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Infectious Disease and Microbiome Program, Infectious Disease and Microbiome

The carbapenem inoculum effect provides insights into the molecular mechanisms underlying carbapenem resistance in the Enterobacterales.

Cartagena AJ, Taylor KL, Lopez LC, et al. The carbapenem inoculum effect provides insights into the molecular mechanisms underlying carbapenem resistance in the Enterobacterales. mBio. 2025:e0154025. doi:10.1128/mbio.01540-25

Bead-based approaches for increased sensitivity and multiplexing of CRISPR diagnostics.

Siddiqui SM, Welch NL, Nguyen TG, et al. Bead-based approaches for increased sensitivity and multiplexing of CRISPR diagnostics. Nature biomedical engineering. 2025. doi:10.1038/s41551-025-01498-2

Circulating tumor human papillomavirus DNA whole genome sequencing enables human papillomavirus-associated oropharynx cancer early detection.

Das D, Hirayama S, Aye L, et al. Circulating tumor human papillomavirus DNA whole genome sequencing enables human papillomavirus-associated oropharynx cancer early detection. Journal of the National Cancer Institute. 2025. doi:10.1093/jnci/djaf249

A generative deep learning approach to de novo antibiotic design.

Krishnan A. A generative deep learning approach to de novo antibiotic design. Cell. 2025. doi:10.1016/j.cell.2025.07.033

Interplay of genetic predisposition, plasma metabolome and Mediterranean diet in dementia risk and cognitive function.

Liu Y, Gu X, Li Y, et al. Interplay of genetic predisposition, plasma metabolome and Mediterranean diet in dementia risk and cognitive function. Nature medicine. 2025. doi:10.1038/s41591-025-03891-5

Elucidating the role of Campylobacter concisus-derived indole metabolites in gut inflammation and immune modulation.

Park JD, Lee SR, Dhennezel C, et al. Elucidating the role of Campylobacter concisus-derived indole metabolites in gut inflammation and immune modulation. Proceedings of the National Academy of Sciences of the United States of America. 2025;122(34):e2514071122. doi:10.1073/pnas.2514071122

Targeted delivery of diverse biomolecules with engineered bacterial nanosyringes.

Kreitz J, Yang V, Friedrich MJ, Pham J, Macrae RK, Zhang F. Targeted delivery of diverse biomolecules with engineered bacterial nanosyringes. Nature biotechnology. 2025. doi:10.1038/s41587-025-02774-x

Marked heterogeneity in malaria infection rate in a Malian longitudinal cohort.

LaVerriere E, Johnson ZM, Shieh M, et al. Marked heterogeneity in malaria infection rate in a Malian longitudinal cohort. Nature communications. 2025;16(1):6512. doi:10.1038/s41467-025-61462-1

The carbapenem inoculum effect provides insight into the molecular mechanisms underlying carbapenem resistance in Enterobacterales.

Cartagena AJ, Taylor KL, Smith JT, et al. The carbapenem inoculum effect provides insight into the molecular mechanisms underlying carbapenem resistance in Enterobacterales. bioRxiv : the preprint server for biology. 2023. doi:10.1101/2023.05.23.541813

Type I interferons and microbial metabolites of tryptophan modulate astrocyte activity and central nervous system inflammation via the aryl hydrocarbon receptor.

Rothhammer V, Mascanfroni ID, Bunse L, et al. Type I interferons and microbial metabolites of tryptophan modulate astrocyte activity and central nervous system inflammation via the aryl hydrocarbon receptor. Nat Med. 2016;22(6):586-97. doi:10.1038/nm.4106