Department of Biochemistry and Molecular Biology
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 Commun, doi: 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 Cell, Cambridge
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
Chip, 11:
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 Phys, 48:
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 Phys, 48:
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 Bioinformatics, Suppl
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.