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  • Angermann C, Heinemann B, Hansen J, Töpfer N, Braun H-P, Hildebrandt TM (2024) Proteome remodeling and amino acid metabolism during germination and seedling establishment in Lupinus albus. Journal of Experimental Botany,


  • Branco-Vieira M, Caetano N-S, Lima A-R-J, Töpfer N (2023) Towards Multiscale Modeling to Predict Diatom Metabolites Production for Biofuels and High-Value Compounds. Environmental Science and Engineering,




  • Töpfer N, Braam T, Shameer S, Ratcliffe RG, Sweetlove LJ (2020) Alternative Crassulacean Acid Metabolism Modes Provide Environment-Specific Water-Saving Benefits in a Leaf Metabolic Model. The Plant Cell,



  • Töpfer N, Fuchs LM, Aharoni A (2017) The PhytoClust tool for metabolic gene clusters discovery in plant genomes. Nucleic Acids Research,
  • Szymanski JJ, Levin Y, Savidor A, Breitel D, Chappell-Maor L, Heinig U, Töpfer N, Aharoni A (2017) Label-free deep shotgun proteomics reveals protein dynamics during tomato fruit tissues development. The Plant Journal,


  • Sajitz-Hermstein M, Töpfer N, Kleessen S, Fernie AR, Nikoloski Z (2016) iReMet-flux: constraint-based approach for integrating relative metabolite levels into a stoichiometric metabolic models. Bioinformatics,



  • Recht L, Töpfer N, Batushansky A, Sikron N, Gibon Y, Fait A, Nikoloski Z, Boussiba S, Zarka A (2014) Metabolite Profiling and Integrative Modeling Reveal Metabolic Constraints for Carbon Partitioning under Nitrogen Starvation in the Green Algae Haematococcus pluvialis. Journal of Biological Chemistry,
  • Töpfer N, Scossa F, Fernie AR, Nikoloski Z (2014) Variability of metabolite levels is linked to differential metabolic pathways in Arabidopsis's responses to abiotic stresses. PLoS Computational Biology,


  • Töpfer N, Niokoloski Z (2013) Large-scale modeling provides insights into Arabidopsis's acclimation to changing light and temperature conditions. Plant Signaling & Behavior,
  • Töpfer N, Caldana C, Grimbs S, Willmitzer L, Fernie AR, Nikoloski Z (2013) Integration of genome-scale modeling and transcript profiling reveals metabolic pathways underlying light and temperature acclimation in Arabidopsis. The Plant Cell,


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