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Research Output

2020

A Mechanically Tunable Quantum Dot in a Graphene Break Junction

Caneva, S., Hermans, M., Lee, M., García-Fuente, A., Watanabe, K., Taniguchi, T., Dekker, C., Ferrer, J., Van Der Zant, H. S. J. & Gehring, P., 2020, In : Nano Letters. 20, 7, p. 4924-4931

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2 Downloads (Pure)

Comparing Current Noise in Biological and Solid-State Nanopores

Fragasso, A., Schmid, S. & Dekker, C., 2020, In : ACS Nano. 14, 2, p. 1338-1349

Research output: Contribution to journalReview articleScientificpeer-review

Open Access
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5 Citations (Scopus)
28 Downloads (Pure)

Direct observation of independently moving replisomes in Escherichia coli

Japaridze, A., Gogou, C., Kerssemakers, J. W. J., Nguyen, H. M. & Dekker, C., 2020, In : Nature Communications. 11, 1, 10 p., 3109.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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3 Downloads (Pure)

DNA-loop extruding condensin complexes can traverse one another

Kim, E., Kerssemakers, J., Shaltiel, I. A., Haering, C. H. & Dekker, C., 2020, In : Nature. 579, 7799, p. 438-442 5 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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7 Citations (Scopus)
1 Downloads (Pure)

Interplay between Confinement and Drag Forces Determine the Fate of Amyloid Fibrils

Smith, K. B., Wehrli, M., Japaridze, A., Assenza, S., Dekker, C. & Mezzenga, R., 2020, In : Physical Review Letters. 124, 11, 6 p., 118102.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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21 Downloads (Pure)

pH-Controlled Coacervate-Membrane Interactions within Liposomes

Last, M. G. F., Deshpande, S. & Dekker, C., 2020, In : ACS Nano. 14, 4, p. 4487-4498

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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3 Citations (Scopus)
9 Downloads (Pure)
2019

1/f noise in solid-state nanopores is governed by access and surface regions

Fragasso, A., Pud, S. & Dekker, C., 2019, In : Nanotechnology. 30, 39, 395202.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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5 Citations (Scopus)
1 Downloads (Pure)

A microfluidic platform for the characterisation of membrane active antimicrobials

Al Nahas, K., Cama, J., Schaich, M., Hammond, K., Deshpande, S., Dekker, C., Ryadnov, M. G. & Keyser, U. F., 2019, In : Lab on a Chip. 19, 5, p. 837-844 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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10 Citations (Scopus)
73 Downloads (Pure)

An Integrated Microfluidic Platform for Quantifying Drug Permeation across Biomimetic Vesicle Membranes

Schaich, M., Cama, J., Al Nahas, K., Sobota, D., Sleath, H., Jahnke, K., Deshpande, S., Dekker, C. & Keyser, U. F., 2019, In : Molecular Pharmaceutics. 16, 6, p. 2494-2501

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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9 Citations (Scopus)
4 Downloads (Pure)

Bacteria-in-paper, a versatile platform to study bacterial ecology

Hol, F. J. H., Whitesides, G. M. & Dekker, C., 2019, In : Ecology Letters. 22, 8, p. 1316-1323 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2 Citations (Scopus)
38 Downloads (Pure)

Cell Boundary Confinement Sets the Size and Position of the E. coli Chromosome

Wu, F., Swain, P., Kuijpers, L., Zheng, X., Felter, K., Guurink, M., Solari, J., Jun, S., Dekker, C. & More Authors, 2019, In : Current Biology. 29, 13, p. 2131-2144.e4

Research output: Contribution to journalArticleScientificpeer-review

10 Citations (Scopus)

Direct imaging of the circular chromosome in a live bacterium

Wu, F., Japaridze, A., Zheng, X., Wiktor, J., Kerssemakers, J. W. J. & Dekker, C., 2019, In : Nature Communications. 10, 1, 9 p., 2194.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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10 Citations (Scopus)
48 Downloads (Pure)

Distinct Roles for Condensin's Two ATPase Sites in Chromosome Condensation

Elbatsh, A. M. O., Kim, E., Eeftens, J. M., Raaijmakers, J. A., van der Weide, R. H., García-Nieto, A., Bravo, S., Ganji, M., Dekker, C. & More Authors, 2019, In : Molecular Cell. 76, 5, p. 724-737.e5

