# Heng Zhu
Heng Zhu is a molecular biologist and proteomics technologist at the Johns Hopkins University School of Medicine, educated in China and known for co-inventing functional protein microarrays, laboratory slides on which thousands of purified proteins are printed at high density so that their activities can be tested in bulk.[1](https://www.hopkinsmedicine.org/profiles/details/heng-zhu) He is a full professor of pharmacology and molecular sciences and oncology, and a member of the university's High Throughput Biology Center.[1](https://www.hopkinsmedicine.org/profiles/details/heng-zhu) • [2](http://english.ipc.cas.cn/news/icn/201307/t20130704_105541.html) His laboratory uses these arrays to characterize the activities of large collections of proteins, to build signaling networks, and to identify biomarkers in human diseases and cancers.[3](https://www.hopkinsmedicine.org/research/labs/z/zhu-lab)
| Fact | Detail |
|---|---|
| Field | Molecular biology; proteomics technology and signaling networks |
| Position | Full professor of pharmacology and molecular sciences and oncology, Johns Hopkins School of Medicine[1](https://www.hopkinsmedicine.org/profiles/details/heng-zhu) |
| Training | B.S. chemistry, Peking University (1990); Ph.D., Clemson University (1999); Damon Runyon postdoctoral fellow with Mike Snyder, Yale University[1](https://www.hopkinsmedicine.org/profiles/details/heng-zhu) • [2](http://english.ipc.cas.cn/news/icn/201307/t20130704_105541.html) |
| Signature work | "Profiling the Human Protein-DNA Interactome Reveals ERK2 as a Transcriptional Repressor of Interferon Signaling," *Cell*, 2009[4](https://www.cell.com/cell/fulltext/S0092-8674(09)01111-8) |
| Core technology | Protein purification at more than 4,000 proteins per day; microarrays carrying more than 15,000 proteins per slide[1](https://www.hopkinsmedicine.org/profiles/details/heng-zhu) |
| Industry role | Cofounder of CDI Laboratories, Inc., which commercializes the HuProt human protein microarray[2](http://english.ipc.cas.cn/news/icn/201307/t20130704_105541.html) • [5](https://www.cdilabs.com/) |
## Education and career
Zhu received his undergraduate degree in chemistry from [Peking University](https://www.edgepedia.org/peking-university) in Beijing in 1990 and earned his Ph.D. from [Clemson University](https://www.edgepedia.org/clemson-university) in 1999.[1](https://www.hopkinsmedicine.org/profiles/details/heng-zhu) According to a [Chinese Academy of Sciences](https://www.edgepedia.org/chinese-academy-of-sciences) news item, he then held a Damon Runyon Postdoctoral Fellowship in Mike Snyder's laboratory at Yale University, where he worked on genetics and proteomics projects and was an inventor of functional protein microarrays; his postdoctoral training at Yale ended in 2004.[2](http://english.ipc.cas.cn/news/icn/201307/t20130704_105541.html) • [6](https://profiles.hopkinsmedicine.org/provider/heng-zhu/2777872) He joined the Johns Hopkins faculty in 2004.[1](https://www.hopkinsmedicine.org/profiles/details/heng-zhu)
At [Johns Hopkins](https://www.edgepedia.org/johns-hopkins) he holds an appointment in the Department of Pharmacology and Molecular Sciences and is a member of the High Throughput Biology Center, with an affiliate faculty position at the Hopkins Oncology Center.[2](http://english.ipc.cas.cn/news/icn/201307/t20130704_105541.html) He was an associate professor as of July 2013 and is now a full professor of pharmacology and molecular sciences and oncology.[2](http://english.ipc.cas.cn/news/icn/201307/t20130704_105541.html) • [1](https://www.hopkinsmedicine.org/profiles/details/heng-zhu)
## Protein microarray technology
According to a review in PMC, a functional protein microarray places many purified proteins at fixed positions on a glass slide, so that one assay can test thousands of proteins at once against a labeled probe. Zhu's 2001 *Science* paper, written during his Yale postdoctoral work, cloned 5,800 yeast open reading frames, overexpressed and purified the corresponding proteins, and printed them onto slides at high spatial density to form a yeast proteome microarray; probing it identified many new calmodulin- and phospholipid-interacting proteins.[7](https://doi.org/10.1126/science.1062191)
His Johns Hopkins lab developed the two technologies that made proteome-scale arrays practical: high-throughput protein purification, exceeding 4,000 proteins per day, and high-density printing, exceeding 15,000 proteins per slide.[1](https://www.hopkinsmedicine.org/profiles/details/heng-zhu) A paper describing the *E. coli* chip reported a purification protocol that yielded all 4,256 proteins encoded by the *E. coli* K12 strain within 10 hours.[8](https://preview-www.nature.com/articles/nmeth1148) The lab has fabricated proteome chips for budding yeast, herpesviruses, and *E. coli* K12.[1](https://www.hopkinsmedicine.org/profiles/details/heng-zhu)
Protein chips of this kind are versatile probes: published assays cover protein-protein, protein-nucleic acid, protein-lipid, enzyme-substrate, and protein-drug interactions.[9](https://bcmb.bs.jhmi.edu/people/heng-zhu/) Reviews of the technology describe its use for binding to DNA, RNA, small molecules, and glycans, and for profiling post-translational modifications such as phosphorylation, ubiquitylation, acetylation, and nitrosylation.[10](https://pmc.ncbi.nlm.nih.gov/articles/PMC3044218/) Using a human protein microarray, Zhu's team identified protein substrates of over 340 human kinases.[2](http://english.ipc.cas.cn/news/icn/201307/t20130704_105541.html) A later application screened 289 individual kinases against 4,191 full-length human proteins, building a network that connects 230 kinases to 2,591 specific in vivo phosphorylation sites on 652 proteins.[11](https://www.genomeweb.com/proteomics/hopkins-led-team-builds-high-res-activity-based-network-kinase-substrate-interac)
After joining Johns Hopkins, Zhu's group set out to extend the approach to the human proteome.
