Welcome to my academic portfolio. I am a Ph.D. candidate at Oregon Health & Science University focusing on alternative polyadenylation mechanisms and their role in cancer biology.

About Me

I am passionate about understanding the complexities of post-transcriptional regulation and how alternative polyadenylation contributes to cancer development and progression. My research combines computational approaches with experimental validation to explore the intricate relationships between RNA processing and disease states.

Currently working in the Xia Lab, I am investigating APA at single-cell RNA-Seq and spatial transcriptomics levels, providing unprecedented insights into 3’ UTR processing dynamics across different cell types and spatial contexts in cancer models. Additionally, I am developing robust computational pipelines for APA analysis using Nextflow and adhering to nf-core standards, ensuring reproducibility and scalability in bioinformatics workflows.

Research Interests

• Alternative Polyadenylation (APA): Investigating mechanisms and functional consequences of APA in normal and disease states
• Single-cell and Spatial Transcriptomics: Exploring APA dynamics at cellular and spatial resolution
• Computational Methods for APA: Developing novel APA analyze tools for scRNA/spatial data & nf-core compatible pipelines for APA analysis

Education

• Ph.D. Candidate (Current)
  Oregon Health & Science University, Portland, US
  Department of Biomedical Engineering
  Advisor: Dr. Zheng Xia

• M.S. (2021)
  Zhejiang University, Hangzhou, CN
  Major: Cell Biology
  Advisor: Dr. Pengyuan Liu

• B.S. (2017)
  East China Normal University, Shanghai, CN
  Major: Biotechnology
  Advisor: Dr. Xiyun Ye

Publications

Preprints

1. Ozaki M, Zhang Y, Bartlett AQ, de Wilde E, Guan X, Yang A, Xia Z, Schedin P. (2024). “Reproductive state controls transcription in the murine liver, with implications for breast cancer liver metastasis.” DOI: 10.1101/2024.08.02.606434

2. Bernhardt SM, Ozaki MK, Betts C, Bleyle LA, DeBarber AE, Fornetti J, Liberty AL, De Wilde E, Zhang Y, Xia Z, et al. (2024). “Altered liver metabolism post-wean abolishes efficacy of vitamin D for breast cancer prevention in a mouse model.” DOI: 10.1101/2024.05.28.596304

Journal Articles

1. Hu RC, Zhang Y, Nitschke L, Johnson SJ, Hurley AE, Lagor WR, Xia Z, Cooper TA. (2025). “MBNL overexpression rescues cardiac phenotypes in a myotonic dystrophy type 1 heart mouse model.” J Clin Invest. Feb 11:e186416. DOI: 10.1172/JCI186416

2. Zhang Y, Liu L, Qiu Q, Zhou Q, Ding J, Lu Y, Liu P. (2021). “Alternative polyadenylation: methods, mechanism, function, and role in cancer.” Journal of Experimental & Clinical Cancer Research. DOI: 10.1186/s13046-021-01852-7

Current Research Projects

• Computational Methods for APA Analysis
  Developing tools to better detect and quantify alternative polyadenylation events from scRNA-seq/spatial data.

• Alternative Polyadenylation in Cancer Progression
  Investigating how changes in polyadenylation site selection affect gene expression programs in cancer cells, with a focus on neuroendocrine tumors.

Technical Skills

• Computational: Bioinformatics pipelines, R, Python, Docker, Nextflow pipelines
• Next-Generation Sequencing: Bulk & single-cell transcriptomics data processing
• Molecular Biology: RNA extraction and library preparation, PCR, RT-qPCR

Conference Presentations

• 2024 Research Week OHSU, poster presentation
• 2023 Oregon Bioengineering Symposium, poster presentation

Contact Information

• Email: zhayi@ohsu.edu
• ORCID: 0000-0001-5680-4647
• Institution: Oregon Health & Science University, Department of Biomedical Engineering
• Lab Website: Xia Lab

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This website was last updated on March 2025.