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
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 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
Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets
  • Berger et al.,
  • Nature Communications,
  • 2020
Biology
Computational Methods
Statistics
Sarah Nyquist
Alex K. Shalek
The tumor microenvironment drives transcriptional phenotypes and their plasticity in metastatic pancreatic cancer
  • Raghavan et al.,
  • bioRxiv,
  • 2020
Biology
Cancer
Cell Atlas
Computational Methods
Genomics
Immunology
Medicine
Technology
Peter Winter
Andrew Navia
Jennyfer Galvez-Reyes
Nolawit Mulugeta
Alex K. Shalek
A Single Human VH-gene Allows for a Broad-Spectrum Antibody Response Targeting Bacterial Lipopolysaccharides in the Blood
  • Sangesland et al.,
  • Cell Reports,
  • 2020
Biology
Computational Methods
Genomics
Immunology
Infectious Disease
Sam Kazer
James Gatter
Alex K. Shalek
Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease
  • Bassler et al.,
  • bioRxiv,
  • 2020
Computational Methods
Genomics
Immunology
Medicine
Marc Wadsworth II
Travis Hughes
Alex K. Shalek
Computational Methods for Single-Cell RNA Sequencing
  • Hie et al.,
  • Annual Reviews,
Biology
Computational Methods
Genomics
Sarah Nyquist
Alex K. Shalek
Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells
  • Muus et al.,
  • bioRxiv,
  • 2020
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Infectious Disease
Statistics
Sam Allon
Sarah Nyquist
José Ordovas-Montañes
Marc Wadsworth II
Carly Ziegler
Alex K. Shalek
The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution
  • Rozenblatt-Rosen et al.,
  • Cell,
  • 2020
Biology
Cancer
Cell Atlas
Computational Methods
Genomics
Immunology
Medicine
Alex K. Shalek
Systematic comparison of single-cell and single-nucleus RNA-sequencing methods
  • Ding et al.,
  • Nature Biotechnology,
  • 2020
Computational Methods
Genomics
R&D
Technology
Travis Hughes
Marc Wadsworth II
Shaina Carroll
Alex K. Shalek
Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
  • Kazer et al.,
  • Nature Medicine,
  • 2020
Biology
Computational Methods
Genomics
Immunology
Infectious Disease
Statistics
Sam Kazer
Toby Aicher
Shaina Carroll
José Ordovas-Montañes
Vincent Miao
Carly Ziegler
Sarah Nyquist
Alex K. Shalek
SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is enriched in specific cell subsets across tissues
  • Ziegler et al.,
  • SSRN,
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Infectious Disease
Medicine
Carly Ziegler
Sam Allon
Sarah Nyquist
Vincent Miao
Marc Wadsworth II
Sam Kazer
Travis Hughes
Benjamin Doran
James Gatter
Marko Vukovic
Constantine Tzouanas
Shaina Carroll
Alex K. Shalek
José Ordovas-Montañes
Sensory neurons innervate peripheral lymph nodes and locally regulate gene expression in postsynaptic endothelium, stromal cells, and innate leukocytes
  • Huang et al.,
  • bioRxiv,
  • 2019
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Carly Ziegler
Marko Vukovic
José Ordovas-Montañes
Alex K. Shalek
Voices in methods development
  • Anikeeva et al.,
  • Nature Methods,
  • 2019
Computational Methods
Genomics
R&D
Technology
Alex K. Shalek
A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers
  • Martin-Gayo et al.,
  • Genome Biology,
  • 2018
Computational Methods
Genomics
Immunology
Infectious Disease
Medicine
Kellie Kolb
José Ordovas-Montañes
Alex K. Shalek
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
  • Macosko et al.,
  • Cell,
  • 2015
Genomics
R&D
Technology
Alex K. Shalek