BN/Nynke Dekker Lab

Research output

Research output per year 2007 2010 2014 2015 2018 2023 2024

• 131 Article
• 12 Dissertation (TU Delft)
• 8 Chapter
• 4 Patent
• 5 More
  • 2 Meeting Abstract
  • 1 Review article
  • 1 Artefact
  • 1 Web publication/site

Research output per year

Research output per year

Search results

• 2007

  Probing DNA and protein-DNA interactions with solid-state nanopores

  Krapf, D., Keyser, UF., Dato, G., van Dorp, S., Smeets, RMM., Wu, MY., Lemay, SG., Dekker, NH. & Dekker, C., 2007, In: Biophysical Journal. p. 6a-6a

  Research output: Contribution to journal › Article › Scientific › peer-review
• 2008

  Controlling the surface properties of nanostructures for studies of polymerases

  Crut, AJE., Koster, DA., Huang, Z., Hage, S. & Dekker, NH., 2008, In: Nanotechnology. 19, 46, p. 85301-1-85301-9

  Research output: Contribution to journal › Article › Scientific › peer-review

  1 Citation (Scopus)

• Dynamics of phosphodiester synthesis by DNA ligase

  Crut, AJE., Nair, PA., Koster, DA., Shuman, S. & Dekker, NH., 2008, In: Proceedings of the National Academy of Sciences of the United States of America. 105, 19, p. 6894-6899 6 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  14 Citations (Scopus)

• End-joining long nucleic acid polymers

  van den Hout, M., Hage, S., Dekker, C. & Dekker, NH., 2008, In: Nucleic Acids Research. 36, 16, p. e104-1-e104-8

  Research output: Contribution to journal › Article › Scientific › peer-review

  4 Citations (Scopus)

• Noise in solid-state nanopores

  Smeets, RMM., Keyser, UF., Dekker, NH. & Dekker, C., 2008, In: Proceedings of the National Academy of Sciences of the United States of America. 105, 2, p. 417-421 5 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  290 Citations (Scopus)

• Reinitiated viral RNA-dependent RNA polymerase resumes replication at a reduced rate

  Vilfan, ID., Candelli, A., Hage, S., Aalto, A., Poranen, M., Bamford, D. & Dekker, NH., 2008, In: Nucleic Acids Research. 36, 22, p. 7059-7067 9 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
  14 Citations (Scopus)

• Single-molecule observations of topotecan-mediated topIB activity at a unique DNA sequence

  Koster, DA., Czerwinski, F., Halby, L., Crut, AJE., Vekhoff, P., Palle, K., Arimondo, PB. & Dekker, NH., 2008, In: Nucleic Acids Research. 36, p. 2301-2310 10 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  17 Citations (Scopus)

• Translocation of RecA-coated dsDNA through solid-state nanopores

  Smeets, RMM., Kowalczyk, SW., Hall, AR., Dekker, NH. & Dekker, C., 2008, In: Nano Letters: a journal dedicated to nanoscience and nanotechnology.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
• 2009

  Control of shape and material composition of solid-state nanopores

  Wu, MY., Smeets, RMM., Zandbergen, M., Ziese, U., Krapf, D., Batson, PE., Dekker, NH., Dekker, C. & Zandbergen, HW., 2009, In: Nano Letters: a journal dedicated to nanoscience and nanotechnology. 9, 1, p. 479-484 6 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  85 Citations (Scopus)

• Distinguishing single- and double-stranded nucleic acid molecules using solid-state nanopores

  Skinner, GM., van den Hout, M., Broekmans, O., Dekker, C. & Dekker, NH., 2009, In: Nano Letters: a journal dedicated to nanoscience and nanotechnology. 9, 8, p. 2953-2960 8 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  139 Citations (Scopus)

• Low-frequency noise in solid-state nanopores

  Smeets, RMM., Dekker, NH. & Dekker, C., 2009, In: Nanotechnology. 20, 9, p. 1-4 4 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  78 Citations (Scopus)

