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Effects of Varying Nitrogen Sources on Amino Acid Synthesis Costs in Arabidopsis thaliana under Different Light and Carbon-Source Conditions

Arnold, A., Sajitz-Hermstein, M., & Nikoloski, Z. (2015) · PLoS ONE · doi:10.1371/journal.pone.0116536 · Cited by 36 · see citing works

Evolution of aromatic amino acid metabolism in plants: a key driving force behind plant chemical diversity in aromatic natural products

Yokoyama, R. (2024) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2023.0352 · Cited by 35 · see citing works

Utilizing systems biology to unravel stomatal function and the hierarchies underpinning its control

Medeiros, D. B., Daloso, D. M., Fernie, A. R., Nikoloski, Z., & Araújo, W. L. (2015) · Plant Cell & Environment · doi:10.1111/pce.12517 · Cited by 35 · see citing works

Plant genome-scale reconstruction: from single cell to multi-tissue modelling and omics analyses

Gomes de Oliveira Dal’Molin, C., & Nielsen, L. K. (2018) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2017.07.009 · Cited by 35 · see citing works

Model-driven insights into the effects of temperature on metabolism

Wendering, P., & Nikoloski, Z. (2023) · Biotechnology Advances · doi:10.1016/j.biotechadv.2023.108203 · Cited by 33 · see citing works

Unveiling the complex molecular dynamics of arbuscular mycorrhizae: A comprehensive exploration and future perspectives in harnessing phosphate-solubilizing microorganisms for sustainable progress

Wahab, A. H., Batool, F., Muhammad, M., Zaman, W., Mikhlef, R. M., Qaddoori, S. M., Ullah, S., Abdi, G., & Saqib, S. (2023) · Environmental and Experimental Botany · doi:10.1016/j.envexpbot.2023.105633 · Cited by 32 · see citing works

Assessing Flux Distribution Associated with Metabolic Specialization of Glandular Trichomes

Zager, J. J., & Lange, B. M. (2018) · Trends in Plant Science · doi:10.1016/j.tplants.2018.04.003 · Cited by 32 · see citing works

Point mutations that boost aromatic amino acid production and CO 2 assimilation in plants

Yokoyama, R., de Oliveira, M. V. V., Takeda, Y., Ishihara, H., Alseekh, S., Arrivault, S., Kukshal, V., Jez, J. M., Stitt, M., Fernie, A. R., et al. (2022) · Science Advances · doi:10.1126/sciadv.abo3416 · Cited by 32 · see citing works

Cell‐type‐specific metabolism in plants

Daloso, D. M., Morais, E. G., Silva, K. F. O. E., & Williams, T. C. R. (2023) · The Plant Journal · doi:10.1111/tpj.16214 · Cited by 32 · see citing works

Dissecting the metabolic reprogramming of maize root under nitrogen-deficient stress conditions

Chowdhury, N. B., Schroeder, W. L., Sarkar, D., Amiour, N., Quilleré, I., Hirel, B. J., Maranas, C. D., & Saha, R. (2021) · Journal of Experimental Botany · doi:10.1093/jxb/erab435 · Cited by 31 · see citing works

Green pathways: Metabolic network analysis of plant systems

Dersch, L. M., Beckers, V., & Wittmann, C. (2015) · Metabolic Engineering · doi:10.1016/j.ymben.2015.12.001 · Cited by 30 · see citing works

iReMet-flux: constraint-based approach for integrating relative metabolite levels into a stoichiometric metabolic models

Sajitz-Hermstein, M., Töpfer, N., Kleeßen, S., Fernie, A. R., & Nikoloski, Z. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw465 · Cited by 30 · see citing works

Metabolomics for understanding stomatal movements

Medeiros, D. B., da Luz, L. M., de Oliveira, H. O., Araújo, W. L., Daloso, D. M., & Fernie, A. R. (2019) · Theoretical and Experimental Plant Physiology · doi:10.1007/s40626-019-00139-9 · Cited by 30 · see citing works

