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Items: 30

1.

Correction: Kinetic analysis methods applied to single motor protein trajectories.

Nord AL, Pols AF, Depken M, Pedaci F.

Phys Chem Chem Phys. 2019 Jun 5;21(22):12044. doi: 10.1039/c9cp90141h.

PMID:
31120464
2.

Kinetic analysis methods applied to single motor protein trajectories.

Nord AL, Pols AF, Depken M, Pedaci F.

Phys Chem Chem Phys. 2018 Jul 11;20(27):18775-18781. doi: 10.1039/c8cp03056a. Erratum in: Phys Chem Chem Phys. 2019 Jun 5;21(22):12044.

PMID:
29961801
3.

Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria.

Dulin D, Bauer DLV, Malinen AM, Bakermans JJW, Kaller M, Morichaud Z, Petushkov I, Depken M, Brodolin K, Kulbachinskiy A, Kapanidis AN.

Nat Commun. 2018 Apr 16;9(1):1478. doi: 10.1038/s41467-018-03902-9.

4.

Hybridization Kinetics Explains CRISPR-Cas Off-Targeting Rules.

Klein M, Eslami-Mossallam B, Arroyo DG, Depken M.

Cell Rep. 2018 Feb 6;22(6):1413-1423. doi: 10.1016/j.celrep.2018.01.045.

5.

What is all this fuss about Tus? Comparison of recent findings from biophysical and biochemical experiments.

Berghuis BA, Raducanu VS, Elshenawy MM, Jergic S, Depken M, Dixon NE, Hamdan SM, Dekker NH.

Crit Rev Biochem Mol Biol. 2018 Feb;53(1):49-63. doi: 10.1080/10409238.2017.1394264. Epub 2017 Nov 6. Review.

PMID:
29108427
6.

Signatures of Nucleotide Analog Incorporation by an RNA-Dependent RNA Polymerase Revealed Using High-Throughput Magnetic Tweezers.

Dulin D, Arnold JJ, van Laar T, Oh HS, Lee C, Perkins AL, Harki DA, Depken M, Cameron CE, Dekker NH.

Cell Rep. 2017 Oct 24;21(4):1063-1076. doi: 10.1016/j.celrep.2017.10.005.

7.

Crowding-induced transcriptional bursts dictate polymerase and nucleosome density profiles along genes.

van den Berg AA, Depken M.

Nucleic Acids Res. 2017 Jul 27;45(13):7623-7632. doi: 10.1093/nar/gkx513.

8.

Switching between Exonucleolysis and Replication by T7 DNA Polymerase Ensures High Fidelity.

Hoekstra TP, Depken M, Lin SN, Cabanas-Danés J, Gross P, Dame RT, Peterman EJG, Wuite GJL.

Biophys J. 2017 Feb 28;112(4):575-583. doi: 10.1016/j.bpj.2016.12.044.

9.

Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation.

Künne T, Kieper SN, Bannenberg JW, Vogel AI, Miellet WR, Klein M, Depken M, Suarez-Diez M, Brouns SJ.

Mol Cell. 2016 Sep 1;63(5):852-64. doi: 10.1016/j.molcel.2016.07.011. Epub 2016 Aug 18.

10.

Why Argonaute is needed to make microRNA target search fast and reliable.

Klein M, Chandradoss SD, Depken M, Joo C.

Semin Cell Dev Biol. 2017 May;65:20-28. doi: 10.1016/j.semcdb.2016.05.017. Epub 2016 May 26. Review.

11.

Backtracking behavior in viral RNA-dependent RNA polymerase provides the basis for a second initiation site.

Dulin D, Vilfan ID, Berghuis BA, Poranen MM, Depken M, Dekker NH.

Nucleic Acids Res. 2015 Dec 2;43(21):10421-9. doi: 10.1093/nar/gkv1098. Epub 2015 Oct 22.

12.

Untangling reaction pathways through modern approaches to high-throughput single-molecule force-spectroscopy experiments.

Dulin D, Berghuis BA, Depken M, Dekker NH.

Curr Opin Struct Biol. 2015 Oct;34:116-22. doi: 10.1016/j.sbi.2015.08.007. Epub 2015 Oct 1. Review.

PMID:
26434413
13.

Strand separation establishes a sustained lock at the Tus-Ter replication fork barrier.

Berghuis BA, Dulin D, Xu ZQ, van Laar T, Cross B, Janissen R, Jergic S, Dixon NE, Depken M, Dekker NH.

Nat Chem Biol. 2015 Aug;11(8):579-85. doi: 10.1038/nchembio.1857. Epub 2015 Jul 6.

PMID:
26147356
14.

Elongation-Competent Pauses Govern the Fidelity of a Viral RNA-Dependent RNA Polymerase.

Dulin D, Vilfan ID, Berghuis BA, Hage S, Bamford DH, Poranen MM, Depken M, Dekker NH.

