Publications of Z. Nikoloski

Journal Article (179)

1.
Journal Article
Huß, S., Judd, R. S., Koper, K., Maeda, H. A. & Nikoloski, Z. An automated workflow that generates atom mappings for large scale metabolic models and its application to Arabidopsis thaliana. The Plant Journal 111, 1486–1500 (2022).
2.
Journal Article
Mbebi, A. J., Breitler, J.-C., Bordeaux, M., Sulpice, R., McHale, M., Tong, H., Toniutti, L., Castillo, J. A., Bertrand, B. & Nikoloski, Z. A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids. G3: Genes, Genomes, Genetics 12, (2022).
3.
Journal Article
Matz, T., Wang, Y., Kulshreshtha, R., Sampathkumar, A. & Nikoloski, Z. Topological properties accurately predict cell division events and organization of shoot apical meristem in Arabidopsis thaliana. Development 149, (2022).
4.
Journal Article
Hashemi, S., Razaghi-Moghadam, Z., Laitinen, R. A. E. & Nikoloski, Z. Relative flux trade-offs and optimization of metabolic network functionalities. Computational and Structural Biotechnology Journal 20, 3963–3971 (2022).
5.
Journal Article
Liu, Z., Østerlund, I., Ruhnow, F., Cao, Y., Huang, G., Cai, W., Zhang, J., Liang, W., Nikoloski, Z., Persson, S. & Zhang, D. Fluorescent cytoskeletal markers reveal associations between the actin and microtubule cytoskeleton in rice cells. Development 149, (2022).
6.
Journal Article
Küken, A., Langary, D. & Nikoloski, Z. The hidden simplicity of metabolic networks is revealed by multireaction dependencies. Science Advances 8, (2022).
7.
Journal Article
Tong, H., Nankar, A. N., Liu, J., Todorova, V., Ganeva, D., Grozeva, S., Tringovska, I., Pasev, G., Radeva-Ivanova, V., Gechev, T., Kostova, D. & Nikoloski, Z. Genomic prediction of morphometric and colorimetric traits in Solanaceous fruits. Horticulture Research 9, (2022).
8.
Journal Article
Wendering, P. & Nikoloski, Z. COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions. PLoS Computational Biology 18, (2022).
9.
Journal Article
Wendering, P. & Nikoloski, Z. Genome-Scale Modeling Specifies the Metabolic Capabilities of Rhizophagus irregularis. mSystems 7, (2022).
10.
Journal Article
Calderan-Rodrigues, M. J., Luzarowski, M., Monte Bello, C. C., Minen, R. I., Zühlke, B. M., Nikoloski, Z., Skirycz, A. & Caldana, C. Proteogenic Dipeptides Are Characterized by Diel Fluctuations and Target of Rapamycin Complex-Signaling Dependency in the Model Plant Arabidopsis thaliana. Frontiers in Plant Science 12, (2021).
11.
Journal Article
Treves, H., Küken, A., Arrivault, S., Ishihara, H., Hoppe, I., Erban, A., Höhne, M., Moraes, T. A., Kopka, J., Szymanski, J., Nikoloski, Z. & Stitt, M. Carbon flux through photosynthesis and central carbon metabolism show distinct patterns between algae, C-3 and C-4 plants. Nature Plants 8, 78–91 (2021).
12.
Journal Article
David, Z., Swart, C., Graf, A., Arrivault, S., Tillich, M., Proost, S., Nikoloski, Z., Stitt, M., Bock, R., Mühlhaus, M. & Boulouis, A. Topology of the redox network during induction of photosynthesis as revealed by time-resolved proteomics in tobacco. Science Advances 7, (2021).
13.
Journal Article
Hashemi, S., Razaghi-Moghadam, Z. & Nikoloski, Z. Identification of flux trade-offs in metabolic networks. Scientific Reports 11, (2021).
14.
Journal Article
Angeleska, A., Omranian, N. & Nikoloski, Z. Coherent network partitions: Characterizations with cographs and prime graphs. Theoretical computer science 894, 3–11 (2021).
15.
Journal Article
Zhu, F., Alseekh, S., Koper, K., Tong, H., Nikoloski, Z., Naake, T., Liu, H., Yan, J., Brotman, Y., Wen, W., Maeda, H., Cheng, Y. & Fernie, A. R. Genome-wide association of the metabolic shifts underpinning dark-induced senescence in Arabidopsis. The Plant Cell 34, 557–578 (2021).
16.
Journal Article
Omranian, N., Angeleska, A. & Nikoloski, Z. Efficient and accurate identification of protein complexes from protein-protein interaction networks based on the clustering coefficient. Computational and Structural Biotechnology Journal 19, 5255–5263 (2021).
17.
Journal Article
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 187, 2419–2434 (2021).
18.
Journal Article
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 37, 3848–3855 (2021).
19.
Journal Article
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 44, 3398–3411 (2021).
20.
Journal Article
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
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