Basler, G.; Grimbs, S.; Selbig, J.; Nikoloski, Z.: Thermodynamic landscapes of randomized large-scale metabolic networks. In: 7th International Workshop on Computational Systems Biology, WCSB 2010, S. 23 - 26 (Hg. Nykter, M.; Ruusuvuori, P.; Carlberg, C.; Yli-Harja, O.). 7th International Workshop on Computational Systems Biology, WCSB 2010, Luxembourg, LUX. Tampere International Center for Signal Processing (2010)

Arnold, A.; Nikoloski, Z.: Design and analysis of a reference model of sugar phosphate metabolism. In . First International Workshop on Differential and Integral Equations with Applications in Biology and Medicine 2010, Karlovassi, Samos, Greece, 2010. (2010)

van Dongen, J. T.; Nikoloski, Z.: Modeling alternatives for interpreting the change in oxygen-consumption rates during hypoxic conditions, New Phytologist 190, S. 273 - 276 (2011)

Dellero, Y.; Nikoloski, Z.: Editorial: Isotopic Labeling Approaches for Exploring Plant Metabolism Dynamics. Frontiers in Plant Science 14, 1356153 (2023)

Hanson, A.D.; Millar, A.H.; Nikoloski, Z.; Way, D.A.: Focus on respiration. Plant Physiology 191 (4), S. 2067 - 2069 (2023)

Arend, M.; Paulitz, E.; Hsieh, Y.; Nikoloski, Z.: Scaling metabolic model reconstruction up to the pan-genome level: A systematic review and prospective applications to photosynthetic organisms. Metabolic Engineering 90, S. 67 - 77 (2025)

Marzban, N.; Psarianos, M.; Herrmann, C.; Schulz-Nielsen, L.; Olszewska-Widdrat, A.; Arefi, A.; Pecenka, R.; Grundmann, P.; Schlüter, O. K.; Hoffmann, T. et al.; Rotter, V. S.; Nikoloski, Z.; Sturm, B.: Smart integrated biorefineries in bioeconomy: A concept toward zero-waste, emission reduction, and self-sufficient energy production. Biofuel Research Journal 12 (1), S. 2319 - 2349 (2025)

Ferreira, M.A.D.M.; Silveira, W.B.D.; Nikoloski, Z.: Protein constraints in genome-scale metabolic models: Data integration, parameter estimation, and prediction of metabolic phenotypes. Biotechnology and Bioengineering 121 (3), S. 915 - 930 (2024)

Wendering, P.; Nikoloski, Z.: Model-driven insights into the effects of temperature on metabolism. Biotechnology Advances 67, 108203 (2023)

Huß, S.; Nikoloski, Z.: Systematic comparison of local approaches for isotopically nonstationary metabolic flux analysis. Frontiers in Plant Science 14, 1178239 (2023)

Østerlund, I.; Persson, S.; Nikoloski, Z.: Tracing and tracking filamentous structures across scales: A systematic review. Computational and Structural Biotechnology Journal 21, S. 452 - 462 (2023)

Omranian, S.; Nikoloski, Z.; Grimm, D.: Computational identification of protein complexes from network interactions: Present state, challenges, and the way forward. Computational and Structural Biotechnology Journal 20, S. 2699 - 2712 (2022)

Tong, H.; Küken, A.; Razaghi-Moghadam, Z.; Nikoloski, Z.: Characterization of effects of genetic variants via genome-scale metabolic modelling. Cellular and Molecular Life Sciences 78, S. 5123 - 5138 (2021)

Estevez, S.; Nikoloski, Z.: Generalized framework for context-specific metabolic model extraction methods. Frontiers in Plant Science 5, S. 491 - 491 (2014)

Arnold, A.; Nikoloski, Z.: Comprehensive classification and perspective for modelling photorespiratory metabolism. Plant Biology 15 (4), S. 667 - 675 (2013)

Arnold, A.; Nikoloski, Z.: A quantitative comparison of CalvinBenson cycle models. Trends in Plant Science 16 (12), S. 676 - 683 (2011)

Kryvych, S.; Kleessen, S.; Ebert, B.; Kersten, B.; Fisahn, J.: Proteomics - The key to understanding systems biology of Arabidopsis trichomes. Phytochemistry 72 (10), S. 1061 - 1070 (2011)