Publications

zDB: bacterial comparative genomics made easy
Marquis, B., Pillonel, T., Carrara, A., Bertelli, C. (2024).
https://doi.org/10.1128/msystems.00473-24
Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions
Causevic, S., Dubey, M., Morales, M., Salazar, G., Sentchilo, V., Carraro, N., Ruscheweyh, H.-J., Sunagawa, S., van der Meer, J. R. (2024).
https://doi.org/10.1038/s41467-024-46933-1
Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags
Daniel, B. B. J., Steiger, Y., Sintsova, A., Field, C. M., Nguyen, B. D., Schubert, C., Cherrak, Y., Sunagawa, S., Hardt, W.-D., Vorholt, J. A. (2024).
https://doi.org/10.1038/s41564-024-01634-9
mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations
Sintsova, A., Ruscheweyh, H.-J., Field, C. M., Feer, L., Nguyen, B., Daniel, B., Hardt, W.-D., Vorholt, J. A., Sunagawa, S. (2024).
https://doi.org/10.1093/bioinformatics/btae078
From microbiome composition to functional engineering, one step at a time
Burz, S. D., Causevic, S., Dal Co, A., Dmitrijeva, M., Vonaesch, P., Vorholt, J., et al. (2023).
https://doi.org/10.1128/mmbr.00063-23
The microbiota conditions a gut milieu that selects for wild-type Salmonella Typhimurium virulence
Gül, E., Hardt, W.-D., et al. (2023).
https://doi.org/10.1371/journal.pbio.3002253
Metabolic interaction models recapitulate leaf microbiota ecology
Schäfer, M., Pacheco, A., Künzler, R., Bortfeld-Miller, M., Field, C. M., Vayena, E., Hatzimanikatis, V., Vorholt, J. (2023).
https://doi.org/10.3929/ethz-b-000621167
Controlled motility in the cyanobacterium Trichodesmium regulates aggregate architecture
Pfreundt, U., Slomka, J., Schneider, G., Sengupta, A., Carrara, F., Fernandez, V., Ackermann, M., Stocker R. (2023).
DOI: 10.1126/science.adf2753
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
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