Simone Webb

TERRA is a foundation model for spatial transcriptomics that predicts tissue behavior under perturbation and identifies multi-scale biological insights across tissues.

Human Developmental Cell Atlas integrates ~4.6 million cells/nuclei from 4-22 post-conception weeks into 454 refined cell types and maps 114 spatial niches across 6PCW whole-embryo sections.

Tripso, a self-supervised transformer model, identifies gene program-specific embeddings and discovers novel gene programs, revealing biological insights in hematopoietic development and disease.

PerturbGen predicts how genetic perturbations affect cellular trajectories across time in human datasets, showing effects on immune responses, hematopoiesis, and skin development.

This study uses single-cell transcriptomics to compare in vitro and in vivo chondrocyte differentiation, identifies off-target differentiation, and improves in vitro protocols by inhibiting FOXO1.

The paper generates a single-cell and spatial transcriptomic atlas of human fetal meninges and finds that meningiomas likely originate from dura lineage cells.

CellHint harmonizes cell types across Human Cell Atlas datasets, revealing new cell states and providing a cross-tissue database with 3.7 million cells.

The paper maps the multi-organ functions of the human yolk sac during early development, revealing its roles in hematopoiesis, nutrition, and oxygen regulation.

The paper identifies a distinct developmental state in KMT2A-rearranged infant B-cell acute lymphoblastic leukemia using single-cell transcriptome analysis.

This study uses single-cell RNA-sequencing to analyze fetal bone marrow development and identifies disruptions in hematopoiesis in Down syndrome.

This paper constructs a single-cell transcriptome atlas of human oral mucosa in health and periodontitis, identifying a stromal-neutrophil axis regulating tissue immunity.