The dynamic response of the Arabidopsis root metabolome to auxin and ethylene is not predicted by changes in the transcriptome

Hildreth, S. B., Foley, E. E., Muday, G. K., Helm, R. F., & Winkel, A. (2020) · Scientific Reports · doi:10.1038/s41598-019-57161-9 · Cited by 30 · see citing works

Assessment of flux through oleoresin biosynthesis in epithelial cells of loblolly pine resin ducts

Turner, G. W., Parrish, A. N., Zager, J. J., Fischedick, J. T., & Lange, B. M. (2018) · Journal of Experimental Botany · doi:10.1093/jxb/ery338 · Cited by 30 · see citing works

Growth in fluctuating light buffers plants against photorespiratory perturbations

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. (2023) · Nature Communications · doi:10.1038/s41467-023-42648-x · Cited by 28 · see citing works

Antioxidant Green Factories: Toward Sustainable Production of Vitamin E in Plant In Vitro Cultures

Muthulakshmi, M., Srinivasan, A., & Srivastava, S. (2023) · ACS Omega · doi:10.1021/acsomega.2c05819 · Cited by 27 · see citing works

On the effects of alternative optima in context-specific metabolic model predictions

Robaina‐Estévez, S., & Nikoloski, Z. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005568 · Cited by 25 · see citing works

Insights into ABA-mediated regulation of guard cell primary metabolism revealed by systems biology approaches

Yoshida, T., dos Anjos, L., Medeiros, D. B., Araújo, W. L., Fernie, A. R., & Daloso, D. M. (2018) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2018.11.006 · Cited by 23 · see citing works

A hybrid kinetic and constraint‐based model of leaf metabolism allows predictions of metabolic fluxes in different environments

Shameer, S., Wang, Y., Bota, P., Ratcliffe, R. G., Long, S. P., & Sweetlove, L. J. (2021) · The Plant Journal · doi:10.1111/tpj.15551 · Cited by 23 · see citing works

Cancer Cell Metabolism as New Targets for Novel Designed Therapies

de Mas, I. M., Aguilar, E., Jayaraman, A., Polat, I. H., Martín-Bernabé, A., Bharat, R., Foguet, C., Milà, E., Papp, B., Centelles, J. J., et al. (2014) · Future Medicinal Chemistry · doi:10.4155/fmc.14.119 · Cited by 23 · see citing works

Photorespiratory Bypasses Lead to Increased Growth in Arabidopsis thaliana: Are Predictions Consistent with Experimental Evidence?

Basler, G., Küken, A., Fernie, A. R., & Nikoloski, Z. (2016) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2016.00031 · Cited by 23 · see citing works

Differential metabolic and coexpression networks of plant metabolism

Omranian, N., Kleeßen, S., Tohge, T., Klie, S., Basler, G., Mueller‐Roeber, B., Fernie, A. R., & Nikoloski, Z. (2015) · Trends in Plant Science · doi:10.1016/j.tplants.2015.02.002 · Cited by 23 · see citing works

Sink/Source Balance of Leaves Influences Amino Acid Pools and Their Associated Metabolic Fluxes in Winter Oilseed Rape (Brassica napus L.)

Dellero, Y., Heuillet, M., Marnet, N., Bellvert, F., Millard, P., & Bouchereau, A. (2020) · Metabolites · doi:10.3390/metabo10040150 · Cited by 22 · see citing works

A multi-organ metabolic model of tomato predicts plant responses to nutritional and genetic perturbations

Gerlin, L., Cottret, L., Escourrou, A., Genin, S., & Baroukh, C. (2021) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiab548 · Cited by 22 · see citing works

The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber

Cunha, E., Silva, M., Chaves, I., Demirci, H., Lagoa, D. R., Lima, D., Rocha, M., Rocha, I., & Dias, Ó. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011499 · Cited by 22 · see citing works

Characterization of maximal enzyme catalytic rates in central metabolism of Arabidopsis thaliana

Küken, A., Gennermann, K., & Nikoloski, Z. (2020) · The Plant Journal · doi:10.1111/tpj.14890 · Cited by 22 · see citing works

