Nynke Dekker

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Nynke Dekker is affiliated with the following schools: Uppsala University, Paris Sciences et Lettres University, Delft University of Technology

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Nynke Dekker

Physics

#8019

World Rank

#10123

Historical Rank

Biophysics

#381

World Rank

#393

Historical Rank

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Physics

Nynke Dekker's Degrees

PhD Physics Delft University of Technology

Why Is Nynke Dekker Influential?

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According to Wikipedia, Nynke Hester Dekker is a Dutch biophysicist who is Professor of Molecular Biophysics at the Kavli Institute of Nanoscience at Delft University of Technology. Dekker studies individual DNA and RNA molecules and how they interact with proteins in bacteria, viruses and eukaryotes. She described how virus proteins build errors into the virus RNA of viruses. In 2020, she was awarded the Spinoza Prize.

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Nynke Dekker's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

Salt dependence of ion transport and DNA translocation through solid-state nanopores. (2006) (713)
Direct force measurements on DNA in a solid-state nanopore (2006) (567)
Noise in solid-state nanopores (2008) (328)
Origin of the electrophoretic force on DNA in solid-state nanopores (2009) (307)
Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB (2005) (305)
Mesoscale conformational changes in the DNA-repair complex Rad50/Mre11/Nbs1 upon binding DNA (2005) (279)
Antitumour drugs impede DNA uncoiling by topoisomerase I (2007) (272)
Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments (2010) (255)
Single-molecule investigations of the stringent response machinery in living bacterial cells (2011) (251)
Stretching of macromolecules and proteins (2003) (232)
Single-molecule measurements of the persistence length of double-stranded RNA. (2005) (228)
Quantitative modeling and optimization of magnetic tweezers. (2009) (175)
Cellular Strategies for Regulating DNA Supercoiling: A Single-Molecule Perspective (2010) (150)
Distinguishing single- and double-stranded nucleic acid molecules using solid-state nanopores. (2009) (138)
Controlling nanopore size, shape and stability (2010) (138)
Optical tweezers for force measurements on DNA in nanopores (2006) (136)
Double-stranded RNA under force and torque: Similarities to and striking differences from double-stranded DNA (2014) (134)
The mechanism of type IA topoisomerases (2002) (133)
Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids (2011) (126)
Translocation of RecA-coated double-stranded DNA through solid-state nanopores. (2009) (125)
Nanobubbles in solid-state nanopores. (2006) (122)
Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I (2004) (119)
Low-frequency noise in solid-state nanopores (2009) (91)
Studying genomic processes at the single-molecule level: introducing the tools and applications (2012) (90)
Quantitative guidelines for force calibration through spectral analysis of magnetic tweezers data. (2010) (86)
An optimized software framework for real-time, high-throughput tracking of spherical beads. (2014) (86)
Torsional sensing of small-molecule binding using magnetic tweezers (2010) (85)
Control of shape and material composition of solid-state nanopores. (2009) (84)
Fast dynamics of supercoiled DNA revealed by single-molecule experiments (2007) (84)
Electromagnetic torque tweezers: a versatile approach for measurement of single-molecule twist and torque. (2012) (79)
Nanopore tomography of a laser focus. (2005) (79)
When a helicase is not a helicase: dsDNA tracking by the motor protein EcoR124I (2006) (74)
High Spatiotemporal-Resolution Magnetic Tweezers: Calibration and Applications for DNA Dynamics. (2015) (70)
Magnetic Tweezers for Single-Molecule Experiments (2009) (69)
Elongation-Competent Pauses Govern the Fidelity of a Viral RNA-Dependent RNA Polymerase. (2015) (68)
Global DNA Compaction in Stationary-Phase Bacteria Does Not Affect Transcription (2018) (63)
Excitable Particles in an Optical Torque Wrench (2011) (60)
