Wendering, P.; Andreou, G.M.; Laitinen, R.A.E.; Nikoloski, Z.: Metabolic modeling identifies determinants of thermal growth responses in Arabidopsis thaliana. New Phytologist 247 (1), S. 178 - 190 (2025)

Langary, D.; Küken, A.; Nikoloski, Z.: Kinetic modules are sources of concentration robustness in biochemical networks. Science Advances 11 (22), eads7269 (2025)

Mbebi, A. J.; Mercado, F.; Hobby, D.; Tong, H.; Nikoloski, Z.: Advances in multi-trait genomic prediction approaches: classification, comparative analysis, and perspectives. Briefings in Bioinformatics 26 (3), bbaf211 (2025)

Hobby, D.; Tong, H.; Heuermann, M.; Mbebi, A. J.; Laitinen, R. A. E.; Dell’Acqua, M.; Altmann, T.; Nikoloski, Z.: Predicting plant trait dynamics from genetic markers. Nature Plants 11, S. 1018 - 1027 (2025)

Seyis, M.; Razaghi-Moghadam, Z.; Nikoloski, Z.: Flux-sum coupling analysis of metabolic network models. PLOS Computational Biology 21 (4), e1012972 (2025)

de Moura Ferreira, M. A.; Menezes de Almeida, E. L.; Batista da Silveira, W.; Nikoloski, Z.: Protein-constrained models pinpoints the role of underground metabolism in robustness of metabolic phenotypes. iScience 28 (3), 112126 (2025)

Yuan, Y.; Iannetta, A.; Kim, M.; Sadecki, P.; Arend, M.; Tsichla, A.; Ruiz-Sola, M.; Kepesidis, G.; Falconet, D.; Thevenon, E. et al.; Tardif, M.; Brugière, S.; Couté, Y.; Kleman, J.; Sizova, I.; Schilling, M.; Jouhet, J.; Hegemann, P.; Li-Beisson, Y.; Nikoloski, Z.; Bastien, O.; Hicks, L.; Petroutsos, D.: Phototropin connects blue light perception to starch metabolism in green algae. Nature Communications 16, 2545 (2025)

Correa Cordoba, S. M.; Burgos, A.; Cuadros-Inostroza, A. C.; Xu, K.; Brotman, Y.; Nikoloski, Z.: A data-integrative modeling approach accurately characterizes the effects of mutations on Arabidopsis lipid metabolism. Plant Physiology 197 (2), kiae615 (2025)

Hsieh, Y. E.; Tandon, K.; Verbruggen, H.; Nikoloski, Z.: Integration of metatranscriptomics data improves the predictive capacity of microbial community metabolic models. The ISME Journal 19 (1), wraf109 (2025)

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)