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
SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues
Biology
Cell Atlas
Genomics
Immunology
Infectious Disease
Statistics
Carly Ziegler
Sam Allon
Sarah Nyquist
Vincent Miao
Constantine Tzouanas
Marc Wadsworth II
Sam Kazer
Travis Hughes
Benjamin Doran
James Gatter
Marko Vukovic
Ben Mead
Shaina Carroll
Alex K. Shalek
José Ordovas-MontañesWe 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.
Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
Biology
Computational MethodsGenomicsImmunologyInfectious DiseaseStatisticsSam Kazer
Toby AicherShaina CarrollJosé Ordovas-MontañesVincent MiaoCarly ZieglerSarah NyquistAlex K. Shalek
Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput
ChemistryGenomics
R&D
Technology
TravelMarc Wadsworth IITravis HughesAlex K. ShalekWe 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.
News
Pre-print on Severity-associated Epithelial Responses to SARS-CoV-2 Now on bioRxiv
Our pre-print detailing how different nasal epithelial and immune populations respond to SARS-CoV-2 infection across the spectrum of COVID-19 severity is now out on bioRxiv. This work was led by Carly Ziegler, Vincent Miao, Andrew Navia, and Josh Bromley in the Shalek lab. Read more here.
Insights into the Immune Response to Stroke in Science Immunology
Our findings detailing the longitudinal response of myeloid cells to stroke are now out in Science Immunology. Read more about the study, co-led by post-doc Britt Goods, here.
Seq-Well S^3 Released
Our improvements to the Seq-Well scRNA-seq platform were release today - read the publication in Immunity here and the press release here.