Torque spectroscopy for the study of rotary motion in biological systems. (2015) (60)
Slow unloading leads to DNA-bound β2-sliding clamp accumulation in live Escherichia coli cells (2014) (56)
Signatures of Nucleotide Analog Incorporation by an RNA-Dependent RNA Polymerase Revealed Using High-Throughput Magnetic Tweezers (2017) (56)
Biological magnetometry: torque on superparamagnetic beads in magnetic fields. (2015) (55)
Direct force measurements on double-stranded RNA in solid-state nanopores. (2010) (54)
A force calibration standard for magnetic tweezers. (2014) (51)
Role of tension and twist in single-molecule DNA condensation. (2007) (50)
Torque-limited RecA polymerization on dsDNA (2005) (49)
Using neutral metastable argon atoms and contamination lithography to form nanostructures in silicon, silicon dioxide, and gold (1996) (45)
Invincible DNA tethers: covalent DNA anchoring for enhanced temporal and force stability in magnetic tweezers experiments (2014) (44)
Dynamics of initiation, termination and reinitiation of DNA translocation by the motor protein EcoR124I (2005) (44)
Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers (2017) (43)
Single-molecule magnetic tweezers studies of type IB topoisomerases. (2009) (40)
Strand separation establishes a sustained lock at the Tus-Ter replication fork barrier. (2015) (37)
Nucleosome assembly dynamics involve spontaneous fluctuations in the handedness of tetrasomes. (2015) (37)
Structural analysis of hyperperiodic DNA from Caenorhabditis elegans (2006) (37)
Distinguishable populations report on the interactions of single DNA molecules with solid-state nanopores. (2010) (36)
Untangling reaction pathways through modern approaches to high-throughput single-molecule force-spectroscopy experiments. (2015) (36)
Electron beam fabrication of a microfluidic device for studying submicron-scale bacteria (2013) (35)
Rapid manufacturing of low-noise membranes for nanopore sensors by trans-chip illumination lithography (2012) (35)
A method to track rotational motion for use in single-molecule biophysics. (2011) (34)
Backtracking behavior in viral RNA-dependent RNA polymerase provides the basis for a second initiation site (2015) (34)
Calibration of the optical torque wrench. (2012) (29)
Structural and torsional properties of the RAD51-dsDNA nucleoprotein filament (2013) (29)
Predicting Intraserotypic Recombination in Enterovirus 71 (2018) (28)
Thermophilic topoisomerase I on a single DNA molecule. (2003) (28)
An RNA toolbox for single-molecule force spectroscopy studies (2007) (27)
Chromatin fibers stabilize nucleosomes under torsional stress (2020) (27)
Single-molecule force spectroscopy on histone H4 tail-cross-linked chromatin reveals fiber folding (2017) (27)
Nanofabrication using neutral atomic beams (1997) (25)
The passage of homopolymeric RNA through small solid-state nanopores. (2011) (24)
Recent insights from in vitro single-molecule studies into nucleosome structure and dynamics (2016) (24)
Hysteresis in DNA compaction by Dps is described by an Ising model (2016) (23)
Electron beam fabrication of birefringent microcylinders. (2011) (23)
High-throughput, high-force probing of DNA-protein interactions with magnetic tweezers. (2016) (22)
Atomic force microscopy shows that vaccinia topoisomerase IB generates filaments on DNA in a cooperative fashion (2005) (22)
Multiple events on single molecules: unbiased estimation in single-molecule biophysics. (2006) (21)
Dynamics of phosphodiester synthesis by DNA ligase (2008) (21)
Single-molecule observations of topotecan-mediated TopIB activity at a unique DNA sequence (2008) (19)
Reinitiated viral RNA-dependent RNA polymerase resumes replication at a reduced rate (2008) (18)
Tracking enzymatic steps of DNA topoisomerases using single-molecule micromanipulation (2002) (18)
Discovery of Enterovirus A71-like nonstructural genomes in recent circulating viruses of the Enterovirus A species (2018) (14)
Joining of long double-stranded RNA molecules through controlled overhangs. (2004) (14)
Applying torque to the Escherichia coli flagellar motor using magnetic tweezers (2017) (14)
