Zhihua Zhang

发表

A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information

Michael Q. Zhang, R. Serfling, Z. Xuan, 2011, Nucleic acids research.

Computational Identification of Active Enhancers in Model Organisms

Zhihua Zhang, Michael Q. Zhang, Chengqi Wang, 2013, Genom. Proteom. Bioinform..

The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos

Zhihua Zhang, Jianguo Zhao, Bingxian Xu, 2020, Genome Biology.

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

Zhihua Zhang, Yiqun Zhang, Bingxian Xu, 2016, bioRxiv.

Evidence of constraint in the 3D genome for trans-splicing in human cells

Zhihua Zhang, Yiqun Zhang, Yan Jia, 2020, Science China Life Sciences.

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

Wenming Zhao, Zhihua Zhang, Bixia Tang, 2017, bioRxiv.

Comparative 3D genome architecture in vertebrates

Zhihua Zhang, Shilin Tian, Long Jin, 2022, BMC biology.

Bivalent-Like Chromatin Markers Are Predictive for Transcription Start Site Distribution in Human

Michael Q. Zhang, Xiaotu Ma, Zhihua Zhang, 2012, PloS one.

An efficient and assumption-free method to approximate protein level distribution in the two-states gene expression model.

Hao Ge, Zhihua Zhang, Bingxian Xu, 2017, Journal of theoretical biology.

DeDoc2 Identifies and Characterizes the Hierarchy and Dynamics of Chromatin TAD‐Like Domains in the Single Cells

Zhihua Zhang, Angsheng Li, Xiao Li, 2022, bioRxiv.

Cell cycle arrest explains the observed bulk 3D genomic alterations in response to long-term heat shock in K562 cells

Zhihua Zhang, Bingxian Xu, Yan Jia, 2022, Genome Research.

DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell

Zhihua Zhang, Angsheng Li, Xiao Li, 2021, Genome Biology.

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

Zhihua Zhang, Xiao Li, 2021, bioRxiv.

A dynamic kissing model for enhancer-promoter communication on the surface of transcriptional condensate

Zhihua Zhang, Qing Zhang, Hualin Shi, 2022, bioRxiv.

Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes

Zhihua Zhang, Michael Q. Zhang, Zhihua Zhang, 2011, BMC Bioinformatics.

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

Zhihua Zhang, Bingxian Xu, Yan Jia, 2021, bioRxiv.

Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study

Zhihua Zhang, Hui Liu, Lei Sun, 2012, BMC Bioinformatics.

DNA transposons mediate duplications via transposition-independent and -dependent mechanisms in metazoans

Graham L. Banes, Jianmin Wu, Zhihua Zhang, 2021, Nature Communications.

Functional diversity of CTCFs is encoded in their binding motifs

Rongxin Fang, Zhihua Zhang, G. Skogerbø, 2015, BMC Genomics.

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

Michael Q. Zhang, Zhihua Zhang, Juntao Gao, 2019, bioRxiv.

Delta.EPI: a probabilistic voting-based enhancer-promoter interaction prediction platform.

Zhihua Zhang, Jing Liu, Haoyu Wang, 2023, Journal of genetics and genomics = Yi chuan xue bao.

Comparison of computational methods for 3D genome analysis at single-cell Hi-C level.

Xiao Li, Ziyang An, Zhihua Zhang, 2020, Methods.

Translational selection in human: more pronounced in housekeeping genes

Peng Cui, Zhang Zhang, Lina Ma, 2014, Biology Direct.

Decoding topologically associating domains with ultra-low resolution Hi-C data by graph structural entropy

Angsheng Li, Zhihua Zhang, Ying Xiong, 2018, Nature Communications.

A hypothetical model of trans-acting R-loops-mediated promoter-enhancer interactions by Alu elements.

Zhihua Zhang, Feifei Li, X. Bai, 2021, Journal of genetics and genomics = Yi chuan xue bao.

Computational inference of physical spatial organization of eukaryotic genomes

Bingxiang Xu, Zhihua Zhang, Zhihua Zhang, 2016, Quantitative Biology.

The Dynamic 3D Genome in Gametogenesis and Early Embryonic Development

Zhihua Zhang, Feifei Li, Ziyang An, 2019, Cells.

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

Zhihua Zhang, Feifei Li, X. Bai, 2021, bioRxiv.

Episo: quantitative estimation of RNA 5-methylcytosine at isoform level by high-throughput sequencing of RNA treated with bisulfite

Feifei Li, Ziyang An, Jing Li, 2019, Bioinform..

The Evolution of Heterogeneities Altered by Mutational Robustness, Gene Expression Noise and Bottlenecks in Gene Regulatory Networks

Zhihua Zhang, 2014, PloS one.

Decoding topologically associating domains with ultra-low resolution Hi-C data by graph structural entropy

Zhihua Zhang, Angsheng Li, Bingxian Xu, 2018, Nature Communications.

ESCRT-0 complex modulates Rbf-mutant cell survival by regulating Rhomboid endosomal trafficking and EGFR signaling

Zhihua Zhang, W. Du, Tianyi Zhang, 2016, Journal of Cell Science.

Functional diversity of CTCFs is encoded in their binding motifs

Rongxin Fang, Zhihua Zhang, G. Skogerbø, 2015, BMC Genomics.

Dynamic chromatin architecture of the porcine adipose tissues with weight gain and loss

Yu Lin, Mingzhou Li, Xuewei Li, 2023, Nature communications.

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

Zhihua Zhang, Bingxian Xu, Yan Jia, 2021, bioRxiv.

3CDB: a manually curated database of chromosome conformation capture data

Zhihua Zhang, Hui Zhang, Bixia Tang, 2016, Database J. Biol. Databases Curation.

A Key to Genome Maze in 3D

Zhihua Zhang, Zhihua Zhang, 2016, Genom. Proteom. Bioinform..

DeCOOC Deconvoluted Hi‐C Map Characterizes the Chromatin Architecture of Cells in Physiologically Distinctive Tissues

Ming Li, Zhihua Zhang, Qing Zhang, 2023, Advanced science.