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Publications

All Publications, excluding chapters and articles not accessed by PubMed, can be found here. Google Scholar page can be found here.

  1. Yan D, Xue J, Xiao J, Lyu Z, Yang X, Protocol for single-molecule labeling and tracking of bacterial cell division proteins, STAR Protocols, 2024.
  2. Cahill J., Holt A., Theodore M., Moreland R., O’Leary C., Martin C., Bettridge K., Xiao J., Young R., Spatial and temporal control of lysis by the lambda holin, mBio,2023 Dec 21:e0129023.
  3. Fu Z, Guo MS, Zhou W, Xiao J., Differential Roles of positive and negative supercoiling in compacting the E. coli genome, Nucleic Acids Research, 2023 (BioRxiv Preprint, 2022.12. 30.522362)
  4. Mahone CR, Yang X, McCausland JW, Payne IP, Xiao J, Goley ED, Integration of cell wall synthesis activation and chromosome segregation during cell division in Caulobacter, (BioRxiv Preprint, 2022.11. 05.515301)
  5. Britton BM, Yovanno RA, Costa SF, McCausland J, Lau AY, Xiao J, Hensel Z, Conformational changes in the essential E. coli septal cell wall synthesis complex suggest an activation mechanism, Nature Communications, 2023 (BioRxiv Preprint, 2022.11. 27.518129)
  6. Bettridge KE, Harris F, Yeyha N, Xiao J, RNAP Promoter Search and Transcription Kinetics in Live E. coli Cells, Journal of Physical Chemistry B, 2023.(BioRxiv Preprint: https://doi.org/10.1101/2022.12.31.522404)
  7. Shachaf LI, Roberts E, Cahan P, Xiao J. Gene regulation network inference using k-nearest neighbor-based mutual information estimation: revisiting an old DREAM, BMC Bioinformatics, 2023, 24(1), p84
  8. Lyu Z, Yahashiri A, Yang X, McCausland JW, Kaus GM, McQuillen R, Weiss DS, Xiao J.FtsN maintains active septal cell wall synthesis by forming a processive complex with the septum-specific peptidoglycan synthases in E. coli, Nature Communications, 2022, 13(1), p5751
  9. Geng Y, Bohrer CH, Yehya N, Hendrix H, Shachaf L, Liu J, Xiao J, Roberts E. A spatially resolved stochastic model reveals the role of supercoiling in transcription regulation, PLoS Computational Biology, 2022, 18(9), e1009788
  10. McQuillen R, Yang X, Bohrer CH, McCausland JW, Xiao J. Light-dependent modulation of protein localization and function in living bacteria cells, BioRxiv. 2022.
  11. Ha T, Kaiser C, Myong S, Wu B, Xiao J. Next generation single-molecule techniques: Imaging, labeling, and manipulation in vitro and in cellulo, Molecular Cell. 2022.
  12. Crespi E, Burnap R, Chen J., Das M, Gassman N, Rosa E, Simmons R, Wada H, Wang ZQ, Xiao J, Yang B, Yin J, Goldstone JV, Resolving the Rules of Robustness and Resilience in Biology Across Scales, Integrative and Comparative Biology. 2021.
  13. Mao C, Wang S, Su Y, Tseng S, He L, Wu AA, Roden RBS, Xiao J, Hung C. Protein detection in blood with single-molecule imaging. Science Advances. 2021. doi: 10.1126/sciadv.abg6522.
  14. Bohrer C, Yang X, Thakur S, Weng X, Tenner B, McQuillen R, Ross B, Wooten M, Chen X, Zhang J, Roberts E, Lakadamyali M, Xiao J. A Pairwise distance distribution correction (DDC) algorithm to eliminate blinking-caused artifacts in SMLM. Nature Methods. 2021. (BioRxiv Preprint: https://doi.org/10.1101/768051)
  15. Gyparaki MT, Arab A, Sorokina EM, Santiago-Ruiz AN, Bohrer CH, Xiao J, Lakadamyali M. Tau forms oligomeric complexes on microtubules that are distinct from pathological oligomers in disease. Proc Natl Acad Sci U S A. 2021 May.; doi: 10.1073/pnas.2021461118. (BioRxiv Preprint: https://doi.org/10.1101/850073.)
