Identification of immune correlates of fatal outcomes in critically ill COVID-19 patients
  • Youngs et al.,
  • PLOS Pathogens,
  • 2021
Biology
Genomics
Immunology
Infectious Disease
Vincent Miao
Alex K. Shalek
HIV infection drives interferon signaling within intestinal SARS-CoV-2 target cells
  • Fardoos et al.,
  • JCI Insight,
  • 2021
Genomics
Immunology
Infectious Disease
Sarah Nyquist
Alex K. Shalek
Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes
  • Genshaft et al.,
  • Nature Communications,
  • 2021
Genomics
R&D
Technology
Alex Genshaft
Carly Ziegler
Constantine Tzouanas
Ben Mead
Andrew Navia
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
Expression of Foxp3 by T follicular helper cells in end-stage germinal centers
  • Jacobsen et al.,
  • Science,
  • 2021
Biology
Genomics
Immunology
Sam Allon
Alex K. Shalek
The cellular architecture of the antimicrobial response network in human leprosy granulomas
  • Ma et al.,
  • Nature Immunology,
  • 2021
Biology
Genomics
Immunology
Infectious Disease
Microbiology
Travis Hughes
Marc Wadsworth II
Alex K. Shalek
Single-cell immunophenotyping of the skin lesion erythema migrans identifies IgM memory B cells
  • Jiang et al.,
  • JCI Insight,
  • 2021
Biology
Genomics
Immunology
Infectious Disease
Ira Fleming
Alex K. Shalek
High-fat diet-activated fatty acid oxidation mediates intestinal stemness and tumorigenicity
  • Mana et al.,
  • Cell Reports,
  • 2021
Biology
Genomics
Constantine Tzouanas
Alex K. Shalek
Targeting Treg cells with GITR activation alleviates resistance to immunotherapy in murine glioblastomas
  • Amoozgar et al.,
  • Nature Communications,
  • 2021
Cancer
Genomics
Immunology
Medicine
Sam Kazer
Alex K. Shalek
COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
  • Delorey et al.,
  • Nature,
  • 2021
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Infectious Disease
Statistics
Carly Ziegler
Alex K. Shalek
Single-cell profiling of environmental enteropathy reveals signatures of epithelial remodeling and immune activation in severe disease
  • Kummerlowe et al.,
  • bioRxiv,
  • 2021
Biology
Genomics
Immunology
Infectious Disease
Conner Kummerlowe
Travis Hughes
Nolawit Mulugeta
Ira Fleming
Marko Vukovic
Benjamin Doran
José Ordovas-Montañes
Alex K. Shalek
MR1-Restricted MAIT Cells From The Human Lung Mucosal Surface Have Distinct Phenotypic, Functional, and Transcriptomic Features That Are Preserved in HIV Infection
  • Khuzwayo et al.,
  • Frontiers in Immunology,
  • 2021
Biology
Genomics
Immunology
Infectious Disease
Microbiology
Jay Prakadan
Sam Kazer
Alex K. Shalek
Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation
  • Dwyer et al.,
  • Science Immunology,
  • 2021
Biology
Genomics
Immunology
José Ordovas-Montañes
Sam Allon
Marko Vukovic
Travis Hughes
Sarah Nyquist
Alex K. Shalek
Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu
  • Goods et al.,
  • JCI Insight,
  • 2021
Biology
Genomics
Immunology
Medicine
Brittany Goods
Riley Drake
Ira Fleming
Alex K. Shalek
How are methodological developments enabling insights into cell behavior in cellular communities?
  • Piddini et al.,
  • Cell Systems,
  • 2021
Biology
Genomics
Immunology
Alex K. Shalek
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
  • Muus et al.,
  • Nature Medicine,
  • 2021
Cell Atlas
Computational Methods
Genomics
Immunology
Infectious Disease
Statistics
Sam Allon
Sarah Nyquist
Marc Wadsworth II
Carly Ziegler
Alex K. Shalek
A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2
  • Delorey et al.,
  • bioRxiv,
  • 2021
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Infectious Disease
Statistics
Carly Ziegler
Alex K. Shalek
Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
  • Ziegler et al.,
  • bioRxiv,
  • 2021
Biology
Genomics
Immunology
Infectious Disease
Microbiology
Carly Ziegler
Vincent Miao
Andrew Navia
Josh Bromley
Micayla George
Riley Drake
Alex K. Shalek
José Ordovas-Montañes
Longitudinal transcriptomics define the stages of myeloid activation in the living human brain after intracerebral hemorrhage
  • Askenase et al.,
  • Science Immunology,
  • 2021
Biology
Genomics
Immunology
Medicine
Brittany Goods
Shaina Carroll
Riley Drake
James Gatter
Alex K. Shalek
Spatiotemporal single-cell profiling reveals that invasive and tissue-resident memory donor CD8+ T cells drive gastrointestinal acute graft-versus-host disease
  • Tkachev et al.,
  • Science Translational Medicine,
  • 2021
Biology
Cell Atlas
Genomics
Immunology
Medicine
Jim Kaminski
José Ordovas-Montañes
Alex K. Shalek