Pro-inflammatory feedback loops define immune responses to pathogenic lentivirus infection
Genomics
Immunology
Infectious Disease
Sam Kazer
Ira Fleming
Vincent Miao
Jennyfer Galvez-Reyes
Alex K. Shalek
Compressed phenotypic screens for complex multicellular models and high-content assays
Biology
Cancer
Chemistry
Computational MethodsGenomics
R&D
Statistics
Technology
Ben Mead
Conner Kummerlowe
Ivy Liu
Walaa Kattan
Thomas Nok Hin Cheng
Peter WinterAlex K. Shalek
Clinical implementation of single-cell RNA sequencing using liver fine needle aspirate tissue sampling and centralized processing captures compartment specific immuno-diversity
Biology
Cell AtlasComputational MethodsGenomicsImmunologyInfectious DiseaseR&DTechnology
Alex Genshaft
Mike Vilme
Riley DrakeIra Fleming
Nancy Tran
Constantine Tzouanas
Jasmin Joseph-ChazanAlex K. Shalek
Cellular and transcriptional diversity over the course of human lactation
BiologyCell AtlasGenomicsImmunologyVincent Miao
Patricia GaoRiley Drake
Kellie KolbBen MeadAlex K. Shalek
Brittany Goods
A Treatment-Naive Cellular Atlas of Pediatric Crohn’s Disease Predicts Disease Severity and Therapeutic Response
BiologyCell AtlasComputational MethodsGenomicsImmunology
Medicine
Benjamin Doran
Kyle KimlerAlex K. Shalek
José Ordovas-Montañes
Single-cell profiling of environmental enteropathy reveals signatures of epithelial remodeling and immune activation in severe disease
BiologyGenomicsImmunologyInfectious DiseaseConner Kummerlowe
Travis Hughes
Nolawit MulugetaIra Fleming
Marko VukovicBenjamin DoranJosé Ordovas-MontañesAlex K. Shalek
A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2
BiologyCell AtlasComputational MethodsGenomicsImmunologyInfectious DiseaseStatistics
Carly ZieglerAlex K. Shalek
Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
BiologyGenomicsImmunologyInfectious Disease
MicrobiologyCarly ZieglerVincent Miao
Andrew Navia
Josh Bromley
Micayla 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 Hughes
Marc Wadsworth IIAlex K. Shalek
Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells
BiologyGenomicsImmunology
Sam AllonJosé Ordovas-MontañesAlex 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 tuberculosis lung granulomas reveals functional lymphocyte signatures of bacterial control
BiologyCell AtlasGenomicsImmunologyInfectious DiseaseTravis HughesMarc Wadsworth IIConner Kummerlowe
Sarah NyquistJosé Ordovas-MontañesAlex K. Shalek
The tumor microenvironment drives transcriptional phenotypes and their plasticity in metastatic pancreatic cancer
BiologyCancerCell AtlasComputational MethodsGenomicsImmunologyMedicineTechnologyPeter WinterAndrew NaviaJennyfer Galvez-ReyesNolawit MulugetaAlex 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
High-throughput organoid screening enables engineering of intestinal epithelial composition
BiologyGenomicsMedicineR&DTechnologyBen MeadMarko VukovicJosé Ordovas-MontañesAlex K. Shalek
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
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 Doran
James GatterMarko VukovicConstantine Tzouanas
Shaina CarrollAlex K. ShalekJosé Ordovas-Montañes
Spatially-resolved live cell tagging and isolation using protected photoactivatable cell dyes
BiologyCancerChemistryGenomicsR&DTechnologyAlex GenshaftCarly ZieglerConstantine TzouanasBen MeadAndrew NaviaAlex 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
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
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 Kazer
Toby AicherShaina CarrollJosé Ordovas-MontañesCarly ZieglerSarah NyquistAlex K. Shalek
Rewiring of the cellular and inter-cellular landscape of the human colon during ulcerative colitis
BiologyCell AtlasComputational MethodsImmunologyMedicineJosé Ordovas-MontañesAlex K. Shalek
Linking single-cell measurements of mass, growth rate, and gene expression
ChemistryGenomicsTechnology
Jay Prakadan
Alejandro GuptaRiley DrakeAlex 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