Natural history of Ebola virus disease in rhesus monkeys shows viral variant emergence dynamics and tissue-specific host responses
Genomics
Infectious Disease
Alex K. Shalek
Sergio Triana
Tammy Lan
Identification of drug candidates targeting monocyte reprogramming in people living with HIV
ImmunologyInfectious DiseaseAlex K. Shalek
CD8+ lymphocytes are critical for early control of tuberculosis in macaques
Computational MethodsInfectious Disease
Medicine
Josh Bromley
Sarah NyquistAlex K. Shalek
Marc Wadsworth II
Travis Hughes
scRNA-Seq reveals elevated interferon responses and TNF-α signaling via NFkB in monocytes in children with clinical malaria
BiologyGenomicsImmunologyInfectious Disease
Microbiology
Riley Drake
Vincent MiaoAlex K. Shalek
Pro-inflammatory feedback loops define immune responses to pathogenic lentivirus infection
GenomicsImmunologyInfectious Disease
Sam Kazer
Ira FlemingVincent Miao
Jennyfer Galvez-ReyesAlex K. Shalek
Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity
Biology
Cell AtlasGenomicsImmunologyInfectious DiseaseAlex K. Shalek
Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19
BiologyCell AtlasGenomicsImmunologyInfectious DiseaseAlex K. Shalek
Myocyte-Specific Upregulation of ACE2 in Cardiovascular Disease: Implications for SARS-CoV-2–Mediated Myocarditis
BiologyCell AtlasGenomicsImmunologyInfectious DiseaseAlex K. Shalek
Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis)
BiologyCell AtlasComputational MethodsGenomicsImmunologyInfectious Disease
R&DSarah Nyquist
Tasneem Jivanjee
Samira IbrahimJosh Bromley
James GatterAlex K. Shalek
HIV specific CD8+ TRM-like cells in tonsils express exhaustive signatures in the absence of natural HIV control
BiologyGenomicsImmunologyInfectious DiseaseSarah NyquistSam Kazer
Son NguyenAlex K. Shalek
Single-cell profiling of environmental enteropathy reveals signatures of epithelial remodeling and immune activation
BiologyCell AtlasGenomicsImmunologyInfectious DiseaseMicrobiology
Conner KummerloweTravis Hughes
Nolawit MulugetaIra Fleming
Marko Vukovic
Benjamin Doran
Toby AicherMarc Wadsworth II
José Ordovas-MontañesAlex K. Shalek
Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control
BiologyCell AtlasGenomicsImmunologyInfectious DiseaseMicrobiologyTravis Hughes
Constantine TzouanasMarc Wadsworth IIConner KummerloweSarah NyquistSamira IbrahimJosé Ordovas-MontañesAlex K. Shalek
A single-cell liver atlas of Plasmodium vivax infection
BiologyCell AtlasGenomicsImmunologyInfectious DiseaseMicrobiology
TechnologyMarc Wadsworth IITravis HughesAlex K. Shalek
Clinical implementation of single-cell RNA sequencing using liver fine needle aspirate tissue sampling and centralized processing captures compartment specific immuno-diversity
BiologyCell AtlasComputational MethodsGenomicsImmunologyInfectious DiseaseR&DTechnology
Alex Genshaft
Mike VilmeRiley DrakeIra Fleming
Nancy TranConstantine Tzouanas
Jasmin Joseph-ChazanAlex K. Shalek
Aggregated Mycobacterium tuberculosis Enhances the Inflammatory Response
BiologyGenomicsImmunologyInfectious DiseaseMicrobiology
Carly ZieglerAlex K. Shalek
Allelic variation in class I HLA determines CD8+ T cell repertoire shape and cross-reactive memory responses to SARS-CoV-2
BiologyGenomicsImmunologyInfectious DiseaseAlex K. Shalek
Enteric Coronavirus Infection and Treatment Modeled With an Immunocompetent Human Intestine-On-A-Chip
BiologyGenomicsImmunologyInfectious DiseaseMedicineR&DTechnologyVincent Miao
Andrew NaviaCarly ZieglerJosé Ordovas-MontañesAlex K. Shalek
Identification of immune correlates of fatal outcomes in critically ill COVID-19 patients
BiologyGenomicsImmunologyInfectious DiseaseVincent MiaoAlex K. Shalek
HIV infection drives interferon signaling within intestinal SARS-CoV-2 target cells
GenomicsImmunologyInfectious DiseaseSarah NyquistAlex K. Shalek
Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
BiologyCell AtlasComputational MethodsGenomicsImmunologyInfectious DiseaseCarly ZieglerVincent MiaoAndrew NaviaJosh Bromley
Micayla GeorgeRiley DrakeAlex K. ShalekJosé Ordovas-Montañes
The cellular architecture of the antimicrobial response network in human leprosy granulomas
BiologyGenomicsImmunologyInfectious DiseaseMicrobiologyTravis HughesMarc Wadsworth IIAlex K. Shalek
Single-cell immunophenotyping of the skin lesion erythema migrans identifies IgM memory B cells
BiologyGenomicsImmunologyInfectious DiseaseIra FlemingAlex K. Shalek
COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
BiologyCell AtlasComputational MethodsGenomicsImmunologyInfectious Disease
StatisticsCarly ZieglerAlex K. Shalek
Single-cell profiling of environmental enteropathy reveals signatures of epithelial remodeling and immune activation in severe disease
BiologyGenomicsImmunologyInfectious DiseaseConner KummerloweTravis HughesNolawit MulugetaIra FlemingMarko VukovicBenjamin DoranJosé Ordovas-MontañesAlex 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
BiologyGenomicsImmunologyInfectious DiseaseMicrobiology
Jay PrakadanSam KazerAlex K. Shalek
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
Cell AtlasComputational MethodsGenomicsImmunologyInfectious DiseaseStatistics
Sam AllonSarah NyquistMarc Wadsworth IICarly ZieglerAlex K. Shalek
A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2
BiologyCell AtlasComputational MethodsGenomicsImmunologyInfectious DiseaseStatisticsCarly ZieglerAlex K. Shalek
Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
BiologyGenomicsImmunologyInfectious DiseaseMicrobiologyCarly ZieglerVincent MiaoAndrew NaviaJosh BromleyMicayla GeorgeRiley DrakeAlex K. ShalekJosé Ordovas-Montañes
Single cell profiling of COVID-19 patients: an international data resource from multiple tissues
BiologyCell AtlasGenomicsImmunologyInfectious DiseaseCarly ZieglerVincent MiaoAndrew NaviaJosh BromleyJosé Ordovas-MontañesAlex K. Shalek
Single cell and spatial transcriptomics defines the cellular architecture of the antimicrobial response network in human leprosy granulomas
BiologyCell AtlasGenomicsImmunologyInfectious DiseaseTravis HughesMarc Wadsworth IIAlex K. Shalek
Evolution and diversity of immune responses during acute HIV infection
BiologyImmunologyInfectious DiseaseMedicineSam KazerAlex K. Shalek
Single-cell profiling of ebola virus disease in vivo reveals viral and host dynamics
BiologyCell AtlasGenomicsImmunologyInfectious DiseaseTravis HughesMarc Wadsworth IINancy TranAlex K. Shalek
Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte signatures of bacterial control
BiologyCell AtlasGenomicsImmunologyInfectious DiseaseTravis HughesMarc Wadsworth IIConner KummerloweSarah NyquistJosé Ordovas-MontañesAlex K. Shalek
Innate Lymphoid Cell Activation and Sustained Depletion in Blood and Tissue of Children Infected with HIV from Birth Despite Antiretroviral Therapy
BiologyGenomicsImmunologyInfectious DiseaseSam KazerAlex K. Shalek
A Single Human VH-gene Allows for a Broad-Spectrum Antibody Response Targeting Bacterial Lipopolysaccharides in the Blood
BiologyComputational MethodsGenomicsImmunologyInfectious DiseaseSam KazerJames GatterAlex K. Shalek
Single-cell profiling of Ebola virus infection in vivo reveals viral and host transcriptional dynamics
BiologyGenomicsImmunologyInfectious DiseaseTravis HughesMarc Wadsworth IINancy TranAlex K. Shalek
SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes
BiologyGenomicsImmunologyInfectious DiseaseJosé Ordovas-MontañesAlex 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
BiologyCell AtlasGenomicsImmunologyInfectious DiseaseStatisticsCarly ZieglerSam AllonSarah NyquistVincent MiaoConstantine TzouanasMarc Wadsworth IISam KazerTravis HughesBenjamin DoranJames GatterMarko Vukovic
Ben Mead
