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
Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
Biology
Computational Methods
Genomics
Immunology
Infectious Disease
Statistics
Sam Kazer
Toby Aicher
Shaina Carroll
José Ordovas-Montañes
Vincent Miao
Carly Ziegler
Sarah Nyquist
Alex K. ShalekWe 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.
Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput
ChemistryGenomics
R&D
Technology
Travel
Marc Wadsworth II
Travis HughesAlex K. ShalekNews
New Study on Immune Dynamics in Untreated HIV-1 Infection Now Out
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.
Pre-print Detailing ACE2 as an Interferon-Stimulated Gene Now Available
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.
COVID-19 scRNA-seq Resource Datasets Released
In light of the spread of SARS-CoV-2, we are sharing multiple unpublished and published scRNA-seq datasets across both health and disease that harbor cells expressing ACE2 (the gene encoding the host receptor) and TMPRSS2 (the gene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…