Xufeng Shu

The paper identifies repeat element-anchored enhancer-promoter interactions (REEPIs) in hormone-resistant breast cancer and links them to transcriptional adaptation and regulatory reprogramming.

The paper maps RNA-DNA interactions in 16 human cell types, showing cell-type-specific and dynamic networks that correlate with gene regulation and disease traits.

The paper identifies hypoacetylation-defined enhancers in luminal breast cancer cells and links them to subtype-specific gene regulation and patient classification.

The paper identifies trans-contacting intronic RNAs (TIRs) in neuronal cells that form nuclear scaffolds called introsomes, influencing 3D genome organization and gene expression.

This paper introduces CFC-seq and SALA to sequence non-poly(A) RNAs, identifies 39,425 novel transcriptional units, and reveals a genomic code governing enhancer RNA fate based on promoter architecture.

The paper introduces RADIP, a new technology for mapping RNA-chromatin interactions mediated by H3K27me3, and demonstrates its application in mouse embryonic stem cells.

The paper performs knockdown of 200 lncRNAs in human iPS cells, identifies 36 with growth inhibition, and finds molecular phenotypes in 29.3% of cases, with higher agreement in molecular than cell growth phenotypes across cell types.