Author

Yi Y. Shi

Shanghai Jiao Tong UniversityORCID 0000-0002-5279-3239Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Organism:human· 3 Approach:statistical model· 3 Research Focus:differential expression· 2 Assay:protein sequence· 2 Research Focus:variant effect prediction· 2 Approach:Bayesian inference· 1 Assay:bulk RNA-seq· 1 Research Focus:clustering· 1

Frequent Co-Authors

Guang HeiD· 3 shared Xianbin SuiD· 3 shared Luming MengiD· 2 shared Mingxuan ZhangiD· 2 shared Qing LuoiD· 2 shared Xin ZouiD· 2 shared Ze‐Guang HaniD· 2 shared Zehua GuoiD· 2 shared

Activity by Year

2020-2024 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

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3 shared papersBioinformatics

Guang HeORCID

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5 papers

Recent·Most cited

Decoding Missense Variants by Incorporating Phase Separation via Machine Learning

Mofan Feng, Xiaoxi Wei, Xi Zheng, Liangjie Liu, Lin Lin, Manying Xia, Guang He, Yi Y. Shi, Qing Lü

PSMutPred predicts the impact of missense variants on phase separation using machine learning, improving the interpretation of variants of unknown significance in intrinsically disordered regions.

Nature Communications · Sep 27, 2024Peer-reviewedBioinformatics

Si-C: method to infer biologically valid super-resolution intact genome structure from single-cell Hi-C data

Luming Meng, Chenxi Wang, Yi Y. Shi, Qiong Luo

Si-C reconstructs biologically valid super-resolution 3D genome structures from sparse single-cell Hi-C data, revealing cell-to-cell variation and hyperfine chromatin features.

Nature Communications · Jul 16, 2021Peer-reviewedBioinformatics

Single-cell and single-variant resolution analysis of clonal evolution in human liver cancer

Xianbin Su, Linan Zhao, Yi Y. Shi, Rui Zhang, Qi Long, Shihao Bai, Qing Luo, Yingxin Lin, Xin Zou, Shila Ghazanfar, Kun Tao, Guoliang Yang, Lan Wang, Kunyan He, Xiaofang Cui, , Ze‐Guang Han

The paper analyzes clonal evolution in liver cancer at single-cell and single-variant resolution, revealing genetic and phenotypic heterogeneity and their evolutionary relationships.

bioRxiv · Dec 30, 2020 · PreprintGenomics

3D Genome Contributes to Protein-Protein Interactome

Yi Y. Shi, Song Cao, Mingxuan Zhang, Xianbin Su, Zehua Guo, Jiayi Wang, Tingting Liu, Hui Shi, Guang He

The paper investigates how 3D genome structure influences protein-protein interactions and shows that gene proximity in 3D space correlates with interaction likelihood.

bioRxiv · Nov 30, 2020 · PreprintBioinformatics

A Novel Neoantigen Discovery Approach based on Chromatin High Order Conformation

Yi Y. Shi, Mingxuan Zhang, Luming Meng, Xianbin Su, Xueying Shang, Zehua Guo, Qingjiao Li, Mengna Lin, Xin Zou, Qing Luo, Yaoliang Yu, Yanting Wu, Lin‐Tai Da, Tom Weidong Cai, Guang He, Ze‐Guang Han

This paper identifies that immuno-positive neoantigens cluster in 3D genome regions and are enriched in active chromosomal compartments, suggesting 3D genome information can improve neoantigen prioritization.

BMC Medical Genomics · Aug 1, 2020Peer-reviewedBioinformatics