The Shalek Lab develops and applies broadly applicable experimental and computational platforms to understand and engineer immune responses in tissues. We employ a comprehensive, five-step approach, building innovative methodologies and leveraging them with partners around the world to facilitate deeper, more mechanistic inquiry into how cells drive tissue-level behaviors across the spectrum of human health and disease.
Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control
We integrate PET and CT imaging, scRNA-seq, and measures of bacterial clearance on TB granulomas from cynomolgus macaques to identify cellular features and programs associated with bacterial control and persistence of granulomas.
We profile metastatic biopsies and matched organoids to show that cancer cell state influences, and can be manipulated to shape, therapeutic response in pancreatic ductal adenocarcinoma.
We analyze the nasopharyngeal cellular landscape of individuals with COVID-19, identifying putative initial target cells of SARS-CoV-2. Further, we find a blunted epithelial anti-viral response is correlated with the development of severe disease.
Alex Profiled in MIT News
Read Alex's new profile in MIT News here.
TB Granuloma Paper Reviewed in Immunity
Check out the preview of our recent paper on TB granulomas here.
Listen to Alex Shalek on the Bioinformatics CRO Podcast
Listen to Alex Shalek on the Bioinformatics CRO Podcast Hear Alex talk about the Shalek Lab's multi-disciplinary approach to answering some of science's toughest and complex questions. https://open.spotify.com/episode/1JLJZfhuEL7TvYvWYexpU4?si=58125b53291e4180&nd=1