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Center for Data and Simulation Science

Nadine Töpfer’s research aims to gain a better understanding of the behaviour of plant metabolic systems and their interactions. Her group uses computational approaches that are centered around the analysis of large-scale metabolic networks and works closely with experimental labs. Key topics include developing flux-balance methods to study plant metabolism at the cell type-, tissue- and whole-plant level as well as plant-environment interactions. Nadine Töpfer develops multi-scale models to better account for genetic, physical, and environmental influences on plant metabolism. On the technical side, the group develops open-source software packages for coherent and reproducible metabolic network curation. The gained knowledge will guide metabolic engineering strategies for improved crop plant productivity and quality.

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Research topics of Nadine Töpfer. Nadine Töpfer uses computational modelling to study plant metabolic networks from the cellular to the ecosystem level.

Selected publications

  1. S. Camborda, J.-N. Weder, N. Töpfer. CobraMod: A pathway-centric curation tool for constraint-based metabolic models. Bioinformatics, btac119 , 2022

  2. N. Töpfer. Environment-coupled models of leaf metabolism. Biochemical Society Transactions, 49 (1), 119-129, 2021

  3. N. Töpfer, T. Braam, S. Shameer, R. G. Ratcliffe, L. J. Sweetlove. Alternative Crassulacean Acid Metabolism modes provide environment-specific water-saving benefits in a leaf metabolic model. The Plant Cell, 32 (12), 3689-3705, 2020

  4. N. Töpfer, L.-M. Fuchs, A. Aharoni. The PhytoClust tool for metabolic gene clusters discovery in plant genomes. Nucleic Acid Research, 45 (12), 7049-7063, 2017

  5. J. Szymanski, Y. Levin, L. Maor-Chapell, U. Heinig, N. Töpfer, A. Aharoni. Label-free deep shotgun proteomics reveals protein dynamics during tomato fruit tissues development. The Plant Journal, 90 (2), 396-417, 2017

  6. M. Sajitz-Hermstein, N. Töpfer, S. Kleessen, A. R. Fernie, Z. Nikoloski. iReMet-flux: constraint-based approach for integrating relative metabolite levels into stoichiometric metabolic models. Bioinformatics, 32 (17), i755-i762, 2016

  7. L. Recht*, N. Töpfer*, A. Batushansky, N. Sikron, A. Zarka, Y. Gibon, Z. Nikoloski, A. Fait, S. Boussiba. Metabolite profiling and integrative modeling reveal metabolic constraints for carbon partitioning under nitrogen-starvation in the green alga Haematococcus pluvialis. Journal of Biological Chemistry, 289 (44), 30387-3040, 2014

  8. N. Töpfer, F. Scossa, A. R. Fernie, Z. Nikoloski. Variability of metabolite levels is linked to differential metabolic pathways in Arabidopsis's responses to abiotic stresses. PLoS Computational Biology, 10 (6), e1003656, 2014

  9. N. Töpfer, C. Caldana, S. Grimbs, L. Willmitzer, A. R. Fernie, Z. Nikoloski. Integration of genome-scale modeling and transcript profiling reveals metabolic pathways underlying light and temperature acclimation in Arabidopsis. The Plant Cell, 25 (4) 1197-1211, 2013

  10. N. Töpfer, S. Józefczuk, Z. Nikoloski. Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli. BMC Systems Biology 6 (1), 1-10, 2012

* authors contributed equally