Mahdi Zamanighomi

The paper introduces coupled nonnegative matrix factorizations to integrate single cell RNA-seq and ATAC-seq data by coupling clustering across samples.

This paper introduces scABC, an R package for unsupervised clustering of scATAC-seq data to classify cell types based on open chromatin regions.

AC-PCA reduces dimensionality and adjusts for confounding variation in biological datasets, recovering anatomical structure and shared variation across species.