## Representative work
The 2009 *Cell* paper "Profiling the Human Protein-DNA Interactome Reveals ERK2 as a Transcriptional Repressor of Interferon Signaling" applied a protein microarray strategy to DNA binding on a proteome scale. It identified 17,718 protein-DNA interactions between 460 DNA motifs predicted to regulate transcription and 4,191 human proteins of various functional classes. More than three hundred of the bound proteins were unconventional DNA-binding proteins, including RNA-binding proteins, mitochondrial proteins, and protein kinases.[4](https://www.cell.com/cell/fulltext/S0092-8674(09)01111-8)
The paper's most striking finding concerned ERK2, a protein kinase and one of these unconventional DNA-binding proteins. Characterization of its DNA binding in vitro and in vivo showed that ERK2 acts as a transcriptional repressor regulating interferon gamma signaling in mammalian cells.[4](https://www.cell.com/cell/fulltext/S0092-8674(09)01111-8)
A second 2009 *Cell* paper, "Protein Acetylation Microarray Reveals that NuA4 Controls Key Metabolic Target Regulating Gluconeogenesis," used an acetylation-focused array to show that NuA4 controls a key metabolic target regulating gluconeogenesis.[13](https://scholar.google.com/citations?hl=en&user=PLQVWdcAAAAJ)
## Current research
Zhu's current work centers on the impacts of DNA epigenetic modifications on transcriptional regulation, the characterization of functional GWAS SNPs, and biomarker discovery.[1](https://www.hopkinsmedicine.org/profiles/details/heng-zhu) Recent chip applications in his lab include RNA-protein, live cell-protein, and lectin-protein interaction assays, protein ubiquitination and acetylation assays, human serum profiling, and biomarker identification in human inflammatory bowel diseases.[1](https://www.hopkinsmedicine.org/profiles/details/heng-zhu) His lab also develops a highly multiplexed DAPPL platform alongside proteome arrays and VirD arrays.[1](https://www.hopkinsmedicine.org/profiles/details/heng-zhu)
## Roles outside academia
Zhu is one of the cofounders of CDI Laboratories, Inc., a firm launched to commercialize the protein microarray technology; as of July 2013 he held two patents with seven pending, and he has planned to offer kinase research services based on his lab's work through the company.[2](http://english.ipc.cas.cn/news/icn/201307/t20130704_105541.html) • [11](https://www.genomeweb.com/proteomics/hopkins-led-team-builds-high-res-activity-based-network-kinase-substrate-interac) CDI Labs produces the HuProt human protein microarray, created by its cofounders, faculty members of the High Throughput Biology Center at Johns Hopkins, with support from the NIH Common Fund.[5](https://www.cdilabs.com/)
## References
1. [Heng Zhu, PhD - Johns Hopkins School of Medicine Faculty](https://www.hopkinsmedicine.org/profiles/details/heng-zhu)
2. [Dr. Heng Zhu from The Johns Hopkins University Visits TIPC, Chinese Academy of Sciences (2013)](http://english.ipc.cas.cn/news/icn/201307/t20130704_105541.html)
3. [Zhu Lab, Johns Hopkins Medicine](https://www.hopkinsmedicine.org/research/labs/z/zhu-lab)
4. https://www.cell.com/cell/fulltext/S0092-8674(09)01111-8
5. [CDI Labs](https://www.cdilabs.com/)
6. [Heng Zhu, PhD - Johns Hopkins Medicine provider profile](https://profiles.hopkinsmedicine.org/provider/heng-zhu/2777872)
7. [Global Analysis of Protein Activities Using Proteome Chips, Science (2001)](https://doi.org/10.1126/science.1062191)
8. [A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli, Nature Methods](https://preview-www.nature.com/articles/nmeth1148)
9. [Heng Zhu - Hopkins BCMB](https://bcmb.bs.jhmi.edu/people/heng-zhu/)
10. [Functional protein microarray technology (review)](https://pmc.ncbi.nlm.nih.gov/articles/PMC3044218/)
11. [Hopkins-led Team Builds High-res Activity-based Network of Kinase-substrate Interactions, GenomeWeb](https://www.genomeweb.com/proteomics/hopkins-led-team-builds-high-res-activity-based-network-kinase-substrate-interac)
12. [From 108 Kinases to the Human Proteome: A 25-Year Journey Toward Proteome-Scale Biology, CDI Labs Blog](https://www.cdilabs.com/blogs/25-year-journey-to-proteome-scale-biology)
13. [Heng Zhu - Google Scholar](https://scholar.google.com/citations?hl=en&user=PLQVWdcAAAAJ)
14. [MAPPING DNA BINDING - US Patent Application US20250101492A1](https://www.patents-review.com/a/20250101492-mapping-dna-binding.html)
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*Topic: Encyclopedia › Life and health › Life and health scientists › Life scientists › Researchers in structural biology, biochemistry, and biophysics*
*Initially written Sep 21, 2026 · Reviewed: Sep 25, 2026; Sep 30, 2026 · Edited: Sep 25, 2026; Sep 30, 2026 · Last review: Sep 30, 2026*
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