Zhihua Zhang

STRIDE: A Sequencing Depth-Insensitive Metric for Robust Comparison between Sparse Chromosome Conformation Capture Data

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

DeLoop: a deep learning model for chromatin loop prediction from sparse ATAC-seq data

DeLoop predicts CTCF-mediated chromatin loops from sparse ATAC-seq data, outperforming existing models under low read depth conditions.

DeDoc2 identifies and characterizes the hierarchy and dynamics of chromatin TAD-like domains in the single cells

DeDoc2 identifies and characterizes the dynamic hierarchy of TAD-like domains in single cells, showing their variability during the cell cycle and across human brain cortex cells.

Cell cycle arrest explained the observed bulk 3D genomic alterations in response to long term heat shock for mammalian cells

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

Evidences for functional trans-acting eRNA-promoter R-loops at Alu sequences

The paper identifies Alu sequences as key mediators of enhancer-promoter interactions through trans-acting R-loops formed by eRNAs, showing their functional and evolutionary significance.

DeTOKI identifies and characterizes the dynamics of chromatin topologically associating domains in a single cell

DeTOKI identifies and characterizes chromatin topologically associating domains (TADs) in single cells using scHi-C data, revealing their dynamic yet regulated nature.

Decoding nucleosome positions with ATAC-seq data at single-cell level

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

Widespread transcriptional responses to the thermal stresses are prewired in human 3D genome

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.

Delta integrates 3D physical structure with topology and genomic data of chromosomes

Delta integrates 3D chromosomal structure with genomic data to visualize and analyze regulatory networks, revealing insights into gene regulation through a case study on the beta-globin region.

Characteristic arrangement of nucleosomes is predictive of chromatin interactions at kilobase resolution

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.