Author

Yi Shi

Icahn School of Medicine at Mount Sinai

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

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Biology Disciplines

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Bioinformatics· 2 Cell Biology· 1 Plant Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 3 Assay:bulk RNA-seq· 2 Research Focus:differential expression· 2 Organism:human· 2 Organism:Arabidopsis· 1 Approach:biophysical modeling· 1 Research Focus:cell signaling & trafficking· 1 Research Focus:cell type annotation· 1

Frequent Co-Authors

Ariele Viacava Follis· 1 shared Guang HeiD· 1 shared Haiyan Xiong· 1 shared Ivan Reyna-Llorens· 1 shared Jarvier N. MohammediD· 1 shared Jerry E. ChipukiD· 1 shared Jesse D. GellesiD· 1 shared Jia Li· 1 shared

Activity by Year

2020-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 12 mutual co-author links

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1 shared paperCell Biology

Ariele Viacava Follis

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4 papers

Recent·Most cited

Comprehensive long-read transcriptome analysis uncovers alternative RNA processing feature and isoform diversity in ovarian cancer progression

Tianxiang Liu, Jianying Lv, Shuo Wang, Yanhua Liu, Yanan Chen, Jia Li, Longlong Wang, Yi Shi, Wei Ding, Yongjun Piao

The paper uses long-read RNA sequencing to analyze isoform diversity in ovarian cancer, identifying key isoform-level changes associated with disease progression and clinical outcomes.

bioRxiv · Mar 14, 2026 · PreprintBioinformatics

A gated hydrophobic funnel within BAX binds long-chain alkenals to potentiate pro-apoptotic function

Jesse D. Gelles, Yiyang Chen, Mark P.A. Luna‐Vargas, Ariele Viacava Follis, Md Abdullah Al Noman, Md Kabir, Stella G. Bayiokos, Jarvier N. Mohammed, Tara M. Sebastian, Ngoc Dung Pham, Yi Shi, Jian Jun Jin, Richard W. Kriwacki, Jerry E. Chipuk

The paper identifies a hydrophobic funnel in BAX that binds 2t-hexadecenal, enhancing BAX activation with BIM, and shows proline 168 regulates this interaction.

Nature Communications · Feb 25, 2026Peer-reviewedCell Biology

PSTP: Decoding Latent Sequence Grammar for Protein Phase Separation through Transfer Learning and Attention

Mofan Feng, Liangjie Liu, Zhuo-Ning Xian, Xiaoxi Wei, Keyi Li, Wenqian Yan, Qing Lü, Yi Shi, Guang He

PSTP predicts protein phase separation regions using transfer learning and attention, achieving 84% accuracy on PhaSePro and improving correlation coefficients over existing models.

Briefings in Bioinformatics · Apr 28, 2025Peer-reviewedBioinformatics

The rice bundle sheath produces reactive oxygen species during high light stress via NADPH oxidase

Haiyan Xiong, Lei Hua, Ivan Reyna-Llorens, Yi Shi, Kun-Ming Chen, Nicholas Smirnoff, Johannes Kromdijk, Julian M. Hibberd

The paper shows that rice bundle sheath cells produce ROS under high light via NADPH oxidase, independent of photosynthesis.

bioRxiv · Jul 6, 2020Plant Biology