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Pre-publication manuscripts (not yet peer reviewed):

Gupta S, et al. A Helicase-tethered ORC Flip Enables Bidirectional Helicase Loading. [preprint] bioRxiv:10.1101/2021.10.06.463322

Ordabayev Y.A., et al. Bayesian machine learning analysis of single-molecule fluorescence colocalization images. [preprint] bioRxiv:2021.09.30.462536

Mumm J.P., et al. Mechanism of upstream promoter element stimulation of transcription at a ribosomal RNA promoter determined by single-molecule imaging. [preprint] bioRxiv:2020.02.17.953182.

Chandrakar P., et al. Microtubule-based active fluids with improved lifetime, temporal stability and miscibility with passive soft materials. [preprint] ArXiv:181105026.


Baek I., et al. Single-molecule studies reveal branched pathways for activator-dependent assembly of RNA polymerase II pre-initiation complexes. Molecular Cell S1097-2765(21)00594-3 (2021). 

Kim L.D.J., et al. DDK regulates replication initiation by controlling the multiplicity of Cdc45-GINS binding to Mcm2-7. eLife 10, e65471 (2021)

Shekhar S, et al., Twinfilin bypasses assembly conditions and actin filament aging to drive barbed end depolymerization. Journal of Cell Biology 220, e202006022 (2021)


Rosen, G.A., Baek, I., et al., Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcription. PNAS [epub]

Harden, T.T., et al.  Alternative transcription cycle for bacterial RNA polymerase. Nature Communications 11, 450 (2020).


Shekhar S. et al.  Synergy between cyclase-associated protein and cofilin accelerates actin filament depolymerization by two orders of magnitude. Nature Communications 10, 5319 (2019).

Champasa, K. et al. A conserved Mcm4 motif is required for Mcm2-7 double-hexamer formation and origin DNA unwinding. eLife 8, e45538 (2019).

Huang B et al. Conformational Cycling within the Closed State of Grp94, an Hsp90-Family Chaperone. Journal of Molecular Biology 431, 3312-3323 (2019).

Stumper, S. K., et al.  Delayed inhibition mechanism for secondary channel factor regulation of ribosomal RNA transcription. eLife 8, e40576 (2019).


Guo, S., et al. Abp1 promotes Arp2/3 complex-dependent actin nucleation and stabilizes branch junctions by antagonizing GMF. Nature Communications 9, 2895 (2018).

Braun, J., et al. Synergistic assembly of human pre-spliceosomes across introns and exons. eLife 7, e37751 (2018).


Ticau, S., et al. Mechanism and timing of Mcm2-7 ring closure during DNA replication origin licensing. Nature Structural and Molecular Biology 24, 309 (2017).

Tetone, L.E., et al. Dynamics of GreB-RNA polymerase interaction allow a proofreading accessory protein to patrol for transcription complexes needing rescue. PNAS 114, E1081 (2017).


Chadda, R., et al. The dimerization equilibrium of a ClC Cl/H+ antiporter in lipid bilayers. eLife 5, e17438 (2016).

Hoskins, A.A. et al. Single molecule analysis reveals reversible and irreversible steps during spliceosome activation. eLife 5, e14166 (2016).

Harden, T.T. et al. Bacterial RNA polymerase can retain σ70 throughout transcription. PNAS 113, 602-607 (2016).


Bombardier, J.P. et al. Single-molecule visualization of a formin-capping protein ‘decision complex’ at the actin filament barbed end. Nature Communications 6, 8707 (2015).

Friedman, L.J. & Gelles, J. Multi-wavelength single-molecule fluorescence analysis of transcription mechanisms. Methods 86, 27–36 (2015).

Jansen, S. et al. Single-molecule imaging of a three-component ordered actin disassembly mechanism. Nature Communications 6, 7202 (2015).

Ticau, S., Friedman, L.J., Ivica, N.A., Gelles, J. & Bell, S.P. Single-Molecule Studies of Origin Licensing Reveal Mechanisms Ensuring Bidirectional Helicase Loading. Cell 161, 1–13 (2015).


Wang, T.Y. et al. The Covalent Trimethoprim Chemical Tag Facilitates Single Molecule Imaging with Organic Fluorophores. Biophysical Journal 106, 272–278 (2014).

Smith, B.A., Gelles, J. & Goode, B.L. Single-Molecule Studies of Actin Assembly and Disassembly Factors. Methods in Enzymology 540, 95–117 (2014).

Paramanathan, T., Reeves, D., Friedman, L.J., Kondev, J. & Gelles, J. A general mechanism for competitor-induced dissociation of molecular complexes. Nature Communications 5, 5207 (2014).


Smith, B.A. et al. Three-color single molecule imaging shows WASP detachment from Arp2/3 complex triggers actin filament branch formation. eLife 2, e01008 (2013).

Smith, B.A., Daugherty-Clarke, K., Goode, B.L. & Gelles, J. Pathway of actin filament branch formation by Arp2/3 complex revealed by single-molecule imaging. PNAS 110, 1285–90 (2013).

Shcherbakova, I. et al. Alternative Spliceosome Assembly Pathways Revealed by Single-Molecule Fluorescence Microscopy. Cell Reports 5, 151–165 (2013).

Friedman, L.J., Mumm, J.P. & Gelles, J. RNA polymerase approaches its promoter without long-range sliding along DNA. PNAS 110, 9740–9745 (2013).

Crawford, D.J., Hoskins, A.A., Friedman, L.J., Gelles, J. & Moore, M.J. Single-molecule colocalization FRET evidence that spliceosome activation precedes stable approach of 5′ splice site and branch site. PNAS 110, 6783–6788 (2013).


Garcia, H.G. et al. Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria. Cell Reports 2, 150–161 (2012).

Friedman, L.J. & Gelles, J. Mechanism of Transcription Initiation at an Activator-Dependent Promoter Defined by Single-Molecule Observation. Cell 148, 679–689 (2012).

Breitsprecher, D. et al. Rocket Launcher Mechanism of Collaborative Actin Assembly Defined by Single-Molecule Imaging. Science 336, 1164–1168 (2012).


Hoskins, A. A., Gelles, J. & Moore, M. J. New insights into the spliceosome by single molecule fluorescence microscopy. Current Opinion in Chemical Biology 15, 864–870 (2011).

Hoskins, A. A. et al. Ordered and Dynamic Assembly of Single Spliceosomes. Science 331, 1289 –1295 (2011).

Sanchez, A., Osborne, M. L., Friedman, L. J., Kondev, J. & Gelles, J. Mechanism of transcriptional repression at a bacterial promoter by analysis of single molecules. EMBO Journal 30, 3940 – 3946 (2011).

Ydenberg, C. A., Smith, B. A., Breitsprecher, D., Gelles, J. & Goode, B. L. Cease‐fire at the leading edge: New perspectives on actin filament branching, debranching, and cross‐linking. Cytoskeleton 68, 598–602 (2011).