Publications

zDB: bacterial comparative genomics made easy
Marquis, B., Pillonel, T., Carrara, A., Bertelli, C. (2024).
https://doi.org/10.1128/msystems.00473-24
Environmental and geographical factors influencing the spread of SARS-CoV-2 over 2 years: a fine-scale spatiotemporal analysis
De Ridder, D., Ladoy, A., Choi, Y., Jacot, D., Vuilleumier, S., Guessous, I., Joost, S., Greub, G. (2024).
https://doi.org/10.3389/fpubh.2024.1298177
Commensal E. coli limits Salmonella gut invasion during inflammation by producing toxin-bound siderophores in a tonB-dependent manner
Cherrak, Y., Salazar, M. A., Yilmaz, K., Kreuzer, M., Hardt, W.-D. (2024).
https://doi.org/10.1371/journal.pbio.3002616
Ectopic colonization by oral bacteria as an emerging theme in health and disease
Hernandez-Cabanyero, C., Vonaesch, P. (2024).
https://doi.org/10.1093/femsre/fuae012
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
An engineered bacterial symbiont allows noninvasive biosensing of the honey bee gut environment
Chhun, A., Moriano-Gutierrez, S., Zoppi, F., Cabirol, A., Engel, P., Schaerli, Y. (2024).
https://doi.org/10.1371/journal.pbio.3002523
Microfluidic approaches in microbial ecology
Ugolini, G. S., Wang, M., Secchi, E., Pioli, R., Ackermann, M., Stocker, R. (2024).
https://doi.org/10.1039/D3LC00784G
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
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