PUBLICATIONS 2017-06-28T16:39:05+00:00

Recent Publications

  • 3D clustering of co-regulated genes and its effect on gene expression.
    Du MY & Bai L (2017)
    Current Genetics, doi: 10.1007/s00294-017-0712-9. Review. [PDF]
  • Three distinct mechanisms of long-distance modulation of gene expression in yeast.
    Du MY, Zhang Q, & Bai L (2017)
    PLOS Genetics, 13(4):e1006736. [PDF]
  • Inter-allelic interaction and gene regulation in budding yeast.
    Zhang DY & Bai L (2016)
    PNAS, 113:4428-33. [PDF]
  • Regulation of cell-to-cell variability in divergent gene expression.
    Yan C, Wu S, Pocetti C, & Bai L (2016)
    Nature Communications, 7: 11099. [PDF]
  • Decoupling of divergent gene regulation by sequence-specific DNA binding factors.
    Yan C, Zhang DY, Garay JA, Mwang MM, & Bai L (2015)
    Nucleic Acid Research, 43: 7292-305. [PDF]
  • The Rts1 regulatory subunit of PP2A phosphatase controls expression of the HO endonuclease via localization of the Ace2 transcription factor.
    Parnell EJ, Yu Y, Lucena R, Yoon Y, Bai L, Kellogg DR, & Stillman DJ (2014)
    JBC, 289:35431-35437. [PDF]
  • Stochastic expression and epigenetic memory at the yeast HO promoter.
    Zhang Q, Yoon Y, Yu Y, Parnell EJ, Garay JA, Mwangi MM, Cross FR, Stillman DJ, & Bai L (2013)
    PNAS, 110: 14012-14017. [PDF]
  • Transcription under torsion
    Ma J, Bai L, & Wang MD. (2013)
    Science, 28:1580-1583. [PDF]
  • Kinetic competition between elongation rate and binding of NELF controls promoter proximal pausing.
    Li J, Liu Y, Rhee HS, Ghosh BS, Bai L, Pugh BF, & Gilmour DS. (2013)
    Molecular Cell, 50: 711–722. [PDF]


Before 2012

  • Nucleosomes and the accessibility problem
    Wang X, Bai L, Bryant GO & Ptashne M (2011)
    Trends Genet, 27: 487-92. Review. [PDF]
  • Multiple sequence-specific factors participate in the formation of nucleosome-depleted-region on the CLN2 promoter.
    Bai L, Ondracka A & Cross FR. (2011)
    Mol. Cell. 42:465-76. [PDF]
  • Comparison of pause predictions of two sequence-dependent transcription models.
    Bai L & Wang MD. (2010)
    Journal of Statistical Mechanics. P12007. [PDF]
  • Gene regulation by nucleosome positioning.
    Bai L & Morozov AV. (2010).
    Trends Genet. 26:476-83. Review. [PDF]
  • Nucleosome depleted regions in cell-cycle-regulated promoters ensure reliable gene expression in every cell cycle.
    Bai L, Charvin G, Siggia ED & Cross FR. (2010)
    Developmental Cell. 18:544-55. [PDF]
  • Overcoming the nucleosomal barrier during transcription elongation.
    Jin J, Bai L, Johnson DS, Fulbright RM, Kireeva ML, Kashlev M, Wang MD (2010)
    Nature Structural and Molecular Biology. 17:745-52. [PDF]
  • High resolution dynamic mapping of histone-DNA interactions in a nucleosome.
    Hall MA, Shundrovsky A, Bai L, Fulbright RM, Lis JT & Wang MD (2009).
    Nature Structural and Molecular Biology 16:124-129. [PDF]
  • Single molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase.
    Johnson DS, Bai L, Smith B, Patel S & Wang MD (2007).
    Cell. 129:1299-309. [PDF]
  • Mechanochemical kinetics of transcription elongation.
    Bai L, Fulbright RM & Wang MD (2007).
    Phys Rev Lett. 98:068103. [PDF]
  • Single molecule analysis of RNA polymerase transcription.
    Bai L, Santangelo T & Wang MD (2006).
    Annu. Rev. Biophys. Biomol. Struct 35:343-360. Review. [PDF]
  • Detection of high affinity mismatch binding and sliding clamp modes for the MSH2-MSH6 mismatch recognition complex by single-molecule unzipping force analysis.
    Jiang J*, Bai L*, Surtees J, Gemici Z, Wang MD & Alani E (2005).
    Mol. Cell. 20:771-81. [PDF]
  • Sequence-dependent kinetic model for transcription elongation by RNA polymerase.
    Bai L, Shundrovsky A. & Wang MD (2004).
    J. Mol. Biol. 344:335-349. [PDF]


News and views:

  • Bind at your own RSC:  Nucleosome phasing and occupancy in a eukaryotic promoter
    Buchler NE & Bai L (2011).
    Current Biology. 21:223-225 [PDF]
  • Nucleosome-depleted regions in promoters: consequences on robustness of transcriptional activation
    Bai L & Charvin G (2010)
    Med Sci (Paris). 26:1035-1037. [PDF]