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.
Learn about how Omer Yilmaz, Associate Professor of Biology at MIT, and Alex combine their expertise to tackle the largest problems in colon cancer here.
Our study on upper respiratory tract epithelial responses to SARS-CoV-2 infection receding mild and severe COVID-19 is now out in Cell. Read more about the study here, here, or here.
Our recent work on neuroimmune interactions in lymph nodes, led by Carly Ziegler in our lab, was recently featured in Science.