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Heng Zhu, Ph.D.

Headshot of Heng Zhu
  • Co-Director, High Throughout Biology Center
  • Professor of Pharmacology and Molecular Sciences

Research Interests

Viral oncology; Transcription regulation; Systems biology; Protein chip approach to study proteomics; Host-pathogen interaction; Protein networks; Signal transduction more


Dr. Heng Zhu is an associate professor of pharmacology and molecular sciences and oncology at the Johns Hopkins School of Medicine. His research focuses on developing and applying protein chip technology to investigate important biological questions and to help clinical research. Dr. Zhu is co-director of the High Throughput Biology Center.

Dr. Zhu is a pioneer proteomics technologist who co-invented protein microarray technology. Currently, his team is engaged in networks and pathways of protein posttranslational modifications, gene transcription regulatory networks, pathogen-host interaction networks and biomarker discovery.

Dr. Zhu received his undergraduate degree in chemistry from Peking University in Beijing, China. He earned his Ph.D. from Clemson University. He completed a fellowship in genetics at Yale University. Dr. Zhu joined the Johns Hopkins faculty in 2004.

Dr. Zhu's work has been recognized with numerous awards and honors, including two Chair's Awards from the Gordon Research Conference. more


  • Co-Director, High Throughout Biology Center
  • Professor of Pharmacology and Molecular Sciences
  • Professor of Oncology

Departments / Divisions

Centers & Institutes



  • Ph.D.; Clemson University (South Carolina) (1999)
  • B.S.; Peking University (China) (1990)

Additional Training

  • Yale University, New Haven, CT, 2004, Proteomics

Research & Publications

Research Summary

Dr. Zhu's research goals are to discover and characterize the activities of large collections of proteins to build signaling networks for better understanding the mechanisms of biological processes, and to identify biomarkers for important human diseases. More specifically, Dr. Zhu and his team are interested in analyzing protein posttranslational modifications, identifying important components involved in various signaling networks and studying host-pathogen interactions on the proteomics level.


Dr. Zhu's lab has developed two key technologies: high-throughput protein purification (>4,000 proteins/day) and high-density protein microarrays/chip (>15,000 protein/slide). So far, they have fabricated proteome chips in the budding yeast, herpesviruses and E. coli (K12). They are also currently working on building a focused protein chip in humans. Previously, they and other researchers demonstrated that protein chips could be used to characterize various protein-binding properties, including protein-protein, protein-DNA, protein-lipid and protein-drug interactions, and to identify downstream targets of protein kinases.

More recently, Dr. Zhu's team and their colleagues have made significant progress in expanding the application of protein chips in the following directions: 1) novel protein binding assays, such as RNA-protein, live cell-protein and lectin-protein interactions; 2) novel enzymatic reactions, including protein ubiquitination and acetylation, 3) human serum profiling and 4) a novel approach in protein chip fabrication. The above new assays or approaches have been applied to investigate host-pathogen interactions, protein glycosylation, cell surface glycan profiles, a ubiquitin E3 enzyme in yeast and biomarker identification in human inflammatory bowel diseases. Their recent progress has been highlighted in five publications. They strongly believe that the protein chip technologies are capable of accumulating massive amount of data to allow comprehensive and systematic analyses of complex eukaryotic proteomes.

Lab Website: Zhu Lab

Selected Publications

Hu S, Wan J, Su Y, Song Q, Zeng Y, Nguyen HN, Shin J, Cox E, Rho HS, Woodard C, Xia S, Liu S, Lyu H, Ming GL, Wade H, Song H, Qian J, Zhu H. "DNA methylation presents distinct binding sites for human transcription factors." Elife. 2013 Sep 3;2:e00726. doi: 10.7554/eLife.00726.

Newman RH, Hu J, Rho HS, Xie Z, Woodard C, Neiswinger J, Cooper C, Shirley M, Clark HM, Hu S, Hwang W, Jeong JS, Wu G, Lin J, Gao X, Ni Q, Goel R, Xia S, Ji H, Dalby KN, Birnbaum MJ, Cole PA, Knapp S, Ryazanov AG, Zack DJ, Blackshaw S, Pawson T, Gingras AC, Desiderio S, Pandey A, Turk BE, Zhang J, Zhu H, Qian J. "Construction of human activity-based phosphorylation networks." Mol Syst Biol. 2013;9:655. doi: 10.1038/msb.2013.12.

Jeong JS, Jiang L, Albino E, Marrero J, Rho HS, Hu J, Hu S, Vera C, Bayron-Poueymiroy D, Rivera-Pacheco ZA, Ramos L, Torres-Castro C, Qian J, Bonaventura J, Boeke JD, Yap WY, Pino I, Eichinger DJ, Zhu H, Blackshaw S. "Rapid identification of monospecific monoclonal antibodies using a human proteome microarray." Mol Cell Proteomics. 2012 Jun;11(6):O111.016253. doi: 10.1074/mcp.O111.016253. Epub 2012 Feb 3.

Lu JY, Lin YY, Sheu JC, Wu JT, Lee FJ, Chen Y, Lin MI, Chiang FT, Tai TY, Berger SL, Zhao Y, Tsai KS, Zhu H, Chuang LM, Boeke JD. "Acetylation of yeast AMPK controls intrinsic aging independently of caloric restriction." Cell. 2011 Sep 16;146(6):969-79. doi: 10.1016/j.cell.2011.07.044. Epub 2011 Sep 9.

Hu S, Xie Z, Onishi A, Yu X, Jiang L, Lin J, Rho HS, Woodard C, Wang H, Jeong JS, Long S, He X, Wade H, Blackshaw S, Qian J, Zhu H. "Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling." Cell. 2009 Oct 30;139(3):610-22. doi: 10.1016/j.cell.2009.08.037.

Contact for Research Inquiries

Edward D. Miller Research Building
733 N. Broadway
Baltimore, MD 21205 map
Phone: 410-502-0878
Fax: 410-502-1872

Academic Affiliations & Courses

Graduate Program Affiliation

BCMB Graduate Program
Chemistry-Biology Interface Program

Activities & Honors


  • Chair's Award, Gordon Research Conference, 2000
  • Chair's Award, Gordon Research Conference, 1998
  • Member of Gamma Sigma Delta, The Honor Society of Agriculture, 1994


  • American Pathopathology Society, 1995 - 1999
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