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
A human liver cell-based system modeling a clinical prognostic liver signature for therapeutic discovery
Biology
CancerGenomicsImmunology
R&D
TechnologyAlex K. Shalek
Mepolizumab targets multiple immune cells in aspirin-exacerbated respiratory disease
BiologyGenomicsImmunology
Medicine
Marko VukovicAlex K. Shalek
José Ordovas-Montañes
An ex vivo ovulation system enables the discovery of novel ovulatory pathways and nonhormonal contraceptive candidates
Biology
Cell AtlasGenomics
Brittany GoodsAlex K. Shalek
Vitrification preserves murine ovarian follicular cell transcriptome in a 3D encapsulated in vitro follicle growth system
BiologyGenomicsImmunologyR&DTechnology
Riley Drake
Daniela RussoAlex K. ShalekBrittany Goods
Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity
BiologyCell 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
IL-5Rα marks nasal polyp IgG4- and IgE-expressing cells in aspirin-exacerbated respiratory disease
BiologyGenomicsImmunologyJosé Ordovas-MontañesMarko VukovicAlex K. Shalek
Compressed phenotypic screens for complex multicellular models and high-content assays
BiologyCancer
Chemistry
Computational MethodsGenomicsR&D
StatisticsTechnology
Ben Mead
Conner Kummerlowe
Ivy Liu
Walaa Kattan
Thomas Nok Hin Cheng
Peter WinterAlex K. Shalek
Spatially Resolved Single-Cell Assessment of Pancreatic Cancer Expression Subtypes Reveals Co-expressor Phenotypes and Extensive Intratumoral Heterogeneity
CancerGenomicsImmunologyR&DTechnologyPeter Winter
Andrew NaviaAlex K. Shalek
NIAID Workshop on T Cell Technologies
BiologyCell AtlasComputational MethodsGenomicsImmunologyR&DAlex K. Shalek
Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis)
BiologyCell AtlasComputational MethodsGenomicsImmunologyInfectious DiseaseR&D
Sarah Nyquist
Tasneem Jivanjee
Samira Ibrahim
Josh 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 transcriptomics of staged oocytes and somatic cells reveal novel regulators of follicle activation
BiologyGenomicsR&DTechnologyDaniela RussoRiley DrakeAlex K. ShalekBrittany Goods
Hypoxic, glycolytic metabolism is a vulnerability of B-acute lymphoblastic leukemia-initiating cells
BiologyCancerGenomicsImmunology
Travis HughesAlex K. Shalek
Single-Cell Multiomics Reveals Clonal T-Cell Expansions and Exhaustion in Blastic Plasmacytoid Dendritic Cell Neoplasm
BiologyCancerCell AtlasGenomicsImmunology
Charles P. CouturierAlex K. Shalek
Identification and tracking of alloreactive T cell clones in Rhesus Macaques through the RM-scTCR-Seq platform
BiologyCell AtlasComputational MethodsGenomicsImmunologyR&DTechnology
Jim KaminskiAlex K. Shalek
PI3K activation allows immune evasion by promoting an inhibitory myeloid tumor microenvironment
BiologyCancerGenomicsImmunologyMedicine
Marc Wadsworth IITravis HughesAlex K. Shalek
Single-cell profiling of environmental enteropathy reveals signatures of epithelial remodeling and immune activation
BiologyCell AtlasGenomicsImmunologyInfectious Disease
MicrobiologyConner KummerloweTravis Hughes
Nolawit MulugetaIra FlemingMarko Vukovic
Benjamin Doran
Toby AicherMarc Wadsworth IIJosé Ordovas-MontañesAlex K. Shalek
Deciphering the immunopeptidome in vivo reveals new tumour antigens
BiologyCancerGenomicsImmunologyPeter WinterAlex 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 DiseaseMicrobiologyTechnologyMarc Wadsworth IITravis HughesAlex K. Shalek
Cellular and transcriptional diversity over the course of human lactation
BiologyCell AtlasGenomicsImmunologyMedicineSarah Nyquist
Patricia GaoRiley Drake
Kellie KolbBen MeadAlex K. ShalekBrittany Goods
Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation
BiologyComputational MethodsGenomicsImmunologyMedicineR&DTechnologyBen MeadMarko VukovicConner KummerloweJosé Ordovas-MontañesAlex K. Shalek
JAK inhibition in a patient with a STAT1 gain-of-function variant reveals STAT1 dysregulation as a common feature of aplastic anemia
BiologyGenomicsImmunologyMedicineTravis HughesAlex K. Shalek
Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states
BiologyCancerGenomicsImmunologyR&DMarc Wadsworth IIAlex K. Shalek
Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer
CancerComputational MethodsGenomicsImmunologyMedicineR&DTechnologyPeter WinterAndrew NaviaJennyfer Galvez-ReyesNolawit MulugetaAlex 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
Cellular and transcriptional diversity over the course of human lactation