What is all this fuss about Tus? Comparison of recent findings from biophysical and biochemical experiments (2018) (14)
Metastable-atom-activated growth of an ultrathin carbonaceous resist for reactive ion etching of SiO2 and Si3N4 (1998) (13)
Magnetic Tweezers for the Measurement of Twist and Torque (2014) (13)
Tunable top-down fabrication and functional surface coating of single-crystal titanium dioxide nanostructures and nanoparticles. (2016) (12)
Quantifying the Precision of Single-Molecule Torque and Twist Measurements Using Allan Variance. (2018) (12)
Comparing the Assembly and Handedness Dynamics of (H3.3-H4)2 Tetrasomes to Canonical Tetrasomes (2015) (12)
Probing Chromatin Structure with Magnetic Tweezers. (2018) (12)
The progression of replication forks at natural replication barriers in live bacteria (2016) (11)
Single-Crystal Rutile TiO2 Nanocylinders are Highly Effective Transducers of Optical Force and Torque (2019) (11)
Inserting and manipulating DNA in a nanopore with optical tweezers. (2009) (10)
DNA replication origins retain mobile licensing proteins (2021) (10)
Low-dimensional resonant tunnelling and Coulomb blockade: a comparison of fabricated versus impurity confinement (1994) (9)
Modification of the histone tetramer at the H3-H3 interface impacts tetrasome conformations and dynamics. (2018) (9)
Essential validation methods for E. coli strains created by chromosome engineering (2015) (8)
Induced intra- and intermolecular template switching as a therapeutic mechanism against RNA viruses. (2021) (7)
Corrigendum: Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids (2015) (7)
High-throughput single-molecule experiments reveal heterogeneity, state switching, and three interconnected pause states in transcription. (2022) (6)
A Unifying Mechanistic Model of Bacterial Transcription with Three Interconnected Pause States and Non-Diffusive Backtrack Recovery (2020) (4)
Nanopores: The Passage of Homopolymeric RNA through Small Solid‐State Nanopores (Small 15/2011) (2011) (4)
End-joining long nucleic acid polymers (2008) (4)
Controlling the surface properties of nanostructures for studies of polymerases (2008) (4)
A unifying mechanistic model of bacterial transcription with three interconnected pause states and non-diffusive backtrack recovery (2019) (4)
Versatile Multilayer Metamaterial Nanoparticles with Tailored Optical Constants for Force and Torque Transduction (2020) (4)
de Broglie wave-front engineering (1998) (4)
DNA sequence is a major determinant of tetrasome dynamics (2019) (4)
Global correction of optical distortions in multicolor single-molecule microscopy using Zernike polynomial gradients (2021) (3)
Observation of the geometric amplitude factor in an optical system (1996) (3)
Using neutral atoms and standing light waves to form a calibration artifact for length metrology (1998) (3)
Induced copy-back RNA synthesis as a novel therapeutic mechanism against RNA viruses (2020) (3)
Observation of novel conductance structure in GaAs/GaxAl1-xAs resonant tunneling heterostructures (1993) (2)
Strand separation suffices to establish a long-lived, foolproof DNA–protein lock at the Tus–Ter replication fork barrier (2018) (2)
Probing the Response of Double-Stranded RNA to Force and Torque at the Single-Molecule Level (2013) (2)
Quantitative Analysis of Intracellular Fluorescent Foci in Live Bacteria. (2015) (2)
Accounting for RNA polymerase heterogeneity reveals state switching and two distinct long-lived backtrack states escaping through cleavage (2021) (2)
de-Broglie WaveFront Engineering (1998) (2)
Real-time observation of replicative helicase assembly onto single-stranded DNA (2016) (1)
Predicting Intra- and Intertypic Recombination in Enterovirus 71 (2018) (1)
Freely Orbiting Magnetic Tweezers: A New Twist on Single Molecule Force Spectroscopy (2011) (1)
Characterizing single-molecule dynamics of viral RNA-dependent RNA polymerases with multiplexed magnetic tweezers (2022) (1)
Towards In Vivo Tracking of the E. coli Replisome Utilizing Single-Molecule Fluorescence Microscopy (2011) (1)
Nucleosome Assembly Dy namics Involve Spontaneous Fluctuations in the Handedness of (2015) (1)
Electron-Beam Fabrication of Micron-Scale Birefringent Quartz Particles for Optical Torque Wrenches (2011) (1)
