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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.

Shalek Lab, September 2024

Shalek Lab, September 2024

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.

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

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

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.

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

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

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

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

Shalek Lab, December 2019.

Shalek Lab, December 2019.

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.

Shalek Lab, 2021.

Shalek Lab, 2021.

Shalek Lab, December 2018.

Shalek Lab, December 2018.

Featured Publications

Scalable, compressed phenotypic screeningusing pooled perturbations
Scalable, compressed phenotypic screeningusing pooled perturbations
  • Liu et al.,
  • Nature Biotechnology,
  • 2024
Biology Biology
Cancer Cancer
Immunology Immunology
Microbiology Microbiology
R&D R&D
Technology Technology
Alex K. Shalek Alex K. Shalek
Ben Mead Ben Mead
Conner Kummerlowe Conner Kummerlowe
Ivy Liu Ivy Liu
Manny Guzman Manny Guzman
Sarah Ingabire Sarah Ingabire
Sergio Triana Sergio Triana
Walaa Kattan Walaa Kattan

High-throughput phenotypic screens using biochemical perturbations and high-content readouts are constrained by limitations of scale. To address this, we establish a method of pooling exogenous perturbations followed by computational deconvolution to reduce required sample size, labor and cost. We demonstrate the increased efficiency of compressed experimental designs compared to conventional approaches through benchmarking with a bioactive small-molecule library and a high-content imaging readout.

CD4+ T cells re-wire granuloma cellularity and regulatory networks to promote immunomodulation following Mtb reinfection
CD4+ T cells re-wire granuloma cellularity and regulatory networks to promote immunomodulation following Mtb reinfection
  • Bromley et al.,
  • Immunity,
  • 2024
Computational Methods Computational Methods
Immunology Immunology
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
Josh Bromley Josh Bromley
Sarah Nyquist Sarah Nyquist

Th1 CD4+ T cells mediate protective antiMtb immunity across biological systems and organisms. Bromley, Ganchua, et al. demonstrate that CD4+ T cells regulate immune tone in TB granulomas and are necessary for immune recall and protection against reinfection. Following reinfection, CD4+ T cells facilitate the development of a growth restrictive niche via the induction of immuno-modulatory genes and cellular interaction networks.

An enhanced IL17 and muted type I interferon nasal epithelial cell state characterizes severe COVID-19 with fungal coinfection
An enhanced IL17 and muted type I interferon nasal epithelial cell state characterizes severe COVID-19 with fungal coinfection
  • Ziegler et al.,
  • American Society for Microbiology,
  • 2024
Computational Methods Computational Methods
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
Sam Kazer Sam Kazer
Vincent Miao Vincent Miao

Recent case reports and epidemiological data suggest that fungal infections represent an underappreciated complication among people with severe COVID-19. However, the frequency of fungal colonization in patients with COVID-19 and associations with specific immune responses in the airways remain incompletely defined.

NEWS

Collaborative work featured in MIT News

Sep 16, 2024

Learn more about this collaborative work featuring Alex Shalek and a discovery that yields a potent immune response, which could be used to develop a potential tumor vaccine.