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Antony K. Chen
Ph.D., Assistant Professor
Department of Biomedical Engineering
Peking University
  • Office Add: Integrated Science and Research Building, Room 112
  • OfficeTel: +86-10-62768343
  • LabAdd: Integrated Science and Research Building, Room 112
  • Email:

Research Interests

DNA/RNA Imaging Probes, CRISPR gene editing/labeling technology, Live-cell Imaging, DNA-RNA-Protein Interactions, Virus-Host Interactions, Super-resolution Imaging, Molecular and Nanomedicine


2004-2008   Ph.D.;   University of Pennsylvania                                (in Bioengineering)

2000-2002   M.S.;    University of California, San Diego                      (in Bioengineering)     

1996-2000   B.S.;     University of California, San Diego                      (in Bioengineering)            

Major Professional Experiences

2013-Present Assistant Professor, Department of Biomedical Engineering, College of Engineering, Peking University

2010-2013    Postdoc; National Institutes of Health;  Jennifer Lippincott-Schwartz’s lab

2010-2012    Postdoc; National Institute of Standards and Technology;  Anne Plant’s lab

2009/2010    Postdoc; University of Pennsylvania;  Andrew Tsourkas’ lab

Selected Honors

·The US. National Research Council (NRC) Research Associate Fellowship (2010-2012)

·Solomon R. Pollack Award for Excellence in Graduate Bioengineering Research (Best Ph.D. Thesis)   (2009)

Major Publications

1. Wu, X., Mao, S., Yachen, Ying., Krueger, C.J. and Chen, A.K.* Progress and Challenges for Live-Cell Imaging of Single Genomic Loci Using CRISPR-Based Platforms. Genomics, proteomics & bioinformatics. 2019; DOI: 10.1016/j.gpb.2018.10.001.

2. Yang, Y., Qu, N., Tan, J., Rushdi, M.N., Krueger, C.J. and Chen, A.K.* Roles of Gag-RNA interactions in HIV-1 virus assembly deciphered by single-molecule localization microscopy. Proc Natl Acad Sci U S A. 2018; 115, 6721-6726.

3. Wu, X., Mao, S., Yang, Y., Rushdi, M.N., Krueger, C.J. and Chen, A.K.* A CRISPR/molecular beacon hybrid system for live-cell genomic imaging. 2018; Nucleic Acids Res, 46, e80.

4. Pak A.J., Grime J.M.A., Sengupta P., Chen A.K., Durumeric A.E.P., Srivastava A., Yeager M., Briggs J.A.G., Lippincott-Schwartz J., Voth G.A.. Proc Natl Acad Sci U S A. 2017; DOI:  10.1073/pnas.1706600114.

5. Ma Z., Wu X., Krueger C.J., and Chen A.K.* Engineering Novel Molecular Beacon Constructs to Study Intracellular RNA Dynamics and Localization. Genomics Proteomics Bioinformatics. 2017; Oct;15(5):279-286. (Review) 

6. Qu, N., Ma, Z., Zhang, M., Rushdi, M.N., Krueger, C.J. and Chen, A.K.* Inhibition of retroviral Gag assembly by non-silencing miRNAs promotes autophagic viral degradation. Protein Cell. 2017; DOI: 10.1007/s13238-017-0461-z

7. Chen, M., Ma, Z., Wu, X., Mao, S., Yang, Y., Tan, J., Krueger, C.J. and Chen, A.K.* A molecular beacon-based approach for live-cell imaging of RNA transcripts with minimal target engineering at the single-molecule level.  Sci Rep. 2017; 7, 1550.

8. Yu, X., Zhang, Y., Li, T., Ma, Z., Jia, H., Chen, Q., Zhao, Y., Zhai, L., Zhong, R., Li, C., Zou, X., Meng, J., Chen, A.K., Puri, P.L., Chen, M., Zhu, D.* Long Non-coding RNA Linc-RAM Enhances Myogenic Differentiation by Interacting with MyoD. Nat. Commun. 2017; 8: 14016

9. Zhao, D., Yang, Y., Qu, N., Chen, M., Ma, Z. Krueger, C.J., Behlke, M.A. and Chen A.K.* Single-Molecule Detection and Tracking of RNA Transcripts in Living Cells Using Phosphorothioate-Optimized 2’-O-Methyl RNA Molecular Beacons. Biomaterials. 2016; 100: 172-183. 

10. Chen, A.K., Sengupta, P., Waki, K., Van Engelenburg, S., Ochiya, T., Ablan, S.D., Freed, E.O. and Lippincott-Schwartz, J.* MicroRNA binding to the HIV-1 Gag protein inhibits Gag assembly and virus production. Proc. Natl. Acad. Sci. U S A., 2014; 111(26):E2676-83.

11. Chung, K.H., Chen, A.K., Anderton, C.R., Bhadriraju, K., Plant, A.L., Bush, B.G., Cook, R.F. and Frank F. Frictional properties of native and functionalized type I collagen thin films. Appl. Phys. Lett. 2013;  103 (14), 143703-143703-5.

12. Chen, A.K. * Delrio, F., Peterson, A.W., Chung, K.H., Bhadriraju, K, and Plant, A.L. Cell spreading and proliferation in response to the composition and mechanics of engineered fibrillar extracellular matrices. Biotechnol Bioeng. 2013: 110: 2731-2741.

13. Chen, A.K.* and Tsourkas A. Developing Molecular-Beacon Constructs for Improved Live-Cell Analysis and Imaging of RNA. Am. Biotech. Lab. 2010; 28 (7): 10-13. (Review).

