Bingxiang Xu

This paper introduces STRIDE, a sequencing depth-insensitive metric for comparing sparse single-cell Hi-C data, enabling robust analysis of 3D genome organization.

The paper shows that mRNA concentration-dependent translation allows Drosophila embryos to create sharp protein patterns despite limited resources.

The paper investigates chromatin structure dynamics during zebrafish HSPC development and identifies PU.1 as a key factor in chromatin loop formation and gene regulation.

The paper shows that long-term heat shock causes chromatin conformation changes in K562 cells due to cell cycle arrest, not chromatin accessibility changes.

The paper introduces deNOPA, a tool for predicting nucleosome positions from ATAC-seq data, showing it outperforms existing tools and works with ultrasparse data.

The paper shows that transcriptional responses to thermal stress in human cells are prewired in the 3D genome, with chromatin and epigenetic settings playing a key role.

The paper introduces CISD and CISD_loop methods to predict chromatin interactions from MNase-seq and Hi-C data, achieving kilobase resolution with low data requirements.