Mettler, T.; Mühlhaus, T.; Hemme, D.; Schöttler, M. A.; Rupprecht, J.; Idoine, A.; Veyel, D.; Pal, S. K.; Yaneva-Roder, L.; Winck, F. V. et al.; 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 (6), pp. 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 (44), pp. 30387 - 30403 (2014)

Sajitz-Hermstein, M.; Nikoloski, Z.: Structural control of metabolic flux. PLoS Computational Biology 9 (12), e1003368 (2013)

Toepfer, N.; Nikoloski, Z.: Large-scale modeling provides insights into Arabidopsis's acclimation to changing light and temperature conditions. Plant Signaling & Behavior 8 (9), e25480 (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 (4), pp. 1197 - 1211 (2013)

Szecowka, M.; Heise, R.; Tohge, T.; Nunes-Nesi, A.; Vosloh, D.; Huege, J.; Feil, R.; Lunn, J.; Nikoloski, Z.; Stitt, M. et al.; Fernie, A. R.; Arrivault, S.: Metabolic Fluxes in an Illuminated Arabidopsis Rosette. The Plant Cell 25 (2), pp. 694 - 714 (2013)

Basler, G.; Grimbs, S.; Nikoloski, Z.: Optimizing metabolic pathways by screening for feasible synthetic reactions. Biosystems 109 (2), pp. 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 (1-2), pp. 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, p. 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 (14), pp. 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, p. 217 (2012)

Kleessen, S.; Nikoloski, Z.: Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations. BMC Systems Biology 6 (1), p. 16 (2012)

Sajitz-Hermstein, M.; Nikoloski, Z.: Restricted cooperative games on metabolic networks reveal functionally important reactions. Journal of Theoretical Biology 314, pp. 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 (1), p. 148 (2012)

Basler, G.; Ebenhoeh, O.; Selbig, J.; Nikoloski, Z.: Mass-balanced randomization of metabolic networks. Bioinformatics 27 (10), pp. 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 (71), pp. 1168 - 1176 (2011)

Basler, G.; Nikoloski, Z.: JMassBalance: mass-balanced randomization and analysis of metabolic networks. Bioinformatics 27 (19), pp. 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 (2), pp. 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, p. 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 (5), p. 054101 (2011)