Alex K. Shalek

The paper identifies cellular and molecular signatures associated with varying severities of West Nile Virus infection using multi-omics analysis of immune responses.

The paper introduces a method to prioritize causal genes for complex traits by integrating GWAS data with gene expression and biological data, achieving high precision in gene-trait pair identification.

The paper introduces a method to compress phenotypic screens using computational deconvolution, demonstrating increased efficiency and applicability to complex multicellular models.

This paper identifies a non-enzymatic HDAC inhibitor with anti-tumor and anti-psychedelic effects, showing reduced gene modulation compared to enzymatic inhibitors.

This study uses scRNA-seq to analyze human breast milk cells over lactation, identifying cell type shifts and functional changes linked to time and maternal factors.

The paper uses single-cell RNA-sequencing to study environmental enteropathy, identifying epithelial and immune correlates of disease severity and suggesting new therapeutic targets.

This study creates a single-cell and spatial atlas of autopsy tissues from COVID-19 patients, revealing altered cellular responses and potential therapeutic targets.

This study uses single-cell RNA-seq and computational methods to analyze macrophage states in COPD patients, revealing transcriptional changes and metabolic shifts associated with the disease.

The paper uses single-cell RNA sequencing to study influenza infection in human nasal washes, identifying a novel goblet cell population and tracking viral variation across infected individuals.

The paper introduces a method to spatially label and isolate cells using photoactivatable dyes, demonstrating its application in organoids and tissue sections to study spatial gene expression and cell behavior.

The paper uses single-cell RNA-sequencing to study immune dynamics in HIV-1 infection, identifying key cellular responses and their temporal progression in untreated individuals.

The paper was withdrawn due to the inclusion of confidential information about a third party.

Seven single-cell and single-nucleus protocols run side by side on the same cell lines, PBMCs and mouse cortex, analysed through one pipeline: 10x Chromium led the high-throughput methods.

This study identifies IL-5Rα-expressing IgG4 and IgE-secreting cells in nasal polyps of AERD patients, linking them to disease severity and local antibody production.

This study shows that T helper cells interact with intestinal stem cells via MHCII to regulate their renewal and differentiation, with distinct effects based on Th subtype and cytokine signaling.