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 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.
We're incredibly grateful to receive an NIH Pioneer Award to define, at unprecedented resolution, how substance use disorders influence immune function and the response to HIV-1 and other pathogens by developing and applying innovative single-cell and bulk profiling and perturbation tools to inform the design of novel cure and prevention…
Our collaborative cell atlases of multiple organs at autopsy from COVID-19 donors - a joint work with many at the Broad Institute and the broader research community - is now available in Nature here, and its accompanying press release here.
Alex was recently features in Cell Systems' "Voices" piece on the future of understanding cell behavior and cellular communities. Read his opinion, and that of other leading voices in the field, here.