William N. Colgan

Pycea: a scverse toolkit for single-cell lineage tracing analysis

Pycea provides a toolkit for analyzing single-cell lineage tracing data, integrating with Scanpy and offering visualization and statistical methods for lineage trees.

Comprehensive Lineage Tracing Maps the Landscape of Cell Fate Decisions in Mouse Embryogenesis

Prime-editing lineage trees for 16 mouse embryos (E7.5 to E10.0, >1.4 million cells) quantify fate restriction timing, progenitor numbers and lineage relationships, and are reproducible across replicate embryos.

Folate deficiency disrupts key metabolic transitions within the developing neural ectoderm

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.

Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumor growth and metastasis

This study uses spatial transcriptomics and lineage tracing to show how tumor subclones drive microenvironmental changes that promote metastasis in a mouse model.

Dissecting context-dependent cancer vulnerabilities using Perturb-seq

The paper uses Perturb-seq to analyze gene knockouts in cancer cell lines, identifying context-specific gene dependencies and transcriptional responses.

Low-heteroplasmy mitochondrial DNA mutations improve clonal reconstruction of human cells

This study shows that low-heteroplasmy mitochondrial DNA mutations provide reliable clonal information, improving clonal reconstruction in human cells.

Atlas of Lysosomal Aging Reveals a Molecular Clock of Storage Disorder-Associated Metabolites

The paper constructs a multi-tissue lysosomal metabolite atlas in mice, revealing age-related accumulation of glycerophosphodiesters and cystine, linked to lysosomal storage disorders, and shows caloric restriction mitigates these changes in some tissues.

High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer

PEtracer maps cell state and lineage dynamics in vivo with high spatial resolution using prime editing and multimodal imaging.