Cell Rep. 2015 Feb 17;10(6):983-992. doi: 10.1016/j.celrep.2015.01.031. Epub 2015 Feb 12.

15.

Slow unloading leads to DNA-bound β2-sliding clamp accumulation in live Escherichia coli cells.

Moolman MC, Krishnan ST, Kerssemakers JW, van den Berg A, Tulinski P, Depken M, Reyes-Lamothe R, Sherratt DJ, Dekker NH.

Nat Commun. 2014 Dec 18;5:5820. doi: 10.1038/ncomms6820.

16.

Visualization and quantification of nascent RAD51 filament formation at single-monomer resolution.

Candelli A, Holthausen JT, Depken M, Brouwer I, Franker MA, Marchetti M, Heller I, Bernard S, Garcin EB, Modesti M, Wyman C, Wuite GJ, Peterman EJ.

Proc Natl Acad Sci U S A. 2014 Oct 21;111(42):15090-5. doi: 10.1073/pnas.1307824111. Epub 2014 Oct 6.

17.

Intermittent transcription dynamics for the rapid production of long transcripts of high fidelity.

Depken M, Parrondo JM, Grill SW.

Cell Rep. 2013 Oct 31;5(2):521-30. doi: 10.1016/j.celrep.2013.09.007. Epub 2013 Oct 10.

18.

Stress-enhanced gelation: a dynamic nonlinearity of elasticity.

Yao NY, Broedersz CP, Depken M, Becker DJ, Pollak MR, Mackintosh FC, Weitz DA.

Phys Rev Lett. 2013 Jan 4;110(1):018103. Epub 2013 Jan 3.

19.

Nonequilibrium fluctuations of a remodeling in vitro cytoskeleton.

Stuhrmann B, Soares E Silva M, Depken M, Mackintosh FC, Koenderink GH.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Aug;86(2 Pt 1):020901. Epub 2012 Aug 23.

PMID:
23005716
20.

Nonlinear viscoelasticity of actin transiently cross-linked with mutant α-actinin-4.

Yao NY, Becker DJ, Broedersz CP, Depken M, Mackintosh FC, Pollak MR, Weitz DA.

J Mol Biol. 2011 Sep 2;411(5):1062-71. doi: 10.1016/j.jmb.2011.06.049. Epub 2011 Jul 6.

21.

Active multistage coarsening of actin networks driven by myosin motors.

Soares e Silva M, Depken M, Stuhrmann B, Korsten M, MacKintosh FC, Koenderink GH.

Proc Natl Acad Sci U S A. 2011 Jun 7;108(23):9408-13. doi: 10.1073/pnas.1016616108. Epub 2011 May 18.

22.

Cross-link-governed dynamics of biopolymer networks.

Broedersz CP, Depken M, Yao NY, Pollak MR, Weitz DA, MacKintosh FC.

Phys Rev Lett. 2010 Dec 3;105(23):238101. Epub 2010 Nov 30.

PMID:
21231506
23.

Anisotropies in cortical tension reveal the physical basis of polarizing cortical flows.

Mayer M, Depken M, Bois JS, Jülicher F, Grill SW.

Nature. 2010 Sep 30;467(7315):617-21. doi: 10.1038/nature09376. Epub 2010 Sep 19.

PMID:
20852613
24.

The origin of short transcriptional pauses.

Depken M, Galburt EA, Grill SW.

Biophys J. 2009 Mar 18;96(6):2189-93. doi: 10.1016/j.bpj.2008.12.3918.

25.

Nucleosome shape dictates chromatin fiber structure.

Depken M, Schiessel H.

Biophys J. 2009 Feb;96(3):777-84. doi: 10.1016/j.bpj.2008.09.055.

26.

Continuum approach to wide shear zones in quasistatic granular matter.

Depken M, van Saarloos W, van Hecke M.

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Mar;73(3 Pt 1):031302. Epub 2006 Mar 7.

PMID:
16605512
27.

Fluctuation-dissipation relation and the Edwards entropy for a glassy granular compaction model.

Depken M, Stinchcombe R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Jun;71(6 Pt 2):065102. Epub 2005 Jun 13.

PMID:
16089799
28.

Exact probability function for bulk density and current in the asymmetric exclusion process.

Depken M, Stinchcombe R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Mar;71(3 Pt 2A):036120. Epub 2005 Mar 18.

PMID:
15903506
29.

Exact joint density-current probability function for the asymmetric exclusion process.

Depken M, Stinchcombe R.

Phys Rev Lett. 2004 Jul 23;93(4):040602. Epub 2004 Jul 22.

PMID:
15323746
30.

Marginal scaling scenario and analytic results for a glassy compaction model.

Stinchcombe R, Depken M.

Phys Rev Lett. 2002 Mar 25;88(12):125701. Epub 2002 Mar 12.

PMID:
11909479

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