Chongyi Chen, Ph.D.

Chongyi Chen, Ph.D.

  • Center for Cancer Research
  • National Cancer Institute


The Chen lab studies DNA topology in the context of chromatin organization and gene expression in human cells, utilizing our strength of developing novel genomic technologies and single-cell assays. We seek to understand how the supercoiling tension of the DNA double helix interact with other chromatin features, contribute to the chromatin environment and gene regulation, as well as the regulatory mechanism and function of DNA supercoiling dynamics and topoisomerase activities during various biological processes. The long-term goal is to apply new scientific discoveries in chromatin biology and new methodologies in single-cell genomics to cancer biology and medicine.

Areas of Expertise

DNA Topology
Chromatin Structure
Gene Expression
Genomic Technology Development
Single-Cell Analysis


Selected Key Publications

Neuronal enhancers are hotspots for DNA single-strand break repair

Wu W, Hill SE, Nathan WJ, Paiano J, Callen E, Wang D, Shinoda K, van Wietmarschen N, Colón-Mercado JM, Zong D, De Pace R, Shih HY, Coon S, Parsadanian M, Pavani R, Hanzlikova H, Park S, Jung SK, McHugh PJ, Canela A, Chen C, Casellas R, Caldecott KW, Ward ME, Nussenzweig A.
Nature. 593: 440-444, 2021. [ Journal Article ]

Single cell genomics to study DNA and chromosome changes in human gametes and embryos

Blanshard RC, Chen C, Xie XS, Hoffmann ER.
Methods in Cell Biology. 144: 441-457, 2018. [ Journal Article ]

Single-cell Whole-genome Analyses by Linear Amplification via Transposon Insertion (LIANTI)

Chen C, Xing D, Tan L, Li H, Zhou G, Huang L, Xie XS.
Science. 356: 189-194, 2017. [ Journal Article ]

Mechanism of Transcriptional Bursting in Bacteria

Chong S, Chen C, Ge H, Xie XS.
Cell. 158: 314-326, 2014. [ Journal Article ]

Job Vacancies

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Shuai Li
Post-doctoral Fellow (Visiting)
Shuai Li, Ph.D.
Jun Lyu
Postdoctoral Fellow (Visiting)
Jun Lyu, Ph.D.
Postbaccalaureate (CRTA)
Charan Vemuri
Qian Yao
Postdoctoral Fellow (Visiting)
Qian Yao, Ph.D.
Linying Zhu
Postdoctoral Fellow (Visiting)
Linying Zhu, Ph.D.


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