• Origin of the electrophoretic force on DNA in solid-state nanopores

  van Dorp, S., Keyser, UF., Dekker, NH., Dekker, C. & Lemay, SG., 2009, In: Nature Physics. 5, 5, p. 347-351 5 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  315 Citations (Scopus)

• Quantitative modeling and optimization of magnetic tweezers

  Lipfert, J., Hao, XM. & Dekker, NH., 2009, In: Biophysical Journal. 96, 12, p. 5040-5049 10 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  148 Citations (Scopus)

• Translocation of RecA-coated double-stranded DNA through solid-state nanopores

  Smeets, RMM., Kowalczyk, SW., Hall, AR., Dekker, NH. & Dekker, C., 2009, In: Nano Letters: a journal dedicated to nanoscience and nanotechnology. 9, 9, p. 3089-3095 7 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  108 Citations (Scopus)
• 2010

  Cellular Strategies for Regulating DNA Supercoiling: A Single-Molecule Perspective

  Koster, AJ., Crut, AJE., Shuman, S., Bjornsti, M. & Dekker, NH., 2010, In: Cell. 142, 4, p. 519-530 12 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  127 Citations (Scopus)

• Controlling Nanopore Size, Shape, and Stability

  van den Hout, M., Hall, AR., Wu, M-Y., Zandbergen, HW., Dekker, C. & Dekker, NH., 2010, In: Nanotechnology. 21, 11

  Research output: Contribution to journal › Article › Scientific › peer-review

  • Nanopore 100%
  • nucleic acids 14%
  • DNA 12%
  • RNA 12%
  • Membrane 12%
  124 Citations (Scopus)

• Der Vorfahr aus der Bronzezeit

  Menze, S., Menze, C., Lipfert, J., Menze, B. & Harsch, G., 2010, In: Praxis der Naturwissenschaften - Chemie in der Schule. 59, 8, p. 6-11 6 p.

  Research output: Contribution to journal › Article › Scientific

• Direct Force Measurements on Double-Stranded RNA in Solid-State Nanopores

  van den Hout, M., Vilfan, ID., Hage, S. & Dekker, NH., 2010, In: Nano Letters: a journal dedicated to nanoscience and nanotechnology. 10, 2, p. 701-707 7 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  58 Citations (Scopus)

• Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding

  Lipfert, J., Sim, AYL., Herschlag, D. & Doniach, S., 2010, In: RNA. 16, 4, p. 708-719 12 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  53 Citations (Scopus)

• Distinguishable Populations Report on the Interactions of Single DNA Molecules with Solid-State Nanopores

  Dekker, NH., van den Hout, M., Krudde, V. & Janssen, XJA., 2010, In: Biophysical Journal. 99, 11, p. 3840-3848 9 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  32 Citations (Scopus)

• Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments

  Lipfert, J., Kerssemakers, JWJ., Jager, T. & Dekker, NH., 2010, In: Nature Methods: techniques for life scientists and chemists. 7, 12, p. 977-980 4 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  239 Citations (Scopus)

• Quantitative guidelines for force calibration through spectral analysis of magnetic tweezers data.

  te Velthuis, AJW., Kerssemakers, JWJ., Lipfert, J. & Dekker, NH., 2010, In: Biophysical Journal. 99, 4, p. 1292-1302 11 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  81 Citations (Scopus)

• The Ligand-Free State of the TPP Riboswitch: A Partially Folded RNA Structure

  Ali, M., Lipfert, J., Seifert, S., Herschlag, D. & Doniach, S., 2010, In: Journal of Molecular Biology. 396, 1, p. 153-165 13 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  61 Citations (Scopus)

• Torsional sensing of small-molecule binding using magnetic tweezers.

