Duy Pham

The Human Gut Cell Atlas v1.0: A Unified, Community-Built Reference of Cellular Diversity Across the Gut

The paper presents the Human Gut Cell Atlas v1.0, a unified reference of gut cell diversity, revealing how tissue structure influences cellular composition and enabling disease and organoid analysis.

Gp130 Orchestrates a Bidirectional Neuron-Microglia Circuit for neuroprotection

This study identifies gp130 as a key receptor for a bidirectional neuron-microglia circuit that enhances neuroprotection after CNS injury.

Spatial lung niches shape Pseudomonas aeruginosa persistence

This study uses spatial transcriptomics to map Pseudomonas aeruginosa niches in lung tissue from CF and COPD patients, revealing distinct bacterial states and host interactions linked to infection persistence.

Integrating 12 Spatial and Single Cell Technologies to Characterise Tumour Neighbourhoods and Cellular Interactions in three Skin Cancer Types

The paper integrates 12 spatial and single-cell technologies to analyze cellular interactions and signatures in three skin cancers, identifying key therapeutic targets and genetic associations.

An atlas of TF driven gene programs across human cells

The paper creates a regulon atlas mapping TF activity across human cell types and uses it to link disease signatures to cell types and TFs, improving disease risk locus analysis.

inVAE: Conditionally invariant representation learning for generating multivariate single-cell reference maps

inVAE improves cell state identification by disentangling biological and technical variation in single-cell data, outperforming existing methods across multiple human tissues.

stLearn: integrating spatial location, tissue morphology and gene expression to find cell types, cell-cell interactions and spatial trajectories within undissociated tissues

Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity

The paper introduces TRIAGE-Cluster and TRIAGE-ParseR to define cell diversity in scRNA-seq data using epigenetic data as a biological anchor.

i-stLearn: An interactive platform for spatial transcriptomics analysis

i-stLearn provides an interactive web platform for analyzing spatial transcriptomics data, enabling cell clustering, interaction analysis, and trajectory inference.

A pluripotent stem cell atlas of multilineage differentiation reveals TMEM88 as a developmental regulator of mammalian blood pressure

The paper creates an iPSC differentiation atlas and identifies TMEM88 as a regulator of mesendodermal development and blood pressure.