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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3 Citations (Scopus)
17 Downloads (Pure)

Electro-Mechanical Conductance Modulation of a Nanopore Using a Removable Gate

Zhao, S., Restrepo-Pérez, L., Soskine, M., Maglia, G., Joo, C., Dekker, C. & Aksimentiev, A., 2019, In : ACS Nano. 13, 2, p. 2398-2409

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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7 Citations (Scopus)
19 Downloads (Pure)

Intercalating Electron Dyes for TEM Visualization of DNA at the Single-Molecule Level

Kabiri, Y., Angelin, A., Ahmed, I., Mutlu, H., Bauer, J., Niemeyer, C. M., Zandbergen, H. & Dekker, C., 2019, In : ChemBioChem. 20, 6, p. 822-830

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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1 Citation (Scopus)
102 Downloads (Pure)

Label-Free Detection of Post-translational Modifications with a Nanopore

Restrepo-Pérez, L., Wong, C. H., Maglia, G., Dekker, C. & Joo, C., 2019, In : Nano Letters. 19, 11, p. 7957-7964 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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4 Citations (Scopus)
28 Downloads (Pure)

Membrane Tension–Mediated Growth of Liposomes

Deshpande, S., Wunnava, S., Hueting, D. & Dekker, C., 2019, In : Small. 15, 38, 10 p., 1902898.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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6 Citations (Scopus)
1 Downloads (Pure)

Movement dynamics of divisome proteins and PBP2x: FtsW in cells of Streptococcus pneumoniae

Perez, A. J., Cesbron, Y., Shaw, S. L., Villicana, J. B., Tsui, H. C. T., Boersma, M. J., Ye, Z. A., Tovpeko, Y., Dekker, C. & More Authors, 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 8, p. 3211-3220 10 p.

Research output: Contribution to journalArticleScientificpeer-review

14 Citations (Scopus)

Nano-Optical Tweezing of Single Proteins in Plasmonic Nanopores

Verschueren, D., Shi, X. & Dekker, C., 2019, In : SMALL METHODS. 3, 5, 9 p., 1800465.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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13 Citations (Scopus)
4 Downloads (Pure)

Resolving Chemical Modifications to a Single Amino Acid within a Peptide Using a Biological Nanopore

Restrepo-Pérez, L., Huang, G., Bohländer, P. R., Worp, N., Eelkema, R., Maglia, G., Joo, C. & Dekker, C., 2019, In : ACS Nano. 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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8 Citations (Scopus)
27 Downloads (Pure)

Shape and Size Control of Artificial Cells for Bottom-Up Biology

Fanalista, F., Birnie, A., Maan, R., Burla, F., Charles, K., Pawlik, G., Deshpande, S., Koenderink, G. H., Dogterom, M. & Dekker, C., 2019, In : ACS Nano. 13, 5, p. 5439-5450

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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16 Citations (Scopus)
59 Downloads (Pure)

Spatiotemporal control of coacervate formation within liposomes

Deshpande, S., Brandenburg, F., Lau, A., Last, M. G. F., Spoelstra, W. K., Reese, L., Wunnava, S., Dogterom, M. & Dekker, C., 2019, In : Nature Communications. 10, 1, 11 p., 1800.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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21 Citations (Scopus)
83 Downloads (Pure)

Visualization of unstained DNA nanostructures with advanced in-focus phase contrast TEM techniques

Kabiri, Y., Ravelli, R. B. G., Lehnert, T., Qi, H., Katan, A. J., Roest, N., Kaiser, U., Dekker, C., Peters, P. J. & Zandbergen, H., 2019, In : Scientific Reports. 9, 1, 7218.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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3 Citations (Scopus)
64 Downloads (Pure)
2018

Active delivery of single DNA molecules into a plasmonic nanopore for label-free optical sensing

Shi, X., Verschueren, D. V. & Dekker, C., 2018, In : Nano Letters. 18, 12, p. 8003-8010

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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16 Citations (Scopus)
47 Downloads (Pure)

A nanopore-based system for trapping, controlled displacement, and sequencing of (bio)macromolecules

Dekker, C. & Aksimentiev, A., 2018, Priority date 7 Sep 2016, Priority No. US 2018/0088104