Review: The case for studying mitochondrial function during plant cryopreservation

Whelehan, L. M., Funnekotter, B., Bunn, E., & Mancera, R. L. (2021) · Plant Science · doi:10.1016/j.plantsci.2021.111134 · Cited by 21 · see citing works

A pathway for every product? Tools to discover and design plant metabolism

Jeffryes, J. G., Seaver, S. M. D., Faria, J. P., & Henry, C. S. (2018) · Plant Science · doi:10.1016/j.plantsci.2018.03.025 · Cited by 21 · see citing works

Mathematical models of plant metabolism

Shi, H., & Schwender, J. (2016) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2015.10.008 · Cited by 21 · see citing works

Metabolic Patterns in Spirodela polyrhiza Revealed by 15N Stable Isotope Labeling of Amino Acids in Photoautotrophic, Heterotrophic, and Mixotrophic Growth Conditions

Evans, E. M., Freund, D. M., Sondervan, V. M., Cohen, J. D., & Hegeman, A. D. (2018) · Frontiers in Chemistry · doi:10.3389/fchem.2018.00191 · Cited by 18 · see citing works

New insights in metabolism modelling to decipher plant–microbe interactions

Blonde, C., Caddeo, A., Nasser, W., Reverchon, S., Peyraud, R., & Haichar, F. E. Z. (2025) · New Phytologist · doi:10.1111/nph.70063 · Cited by 17 · see citing works

Environment-coupled models of leaf metabolism

Töpfer, N. (2021) · Biochemical Society Transactions · doi:10.1042/bst20200059 · Cited by 16 · see citing works

Characterization of effects of genetic variants via genome-scale metabolic modelling

Tong, H., Küken, A., Razaghi‐Moghadam, Z., & Nikoloski, Z. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03844-4 · Cited by 16 · see citing works

Metabolic modeling reveals distinct roles of sugars and carboxylic acids in stomatal opening as well as unexpected carbon fluxes

Sprent, N., Cheung, C. Y. M., Shameer, S., Ratcliffe, R. G., Sweetlove, L. J., & Töpfer, N. (2024) · The Plant Cell · doi:10.1093/plcell/koae252 · Cited by 15 · see citing works

Computational Prediction of Essential Metabolic Genes Using Constraint-Based Approaches

Basler, G. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-2398-4_12 · Cited by 15 · see citing works

ChloroKB, a cell metabolism reconstruction of the model plant Arabidopsis thaliana

Gloaguen, P., Vandenbrouck, Y., Joyard, J., & Curien, G. (2021) · Comptes Rendus Biologies · doi:10.5802/crbiol.49 · Cited by 15 · see citing works

A structural property for reduction of biochemical networks

Küken, A., Wendering, P., Langary, D., & Nikoloski, Z. (2021) · Scientific Reports · doi:10.1038/s41598-021-96835-1 · Cited by 15 · see citing works

Metabolic flux from the chloroplast provides signals controlling photosynthetic acclimation to cold in Arabidopsis thaliana

Herrmann, H. A., Dyson, B. C., Miller, M., Schwartz, J., & Johnson, G. N. (2020) · Plant Cell & Environment · doi:10.1111/pce.13896 · Cited by 14 · see citing works

Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism

Correa, S. M., Tong, H., Burgos, A., Zhu, F., Alseekh, S., Fernie, A. R., & Nikoloski, Z. (2023) · Nature Communications · doi:10.1038/s41467-023-40644-9 · Cited by 14 · see citing works

Metabolic modeling identifies determinants of thermal growth responses in Arabidopsis thaliana

Wendering, P., Andreou, G. M., Laitinen, R. A. E., & Nikoloski, Z. (2025) · New Phytologist · doi:10.1111/nph.20420 · Cited by 13 · see citing works

Simulation of heterosis in a genome-scale metabolic network provides mechanistic explanations for increased biomass production rates in hybrid plants

