Journal articles

Anglada-Girotto, M., Handschin, G., Ortmayr, K., Campos, A.I., Gillet, L., Manfredi, P., Mulholland, C.V., Berney, M., Jenal, U., Picotti, P., and Zampieri, M. Combining CRISPRi and metabolomics for functional annotation of compound libraries. Nature Chemical Biology 2022 https://identifiers.org//doi:10.1038/s41589-022-00970-3

de Bakker, V., Liu, X., Bravo, A.M., and Veening, J.W. CRISPRi-seq for genome-wide fitness quantification in bacteria. Nature Protocols 2022 Vol. 17 Issue 2 https://identifiers.org//doi:10.1038/s41596-021-00639-6




Journal articles

Maffei, E., Shaidullina, A., Burkolter, M., Heyer, Y., Estermann, F., Druelle, V., Sauer, P., Willi, L., Michaelis, S., Hilbi, H., Thaler, D. S., and Harms, A. Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection. PLoS Biology 2021 Vol. 19 Issue 1. https://identifiers.org/doi:10.1371/journal.pbio.3001424

Díaz-Pascual, F., Lempp, M., Nosho, K., Jeckel, H., Jo, J.K., Neuhaus, K., Hartmann, R., Jelli, E., Hansen, M.F., Price-Whelan, A., Dietrich, L.E. P., Link, H., and Drescher, K. Spatial alanine metabolism determines local growth dynamics of Escherichia coli colonies. Elife 2021 Vol. 10. https://identifiers.org//doi:10.7554/eLife.70794

Ude, J., Tripathi, V., Buyck, J.M., Soderholm, S., Cunrath, O., Fanous, J., Claudi, B., Egli, A., Schleberger, C., Hiller, S., and Bumann, D. Outer membrane permeability: Antimicrobials and diverse nutrients bypass porins in Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences of the United States of America 2021 Vol. 118 Issue 31. https://identifiers.org//doi:10.1073/pnas.2107644118

Sharma, K., Thacker, V.V., Dhar, N., Clapes Cabrer, M., Dubois, A., Signorino-Gelo, F., Mullenders, J., Knott, G.W., Clevers, H., and McKinney, J.D. Early invasion of the bladder wall by solitary bacteria protects UPEC from antibiotics and neutrophil swarms in an organoid model. Cell Reports 2021 Vol. 36 Issue 3. https://identifiers.org/doi:10.1016/j.celrep.2021.109351

Sharma, K., Dhar, N., Thacker, V.V., Simonet, T.M., Signorino-Gelo, F., Knott, G.W., and McKinney, J.D. Dynamic persistence of UPEC intracellular bacterial communities in a human bladder-chip model of urinary tract infection. Elife 2021 Vol. 10. https://identifiers.org/doi:10.7554/eLife.66481

Fuentes, D.A.F., Manfredi, P., Jenal, U., and Zampieri, M. Pareto optimality between growth-rate and lag-time couples metabolic noise to phenotypic heterogeneity in Escherichia coli. Nature Communications 2021 Vol. 12 Issue 1. https://identifiers.org//doi:10.1038/s41467-021-23522-0

Kaur, H., Jakob, R. P., Marzinek, J. K., Green, R., Imai, Y., Bolla, J. R., Agustoni, E., Robinson, C. V., Bond, P. J., Lewis, K., Maier, T., and Hiller, S. The antibiotic darobactin mimics a beta-strand to inhibit outer membrane insertase. Nature 2021 Vol. 593 Issue 7857. https://identifiers.org//doi:10.1038/s41586-021-03455-w

Santi, I., Manfredi, P., Maffei, E., Egli, A., and Jenal, U. Evolution of Antibiotic Tolerance Shapes Resistance Development in Chronic Pseudomonas aeruginosa Infections. mBio 2021 Vol. 12 Issue 1. https://identifiers.org//doi:10.1128/mBio.03482-20

Liu, X., Kimmey, J.M., Matarazzo, L., de Bakker, V., Van Maele, L., Sirard, J.C., Nizet, V., and Veening, J.W. Exploration of Bacterial Bottlenecks and Streptococcus pneumoniae Pathogenesis by CRISPRi-Seq. Cell Host Microbe 2021 Vol. 29 Issue 1. https://identifiers.org//doi:10.1016/j.chom.2020.10.001


Book chapters

Maffei, E., Fino, C., and Harms, A. Antibiotic Tolerance and Persistence Studied Throughout Bacterial Growth Phases. Methods in Molecular Biology 2021 Vol. 2357. https://identifiers.org//doi:10.1007/978-1-0716-1621-5_2