Research output: Patent

Detection of CRISPR-dCas9 on DNA with Solid-State Nanopores

Yang, W., Restrepo-Pérez, L., Bengtson, M., Heerema, S. J., Birnie, A., Van Der Torre, J. & Dekker, C., 2018, In : Nano Letters. 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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15 Citations (Scopus)
32 Downloads (Pure)

Direct observation of end resection by RecBCD during double-stranded DNA break repair in vivo

Wiktor, J., Van Der Does, M., Büller, L., Sherratt, D. J. & Dekker, C., 2018, In : Nucleic Acids Research. 46, 4, p. 1821-1833 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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10 Citations (Scopus)
14 Downloads (Pure)

Dividing the Archaeal Way: The Ancient Cdv Cell-Division Machinery

Caspi, Y. & Dekker, C., 2018, In : Frontiers in Microbiology. 9, 25 p., 174.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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11 Citations (Scopus)
59 Downloads (Pure)

DNA origami scaffold for studying intrinsically disordered proteins of the nuclear pore complex

Ketterer, P., Ananth, A. N., Laman Trip, D. S., Mishra, A., Bertosin, E., Ganji, M., Van Der Torre, J., Onck, P., Dietz, H. & Dekker, C., 2 Mar 2018, In : Nature Communications. 9, 1, 902.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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30 Citations (Scopus)
25 Downloads (Pure)

DNA sequence encodes the position of DNA supercoils

Kim, S. H., Ganji, M., Kim, E., van der Torre, J., Abbondanzieri, E. & Dekker, C., 2018, In : eLife. 7, 23 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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4 Citations (Scopus)
33 Downloads (Pure)

Double Barrel Nanopores as a New Tool for Controlling Single-Molecule Transport

Cadinu, P., Campolo, G., Pud, S., Yang, W., Edel, J. B., Dekker, C. & Ivanov, A. P., 2018, In : Nano Letters. 18, 4, p. 2738-2745 8 p.

Research output: Contribution to journalArticleScientificpeer-review

19 Citations (Scopus)

FtsZ-Induced Shape Transformation of Coacervates

Fanalista, F., Deshpande, S., Lau, A., Pawlik, G. & Dekker, C., 2018, In : ADVANCED BIOSYSTEMS. 2, 9, 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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10 Citations (Scopus)
34 Downloads (Pure)

High-Speed Atomic Force Microscopy of SMC Proteins

Ryu, J-K., Katan, A., Minamino, M., Bouchoux, C., Bisht, S., Eeftens, J., Hearing, C., Uhlmann, F. & Dekker, C., 2018, In : Biophysical Journal. 114, 3, p. 564A-564A

Research output: Contribution to journalMeeting AbstractScientific

How we made the carbon nanotube transistor

Dekker, C., 2018, In : Nature Electronics. 1, 9, 3 p.

Research output: Contribution to journalComment/Letter to the editorScientificpeer-review

Open Access
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5 Citations (Scopus)

Label-Free Optical Detection of DNA Translocations through Plasmonic Nanopores

Verschueren, D. V., Pud, S., Shi, X., De Angelis, L., Kuipers, L. & Dekker, C., 2018, In : ACS Nano.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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26 Citations (Scopus)
29 Downloads (Pure)

Lithography-based fabrication of nanopore arrays in freestanding SiN and graphene membranes

Verschueren, D. V., Yang, W. & Dekker, C., 2018, In : Nanotechnology. 29, 14, 145302.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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24 Citations (Scopus)
21 Downloads (Pure)

Mechanical Division of Cell-Sized Liposomes

Deshpande, S., Spoelstra, W. K., Van Doorn, M., Kerssemakers, J. & Dekker, C., 2018, In : ACS Nano. 12, 3, p. 2560-2568 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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29 Citations (Scopus)
40 Downloads (Pure)

Mechanically controlled quantum interference in graphene break junctions

Caneva, S., Gehring, P., García-Suárez, V. M., García-Fuente, A., Stefani, D., Olavarria-Contreras, I. J., Ferrer, J., Dekker, C. & van der Zant, H. S. J., 2018, In : Nature Nanotechnology. p. 1126-1131

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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20 Citations (Scopus)
28 Downloads (Pure)

On-chip microfluidic production of cell-sized liposomes

Deshpande, S. & Dekker, C., 2018, In : Nature Protocols. 13, 5, p. 856-874 19 p.

