Chongyi Chen, Ph.D.

Chongyi Chen, Ph.D.

  • Center for Cancer Research
  • National Cancer Institute


The Chen lab study chromatin structure, DNA topology, and gene expression regulation in human cells, by newly invented genomic technologies and single-cell assays. We seek to understand how the topological tension of the double helix interacts with other chromatin features during fundamental biological processes. The lab also develops new techniques in single-cell genomics, epigenomics, and transcriptomics. The long-term goal is to apply the new knowledge in chromatin biology and the new methodologies in single-cell omics 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 ]

Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria

Wang W, Li G, Chen C, Xie XS, Zhuang X
Science. 333: 1445-1449, 2011. [ Journal Article ]

Job Vacancies

Position Degree Required Contact Name Contact Email
Post-doctoral Fellow - DNA topology, chromatin structure Ph.D. or equivalent Chongyi Chen


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