Signatures of Nucleotide A nalog Incorporation by an RNA-Dependent RNA Polymerase Revealed Using High-Throughput Magnetic Tweezers Graphical (2017) (0)
Resist-based neutral atom lithography (1997) (0)
A Magnetic Tweezers Study of a RNA-Dependant RNA Polymerase (2012) (0)
Plat Lipid Bilayer Influences Rhodopsin Activation Probed by FTIR and UV-Visible Spectroscopy (2013) (0)
Investigating DNA Replication in Escherichia Coli on the Single Cell Level Utilizing Microfluidics and Single-Molecule Fluorescence Microscopy (2013) (0)
Unravelling the Role of Linker Histone H1 and the H4-Tail in Chromatin (Un-)Folding (2016) (0)
Visualizing an RNA-dependent RNA Polymerase at Work: Polymerization And Strand-switching (2009) (0)
CAF-1 deposits newly synthesized histones during DNA replication using distinct mechanisms on the leading and lagging strands (2022) (0)
In Vivo Investigation of DNA Replication in Escherichia Coli using Single-Molecule Fluorescence Microscopy (2012) (0)
Improved Axial Super-Resolution of Single Emitters Through Rapid Tirf Angle Scanning (2022) (0)
Emerging Single Molecule Techniques II (0)
Fabrication and Surface Functionalization of Highly Birefringent Particles for Optical Torque Wrench (2014) (0)
Camptothecin binding to topoisomerase I-DNA complexes impedes DNA uncoiling and induces the accumulation of positive supercoils (2007) (0)
Local probe studies of single biomolecules: Type I restriction enzymes (2003) (0)
The RNA Molecule and its Processing by Molecular Motors (2013) (0)
A method for making a double-stranded polyribonucleotide sequence with terminal overhang, as well as a method of forming a double-stranded polynucleotidenconstruct and an application. (2004) (0)
RNA Structure, Function, and (Thermo-) Dynamics: A SAXS and Single-Molecule Perspective (2011) (0)
Chromatin fibers stabilize nucleosomes under torsional stress (2020) (0)
1 Real-time observation of replicative helicase assembly onto single-stranded DNA (2016) (0)
dsDNA and nanobubble studies using solid-state nanopores (2007) (0)
Supercoiling Double-Stranded RNA (2010) (0)
Towards DNA-AddAB Interactions In Magnetic Tweezers (2008) (0)
Magnetic Torque Tweezers and Their Application in Probing the Torsional Properties of DNA, RNA, and DNA Filaments (2011) (0)
Physics meets biology: The joining of two forces to further our understanding of cellular function. (2021) (0)
Supplementary Section to “ When a helicase is not a helicase : dsDNA tracking by the motor protein EcoR 124 I ” (2006) (0)
Computational Analysis of Electron Tunneling Pathways of Blue-Light Photoreceptors (2012) (0)
Single Molecule Tracking Inside Individual Living Bacterial Cells (2010) (0)
Zero-Mode Waveguides for Real-Time Observation of Single Nucleotide Incorporation (2009) (0)
High-Speed Magnetic Tweezers Studies of the E. coli Replisome (2018) (0)
Investigation of the Tus-ter Blocking Efficacy during the Chromosome Replication of Live Escherichia Coli Cells (2015) (0)
An Ising Model Describes Hysteresis in a Novel form of Cooperative Binding (2016) (0)
Small-Molecule Binding to DNA under Tension and Twist Studied by Magnetic Tweezers (2009) (0)
- 1-Supplementary information to “ Dynamics of initiation , termination and reinitiation of DNA translocation by the motor protein EcoR 124 I ” (2005) (0)
Highly birefringent TiO2 nanocylinders : characterization and application in the optical torque wrench (2016) (0)
Preparation and characterization of a silicon nanoparticle/DNA conjugate (2003) (0)
Probing the Structural Properties of RNA using Solid-State Nanopores (2009) (0)
Principles and best practices of optimizing a micromirror-based multicolor TIRF microscopy system (2023) (0)
FUEL CYCLE COST CALCULATIONS FOR A 120,000 SHP PWR FOR SHIP PROPULSION. (1972) (0)
A biochemical portrait of the nidovirus RNA polymerases and helicase (2007) (0)
Fabrication and Surface Functionalization of Highly Birefringent Rutile Particles for Trapping in an Optical Torque Wrench (2015) (0)
RNA-Dependent RNA Pausing or Taking a Long Coffee Break (2010) (0)
Measurements of DNA Twist Using the Freely-orbiting Magnetic Tweezers (2015) (0)
