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Jingyi Fei

TitleAssistant Professor
InstitutionUniversity of Chicago
DepartmentBiochemistry and Molecular Biology
AddressChicago IL 60637
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    The main focus of my research is to understand the mechanisms by which RNAs mediate gene expression and regulation in both bacterial and eukaryotic systems. We are currently studying regulatory RNAs and RNA modifications using various single-molecule fluorescence microscopy and super-resolution imaging tools. my group is also interested in the development of new labeling, imaging and data analysis methods.
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    2024Kavli Fellow, National Academy of Sciences
    2018Scialog Fellow, Research Corporation for Science Advancement
    2017 - 2022NIH Director’s New Innovator Award, NIH
    2017 - 2020Searle Scholar, Searle Scholars Program
    2010Hammett Award, Columbia University
    2007Blanche R. and David Kasindorf Fellowship Award, Columbia University

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    2246530     (FEI, JINGYI; REGEV ODED)Aug 1, 2023 - Jul 31, 2026
    NSF
    Connecting the sequence logic of RNA splicing to nuclear localization
    Role: Principal Investigator

    R21GM141670     (FEI, JINGYI ;TANG, WEIXIN)Jun 1, 2021 - May 31, 2023
    NIH
    Spatially resolved high throughput lineage tracing by targeted in situ DNA diversification
    Role: Principal Investigator

    DP2GM128185     (FEI, JINGYI)Sep 30, 2017 - May 31, 2022
    NIH
    Quantitative imaging of epitranscriptomic regulation mediated by RNA modification
    Role: Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Glauninger H, Bard JAM, Wong Hickernell CJ, Airoldi EM, Li W, Singer RH, Paul S, Fei J, Sosnick TR, Wallace EWJ, Drummond DA. Transcriptome-wide mRNA condensation precedes stress granule formation and excludes stress-induced transcripts. bioRxiv. 2024 May 02. PMID: 38659805; PMCID: PMC11042329.
      Citations:    
    2. Paul S, Arias MA, Wen L, Liao SE, Zhang J, Wang X, Regev O, Fei J. RNA molecules display distinctive organization at nuclear speckles. iScience. 2024 May 17; 27(5):109603. PMID: 38638569; PMCID: PMC11024929.
      Citations:    
    3. Wu J, Xiao Y, Liu Y, Wen L, Jin C, Liu S, Paul S, He C, Regev O, Fei J. Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency. bioRxiv. 2024 Feb 29. PMID: 38464148; PMCID: PMC10925297.
      Citations:    
    4. Wu T, Cheng AY, Zhang Y, Xu J, Wu J, Wen L, Li X, Liu B, Dou X, Wang P, Zhang L, Fei J, Li J, Ouyang Z, He C. KARR-seq reveals cellular higher-order RNA structures and RNA-RNA interactions. Nat Biotechnol. 2024 Jan 18. PMID: 38238480.
      Citations:    Fields:    
    5. Xiao Y, Chen YM, Zou Z, Ye C, Dou X, Wu J, Liu C, Liu S, Yan H, Wang P, Zeng TB, Liu Q, Fei J, Tang W, He C. Profiling of RNA-binding protein binding sites by in situ reverse transcription-based sequencing. Nat Methods. 2024 Feb; 21(2):247-258. PMID: 38200227; PMCID: PMC10864177.
      Citations: 1     Fields:    Translation:Cells
    6. Ousalem F, Singh S, Bailey NA, Wong KH, Zhu L, Neky MJ, Sibindi C, Fei J, Gonzalez RL, Boël G, Hunt JF. Comparative genetic, biochemical, and biophysical analyses of the four E. coli ABCF paralogs support distinct functions related to mRNA translation. bioRxiv. 2023 Jun 12. PMID: 37398404; PMCID: PMC10312648.
      Citations:    
    7. Ray KK, Kinz-Thompson CD, Fei J, Wang B, Lin Q, Gonzalez RL. Entropic control of the free-energy landscape of an archetypal biomolecular machine. Proc Natl Acad Sci U S A. 2023 05 23; 120(21):e2220591120. PMID: 37186858; PMCID: PMC10214133.
      Citations: 2     Fields:    Translation:Cells
    8. Luo Z, Zhang J, Fei J, Ke S. Deep learning modeling m6A deposition reveals the importance of downstream cis-element sequences. Nat Commun. 2022 05 17; 13(1):2720. PMID: 35581216; PMCID: PMC9114009.
