The University of Chicago · Biochemistry and Molecular Biology GCIS W125 · 929 E. 57th Street, Chicago, IL
Fei LabRNA Biophysics & Gene Regulation
Publications

Publications

Click a title to open the article on the publisher's site. The full list is also on Google Scholar.

# equal contribution · * co-corresponding

2026

  1. 51
    Super-resolved spatial organization of the nucleolar transcriptome.Fan X, Tan C, Mu JH, Chiang SM, Xiao Y, He C, Li ITS, Wu WS, Fei J · bioRxiv 2026.05.19.726041
  2. 50
    RNA localization to nuclear speckles follows splicing logic.Wen L#, Arias MA#, Fan X, Paul S, Liao SE, Sobczyk M, Regev O*, Fei J* · Nucleic Acids Research 54: gkag174

2025

  1. 49
    Structural dependence of ProQ–mRNA interactions in live bacterial cells.Zhou Z, Prévost K, Carrier M-C, El Ashry N, Mu JH, Valle CDV, Park S, Guzman A, Massé E, Fei J · Communications Biology 8: 1780
  2. 48
    Transcriptome-wide mRNP condensation precedes stress granule formation and excludes new mRNAs.Glauninger H, Bard JAM, Wong Hickernell CJ, Velez KM, Airoldi EM, Li W, Singer RH, Paul S, Fei J, Sosnick TR, Wallace EWJ, Drummond DA · Molecular Cell 85(23): 4393–4409

2024

  1. 47
    Translational T-box riboswitches bind tRNA by modulating conformational flexibility.Campos-Chavez E#, Paul S#, Zhou Z, Alonso D, Verma AR, Fei J*, Mondragón A* · Nature Communications 15: 6592
  2. 46
    Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency.Wu J#, Xiao Y#, Liu Y#, Wen L, Jin C, Liu S, Paul S, He C, Regev O*, Fei J* · Science Advances 10: eadp7727
  3. 45
    RNA molecules display distinctive organization at nuclear speckles.Paul S#, Arias MA#, Wen L, Liao SE, Zhang J, Wang X, Regev O*, Fei J* · iScience 27(5): 109603
  4. 44
    Fluorescence resonance energy transfer at the single-molecule level.Ha T, Fei J, Schmid S, Lee NK, Gonzalez RL Jr, Paul S, Yeou S · Nature Reviews Methods Primers 4: 21
  5. 43
    KARR-seq reveals cellular RNA higher-order structures and RNA–RNA interactions.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 · Nature Biotechnology
  6. 42
    Profiling of RNA-binding protein binding sites by in situ reverse transcription-based sequencing.Xiao Y, Chen Y-M, Zou Z, Ye C, Dou X, Wu J, Liu C, Liu S, Yan H, Wang P, Zeng T, Liu Q, Fei J, Tang W, He C · Nature Methods 21(2): 247

2023

  1. 41
    Entropic control of the free-energy landscape of an archetypal biomolecular machine.Ray KK, Kinz-Thompson CD, Fei J, Wang B, Lin Q, Gonzalez RL · Proc Natl Acad Sci USA 120: e2220591120