  Lipfert, J., Klijnhout, S. & Dekker, NH., 2010, In: Nucleic Acids Research. 38, 20, p. 7122-7132 11 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  82 Citations (Scopus)
• 2011

  A method to track rotational motion for use in single-molecule biophysics

  Lipfert, J., Kerssemakers, JWJ., Rojer, SF. & Dekker, NH., 2011, In: Review of Scientific Instruments. 82, 10, p. 1-12 12 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  30 Citations (Scopus)

• Electron beam fabrication of birefringent microcylinders

  Huang, Z., Pedaci, F., Oene, M., Wiggin, MJ. & Dekker, NH., 2011, In: ACS Nano. 5, 2, p. 1418-1427 10 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  18 Citations (Scopus)

• Excitable Particles in an Optical Torque Wrench.

  Pedaci, F., Huang, Z., Oene, M., Barland, S. & Dekker, NH., 2011, In: Nature Physics.

  Research output: Contribution to journal › Article › Scientific › peer-review

  75 Citations (Scopus)

• Freely-orbiting magnetic tweezers directly report on changes in the twist of nucleic acids.

  Lipfert, J., Wiggin, MJ., Kerssemakers, JWJ., Pedaci, F. & Dekker, NH., 2011, In: Nature Communications. 2, 439, p. 1-33 33 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

• Single Molecule Investigations of the Stringent Response Machinery in Individual Living Bacterial Cells.

  English, BP., Hauryliuk, V., Sanamrad, A., Tankov, S., Dekker, NH. & Elf, J., 2011, In: Proceedings of the National Academy of Sciences of the United States of America. 108, 31, p. 365-373 9 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

• The Passage of Homopolymeric RNA through Small Solid-State Nanopores.

  van den Hout, M., Skinner, GM., Klijnhout, S., Krudde, V. & Dekker, NH., 2011, In: Small. 7, 15, p. 2217-2224 8 p.

  Research output: Contribution to journal › Article › Scientific › peer-review
  23 Citations (Scopus)
• 2012

  Calibration of the optical torque wrench

  Pedaci, F., Huang, Z., van Oene, MM. & Dekker, NH., 2012, In: Optics Express. 20, 4, p. 3787-3802 16 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  26 Citations (Scopus)

• Electromagnetic torque tweezers for single-molecule studies

  Janssen, XJA., Lipfert, J., Daudey, R., Beekman, J. & Dekker, NH., 2012, In: Nano Letters: a journal dedicated to nanoscience and nanotechnology. 12, 7, p. 3634-3639 6 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

• Genomic processes studied at the single-molecule level: Introducing the tools and applications

  Dulin, D., Lipfert, J., Moolman, MC. & Dekker, NH., 2012, In: Nature Reviews. Genetics. p. 1-15 15 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

• Rapid manifacturing of low-noise membranes for nanopore sensors by trans-chip illumination lithograpy

  Janssen, XJA., Jonsson, PM., Plesa, C., Soni, GV., Dekker, C. & Dekker, NH., 2012, In: Nanotechnology. 23, 47, p. 75302-75309 8 p.

  Research output: Contribution to journal › Article › Scientific › peer-review
• 2013

  Backtracking and other off-path pauses control the dynamic of viral RNA dependent RNA polymerases

  Dulin, D., Vilfan, ID., Berghuis, BA., Hage, S., Bamford, D., Poranen, M., Depken, SM. & Dekker, NH., 2013, In: Biophysical Journal. 104, 2, p. 364A-364A

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

• Dependence of Micelle size and shape on detergent alkyl chain length and head group

  Oliver, RC., Lipfert, J., Fox, DA., Lo, RH., Doniach, S. & Columbus, L., 2013, In: PLoS ONE. 8, 5, p. 1-7 7 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
  166 Citations (Scopus)

• Electron-beam fabrication of a microfluidic device for submicron-scale bacteria

  Moolman, MC., Huang, Z., Tiruvadi Krishnan, S. & Dekker, NH., 2013, In: Journal of Nanobiotechnology. 11, 12, p. 1-10 10 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
  28 Citations (Scopus)

• Investigating DNA replication in Escherichia coli on the single cell level utilizing microfluidics and single-molecule fluorescence microscopy

