Emily Stephenson

The paper builds a spatiotemporal map of human pilosebaceous unit development using single-cell multiomics and machine learning, showing how epithelial-mesenchymal interactions drive organogenesis and how sebaceous gland programs are disrupted in tumors.

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.

This study creates a spatially-resolved molecular atlas of human skin and uses deep learning to identify 26 niches, revealing novel immune memory structures in inflammatory skin diseases.

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

This study identifies non-canonical NF-κB signalling as a therapeutic target in CYLD cutaneous syndrome and shows that IKK inhibition reduces tumor viability in patient-derived models.

The paper maps the spatial organization of the human thymus across developmental stages using a multimodal atlas and identifies key cellular and molecular features of T cell development.

The paper integrates single-cell RNA-seq datasets across the GI tract to identify epithelial metaplasia in inflammatory diseases, showing its role in inflammation through immune cell interactions.

The paper identifies Th2-like malignant cells in CTCL supported by a B cell-rich microenvironment through single-cell and spatial transcriptomics analysis.

This study creates a prenatal human skin cell atlas, revealing immune cells' role in skin development and showing their impact on vascular and hair follicle formation.

The paper develops GASPACHO to identify dynamic eQTLs in antiviral responses using single-cell RNA-seq, uncovering thousands of eQTLs and linking them to disease risk loci.

This study creates a single-cell atlas of human liver development, identifying pathways and factors that guide hepatic cell fates and improving hepatocyte-like cell functionality.

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

MultiMAP integrates multimodal data by reducing dimensionality and preserving structure, outperforming existing methods in various tasks.

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

The paper uses single-cell transcriptomics to map hematopoiesis in human fetal liver, identifying cell differentiation trajectories and shifts in hematopoietic composition during development.

The paper profiles single-cell transcriptomes from the human first trimester fetal-maternal interface, revealing cellular composition and interactions critical for placentation.