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    The 3D Human Genome

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    Genome Editing

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    Monocyte Differentiation

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    Software Development

Research Interests

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    3D Chromatin Structure

    We study how DNA loops regulate gene transcription and human development.

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    Genome editing

    We are developing and applying new techniques manipulate non-coding regulatory DNA and 3D chromatin structure.

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    Cellular Differentiation

    We are interested in the complex network of molecular events that drive lineage specification and the maintenance of cellular identity.

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    Software Development

    We are developing novel software to analyze and visualize data from genomic and proteomic data sets.

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Mission Statement

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It is estimated that only 2% of the human genome codes for functional proteins. Scattered throughout the rest of the genome are regulatory regions that can exert control over genes hundreds of thousands of base pairs away through the formation of DNA loops. These promoter-distal regulatory regions play critical roles in establishing proper transcriptional profiles during human development and harbor the vast majority of disease-related variants. Over the past decade, rapid improvements in DNA sequencing technology and computing power have produced breakthroughs in our knowledge regarding the components governing loop establishment in cells grown in steady state. However, despite these advances and the known importance of loops in transcriptional control during development, we very little about the molecules and mechanisms that govern cell-type specific loop formation during dynamic biological processes such as cellular differentiation. This knowledge gap stems from: (1) lack of high-resolution time-course data characterizing DNA loops during differentiation, (2) a dearth of software for differential loop analysis, interpretation, and visualization, and (3) limitations in current genome editing methods. The long-term goal of our research is to develop and apply new tools to uncover the mechanisms and functions of dynamic DNA looping during cellular differentiation of human cells.

Funding sources

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    1 Jan 2012 - 31 Dec 2015

    Post-doctoral fellowship

    Exploring the regulatory role of long-range chromatin interactions.

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    31 July 2015 - 1 June 2020

    K99/R00

    The development and application of tools to characterize the 4D nucleome.