Publications of Z. Nikoloski

Pratx, L.; Wendering, P.; Kappel, C.; Nikoloski, Z.; Bäurle, I.: Histone retention preserves epigenetic marks during heat stress-induced transcriptional memory in plants. The EMBO Journal 42, e113595 (2023)

von Bismarck, T.; Wendering, P.; de Souza, L. P.; Ruß, J.; Strandberg, L.; Heyneke, E.; Walker, B. J.; Schöttler, M. A.; Fernie, A. R.; Nikoloski, Z. et al.; Armbruster, U.: Growth in fluctuating light buffers plants against photorespiratory perturbations. Nature Communications 14 (1), 7052 (2023)

Ferreira, M. A. d. M.; Silveira, W. B. d.; Nikoloski, Z.: PARROT: Prediction of enzyme abundances using protein-constrained metabolic models. PLoS Computational Biology 19 (10), e1011549 (2023)

Tong, H.; Laitinen, R.A.E.; Nikoloski, Z.: Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana. New Phytologist 240 (1), pp. 426 - 438 (2023)

Bezold, F.; Scheffer, J.; Wendering, P.; Razaghi-Moghadam, Z.; Trauth, J.; Pook, B.; Nußhär, H.; Hasenjäger, S.; Nikoloski, Z.; Essen, L.-O. et al.; Taxis, C.: Optogenetic control of Cdc48 for dynamic metabolic engineering in yeast. Metabolic Engineering 79, pp. 97 - 107 (2023)

Hashemi, S.; Razaghi-Moghadam, Z.; Nikoloski, Z.: Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony. PLoS Computational Biology 19 (9), e1011489 (2023)

Langary, D.; Küken, A.; Nikoloski, Z.: The effective deficiency of biochemical networks. Scientific Reports 13, 14589 (2023)

Arend, M.; Zimmer, D.; Xu, R.; Sommer, F.; Mühlhaus, T.; Nikoloski, Z.: Proteomics and constraint-based modelling reveal enzyme kinetic properties of Chlamydomonas reinhardtii on a genome scale. Nature Communications 14 (1), 4781 (2023)

Correa Cordoba, S.; Tong, H.; Burgos, A.; Zhu, F.; Alseekh, S.; Fernie, A. R.; Nikoloski, Z.: Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism. Nature Communications 14 (1), 4897 (2023)

Mbebi, A. J.; Nikoloski, Z.: Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection. PLoS Computational Biology 19 (7), e1010832 (2023)

Hashemi, S.; Laitinen, R.; Nikoloski, Z.: Models and molecular mechanisms for trade-offs in the context of metabolism. Molecular Ecology 33 (10), e16879 (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)

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)

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)