Publications of Z. Nikoloski

Arnold, A. & Nikoloski, Z. Design and analysis of a reference model of sugar phosphate metabolism. in (2010). at <http://hdl.handle.net/11858/00-001M-0000-0014-2477-5>

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

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

Hanson, A. D., Millar, A. H., Nikoloski, Z. & Way, D. A. Focus on respiration. Plant Physiology 191, 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, 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., 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, 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, 915–930 (2024).

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

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

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

Omranian, S., Nikoloski, Z. & Grimm, D. G. Computational identification of protein complexes from network interactions: Present state, challenges, and the way forward. Computational and Structural Biotechnology Journal 20, 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, 5123–5138 (2021).

Medeiros, D. B., Daloso, D. M., Fernie, A. R., Nikoloski, Z. & Araujo, W. L. Utilizing systems biology to unravel stomatal function and the hierarchies underpinning its control. Plant, Cell and Environment 38, 1457–1470 (2015).

Toepfer, N., Kleessen, S. & Nikoloski, Z. Integration of metabolomics data into metabolic networks. Frontiers in Plant Science 6, (2015).

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

Arnold, A. & Nikoloski, Z. Comprehensive classification and perspective for modelling photorespiratory metabolism. Plant Biology 15, 667–675 (2013).

Fernie, A. R., Bauwe, H., Eisenhut, M., Florian, A., Hanson, D. T., Hagemann, M., Keech, O., Mielewczik, M., Nikoloski, Z., Peterhansel, C., Roje, S., Sage, R., Timm, S., von Cammerer, S., Weber, A. P. & Westhoff, P. Perspectives on plant photorespiratory metabolism. Plant Biology 15, 748–753 (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).

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).

Larhlimi, A., Blachon, S., Selbig, J. & Nikoloski, Z. Robustness of metabolic networks: A review of existing definitions. Biosystems 106, 1–8 (2011).