Comparative analysis of cell–cell communication at single-cell resolution
Computational Methods
Genomics
R&D
Statistics
Alex K. Shalek
Compressed phenotypic screens for complex multicellular models and high-content assays
Biology
Cancer
ChemistryComputational MethodsGenomicsR&DStatistics
Technology
Ben Mead
Conner Kummerlowe
Ivy Liu
Walaa Kattan
Thomas Nok Hin Cheng
Peter WinterAlex K. Shalek
NIAID Workshop on T Cell Technologies
Biology
Cell AtlasComputational MethodsGenomics
ImmunologyR&DAlex K. Shalek
Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis)
BiologyCell AtlasComputational MethodsGenomicsImmunology
Infectious DiseaseR&D
Sarah Nyquist
Tasneem Jivanjee
Samira Ibrahim
Josh Bromley
James GatterAlex 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
Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation
BiologyComputational MethodsGenomicsImmunology
MedicineR&DTechnologyBen Mead
Marko VukovicConner Kummerlowe
José Ordovas-MontañesAlex K. Shalek
Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer
CancerComputational MethodsGenomicsImmunologyMedicineR&DTechnologyPeter Winter
Andrew Navia
Jennyfer Galvez-Reyes
Nolawit 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 Vilme
Riley Drake
Ira Fleming
Nancy Tran
Constantine Tzouanas
Jasmin Joseph-ChazanAlex K. Shalek
A Treatment-Naive Cellular Atlas of Pediatric Crohn’s Disease Predicts Disease Severity and Therapeutic Response
BiologyCell AtlasComputational MethodsGenomicsImmunologyMedicine
Benjamin Doran
Kyle KimlerAlex K. ShalekJosé Ordovas-Montañes
Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
BiologyCell AtlasComputational MethodsGenomicsImmunologyInfectious Disease
Carly Ziegler
Vincent MiaoAndrew NaviaJosh Bromley
Micayla GeorgeRiley DrakeAlex K. ShalekJosé Ordovas-Montañes
COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
BiologyCell AtlasComputational MethodsGenomicsImmunologyInfectious DiseaseStatisticsCarly ZieglerAlex K. Shalek
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
Cell AtlasComputational MethodsGenomicsImmunologyInfectious DiseaseStatistics
Sam 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
Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets
BiologyComputational MethodsStatisticsSarah NyquistAlex 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 Disease
Sam KazerJames GatterAlex K. Shalek
Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease
Computational MethodsGenomicsImmunologyMedicineMarc Wadsworth II
Travis HughesAlex K. Shalek
Computational Methods for Single-Cell RNA Sequencing
BiologyComputational MethodsGenomicsSarah NyquistAlex 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
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 II
Shaina CarrollAlex 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
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
Voices in methods development
Computational MethodsGenomicsR&DTechnologyAlex K. Shalek
A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers
Computational MethodsGenomicsImmunologyInfectious DiseaseMedicine
Kellie KolbJosé Ordovas-MontañesAlex K. Shalek
MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data
Computational MethodsStatisticsAlex K. Shalek
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
GenomicsR&DTechnologyAlex K. Shalek