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.
Our Research
Featured Publications
We analyze multiple datasets spanning organ systems in human and non-human primate to identify putative target cells of SARS-CoV-2. We establish the entry receptor, ACE2, to be an interferon-stimulated gene in human, but not murine, airway cells.
We profile the longitudinal immune dynamics of untreated HIV-1 infection in multiple individuals from pre-infection through chronic infection. We develop a framework to characterize temporally-correlated gene programs in different cell types.
We develop Seq-Well, a portable and inexpensive platform for high-throughput single-cell RNA sequencing. We report robust transcriptional profiling on cell lines and primary human cells - and envision its use in dissecting complex clinical samples.
News
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
Pancreatic Cancer Study Now Out in Cell
Our study on pancreatic cancer with collaborators at MIT, the Broad Institute, and Dana-Farmer Cancer Institute is now out in Cell - read the publication here and about the study here.