Publikationen von Z. Nikoloski

Zeitschriftenartikel (163)

1.
Zeitschriftenartikel
Aarabi, F., Rakpenthai, A., Barahimipour, R., Gorka, M., Alseekh, S., Zhang, Y. J., Salem, M. A., Brückner, F., Omranian, N., Watanabe, M., Nikoloski, Z., Giavalisco, P., Tohge, T., Graf, A., Fernie, A. R. & Hoefgen, R. Sulfur Deficiency Induced genes affect seed protein accumulation and composition under sulfate deprivation. Plant Physiology (2021). doi:10.1093/plphys/kiab386
2.
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Xu, R., Razaghi-Moghadam, Z. & Nikoloski, Z. Maximization of non-idle enzymes improves the coverage of the estimated maximal in vivo enzyme catalytic rates in Escherichia coli. Bioinformatics (2021). doi:10.1093/bioinformatics/btab575
3.
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Moreno, J. C., Rojas, B. E., Vicente, R., Gorka, M., Matz, T., Kosmacz, M., Peralta-Ariza, J. S., Zhang, Y. J., Alseekh, S., Childs, D., Luzarowski, M., Nikoloski, Z., Zarivach, R., Walther, D., Hartman, M. D., Figueroa, C. M., Iglesias, A. A., Fernie, A. R. & Skirycz, A. Tyr-Asp inhibition of glyceraldehyde 3-phosphate dehydrogenase affects plant redox metabolism. EMBO Journal (2021). doi:10.15252/embj.2020106800
4.
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Eng, R. C., Schneider, R., Matz, T., Carter, R., Ehrhardt, D. W., Jönsson, H., Nikoloski, Z. & Sampathkumar, A. KATANIN and CLASP function at different spatial scales to mediate microtubule response to mechanical stress in Arabidopsis cotyledons. Current Biology 31, 3262–3274 (2021).
5.
Zeitschriftenartikel
Nowak, J., Eng, R. C., Matz, T., Waack, M., Persson, S., Sampathkumar, A. & Nikoloski, Z. A network-based framework for shape analysis enables accurate characterization of leaf epidermal cells. Nature Communications 12, (2021).
6.
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Beleggia, R., Omranian, N., Holtz, Y., Gioia, T., Fiorani, F., Nigro, F. M., Pecchioni, N., De Vita, P., Schurr, U., David, J. L., Nikoloski, Z. & Papa, R. Comparative analysis based on transcriptomics and metabolomics data reveal differences between emmer and durum wheat in response to nitrogen starvation. International Journal of Molecular Sciences 22, (2021).
7.
Zeitschriftenartikel
Duarte, G. T., Pandey, P. K., Vaid, N., Alseekh, S., Fernie, A. R., Nikoloski, Z. & Laitinen, R. Plasticity of rosette size in response to nitrogen availability is controlled by an RCC1-family protein. Plant, Cell and Environment (2021). doi:10.1111/pce.14146
8.
Zeitschriftenartikel
Küken, A., Wendering, P., Langary, D. & Nikoloski, Z. A structural property for reduction of biochemical networks. Scientific Reports 11, (2021).
9.
Zeitschriftenartikel
Mbebi, A. J., Tong, H. & Nikoloski, Z. L2,1-norm regularized multivariate regression model with applications to genomic prediction. Bioinformatics (2021). doi:10.1093/bioinformatics/btab212
10.
Zeitschriftenartikel
Omranian, N., Angeleska, A. & Nikoloski, Z. PC2P: parameter-free network-based prediction of protein complexes. Bioinformatics 37, 73–81 (2021).
11.
Zeitschriftenartikel
Pries, C., Razaghi-Moghadam, Z., Kopka, J. & Nikoloski, Z. Integration of relative metabolomics and transcriptomics time-course data in a metabolic model pinpoints effects of ribosome biogenesis defects on Arabidopsis thaliana metabolism. Scientific Reports 11, (2021).
12.
Zeitschriftenartikel
Razaghi-Moghadam, Z., Sokolowska, E., Sowa, M. A., Skirycz, A. & Nikoloski, Z. Combination of network and molecule structure accurately predicts competitive inhibitory interactions. Computational and Structural Biotechnology Journal 19, 2170–2178 (2021).
13.
Zeitschriftenartikel
Seep, L., Razaghi-Moghadam, Z. & Nikoloski, Z. Reaction lumping in metabolic networks for application with thermodynamic metabolic flux analysis. Scientific Reports 11, (2021).
14.
Zeitschriftenartikel
Tong, H., Küken, A., Razaghi-Moghadam, Z. & Nikoloski, Z. Characterization of effects of genetic variants via genome-scale metabolic modelling. Cellular and Molecular Life Sciences 78, 5123–5138 (2021).
15.
Zeitschriftenartikel
Tong, H. & Nikoloski, Z. Machine learning approaches for crop improvement: Leveraging phenotypic and genotypic big data. Journal of Plant Physiology 257, (2021).
16.
Zeitschriftenartikel
Razaghi-Moghadam, Z. & Nikoloski, Z. GeneReg: A constraint-based approach for design of feasible metabolic engineering strategies at the gene level. Bioinformatics (2020). doi:10.1093/bioinformatics/btaa996
17.
Zeitschriftenartikel
Nowak, J., Gennermann, K., Persson, S. & Nikoloski, Z. CytoSeg 2.0: automated extraction of actin filaments. Bioinformatics 36, 2950–2951 (2020).
18.
Zeitschriftenartikel
Clemente-Moreno, M. J., Omranian, N., Sáez, P. L., Figueroa, C. M., Del-Saz, N., Elso, M., Poblete, L., Orf, I., Cuadros-Inostroza, A., Cavieres, L. A., 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, 1376–1393 (2020).
19.
Zeitschriftenartikel
Correa, S. M., Alseekh, S., Atehortúa, L., Brotman, Y., Ríos-Estepa, R., Fernie, A. R. & Nikoloski, Z. Model-assisted identification of metabolic engineering strategies for Jatropha curcas lipid pathways. The Plant Journal 104, 76–95
20.
Zeitschriftenartikel
Correa, S. M., Fernie, A. R., Nikoloski, Z. & Brotman, Y. Towards model-driven characterization and manipulation of plant lipid metabolism. Progress in Lipid Research 80, (2020).
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