Nadia Grenningloh

COSMIC, a generative model, quantifies the relationship between nuclear morphology and gene expression using paired single-cell data, revealing morphology-associated genes in prostate cancer and spatial transcriptomics of zebrafish embryos.

This study identifies DNA binding motifs for 98 human transcription factors using meSMiLE-seq, revealing methylation-sensitive binding preferences for some TFs.

The paper introduces IRIS, a platform integrating high-resolution imaging and single-cell RNA sequencing to link morphology with transcriptomes, revealing new nuclear-ER architectures in CD8+ T cells.

EXTRA-seq quantifies enhancer-promoter communication in endogenous contexts, revealing the TATA-box's role in modulating expression and improving gene expression prediction when integrated with deep learning models.