Author

Haojie Chen

Chinese Academy of SciencesORCID 0000-0002-4142-9829Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:ChIP-seq· 3 Approach:statistical model· 3 Assay:ATAC-seq· 2 Research Focus:database / resource· 2 Research Focus:differential expression· 2 Organism:human· 2 Research Focus:benchmarking· 1 Approach:experimental assay· 1

Frequent Co-Authors

Shiqi TuiD· 3 shared Zhen ShaoiD· 3 shared Yijing ZhangiD· 2 shared Anqin Zheng· 1 shared Chongze YuaniD· 1 shared David J. WaxmaniD· 1 shared Feng TianiD· 1 shared Fengxiang Tan· 1 shared

Activity by Year

2021-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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3 shared papersBioinformatics

Shiqi TuORCID

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Author profile →

4 papers

Recent·Most cited

Synora: vector-based boundary detection for spatial omics

Jun-Teng Li, Zhuoran Liang, Zhe Fu, Haojie Chen, Ye‐Lin Liang, Na Liu, Qianyu Wu, Zexian Liu, Yongqiang Zheng, Jihui Huo, Xiaoxing Li, Zhi-Xiang Zuo, Qi Zhao

Synora identifies tumor-stroma boundaries in spatial omics data using cell coordinates and tumor/non-tumor labels, achieving robust boundary detection across datasets and modalities.

bioRxiv · Mar 2, 2026 · PreprintBioinformatics

EAP: a versatile cloud-based platform for comprehensive and interactive analysis of large-scale ChIP/ATAC-seq data sets

Guangyong Zheng, Haojie Chen, Zhijie Guo, Liangxiao Ma, Anqin Zheng, Tao Huang, Weiran Chen, Shiqi Tu, Yixue Li, Zhen Shao

EAP provides a cloud-based platform for analyzing large-scale ChIP/ATAC-seq data, generating publication-ready results and enabling epigenomic analysis in cancer and therapeutic target discovery.

Computational and Structural Biotechnology Journal · Jan 1, 2025Peer-reviewedBioinformatics

HyperChIP for identifying hypervariable signals across ChIP/ATAC-seq samples

Haojie Chen, Shiqi Tu, Chongze Yuan, Feng Tian, Yijing Zhang, Yihua Sun, Zhen Shao

HyperChIP identifies hypervariable genomic regions across ChIP/ATAC-seq samples to reveal tumor heterogeneity and associated transcription factors.

Genome biology · Feb 28, 2022Peer-reviewedBioinformatics

MAnorm2 for quantitatively comparing groups of ChIP-seq samples

Shiqi Tu, Mushan Li, Fengxiang Tan, Haojie Chen, Jian Xu, David J. Waxman, Yijing Zhang, Zhen Shao

MAnorm2 is a tool for comparing ChIP-seq samples across groups, improving differential binding detection by accounting for within-group variability and outperforming existing methods.

Genome Research · Jan 1, 2021Peer-reviewedBioinformatics