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Systematic deconstruction of myeloid cell signaling in tuberculosis granulomas reveals IFN-γ, TGF-β, and time are associated with conserved myeloid diversity
Peters et al.,
biorxiv,
2024
Alex K. Shalek
Josh Bromley
Sarah Nyquist
Travis Hughes
Intrahepatic plasma cells, but not atypical memoryB cells, associate with clinical phases of chronichepatitis B
Osmani et al.,
European Journal of Immunology,
2024
Immunology
Alex K. Shalek
Jasmin Joseph-Chazan
Tobacco smoke exposure recruits inflammatory airspace monocytes that establish permissive lung niches for Mycobacterium tuberculosis
Corleis et al.,
Science Translational Medicine,
2023
Computational Methods
Infectious Disease
Medicine
Alex K. Shalek
Constantine Tzouanas
Marc Wadsworth II
Natural history of Ebola virus disease in rhesus monkeys shows viral variant emergence dynamics and tissue-specific host responses
Normandin et al.,
Cell Genomics,
2023
Genomics
Infectious Disease
Alex K. Shalek
Sergio Triana
Tammy Lan
Identification of drug candidates targeting monocyte reprogramming in people living with HIV
Knoll et al.,
Frontiers in Immunology,
2023
Immunology
Infectious Disease
Alex K. Shalek
CD8+ lymphocytes are critical for early control of tuberculosis in macaques
Winchell et al.,
Journal of Experimental Medicine,
2023
Computational Methods
Infectious Disease
Medicine
Alex K. Shalek
Josh Bromley
Marc Wadsworth II
Sarah Nyquist
Travis Hughes
scRNA-Seq reveals elevated interferon responses and TNF-α signaling via NFkB in monocytes in children with clinical malaria
Morang’a et al.,
medRxiv,
2023
Biology
Genomics
Immunology
Infectious Disease
Microbiology
Alex K. Shalek
Riley Drake
Vincent Miao
Pro-inflammatory feedback loops define immune responses to pathogenic lentivirus infection
Wilk et al.,
bioRxiv,
2023
Genomics
Immunology
Infectious Disease
Alex K. Shalek
Ira Fleming
Jennyfer Galvez-Reyes
Sam Kazer
Vincent Miao
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,
2023
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,
2023
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
Alex K. Shalek
James Gatter
Josh Bromley
Samira Ibrahim
Sarah Nyquist
Tasneem Jivanjee
HIV specific CD8+ TRM-like cells in tonsils express exhaustive signatures in the absence of natural HIV control
Fardoos et al.,
Frontiers in Immunology,
2023
Biology
Genomics
Immunology
Infectious Disease
Alex K. Shalek
Sam Kazer
Sarah Nyquist
Son Nguyen
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
Alex K. Shalek
Benjamin Doran
Conner Kummerlowe
Ira Fleming
José Ordovas-Montañes
Marc Wadsworth II
Marko Vukovic
Nolawit Mulugeta
Toby Aicher
Travis Hughes
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
Alex K. Shalek
Conner Kummerlowe
Constantine Tzouanas
José Ordovas-Montañes
Marc Wadsworth II
Samira Ibrahim
Sarah Nyquist
Travis Hughes
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
Alex K. Shalek
Marc Wadsworth II
Travis Hughes
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
Alex K. Shalek
Constantine Tzouanas
Ira Fleming
Jasmin Joseph-Chazan
Mike Vilme
Nancy Tran
Riley Drake
Aggregated Mycobacterium tuberculosis Enhances the Inflammatory Response
Rodel et al.,
Frontiers in Microbiology,
2021
Biology
Genomics
Immunology
Infectious Disease
Microbiology
Alex K. Shalek
Carly Ziegler
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
Alex K. Shalek
Andrew Navia
Carly Ziegler
José Ordovas-Montañes
Vincent Miao
Identification of immune correlates of fatal outcomes in critically ill COVID-19 patients
Youngs et al.,
PLOS Pathogens,
2021
Biology
Genomics
Immunology
Infectious Disease
Alex K. Shalek
Vincent Miao
HIV infection drives interferon signaling within intestinal SARS-CoV-2 target cells
Fardoos et al.,
JCI Insight,
2021
Genomics
Immunology
Infectious Disease
Alex K. Shalek
Sarah Nyquist
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
Alex K. Shalek
Andrew Navia
Carly Ziegler
Josh Bromley
José Ordovas-Montañes
Micayla George
Riley Drake
Vincent Miao
The cellular architecture of the antimicrobial response network in human leprosy granulomas
Ma et al.,
Nature Immunology,
2021
Biology
Genomics
Immunology
Infectious Disease
Microbiology
Alex K. Shalek
Marc Wadsworth II
Travis Hughes
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
Alex K. Shalek
Ira Fleming
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
Alex K. Shalek
Ira Fleming
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
Alex K. Shalek
Carly Ziegler
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
Alex K. Shalek
Benjamin Doran
Conner Kummerlowe
Ira Fleming
José Ordovas-Montañes
Marko Vukovic
Nolawit Mulugeta
Travis Hughes
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
Alex K. Shalek
Jay Prakadan
