Publications of the Group

Wendering, P.; Ferguson, J.; Xu, R.; Kromdijk, J.; Nikoloski, Z.: Kinetic parameter prediction using neural networks identifies limitations toC4photosynthesis. New Phytologist 251 (3), pp. 1578 - 1594 (2026)

Wang, Q.; Gong, Y.; Wang, L.; Lv, N.; Du, X.; Zhang, J.; Xin, Y.; Nikoloski, Z.; Li-Beisson, Y.; Sun, L. et al.; Ma, B.; Wang, X.; Xu, J.: High-throughput Raman-activated cell sorting of microalgal genome-wide edited library revealed a regulatory pathway for carotenoid synthesis. Nature Communications (2026)

Hoffmann, J.; Andreou, G. M.; Nikoloski, Z.; Laitinen, R.: Temperature-mediated plasticity of floral and fitness traits inArabidopsis thaliana. Quantitative Plant Biology 7, e11 (2026)

Rahimi-Majd, M.; Xu, R.; Bauermeister, S.; Nikoloski, Z.: Machine learning surrogate for the leaf PROSPECT-D model and its applications across plant species. Scientific Reports 16, 15602 (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 49 (4), pp. 2024 - 2027 (2026)

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 24 (4), pp. 2076 - 2078 (2026)

Østerlund, I.; Neumann, A.; Ma, Z.; Miao, Y.; Persson, S.; Nikoloski, Z.: GraFT: A robust network-based spatiotemporal analysis of filamentous structures. Science Advances 12 (13), eadz4132 (2026)

Rahimi-Majd, M.; Ferguson, J.; Genty, B.; Kromdijk, J.; Nikoloski, Z.: Unraveling a hidden effective signal in leaf hyperspectral reflectance data. Science of Remote Sensing 13, 100405 (2026)

Soleymani Babadi, F.; Razaghi-Moghadam, Z.; Nikoloski, Z.: Accurate prediction of flux distributions compatible with metabolite concentration effects in genome-scale metabolic networks. PLOS Computational Biology 22, e1014066 (2026)

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)

Liu, P.; Yang, J.; Xu, Z.; Han, Y.; Wang, S.; Nikoloski, Z.; Yang, J.: Precision modification and de novo design of metabolic pathways to enhance crop nutritional quality and stress tolerance. The Crop Journal 14 (1), pp. 37 - 47 (2026)

Wu, C.-Y.; Cheng, H.-Y.; Lin, Y.-C.; Wang, Y.-C.; Meng, Y.-Z.; Hsieh, Y. E.; Liu, A.-C.; Yang, S.-H.: Role of core microbiome shifts in octocoral litophyton under diurnal temperature fluctuations. Microbial Ecology 89, 62 (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)

Zhang, S.-C.; Lin, Y.-C.; Wu, C.-Y.; Hsieh, Y. E.; Meng, Y.-Z.; Yang, S.-H.; Fan, T.-Y.: Effects of blue light and feeding on the physiological performance of reef corals, Stylophora pistillata and Pocillopora damicornis. Zoological Studies 65, 6 (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)

Xu, R.; Ferguson, J.; Hobby, D.; Rahimi-Majd, M.; Wendering, P.; Kromdijk, J.; Nikoloski, Z.: KineticGP: A computational framework for genomic prediction of leaf photosynthetic traits. Plant Communications 7 (5), 101685 (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)