Shu Yi Shen

This study benchmarks CUT&RUN peak callers using motif enrichment, finding that MACS2 outperforms SEACR in most scenarios with optimal preprocessing.

The paper uses cfMeDIP-seq to analyze cell-free placental DNA methylation in maternal plasma, identifying enriched regions associated with preterm birth and IUGR.

The paper develops methods to model transcription factor binding in modified DNA by expanding the DNA alphabet and adapting existing tools to handle custom alphabets, identifying modification-sensitive motifs and validating them with experimental data.

This paper introduces synthetic spike-in controls for cfMeDIP-seq to enable accurate and reproducible quantification of DNA methylation, reducing batch effects and technical biases.