Single cell profiling of COVID-19 patients: an international data resource from multiple tissues
Single cell profiling of COVID-19 patients: an international data resource from multiple tissues
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  • medRxiv,
  • 2020
Biology Biology
Cell Atlas Cell Atlas
Genomics Genomics
Immunology Immunology
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
Vincent Miao Vincent Miao
Lymph nodes are innervated by a unique population of sensory neurons with immunomodulatory potential
Lymph nodes are innervated by a unique population of sensory neurons with immunomodulatory potential
  • Huang et al.,
  • Cell,
  • 2020
Biology Biology
Genomics Genomics
Immunology Immunology
Alex K. Shalek Alex K. Shalek
Carly Ziegler Carly Ziegler
José Ordovas-Montañes José Ordovas-Montañes
Marko Vukovic Marko Vukovic
Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells
Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells
  • Pae et al.,
  • Journal of Experimental Medicine,
  • 2020
Biology Biology
Genomics Genomics
Immunology Immunology
Alex K. Shalek Alex K. Shalek
José Ordovas-Montañes José Ordovas-Montañes
Sam Allon Sam Allon
The Human Cell Atlas and equity: lessons learned
The Human Cell Atlas and equity: lessons learned
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  • Nature Medicine,
  • 2020
Cell Atlas Cell Atlas
Genomics Genomics
Alex K. Shalek Alex K. Shalek
Single cell and spatial transcriptomics defines the cellular architecture of the antimicrobial response network in human leprosy granulomas
Single cell and spatial transcriptomics defines the cellular architecture of the antimicrobial response network in human leprosy granulomas
  • Ma et al.,
  • bioRxiv,
  • 2020
Biology Biology
Cell Atlas Cell Atlas
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
Marc Wadsworth II Marc Wadsworth II
Travis Hughes Travis Hughes
Functional compensation precedes recovery of tissue mass following acute liver injury
Functional compensation precedes recovery of tissue mass following acute liver injury
  • Walesky et al.,
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  • 2020
Biology Biology
Genomics Genomics
Immunology Immunology
Alex K. Shalek Alex K. Shalek
Ira Fleming Ira Fleming
Kellie Kolb Kellie Kolb
Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells
Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells
  • Pae et al.,
  • bioRxiv,
  • 2020
Biology Biology
Genomics Genomics
Immunology Immunology
Alex K. Shalek Alex K. Shalek
José Ordovas-Montañes José Ordovas-Montañes
Sam Allon Sam Allon
Inflammasomes within hyperactive murine dendritic cells stimulate long-lived T cell-mediated anti-tumor immunity
Inflammasomes within hyperactive murine dendritic cells stimulate long-lived T cell-mediated anti-tumor immunity
  • Zhivaki et al.,
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  • 2020
Biology Biology
Cancer Cancer
Genomics Genomics
Immunology Immunology
Medicine Medicine
Alex K. Shalek Alex K. Shalek
Benjamin Doran Benjamin Doran
Ira Fleming Ira Fleming
Evolution and diversity of immune responses during acute HIV infection
Evolution and diversity of immune responses during acute HIV infection
  • Kazer et al.,
  • Immunity,
  • 2020
Biology Biology
Immunology Immunology
Infectious Disease Infectious Disease
Medicine Medicine
Alex K. Shalek Alex K. Shalek
Sam Kazer Sam Kazer
Single-cell profiling of ebola virus disease in vivo reveals viral and host dynamics
Single-cell profiling of ebola virus disease in vivo reveals viral and host dynamics
  • Kotliar et al.,
  • Cell,
  • 2020
Biology Biology
Cell Atlas Cell Atlas
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
Marc Wadsworth II Marc Wadsworth II
Nancy Tran Nancy Tran
Travis Hughes Travis Hughes
Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte signatures of bacterial control
Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte signatures of bacterial control
  • Gideon et al.,
  • bioRxiv,
  • 2020
Biology Biology
Cell Atlas Cell Atlas
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
Conner Kummerlowe Conner Kummerlowe
José Ordovas-Montañes José Ordovas-Montañes
Marc Wadsworth II Marc Wadsworth II
Sarah Nyquist Sarah Nyquist
Travis Hughes Travis Hughes
Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies
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 Biology
Cell Atlas Cell Atlas
Chemistry Chemistry
Genomics Genomics
Immunology Immunology
R&D R&D
