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Our Research

The Shalek Lab develops and applies broadly applicable experimental and computational platforms to understand and engineer immune responses in tissues. We employ a comprehensive, five-step approach, building innovative methodologies and leveraging them with partners around the world to facilitate deeper, more mechanistic inquiry into how cells drive tissue-level behaviors across the spectrum of human health and disease.

Celebrating International Women's Day at Shalek Lab-lead training workshop in Accra, Ghana.

Celebrating International Women's Day at Shalek Lab-lead training workshop in Accra, Ghana.

Shalek Lab, 2021.

Shalek Lab, 2021.

The Shalek Lab aims to understand the beauty in each and every single cell.

The Shalek Lab aims to understand the beauty in each and every single cell.

The lab isn't afraid to embody their favorite animals in lab.

The lab isn't afraid to embody their favorite animals in lab.

Seq-Well, our new high-throughput single-cell RNA-sequencing technology.

Seq-Well, our new high-throughput single-cell RNA-sequencing technology.

Hexagons around the site describe who we are and what we like.

Hexagons around the site describe who we are and what we like.

We use single-cell transcriptomics to profile several tissues within a single organism.

We use single-cell transcriptomics to profile several tissues within a single organism.

Shalek Lab, December 2018.

Shalek Lab, December 2018.

Shalek Lab, December 2019.

Shalek Lab, December 2019.

Featured Publications

Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control
Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control
  • Gideon et al.,
  • Immunity,
  • 2022
Biology Biology
Cell Atlas Cell Atlas
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Microbiology Microbiology
Alex K. Shalek Alex K. Shalek
Conner Kummerlowe Conner Kummerlowe
Constantine Tzouanas Constantine Tzouanas
José Ordovas-Montañes José Ordovas-Montañes
Marc Wadsworth II Marc Wadsworth II
Samira Ibrahim Samira Ibrahim
Sarah Nyquist Sarah Nyquist
Travis Hughes Travis Hughes

We integrate PET and CT imaging, scRNA-seq, and measures of bacterial clearance on TB granulomas from cynomolgus macaques to identify cellular features and programs associated with bacterial control and persistence of granulomas.

Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer
Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer
  • Raghavan et al.,
  • Cell,
  • 2021
Cancer Cancer
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Medicine Medicine
R&D R&D
Technology Technology
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Jennyfer Galvez-Reyes Jennyfer Galvez-Reyes
Nolawit Mulugeta Nolawit Mulugeta
Peter Winter Peter Winter

We profile metastatic biopsies and matched organoids to show that cancer cell state influences, and can be manipulated to shape, therapeutic response in pancreatic ductal adenocarcinoma.

Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
  • Ziegler et al.,
  • Cell,
  • 2021
Biology Biology
Cell Atlas Cell Atlas
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Carly Ziegler Carly Ziegler
Josh Bromley Josh Bromley
José Ordovas-Montañes José Ordovas-Montañes
Micayla George Micayla George
Riley Drake Riley Drake
Vincent Miao Vincent Miao

We analyze the nasopharyngeal cellular landscape of individuals with COVID-19, identifying putative initial target cells of SARS-CoV-2. Further, we find a blunted epithelial anti-viral response is correlated with the development of severe disease.

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