Publications of the Group

Journal Article (146)

1.
Journal Article
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)
2.
Journal Article
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 (2024)
3.
Journal Article
Razaghi-Moghadam, Z.; Soleymani Babadi, F.; Nikoloski, Z.: Harnessing the optimization of enzyme catalytic rates in engineering of metabolic phenotypes. PLOS Computational Biology 20 (11), e1012576 (2024)
4.
Journal Article
Habibpour , M.; Razaghi-Moghadam, Z.; Nikoloski, Z.: Machine learning of metabolite-protein interactions from model-derived metabolic phenotypes. NAR: genomics and bioinformatics 6 (3), lqae114 (2024)
5.
Journal Article
Qian, L.; Yan, B.; Zhou, J.; Fan, Y.; Tao, M.; Zhu, W.; Wang, C.; Tu, Q.; Tian, Y.; He, Q. et al.; 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, 173961 (2024)
6.
Journal Article
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 (12), pp. 5158 - 5171 (2024)
7.
Journal Article
Pieri, A.; Beleggia, R.; Gioia, T.; Tong, H.; Di Vittori, V.; Frascarelli, G.; Bitocchi, E.; Nanni, L.; Bellucci, E.; Fiorani, F. et al.; Pecchioni, N.; Marzario, S.; De Quattro, C.; Limongi, A.; De Vita, P.; Rossato, M.; Schurr, U.; David, J.; Nikoloski, Z.; Papa, R.: Transcriptomic response to nitrogen availability reveals signatures of adaptive plasticity during tetraploid wheat domestication. Plant Cell 36 (9), pp. 3809 - 3823 (2024)
8.
Journal Article
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 (1), 54 (2024)
9.
Journal Article
Laitinen, R. A. E.; Nikoloski, Z.: Strategies to identify and dissect trade-offs in plants. Molecular Ecology 33 (10), e16780 (2024)
10.
Journal Article
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 (1), 117 (2024)
11.
Journal Article
Habibpour, M.; Razaghi-Moghadam, Z.; Nikoloski, Z.: Prediction and integration of metabolite-protein interactions with genome-scale metabolic models. Metabolic Engineering 82, pp. 216 - 224 (2024)
12.
Journal Article
Hsieh, Y.; Lu, C.-Y.; Liu, P.-Y.; Kao, J.-M.; Yang, S.-Y.; Wu, C.-Y.; Wong, J.-W.M.; Shikina, S.; Fan, T.-Y.; Yang, S.-H.: Successive responses of three coral holobiont components (coral hosts, symbiotic algae, and bacteria) to daily temperature fluctuations. Ecological Indicators 158, 111515 (2024)
13.
Journal Article
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 (1), 2687 (2023)
14.
Journal Article
Langary, D.; Küken, A.; Nikoloski, Z.: The unraveling of balanced complexes in metabolic networks. Scientific Reports 13 (1), 5712 (2023)
15.
Journal Article
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 (1), 986 (2023)
16.
Journal Article
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, 1140829 (2023)
17.
Journal Article
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, pp. 184 - 192 (2023)
18.
Journal Article
Pratx, L.; Wendering, P.; Kappel, C.; Nikoloski, Z.; Bäurle, I.: Histone retention preserves epigenetic marks during heat stress-induced transcriptional memory in plants. The EMBO Journal 42, e113595 (2023)
19.
Journal Article
von Bismarck, T.; Wendering, P.; de Souza, L. P.; Ruß, J.; Strandberg, L.; Heyneke, E.; Walker, B. J.; Schöttler, M. A.; Fernie, A. R.; Nikoloski, Z. et al.; Armbruster, U.: Growth in fluctuating light buffers plants against photorespiratory perturbations. Nature Communications 14 (1), 7052 (2023)
20.
Journal Article
Ferreira, M. A. d. M.; Silveira, W. B. d.; Nikoloski, Z.: PARROT: Prediction of enzyme abundances using protein-constrained metabolic models. PLoS Computational Biology 19 (10), e1011549 (2023)
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