Publications

2023

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, https://doi.org/10.1007/978-3-031-43559-1_31

Camborda S, Weder J-N, Töpfer N (2022) CobraMod: A pathway-centric curation tool for constraint-based metabolic models. Bioinformatics, https://doi.org/10.1093/bioinformatics/btac119

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, https://doi.org/10.1016/j.csbj.2021.08.004
Töpfer N (2021) Environment-coupled models of leaf metabolism. Biochemical Society Transactions, https://doi.org/10.1042/BST20200059

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, https://doi.org/10.1105/tpc.20.00132

Töpfer N, Seaver SMD, Aharoni A (2018) Integration of Plant Metabolomics Data with Metabolic Networks: Progresses and Challenges. Plant Metabolomics, https://doi.org/10.1007/978-1-4939-7819-9_21

Töpfer N, Fuchs LM, Aharoni A (2017) The PhytoClust tool for metabolic gene clusters discovery in plant genomes. Nucleic Acids Research, https://doi.org/10.1093/nar/gkx404
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, https://doi.org/10.1111/tpj.13490

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, https://doi.org/10.1093/bioinformatics/btw465

Töpfer N, Kleessen S, Nikoloski Z (2015) Integration of metabolomics data into metabolic networks. Frontiers in plant science, https://doi.org/10.3389/fpls.2015.00049

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, https://doi.org/10.1074/jbc.M114.555144
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, https://doi.org/10.1371/journal.pcbi.1003656

Töpfer N, Niokoloski Z (2013) Large-scale modeling provides insights into Arabidopsis's acclimation to changing light and temperature conditions. Plant Signaling & Behavior, https://doi.org/10.4161/psb.25480
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, https://doi.org/10.1105/tpc.112.108852

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, https://doi.org/10.1186/1752-0509-6-148