Yubo Zhang

Hyper3D-lite: count-preserving representation auditing for long-read multi-contact genome data

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

A single-cell genomic strategy for alternative transcript start sites identification

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.

Genome-wide identification of silencers in human cells

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.

Induce Pluripotency via Specific distal enhancer-promoter associations

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.

Start from Scratch: Precisely Identify Massive Active Enhancers by Sequencing

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

Enhancer-promoter association determines Sox2 transcription regulation in mouse pluripotent cells

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