* co-first authors. # co-correspondence

1.Junmei Wang*, Lu Lu*, Shiqi Zheng, Danyang Wang, Long Jin, Qing Zhang#, Mingzhou Li# and Zhihua Zhang#. DeCOOC deconvoluted Hi-C map characterizes the chromatin architecture of cells in physiologically distinctive tissues. Advanced Science, 2023, 2301058.

2.Long Jin*, Danyang Wang*, Jiaman Zhang*, Pengliang Liu, Yujie Wang, Yu Lin, Can Liu, Ziyin Han,6, Keren Long, Diyan Li, Yu Jiang, Guisen Li, Yu Zhang, Jingyi Bai, Xiaokai Li, Jing Li, Lu Lu, Fanli Kong, Xun Wang, Hua Li, Zhiqing Huang0, Jideng Ma, Xiaolan Fan, Linyuan Shen, Li Zhu, Yanzhi Jiang, Guoqing Tang, Bin Feng, Bo Zeng, Liangpeng Ge, Xuewei Li, Qianzi Tang, Zhihua Zhang#, and Mingzhou Li#, Dynamic chromatin architecture of the porcine adipose tissues with weight gain and loss, 2023, Nature Communications 2023,14:3457.

3.Angsheng Li,#,* Guangjie Zeng,*, Haoyu Wang,*, Xiao Li , and Zhihua Zhang#. DeDoc2 identifies and characterizes the hierarchy and dynamics of chromatin TAD-like domains in the single cells. 2023, Advanced Science, 2300366.

4.Yuyang Zhang, Haoyu Wang, Jing Liu, Junlin Li, Qing Zhang#, Bixia Tang#, Zhihua Zhang#. Delta.EPI: a probabilistic voting-based enhancer-promoter interaction prediction platform. Journal of Genetics and Genomics, 2023 (23): S1673-8527.

5.Lei Sun, Gongming Wang, Zhihua Zhang# SimCH: simulation of single-cell RNA sequencing data by modeling cellular heterogeneity at gene expression level，Briefings in Bioinformatics, 2022, bbac590.

6.Qingzhu Yang, Zhihua Zhang# Lattice Simulation-based diffusion modelling of 3D chromatin structure, Computational and Structural Biotechnology Journal, 2022, 20: 3351-3358;

7.Bingxiang Xu#*, Xiaomeng Gao*, Xiaoli Li, Yan Jia, Feifei Li#, Zhihua Zhang#, Cell cycle arrest explained the observed bulk 3D genomic alterations in response to long term heat shock in K562 cells. Genome Research, 2022, 32:1285–1297;

8.Diyan Li*, Mengnan He*, Qianzi Tang*, Shilin Tian*, Jiaman Zhang*, Yan Li, Danyang Wang, Long Jin, Chunyou Ning, Wei Zhu, Silu Hu, Keren Long, Jideng Ma, Jing Liu, Zhihua Zhang#, Mingzhou Li#，Comparative 3D genome architecture in vertebrates，BMC Biology, 2022, 20:99.

9.Bingxiang Xu #, Xiaoli Li, Xiaomeng Gao, Yan Jia, Jing Liu, Feifei Li and Zhihua Zhang#, DeNOPA: decoding nucleosome positions sensitively with sparse ATAC-seq data, Briefings in Bioinformatics, 2022, bbab469.

10.Xiao Li, Guangjie Zeng, Angsheng Li and Zhihua Zhang#, DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell, Genome Biology, 2021, 22, 217.

11.Xue Bai, Feifei Li, Zhihua Zhang#, A hypothetical model of trans-acting R-loops-mediated promoter-enhancer interactions by Alu elements, Journal of Genetics and Genomics, 2021 V48 (11):1007-1019.

12.Bixia Tang, Xiaoxing Li, Guan Li, Dong Tian, Feifei Li, and Zhihua Zhang#, Exploring multiomics data in 3D genomic space using augmented reality based visualization platform Delta.AR. The Innovation, 2021, 2(3),100149.

13.Feifei Li*, Danyang Wang*, Ruigao Song*, Chunwei Cao*, Zhihua Zhang*#, Yu Wang, Xiaoli Li, Jiaojiao Huang, Qiang Liu, Naipeng Hou, Bingxiang Xu, Xiao Li, Xiaomeng Gao, Yan Jia, Jianguo Zhao, Yanfang Wang# The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos. Genome Biology, 2020, 21:203.

14.Cong Liu, Yiqun Zhang, Xiaoli Li, Yan Jia, Feifei Li#, Jing Li#, Zhihua Zhang# (2020) Evidence of constraint in the 3D genome for trans-splicing in human cells. SCIENCE CHINA Life Sciences, 2020, 63(9):1380-1393.

15.Junfeng Liu*, Ziyang An*, Jianjun Luo, Jing Li, Feifei Li#, Zhihua Zhang#, (2020) Episo: quantitative estimation of RNA 5-methylcytosine at isoform level by high-throughput sequencing of RNA treated with bisulfite, Bioinformatics, 36(7), 2033–2039.

16.Angsheng Li#, Xianchen Yin, Bingxiang Xu, Danyang Wang, Jimin Han, Yi Wei, Yun Deng, Ying Xiong and Zhihua Zhang# (2018) Decoding Topologically Associating Domains with Ultra-low resolution Hi-C Data by Graph Structural Entropy. Nature Communications, 2018 9:3265.

17.Bixia Tang, Feifei Li, Jing Li, Wenming Zhao#, Zhihua Zhang# (2017) Delta: a new Web-based 3D genome visualization and analysis platform. Bioinformatics, 2017, 34:1409–1410.

18.Hui Zhang*, Feifei Li*, Yan Jia, Bingxiang Xu, Yiqun Zhang, Xiaoli Li, Zhihua Zhang# (2017) Characteristic arrangement of nucleosomes is predictive of chromatin interactions at kilobase resolution. Nucleic Acids Research, 2017 V45, 12739 - 12751.

19.Bingxiang Xu, Hao Ge, Zhihua Zhang# (2017) An efficient and assumption-free method to approximate protein level distribution in the two-states gene expression model. Journal of Theoretical Biology, 2017, 433:1-7.

20.Zhihua Zhang# (2014) The Evolution of Heterogeneities Altered by Mutational Robustness, Gene Expression Noise and Bottlenecks in Gene Regulatory Networks. PLoS ONE, 9(12): e116167.

21.Zhihua Zhang., Wenfeng Qian and Jianzhi Zhang (2009) Positive selection for elevated gene expression noise in yeast. Molecular Systems Biology, 5:299.

22.Zhihua Zhang and Jianzhi Zhang (2009) A Big World Inside Small-World Networks. PLoS ONE, 4: e5686.

23.Zhihua Zhang and Jianzhi Zhang (2008) Accuracy and application of the motif expression decomposition method in dissecting transcriptional regulation. Nucleic Acids Research, 36(10):3185-3193.

24.Zhihua Zhang., Changning Liu., Geir Skogerbo., Xiaopeng Zhu., Hongchao Lu.,Lan Chen., Baochen Shi., Yong Zhang., Tao Wu., Jie Wang and Runsheng Chen (2006) Dynamic Changes in Subgraph Preference Profiles of Crucial Transcription Factors. PLoS Computational Biology, 2(5): e47.

25.Zhang Zhihua (2002) On Short Exact Categorie CRM. Journal of Natural Science of Hunan Normal University, Vol.25:13-17. (In Chinese).

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