Sam Kazer
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
Alex K. Shalek
Carly Ziegler
Marc Wadsworth II
Sam Allon
Sarah Nyquist
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
Alex K. Shalek
Carly Ziegler
Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
Ziegler et al.,
bioRxiv,
2021
Biology
Genomics
Immunology
Infectious Disease
Microbiology
Alex K. Shalek
Andrew Navia
Carly Ziegler
Josh Bromley
José Ordovas-Montañes
Micayla George
Riley Drake
Vincent Miao
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
Alex K. Shalek
Andrew Navia
Carly Ziegler
Josh Bromley
José Ordovas-Montañes
Vincent Miao
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
Alex K. Shalek
Marc Wadsworth II
Travis Hughes
Evolution and diversity of immune responses during acute HIV infection
Kazer et al.,
Immunity,
2020
Biology
Immunology
Infectious Disease
Medicine
Alex K. Shalek
Sam Kazer
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
Alex K. Shalek
Marc Wadsworth II
Nancy Tran
Travis Hughes
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
Alex K. Shalek
Conner Kummerlowe
José Ordovas-Montañes
Marc Wadsworth II
Sarah Nyquist
Travis Hughes
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
Alex K. Shalek
Sam Kazer
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
Alex K. Shalek
James Gatter
Sam Kazer
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
Alex K. Shalek
Marc Wadsworth II
Nancy Tran
Travis Hughes
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
Alex K. Shalek
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
Ziegler et al.,
Cell,
2020
Biology
Cell Atlas
Genomics
Immunology
Infectious Disease
Statistics
Ben Mead
Benjamin Doran
Carly Ziegler
Constantine Tzouanas
James Gatter
Marc Wadsworth II
Marko Vukovic
Sam Allon
Sarah Nyquist
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
Muus et al.,
bioRxiv,
2020
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Infectious Disease
Statistics
Alex K. Shalek
Carly Ziegler
José Ordovas-Montañes
Marc Wadsworth II
Sam Allon
Sarah Nyquist
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
Alex K. Shalek
José Ordovas-Montañes
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
Alex K. Shalek
Carly Ziegler
José Ordovas-Montañes
Sam Kazer
Sarah Nyquist
Shaina Carroll
Toby Aicher
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
Ziegler et al.,
SSRN,
2020
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Infectious Disease
Medicine
Benjamin Doran
Carly Ziegler
Constantine Tzouanas
James Gatter
Marc Wadsworth II
Marko Vukovic
Sam Allon
Sarah Nyquist
Shaina Carroll
Vincent Miao
Distribution and storage of inflammatory memory in barrier tissues
Ordovas-Montanes et al.,
Nature Reviews Immunology,
2020
Biology
Genomics
Immunology
Infectious Disease
Alex K. Shalek
José Ordovas-Montañes
Immunological Fingerprints of Controllers Developing Neutralizing HIV-1 Antibodies
Martin-Gayo et al.,
Cell Reports,
2020
Biology
Genomics
Immunology
Infectious Disease
Medicine
Alex K. Shalek
Kellie Kolb
Identification of a master regulator of differentiation in toxoplasma
Waldman et al.,
Cell,
2020
Biology
Genomics
Immunology
Infectious Disease
Microbiology
Alex K. Shalek
Marc Wadsworth II
Prevention of tuberculosis in macaques after intravenous BCG immunization
Darrah et al.,
Nature,
2020
Biology
Genomics
Immunology
Infectious Disease
Medicine
Alex K. Shalek
Marc Wadsworth II
Travis Hughes
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
Alex K. Shalek
Sam Kazer
Group 3 innate lymphoid cells mediate early protective immunity against tuberculosis
Ardain A. et al.,
Nature,
2019
Biology
Immunology
Infectious Disease
Alex K. Shalek
Sam Kazer
Identification of a Master Regulator of Differentiation in Toxoplasma
Waldman B.S. et al.,
bioRxiv,
2019
Biology
Infectious Disease
Microbiology
Alex K. Shalek
Marc Wadsworth II
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
Alex K. Shalek
Carly Ziegler
José Ordovas-Montañes
Sam Kazer
Sarah Nyquist
Shaina Carroll
Toby Aicher
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
Alex K. Shalek
Sam Kazer
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
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
Alex K. Shalek
Sam Kazer
Toby Aicher
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
Alex K. Shalek
José Ordovas-Montañes
Kellie Kolb
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
Alex K. Shalek
José Ordovas-Montañes
Sam Kazer
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
Alex K. Shalek
Kellie Kolb
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
Alex K. Shalek
Sam Kazer
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
Alex K. Shalek
Sam Kazer
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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