TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures
Biology
Cell Atlas
Genomics
Immunology
R&D
Technology
Alex 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 Atlas
Computational MethodsGenomicsImmunology
Carly Ziegler
José Ordovas-MontañesAlex K. Shalek
Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration
BiologyCell AtlasGenomicsImmunology
Medicine
Brittany GoodsAlex K. Shalek
Induction of metabolic quiescence defines the transitional to follicular B cell switch
BiologyGenomicsImmunology
Toby 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
BiologyGenomicsImmunology
Infectious DiseaseMedicine
Sam KazerAlex K. Shalek
Highly efficient, massively-parallel single-cell RNA-Seq reveals cellular states and molecular features of human skin pathology
BiologyGenomicsImmunologyR&DTechnology
Travis Hughes
Marc 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 Aicher
Shaina CarrollJosé Ordovas-MontañesCarly Ziegler
Sarah 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
Biology
CancerImmunology
Kellie Kolb
Jay 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 NyquistTravis HughesMarc Wadsworth IISam 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
GenomicsImmunology
Andrew 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 DiseaseMedicine
MicrobiologySam 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
Biology
ChemistryImmunologyTechnologyAlex K. Shalek
Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits
GenomicsImmunologyInfectious DiseaseAlex K. Shalek