Welcome to Fei Lab
Department of Biochemistry and Molecular Biology


32. S Park, J Zhang, MA Reyer, J Zareba, AA Troy, J Fei. (2018) Conducting Multiple Imaging Modes with One Fluorescence Microscope. JoVE (Journal of Visualized Experiments), e58320 [PDF].

31. J Zhang#, B Chetnani#, ED Cormack, W Liu, A Mondragón, J Fei. (2018) Specific structural elements of the T-box riboswitch drive the two-step binding of the tRNA ligand. eLife 7: e39518 [PDF][SI]. (#Co-authorship)

30. J Fei, CM Sharma. (2018) RNA localization in baceria. Microbiology Spectrum 6: no. 5 doi:10.1128/microbiolspec.RWR-0024-2018 [PDF].

29. D Singh, Y Wang, J Mallon, O Yang, J Fei, A Poddar, D Ceylan, S Bailey, T Ha. (2018) Mechanisms of improved specificity of engineered Cas9s revealed by single-molecule FRET analysis. Nat Struct Mol Biol 25: 347 [PDF].

28. S Park, M Bujnowska, EL McLean, J Fei. (2018)  Quantitative Super-Resolution Imaging of Small RNAs in Bacterial Cells. Methods in Molecular Biology  Bacterial Regulatory RNA:199-212 [PDF].


27. MA Reyer, EL McLean, S Chennakesavalu, J Fei. (2017) An Automated Image Analysis Method for Segmenting Fluorescent Bacteria in Three Dimensions. Biochemistry DOI: 10.1021/acs.biochem.7b00839 [PDF].

26. J Fei*, M Jadaliha, TS Harmon, ITS Li, B Hua, Q Hao, AlS Holehouse, M Reyer, Q Sun, SM Freier, RV Pappu, KV Prasanth*, T Ha. (2017)  Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution. J Cell Sci 130(24): 4180-4192. (*Co-correspondence) [PDF].

25. S Jiang, S Park, SD Shallapalli, J Fei and Y Wang. (2017)  Robust nonparametric quantification of clustering density of molecules in single-molecule localization microscopy. PloS one 12(6): e0179975 [PDF].

24. CR Lloyd, S Park, J Fei and CK Vanderpool. (2017) The small protein Sgrt controls transport activity of the glucose-specific phosphotransferase system. Journal of Bacteriology, 199: e00869-16. [PDF]. Also see commentary by Raina and Storz [PDF].


23.  Singh, D., Sternberg, S.H., Fei, J., Doudna, J.A., and Ha, T. (2016) Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9. Nat Commundoi: 10.1038/ncomms12778. [PDF][SI]

22.  Balasubramanian, D., Ragunathan, P.T., Fei, J., and Vanderpool, C.K. (2016) A prophage-encoded small RNA controls metabolism and cell division in Escherichia coli. mSystems, 1: e00021-15. [PDF]

21.  Zong, X., Nakagawa, S., Freier S.M., Fei, J., Ha, T., Prasanth, S.G., and Prasanth, K.V. (2016) Natural antisense RNA promotes 3' end processing and maturation of MALAT1 lncRNA. Nucleic Acids Research, doi: 10.1093/nar/gkw047. [PDF][SI]


20.  Peterson, J.R., Cole, J.A., Fei, J., Ha, T. and Luthey-Schulten, Z.A. (2015) Effects of DNA replication on mRNA noise. Proc Natl Acad Sci, USA, 112:15886. [PDF]

19.  Zhang, J., Fei, J., Leslie, B.J., Han, K.Y., Kuhlman, T.E., and Ha, T. (2015) Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells. Scientific reports, 5: 17295. [PDF][SI]

18.  Fei, J., Singh, D., Zhang, Q., Park, S., Balasubramanian, D., Golding, I., Vanderpool, C.K. and Ha, T. (2015) Determination of in vivo target search kinetics of regulatory non-coding RNA. Science, 347: 1371-1374.  [PDF][SI

17. Tripathi, V., Fei, J., Ha, T. and Prasanth, K.V. (2015). RNA fluorescence in situ hybridization in cultured mammalian cells. Regulatory non-coding RNAs,Springer New York.  [PDF]


16.   Ning, W., Fei, J. and Gonzalez, R.L., Jr. (2014) The ribosome uses cooperative conformational changes to maximize and regulate the efficiency of translation. Proc Natl Acad Sci, USA, 111: 12073–12078. [PDF][SI

