Lindsey A. Muir

The paper develops an agent-based model of fibroblast scratch assays to simulate wound healing, achieving high accuracy in predicting cell behavior across different geometries.

The paper develops a single-cell transcriptomic reference atlas and evaluates a transcription factor recipe for reprogramming fibroblasts into hematopoietic stem cells, revealing intermediate transcriptomic states and transcriptional remodeling.

The paper maps multi-way chromatin contacts using long reads and identifies cell type-specific transcription clusters by integrating contacts with chromatin accessibility and gene expression.

This study shows that WAPL regulates T cell 3D genome structure, affecting activation, proliferation, and GVHD severity.

The paper investigates allele-specific relationships between gene expression and genome structure in human cells using integrated haplotype-resolved data.

This study shows that MYOD1-mediated reprogramming of human fibroblasts into muscle cells involves a genome architecture bifurcation point preceding transcriptional changes.

The paper introduces a data-guided algorithm for cellular reprogramming using transcription factors, validated on human fibroblasts and showing potential for tissue regeneration and cancer cell reprogramming.