Center for Epigenomics:
Dr. Nathan Zemke

Mapping the Epigenome and 3D Genome at Single-Cell Resolution

Dr. Nathan Zemke is a principal investigator at the UC San Diego Center for Epigenomics (C4E), where he leads the Center’s single-cell genomics platform and drives high-impact research into chromatin regulation and enhancer biology. A molecular biologist by training and systems thinker by nature, Dr. Zemke is advancing our understanding of how regulatory DNA and chromatin dynamics control cell identity, development, and disease — one cell at a time.

His group develops and applies cutting-edge single-cell multiomic assays to profile DNA methylation, 3D genome architecture, histone modifications, and chromatin accessible landscapes to interrogate gene regulatory programs with precision. He plays a central role in many of C4E’s collaborative efforts, enabling researchers across disciplines to deploy state-of-the-art single-cell epigenomic tools in projects ranging from cancer and aging to development and evolution.

Dr. Zemke also leads integrative functional genomics projects that bridge experimental and computational biology. His work helps define the roles of enhancers, transcription factors, and cis-regulatory elements in orchestrating cell fate transitions — and in unraveling what goes wrong in disease.

As head of C4E’s single-cell genomics platform, Dr. Zemke builds customized strategies for internal and external collaborators, optimizing experimental design, execution, and downstream analysis across tissues, species, and disease models. His platform supports initiatives in cancer, neuroscience, immunology, and beyond.

Dr. Zemke’s innovative research and leadership in single-cell genomics place him at the forefront of efforts to translate epigenomic discoveries into therapeutic strategies for complex diseases.

Q&A with Nathan Zemke

Meet Dr. Nathan Zemke: Mapping the Epigenome Cell by Cell

Q: What’s the big idea driving your work?
We want to know how the genome encodes gene regulatory networks — and how these networks promote cell identity, developmental stages, and disease.

Q: What does your single-cell platform offer to collaborators?
We can profile multiple layers of epigenetics at the resolution of individual cells, to resolve gene regulatory networks of different cell types and states, across space and time. And we help collaborators do it with rigor and impact.

Q: What excites you most about being at C4E?
The integration of technology and biology here is next-level. We explore the molecular basis for human diseases at unprecedented resolution — and we get to collaborate with brilliant people across UC San Diego and beyond.

Q: Where do you see this field going?
We’re heading toward truly understanding the human genome. If we know how the genome functions we can understand genetic and environmental influence on gene regulation revealing new therapeutic targets to prevent and treat disease.

Nathan Zemke, PhD

Principal Investigator
Molecular Biologist
Bioinformatician
Single-Cell Genomics

nzemke@health.ucsd.edu

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