  16. , , , , , , , , , . Treadmilling FtsZ polymers drive the directional movement of sPG-synthesis enzymes via a Brownian ratchet mechanism. Nature Communications. 2021. https://doi.org/10.1038/s41467-020-20873-y (BioRxiv Preprint: https://doi.org/10.1101/857813)
  17. Yang X, McQuillen R, Lyu Z, Phillips-Mason P, De La Cruz A, McCausland JW, Liang H, DeMeester KE, Santiago CC,  Grimes CL, de Boer P & Xiao J. A two-track model for the spatiotemporal coordination of bacterial septal cell wall synthesis revealed by single-molecule imaging of FtsW. Nature Microbiology. 2021. doi: https://doi.org/10.1038/s41564-020-00853-0 (BioRxiv Preprint: https://doi.org/10.1101/850073.)
  18. Tenner B, Getz M, Ross B, Ohadi D, Bohrer CH, Greenwald E, Mehta S, Xiao J, Rangamani P, Zhang J. Spatially compartmentalized phase regulation of a Ca2+-cAMP-PKA oscillatory circuit. Elife. 2020 Nov 17;9. doi: 10.7554/eLife.55013. PubMed PMID: 33201801; PubMed Central PMCID: PMC7671691.
  19. Bettridge K, Verma S, Weng X, Adhya S, Xiao J. Single-molecule tracking reveals that the nucleoid-associated protein HU plays a dual role in maintaining proper nucleoid volume through differential interactions with chromosomal DNA. Mol Microbiol. 2020 Jul 8;. doi: 10.1111/mmi.14572. [Epub ahead of print] PubMed PMID: 32640056
  20. McQuillen R, Xiao J. Insights into the Structure, Function, and Dynamics of the Bacterial Cytokinetic FtsZ-Ring. Annu Rev Biophys. 2020 May 6;49:309-341. doi: 10.1146/annurev-biophys-121219-081703. Epub 2020 Feb 24. PubMed PMID: 32092282.
  21. Bohrer C.H., Xiao J. Complex Diffusion in Bacteria. In: Duménil G., van Teeffelen S. (eds) Physical Microbiology. Advances in Experimental Medicine and Biology, vol 1267. Springer, Cham. 2020 September; https://doi.org/10.1007/978-3-030-46886-6_2
  22. Weng X, Bohrer CH, Bettridge K, Lagda AC, Cagliero C, Jin DJ, Xiao J. Spatial organization of RNA polymerase and its relationship with transcription in Escherichia coli. Proc Natl Acad Sci U S A. 2019 Sep 16;. doi: 10.1073/pnas.1903968116
  23. Wooten M, Snedeker J, Nizami ZF, Yang X, Ranjan R, Urban E, Kim JM, Gall J, Xiao J, Chen X. Asymmetric histone inheritance via strand-specific incorporation and biased replication fork movement. Nat Struct Mol Biol. 2019 Aug;26(8):732-743.
  24. Syu GD, Wang SC, Ma G, Liu S, Pearce D, Prakash A, Henson B, Weng LC, Ghosh D, Ramos P, Eichinger D, Pino I, Dong X, Xiao J, Wang S, Tao N, Kim KS, Desai PJ, Zhu H. Development and application of a high-content virion display human GPCR array. Nat Commun. 2019 Apr 30;10(1):1997.
  25. Holt A, Cahill J, Ramsey J, O’Leary C, Moreland R, Martin C, Thushara Galbadage D, Sharan R, Sule P, Bettridge K, Xiao J, Cirillo J, Young R. Phage-encoded cationic antimicrobial peptide used for outer membrane disruption in lysis. bioRxiv. 2019 January; doi: https://doi.org/10.1101/515445
  26. Fang X, Liu Q, Bohrer C, Hensel Z, Han W, Wang J, Xiao J. Cell fate potentials and switching kinetics uncovered in a classic bistable genetic switch. Nat Commun. 2018 Jul 17;9(1):2787.