BiologyCell AtlasGenomicsImmunologyVincent MiaoPatricia GaoRiley DrakeKellie KolbBen MeadAlex K. ShalekBrittany Goods
Enteric Coronavirus Infection and Treatment Modeled With an Immunocompetent Human Intestine-On-A-Chip
BiologyGenomicsImmunologyInfectious DiseaseMedicineR&DTechnologyVincent MiaoAndrew NaviaCarly ZieglerJosé Ordovas-MontañesAlex K. Shalek
Measuring kinetics and metastatic propensity of CTCs by blood exchange between mice
BiologyCancerGenomicsImmunology
PhysicsR&DTechnologyNolawit MulugetaAlex K. Shalek
Single cell biology—a Keystone Symposia report
BiologyCell AtlasGenomicsAlex K. Shalek
Genomic and transcriptomic correlates of immunotherapy response within the tumor microenvironment of leptomeningeal metastases
BiologyCancerGenomicsImmunologyMedicine
Jay PrakadanAndrew NaviaKellie KolbMarc Wadsworth IIAlex K. Shalek
A Treatment-Naive Cellular Atlas of Pediatric Crohn’s Disease Predicts Disease Severity and Therapeutic Response
BiologyCell AtlasComputational MethodsGenomicsImmunologyMedicineBenjamin Doran
Kyle KimlerAlex K. ShalekJosé Ordovas-Montañes
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
Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes
GenomicsR&DTechnologyAlex GenshaftCarly ZieglerConstantine TzouanasBen MeadAndrew NaviaAlex 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
Expression of Foxp3 by T follicular helper cells in end-stage germinal centers
BiologyGenomicsImmunology
Sam AllonAlex K. Shalek
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
High-fat diet-activated fatty acid oxidation mediates intestinal stemness and tumorigenicity
BiologyGenomicsConstantine TzouanasAlex K. Shalek
Targeting Treg cells with GITR activation alleviates resistance to immunotherapy in murine glioblastomas
CancerGenomicsImmunologyMedicineSam KazerAlex K. Shalek
COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
BiologyCell AtlasComputational MethodsGenomicsImmunologyInfectious DiseaseStatisticsCarly 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 DiseaseMicrobiologyJay PrakadanSam KazerAlex K. Shalek
Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation
BiologyGenomicsImmunologyJosé Ordovas-MontañesSam AllonMarko VukovicTravis HughesSarah NyquistAlex K. Shalek
Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu
BiologyGenomicsImmunologyMedicineBrittany GoodsRiley 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 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
Longitudinal transcriptomics define the stages of myeloid activation in the living human brain after intracerebral hemorrhage
BiologyGenomicsImmunologyMedicineBrittany Goods
Shaina CarrollRiley DrakeJames 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 AtlasGenomicsImmunologyMedicineJim 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
BiologyGenomicsImmunologyKellie 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
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 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
Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies
BiologyCell AtlasChemistryGenomicsImmunologyR&DTechnologyTravis HughesMarc Wadsworth IIJosé Ordovas-MontañesAlex K. Shalek
Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets
BiologyComputational MethodsStatisticsSarah NyquistAlex 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 MethodsGenomicsImmunologyMedicineTechnologyPeter WinterAndrew NaviaJennyfer 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
Computational Methods for Single-Cell RNA Sequencing
BiologyComputational MethodsGenomicsSarah NyquistAlex K. Shalek
High-throughput organoid screening enables engineering of intestinal epithelial composition
BiologyGenomicsMedicineR&DTechnologyBen MeadMarko VukovicJosé Ordovas-MontañesAlex 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 VukovicBen 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
Systematic comparison of single-cell and single-nucleus RNA-sequencing methods
Computational MethodsGenomicsR&DTechnologyTravis HughesMarc Wadsworth IIShaina CarrollAlex 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
Spatially-resolved live cell tagging and isolation using protected photoactivatable cell dyes
BiologyCancerChemistryGenomicsR&DTechnologyAlex GenshaftCarly ZieglerConstantine TzouanasBen MeadAndrew NaviaAlex K. Shalek
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
Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression
BiologyGenomicsMarc Wadsworth IISam AllonBen MeadRiley DrakeAlex K. Shalek