Xinsong Chen

SIMPlex generates matched spatial and single-nucleus transcriptomic profiles from the same tissue section to resolve cell states with spatial signatures in mouse and human cancer tissues.

The paper analyzes subclonal gene dosage effects in cancer using DNTR-seq, finding additive and compensatory transcriptional impacts and identifying transient clonality in ovarian and soft tissue sarcomas.

This paper introduces spatial ATAC, a method for spatially resolved chromatin accessibility profiling, and demonstrates its application in studying gene regulation in mouse development and human disease.

PhylEx reconstructs clonal structure by integrating bulk DNA-seq and scRNA-seq data, outperforming existing methods in clonal-tree reconstruction and mutation clustering.