  27. Bohrer CH, Yang X, Lyu Z, Wang S, Xiao J. Improved single-molecule localization precision in astigmatism-based 3D superresolution imaging using weighted likelihood estimation. bioRxiv. 2018 April; doi: https://doi.org/10.1101/304816.
  28. Woldemeskel SA, McQuillen R, Hessel AM, Xiao J, Goley ED. A conserved coiled-coil protein pair focuses the cytokinetic Z-ring in Caulobacter crescentus. Mol Microbiol. 2017 Sep;105(5):721-740
  29.  Mo GC, Ross B, Hertel F, Manna P, Yang X, Greenwald E, Booth C, Plummer AM, Tenner B, Chen Z, Wang Y, Kennedy EJ, Cole PA, Fleming KG, Palmer A, Jimenez R, Xiao J, Dedecker P, Zhang J. Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution. Nat Methods. 2017 Apr;14(4):427-434
  30. Buss JA, Peters NT, Xiao J, Bernhardt TG. ZapA and ZapB form an FtsZ-independent structure at midcell. Mol Microbiol. 2017 May;104(4):652-663. doi: 10.1111/mmi.13655. Epub 2017 Mar 26. PubMed PMID: 28249098; PubMed Central PMCID: PMC5426985.
  31.  Yang X, Lyu Z, Miguel A, McQuillen R, Huang KC, Xiao J. GTPase activity-coupled treadmilling of the bacterial tubulin FtsZ organizes septal cell wall synthesis. Science. 2017 Feb 17;355(6326):744-747
  32.  Xiao J, Ha T. Flipping nanoscopy on its head. Science. 2017 Feb 10;355(6325):582-584
  33. Bohrer CH, Bettridge K, Xiao J. Reduction of Confinement Error in Single-Molecule Tracking in Live Bacterial Cells Using SPICER. Biophys J. 2017 Feb 28;112(4):568-574
  34. Coltharp C, Xiao J. Beyond force generation: Why is a dynamic ring of FtsZ polymers essential for bacterial cytokinesis?. Bioessays. 2017 Jan;39(1):1-11.
  35. Xiao J, Dufrêne YF. Optical and force nanoscopy in microbiology. Nat Microbiol. 2016 Oct 26;1(11):16186.
  36. Xiao J, Goley ED. Redefining the roles of the FtsZ-ring in bacterial cytokinesis. Curr Opin Microbiol. 2016 Dec;34:90-96.
  37. Luo Y, Yang X, Tan X, Xu L, Liu Z, Xiao J, Peng R. Functionalized graphene oxide in microbial engineering: An effective stimulator for bacterial growth. Carbon. 2016 March; 103:172-180
  38.  Lyu Z, Coltharp C, Yang X, Xiao J. Influence of FtsZ GTPase activity and concentration on nanoscale Z-ring structure in vivo revealed by three-dimensional Superresolution imaging. Biopolymers. 2016 Oct;105(10):725-34.
  39. Coltharp C, Buss J, Plumer TM, Xiao J. Defining the rate-limiting processes of bacterial cytokinesis. Proc Natl Acad Sci U S A. 2016 Feb 23;113(8):E1044-53. doi: 10.1073/pnas.1514296113.
  40. Buss J, Coltharp C, Shtengel G, Yang X, Hess H, Xiao J. A multi-layered protein network stabilizes the Escherichia coli FtsZ-ring and modulates constriction dynamics. PLoS Genet. 2015 Apr;11(4):e1005128.
  41. Coltharp C, Yang X, Xiao J. Quantitative analysis of single-molecule superresolution images. Curr Opin Struct Biol. 2014 Oct;28:112-21.
  42. Weng X, Xiao J. Spatial organization of transcription in bacterial cells. Trends Genet. 2014 Jul;30(7):287-97.
  43. Buss J, Coltharp C, Huang T, Pohlmeyer C, Wang SC, Hatem C, Xiao J. In vivo organization of the FtsZ-ring by ZapA and ZapB revealed by quantitative super-resolution microscopy. Mol Microbiol. 2013 Sep;89(6):1099-120. (cover image)
  44. Hensel Z., Xiao J., Single molecule methods for studying gene regulation in vivo, Pflügers Arch-European Journal of Physiology, 2013, Mar;465(3):383-95.
