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S. C. Bera et al., “The nucleotide addition cycle of the SARS-CoV-2 polymerase,” Cell Reports, vol. 36, no. 9, 2021.

M. Seifert et al., “Temperature controlled high-throughput magnetic tweezers show striking difference in activation energies of replicating viral RNA-dependent RNA polymerases,” Nucleic acids research, vol. 48, no. 10, pp. 5591–5602, 2020.

T. J. C. Cui et al., “Argonaute bypasses cellular obstacles without hindrance during target search,” Nature Communications (in press), vol. 10, no. 1, Dec. 2019, doi: 10.1038/s41467-019-12415-y.

B. A. Berghuis et al., What is all this fuss about Tus? Comparison of recent findings from biophysical and biochemical experiments, vol. 53. Taylor & Francis, 2018, pp. 49–63. doi: 10.1080/10409238.2017.1394264.

A. L. Nord, A. F. Pols, M. Depken, and F. Pedaci, “Kinetic analysis methods applied to single motor protein trajectories,” Physical Chemistry Chemical Physics, vol. 20, no. 27, pp. 18775–18781, 2018.

D. Dulin et al., “Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria,” Nature Communications, vol. 9, no. 1, p. 1478, Dec. 2018, doi: 10.1038/s41467-018-03902-9.

M. Klein, B. Eslami-Mossallam, D. G. Arroyo, and M. Depken, “Hybridization Kinetics Explains CRISPR-Cas Off-Targeting Rules,” Cell Reports, vol. 22, no. 6, pp. 1413–1423, 2018, doi: 10.1016/j.celrep.2018.01.045.

D. Dulin et al., “Signatures of Nucleotide Analog Incorporation by an RNA-Dependent RNA Polymerase Revealed Using High-Throughput Magnetic Tweezers,” Cell Reports, vol. 21, no. 4, pp. 1063–1076, Oct. 2017, doi: 10.1016/j.celrep.2017.10.005.

A. A. van den Berg and M. Depken, “Crowding-induced transcriptional bursts dictate polymerase and nucleosome density profiles along genes,” Nucleic Acids Research, vol. 45, no. 13, pp. 7623–7632, Jul. 2017, doi: 10.1093/nar/gkx513.

M. Klein, S. D. Chandradoss, M. Depken, and C. Joo, “Why Argonaute is needed to make microRNA target search fast and reliable,” in Seminars in cell & developmental biology, 2017, vol. 65, pp. 20–28.

T. Künne et al., “Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation,” Molecular Cell, vol. 63, no. 5, pp. 852–864, Sep. 2016, doi: 10.1016/j.molcel.2016.07.011.

D. Dulin et al., “Elongation-Competent Pauses Govern the Fidelity of a Viral RNA-Dependent RNA Polymerase,” Cell Reports, vol. 10, no. 6, pp. 983–992, Feb. 2015, doi: 10.1016/j.celrep.2015.01.031.

D. Dulin, B. A. Berghuis, M. Depken, and N. H. Dekker, Untangling reaction pathways through modern approaches to high-throughput single-molecule force-spectroscopy experiments, vol. 34. Elsevier Current Trends, 2015, pp. 116–122. doi: 10.1016/j.sbi.2015.08.007.

D. Dulin, I. D. Vilfan, B. A. Berghuis, M. M. Poranen, M. Depken, and N. H. Dekker, “Backtracking behavior in viral RNA-dependent RNA polymerase provides the basis for a second initiation site,” Nucleic Acids Research, vol. 43, no. 21, p. gkv1098, Oct. 2015, doi: 10.1093/nar/gkv1098.

B. a Berghuis et al., “Strand separation establishes a sustained lock at the Tus-Ter replication fork barrier.,” Nature chemical biology, vol. 11, no. 8, pp. 579–85, Aug. 2015, doi: 10.1038/nchembio.1857.

A. Candelli et al., “Visualization and quantification of nascent RAD51 filament formation at single-monomer resolution,” Proceedings of the National Academy of Sciences, vol. 111, no. 42, pp. 15090–15095, 2014, doi: 10.1073/pnas.1307824111.