Vacher, M. A., & Small, I. (2019) · npj Systems Biology and Applications · doi:10.1038/s41540-019-0101-8 · Cited by 13 · see citing works

An automated workflow that generates atom mappings for large‐scale metabolic models and its application to Arabidopsis thaliana

Huß, S., Judd, R., Koper, K., Maeda, H. A., & Nikoloski, Z. (2022) · The Plant Journal · doi:10.1111/tpj.15903 · Cited by 12 · see citing works

Model‐assisted identification of metabolic engineering strategies for Jatropha curcas lipid pathways

Correa, S. M., Alseekh, S., Atehortúa, L., Brotman, Y., Ríos‐Estepa, R., Fernie, A. R., & Nikoloski, Z. (2020) · The Plant Journal · doi:10.1111/tpj.14906 · Cited by 12 · see citing works

How does metabolic rate in plant shoot tips change after cryopreservation?

Whelehan, L. M., Dalziell, E. L., Bunn, E., Mancera, R. L., & Funnekotter, B. (2022) · Cryobiology · doi:10.1016/j.cryobiol.2022.10.003 · Cited by 11 · see citing works

Integration of relative metabolomics and transcriptomics time-course data in a metabolic model pinpoints effects of ribosome biogenesis defects on Arabidopsis thaliana metabolism

Pries, C., Razaghi‐Moghadam, Z., Kopka, J., & Nikoloski, Z. (2021) · Scientific Reports · doi:10.1038/s41598-021-84114-y · Cited by 11 · see citing works

Shifts in carbon partitioning by photosynthetic activity increase terpenoid synthesis in glandular trichomes

Saadat, N. P., van Aalst, M., Brand, A., Ebenhöh, O., Tissier, A. F., & Matuszyńska, A. (2023) · The Plant Journal · doi:10.1111/tpj.16352 · Cited by 10 · see citing works

Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana

Tong, H., Laitinen, R. A. E., & Nikoloski, Z. (2023) · New Phytologist · doi:10.1111/nph.19154 · Cited by 10 · see citing works

Toward mechanistic modeling and rational engineering of plant respiration

Wendering, P., & Nikoloski, Z. (2023) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiad054 · Cited by 10 · see citing works

Accurate flux predictions using tissue-specific gene expression in plant metabolic modeling

Kaste, J. A. M., & Shachar‐Hill, Y. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad186 · Cited by 10 · see citing works

Scaling metabolic model reconstruction up to the pan-genome level: A systematic review and prospective applications to photosynthetic organisms

Arend, M., Paulitz, E., Hsieh, Y. E., & Nikoloski, Z. (2025) · Metabolic Engineering · doi:10.1016/j.ymben.2025.02.015 · Cited by 9 · see citing works

Plant cold acclimation and its impact on sensitivity of carbohydrate metabolism

Adler, S. O., Kitashova, A., Bulović, A., Nägele, T., & Klipp, E. (2025) · npj Systems Biology and Applications · doi:10.1038/s41540-025-00505-1 · Cited by 9 · see citing works

The hidden simplicity of metabolic networks is revealed by multireaction dependencies

Küken, A., Langary, D., & Nikoloski, Z. (2022) · Science Advances · doi:10.1126/sciadv.abl6962 · Cited by 9 · see citing works

TCA Cycle and Its Relationship with Clavulanic Acid Production: A Further Interpretation by Using a Reduced Genome-Scale Metabolic Model of Streptomyces clavuligerus

Ramírez-Malule, H., López-Agudelo, V. A., Gómez-Ríos, D., Ochoa, S., Ríos‐Estepa, R., Junne, S. G., & Neubauer, P. B. (2021) · Bioengineering · doi:10.3390/bioengineering8080103 · Cited by 9 · see citing works

Selection on genome‐wide gene expression plasticity of rice in wet and dry field environments

Hamann, E., Groen, S. C., Dunivant, T. S., Ćalić, I., Cochran, C., Konshok, R., Purugganan, M. D., & Franks, S. J. (2024) · Molecular Ecology · doi:10.1111/mec.17522 · Cited by 8 · see citing works

