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 II
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


Paired Single-cell Transcriptome-TCR Methods in Nature Immunology

Our recent paper details a strategy, co-developed with the Love Lab at MIT, for pairing TCR sequencing with whole-transcriptome profiling in single-cells via 3'-barcoded techniques. Using a targeted pulldown and amplification method, we are able to sequence TCR CDR3 regions from pre-existing scRNA-seq libraries, increasing the amount of orthogonal information…

New Paper on Neuroimmune Interactions on BioRxiv

We’re stoked to have this paper up! We present our work finding new roles for sensory neurons within inflammatory responses and previously unappreciated axes of neuro-immune crosstalk. Led by Shalek lab MD-PhD student Carly Ziegler and post doc Tracy Huang with Uli von Andrian, we find that lymph nodes are…

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…