Technology Technology
Alex K. Shalek Alex K. Shalek
José Ordovas-Montañes José Ordovas-Montañes
Marc Wadsworth II Marc Wadsworth II
Travis Hughes Travis Hughes
Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets
Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets
  • Berger et al.,
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  • 2020
Biology Biology
Computational Methods Computational Methods
Statistics Statistics
Alex K. Shalek Alex K. Shalek
Sarah Nyquist Sarah Nyquist
Innate Lymphoid Cell Activation and Sustained Depletion in Blood and Tissue of Children Infected with HIV from Birth Despite Antiretroviral Therapy
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 Biology
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
Sam Kazer Sam Kazer
The tumor microenvironment drives transcriptional phenotypes and their plasticity in metastatic pancreatic cancer
The tumor microenvironment drives transcriptional phenotypes and their plasticity in metastatic pancreatic cancer
  • Raghavan et al.,
  • bioRxiv,
  • 2020
Biology Biology
Cancer Cancer
Cell Atlas Cell Atlas
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Medicine Medicine
Technology Technology
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Jennyfer Galvez-Reyes Jennyfer Galvez-Reyes
Nolawit Mulugeta Nolawit Mulugeta
Peter Winter Peter Winter
A Single Human VH-gene Allows for a Broad-Spectrum Antibody Response Targeting Bacterial Lipopolysaccharides in the Blood
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 Biology
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
James Gatter James Gatter
Sam Kazer Sam Kazer
Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn’s Disease
Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn’s Disease
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  • Gastroenterology,
  • 2020
Biology Biology
Genomics Genomics
Immunology Immunology
Alex K. Shalek Alex K. Shalek
José Ordovas-Montañes José Ordovas-Montañes
Marko Vukovic Marko Vukovic
Spatiotemporal single-cell profiling of gastrointestinal GVHD reveals invasive and resident memory T cell states
Spatiotemporal single-cell profiling of gastrointestinal GVHD reveals invasive and resident memory T cell states
  • Tkachev et al.,
  • bioRxiv,
  • 2020
Biology Biology
Genomics Genomics
Immunology Immunology
Alex K. Shalek Alex K. Shalek
Jim Kaminski Jim Kaminski
José Ordovas-Montañes José Ordovas-Montañes
Single-cell profiling of Ebola virus infection ​in vivo​ reveals viral and host transcriptional dynamics
Single-cell profiling of Ebola virus infection ​in vivo​ reveals viral and host transcriptional dynamics
  • Kotliar et al.,
  • bioRxiv,
  • 2020
Biology Biology
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
Marc Wadsworth II Marc Wadsworth II
Nancy Tran Nancy Tran
Travis Hughes Travis Hughes
Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease
Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease
  • Bassler et al.,
  • bioRxiv,
  • 2020
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Medicine Medicine
Alex K. Shalek Alex K. Shalek
Marc Wadsworth II Marc Wadsworth II
Travis Hughes Travis Hughes
Computational Methods for Single-Cell RNA Sequencing
Computational Methods for Single-Cell RNA Sequencing
  • Hie et al.,
  • Annual Reviews,
  • 2020
Biology Biology
Computational Methods Computational Methods
Genomics Genomics
Alex K. Shalek Alex K. Shalek
Sarah Nyquist Sarah Nyquist
High-throughput organoid screening enables engineering of intestinal epithelial composition
High-throughput organoid screening enables engineering of intestinal epithelial composition
  • Mead et al.,
  • bioRxiv,
  • 2020
Biology Biology
Genomics Genomics
Medicine Medicine
R&D R&D
Technology Technology
Alex K. Shalek Alex K. Shalek
Ben Mead Ben Mead
José Ordovas-Montañes José Ordovas-Montañes
Marko Vukovic Marko Vukovic
SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes
SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes
  • Sungnak et al.,
  • Nature Medicine,
  • 2020
Biology Biology
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
José Ordovas-Montañes José Ordovas-Montañes
SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues
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 Biology
Cell Atlas Cell Atlas
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Statistics Statistics
Ben Mead Ben Mead
Benjamin Doran Benjamin Doran
Carly Ziegler Carly Ziegler
Constantine Tzouanas Constantine Tzouanas
