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Research

My research focuses on understanding the complex interplay between genomic structure, regulatory elements, and gene expression. Here are the main areas of my PhD work:

I. Integration of Cis-Regulatory Information in the Genome
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I investigated how different genomic elements work together to control gene expression. This project explored the “grammar” of gene regulation, revealing how various regulatory elements combine to influence gene activity in mouse embryonic stem cells.

II. Impact of Genomic Environments on Gene Expression Noise
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I studied how the surrounding genomic context affects the variability of gene expression. This work demonstrated that genomic environments can scale the activities of core promoters, providing insights into the factors that contribute to gene expression noise.

III. High-Throughput Discovery of Cell-Type Specific Enhancers
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Using innovative single-cell techniques, I developed a method to identify cell-type specific enhancers in mouse brains. This project utilized a single-cell massively parallel reporter assay (scMPRA) to detect cell-type-specific gene regulation, advancing our understanding of tissue-specific gene expression.

IV. Characterization of Insulator Activity Across the Genome
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I conducted a large-scale study to characterize insulator activity throughout the genome. This work provided a comprehensive map of insulator function, contributing to our understanding of how these elements help organize the genome and regulate gene expression.

Selected Publications
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  1. Hong, C. K. Y., et al. (2024). Effect of genomic and cellular environments on gene expression noise. Genome Biology.

  2. Hong, C. K. Y., et al. (2024). Massively parallel characterization of insulator activity across the genome. Nature Communications.

  3. Zhao, S., Hong, C. K. Y., et al. (2023). A single-cell massively parallel reporter assay detects cell-type-specific gene regulation. Nature Genetics.

  4. Hong, C. K. Y. & Cohen, B. A. (2022). Genomic environments scale the activities of diverse core promoters. Genome Research.