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, pp. 5255 - 5263 (2021)

Aarabi, F.; Rakpenthai, A.; Barahimipour, R.; Gorka, M.; Alseekh, S.; Zhang, Y.; Salem, M.A.; Brückner, F.; Omranian, N.; Watanabe, M. et al.; 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 (4), pp. 2419 - 2434 (2021)

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 (21), pp. 3848 - 3855 (2021)

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 (10), pp. 3398 - 3411 (2021)

Moreno, J.C.; Rojas, B.E.; Vicente, R.; Gorka, M.; Matz, T.; Kosmacz, M.; Peralta-Ariza, J.S.; Zhang, Y.; Alseekh, S.; Childs, D. et al.; 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 40 (15), e106800 (2021)

Razaghi-Moghadam, Z.; Nikoloski, Z.: GeneReg: a constraint-based approach for design of feasible metabolic engineering strategies at the gene level. Bioinformatics 37 (12), pp. 1717 - 1723 (2021)

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 (15), pp. 3262 - 3274 (2021)

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 (1), 458 (2021)

Beleggia, R.; Omranian, N.; Holtz, Y.; Gioia, T.; Fiorani, F.; Nigro, F.M.; Pecchioni, N.; De Vita, P.; Schurr, U.; David, J.L. et al.; 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 (9), 4790 (2021)

Küken, A.; Wendering, P.; Langary, D.; Nikoloski, Z.: A structural property for reduction of biochemical networks. Scientific Reports 11 (1), 17415 (2021)

Mbebi, A. J.; Tong, H.; Nikoloski, Z.: L2,1-norm regularized multivariate regression model with applications to genomic prediction. Bioinformatics 37 (18), pp. 2896 - 2904 (2021)

Omranian, N.; Angeleska, A.; Nikoloski, Z.: PC2P: parameter-free network-based prediction of protein complexes. Bioinformatics 37 (1), pp. 73 - 81 (2021)

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 (1), 4787 (2021)

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, pp. 2170 - 2178 (2021)

Seep, L.; Razaghi-Moghadam, Z.; Nikoloski, Z.: Reaction lumping in metabolic networks for application with thermodynamic metabolic flux analysis. Scientific Reports 11, 8544 (2021)

Tong, H.; Nikoloski, Z.: Machine learning approaches for crop improvement: Leveraging phenotypic and genotypic big data. Journal of Plant Physiology 257, 153354 (2021)

Nowak, J.; Gennermann, K.; Persson, S.; Nikoloski, Z.: CytoSeg 2.0: automated extraction of actin filaments. Bioinformatics 36 (9), pp. 2950 - 2951 (2020)

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)

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 (accepted)

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, 101051 (2020)