M. C. Moolman et al., “Slow unloading leads to DNA-bound beta2-sliding clamp accumulation in live Escherichia coli cells,” Nat Commun, vol. 5, p. 5820, 2014, doi: 10.1038/ncomms6820.

N. Y. Yao et al., “Stress-Enhanced Gelation: A Dynamic Nonlinearity of Elasticity,” Physical Review Letters, vol. 110, no. 1, p. 018103, Jan. 2013, doi: 10.1103/PhysRevLett.110.018103.

M. Depken, J. Parrondo, and S. Grill, “Intermittent Transcription Dynamics for the Rapid Production of Long Transcripts of High Fidelity,” Cell Reports, vol. 5, pp. 1–10, 2013.

B. Stuhrmann, M. Soares E Silva, M. Depken, F. C. MacKintosh, and G. H. Koenderink, “Nonequilibrium fluctuations of a remodeling in vitro cytoskeleton,” Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, vol. 86, no. 2, 2012, doi: 10.1103/PhysRevE.86.020901.

N. Y. N. Y. Yao et al., “Nonlinear viscoelasticity of actin transiently cross-linked with mutant α-actinin-4.,” Journal of Molecular Biology, vol. 411, no. 5, pp. 1062–71, Sep. 2011, doi: 10.1016/j.jmb.2011.06.049.

M. e Silva, M. Depken, B. Stuhrmann, M. Korsten, F. C. MacKintosh, and G. H. Koenderink, “Active multistage coarsening of actin networks driven by myosin motors,” Proceedings of the National Academy of Sciences, vol. 108, no. 23, pp. 9408–9413, 2011.

M. Mayer et al., “Anisotropies in cortical tension reveal the physical basis of polarizing cortical flows.,” Nature, vol. 467, no. 7315, pp. 617–621, 2010, doi: 10.1038/nature09376.

C. Broedersz, M. Depken, N. Yao, M. Pollak, D. Weitz, and F. MacKintosh, “Cross-Link-Governed Dynamics of Biopolymer Networks,” Physical Review Letters, vol. 105, no. 23, Nov. 2010, doi: 10.1103/PhysRevLett.105.238101.

M. Depken, E. A. Galburt, and S. W. Grill, “The origin of short transcriptional pauses,” Biophysical Journal, vol. 96, no. 6, pp. 2189–2193, 2009, doi: 10.1016/j.bpj.2008.12.3918.

M. Depken and H. Schiessel, “Nucleosome shape dictates chromatin fiber structure.,” Biophysical journal, vol. 96, no. 3, pp. 777–784, Feb. 2009, doi: 10.1016/j.bpj.2008.09.055.

M. Depken, J. B. Lechman, M. van Hecke, W. van Saarloos, and G. S. Grest, “Stresses in smooth flows of dense granular media,” Europhysics Letters, vol. 78, no. 5, p. 58001, 2007.

M. Depken, W. Van Saarloos, and M. Van Hecke, “Continuum approach to wide shear zones in quasistatic granular matter,” Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, vol. 73, no. 3, 2006, doi: 10.1103/PhysRevE.73.031302.

M. Depken and R. Stinchcombe, “Exact probability function for bulk density and current in the asymmetric exclusion process,” Physical Review E, vol. 71, no. 3, p. 36120, 2005.

M. Depken and R. Stinchcombe, “Fluctuation-dissipation relation and the Edwards entropy for a glassy granular compaction model,” Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, vol. 71, no. 6, 2005, doi: 10.1103/PhysRevE.71.065102.

M. Depken and R. Stinchcombe, “Exact joint density-current probability function for the asymmetric exclusion process,” Physical Review Letters, vol. 93, no. 4, pp. 040602–1, 2004, doi: 10.1103/PhysRevLett.93.040602.

R. Stinchcombe and M. Depken, “Marginal Scaling Scenario And Analytic Results For A Glassy Compaction Model,” Physical Review Letters, vol. 88, no. 12, p. 125701, Mar. 2002, doi: 10.1103/PhysRevLett.88.125701.

M. Depken, “On the gallavotti-cohen symmetry and the fluctuation theorem for stochastic processes,” Los Alamos archive: http://www. arxiv. org, 2002.