Papers

Practical considerations for accurate estimation of diffusion parameters from single-particle tracking in living cells
Ghosal A, Wang Y-H, Nguyen N, Troyer L, and Kim S Journal of Chemical Physics, 2025.
[OpenAccess][bioRxiv][github]

OLD amputates the anticodon arm of tRNAs during P2–Lambda interference
Tovande AA, Matibag BD, Ünlü I, Wolf, EJ, Sargen MR, Ramsey B, Kim S, Helaine S, Corrêa, Jr. IR, Lim HC Nucleic Acids Research, 2025.
[OpenAccess][Pubmed]

Rif-seq reveals Caulobacter crescentus mRNA decay is globally coordinated with transcription and translation
Kulathungage H, Aretakis JR, Vaidya K, Al-Husini N, Muthunayake NS, Kim S, and Schrader JM 2025.
[bioRxiv]

Single-molecule imaging reveals the role of membrane-binding motif and C-terminal domain of RNase E in its localization and diffusion in Escherichia coli
Troyer L*, Wang Y-H*, Shobhna, Kim S, Woo J, Tajkhorshid E, and Kim S 2024.
[bioRxiv][github]

Re-defining how mRNA degradation is coordinated with transcription and translation in bacteria
Kim S, Wang Y-H, Hassan A, and Kim S 2024.
[bioRxiv]

DNA supercoiling drives a transition between collective modes of gene synthesis
Chatterjee P, Goldenfeld N, and Kim S Physical Review Letters, 2021.
[OpenAccess] [bioRxiv][github]

Probing mRNA kinetics in space and time in Escherichia coli using two-color single-molecule fluorescence in situ hybridization
Kim S and Vaidya K Journal of Visualized Experiments, 2020.
[OpenAccess] [github]

Better together: Cooperation and antagonism between RNA polymerases during transcription in vivo
Kim S Bioessays, 2020.
[PubMed] [OpenAccess]

Long-distance cooperative and antagonistic RNA polymerase dynamics via DNA supercoiling
Kim S, Beltran B, Irnov I, and Jacobs-Wagner C Cell, 2019.
[PubMed] [PDF] [github]

Nucleoid size scaling and intracellular organization of translation across bacteria
Gray WT, Govers SK, Xiang Y, Parry BR, Campos M, Kim S, and Jacobs-Wagner C Cell, 2019.
[PubMed] [PDF] [github]

Effects of mRNA degradation and site-specific transcriptional pausing on protein expression noise
Kim S and Jacobs-Wagner C Biophysical Journal, 2018.
[PubMed] [PDF] [Supp] [github]

Probing allostery through DNA
Kim S*, Broströmer E*, Xing D*, Jin J*, Chong S, Ge H, Wang S, Gu C, Yang L, Gao YQ, Su X-D, Sun Y, and Xie XS Science, 2013.
[PubMed] [PDF] [Supp]

Single-molecule study of DNA polymerization activity of HIV-1 reverse transcriptase on DNA template
Kim S, Schroeder CM, and Xie XS Journal of Molecular Biology, 2010.
[PubMed] [PDF] [Supp]

Hydrodynamic flow-stretching assay for single-molecule studies of nucleic acid–protein interactions
Schroeder CM, Blainey PC, Kim S, and Xie XS Single-Molecule Techniques: A Laboratory Manual, 2008.

Multiplexed single-molecule assay for enzymatic activity on flow-stretched DNA
Kim S, Blainey PC, Schroeder CM, and Xie XS Nature Methods, 2007.
[PubMed] [PDF] [Supp]

Direct observation of an intermediate state for a surface photochemical reaction initiated by hot electron transfer
Lee J, Ryu S, Chang J, Kim S, and Kim SK The Journal of Physical Chemistry B, 2005.
[PubMed]