Dark Genes

In traditional transcriptomics, researchers often focus on genes that show significant changes in expression levels between different biological states—known as differentially expressed genes (DEGs). However, a vast number of genes, often referred to as “Dark Genes,” remain hidden from these standard analyses. By developing novel computational frameworks to detect these subtle shifts in network topology, we aim to provide the researchers with a bioinformatic pipeline to understand how dark genes modulate biological functions under diverse contexts from single-cell RNA-seq and ATAC-seq data, ultimately revealing a critical layer of genomic regulation that remains invisible to standard analytical methods.