  Moolman, MC., Krishnan, ST., Kerssemakers, JWJ., Hage, S., Reyes-Lamothe, R., Sherratt, DJ. & Dekker, NH., 2013, In: Biophysical Journal. 104, 2, p. 368A-369A

  Research output: Contribution to journal › Article › Scientific › peer-review

• Investigation stator dynamics of the Escherichia coli flagellar motor

  Dickinson, LE., van Oene, MM., Pedaci, F., Cross, B., Lim, R., Berry, RM. & Dekker, NH., 2013, In: Biophysical Journal. 104, 2, p. 640A-640A

  Research output: Contribution to journal › Article › Scientific › peer-review

• Modulating the physical properties of micelles for membrane protein investigations

  Oliver, RC., Lipfert, J. & Columbus, L., 2013, In: Biophysical Journal. 104, 2, p. 44a-44a

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

• Probing the response of double-stranded RNA to force and torque at the single-molecule level

  Lipfert, J., Skinner, GM., Keegstra, JM., Hensgens, T., Jager, T., Dulin, D., Donkers, SP. & Dekker, NH., 2013, In: Biophysical Journal. 104, 2, p. 1A-2A

  Research output: Contribution to journal › Article › Scientific › peer-review

• Structural and torsional properties of the RAD51-dsDNA nucleoprotein filament

  Lee, M., Lipfert, J., Sanchez, H., Wyman, C. & Dekker, NH., 2013, In: Nucleic Acids Research. 41, p. 7023-7030 8 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  21 Citations (Scopus)

• Studying genomic processes at the single-molecule level: introducing the tools and applications

  Dulin, D., Lipfert, J., Moolman, MC. & Dekker, NH., 2013, In: Nature Reviews. Genetics. 14, 1, p. 9-22 14 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

  • Molecule 100%
  • Transcription 33%
  • Facilitated Diffusion 33%
  • Conformation 33%
  • transcription 33%
  72 Citations (Scopus)

  58 Downloads (Pure)
• 2014

  Accurate high throughput bright field bead tracking using Gpu hardware

  Cnossen, JP., Dulin, D. & Dekker, NH., 2014, In: Biophysical Journal. 106, 2, p. 1-3 3 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

• Actin-microtubule coordination at growing microtubule ends

  Preciado Lopez, M., Huber, F., Grigoriev, I., Steinmetz, MO., Akhmanova, A., Koenderink, GH. & Dogterom, AM., 2014, In: Nature Communications. 5, p. 1-4 4 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  97 Citations (Scopus)

• An optimized software framework for real-time, high-throughput tracking of spherical beads

  Cnossen, JP., Dulin, D. & Dekker, NH., 2014, In: Review of Scientific Instruments. 85, 10, p. 1-11 11 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  63 Citations (Scopus)

• Blind predictions of DNA and RNA tweezers experiments with force and torque

  Chou, FC., Lipfert, J. & Das, R., 2014, In: PLoS Computational Biology (Print). 10, 8, p. 1-19 19 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  31 Citations (Scopus)

• Double-stranded RNA under force and torque: similarities and striking differences to double-stranded DNA

  Lipfert, J., Skinner, GM., Keegstra, JM., Hensgens, T., Jager, T., Dulin, D., Donkers, SP., Chou, FC., Das, R. & Dekker, NH., 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 43, p. 15408-15413 6 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  126 Citations (Scopus)

• Efficient illumination for microsecond tracking microscopy

  Dulin, D., Barland, S., Hachair, X. & Pedaci, F., 2014, In: PLoS ONE. 9, 9, p. 1-9 9 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  23 Citations (Scopus)

• Fabrication and surface functionalization of highly birefringent particles for optical torque wrench

  Ha, S., van Oene, MM., Janissen, R. & Dekker, NH., 2014, In: Biophysical Journal. 106, 2, p. 1-3 3 p.

  Research output: Contribution to journal › Article › Scientific › peer-review