You are here: Home FACULTY Faculty A-Z
Antony K. Chen
Ph.D., Associate 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

    2019.08-Present Associate Professor, Department of Biomedical Engineering, College of Engineering, Peking University

    2013.04-2019.07 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. Mao, S., Ying, Y., Wu, X., Krueger, C.J. and Chen, A.K.* CRISPR/Dual-FRET Molecular Beacon for Sensitive Live-Cell Imaging of Non-Repetitive Genomic Loci. Nucleic Acids Res, 2019; DOI: 10.1093/nar/gkz752

    2. Ding, T., Chen, A.K.* and Lu, Z.* The applications of nanopores in studies of proteins. Sci. Bull. 2019; DOI:  10.1016/j.scib.2019.07.029. (Review)

    3.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.

    4.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.

    5. 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.

    6. 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.

    7. 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) 

    8. 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

    9.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.

    10. 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

    11. 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. 

    12. 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.

    13. 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.

    14. 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.

    15. 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).

    16. 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.

    17. 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.

    18. 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.

    19. 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) 

    20. 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.

    21. 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.   

    22. 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).

    23. 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.

    24. 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.

    25. 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).

    26. 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. Ying Y., Mao S., Krueger C.J., Chen A.K.* (2019) Live-Cell Imaging of Long Noncoding RNAs Using Molecular Beacons. In: Shav-Tal Y. (eds) Imaging Gene Expression. Methods in Molecular Biology, vol 2038. Humana, New York, NY

    2. 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.

    3. 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.

    4. 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.

    5. 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. 

    6. 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.

    7. 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. 

    8. 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.