Sajitz-Hermstein, M.; Nikoloski, Z.: A novel approach for determining environment-specific protein costs: the case of Arabidopsis thaliana. Bioinformatics 26 (18), pp. i582 - i588 (2010)

Childs, L.; Nikoloski, Z.; May, P.; Walther, D.: Identification and classification of ncRNA molecules using graph properties. Nucleic Acids Research 37 (9), p. e66 (2009)

Szymanski, J.; Jozefczuk, S.; Nikoloski, Z.; Selbig, J.; Nikiforova, V.; Catchpole, G.; Willmitzer, L.: Stability of Metabolic Correlations under Changing Environmental Conditions in Escherichia coli - A Systems Approach. PLoS One 4 (10), p. e7441 (2009)

Basler, G.; Nikoloski, Z.; Ebenhoeh, O.; Handorf, T.: Biosynthetic potentials from species-specific metabolic networks. Genome Informatics 20, pp. 135 - 148 (2008)

Brandes, U.; Delling, D.; Gaertler, M.; Gorke, R.; Hoefer, M.; Nikoloski, Z.; Wagner, D.: On modularity clustering. IEEE Transactions on Knowledge and Data Engineering 20 (2), pp. 172 - 188 (2008)

Nikoloski, Z.; Grimbs, S.; May, P.; Selbig, J.: Metabolic networks are NP-hard to reconstruct. Journal of Theoretical Biology 254 (4), pp. 807 - 816 (2008)

Nikoloski, Z.; Grimbs, S.; Selbig, J.; Ebenhoeh, O.: Hardness and Approximability of the Inverse Scope Problem. Algorithms in Bioinformatics, Wabi 2008 5251, pp. 99 - 112 (2008)

de Abreu e Lima, F.; Leifels, L.; Nikoloski, Z.: Regression-Based Modeling of Complex Plant Traits Based on Metabolomics Data. In: Plant Metabolomics: Methods and Protocols, pp. 321 - 327 (Ed. António, C.). Humana Press, New York (2018)

Küken, A.; Nikoloski, Z.: Genome-scale modeling of photorespiratory pathway manipulation. In: Methods in Molecular Biology, Vol. 1653, pp. 195 - 202. Elsevier, Cambridge, MA (2017)

Omranian, N.; Nikoloski, Z.: Computational Approaches to Study Gene Regulatory Networks. In: Plant gene Regulatory Networks, Vol. 1629, pp. 283 - 295. Springer, heidelberg (2017)

Kleessen, S.; Nikoloski, Z.: Computational Approaches to Dissect and Understand Mechanisms of Adaptation. In: Molecular Mechanisms in Plant Adaptation, pp. 193 - 215. Wiley-Blackwell, Malden (2015)

Angeleska, A.; Kleessen, S.; Nikoloski, Z.: The Sequence Reconstruction Problem. In: Discrete and Topological Models in Molecular Biology, pp. 23 - 43 (Eds. Jonoska , N.; Saito, M.). Springer-Verlag, Berlin, Heidelberg (2014)

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)

Sajitz-Hermstein, M.; Nikoloski, Z.: Sensitivity of Contending Cellular Objectives in the Central Carbon Metabolism of Escherichia Coli. In: Information Processing in Cells and Tissues, pp. 169 - 172. 10th International Conference on Information Processing in Cells and Tissues (IPCAT), San Diego, CA, September 14, 2015 - September 16, 2015. (2015)

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)