Single-cell immunophenotyping of the skin lesion erythema migrans identifies IgM memory B cells
Biology
Genomics
Immunology
Infectious Disease
Ira Fleming
Alex K. Shalek
Targeting Treg cells with GITR activation alleviates resistance to immunotherapy in murine glioblastomas
CancerGenomicsImmunology
Medicine
Sam KazerAlex K. Shalek
COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
Biology
Cell Atlas
Computational MethodsGenomicsImmunologyInfectious Disease
Statistics
Carly ZieglerAlex K. Shalek
Single-cell profiling of environmental enteropathy reveals signatures of epithelial remodeling and immune activation in severe disease
BiologyGenomicsImmunologyInfectious Disease
Conner Kummerlowe
Travis Hughes
Nolawit MulugetaIra Fleming
Marko Vukovic
Benjamin Doran
José 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 Disease
Microbiology
Jay PrakadanSam KazerAlex K. Shalek
Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation
BiologyGenomicsImmunologyJosé Ordovas-Montañes
Sam AllonMarko VukovicTravis Hughes
Sarah NyquistAlex K. Shalek
Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu
BiologyGenomicsImmunologyMedicine
Brittany Goods
Riley DrakeIra FlemingAlex K. Shalek
How are methodological developments enabling insights into cell behavior in cellular communities?
BiologyGenomicsImmunologyAlex K. Shalek
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
Cell AtlasComputational MethodsGenomicsImmunologyInfectious DiseaseStatisticsSam AllonSarah Nyquist
Marc 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 Ziegler
Vincent Miao
Andrew Navia
Josh Bromley
Micayla GeorgeRiley DrakeAlex K. ShalekJosé Ordovas-Montañes
Longitudinal transcriptomics define the stages of myeloid activation in the living human brain after intracerebral hemorrhage
BiologyGenomicsImmunologyMedicineBrittany Goods
Shaina CarrollRiley Drake
James GatterAlex K. Shalek
Spatiotemporal single-cell profiling reveals that invasive and tissue-resident memory donor CD8+ T cells drive gastrointestinal acute graft-versus-host disease
BiologyCell AtlasGenomicsImmunologyMedicine
Jim KaminskiJosé Ordovas-MontañesAlex K. Shalek
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
Lymph nodes are innervated by a unique population of sensory neurons with immunomodulatory potential
BiologyGenomicsImmunologyCarly ZieglerMarko VukovicJosé Ordovas-MontañesAlex K. Shalek
Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells
BiologyGenomicsImmunologySam AllonJosé 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
Functional compensation precedes recovery of tissue mass following acute liver injury
BiologyGenomicsImmunology
Kellie KolbIra FlemingAlex K. Shalek
Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells
BiologyGenomicsImmunologySam AllonJosé Ordovas-MontañesAlex K. Shalek
Inflammasomes within hyperactive murine dendritic cells stimulate long-lived T cell-mediated anti-tumor immunity
BiologyCancerGenomicsImmunologyMedicineBenjamin DoranIra FlemingAlex K. Shalek
Evolution and diversity of immune responses during acute HIV infection
BiologyImmunologyInfectious DiseaseMedicineSam KazerAlex K. Shalek
Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu
BiologyGenomicsImmunologyMedicineBrittany GoodsRiley DrakeIra FlemingAlex K. Shalek
Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states
BiologyCancerGenomicsImmunologyMarc Wadsworth IIAlex K. Shalek
Single-cell profiling of ebola virus disease in vivo reveals viral and host dynamics
BiologyCell AtlasGenomicsImmunologyInfectious DiseaseTravis HughesMarc Wadsworth II
Nancy 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
Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies
BiologyCell Atlas
ChemistryGenomicsImmunology
R&D
TechnologyTravis HughesMarc Wadsworth IIJosé 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
The tumor microenvironment drives transcriptional phenotypes and their plasticity in metastatic pancreatic cancer
BiologyCancerCell AtlasComputational MethodsGenomicsImmunologyMedicineTechnology
Peter WinterAndrew Navia
Jennyfer Galvez-ReyesNolawit MulugetaAlex 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 Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn’s Disease
BiologyGenomicsImmunologyJosé Ordovas-MontañesMarko VukovicAlex K. Shalek
Spatiotemporal single-cell profiling of gastrointestinal GVHD reveals invasive and resident memory T cell states
BiologyGenomicsImmunologyJim KaminskiJosé Ordovas-MontañesAlex 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
Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease
Computational MethodsGenomicsImmunologyMedicineMarc Wadsworth IITravis HughesAlex 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 Miao
Constantine TzouanasMarc Wadsworth IISam KazerTravis HughesBenjamin DoranJames GatterMarko Vukovic
Ben MeadShaina 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
