Chuan Xu

  • Tel: +86-021
  • Email: chuanx@at@sjtu.edu.cn (需去除：at@)
  • Lab Web: https://gpd.sjtu.edu.cn/XuLab/index.html
  • PI, Bio-X institutes at SJTU. My research involves Bioinformatics, Fungal Pathogens, Evolutionary Genomics and Systems Biology. Researches are published in Cell Syst., Cell Rep., PLoS Biol., Mol. Biol. Evol., Nat. Rev. Genet., etc. International students are welcome to apply for my lab's Master/Ph.D. programs.

Education and Research Experience

  • PI, Bio-X institutes at SJTU, Shanghai, China.
  • Postdoctoral Researcher at UMich, USA.
  • Ph.D. at Zhejiang Unviersity, China.

Research Interests

Genome-wide mechanism of eukaryotic transcription and translation and its si...

1. Genome-wide mechanism of eukaryotic transcription and translation and its significance in species evolution.

This direction includes alternative transcription starts, alternative splicing, back-splicing, alternative polyadenylation, alterantive translation, and many RNA modications (such as m6A, m5C, and RNA editing).

Human diseases

2. Human diseases, especially for the brain disorders (such as depression, anxiety, schizophrenia, Alzheimers' disease, autism...) and cancers.
 

Virulence evolution of pathogenic fungi

3. Virulence evolution of pathogenic fungi.

I am interested in how pathogenic fungi adapt to the infection process. We combine computational and molecular experiments to study it.

Selected Publications

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    Mi, K., Guan, L., Sarker, B., Song, S., Zhou, T., Yi, H., Zhang, J. & Xu, C. (2026). Transcript diversity reflects deleterious RNA processing errors shaped by population size in metazoans. PLOS Biology, 24(3), e3003671.

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    Sarker, B., Zhou, T., Deng, X., Zhang, L., Zhao, X., Huang, W., Yi, H., Jiang, H., & Xu, C. (2026). APAdeg enhances differentially expressed gene inference by leveraging site-specific signals in APA-seq data. Briefings in Bioinformatics, 27(3), bbag295.

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    Li, Z., Mi, K., & Xu, C. (2025). Most m5C modifications in mammalian mRNAs are nonadaptive. Molecular Biology and Evolution, msaf008.
     

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    Li, Z., Sarker, B., Zhao, F., Zhou, T., Zhang, J., & Xu, C. (2024). COL: a method for identifying putatively functional circular RNAs. Journal of genetics and genomics, 51(11), 1338.
     

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    Zhang, J., and Xu, C.  (2022) Gene product diversity: adaptive or not? Trends in Genetics, In press

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    Xu, C., and Zhang, J (2021) Mammalian circular RNAs result largely from splicing errors. Cell Reports., 36:109439.

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    Xu, C., and Zhang, J. (2020). Mammalian alternative translation initiation is mostly nonadaptive. Molecular Biology and Evolution. Mar 7. pii: msaa063. doi: 10.1093/molbev/msaa063.

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    Xu, C., and Zhang, J. (2020) A different perspective on alternative cleavage and polyadenylation. Nature Review Genetics., doi: 10.1038/s41576-019-0198-z

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    Xu, C., Park, J. K., and Zhang, J. (2019). Evidence that alternative transcriptional initiation is largely nonadaptive. PLoS biology, 17(3), e3000197.

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    Xu, C., and Zhang, J. (2018). Alternative Polyadenylation of Mammalian Transcripts Is Generally Deleterious, Not Adaptive. Cell systems. 6 (6), 734-742.e4

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