Redestig, H.; Szymanski, J.; Hirai, M. Y.; Selbig, J.; Willmitzer, L.; Saito, K.; Nikoloski, Z.: Data integration, Metabolic Networks and Systems Biology. In: Biology of Plant Metabolomics, 9 (Ed. Hall, R. D.). Wiley-Blackwell, Oxford, UK (2011)

CUBCO: Prediction of Protein Complexes Based on Min-cut Network Partitioning into Biclique Spanned Subgraphs. Springer International Publishing, Cham (2022)

Razaghi-Moghadam, Z.; Masoudi-Nejad, A.; Nowzari-Dalini, A.: ParaKavosh: A Parallel Algorithm for Finding Biological Network Motifs. In: 2020 11th International Conference on Information and Knowledge Technology (IKT), pp. 45 - 49. (2020)

Larhlimi, A.; Basler, G.; Grimbs, S.; Selbig, J.; Nikoloski, Z.: Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks. In: 11th European Conference on Computational Biology (ECCB) / Conference of the Intelligent Systems in Molecular Biology (ISMB), pp. I502 - I508. 11th European Conference on Computational Biology (ECCB) / Conference of the Intelligent Systems in Molecular Biology (ISMB) , Basel, SWITZERLAND. (2012)

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, pp. 23 - 26 (Eds. 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, pp. 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), pp. 2067 - 2069 (2023)

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. (2024)

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

Huß, S.; Nikoloski, Z.: Systematic comparison of local approaches for isotopically nonstationary metabolic flux analysis. (2023)

Østerlund, I.; Persson, S.; Nikoloski, Z.: Tracing and tracking filamentous structures across scales: A systematic review. (2023)

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

Tong, H.; Küken, A.; Razaghi-Moghadam, Z.; Nikoloski, Z.: Characterization of effects of genetic variants via genome-scale metabolic modelling. (2021)

Estevez, S.; Nikoloski, Z.: Generalized framework for context-specific metabolic model extraction methods. (2014)

Arnold, A.; Nikoloski, Z.: Comprehensive classification and perspective for modelling photorespiratory metabolism. (2013)

Arnold, A.; Nikoloski, Z.: A quantitative comparison of CalvinBenson cycle models. (2011)

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