Author

Hongshun Shi

Emory University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

Click to filter author papers

Bioinformatics· 1 Cell Biology· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:cell type annotation· 2 Organism:human· 2 Assay:proteomics· 2 Assay:spatial transcriptomics· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Research Focus:cancer & tumor microenvironment· 1 Research Focus:cell signaling & trafficking· 1

Frequent Co-Authors

Jindan YuiD· 3 shared Abhijeet Venkataraman· 1 shared Ahmet F. CoskuniD· 1 shared Ajie Liu· 1 shared Bing YaoiD· 1 shared Chenyang YuaniD· 1 shared Felix G. Rivera MoctezumaiD· 1 shared Feng WangiD· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

3 shared papersSystems Biology

Jindan YuORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

Morphomechanically-Informed Spatial Curvature Sequencing in Prostate Cancer

Ivan Kordic, Felix G. Rivera Moctezuma, Hoseyn A. Amiri, Ajie Liu, Shuangyi Cai, Mehdia Nadeem Rajab Ali, Lourdes T. Brea, Abhijeet Venkataraman, Hongshun Shi, Lara Rabih Harik, Todd Sulchek, Jindan Yu, Ahmet F. Coskun

This paper introduces CurvSeq and CurvSee to analyze prostate cancer morphology and molecular profiles, identifying cancer-associated genes and morphomechanical niches linked to progression.

bioRxiv · Jul 23, 2026 · PreprintSystems Biology

RNA-Binding Protein NF90 Mediates Polycomb-Independent Transactivation by EZH2 to Promote Cancer Growth

Yuan Wang, Peng Liu, Xiaodong Lü, Hongshun Shi, Mohan Zheng, Sambhavi Senthil, Jawad Akhtar, Yongik Lee, Hana Chandonnet, Jonathan D. Licht, Ximing J. Yang, Jonathan C. Zhao, Jindan Yu

This study identifies NF90 as a coactivator of EZH2's polycomb-independent transactivation function in prostate cancer, promoting cell growth and poor clinical outcomes.

bioRxiv · Dec 3, 2025 · PreprintCell Biology

Uncovering the dark transcriptome in polarized neuronal compartments with mcDETECT

Chenyang Yuan, Krupa Patel, Hongshun Shi, Hsiao‐Lin V. Wang, Feng Wang, Rong-Hua Li, Yangping Li, Victor G. Corces, Hailing Shi, Sulagna Das, Jindan Yu, Peng Jin, Bing Yao, Jian Hu

The paper introduces mcDETECT, a machine learning framework for detecting RNA granules in spatial transcriptomics data, revealing functionally distinct neuronal substates and early Alzheimer's disease pathology.

bioRxiv · Mar 27, 2025 · PreprintBioinformatics