James Gatter James Gatter
Marc Wadsworth II Marc Wadsworth II
Marko Vukovic Marko Vukovic
Sam Allon Sam Allon
Sarah Nyquist Sarah Nyquist
Vincent Miao Vincent Miao
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
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 Biology
Cell Atlas Cell Atlas
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Statistics Statistics
Alex K. Shalek Alex K. Shalek
Carly Ziegler Carly Ziegler
José Ordovas-Montañes José Ordovas-Montañes
Marc Wadsworth II Marc Wadsworth II
Sam Allon Sam Allon
Sarah Nyquist Sarah Nyquist
Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults
Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults
  • Cao et al.,
  • bioRxiv,
  • 2020
Biology Biology
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Microbiology Microbiology
Alex K. Shalek Alex K. Shalek
José Ordovas-Montañes José Ordovas-Montañes
The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution
The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution
  • Rozenblatt-Rosen et al.,
  • Cell,
  • 2020
Biology Biology
Cancer Cancer
Cell Atlas Cell Atlas
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Medicine Medicine
Alex K. Shalek Alex K. Shalek
Systematic comparison of single-cell and single-nucleus RNA-sequencing methods
Systematic comparison of single-cell and single-nucleus RNA-sequencing methods
  • Ding et al.,
  • Nature Biotechnology,
  • 2020
Computational Methods Computational Methods
Genomics Genomics
R&D R&D
Technology Technology
Alex K. Shalek Alex K. Shalek
Marc Wadsworth II Marc Wadsworth II
Shaina Carroll Shaina Carroll
Travis Hughes Travis Hughes
Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
  • Kazer et al.,
  • Nature Medicine,
  • 2020
Biology Biology
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Statistics Statistics
Alex K. Shalek Alex K. Shalek
Carly Ziegler Carly Ziegler
José Ordovas-Montañes José Ordovas-Montañes
Sam Kazer Sam Kazer
Sarah Nyquist Sarah Nyquist
Shaina Carroll Shaina Carroll
Toby Aicher Toby Aicher
Vincent Miao Vincent Miao
SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is enriched in specific cell subsets across tissues
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 Biology
Cell Atlas Cell Atlas
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Medicine Medicine
Benjamin Doran Benjamin Doran
Carly Ziegler Carly Ziegler
Constantine Tzouanas Constantine Tzouanas
James Gatter James Gatter
Marc Wadsworth II Marc Wadsworth II
Marko Vukovic Marko Vukovic
Sam Allon Sam Allon
Sarah Nyquist Sarah Nyquist
Shaina Carroll Shaina Carroll
Vincent Miao Vincent Miao
Spatially-resolved live cell tagging and isolation using protected photoactivatable cell dyes
Spatially-resolved live cell tagging and isolation using protected photoactivatable cell dyes
  • Genshaft et al.,
  • bioRxiv,
  • 2020
Biology Biology
Cancer Cancer
Chemistry Chemistry
Genomics Genomics
R&D R&D
Technology Technology
Alex Genshaft Alex Genshaft
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Ben Mead Ben Mead
Carly Ziegler Carly Ziegler
Constantine Tzouanas Constantine Tzouanas
Distribution and storage of inflammatory memory in barrier tissues
Distribution and storage of inflammatory memory in barrier tissues
  • Ordovas-Montanes et al.,
  • Nature Reviews Immunology,
  • 2020
Biology Biology
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
José Ordovas-Montañes José Ordovas-Montañes
Immunological Fingerprints of Controllers Developing Neutralizing HIV-1 Antibodies
Immunological Fingerprints of Controllers Developing Neutralizing HIV-1 Antibodies
  • Martin-Gayo et al.,
  • Cell Reports,
  • 2020
Biology Biology
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Medicine Medicine
Alex K. Shalek Alex K. Shalek
Kellie Kolb Kellie Kolb
Identification of a master regulator of differentiation in toxoplasma
Identification of a master regulator of differentiation in toxoplasma
  • Waldman et al.,
  • Cell,
  • 2020
Biology Biology
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Microbiology Microbiology
Alex K. Shalek Alex K. Shalek
Marc Wadsworth II Marc Wadsworth II
Prevention of tuberculosis in macaques after intravenous BCG immunization
Prevention of tuberculosis in macaques after intravenous BCG immunization
  • Darrah et al.,
  • Nature,
  • 2020
Biology Biology
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Medicine Medicine
Alex K. Shalek Alex K. Shalek
Marc Wadsworth II Marc Wadsworth II
Travis Hughes Travis Hughes