Jingyi Fei_publications

53. Z Zhou, K Prévost, M-C Carrier, N El Ashry, JH Mu, CDV Valle, S Park, A Guzman, E Massé, J Fei, (2025) Structural dependence of ProQ-mRNA interactions in live bacterial cells. Communications Biology , (2025)8: 1780.

52. H Glauninger, JAM Bard, CJ Wong Hickernell, KM Velez, EM Airoldi, W Li, RH Singer, S Paul, J Fei, TR Sosnick, EWJ Wallace, DA Drummond, (2025) Transcriptome-wide mRNP condensation precedes stress granule formation and excludes new mRNAs. 'Molecular Cell, 85(23): p4393-4409.e11.

51. L Wen^#, MA Arias^#, X Fan, S Paul, SE Liao, M Sobczyk, O Regev*, J Fei*, (2025) RNA localization to nuclear speckles follows splicing logic. BioRxiv, 2025.05. 28.6564. (*co-correspondence).

50. E Campos-Chavez ^#, S Paul^#, Z Zhou, D Alonso, AR Verma, J Fei*, A Mondragon*, (2024) Translational T-box riboswitches bind tRNA by modulating conformational flexibility. Nature Communications 15(1): 6592. (*co-correspondence).

49. J Wu, Y Xiao, Y Liu, L Wen, C Jin, S Liu, S Paul, C He, O Regev*, J Fei*, (2024) Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency. Science Advances, 10, eadp727. (*co-correspondence).

48. S Paul^#, MA Hernandez^#, L Wen, SE Liao, J Zhang, X Wang, O Regev*, J Fei* (2024) RNA molecules display distinctive organization at nuclear speckles, iScience, 27(5): 109603.

47. T Ha, J Fei, S Schmid, NK Lee, RL Gonzalez, Jr., S Paul, S Yeou (2024). Fluorescence resonance energy transfer at the single-molecule level. Nature Reviews Methods Primers, 4:21

46. T Wu, A Cheng, X Li, J Wu, Y Zhang, J Xu, B Liu, X Dou, P Wang, L Zhang, J Fei, J Li, Z Ouyang, C He (2024). KARR-seq reveals cellular RNA higher-order structures and RNA-RNA interactions. Nature Biotechnology.

45. Y Xiao, Y-M Chen, Z Zou, C Ye, X Dou, J Wu, C Liu, S Liu, H Yan, P Wang, T Zeng, Q Liu, J Fei, W Tang, C He (2024). Profiling of RNA-binding protein binding sites by in-situ reverse transcription-based sequencing, Nature Methods. 21(2):247

44. KK Ray, CD Kinz-Thompson, J Fei, B Wang, Q Lin, RL Gonzalez (2023) Entropic control of the free-energy landscape of an archetypal biomolecular machine, Proc Natl Acad Sci, USA, 120: e2220591120.

43. Z Luo, J Zhang, J Fei, S Ke, (2022) Deep learning modeling m6A deposition reveals the importance of downstream cis-element sequences, Nature Communications, 13: 2720.

42. MA Reyer, S Chennakesavalu^#, EM Heideman^#, X Ma, M Bujnowska, L Hong, AR Dinner, CK Vanderpool, J Fei, (2021) Kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional sRNA regulators, Cell Reports, 36: 109764. (^#co-authorship)

41. D Lalaouna, K Prevost^#, S Park^#, T Chenard, M Bouchard, M Caron, CK Vanderpool, J Fei*, E Masse*, (2021) Binding of the RNA chaperone Hfq on target mRNAs promotes the small RNA RyhB-induced degradation in Escherichia coli, Non-Coding RNA, 7: 64. (*co-correspondence)

40. Yu Y^#, Zheng Q^#, Erramilli SK^#, Pan M^#, Park S, Xie Y, Li J, Fei J, Kossiakoff AA*, Liu L*, Zhao M*, (2021) K29-linked ubiquitin signaling regulates proteotoxic stress response and cell cycle, Nature Chemical Biology, 17: 896. (*co-correspondence, ^#co-authorship)

39. E Lerner†*, A Barth†*, J Hendrix†*, B Ambrose , V Birkedal , SC Blanchard , R Borner, HS Chung , T Cordes , TD Craggs, AA Deniz, J Diao, J Fei , RL Gonzalez, IV Gopich, T Ha, C A Hanke, G Haran, NS Hatzakis, S Hohng, S-C Hong, T Hugel, A Ingargiola, C Joo, AN Kapanidis, HD Kim, T Laurence, NK Lee, T-H Lee, EA Lemke, E Margeat, J Michaelis, X Michalet, S Myong, D Nettels, T-O Peulen, E Ploetz, Y Razvag, NC Robb, B Schuler, H Soleimaninejad, C Tang, R Vafabakhsh, DC Lamb*, CAM Seidel*, S Weiss*, (2021) FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices, eLife, 10:e60416.

38. S Park^#, K Prevost^#, EM Heideman†, M-C Carrier†, MS Azam, MA Reyer, W Liu, E Masse*, J Fei*, (2021) Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs and mRNAs in live bacterial cells, eLife, 10:e64207 . (*Co-correspondence; ^#,^ Co-authorship)

37. A Poddar, MS Azam, T Kayikcioglu, M Bobrovskyy, J Zhang, X Ma, P Labhsetwar, J Fei, D Singh, Z Luthey-Schulten, CK Vanderpool, T Ha, (2021) Nature Communications, 12:874.

36. M Bujnowska, J Zhang, Q Dai, EM Heideman, J Fei, (2020) Deoxyribozyme-based method for absolute quantification of N⁶-methyladenosine fraction at specific sites of RNA, Journal of Biological Chemistry, 295:6992 [PDF][SI].

35. Y Fan, Y Lim, LS Wyss, S Park, C Xu, H Fu, J Fei, Y Hong, B Wang, (2020) Mechanical expansion microscopy, Methods in Cell Biology [PDF]

34. Y Wang*, J Fei*, (220) Continuous active development of super-resolution fluorescence microscopy, Physical Biology, 17:030401 [PDF]

33. S Park, MA Reyer, EL McLean, W Liu, J Fei, (2019) An improved method for bacterial immunofluorescence staining to eliminate antibody exclusion from the fixed nucleoid, Biochemistry 58: 4457 [PDF][SI].

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 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.