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


Sahu A, Blätke M-A, Szymanski JJ, Töpfer N (2021) Advances in Flux Balance Analysis by Integrating Machine Learning and Mechanism-based Models. Computational and Structural Biotechnology Journal,

Töpfer N (2021) Environment-coupled models of leaf metabolism. Biochemical Society Transactions,


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, Seaver SMD, Aharoni A (2018) Integration of Plant Metabolomics Data with Metabolic Networks: Progresses and Challenges,


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,


Töpfer N, Kleessen S, Nikoloski Z (2015) Integration of metabolomics data into metabolic networks. Frontiers in plant science,


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 Comput Biol,


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,

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