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 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.
Seq-Well is a portable and inexpensive platform for high-throughput single-cell RNA sequencing. We report robust single-cell transcriptional profiling on cell lines and primary human cells.
Our study of untreated HIV-1 infection is now out in Nature Medicine! We profile longitudinal peripheral blood samples from pre-infection through chronic infection to characterize gene programs that are temporally-correlated in and between cell types. Read the press release here.
Our pre-print work detailing ACE2 upregulation in response to interferons, and type I interferons in particular, is now available here. Descriptions of the datasets analyzed in the study are found here on our COVID-19 Resource page, along with links to the data themselves.
In light of the spread of SARS-CoV-2, we are sharing multiple unpublished and published scRNA-seq datasets across both health and disease that harbor cells expressing ACE2 (the gene encoding the host receptor) and TMPRSS2 (the gene involved in processing the viral spike protein). We are sharing these resources for SARS-CoV-2…