Publications of Z. Nikoloski

Langary, D.; Küken, A.; Nikoloski, Z.: The unraveling of balanced complexes in metabolic networks. Scientific Reports 13 (1), 5712 (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 (1), 986 (2023)

Campana, P.; Nikoloski, Z.: Self- and cross-attention accurately predicts metabolite–protein interactions. NAR: genomics and bioinformatics 5 (1), lqad008 (2023)

Wendering, P.; Arend, M.; Razaghi-Moghadam, Z.; Nikoloski, Z.: Data integration across conditions improves turnover number estimates and metabolic predictions. Nature Communications 14, 1485 (2023)

Águila Ruiz-Sola, M.; Flori, S.; Yuan, Y.; Villain, G.; Sanz-Luque, E.; Redekop, P.; Tokutsu, R.; Küken, A.; Tsichla, A.; Kepesidis, G. et al.; Allorent, G.; Arend, M.; Iacono, F.; Finazzi, G.; Hippler, M.; Nikoloski, Z.; Minagawa, J.; Grossman, A. R.; Petroutsos, D.: Light-independent regulation of algal photoprotection by CO2 availability. Nature Communications 14, 1977 (2023)

Andreou, G.M.; Messer, M.; Tong, H.; Nikoloski, Z.; Laitinen, R. A.E.: Heritability of temperature-mediated flower size plasticity in Arabidopsis thaliana. Quantitative Plant Biology 4, e4 (2023)

Hashemi, S.; Laitinen, R.; Nikoloski, Z.: Models and molecular mechanisms for trade-offs in the context of metabolism. Molecular Ecology (2023)

Omranian, N.; Nikoloski, Z.: CUBCO+: prediction of protein complexes based on min-cut network partitioning into biclique spanned subgraphs. Applied Network Science 7, 71 (2022)

Wiszniewski, A.A.G.; Uberegui, E.; Messer, M.; Sultanova, G.; Borghi, M.; Duarte, G. T.; Vicente, R.; Sageman-Furnas, K.; Fernie, A. R.; Nikoloski, Z. et al.; Laitinen, R. A.E.: Temperature-mediated flower size plasticity in Arabidopsis. iScience 25 (11), 105411 (2022)

Laitinen, R. A. E.; Nikoloski, Z.: Strategies to identify and dissect trade-offs in plants. Molecular Ecology (2022)

Orf, I.; Tenenboim, H.; Omranian, N.; Nikoloski, Z.; Fernie, A. R.; Lisec, J.; Brotman, Y.; Bromke, M.A.: Transcriptomic and Metabolomic Analysis of a Pseudomonas-Resistant versus a Susceptible Arabidopsis Accession. International Journal of Molecular Sciences 23 (20), 12087 (2022)

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 (5), pp. 1486 - 1500 (2022)

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 (9), jkac170 (2022)

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 (16), dev201024 (2022)

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, pp. 3963 - 3971 (2022)

Liu, Z.; Østerlund, I.; Ruhnow, F.; Cao, Y.; Huang, G.; Cai, W.; Zhang, J.; Liang, W.; Nikoloski, Z.; Persson, S. et al.; Zhang, D.: Fluorescent cytoskeletal markers reveal associations between the actin and microtubule cytoskeleton in rice cells. Development 149 (12), dev.200415 (2022)

Küken, A.; Langary, D.; Nikoloski, Z.: The hidden simplicity of metabolic networks is revealed by multireaction dependencies. Science Advances 8 (13), eabl6962 (2022)

Tong, H.; Nankar, A.N.; Liu, J.; Todorova, V.; Ganeva, D.; Grozeva, S.; Tringovska, I.; Pasev, G.; Radeva-Ivanova, V.; Gechev, T. et al.; Kostova, D.; Nikoloski, Z.: Genomic prediction of morphometric and colorimetric traits in Solanaceous fruits. Horticulture Research 9, uhac072 (2022)

Wendering, P.; Nikoloski, Z.: COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions. PLoS Computational Biology 18 (3), e1009906 (2022)

Wendering, P.; Nikoloski, Z.: Genome-Scale Modeling Specifies the Metabolic Capabilities of Rhizophagus irregularis. mSystems 7 (1), e01216-21 (2022)