      Citations: 4     Fields:    Translation:Cells
    9. Reyer MA, Chennakesavalu S, Heideman EM, Ma X, Bujnowska M, Hong L, Dinner AR, Vanderpool CK, Fei J. Kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional sRNA regulators. Cell Rep. 2021 09 28; 36(13):109764. PMID: 34592145; PMCID: PMC8634553.
      Citations: 4     Fields:    Translation:Cells
    10. Park S, Vanderpool CK, Fei J, Lalaouna D, Prévost K, Chénard T, Bouchard MP, Caron MP, Massé E. Binding of the RNA Chaperone Hfq on Target mRNAs Promotes the Small RNA RyhB-Induced Degradation in Escherichia coli. Noncoding RNA. 2021 Sep 28; 7(4). PMID: 34698252; PMCID: PMC8544716.
      Citations: 3     
    11. Yu Y, Zheng Q, Erramilli SK, Pan M, Park S, Xie Y, Li J, Fei J, Kossiakoff AA, Liu L, Zhao M. K29-linked ubiquitin signaling regulates proteotoxic stress response and cell cycle. Nat Chem Biol. 2021 08; 17(8):896-905. PMID: 34239127; PMCID: PMC8717942.
      Citations: 23     Fields:    Translation:HumansCells
    12. Lerner E, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Sung Chung H, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, Ha T, Haran G, Hatzakis NS, Hohng S, Hong SC, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee TH, Lemke EA, Michalet X, Myong S, Nettels D, Peulen TO, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Weiss S, Barth A, Börner R, Cordes T, Hanke CA, Margeat E, Michaelis J, Ploetz E, Lamb DC, Seidel CA. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. Elife. 2021 03 29; 10. PMID: 33779550; PMCID: PMC8007216.
      Citations: 74     Fields:    Translation:Cells
    13. Park S, Heideman EM, Carrier MC, Azam MS, Reyer MA, Liu W, Fei J, Prévost K, Massé E. Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs, and mRNAs in live bacterial cells. Elife. 2021 02 22; 10. PMID: 33616037; PMCID: PMC7987339.
      Citations: 14     Fields:    Translation:Cells
    14. Poddar A, Azam MS, Kayikcioglu T, Bobrovskyy M, Zhang J, Ma X, Labhsetwar P, Fei J, Singh D, Luthey-Schulten Z, Vanderpool CK, Ha T. Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA. Nat Commun. 2021 02 08; 12(1):874. PMID: 33558533; PMCID: PMC7870926.
      Citations: 1     Fields:    Translation:Cells
    15. Fan Y, Lim Y, Wyss LS, Park S, Xu C, Fu H, Fei J, Hong Y, Wang B. Mechanical expansion microscopy. Methods Cell Biol. 2021; 161:125-146. PMID: 33478686.
      Citations: 3     Fields:    Translation:AnimalsCells
    16. Bujnowska M, Zhang J, Dai Q, Heideman EM, Fei J. Deoxyribozyme-based method for absolute quantification of N6-methyladenosine fractions at specific sites of RNA. J Biol Chem. 2020 05 15; 295(20):6992-7000. PMID: 32269077; PMCID: PMC7242713.
      Citations: 4     Fields:    Translation:HumansCells
    17. Wang Y, Fei J. Continuous active development of super-resolution fluorescence microscopy. Phys Biol. 2020 04 07; 17(3):030401. PMID: 32066124; PMCID: PMC7658958.
      Citations:    Fields:    
    18. Park S, Reyer MA, McLean EL, Liu W, Fei J. An Improved Method for Bacterial Immunofluorescence Staining To Eliminate Antibody Exclusion from the Fixed Nucleoid. Biochemistry. 2019 11 12; 58(45):4457-4465. PMID: 31657208.
      Citations: 8     Fields:    Translation:Cells
    19. Park S, Zhang J, Reyer MA, Zareba J, Troy AA, Fei J. Conducting Multiple Imaging Modes with One Fluorescence Microscope. J Vis Exp. 2018 10 28; (140). PMID: 30417870; PMCID: PMC6235614.
      Citations: 2     Fields:    Translation:Cells
    20. Zhang J, Chetnani B, Cormack ED, Alonso D, Liu W, Fei J, Mondragón A. Specific structural elements of the T-box riboswitch drive the two-step binding of the tRNA ligand. Elife. 2018 09 25; 7. PMID: 30251626; PMCID: PMC6197855.
      Citations: 16     Fields:    Translation:Cells
    21. Fei J, Sharma CM. RNA Localization in Bacteria. Microbiol Spectr. 2018 09; 6(5). PMID: 30191804; PMCID: PMC6264921.
      Citations: 16     Fields:    Translation:Cells
    22. Singh D, Wang Y, Mallon J, Yang O, Fei J, Poddar A, Ceylan D, Bailey S, Ha T. Mechanisms of improved specificity of engineered Cas9s revealed by single-molecule FRET analysis. Nat Struct Mol Biol. 2018 04; 25(4):347-354. PMID: 29622787; PMCID: PMC6195204.