  45. Hensel Z, Weng X, Lagda AC, Xiao J. Transcription-factor-mediated DNA looping probed by high-resolution, single-molecule imaging in live E. coli cells. PLoS Biol. 2013;11(6):e1001591.  Editor’s Synopsis*, DNA Looping in the News*
  46. Buss J, Coltharp C, Xiao J. Super-resolution imaging of the bacterial division machinery. J Vis Exp. 2013 Jan 21;(71).
  47. Hensel Z, Fang X, Xiao J. Single-molecule imaging of gene regulation in vivo using cotranslational activation by Cleavage (CoTrAC). J Vis Exp. 2013 Mar 15;(73):e50042.
  48. Coltharp C, Kessler RP, Xiao J. Accurate construction of photoactivated localization microscopy (PALM) images for quantitative measurements. PLoS One. 2012;7(12):e51725.
  49. Coltharp C, Xiao J. Superresolution microscopy for microbiology. Cell Microbiol. 2012 Dec;14(12):1808-18.
  50. Hensel Z, Feng H, Han B, Hatem C, Wang J, Xiao J. Stochastic expression dynamics of a transcription factor revealed by single-molecule noise analysis. Nat Struct Mol Biol. 2012 Aug;19(8):797-802. (cover image)
  51. Feng H, Hensel Z, Xiao J, Wang J. Analytical calculation of protein production distributions in models of clustered protein expression. Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Mar;85(3 Pt 1):031904.
  52. Fu G, Huang T, Buss J, Coltharp C, Hensel Z, Xiao J. In vivo structure of the E. coli FtsZ-ring revealed by photoactivated localization microscopy (PALM). PLoS One. 2010 Sep 13;5(9):e12682.
  53. Xiao J. Single molecule imaging in live cells . In: Handbook of Single-molecule Biophysics. van Oijen A, Hinterdorfer P, editors. NY: Springer; 2009.
  54. Hensel Z, Xiao J. A mechanism for stochastic decision making by bacteria. Chembiochem. 2009 Apr 17;10(6):974-6.
  55. Singleton SF, Roca AI, Lee AM, Xiao J. Probing the structure of RecA-DNA filaments. Advantages of a fluorescent guanine analog. Tetrahedron. 2007 Apr 23;63(17):3553-3566.
  56. Xiao J, Elf J, Li G, Ji Y, Xie XS. Imaging gene expression in living cells at the single molecule level . In: Single Molecules: A Laboratory Manual. Selvin P, Ha T, editors. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 2007.
  57. Yu J, Xiao J, Ren X, Lao K, Xie XS. Probing gene expression in live cells, one protein molecule at a time. Science. 2006 Mar 17;311(5767):1600-3.
  58. Xiao J, Lee AM, Singleton SF. Construction and evaluation of a kinetic scheme for RecA-mediated DNA strand exchange. Biopolymers. 2006 Apr 15;81(6):473-96.
  59. Xiao J, Lee AM, Singleton SF. Direct evaluation of a kinetic model for RecA-mediated DNA-strand exchange: the importance of nucleic acid dynamics and entropy during homologous genetic recombination. Chembiochem. 2006 Aug;7(8):1265-78. (cover image)
  60. Lee AM, Xiao J, Singleton SF. Origins of sequence selectivity in homologous genetic recombination: insights from rapid kinetic probing of RecA-mediated DNA strand exchange. J Mol Biol. 2006 Jul 7;360(2):343-59.
  61. Xiao J, Singleton SF. Elucidating a key intermediate in homologous DNA strand exchange: structural characterization of the RecA-triple-stranded DNA complex using fluorescence resonance energy transfer. J Mol Biol. 2002 Jul 12;320(3):529-58.
  62. Singleton SF, Xiao J. The stretched DNA geometry of recombination and repair nucleoprotein filaments. Biopolymers. 2001-2002;61(3):145-58.
  63. Martin SR, Lu AQ, Xiao J, Kleinjung J, Beckingham K, Bayley PM. Conformational and metal-binding properties of androcam, a testis-specific, calmodulin-related protein from Drosophila. Protein Sci. 1999 Nov;8(11):2444-54.