15.   Kim, H.K., Liu, F., Fei, J., Bustamante, C. Gonzalez, R.L., Jr. and Tinoco, I. (2014) A frameshifting stimulatory stem loop destabilizes the hybrid state and impedes ribosomal translocation. Proc Natl Acad Sci, USA, 111: 5538-5543.  [PDF][SI

14.   Chen, B., Boel, G., Hashem, Y., Ning W., Fei, J., Wang, C., Gonzalez, R.L., Jr., Hunt, J.F., and Frank, J. (2014) EttA binds at ribosomal E site and regulates translation by restricting ribosome dynamics. Nat Struct Mol Biol, 21: 152–159.  [PDF][SI


13.   Han, K.Y., Leslie, B.J., Fei, J., Zhang, J. and Ha, T. (2013) Understanding the photophysics of the Spinach-DFHBI RNA aptamer-fluorogen complex to improve live cell RNA imaging. J. Am. Chem. Soc. 135: 19033–19038. [PDF][SI

12.  Fei, J. and Ha, T. (2013). Watching DNA breath one molecule at a time. Proc Natl Acad Sci, USA, 110: 17173-17174. [PDF]


11.  Fei, J., Richard, A.C., Bronson, J.E. and Gonzalez, R.L., Jr. (2011). Transfer RNA-mediated control of ribosome dynamics during translation. Nat Struct Mol Biol, 18:1043-51.  [PDF][SI

10. MacDougall, D., Fei, J., and Gonzalez, R.L., Jr. (2011). Single-molecule fluorescence resonance energy transfer investigations of ribosome-catalyzed protein synthesis. Molecular Machines in Biology: Workshop of the CellCambridge University Press.  [PDF]

9.  Wang, B., Ho, J., Fei, J., Gonzalez, R.L., Jr and Lin, Q. (2011) A microfluidic approach for investigating the temperature dependence of biomolecular activity with single-molecule resolution. Lab Chip11: 274-81. [PDF][SI


8. Ye, X., Fei, J., Xu, K. and Bai, R. (2010) Effect of polystyrene-b-poly(ethylene oxide) on self-assembly of polystyrene-b-poly(N-isopropylacrylamide) in aqueous solution. J Polym Sci B: Polym Phys48: 1168-74.  [PDF]

7. Ye, X., Fei, J., Guan, J., Zhou, X. and Zhang, G. (2010) Dispersion of polystyrene inside polystyrene-b-poly(N-isopropylacrylamide) micelles in water. J Polym Sci B: Polym Phys48: 749-55.  [PDF]

6.  Fei, J., Wang, J., Sternberg, S.H., MacDougall, D.D., Elvekrog, M.M., Pulukkunat, D., and Gonzalez, R.L., Jr. (2010) A highly-purified, fluorescently-labeled in vitro translation system for single molecule studies of protein synthesis. Methods Enzymol, 472: 221-259. [PDF]

5.  Bronson, J.E., Hofman, J.M., Fei, J., Gonzalez, R.L., Jr. and Wiggins, C.H. (2010) Graphical models for inferring single molecule dynamics. BMC BioinformaticsSuppl 8: S2. [PDF]


4.  Bronson, J.E., Fei, J., Hofman, J.M. Gonzalez, R.L, Jr. and Wiggins, C.H. (2009). Learning rates and states from biophysical time series: A Bayesian approach to model selection and single-molecule FRET data. Biophys J, 97: 3196-3205. [PDF][SI
†This work was selected and evaluated by Faculty of 1000 Biology  (http://www.f1000biology.com/article/id/2278956). 

3.  Fei, J., Bronson, J.E., Hofman, J.M., Srinivas, R.L., Wiggins, C.H. and Gonzalez, R.L., Jr. (2009). Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation. Proc Natl Acad Sci, USA,106:15702-15707.  [PDF][SI
†This work was featured as a Science and Technology News Item in Chem Eng News 87, 29 

2. Sternberg, S.H., Fei, J., Prywes, N., McGrath, K.A. and Gonzalez, R.L., Jr. (2009). Translation factors direct intrinsic ribosome dynamics during termination and ribosome recycling. Nat Struct Mol Biol, 16: 861-868. [PDF][SI
†This paper was featured as a Research Highlight in Nat Chem Biol 5, 540 and the work was featured as a Science and Technology News Item in Chem Eng News 87, 29.


1.   Fei, J. , Kosuri, P., MacDougall, D. and Gonzalez, R.L., Jr. (2008). Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. Mol Cell, 30: 348-359. [PDF][SI]

You can also find the full publication list at my Google Scholar.