2022

  1. 40

2021

  1. 39
    Kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional sRNA regulators.Reyer MA, Chennakesavalu S#, Heideman EM#, Ma X, Bujnowska M, Hong L, Dinner AR, Vanderpool CK, Fei J · Cell Reports 36: 109764
  2. 38
    Binding of the RNA chaperone Hfq on target mRNAs promotes the small RNA RyhB-induced degradation in Escherichia coli.Lalaouna D, Prévost K#, Park S#, Chénard T, Bouchard M, Caron M, Vanderpool CK, Fei J*, Massé E* · Non-Coding RNA 7: 64
  3. 37
    K29-linked ubiquitin signaling regulates proteotoxic stress response and cell cycle.Yu Y#, Zheng Q#, Erramilli SK#, Pan M#, Park S, Xie Y, Li J, Fei J, Kossiakoff AA*, Liu L*, Zhao M* · Nature Chemical Biology 17: 896
  4. 36
    FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices.Lerner E#*, Barth A#*, Hendrix J#*, … Fei J, … Lamb DC*, Seidel CAM*, Weiss S* · eLife 10: e60416
  5. 35
    Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs and mRNAs in live bacterial cells.Park S#, Prévost K#, Heideman EM, Carrier M-C, Azam MS, Reyer MA, Liu W, Massé E*, Fei J* · eLife 10: e64207
  6. 34
    Effects of individual base-pairs on in vivo target search and destruction kinetics of small RNA.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 · Nature Communications 12: 874
  7. 33
    Mechanical expansion microscopy.Fan Y, Lim Y, Wyss LS, Park S, Xue C, Fu H, Fei J, Hong Y, Wang B · Methods in Cell Biology 161: 125

2020

  1. 32
    Deoxyribozyme-based method for absolute quantification of N6-methyladenosine fraction at specific sites of RNA.Bujnowska M, Zhang J, Dai Q, Heideman EM, Fei J · Journal of Biological Chemistry 295: 6992
  2. 31

2019

  1. 30

2018

  1. 29
    Specific structural elements of the T-box riboswitch drive the two-step binding of the tRNA ligand.Zhang J#, Chetnani B#, Cormack ED, Alonso D, Liu W, Mondragón A, Fei J · eLife 7: e39518
  2. 28
    RNA localization in bacteria.Fei J*, Sharma CM* · Microbiology Spectrum 6(5)
  3. 27
    Conducting multiple imaging modes with one fluorescence microscope.Park S, Zhang J, Reyer MA, Zareba J, Troy AA, Fei J · Journal of Visualized Experiments 140: e58320
  4. 26
    Mechanisms of improved specificity of engineered Cas9s revealed by single-molecule FRET analysis.Singh D, Wang Y, Mallon J, Yang O, Fei J, Poddar A, Ceylan D, Bailey S, Ha T · Nat Struct Mol Biol 25: 347

2017

  1. 25
    Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution.Fei J*#, Jadaliha M#, Harmon TS, Li ITS, Hua B, Hao Q, Holehouse AS, Reyer MA, Sun Q, Freier SM, Pappu RV, Prasanth KV*, Ha T · Journal of Cell Science 130(24): 4180–4192
  2. 24
    An automated image analysis method for segmenting fluorescent bacteria in 3D.Reyer MA, McLean EL, Chennakesavalu S, Fei J · Biochemistry 57: 209
  3. 23
  4. 22
    The small protein SgrT controls transport activity of the glucose-specific phosphotransferase system.Lloyd CR, Park S, Fei J, Vanderpool CK · Journal of Bacteriology 199: e00869-16

2016

  1. 21
    Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9.Singh D, Sternberg SH, Fei J, Doudna JA, Ha T · Nature Communications 7: 12778
  2. 20
    A prophage-encoded small RNA controls metabolism and cell division in Escherichia coli.Balasubramanian D, Ragunathan PT, Fei J, Vanderpool CK · mSystems 1: e00021-15
  3. 19
    Natural antisense RNA promotes 3′ end processing and maturation of MALAT1 lncRNA.Zong X, Nakagawa S, Freier SM, Fei J, Ha T, Prasanth SG, Prasanth KV · Nucleic Acids Research 44: 2898–2908

2015

  1. 18
    Effects of DNA replication on mRNA noise.Peterson JR, Cole JA, Fei J, Ha T, Luthey-Schulten ZA · Proc Natl Acad Sci USA 112: 15886–15891
  2. 17
    Tandem Spinach array for mRNA imaging in living bacterial cells.Zhang J, Fei J, Leslie BJ, Han KY, Kuhlman TE, Ha T · Scientific Reports 5: 17295
  3. 16
    Determination of in vivo target search kinetics of regulatory noncoding RNA.Fei J, Singh D, Zhang Q, Park S, Balasubramanian D, Golding I, Vanderpool CK, Ha T · Science 347: 1371–1374

