Publications of Zoran Nikoloski

Hobby, D.; Lindner, R.; Mbebi, A. J.; Tong, H.; Nikoloski, Z.: Comparative analysis of genomic prediction approaches for multiple time-resolved traits in maize. Theoretical and Applied Genetics 139, 63 (2026)

Andreou-Huotari, G.M.; Brosché, M.; Hoffmann, J.; Nikoloski, Z.; Laitinen, R.A.E.: Spliceosomal Factor SmF Modulates Temperature-Mediated Flower and Leaf Size Plasticity in Arabidopsis thaliana. Plant, Cell and Environment (2026)

Annunziata, M. G.; Feil, R.; Lohse, M.; Figueroa, C. M.; Hartman, M. D.; Esmailpour , M.; Nikoloski, Z.; Koehl, K. I.; Stitt, M.; Lunn, J. E. et al.; Fichtner, F.: The sucrose:trehalose 6-phosphate nexus is conserved in flowering plants with different phloem loading and carbon storage strategies. Journal of Experimental Botany 77 (2), pp. 578 - 591 (2026)

Xu, R.; Ferguson, J.; Breil-Aubert, M.; Kromdijk, J.; Nikoloski, Z.: Generalizability and transferability of machine learning models using hyperspectral reflectance data for maize traits. Scientific Reports 16, 5865 (2026)

Østerlund, I.; Nyboe Ørting, S.; Leverett, A.; Théroux-Rancourt, G.; Ebrahimi, S.; Wang, Y.; Nikoloski, Z.; Kromdijk, J.; Persson, S.: Rho GTPase overexpression impacts leaf internal architecture and mesophyll conductance in Arabidopsis. New Phytologist 248 (6), pp. 3053 - 3066 (2025)

Soleymani Babadi, F.; Correa Cordoba, S. M.; Arend, M.; Forghanisardaghi, N.; Treves, H.; Razaghi-Moghadam, Z.; Nikoloski, Z.: Constraint-based metabolic modeling reveals metabolic properties underpinning the unprecedented growth of Chlorella ohadii. New Phytologist 248 (3), pp. 1572 - 1583 (2025)

Küken, A.; Langary, D.; Angeleska, A.; Nikoloski, Z.: A constraint-based framework for exploring the impact of multireaction dependencies on metabolic functions. npj Systems biology and applications 11, 118 (2025)

Wendering, P.; Nikoloski, Z.: Predicting plant thermal responses using a temperature-aware plant metabolic model: a primer. IN SILICO PLANTS 7 (2), diaf020 (2025)

Koper, K.; de Oliveira; V., M. V.; Huß, S.; Hataya, S.; Soleymani Babadi, F.; Hawkins, C.; Rhee, S. Y.; Takasuka, T. E.; Nikoloski, Z. et al.; Maeda, H. A.: Mapping multi-substrate specificity of Arabidopsis aminotransferases. Nature Plants 11 (9), pp. 1863 - 1876 (2025)

Zrimec, J.; Correa, S.; Zagorščak, M.; Petek, M.; Bleker, C.; Stare, K.; Schuy, C.; Sonnewald, S.; Gruden, K.; Nikoloski, Z.: Evaluating plant growth-defense trade-offs by modeling the interaction between primary and secondary metabolism. Proceedings of the National Academy of Sciences of the United States of America 122 (32), e2502160122 (2025)

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), pp. 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, pp. 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)

Huß, S.; Nikoloski, Z.: NeuralFlux: Estimation of Reaction Fluxes at a Genome-Scale Level From Time-Resolved Isotope Labelling Patterns Using Deep Learning. Plant Biotechnology Journal (2025)