Publications

Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations
Sahin, A., Weilandt, D. R., Hatzimanikatis, V. (2023).
https://doi.org/10.1038/s41467-023-38159-4
A MALDI-TOF MS library for rapid identification of human commensal gut bacteria from the class Clostridia
Asare, P. T., Lee, C.-H., Hürlimann, V., Teo, Y., Vonaesch, P., et al. (2023).
https://doi.org/10.3389/fmicb.2023.1104707
Spatial self-organization of metabolism in microbial systems: A matter of enzymes and chemicals
Dal Co, A., Ackermann, M., van Vliet, S. (2023).
https://doi.org/10.1016/j.cels.2022.12.009
Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota
Hoces, D., Greter, G., Arnoldini, M., Stäubli, M., Moresi, C., Sintsova, A., Slack, E., et al. (2023).
https://doi.org/10.7554/eLife.81212
Encounter rates prime interactions between microorganisms
Slomka, J., Alcolombri, U., Carrara, F., Foffi, R., Peaudecerf, F. J., Zbinden, M., Stocker, R. (2023).
https://doi.org/10.1098/rsfs.2022.0059
Chemotaxis and autoinducer-2 signalling mediate colonization and contribute to co-existence of Escherichia coli strains in the murine gut
Laganenka, L., Lee, J.-W., Malfertheiner, L., Dieterich, C. L., Fuchs, L., Piel, J., von Mering, C., Sourjik, V., Hardt, W.-D. (2023).
https://doi.org/10.1038/s41564-022-01286-7
Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models
Weilandt, D. R., Salvy, P., Masid, M., Fengos, G., Hatzimanikatis, V., et al. (2023).
https://doi.org/10.1093/bioinformatics/btac787
Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments
Ruscheweyh, H.-J., Milanese, A., Paoli, L., Karcher, N., Sunagawa, S., et al. (2022).
https://doi.org/10.1186/s40168-022-01410-z
A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions
Vayena, E., Chiappino-Pepe, A., MohammadiPeyhani, H., Francioli, Y., Hatzimanikatis, V., et al. (2022).
https://doi.org/10.1073/pnas.2211197119
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