JOURNAL PUBLICATIONS


34. Ying, Y., Yang, Y., and Chen, A.K.* Roles of RNA scaffolding in nanoscale Gag multimerization and selective protein sorting at HIV membranes. Sci. Adv. 2024 Feb 23;10(8):eadk8297.

33.Dong, J., Wu, X., Zhou, X., Gao, Y., Wang, C., Wang, W., He, W., Li, J., Deng, W., Liao, J., Wu, X., Lu, Y., Chen, A.K., Wen, L., Fu, W., Tang, F. Spatially resolved expression landscape and gene-regulatory network of human gastric corpus epithelium. Protein Cell. 2023 Jun 7;14(6):433-447.

32. Wang, R., Chen, F., Chen, Q., Wan, X., Shi, M., Chen, A.K., Ma, Z., Li, G., Wang, M., Ying, Y., Liu Q, Li, H., Zhang X., Ma, J., Zhong, J., Chen, M., Zhang, M., Zhang, Y., Chen, Y., Zhu, D. MyoD is a 3D genome structure organizer for muscle cell identity. Nat Commun. 2022 Jan 11;13(1):205.

31. Qu, N., Ying, Y., Qin, J., and Chen, A.K.* Rational design of self-assembled RNA nanostructures for HIV-1 virus assembly blockade. Nucleic Acids Res. 2021; gkab1282

30. Mao, S., Ying, Y., Zhao, M., Yang, Y., and Chen, A.K.* A Background Assessable and Correctable Bimolecular Fluorescence Complementation System for Nanoscopic Single-Molecule Imaging of Intracellular Protein-Protein Interactions. ACS Nano. 2021；15, 14338-14346.

29. Jin, M., Tang, S., Chen, J., Yu, X., Shu, H., Tao Y, Chen, A.K., Gong Q, Wang X, Xiao Y. 1/f-noise-free optical sensing with an integrated heterodyne interferometer. Nat. Commun. 2021; 12(1), 1973.

28. Mao, S., Ying, Y., Wu, R., and Chen, A.K.* Recent Advances in the Molecular Beacon Technology for Live-Cell Single-Molecule Imaging. iScience. 2020; 23, 101801. (Review)

27. Kang Y, Wan C, Lu S, Fu Z, Chen, A.K., Lu, Z. A new metagenome binning method based on gene uniqueness. Genes Genomics. 2020 Aug;42(8):883-892.

26. 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; 47, e131.

25. Ding, T., Chen, A.K.* and Lu, Z.* The applications of nanopores in studies of proteins. Sci Bull. 2019; 64, 1456-1467. (Review).

24. Wu, X., Mao, S., Ying, Y., 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; 17(2): 119-128.

23. 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.

22. 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.

21. 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. Immature HIV-1 lattice assembly dynamics are regulated by scaffolding from nucleic acid and the plasma membrane. Proc Natl Acad Sci U S A. 2017; 114(47): E10056-E10065

20. 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; 15, 279-286.

19. 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 2018; 9, 640-651.

18. 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.

17. 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

16. 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.

15. 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.

14. 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.

13. 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.

12. 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).

11. 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.

10. 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.

9. 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.

8. 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)

7. 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.

6. 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.

5. 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).

4. 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.

3. 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.

2. 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).

1. 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


10. Wu X., Ying Y., Mao S., Krueger C.J., Chen A.K.* (2020) Live-Cell Imaging of Genomic Loci Using CRISPR/Molecular Beacon Hybrid Systems. In: Heinlein M. (eds) RNA Tagging. Methods in Molecular Biology, vol 2166. Humana, New York, NY. pp 357-372.

9. Mao S., Ying Y., Wu X., Chen A.K.* (2020) Delivering Molecular Beacons via an Electroporation-Based Approach Enables Live-Cell Imaging of Single RNA Transcripts and Genomic Loci. In: Heise T. (eds) RNA Chaperones. Methods in Molecular Biology, vol 2106. Humana, New York, NY. pp 241-252.

8. 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. pp 21-33.

7. 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.

6. 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.

5. 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.

3. 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.

2. 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.

1. 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.

PATENTS


  • 陈匡时，吴若楠，秦金珊，应亚宸，杨艳涛。一种对单分子荧光共振能量转移信号进行分析的方法。中国发明专利，专利号：202110687125.6

  • 陈匡时，马昭，毛诗琦，应亚宸。一种可有效识别假阳性信号的双分子荧光互补技术。中国发明专利，专利号：202110440775

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

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