Publikationen von Z. Nikoloski

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 (2025). auf <http://hdl.handle.net/21.11116/0000-0011-0CEA-9>

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

Yuan, Y. Z., Iannetta, A. A., Kim, M., Sadecki, P. W., Arend, M., Tsichla, A., Ruiz-Sola, M. A., Kepesidis, G., Falconet, D., Thevenon, E., Tardif, M., Brugière, S., Couté, Y., Kleman, J. P., Sizova, I., Schilling, M., Jouhet, J., Hegemann, P., Li-Beisson, Y., Nikoloski, Z., Bastien, O., Hicks, L. M. & Petroutsos, D. Phototropin connects blue light perception to starch metabolism in green algae. Nature Communications 16, (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, (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 (2025). doi:10.1111/nph.20420

Razaghi-Moghadam, Z., Soleymani Babadi, F. & Nikoloski, Z. Harnessing the optimization of enzyme catalytic rates in engineering of metabolic phenotypes. PLOS Computational Biology 20, (2024).

Habibpour , M., Razaghi-Moghadam, Z. & Nikoloski, Z. Machine learning of metabolite-protein interactions from model-derived metabolic phenotypes. NAR: genomics and bioinformatics 6, (2024).

Qian, L., Yan, B., Zhou, J., Fan, Y., Tao, M., Zhu, W., Wang, C., Tu, Q., Tian, Y., He, Q., Wu, K., Niu, M., Yan, Q., Nikoloski, Z., Liu, G., Yu, X. & He, Z. Comprehensive profiles of sulfur cycling microbial communities along a mangrove sediment depth. Science of the Total Environment 944, (2024).

Rahimi-Majd, M., Leverett, A., Neumann, A., Kromdijk, J. & Nikoloski, Z. Nonlinear models based on leaf architecture traits explain the variability of mesophyll conductance across plant species. Plant, Cell and Environment 47, 5158–5171 (2024).

Pieri, A., Beleggia, R., Gioia, T., Tong, H., Di Vittori, V., Frascarelli, G., Bitocchi, E., Nanni, L., Bellucci, E., Fiorani, F., Pecchioni, N., Marzario, S., De Quattro, C., Limongi, A. R., De Vita, P., Rossato, M., Schurr, U., David, J. L., Nikoloski, Z. & Papa, R. Transcriptomic response to nitrogen availability reveals signatures of adaptive plasticity during tetraploid wheat domestication. Plant Cell 36, 3809–3823 (2024).

Hsieh, Y. E., Tandon, K., Verbruggen, H. & Nikoloski, Z. Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches. npj Systems biology and applications 10, (2024).

Laitinen, R. A. E. & Nikoloski, Z. Strategies to identify and dissect trade-offs in plants. Molecular Ecology 33, (2024).

Gupta, S., Petrov, V., Garg, V., Mueller-Roeber, B., Fernie, A. R., Nikoloski, Z. & Gechev, T. The genome of Haberlea rhodopensis provides insights into the mechanisms for tolerance to multiple extreme environments. Cellular and Molecular Life Sciences 81, (2024).

Habibpour, M., Razaghi-Moghadam, Z. & Nikoloski, Z. Prediction and integration of metabolite-protein interactions with genome-scale metabolic models. Metabolic Engineering 82, 216–224 (2024).

Arend, M., Yuan, Y., Ruiz-Sola, M. Á., Omranian, N., Nikoloski, Z. & Petroutsos, D. Widening the landscape of transcriptional regulation of green algal photoprotection. Nature Communications 14, (2023).

Langary, D., Küken, A. & Nikoloski, Z. The unraveling of balanced complexes in metabolic networks. Scientific Reports 13, (2023).

Tan, Q. W., Lim, P. K., Chen, Z., Pasha, A., Provart, N., Arend, M., Nikoloski, Z. & Mutwil, M. Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses. Nature Communications 14, (2023).

Küken, A., Treves, H. & Nikoloski, Z. A simulation-free constrained regression approach for flux estimation in isotopically nonstationary metabolic flux analysis with applications in microalgae. Frontiers in Plant Science 14, (2023).

Moura Ferreira, M. A. D., Wendering, P., Arend, M., Batista da Silveira, W. & Nikoloski, Z. Accurate prediction of in vivo protein abundances by coupling constraint-based modelling and machine learning. Metabolic Engineering 80, 184–192 (2023).