Research output: Contribution to journalArticleScientificpeer-review

34 Citations (Scopus)

Paving the way to single-molecule protein sequencing

Restrepo-Pérez, L., Joo, C. & Dekker, C., 2018, In : Nature Nanotechnology. 13, 9, p. 786-796

Research output: Contribution to journalReview articleScientificpeer-review

Open Access
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66 Citations (Scopus)
297 Downloads (Pure)

Probing DNA Translocations with Inplane Current Signals in a Graphene Nanoribbon with a Nanopore

Heerema, S., Vicarelli, L., Pud, S., Schouten, R., Zandbergen, H. & Dekker, C., 2018, In : ACS Nano (online). 12, 3, p. 2623-2633

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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35 Citations (Scopus)
24 Downloads (Pure)

Real-time imaging of DNA loop extrusion by condensin

Ganji, M., Shaltiel, I. A., Bisht, S., Kim, E., Kalichava, A., Haering, C. H. & Dekker, C., 2018, In : Science. 360, 6384, p. 102-105 4 p.

Research output: Contribution to journalArticleScientificpeer-review

170 Citations (Scopus)

Reversible Immobilization of Proteins in Sensors and Solid-State Nanopores

Ananth, A., Genua, M., Aissaoui, N., Díaz, L., Eisele, N. B., Frey, S., Dekker, C., Richter, R. P. & Görlich, D., 3 May 2018, In : Small. 14, 18, 1703357.

Research output: Contribution to journalArticleScientificpeer-review

14 Citations (Scopus)

Spatial structure of disordered proteins dictates conductance and selectivity in nuclear pore complex mimics

Ananth, A. N., Mishra, A., Frey, S., Dwarkasing, A., Versloot, R., van der Giessen, E., Görlich, D., Onck, P. & Dekker, C., 2018, In : eLife. 7, e31510.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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7 Citations (Scopus)
11 Downloads (Pure)

Tailoring the appearance: what will synthetic cells look like?

Spoelstra, W. K., Deshpande, S. & Dekker, C., 2018, In : Current Opinion in Biotechnology. 51, p. 47-56 10 p.

Research output: Contribution to journalReview articleScientificpeer-review

Open Access
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24 Citations (Scopus)
20 Downloads (Pure)
2017

Annealing helicase HARP closes RPA-stabilized DNA bubbles non-processively

Burnham, D. R., Nijholt, B., De Vlaminck, I., Quan, J., Yusufzai, T. & Dekker, C., 2017, In : Nucleic Acids Research. 45, 8, p. 4687-4695 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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1 Citation (Scopus)
19 Downloads (Pure)

Catching DNA with hoops-biophysical approaches to clarify the mechanism of SMC proteins

Eeftens, J. & Dekker, C., 7 Dec 2017, In : Nature Structural and Molecular Biology. 24, 12, p. 1012-1020 9 p.

Research output: Contribution to journalReview articleScientificpeer-review

Open Access
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4 Citations (Scopus)
23 Downloads (Pure)

Distortion of DNA Origami on Graphene Imaged with Advanced TEM Techniques

Kabiri, Y., Ananth, A. N., van der Torre, J., Katan, A., Hong, J. Y., Malladi, S., Kong, J., Zandbergen, H. & Dekker, C., 18 Aug 2017, In : Small. 13, 31, p. 1-8 8 p., 1700876.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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10 Citations (Scopus)
22 Downloads (Pure)

DNA Sequence can Pin the Position of DNA Supercoils

Kim, S. H., Ganji, M., van der Torre, J., Abbondanzieri, E. & Dekker, C., 2017, In : Biophysical Journal. 112, 3, p. 214A-214A

Research output: Contribution to journalMeeting AbstractScientific

Human centromeric CENP-A chromatin is a homotypic, octameric nucleosome at all cell cycle points

Nechemia-Arbely, Y., Fachinetti, D., Miga, K. H., Sekulic, N., Soni, G. V., Kim, D. H., Wong, A. K., Lee, A. Y., Nguyen, K., Dekker, C., Ren, B., Black, B. E. & Cleveland, D. W., 6 Mar 2017, In : The Journal of Cell Biology. 216, 3, p. 607-621 15 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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22 Citations (Scopus)
17 Downloads (Pure)