Publications

2020 - Current

  • Ide, N.A., Gentry, R.C., Rudbach, M.A., Yoo, K., Velez, P.K., Comunale, V.M., Hartwick, E.W., Kinz-Thompson, C.D., Gonzalez Jr, R.L., Aitken, C.E., (2024) A dynamic compositional equilibrium governs mRNA recognition by eIF3. bioRxiv. DOI:10.1101/2024.04.25.581977 [Preprint]

  • Verma, A. R., Ray, K. K., Bodick, M., Kinz-Thompson, C. D. & Gonzalez, Jr., R. L. (2024) Increasing the accuracy of single-molecule data analysis using tMAVEN. Biophysical Journal, 123, 1-15. DOI:10.1101/2023.08.15.553409. [Link] [Preprint]

  • Gentry, R.C., Ide, N.A., Comunale, V.M., Hartwick, E.W., Kinz-Thompson, C.D., Gonzalez Jr., R.L. (2023) The mechanism of mRNA activation. bioRxiv, DOI:10.1101/2023.11.15.567265. [Preprint]

  • Ray, K. K. & Kinz-Thompson, C. D. (2023) Scale-dependent hierarchical resolution: applications to atomic resolution and model validation in cryoEM. bioRxiv, DOI:10.1101/2023.10.17.562748. [Preprint] [Zenodo Dataset]

  • Ray, K.K., Kinz-Thompson, C.D., Fei, J., Wang, B., Lin, Q., Gonzalez, Jr., R.L. (2023) Entropic control of the free energy landscape of an archetypal biomolecular machine. Proceedings of the National Academy of Sciences 120, e2220591120. DOI:10.1073/pnas.2220591120. [Link] [Preprint]

  • Zhu, L., Kim, J., Leng, K., Ramos, J.E., Kinz-Thompson, C.D., Karpowich, N.K., Gonzalez Jr., R.L., Hunt, J.F. (2022) Realtime observation of ATP-driven single B12 molecule translocation through BtuCD-F. bioRxiv. DOI:10.1101/2022.12.02.518935. [Preprint]

  • Zhu, L., Kim, J., Leng, K., Ramos, J.E., Kinz-Thompson, C.D., Karpowich, N.K., Gonzalez Jr., R.L., Hunt, J.F. (2022) Mechanistic implications of the interaction of the soluble substrate-binding protein with a type II ABC importer, bioRxiv. DOI:10.1101/2022.12.02.518933. [Preprint]

  • Kinz-Thompson, C.D., Lopez Redondo, M., Mulligan C., Sauer, D.B., Marden, J.J., Song, J. Tajkhorshid, E., Hunt, J.F., Stokes, D.L., Mindell, J.A., Wang, D.N, Gonzalez, Jr., R.L. (2022) Elevator mechanism dynamics in a sodium-coupled dicarboxylate transporter, bioRxiv. DOI:10.1101/2022.05.01.490196. [Preprint]

  • Ray, K.K., Verma, A.R., Gonzalez, Jr., R.L., Kinz-Thompson, C.D. (2022) Inferring the shape of data: a probabilistic framework for analysing experiments in the natural sciences. Proceedings of the Royal Society A, 478, 20220177. DOI:10.1098/rspa.2022.0177. [Link] [Preprint]

  • Kinz-Thompson, C.D., Ray, K.K., Gonzalez, Jr., R.L. (2021) Bayesian inference: the comprehensive approach to analyzing single-molecule experiments. Annual Review of Biophysics, 50, 191-208. DOI:10.1146/annurev-biophys-082120-103921. [Link] [PMC] [Preprint]

Prior to 2020

  • Subramanyam, S., Kinz-Thompson, C.D., Gonzalez, R.L., Jr., Spies, M. (2018) Observation and Analysis of RAD51 Nucleation Dynamics at Single-monomer Resolution. Methods in Enzymology, 600, 201-232. [Link] [PMC]

  • Kinz-Thompson, C.D.,† Gonzalez, R.L., Jr. (2018) Increasing the Time Resolution of Single-molecule Experiments with Bayesian Inference. Biophysical Journal, 114, 289-300. [Link] [PMC] [Preprint]

  • Kinz-Thompson, C.D., Bailey, N.A., Gonzalez, R.L., Jr. (2016) Precisely and Accurately Inferring Single-molecule Rate Constants. Methods in Enzymology, 581, 187-225. [Link] [PMC]

  • Kinz-Thompson, C.D., Sharma, A.K., Frank, J., Gonzalez, R.L., Jr. Chowdhury, D. (2015) Quantitative Connection between Ensemble Thermodynamics and Single-Molecule Kinetics: A Case Study Using Cryogenic Electron Microscopy and Single-Molecule Fluorescence Resonance Energy Transfer Investigations of the Ribosome. Journal of Physical Chemistry B, 119(34), 10888-10901. [Link] [PMC]

  • Kinz-Thompson, C.D., Gonzalez, R.L., Jr. (2014) smFRET Studies of the “Encounter” Complexes and Subsequent Intermediate States that Regulate the Selectivity of Ligand Binding. FEBS Letters, 588(19), 3526-3538. [Link] [PMC]

  • Kinz-Thompson, C.D., Palma, M., Pulukkunat, D.K., Chenet, D., Hone, J., Wind, S.J., Gonzalez, R.L., Jr. (2013) Robustly Passivated, Gold Nanoaperture Arrays for Single-Molecule Fluorescence Microscopy. ACS Nano, 7(9), 8159-8166. [Link] [PMC]

  • Kravec, S.M., Kinz-Thompson, C.D., Conwell, E.M. (2011) Localization of a Hole on an Adenine-Thymine Radical Cation Embedded in B-Form DNA in Water. Journal of Physical Chemistry B, 115(19), 6166-6171. [Link]

  • Kinz-Thompson, C., Conwell, E. (2010) Proton Transfer in Adenine-Thymine Radical Cation Embedded in B-Form DNA. Journal of Physical Chemistry Letters, 1(9), 1403-1407. [Link]

  • Kucherov, V.M., Kinz-Thompson, C.D., Conwell, E.M. (2010) Polarons in DNA Oligomers. Journal of Physical Chemistry C, 114(3), 1663-1666. [Link]