Allon Wagner

This study profiles intestinal T cell responses to the microbiota, revealing antigen-specific dependencies on early-life programming for generating microbiota-reactive Tregs.

The paper introduces MeRN, a graph-guided variational autoencoder for learning single-cell metabolic states from transcriptomes, and identifies metabolic drivers in various biological contexts.

This study uses a deep-learning model to analyze scRNA-seq data and identifies how folate deficiency disrupts metabolic transitions in developing mouse neural ectoderm, leading to morphological defects.

Intra-tumoral Treg ablation enhances NK cell-mediated tumor control by restoring IL-2 production, effective against both MHC I+ and MHC I- cancers without systemic toxicity.

This study shows neonatal human naive CD4+ T cells have higher CD38 expression, linking it to glycolytic metabolism and tolerogenic function compared to adult cells.

Harreman identifies metabolic crosstalk in spatial transcriptomics data by analyzing co-localized metabolite transporter expression, revealing tissue-specific metabolic exchanges in human and mouse models.

MEBOCOST infers metabolite-mediated cell communications from single-cell RNA-seq data, identifying known and novel interactions in mouse brown adipose tissue.

This study identifies PGAM as a negative regulator of Th17 pathogenicity using single-cell RNA-seq and metabolic flux analysis.

The paper identifies a poxvirus effector that triggers an NF-κB response by disrupting anti-viral complexes, revealing a novel ETI pathway.

The paper introduces DestVI, a method for multi-resolution spatial transcriptomics analysis that captures continuous cell state variation, and applies it to study inflammation in lymph nodes and tumors.

The paper introduces Compass, an algorithm that uses single-cell RNA-Seq and flux balance analysis to characterize metabolic states in Th17 cells, revealing a metabolic switch and novel anti-inflammatory regulators.

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.

This paper evaluates normalization methods for scRNA-seq using a framework called scone, showing that top methods improve agreement with validation data.

The paper proposes the Human Cell Atlas project to catalog all human cell types through molecular profiling and connects this data with classical cellular descriptions.