Stephen Lindsly

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.

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

The paper introduces 4DNvestigator, a toolbox for analyzing time series Hi-C and RNA-seq data, with methods to quantify network and tensor entropy and detect significant changes over time.

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.