pathways in Arabidopsis's Responses to Abiotic Stresses. PLoS Computational Biology 10, (2014).

Sajitz-Hermstein, M. & Nikoloski, Z. Structural control of metabolic flux. PLoS Computational Biology 9, (2013).

Hochberg, U., Degu, A., Toubiana, D., Gendler, T., Nikoloski, Z., Rachmilevitch, S. & Fait, A. Metabolic profiling and network analysis reveal coordinated changes in grapevine water stress response. BMC Plant Biology 13, (2013).

Toepfer, N. & Nikoloski, Z. Large-scale modeling provides insights into Arabidopsis's acclimation to changing light and temperature conditions. Plant Signaling & Behavior 8, (2013).

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).

Toepfer, N., Caldana, C., Grimbs, S., Willmitzer, L., Fernie, A. R. & Nikoloski, Z. Integration of Genome-Scale Modeling and Transcript Profiling Reveals Metabolic Pathways Underlying Light and Temperature Acclimation in Arabidopsis. The Plant Cell 25, 1197–1211 (2013).

Neigenfind, J., Grimbs, S. & Nikoloski, Z. On the relation between reactions and complexes of (bio)chemical reaction networks. Journal of Theoretical Biology 317, 359–365 (2013).

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).

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).