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

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

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.

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.

Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer
  • Raghavan et al.,
  • Cell,
  • 2021
Cancer
Computational Methods
Genomics
Immunology
Medicine
R&D
Technology
Peter Winter
Andrew Navia
Jennyfer Galvez-Reyes
Nolawit Mulugeta
Alex K. Shalek
Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
  • Ziegler et al.,
  • Cell,
  • 2021
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Infectious Disease
Carly Ziegler
Vincent Miao
Andrew Navia
Josh Bromley
Micayla George
Riley Drake
Alex K. Shalek
José Ordovas-Montañes

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.

News

Listen to Alex Shalek on the Bioinformatics CRO Podcast

Listen to Alex Shalek on the Bioinformatics CRO Podcast Hear Alex talk about the Shalek Lab's multi-disciplinary approach to answering some of science's toughest and complex questions. https://open.spotify.com/episode/1JLJZfhuEL7TvYvWYexpU4?si=58125b53291e4180&nd=1