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, (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. & Armbruster, U. Growth in fluctuating light buffers plants against photorespiratory perturbations. Nature Communications 14, (2023).

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

Tong, H., Laitinen, R. A. E. & Nikoloski, Z. Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana. New Phytologist 240, 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. & Taxis, C. Optogenetic control of Cdc48 for dynamic metabolic engineering in yeast. Metabolic Engineering 79, 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, (2023).

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

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

Hashemi, S., Laitinen, R. & Nikoloski, Z. Models and molecular mechanisms for trade-offs in the context of metabolism. Molecular Ecology 33, (2023).

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

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

Águila Ruiz-Sola, M., Flori, S., Yuan, Y., Villain, G., Sanz-Luque, E., Redekop, P., Tokutsu, R., Küken, A., Tsichla, A., Kepesidis, G., 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, (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, (2023).

Omranian, N. & Nikoloski, Z. CUBCO+: prediction of protein complexes based on min-cut network partitioning into biclique spanned subgraphs. Applied Network Science 7, (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. & Laitinen, R. A. E. Temperature-mediated flower size plasticity in Arabidopsis. iScience 25, (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, (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, 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, (2022).