Fitness costs and benefits of gene expression plasticity in rice under droughtPreprint

Groen, S. C., Hamann, E., Ćalić, I., Cochran, C., Konshok, R., Purugganan, M. D., & Franks, S. J. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.16.435597 · Cited by 8 · see citing works

Response of lignin and flavonoid metabolic pathways in Capsicum annuum to drought and waterlogging stresses

Lv, X., Huangqiao, X. I. A. O., Jie, H., Ma, Y., Zhao, L. O. N. G., He, P., Xing, H., & Jie, Y. (2024) · Notulae Botanicae Horti Agrobotanici Cluj-Napoca · doi:10.15835/nbha52213819 · Cited by 7 · see citing works

Resource allocation modeling for autonomous prediction of plant cell phenotypes

Goelzer, A., Rajjou, L., Chardon, G., Loudet, O., & Fromion, V. (2024) · Metabolic Engineering · doi:10.1016/j.ymben.2024.03.009 · Cited by 7 · see citing works

Cytosolic fumarase acts as a metabolic fail-safe for both high and low temperature acclimation of Arabidopsis thaliana

Herrmann, H. A., Calzadilla, P. I., Schwartz, J., & Johnson, G. N. (2021) · Journal of Experimental Botany · doi:10.1093/jxb/erab560 · Cited by 7 · see citing works

Systematic comparison of local approaches for isotopically nonstationary metabolic flux analysis

Huß, S., & Nikoloski, Z. (2023) · Frontiers in Plant Science · doi:10.3389/fpls.2023.1178239 · Cited by 7 · see citing works

Identification of flux trade-offs in metabolic networks

Hashemi, S., Razaghi‐Moghadam, Z., & Nikoloski, Z. (2021) · Scientific Reports · doi:10.1038/s41598-021-03224-9 · Cited by 6 · see citing works

Relative flux trade-offs and optimization of metabolic network functionalities

Hashemi, S., Razaghi‐Moghadam, Z., Laitinen, R. A. E., & Nikoloski, Z. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.07.038 · Cited by 6 · see citing works

The activity of RubisCO and energy demands for its biosynthesis. Comparative studies with CO2-reductases

Ślesak, I., & Ślesak, H. (2020) · Journal of Plant Physiology · doi:10.1016/j.jplph.2020.153337 · Cited by 5 · see citing works

The unraveling of balanced complexes in metabolic networks

Langary, D., Küken, A., & Nikoloski, Z. (2023) · Scientific Reports · doi:10.1038/s41598-023-32666-6 · Cited by 5 · see citing works

Predictive Algal Systems Biology: Integrating Omics, Genome-Scale Metabolic Models, and Machine Learning

Tec-Campos, D., Kumar, M., Parra, N., Bracamonte, A., Castillo-Sanchez, A., Pae, J., Zúñiga, C., & Zengler, K. (2026) · Bioengineering · doi:10.3390/bioengineering13060633 · Cited by 4 · see citing works

A Double Edge‐Sword in Antarctica: In Situ Passive Warming Exacerbates Drought and Heat Stress Differentially in the Native Vascular Species

Gago, J., Carriquí, M., Ayuso, M., Nunes‐Nesi, A., Figueroa, C. M., Fernie, A. R., Clemente‐Moreno, M. J., Gulías, J., Flexas, J., Cavieres, L. A., et al. (2025) · Physiologia Plantarum · doi:10.1111/ppl.70399 · Cited by 4 · see citing works

A Genome-Scale Metabolic Model of Arabidopsis and Some of Its Properties

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Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity

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Genome-scale reconstruction and constraint-based modelling of Arabidopsis thaliana energy metabolism

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BIOT 273-Genome-scale metabolic network model of Arabidopsis

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Genome Scale Metabolic Modelling of Arabidopsis thaliana and Chlamydomonas reinhardtii

Adhikari, K. (2022) · Radar (Oxford Brookes University) · doi:10.24384/3jd0-x523