2014

  1. 15
  2. 14
    A frameshifting stimulatory stem loop destabilizes the hybrid state and impedes ribosomal translocation.Kim HK, Liu F, Fei J, Bustamante C, Gonzalez RL, Tinoco I · Proc Natl Acad Sci USA 111: 5538–5543
  3. 13
    EttA binds at ribosomal E site and regulates translation by restricting ribosome dynamics.Chen B, Boël G, Hashem Y, Ning W, Fei J, Wang C, Gonzalez RL Jr, Hunt JF, Frank J · Nat Struct Mol Biol 21: 152–159

2013

  1. 12
  2. 11
    Watching DNA breath one molecule at a time.Fei J, Ha T · Proc Natl Acad Sci USA 110: 17173–17174

2011

  1. 10
    Transfer RNA-mediated control of ribosome dynamics during translation.Fei J, Richard AC, Bronson JE, Gonzalez RL Jr · Nat Struct Mol Biol 18: 1043–1051
  2. 9

2010

  1. 8
  2. 7
    Dispersion of polystyrene inside polystyrene-b-poly(N-isopropylacrylamide) micelles in water.Ye X, Fei J, Guan J, Zhou X, Zhang G · J Polym Sci B: Polym Phys 48: 749–755
  3. 6
    A highly-purified, fluorescently-labeled in vitro translation system for single-molecule studies of protein synthesis.Fei J, Wang J, Sternberg SH, MacDougall DD, Elvekrog MM, Pulukkunat D, Gonzalez RL Jr · Methods Enzymol 472: 221–259
  4. 5
    Graphical models for inferring single molecule dynamics.Bronson JE, Hofman JM, Fei J, Gonzalez RL, Wiggins CH · BMC Bioinformatics Suppl 8: S2

2008–2009

  1. 4
    Learning rates and states from biophysical time series: A Bayesian approach to model selection and single-molecule FRET data.Bronson JE, Fei J, Hofman JM, Gonzalez RL, Wiggins CH · Biophys J 97: 3196–3205 (2009)Evaluated by Faculty of 1000.
  2. 3
    Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation.Fei J, Bronson JE, Hofman JM, Srinivas RL, Wiggins CH, Gonzalez RL · Proc Natl Acad Sci USA 106: 15702–15707 (2009)Featured as a Science and Technology News item in Chem Eng News 87, 29.
  3. 2
    Translation factors direct intrinsic ribosome dynamics during termination and ribosome recycling.Sternberg SH, Fei J, Prywes N, McGrath KA, Gonzalez RL · Nat Struct Mol Biol 16: 861–868 (2009)Featured as a Research Highlight in Nat Chem Biol 5, 540 and in Chem Eng News 87, 29.
  4. 1
    Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation.Fei J, Kosuri P, MacDougall DD, Gonzalez RL · Mol Cell 30: 348–359 (2008)

Book chapters

  1. 3
    Quantitative super-resolution imaging of small RNAs in bacterial cells.Park S, Bujnowska M, McLean EL, Fei J · Bacterial Regulatory RNA: Methods and Protocols (Arluison V, Valverde C, eds.), pp. 199–212, Springer New York (2018)
  2. 2
    RNA fluorescence in situ hybridization in cultured mammalian cells.Tripathi V, Fei J, Ha T, Prasanth KV · Regulatory Non-Coding RNAs (Carmichael GG, ed.), pp. 123–136, Springer New York (2015)
  3. 1
    Single-molecule fluorescence resonance energy transfer investigations of ribosome-catalyzed protein synthesis.MacDougall DD, Fei J, Gonzalez RL Jr · Molecular Machines in Biology: Workshop of the Cell (Frank J, ed.), pp. 93–116, Cambridge University Press (2011)