Essential validation methods for E. coli strains created by chromosome engineering (2015) (0)
Recent insights from in vitro single-molecule studies into nucleosome structure and dynamics (2016) (0)
Publisher's Note: Biological Magnetometry: Torque on Superparamagnetic Beads in Magnetic Fields [Phys. Rev. Lett. 114, 218301 (2015)]. (2018) (0)
Measuring In Vivo Protein Dynamics Throughout the Cell Cycle Using Microfluidics. (2017) (0)
Backtracking and Other Off-Path Pauses Control the Dynamic of Viral RNA Dependent RNA Polymerases (2013) (0)
Static and Dynamic Investigations of RecA-DNA Complex with a Solid-State Nanopore (2009) (0)
Chromosome Reorganization by the Highly Cooperative Dps Protein (2015) (0)
Nanopores as a Single-Molecule Probe for Protein-DNA Complexes (2009) (0)
Stretched Oriented DNA Arrays (SODA) as a Tool for Studying Protein-DNA Interactions (2016) (0)
Roadblocks on the E.Coli Genome: The Workings of a Molecular Mouse Trap at the Single-Molecule Level (2014) (0)
[Enzymes that relax supercoiled DNA]. (2003) (0)
Local probe studies of single biomolecules: Magnetic tweezer studies of topoisomerase (2002) (0)
Dissection of E.Coli DNA Replication in High Resolution with Temperature-Controlled Magnetic Tweezers (2016) (0)
Title Single-molecule force spectroscopy on histone H 4 tail-cross-linked chromatin reveals fiber folding (2019) (0)
13 Magnetic Tweezers for Single-Molecule Experiments (2009) (0)
Studying the Bacterial Flagellar Motor using an Optical Torque Wrench (2012) (0)
Optical Torque Wrench for Single Molecule Studies (2010) (0)
The Mechanical Properties of Double-Stranded RNA in Response to Force and Torque (2012) (0)
Stretched, Oriented DNA Arrays (SODA) for Fluorescence Based Single-Molecule Experiments in Complex Environment (2015) (0)
Introducing the Electromagnetic Torque Tweezers (2012) (0)
Optimizing single-molecule experimental approaches for the study of complex protein assemblies on DNA. (2023) (0)
Torque-limited RecA polymerization on dsDNA (2005) (0)
Corrigendum: Applying torque to the Escherichia coli flagellar motor using magnetic tweezers (2018) (0)
Characterization of Supercoiled Double-Stranded RNA, and Comparison to Double-Stranded DNA (2011) (0)
Investigation of the Bacterial Flagellar Motors through Magnetic Torque Wrench (2016) (0)
Magnetization Properties of Superparamagnetic Beads (2014) (0)
SV40 Helicase Unwinds DNA against Force (2014) (0)
Elongation-Competent Pa uses Govern the Fidelity of a Viral RNA-Dependent RNA Polymerase Graphical Abstract Highlights (2015) (0)
Zero Mode Waveguides: a Powerful Tool for Single Molecule Optical Studies (2010) (0)
Investigating Stator Dynamics of the Escherichia Coli Flagellar Motor (2013) (0)
Investigating the Dynamics of the β2 Sliding Clamp in Escherichia Coli at the Single-Cell Level Utilizing Single-Molecule Fluorescence Microscopy (2014) (0)
Investigating the Handedness Dynamics of Tetrasomes (2016) (0)
Local probe studies of single biomolecules: Translocation through alpha-hemolysin nanopores (2003) (0)
Nucleotide binding halts diffusion of the eukaryotic replicative helicase during activation (2022) (0)
Accurate High Throughput Bright Field Bead Tracking using Gpu Hardware (2014) (0)
Measuring Direct Forces on dsRNA in Solid State Nanopores (2010) (0)
Real-time observation of DNA translocation by the type I restriction modification enzyme Eco R 124 I (0)
Topoisomerase IB Activity Investigated By Single Molecule Magnetic Tweezers: Mechanisms of Cytotoxicity (2010) (0)
Single Molecule Studies of DNA-Binding Proteins: Development of New Covalent DNA Anchoring Techniques for the Study of Rupture Forces of Replication Blocks (2014) (0)
Protein-DNA Interactions Studies using Magnetic Tweezers (2010) (0)
Trapping of highly birefringent rutile nanocylinders in the optical torque wrench (2016) (0)
Salt Dependence Of RNA Translocations Through Solid State Nanopores (2009) (0)
Quantifying the Resolution of Single-Molecule Torque Measurements by Allan Variance (2014) (0)

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What Schools Are Affiliated With Nynke Dekker?

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