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.
Our improvements to the Seq-Well scRNA-seq platform were release today - read the publication in Immunity here and the press release here.
Alex, along with HCA Equity Working Group co-leaders Partha Majumder and Musa Mhlanga, details some of the lessons they've learned in their timing leading the initiative and their thoughts moving forward in this piece for Nature Medicine.
Congratulations to Alex for being awarded a Young Mentor Award from Harvard Medical School! Read more here.