      Citations: 56     Fields:    Translation:Cells
    23. Park S, Bujnowska M, McLean EL, Fei J. Quantitative Super-Resolution Imaging of Small RNAs in Bacterial Cells. Methods Mol Biol. 2018; 1737:199-212. PMID: 29484595.
      Citations: 2     Fields:    Translation:Cells
    24. Fei J, Jadaliha M, Harmon TS, Li ITS, Hua B, Hao Q, Holehouse AS, Reyer M, Sun Q, Freier SM, Pappu RV, Prasanth KV, Ha T. Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution. J Cell Sci. 2017 Dec 15; 130(24):4180-4192. PMID: 29133588; PMCID: PMC5769577.
      Citations: 125     Fields:    Translation:HumansCells
    25. Reyer MA, McLean EL, Chennakesavalu S, Fei J. An Automated Image Analysis Method for Segmenting Fluorescent Bacteria in Three Dimensions. Biochemistry. 2018 01 16; 57(2):209-215. PMID: 29083867.
      Citations: 4     Fields:    Translation:AnimalsCells
    26. Jiang S, Park S, Challapalli SD, Fei J, Wang Y. Robust nonparametric quantification of clustering density of molecules in single-molecule localization microscopy. PLoS One. 2017; 12(6):e0179975. PMID: 28636661; PMCID: PMC5479598.
      Citations: 2     Fields:    Translation:Cells
    27. Lloyd CR, Park S, Fei J, Vanderpool CK. The Small Protein SgrT Controls Transport Activity of the Glucose-Specific Phosphotransferase System. J Bacteriol. 2017 06 01; 199(11). PMID: 28289085; PMCID: PMC5424253.
      Citations: 35     Fields:    Translation:Cells
    28. Singh D, Sternberg SH, Fei J, Doudna JA, Ha T. Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9. Nat Commun. 2016 09 14; 7:12778. PMID: 27624851; PMCID: PMC5027287.
      Citations: 121     Fields:    Translation:Cells
    29. Balasubramanian D, Ragunathan PT, Fei J, Vanderpool CK. A Prophage-Encoded Small RNA Controls Metabolism and Cell Division in Escherichia coli. mSystems. 2016 Jan-Feb; 1(1). PMID: 27822514; PMCID: PMC5069750.
      Citations: 22     Fields:    
    30. Zong X, Nakagawa S, Freier SM, Fei J, Ha T, Prasanth SG, Prasanth KV. Natural antisense RNA promotes 3' end processing and maturation of MALAT1 lncRNA. Nucleic Acids Res. 2016 Apr 07; 44(6):2898-908. PMID: 26826711; PMCID: PMC4824109.
      Citations: 37     Fields:    Translation:HumansCells
    31. Peterson JR, Cole JA, Fei J, Ha T, Luthey-Schulten ZA. Effects of DNA replication on mRNA noise. Proc Natl Acad Sci U S A. 2015 Dec 29; 112(52):15886-91. PMID: 26669443; PMCID: PMC4702981.
      Citations: 24     Fields:    Translation:Cells
    32. Zhang J, Fei J, Leslie BJ, Han KY, Kuhlman TE, Ha T. Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells. Sci Rep. 2015 Nov 27; 5:17295. PMID: 26612428; PMCID: PMC4661537.
      Citations: 42     Fields:    Translation:AnimalsCells
    33. Fei J, Singh D, Zhang Q, Park S, Balasubramanian D, Golding I, Vanderpool CK, Ha T. RNA biochemistry. Determination of in vivo target search kinetics of regulatory noncoding RNA. Science. 2015 Mar 20; 347(6228):1371-4. PMID: 25792329; PMCID: PMC4410144.
      Citations: 59     Fields:    Translation:Cells
    34. Tripathi V, Fei J, Ha T, Prasanth KV. RNA fluorescence in situ hybridization in cultured mammalian cells. Methods Mol Biol. 2015; 1206:123-36. PMID: 25240892.
      Citations: 12     Fields:    Translation:AnimalsCells
    35. Ning W, Fei J, Gonzalez RL. The ribosome uses cooperative conformational changes to maximize and regulate the efficiency of translation. Proc Natl Acad Sci U S A. 2014 Aug 19; 111(33):12073-8. PMID: 25085895; PMCID: PMC4143051.
