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Journal Article (143)

1. 1.
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   Nowak, J.; Gennermann, K.; Persson, S.; Nikoloski, Z.: CytoSeg 2.0: automated extraction of actin filaments. Bioinformatics 36 (9), pp. 2950 - 2951 (2020)
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   Clemente-Moreno, M.; Omranian, N.; Sáez, P.; Figueroa, C.; Del-Saz, N.; Elso, M.; Poblete, L.; Orf, I.; Cuadros-Inostroza, A.; Cavieres, L.A. et al.; Bravo, L.; Fernie, A. R.; Ribas-Carbó, M.; Flexas, J.; Nikoloski, Z.; Brotman, Y.; Gago, J.: Low temperature tolerance of the Antarctic species Deschampsia antarctica: a complex metabolic response associated with nutrient remobilization. Plant, Cell and Environment 43 (6), pp. 1376 - 1393 (2020)
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   Razaghi-Moghadam, Z.; Nikoloski, Z.: Supervised Learning of Gene Regulatory Networks. Current Protocols in Plant Biology 5 (2), e20106 (2020)
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   Robaina-Estévez, S.; Nikoloski, Z.: Flux-based hierarchical organization of Escherichia coli’s metabolic network. PLoS Computational Biology 16 (4), e1007832 (2020)
5. 5.
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   Tong, H.; Küken, A.; Nikoloski, Z.: Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth. Nature Communications 11 (1), 2410 (2020)
6. 6.
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   Angeleska, A.; Nikoloski, Z.: Coherent network partitions. Discrete applied mathematics 266, pp. 283 - 290 (2019)
7. 7.
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   Clemente-Moreno, J. M.; Omranian, N.; Sáez, P.; Figueroa, C. M.; Del-Saz, N.; Elso, M.; Poblete, L.; Orf, I.; Cuadros-Inostroza, A.; Cavieres, L. et al.; Bravo, L.; Fernie, A. R.; Ribas-Carbó, M.; Flexas, J.; Nikoloski, Z.; Brotman, Y.; Gago, J.: Cytochrome respiration pathway and sulphur metabolism sustain stress tolerance to low temperature in the Antarctic species Colobanthus quitensis. New Phytologist 225 (2), pp. 754 - 768 (2019)
8. 8.
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   Ferrari, C.; Proost, S.; Janowski, M.; Becker, J.; Nikoloski, Z.; Bhattacharya, D.; Price, D.; Tohge, T.; Bar-Even, A.; Fernie, A. R. et al.; Stitt, M.; Mutwil, M.: Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida. Nature Communications 10, 737 (2019)
9. 9.
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   Küken, A.; Eloundou-Mbebi, J. M. O.; Basler, G.; Nikoloski, Z.: Cellular determinants of metabolite concentration ranges. PLoS Computational Biology 15 (1), e1006687 (2019)
10. 10.
    MPG.PuRe

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    Küken, A.; Nikoloski, Z.: Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways. Plant Physiology 179 (3), pp. 894 - 906 (2019)
11. 11.
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    Laitinen, R.; Nikoloski, Z.: Genetic basis of plasticity in plants. Journal of Experimental Botany 70 (3), pp. 739 - 745 (2019)
12. 12.
    MPG.PuRe

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    Langary, D.; Nikoloski, Z.: Inference of chemical reaction networks based on concentration profiles using an optimization framework. Chaos: An Interdisciplinary Journal of Nonlinear Science 29 (11), 113121, p. 113121 (2019)
13. 13.
    MPG.PuRe

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    Nunes-Nesi, A.; Alseekh, S.; de Silva, O.; Magnum, F.; Omranian, N.; Lichtenstein, G.; Mirnezhad, M.; González, R. R. R.; Garcia, J. S. y.; Conte, M. et al.; Leiss, K. A.; Klinkhamer, P. G. L.; Nikoloski, Z.; Carrari, F.; Fernie, A. R.: Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds. Metabolomics 15 (4), 46 (2019)
14. 14.
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    Pandey, P. K.; Yu, J.; Omranian, N.; Alseekh, S.; Vaid, N.; Fernie, A. R.; Nikoloski, Z.; Laitinen, R.: Plasticity in metabolism underpins local responses to nitrogen in Arabidopsis thaliana populations. Plant Direct 3 (11), e00186 (2019)
15. 15.
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    Song, Y.; Li, G.; Nowak, J.; Zhang, X.; Xu, D.; Yang, X.; Huang, G.; Liang, W.; Yang, L.; Wang, C. et al.; Bulone, V.; Nikoloski, Z.; Hu, J.; Persson, S.; Zhang, D.: The Rice Actin-Binding Protein RMD Regulates Light-Dependent Shoot Gravitropism. Plant Physiology 181 (2), pp. 630 - 644 (2019)
16. 16.
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    Yu, Y.; Wu, S.; Nowak, J.; Wang, G.; Han, L.; Feng, Z.; Mendrinna, A.; Ma, Y.; Wang, H.; Zhang, X. et al.; Tian, J.; Dong, L.; Nikoloski, Z.; Persson, S.; Kong, Z.: Live-cell imaging of the cytoskeleton in elongating cotton fibres. Nature Plants 5 (5), pp. 498 - 504 (2019)
17. 17.
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    Janowski, M.; Zoschke, R.; Scharff, L. B.; Martinez-Jaime, S.; Ferrari, C.; Proost, S.; Ng Wei Xiong, J.; Omranian, N.; Musialak-Lange, M.; Nikoloski, Z. et al.; Graf, A.; Schöttler, M. A.; Sampathkumar, A.; Vaid, N.; Mutwil, M.: AtRsgA from Arabidopsis thaliana is important for maturation of the small subunit of the chloroplast ribosome. The Plant Journal 96 (2), pp. 404 - 420 (2018)
18. 18.
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    Basler, G.; Fernie, A. R.; Nikoloski, Z.: Advances in metabolic flux analysis toward genome-scale profiling of higher organisms. Bioscience Reports 38 (6), 6 (2018)
19. 19.
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    Cubillos, A.; Tong, H.; Alseekh, S.; de Abreu e Lima, F.; Yu, J.; Fernie, A. R.; Nikoloski, Z.; Laitinen, R.: Inheritance patterns in metabolism and growth in diallel crosses of Arabidopsis thaliana from a single growth habitat. Heredity 120, pp. 463 - 473 (2018)
20. 20.
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    de Abreu e Lima, F.; Li, K.; Wen, W.; Yan, J.; Nikoloski, Z.; Willmitzer, L.; Brotman, Y.: Unraveling lipid metabolism in maize with time-resolved multi-omics data. The Plant Journal 93 (6), pp. 1102 - 1115 (2018)