Publications of Zoran Nikoloski
Journal Article (195)
1.
Journal Article
81 (1), 117 (2024)
The genome of Haberlea rhodopensis provides insights into the mechanisms for tolerance to multiple extreme environments. Cellular and Molecular Life Sciences 2.
Journal Article
82, pp. 216 - 224 (2024)
Prediction and integration of metabolite-protein interactions with genome-scale metabolic models. Metabolic Engineering 3.
Journal Article
14 (1), 2687 (2023)
Widening the landscape of transcriptional regulation of green algal photoprotection. Nature Communications 4.
Journal Article
13 (1), 5712 (2023)
The unraveling of balanced complexes in metabolic networks. Scientific Reports 5.
Journal Article
14 (1), 986 (2023)
Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses. Nature Communications 6.
Journal Article
14, 1140829 (2023)
A simulation-free constrained regression approach for flux estimation in isotopically nonstationary metabolic flux analysis with applications in microalgae. Frontiers in Plant Science 7.
Journal Article
80, pp. 184 - 192 (2023)
Accurate prediction of in vivo protein abundances by coupling constraint-based modelling and machine learning. Metabolic Engineering 8.
Journal Article
42, e113595 (2023)
Histone retention preserves epigenetic marks during heat stress-induced transcriptional memory in plants. The EMBO Journal 9.
Journal Article
14 (1), 7052 (2023)
Growth in fluctuating light buffers plants against photorespiratory perturbations. Nature Communications 10.
Journal Article
19 (10), e1011549 (2023)
PARROT: Prediction of enzyme abundances using protein-constrained metabolic models. PLoS Computational Biology 11.
Journal Article
240 (1), pp. 426 - 438 (2023)
Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana. New Phytologist 12.
Journal Article
79, pp. 97 - 107 (2023)
Optogenetic control of Cdc48 for dynamic metabolic engineering in yeast. Metabolic Engineering 13.
Journal Article
19 (9), e1011489 (2023)
Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony. PLoS Computational Biology 14.
Journal Article
13, 14589 (2023)
The effective deficiency of biochemical networks. Scientific Reports 15.
Journal Article
14 (1), 4781 (2023)
Proteomics and constraint-based modelling reveal enzyme kinetic properties of Chlamydomonas reinhardtii on a genome scale. Nature Communications 16.
Journal Article
14 (1), 4897 (2023)
Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism. Nature Communications 17.
Journal Article
19 (7), e1010832 (2023)
Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection. PLoS Computational Biology 18.
Journal Article
5 (1), lqad008 (2023)
Self- and cross-attention accurately predicts metabolite–protein interactions. NAR: genomics and bioinformatics 19.
Journal Article
14, 1485 (2023)
Data integration across conditions improves turnover number estimates and metabolic predictions. Nature Communications 20.
Journal Article
Models and molecular mechanisms for trade-offs in the context of metabolism. Molecular Ecology (2023)
21.
Journal Article
14, 1977 (2023)
Light-independent regulation of algal photoprotection by CO2 availability. Nature Communications 22.
Journal Article
4, e4 (2023)
Heritability of temperature-mediated flower size plasticity in Arabidopsis thaliana. Quantitative Plant Biology 23.
Journal Article
7, 71 (2022)
CUBCO+: prediction of protein complexes based on min-cut network partitioning into biclique spanned subgraphs. Applied Network Science 24.
Journal Article
25 (11), 105411 (2022)
Temperature-mediated flower size plasticity in Arabidopsis. iScience 25.
Journal Article
Strategies to identify and dissect trade-offs in plants. Molecular Ecology (2022)
26.
Journal Article
23 (20), 12087 (2022)
Transcriptomic and Metabolomic Analysis of a Pseudomonas-Resistant versus a Susceptible Arabidopsis Accession. International Journal of Molecular Sciences 27.
Journal Article
111 (5), pp. 1486 - 1500 (2022)
An automated workflow that generates atom mappings for large-scale metabolic models and its application to Arabidopsis thaliana. The Plant Journal 28.
Journal Article
12 (9), jkac170 (2022)
A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids. G3: Genes, Genomes, Genetics 29.
Journal Article
149 (16), dev201024 (2022)
Topological properties accurately predict cell division events and organization of shoot apical meristem in Arabidopsis thaliana. Development 30.
Journal Article
20, pp. 3963 - 3971 (2022)
Relative flux trade-offs and optimization of metabolic network functionalities. Computational and Structural Biotechnology Journal 31.
Journal Article
149 (12), dev.200415 (2022)
Fluorescent cytoskeletal markers reveal associations between the actin and microtubule cytoskeleton in rice cells. Development 32.
Journal Article
8 (13), eabl6962 (2022)
The hidden simplicity of metabolic networks is revealed by multireaction dependencies. Science Advances 33.
Journal Article
9, uhac072 (2022)
Genomic prediction of morphometric and colorimetric traits in Solanaceous fruits. Horticulture Research