      Citations: 26     Fields:    Translation:Cells
    36. Kim HK, Liu F, Fei J, Bustamante C, Gonzalez RL, Tinoco I. A frameshifting stimulatory stem loop destabilizes the hybrid state and impedes ribosomal translocation. Proc Natl Acad Sci U S A. 2014 Apr 15; 111(15):5538-43. PMID: 24706807; PMCID: PMC3992627.
      Citations: 70     Fields:    Translation:Cells
    37. Chen B, Hashem Y, Ning W, Fei J, Wang C, Gonzalez RL, Hunt JF, Frank J, Boël G. EttA regulates translation by binding the ribosomal E site and restricting ribosome-tRNA dynamics. Nat Struct Mol Biol. 2014 Feb; 21(2):152-9. PMID: 24389465; PMCID: PMC4143144.
      Citations: 46     Fields:    Translation:Cells
    38. Han KY, Leslie BJ, Fei J, Zhang J, Ha T. Understanding the photophysics of the spinach-DFHBI RNA aptamer-fluorogen complex to improve live-cell RNA imaging. J Am Chem Soc. 2013 Dec 18; 135(50):19033-8. PMID: 24286188; PMCID: PMC3908778.
      Citations: 56     Fields:    Translation:AnimalsCells
    39. Fei J, Ha T. Watching DNA breath one molecule at a time. Proc Natl Acad Sci U S A. 2013 Oct 22; 110(43):17173-4. PMID: 24096577; PMCID: PMC3808658.
      Citations: 17     Fields:    Translation:Cells
    40. Fei J, Richard AC, Bronson JE, Gonzalez RL. Transfer RNA-mediated regulation of ribosome dynamics during protein synthesis. Nat Struct Mol Biol. 2011 Aug 21; 18(9):1043-51. PMID: 21857664; PMCID: PMC3167956.
      Citations: 37     Fields:    Translation:Cells
    41. Wang B, Ho J, Fei J, Gonzalez RL, Lin Q. A microfluidic approach for investigating the temperature dependence of biomolecular activity with single-molecule resolution. Lab Chip. 2011 Jan 21; 11(2):274-81. PMID: 20981364; PMCID: PMC3766768.
      Citations: 11     Fields:    Translation:Cells
    42. Bronson JE, Hofman JM, Fei J, Gonzalez RL, Wiggins CH. Graphical models for inferring single molecule dynamics. BMC Bioinformatics. 2010 Oct 26; 11 Suppl 8:S2. PMID: 21034427; PMCID: PMC2966289.
      Citations: 12     Fields:    Translation:Cells
    43. Fei J, Wang J, Sternberg SH, MacDougall DD, Elvekrog MM, Pulukkunat DK, Englander MT, Gonzalez RL. A highly purified, fluorescently labeled in vitro translation system for single-molecule studies of protein synthesis. Methods Enzymol. 2010; 472:221-59. PMID: 20580967; PMCID: PMC4748369.
      Citations: 30     Fields:    Translation:Cells
    44. Bronson JE, Fei J, Hofman JM, Gonzalez RL, Wiggins CH. Learning rates and states from biophysical time series: a Bayesian approach to model selection and single-molecule FRET data. Biophys J. 2009 Dec 16; 97(12):3196-205. PMID: 20006957; PMCID: PMC2793368.
      Citations: 196     Fields:    Translation:Cells
    45. Fei J, Bronson JE, Hofman JM, Srinivas RL, Wiggins CH, Gonzalez RL. Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation. Proc Natl Acad Sci U S A. 2009 Sep 15; 106(37):15702-7. PMID: 19717422; PMCID: PMC2747183.
      Citations: 90     Fields:    Translation:Cells
    46. Sternberg SH, Fei J, Prywes N, McGrath KA, Gonzalez RL. Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling. Nat Struct Mol Biol. 2009 Aug; 16(8):861-8. PMID: 19597483; PMCID: PMC4748396.
      Citations: 46     Fields:    Translation:Cells
    47. Huang WW, Shen LX, Zhu WM, Qian MC, Chen ZM, Tang W, Fang XM, Feng M, Fei JF, Luo JW. [A comparative study on mental health among students and adults in the earthquake-hit areas]. Zhonghua Yu Fang Yi Xue Za Zhi. 2008 Nov; 42(11):806-9. PMID: 19176139.
      Citations:    Fields:    Translation:Humans
    48. Fei J, Kosuri P, MacDougall DD, Gonzalez RL. Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. Mol Cell. 2008 May 09; 30(3):348-59. PMID: 18471980.
      Citations: 190     Fields:    Translation:Cells
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