Chelsea M. Pagan

SCALPEL: A pipeline for processing large-scale spatial transcriptomics data

SCALPEL processes large-scale spatial transcriptomics data with improved 3D segmentation, doublet detection, and spatial alignment, showing better performance than previous methods.

The transcriptomic and spatial organization of telencephalic GABAergic neuronal types

The paper analyzes the transcriptomic and spatial organization of GABAergic neurons in the mouse telencephalon, revealing complex developmental and spatial relationships across multiple brain regions.

MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics

The paper introduces MerQuaCo, an open-source tool to automatically detect and quantify imperfections in spatial transcriptomics data, improving quality assessment.

Integrated multimodal cell atlas of Alzheimer's disease

This study creates an integrated multimodal cell atlas of Alzheimer's disease by analyzing single nuclei transcriptomes, epigenomes, and spatial coordinates across AD stages.

Continuous cell type diversification throughout the embryonic and postnatal mouse visual cortex development

The paper constructs a high-resolution transcriptomic and epigenomic atlas of the developing mouse visual cortex, revealing continuous cell type diversification across embryonic and postnatal stages.

Known pathogenic gene variants and new candidates detected in Sudden Unexpected Infant Death using Whole Genome Sequencing

This study identifies known pathogenic variants and new candidates in SUID using WGS, highlighting genetic factors related to heart disease and redox metabolism.

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

This paper creates a high-resolution transcriptomic and spatial cell type atlas of the whole adult mouse brain, revealing spatial organization and transcription factor codes for cell types.