Single cell profiling of COVID-19 patients: an international data resource from multiple tissues
  • Chan Zuckerberg Initiative Single-Cell COVID-19 Consortia et al.,
  • medRxiv,
  • 2020
Biology
Cell Atlas
Genomics
Immunology
Infectious Disease
Carly Ziegler
Vincent Miao
Andrew Navia
Josh Bromley
José Ordovas-Montañes
Alex K. Shalek
Lymph nodes are innervated by a unique population of sensory neurons with immunomodulatory potential
  • Huang et al.,
  • Cell,
  • 2020
Biology
Genomics
Immunology
Carly Ziegler
Marko Vukovic
José Ordovas-Montañes
Alex K. Shalek
Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells
  • Pae et al.,
  • Journal of Experimental Medicine,
  • 2020
Biology
Genomics
Immunology
Sam Allon
José Ordovas-Montañes
Alex K. Shalek
The Human Cell Atlas and equity: lessons learned
  • Majumder et al.,
  • Nature Medicine,
  • 2020
Cell Atlas
Genomics
Alex K. Shalek
Single cell and spatial transcriptomics defines the cellular architecture of the antimicrobial response network in human leprosy granulomas
  • Ma et al.,
  • bioRxiv,
  • 2020
Biology
Cell Atlas
Genomics
Immunology
Infectious Disease
Travis Hughes
Marc Wadsworth II
Alex K. Shalek
Functional compensation precedes recovery of tissue mass following acute liver injury
  • Walesky et al.,
  • Nature Communications,
  • 2020
Biology
Genomics
Immunology
Kellie Kolb
Ira Fleming
Alex K. Shalek
Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells
  • Pae et al.,
  • bioRxiv,
  • 2020
Biology
Genomics
Immunology
Sam Allon
José Ordovas-Montañes
Alex K. Shalek
Inflammasomes within hyperactive murine dendritic cells stimulate long-lived T cell-mediated anti-tumor immunity
  • Zhivaki et al.,
  • Cell Reports,
  • 2020
Biology
Cancer
Genomics
Immunology
Medicine
Benjamin Doran
Ira Fleming
Alex K. Shalek
Evolution and diversity of immune responses during acute HIV infection
  • Kazer et al.,
  • Immunity,
  • 2020
Biology
Immunology
Infectious Disease
Medicine
Sam Kazer
Alex K. Shalek
Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu
  • Goods et al.,
  • biorXiv,
  • 2020
Biology
Genomics
Immunology
Medicine
Brittany Goods
Riley Drake
Ira Fleming
Alex K. Shalek
Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states
  • Song et al.,
  • bioRxiv,
  • 2020
Biology
Cancer
Genomics
Immunology
Marc Wadsworth II
Alex K. Shalek
Single-cell profiling of ebola virus disease in vivo reveals viral and host dynamics
  • Kotliar et al.,
  • Cell,
  • 2020
Biology
Cell Atlas
Genomics
Immunology
Infectious Disease
Travis Hughes
Marc Wadsworth II
Nancy Tran
Alex K. Shalek
Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte signatures of bacterial control
  • Gideon et al.,
  • bioRxiv,
  • 2020
Biology
Cell Atlas
Genomics
Immunology
Infectious Disease
Travis Hughes
Marc Wadsworth II
Conner Kummerlowe
Sarah Nyquist
José Ordovas-Montañes
Alex K. Shalek
Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies
  • Hughes et al.,
  • Immunity,
  • 2020
Biology
Cell Atlas
Chemistry
Genomics
Immunology
R&D
Technology
Travis Hughes
Marc Wadsworth II
José Ordovas-Montañes
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
Innate Lymphoid Cell Activation and Sustained Depletion in Blood and Tissue of Children Infected with HIV from Birth Despite Antiretroviral Therapy
  • Singh et al.,
  • Cell Reports,
  • 2020
Biology
Genomics
Immunology
Infectious Disease
Sam Kazer
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
Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn’s Disease
  • Mitsialis et al.,
  • Gastroenterology,
  • 2020
Biology
Genomics
Immunology
José Ordovas-Montañes
Marko Vukovic
Alex K. Shalek
Spatiotemporal single-cell profiling of gastrointestinal GVHD reveals invasive and resident memory T cell states
  • Tkachev et al.,
  • bioRxiv,
  • 2020
Biology
Genomics
Immunology
Jim Kaminski
José Ordovas-Montañes
Alex K. Shalek
Single-cell profiling of Ebola virus infection ​in vivo​ reveals viral and host transcriptional dynamics
  • Kotliar et al.,
  • bioRxiv,
  • 2020
Biology
Genomics
Immunology
Infectious Disease
Travis Hughes
Marc Wadsworth II
Nancy Tran
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,
  • 2020
Biology
Computational Methods
Genomics
Sarah Nyquist
Alex K. Shalek
High-throughput organoid screening enables engineering of intestinal epithelial composition
  • Mead et al.,
  • bioRxiv,
  • 2020
Biology
Genomics
Medicine
R&D
Technology
Ben Mead
Marko Vukovic
José Ordovas-Montañes
Alex K. Shalek
SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes
  • Sungnak et al.,
  • Nature Medicine,
  • 2020
Biology
Genomics
Immunology
Infectious Disease
José Ordovas-Montañes
Alex K. Shalek
SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues
  • Ziegler et al.,
  • Cell,
  • 2020
Biology
Cell Atlas
Genomics
Immunology
Infectious Disease
Statistics
Carly Ziegler
Sam Allon
Sarah Nyquist
Vincent Miao
Constantine Tzouanas
Marc Wadsworth II
Sam Kazer
Travis Hughes
Benjamin Doran
James Gatter
Marko Vukovic
Ben Mead
Shaina Carroll
Alex K. Shalek
José Ordovas-Montañes
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
Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults
  • Cao et al.,
  • bioRxiv,
  • 2020
Biology
Genomics
Immunology
Infectious Disease
Microbiology
José Ordovas-Montañes
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,
  • 2020
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
Spatially-resolved live cell tagging and isolation using protected photoactivatable cell dyes
  • Genshaft et al.,
  • bioRxiv,
  • 2020
Biology
Cancer
Chemistry
Genomics
R&D
Technology
Alex Genshaft
Carly Ziegler
Constantine Tzouanas
Ben Mead
Andrew Navia
Alex K. Shalek
Distribution and storage of inflammatory memory in barrier tissues
  • Ordovas-Montanes et al.,
  • Nature Reviews Immunology,
  • 2020
Biology
Genomics
Immunology
Infectious Disease
José Ordovas-Montañes
Alex K. Shalek
Immunological Fingerprints of Controllers Developing Neutralizing HIV-1 Antibodies
  • Martin-Gayo et al.,
  • Cell Reports,
  • 2020
Biology
Genomics
Immunology
Infectious Disease
Medicine
Kellie Kolb
Alex K. Shalek
Identification of a master regulator of differentiation in toxoplasma
  • Waldman et al.,
  • Cell,
  • 2020
Biology
Genomics
Immunology
Infectious Disease
Microbiology
Marc Wadsworth II
Alex K. Shalek
Prevention of tuberculosis in macaques after intravenous BCG immunization
  • Darrah et al.,
  • Nature,
  • 2020
Biology
Genomics
Immunology
Infectious Disease
Medicine
Marc Wadsworth II
Travis Hughes
Alex K. Shalek