Shaina CarrollAlex K. ShalekJosé 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
BiologyCell AtlasComputational MethodsGenomicsImmunologyInfectious DiseaseStatisticsSam AllonSarah NyquistJosé Ordovas-MontañesMarc Wadsworth IICarly ZieglerAlex K. Shalek
Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults
BiologyGenomicsImmunologyInfectious DiseaseMicrobiologyJosé Ordovas-MontañesAlex K. Shalek
Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
BiologyComputational MethodsGenomicsImmunologyInfectious DiseaseStatisticsSam KazerToby AicherShaina CarrollJosé Ordovas-MontañesVincent MiaoCarly ZieglerSarah NyquistAlex 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
BiologyCell AtlasComputational MethodsGenomicsImmunologyInfectious DiseaseMedicineCarly ZieglerSam AllonSarah NyquistVincent MiaoMarc Wadsworth IISam KazerTravis HughesBenjamin DoranJames GatterMarko VukovicConstantine TzouanasShaina CarrollAlex K. ShalekJosé Ordovas-Montañes
Distribution and storage of inflammatory memory in barrier tissues
BiologyGenomicsImmunologyInfectious DiseaseJosé Ordovas-MontañesAlex K. Shalek
Immunological Fingerprints of Controllers Developing Neutralizing HIV-1 Antibodies
BiologyGenomicsImmunologyInfectious DiseaseMedicine
Kellie KolbAlex K. Shalek
Identification of a master regulator of differentiation in toxoplasma
BiologyGenomicsImmunologyInfectious DiseaseMicrobiologyMarc Wadsworth IIAlex K. Shalek
Prevention of tuberculosis in macaques after intravenous BCG immunization
BiologyGenomicsImmunologyInfectious DiseaseMedicineMarc Wadsworth IITravis HughesAlex K. Shalek
Germline-encoded affinity for cognate antigen enables vaccine amplification of a human broadly neutralizing response against influenza virus
BiologyGenomicsImmunologyInfectious DiseaseMedicineSam KazerAlex K. Shalek
Group 3 innate lymphoid cells mediate early protective immunity against tuberculosis
BiologyImmunologyInfectious DiseaseSam KazerAlex K. Shalek
Identification of a Master Regulator of Differentiation in Toxoplasma
BiologyInfectious DiseaseMicrobiologyMarc Wadsworth IIAlex K. Shalek
Integrated Single-Cell Analysis of Multicellular Immune Dynamics during Hyper-Acute HIV-1 Infection
BiologyGenomicsImmunologyInfectious DiseaseSam KazerToby AicherShaina CarrollJosé Ordovas-MontañesCarly ZieglerSarah NyquistAlex K. Shalek
Augmentation of HIV-specific T cell function by immediate treatment of hyperacute HIV-1 infection
GenomicsImmunologyMedicineSam KazerAlex K. Shalek
Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses
BiologyGenomicsImmunologyInfectious DiseaseAlex K. ShalekCarly Ziegler
High-Frequency, Functional HIV-Specific T-Follicular Helper and Regulatory Cells Are Present Within Germinal Centers in Children but Not Adults
Toby AicherSam KazerAlex K. Shalek
A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers
Computational MethodsGenomicsImmunologyInfectious DiseaseMedicineKellie KolbJosé Ordovas-MontañesAlex K. Shalek
Single-cell analyses to tailor treatments
ImmunologyInfectious DiseaseMedicineTechnologyAlex K. Shalek
Novel in vitro booster vaccination to rapidly generate antigen-specific human monoclonal antibodies
GenomicsImmunologyInfectious DiseaseMedicineMicrobiologySam KazerJosé Ordovas-MontañesAlex K. Shalek
Circulating CXCR5+CXCR3+PD-1lo Tfh-like Cells in HIV-1 Controllers with Neutralizing Antibody Breadth
BiologyImmunologyInfectious DiseaseKellie KolbAlex K. Shalek
Antiviral CD8+ T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion
BiologyImmunologyInfectious DiseaseSam KazerAlex K. Shalek
Innate Lymphoid Cells Are Depleted Irreversibly during Acute HIV-1 Infection in the Absence of Viral Suppression
BiologyGenomicsImmunologyInfectious DiseaseSam KazerAlex K. Shalek
Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses
BiologyGenomicsImmunologyInfectious DiseaseMicrobiologyTechnologyAlex K. Shalek