Yubo Zhang

Hyper3D-lite audits long-read multi-contact genome data by preserving counts during all-pair projections to avoid overcounting contact evidence.

The paper introduces a single-cell genomic method to identify alternative TSSs in mouse cells and shows it is accurate and sensitive, revealing more TSSs than previous methods.

The paper identifies silencer regions in three human cell lines using MPRAs, finding 739,434, 643,484, and 491,952 silencer regions with inhibitory activity and enriched inhibitory motifs.

This study identifies specific distal enhancer-promoter associations that can reprogram MEF cells into iPS-like clones, demonstrating a method to generate pluripotent cells through 3D chromatin conformation.

The paper introduces MAE-Seq, an experimental method to identify active enhancer sequences, and reports the discovery of known enhancers and unmarked regulatory elements.

The paper investigates how different enhancer-promoter associations influence Sox2 transcription in mouse embryonic stem cells, revealing distinct biological effects based on interaction type.