14. Chen, A.K., Davydenko, O., Behlke, M., and Tsourkas A.* Ratiometric Bi-Molecular Beacons: Ratiometric Bimolecular Beacons for the Sensitive Detection of RNA in Single Living Cells. Nucleic Acids Res. 2010; 38 (14): e148.

15. Cheng, Z., Chen, A.K., Lee H-Y., and Tsourkas, A.* Examination of Folate-Targeted Liposomes with Encapsulated Poly(2-Propylacrylic acid) as a pH-responsive Nanoplatform for Cytosolic Drug Delivery. Small. 2010; 6 (13): 1398-401.

16. Chen, A.K., Behlke, M., and Tsourkas, A.* Subcellular Trafficking and Functionality of 2'-O-methyl and 2'-O-methy-phosphorothioate Molecular Beacons. Nucleic Acids Res. 2009; 37 (22): e149.

17. Chen, A.K. and Tsourkas, A.* Imaging RNA in Living Cells with Molecular Beacons: Current Perspectives and Challenges. J. Innov. Opt. Health Sc. 2009; 2 (4): 315-324. (Review) 

18. Chen, A.K., Cheng, Z., Behlke, M., and Tsourkas, A.* “Assessing the Sensitivity of Commercially Available Fluorophores to the Intracellular Environment”. Anal Chem. 2008; 80 (19): 7437-44.

19. Chen, A.K., Behlke, M., and Tsourkas, A.* “Efficient Cytosolic Delivery of Molecular Beacon Conjugates and Flow Cytometric Analysis of Target RNA”. Nucleic Acids Res. 2008; 36 (12): e69.   

20. Elias, D.R., Thorek, D.L., Chen, A.K., Czupryna, J., and Tsourkas, A.* “In vivo Imaging of Cancer Biomarkers Using Activatable Molecular Probes”. Cancer Biomarkers. 2008; 4 (6): 287-305. (Review).

21. Chen, A.K., Behlke, M., and Tsourkas, A.* “Avoiding False-Positive Signals with Nuclease-Vulnerable Molecular Beacons in Single Living Cells”. Nucleic Acids Res. 2007; 35 (16): e105.

22. Chen, A.K., Latz, M.I., Sobolewski, P., and Frangos, J.A.* “Evidence for the Role of G-Proteins in Flow Stimulation of Dinoflagellate Bioluminescence.” Am J Physiol Regul Integr Comp Physiol. 2007; 292(5): R2020-7.

23. Thorek, D.L.J., Chen, A.K., Czupryna, J., and Tsourkas, A.* “Superparamagnetic Iron Oxide Nanoparticle Probes for Molecular Imaging.” Ann Biomed Eng. 2006; Jan;34(1):23-38 (Review).

24. Chen, A.K., Latz, M.I., and Frangos, J.A.* The Use of Dinoflagellate Bioluminescence to Characterize Cell Stimulation in Bioreactors.” Biotechnol Bioeng. 2003; 83(1): 93-103.

Book Chapters

            1. Chen, M., Mao, S., Wu, X., Mao, S., Ma., Z., Yang, Y., Krueger, C.J. and Chen, A.K.* (2019) Single-Molecule Analysis of RNA Dynamics in Living Cells Using Molecular Beacons. In: Wajapeyee, Narendra, Gupta, Romi (eds) Epitranscriptomics. Methods in Molecular Biology, vol 1870. Humana Press, New York, NY.

            2. Chen M., Yang Y., Krueger C.J., Chen A.K.* (2018) Optimizing Molecular Beacons for Intracellular Analysis of RNA. In: Gaspar I. (eds) RNA Detection. Methods in Molecular Biology, vol 1649. Humana Press, New York, NY. pp 243-257.

3. Yang Y., Chen M., Krueger C.J., Tsourkas A., Chen A.K.* (2018) Quantifying Gene Expression in Living Cells with Ratiometric Bimolecular Beacons. In: Gaspar I. (eds) RNA Detection. Methods in Molecular Biology, vol 1649. Humana Press, New York, NY. pp 231-242.

4 Crayton, S.H., Chen, A.K., Liu, J.F., Higbee-Dempsey, E.M., Huang, C.-H., Tsourkas, A. and Cheng Z. (2017) Molecular Imaging In Comprehensive Biomaterials II, edited by Ducheyne, P., Grainger, D.W., Healy, K.E., Hutmacher, D.W., Kirkpatrick, C.J., Elsevier Inc., pp 424-466. 

5. Chen, A.K., Rhee, W.J., Bao G. and Tsourkas, A.* (2011)Delivery of Molecular Beacons for Live-cell Imaging and Analysis of RNA, RNA Detection and Visualization, Jeffrey E. Gerst, Humana Press, pp 159-174.

6. Crayton, S.H., Chen, A.K., Cheng, Z., Tsourkas, A.* (2010) Molecular Imaging In Comprehensive Biomaterials, edited by Ducheyne, P., Healy, K., Hutmacher, D., Kirkpatrick, C.J., Elsevier Inc., pp 305-328. 

7. Thorek, D.L.J., Czupryna, J., Chen, A.K., Tsourkas, A.* (2006) Molecular Imaging of Cancer with Superparamagnetic Iron Oxide Nanoparticles. In Cancer Imaging, edited by M.A. Hayat. Elsevier Science/Academic Press, pp 85-95.

Patent Applications

1. Andrew Tsourkas and Antony Chen. Quantitative Molecular Probes, 2007. US Application Number: 12/282.612; International Application Number: PCT/US07/064099.

2. Andrew Tsourkas and Antony Chen. Novel Molecular Beacons. 2009. US Application Number: 61/244,378; International Application Number: PCT/US10/49301.