Michael J. Apostolides

This paper introduces MPAQT, a framework that improves isoform quantification in bulk and single-cell RNA-seq by integrating short- and long-read data and using sequence-to-expression models.

MetaFusion improves fusion detection by combining multiple callers, achieving higher precision and recall through standardized annotation and graph clustering.

The paper identifies RNA-specific gene fusions in tumors and normal tissues, showing they are linked to spliceosomal gene dysregulation and may contribute to cancer development.