Research in the Shalek Lab is directed towards the creation and implementation of new technologies to understand how cells collectively perform systems-level functions in healthy and diseased states. We employ a comprehensive, five-step approach , developing innovative methodologies and applying them across multiple systems to empower more mechanistic inquiry and a deeper understanding of the rules that govern ensemble cellular behaviors.
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.
Read Alex's new profile in MIT News here.
Check out the preview of our recent paper on TB granulomas here.
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