Emily Stephenson

Function-driven geometry directs human pilosebaceous unit development

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.

An integrated single cell and spatial omics atlas of human prenatal development

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.

Self-supervised learning for a gene program-centric view of cell states

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

Hidden immune memory niches in inflammatory skin diseases

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.

Predicting how perturbations reshape cellular trajectories with PerturbGen

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

Targeting non-canonical NF-κB signalling in CYLD cutaneous syndrome by selective inhibition of IκB kinase alpha.

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.

Single Cell Integration Characterises Metaplasia in Inflammatory Intestinal Diseases

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.

Cutaneous T cell lymphoma atlas reveals malignant Th2 cells supported by a B cell-rich microenvironment

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

A human prenatal skin cell atlas reveals immune cell regulation of skin morphogenesis

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.

Mapping interindividual dynamics of innate immune response at single-cell resolution

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.

Single-cell atlas of human liver development reveals pathways directing hepatic cell fates

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.

Multi-organ functions of yolk sac during human early development

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: Dimensionality Reduction and Integration of Multimodal Data

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

Intrinsic and extrinsic regulation of human fetal bone marrow haematopoiesis and perturbations in Down syndrome

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

Decoding the development of the blood and immune systems during human fetal liver haematopoiesis

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

Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics

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