The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution
BiologyCancerCell AtlasComputational MethodsGenomicsImmunologyMedicineAlex K. Shalek
Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
BiologyComputational MethodsGenomicsImmunologyInfectious DiseaseStatisticsSam Kazer
Toby 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 DiseaseMedicineKellie 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
TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures
BiologyCell AtlasGenomicsImmunologyR&DTechnologyAlex K. Shalek
Revisiting airway epithelial remodeling in type 2 immunity: Beyond goblet cell metaplasia
BiologyGenomicsImmunologyAlex K. Shalek
Sensory neurons innervate peripheral lymph nodes and locally regulate gene expression in postsynaptic endothelium, stromal cells, and innate leukocytes
BiologyCell AtlasComputational MethodsGenomicsImmunologyCarly ZieglerMarko VukovicJosé Ordovas-MontañesAlex K. Shalek
Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration
BiologyCell AtlasGenomicsImmunologyMedicineBrittany GoodsAlex K. Shalek
Induction of metabolic quiescence defines the transitional to follicular B cell switch
BiologyGenomicsImmunologyToby AicherAlex K. Shalek
The next quarter century
BiologyGenomicsImmunologyAlex 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
Highly efficient, massively-parallel single-cell RNA-Seq reveals cellular states and molecular features of human skin pathology
BiologyGenomicsImmunologyR&DTechnologyTravis HughesMarc Wadsworth IIJosé Ordovas-MontañesAlex K. Shalek
Group 3 innate lymphoid cells mediate early protective immunity against tuberculosis
BiologyImmunologyInfectious DiseaseSam KazerAlex 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
Mechanisms of lymphoma clearance induced by high-dose alkylating agents
BiologyCancerImmunologyKellie KolbJay PrakadanAlex K. Shalek
Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity
Marc Wadsworth IITravis HughesAlex K. Shalek
Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses
BiologyGenomicsImmunologyInfectious DiseaseAlex K. ShalekCarly Ziegler
T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation
GenomicsImmunologyMedicineJosé Ordovas-MontañesAlex K. Shalek
A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade
Alex K. Shalek
Rewiring of the cellular and inter-cellular landscape of the human colon during ulcerative colitis
BiologyCell AtlasComputational MethodsImmunologyMedicineJosé Ordovas-MontañesAlex K. Shalek
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
Allergic Inflammatory Memory in Human Respiratory Epithelial Progenitor Cells
BiologyCell AtlasImmunologyMedicineJosé Ordovas-MontañesSarah NyquistMarko VukovicMarc Wadsworth IITravis HughesSam 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
Initiation of Antiviral B Cell Immunity Relies on Innate Signals from Spatially Positioned NKT Cells
GenomicsImmunologyAndrew NaviaAlex K. Shalek
Reduced cellular diversity and an altered basal progenitor cell state inform epithelial barrier dysfunction in human type 2 immunity
Cell AtlasImmunologyMedicineJosé Ordovas-MontañesSarah NyquistMarc Wadsworth IITravis HughesSam KazerAlex 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
IFNγ-Dependent Tissue-Immune Homeostasis is Co-opted in the Tumor Microenvironment
CancerGenomicsImmunologyJay PrakadanAlex 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
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
BiologyCancerGenomicsMedicineJay PrakadanMarc Wadsworth II
Alex GenshaftTravis HughesCarly ZieglerSam Kazer
Aleth GaillardKellie KolbAlex K. Shalek
Innate Lymphoid Cells Are Depleted Irreversibly during Acute HIV-1 Infection in the Absence of Viral Suppression
BiologyGenomicsImmunologyInfectious DiseaseSam KazerAlex K. Shalek
A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages
BiologyGenomicsImmunologyR&DTechnologyAlex GenshaftSam KazerAlex K. Shalek
Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity
BiologyGenomicsImmunologyAlex K. Shalek
Oct1 and OCA-B are selectively required for CD4 memory T cell function
BiologyGenomicsImmunologyAlex K. Shalek
Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses
BiologyGenomicsImmunologyInfectious DiseaseMicrobiologyTechnologyAlex K. Shalek
Heterogeneity in immune responses: from populations to single cells
GenomicsImmunologyTechnologyAlex K. Shalek
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
BiologyGenomicsImmunologyAlex K. Shalek
Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli
BiologyImmunologyAlex K. Shalek
Dynamic regulatory network controlling TH17 cell differentiation
BiologyGenomicsImmunologyAlex K. Shalek
Probing Enzymatic Activity inside Living Cells Using a Nanowire−Cell “Sandwich” Assay
BiologyChemistryImmunologyTechnologyAlex K. Shalek
Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits
GenomicsImmunologyInfectious DiseaseAlex K. Shalek