WP6 Archives

Publications

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

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