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Code Repositories

Here you will find links to the code repositories for some of the publications by researchers at Simpson Querrey Lung Institute for Translational Science (SQLIFTS).

General

Successful Clinical Response In Pneumonia Therapy (SCRIPT)

Division of Pulmonary and Critical Care

Specific Publications

Grant RA, Morales-Nebreda L, Markov NS, et al. Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia. Nature. 2021; 590(7847):635-641.

Stoeger T, et al. Aging is associated with a systemic length-associated transcriptome imbalance. Nature Aging. 2022; 2(12):1191-1206.

Gao CA, Markov NS, Stoeger T, et al. Machine learning links unresolving secondary pneumonia to mortality in patients with severe pneumonia, including COVID-19. Journal of Clinical Investigation. 2203; 133(12):e170682.

Grant RA, Poor TA, et al. Prolonged exposure to lung-derived cytokines is associated with activation of microglia in patients with COVID-19. JCI Insight2024; 9(8):e178859.

Bailey JI, Puritz CH, Senkow KJ, et al. Profibrotic monocyte-derived alveolar macrophages are expanded in patients with persistent respiratory symptoms and radiographic abnormalities after COVID-19. Nature Immunology2024. doi: 10.1038/s41590-024-01975-x. Online ahead of print.

Markov NS, et al. Distinctive evolution of alveolar T cell responses is associated with clinical outcomes in unvaccinated patients with SARS-CoV-2 pneumonia. Nature Immunology2024; 25(9):1607-1622.

Fenske SW, Peltekian A, et al. Developing and validating a machine learning model to predict successful next-day extubation in the ICU (preprint). 

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