Tools for Integrated Analysis of Single-Cell Epigenomic and Transcriptomic Data

To develop computation methods and algorithms for integrating single-cell epigenome and transcriptome data sets to classify cell types and their biological regulation.

During this project, the Mukamel lab developed a software package, SingleCellFusion, which uses bigraph imputation to link measurements of single-cell or single-nucleus transcriptomes and epigenomes. They take advantage of robust correlations between gene expression and epigenetic marks in the gene body to identify the best matched groups of cells across datasets from different modalities, taking into account systematic differences across experimental batches and platforms.