Publications

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
Metabolic reconstitution of germ-free mice by a gnotobiotic microbiota varies over the circadian cycle
Hoces, D., Lan, J., Sun, W., Geiser, T., Stäubli, M., Barazzone, E., Arnoldini, M., Challa, T.D., Klug, M., Kellenberger, A., Nowok, S., Faccin, E., Macpherson, A.J., Stecher, B., Sunagawa, S., Zenobi, R., Hardt, W.-D., Wolfrum, C., Slack, E. (2022).
https://doi.org/10.1371/journal.pbio.3001743
Computational tools and resources for designing new pathways to small molecules
Sveshnikova, A., Mohammadi Peyhani, H., Hatzimanikatis, V. (2022).
https://doi.org/10.1016/j.copbio.2022.102722
ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds
Sveshnikova, A., Mohammadi Peyhani, H., Hatzimanikatis, V. (2022).
https://doi.org/10.1016/j.ymben.2022.03.013
Reproducible Propagation of Species-Rich Soil Bacterial Communities Suggests Robust Underlying Deterministic Principles of Community Formation
Causevic, S., Tackmann, J., Sentchilo, V., von Mering, C., van der Meer, J. R. (2022).
https://doi.org/10.1128/msystems.00160-22
Load more
THEMES
AUTHORS