Our Research

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.

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Featured Publications

Allergic Inflammatory Memory in Human Respiratory Epithelial Progenitor Cells
  • Ordovas-Montanes et al.,
  • Nature,
  • 2018
Cell Atlas
José Ordovas-Montañes
Sarah Nyquist
Marko Vukovic
Marc Wadsworth II
Travis Hughes
Sam Kazer
Alex K. Shalek

We used single-cell RNA-seq to uncover basal cell reprogramming in allergic airway disease.

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
  • Gierahn et al.,
  • Nature Methods,
  • 2017
Marc Wadsworth II
Travis Hughes
Alex K. Shalek


Jay Prakadan Graduates from the Shalek Lab!

Congratulations to Jay Prakadan for successfully defending his thesis! We wish Jay the best of luck in his future endeavors, and we’re excited for all the upcoming defenses this year!

New Study on Increased TB Vaccine Efficacy Now Out

Our paper on increased tuberculosis (TB) vaccine efficacy with intravenous injection in nonhuman primates is now out in Nature. With collaborators at the National Institutes of Health's National Institute of Allergy and Infectious Diseases and others, we show greatly enhanced immune protection and outcome compared to traditional intradermal injection of…