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 J. et al.,
  • Nature,
  • 2018
Cell Atlas
José Ordovas-Montañes
Sarah Nyquist
Travis Hughes
Marc Wadsworth
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
Travis Hughes
Alex K. Shalek


Alex Shalek Featured in Nature Methods: “Voices in Methods Development”

Alex was recently featured in Nature Methods to discuss challenges and future opportunities in high-throughput genomics techniques. He joins researchers spanning across the spectrum of biology disciplines in laying out technological challenges of their respective fields and the great potential next-generation techniques hold in better understanding complex biological systems. Read…

Human Cell Atlas Launches in Latin America

Alex was recently in Sao Paulo to kick off work with the the Human Cell Atlas in Latin America. Alongside both Brazilian and international researchers, Alex introduced the scope and potential impact of the initiative, which seeks to create comprehensive reference maps of all human cells—the fundamental units of life—as a…

Kellie Kolb Graduates from the Shalek Lab!

Congratulations to Kellie Kolb, the first student from the Shalek Lab to receive her PhD! We wish Kellie the best of luck in her future endeavors, and we're excited for many more graduations in the coming years!