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Infectious Disease
Pro-inflammatory feedback loops define immune responses to pathogenic lentivirus infection
Wilk et al.,
bioRxiv,
2023
Genomics
Immunology
Infectious Disease
Sam Kazer
Ira Fleming
Vincent Miao
Jennyfer Galvez-Reyes
Alex K. Shalek
Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity
Bui et al.,
Nature Communications,
2023
Biology
Cell Atlas
Genomics
Immunology
Infectious Disease
Alex K. Shalek
Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19
Bernardes et al.,
Immunity,
Biology
Cell Atlas
Genomics
Immunology
Infectious Disease
Alex K. Shalek
Myocyte-Specific Upregulation of ACE2 in Cardiovascular Disease: Implications for SARS-CoV-2–Mediated Myocarditis
Tucker et al.,
Circulation,
Biology
Cell Atlas
Genomics
Immunology
Infectious Disease
Alex K. Shalek
Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis)
Jaiswal et al.,
BMC Genomics,
2023
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Infectious Disease
R&D
Sarah Nyquist
Tasneem Jivanjee
Samira Ibrahim
Josh Bromley
James Gatter
Alex K. Shalek
HIV specific CD8+ TRM-like cells in tonsils express exhaustive signatures in the absence of natural HIV control
Fardoos et al.,
Frontiers in Immunology,
Biology
Genomics
Immunology
Infectious Disease
Sarah Nyquist
Sam Kazer
Son Nguyen
Alex K. Shalek
Single-cell profiling of environmental enteropathy reveals signatures of epithelial remodeling and immune activation
Kummerlowe et al.,
Science Translational Medicine,
2022
Biology
Cell Atlas
Genomics
Immunology
Infectious Disease
Microbiology
Conner Kummerlowe
Travis Hughes
Nolawit Mulugeta
Ira Fleming
Marko Vukovic
Benjamin Doran
Toby Aicher
Marc Wadsworth II
José Ordovas-Montañes
Alex K. Shalek
Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control
Gideon et al.,
Immunity,
2022
Biology
Cell Atlas
Genomics
Immunology
Infectious Disease
Microbiology
Travis Hughes
Constantine Tzouanas
Marc Wadsworth II
Conner Kummerlowe
Sarah Nyquist
Samira Ibrahim
José Ordovas-Montañes
Alex K. Shalek
A single-cell liver atlas of Plasmodium vivax infection
Mancio-Silva et al.,
Cell Host & Microbe,
2022
Biology
Cell Atlas
Genomics
Immunology
Infectious Disease
Microbiology
Technology
Marc Wadsworth II
Travis Hughes
Alex K. Shalek
Clinical implementation of single-cell RNA sequencing using liver fine needle aspirate tissue sampling and centralized processing captures compartment specific immuno-diversity
Genshaft et al.,
bioRxiv,
2021
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Infectious Disease
R&D
Technology
Alex Genshaft
Mike Vilme
Riley Drake
Ira Fleming
Nancy Tran
Constantine Tzouanas
Jasmin Joseph-Chazan
Alex K. Shalek
Aggregated Mycobacterium tuberculosis Enhances the Inflammatory Response
Rodel et al.,
Frontiers in Microbiology,
Biology
Genomics
Immunology
Infectious Disease
Microbiology
Carly Ziegler
Alex K. Shalek
Allelic variation in class I HLA determines CD8+ T cell repertoire shape and cross-reactive memory responses to SARS-CoV-2
Francis et al.,
Science Immunology,
2021
Biology
Genomics
Immunology
Infectious Disease
Alex K. Shalek
Enteric Coronavirus Infection and Treatment Modeled With an Immunocompetent Human Intestine-On-A-Chip
Bein et al.,
Frontiers in Pharmacology,
2021
Biology
Genomics
Immunology
Infectious Disease
Medicine
R&D
Technology
Vincent Miao
Andrew Navia
Carly Ziegler
José Ordovas-Montañes
Alex K. Shalek
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
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
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
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
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
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
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
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
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
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
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 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
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,
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
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
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
Germline-encoded affinity for cognate antigen enables vaccine amplification of a human broadly neutralizing response against influenza virus
Sangesland et al.,
Immunity,
2019
Biology
Genomics
Immunology
Infectious Disease
Medicine
Sam Kazer
Alex K. Shalek
Group 3 innate lymphoid cells mediate early protective immunity against tuberculosis
Ardain A. et al.,
Nature,
2019
Biology
Immunology
Infectious Disease
Sam Kazer
Alex K. Shalek
Identification of a Master Regulator of Differentiation in Toxoplasma
Waldman B.S. et al.,
bioRxiv,
Biology
Infectious Disease
Microbiology
Marc Wadsworth II
Alex K. Shalek
Integrated Single-Cell Analysis of Multicellular Immune Dynamics during Hyper-Acute HIV-1 Infection
Kazer S.W. et al.,
bioRxiv,
2019
Biology
Genomics
Immunology
Infectious Disease
Sam Kazer
Toby Aicher
Shaina Carroll
José Ordovas-Montañes
Carly Ziegler
Sarah Nyquist
Alex K. Shalek
Augmentation of HIV-specific T cell function by immediate treatment of hyperacute HIV-1 infection
Ndhlovu et al.,
Science Translational Medicine,
2019
Genomics
Immunology
Medicine
Sam Kazer
Alex K. Shalek
Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses
Douam F. et al.,
Nature Communications,
2018
Biology
Genomics
Immunology
Infectious Disease
Alex K. Shalek
Carly Ziegler
High-Frequency, Functional HIV-Specific T-Follicular Helper and Regulatory Cells Are Present Within Germinal Centers in Children but Not Adults
Roider et al.,
frontiers in Immunology,
2018
Toby Aicher
Sam Kazer
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
Single-cell analyses to tailor treatments
Shalek A.K. et al.,
Science Translational Medicine,
2017
Immunology
Infectious Disease
Medicine
Technology
Alex K. Shalek
Novel in vitro booster vaccination to rapidly generate antigen-specific human monoclonal antibodies
Nandin I.S. et al.,
Journal of Experimental Medicine,
2017
Genomics
Immunology
Infectious Disease
Medicine
Microbiology
Sam Kazer
José Ordovas-Montañes
Alex K. Shalek
Circulating CXCR5+CXCR3+PD-1lo Tfh-like Cells in HIV-1 Controllers with Neutralizing Antibody Breadth
Martin-Gayo et al.,
JCI Insight,
2017
Biology
Immunology
Infectious Disease
Kellie Kolb
Alex K. Shalek
Antiviral CD8+ T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion
Ranasinghe et al.,
Immunity,
2016
Biology
Immunology
Infectious Disease
Sam Kazer
Alex K. Shalek
Innate Lymphoid Cells Are Depleted Irreversibly during Acute HIV-1 Infection in the Absence of Viral Suppression
Kløverpris et al.,
Immunity,
2016
Biology
Genomics
Immunology
Infectious Disease
Sam Kazer
Alex K. Shalek
Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses
Avraham et al.,
Cell,
2015
Biology
Genomics
Immunology
Infectious Disease
Microbiology
Technology
Alex K. Shalek
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