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Filius, M. (author), van Wee, R.G. (author), de Lannoy, C.V. (author), Westerlaken, I. (author), Li, Zeshi (author), Kim, S.H. (author), de Agrela Pinto, C. (author), Wu, Yunfei (author), Boons, Geert-Jan (author), Pabst, Martin (author), de Ridder, Dick (author), Joo, C. (author)Proteins are the primary functional actors of the cell. While proteoform diversity is known to be highly biologically relevant, current protein analysis methods are of limited use for distinguishing proteoforms. Mass spectrometric methods, in particular, often provide only ambiguous information on post-translational modification sites, and...journal article 2024
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Gillies, Natasha (author), Martín López, Lucía Martina (author), den Ouden, O.F.C. (author), Assink, Jelle D. (author), Basille, Mathieu (author), Clay, Thomas A. (author), Clusella-Trullas, Susana (author), Joo, Rocío (author), Weimerskirch, Henri (author)The ways in which seabirds navigate over very large spatial scales remain poorly understood. While olfactory and visual information can provide guidance over short distances, their range is often limited to 100s km, far below the navigational capacity of wide-ranging animals such as albatrosses. Infrasound is a form of low-frequency sound...journal article 2023
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Filius, M. (author), van Wee, R.G. (author), Joo, C. (author)Fluorescence resonance energy transfer (FRET) is a photophysical phenomenon that has been repurposed as a biophysical tool to measure nanometer distances. With FRET by DNA eXchange, or FRET X, many points of interest (POIs) in a single object can be probed, overcoming a major limitation of conventional single-molecule FRET. In FRET X, short...book chapter 2023
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Shin, D. (author), Kim, Hakseong (author), Kim, S.H. (author), Cheong, Hyeonsik (author), Steeneken, P.G. (author), Joo, C. (author), Lee, Sang Wook (author)The inherent properties of 2D materials—light mass, high out-of-plane flexibility, and large surface area—promise great potential for precise and accurate nanomechanical mass sensing, but their application is often hampered by surface contamination. Here we demonstrate a tri-layer graphene nanomechanical resonant mass sensor with sub-attogram...journal article 2023
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- Kim, S.H. (author), Severins, I.W.H. (author), Brandenburg, Frank (author), Bastiaanssen, C.K.J.M.L. (author), Joo, C. (author) journal article 2023
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Severins, I.W.H. (author), Joo, C. (author), van Noort, John (author)Next-generation sequencing techniques have led to a new quantitative dimension in the biological sciences. In particular, integrating sequencing techniques with biophysical tools allows sequence-dependent mechanistic studies. Using the millions of DNA clusters that are generated during sequencing to perform high-throughput binding affinity...review 2022
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Seo, Miri (author), Yang, Eunseo (author), Shin, D. (author), Je, Yugyeong (author), Joo, C. (author), Lee, Kookjin (author), Lee, Sang Wook (author)Nanomechanical resonator devices are widely used as ultrasensitive mass detectors for fundamental studies and practical applications. The resonance frequency of the resonators shifts when a mass is loaded, which is used to estimate the mass. However, the shift signal is often blurred by the thermal noise, which interferes with accurate mass...journal article 2022
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Joo, C. (author), Meller, Amit (author)In recent years, single molecule technology has experienced a rapid growth, with exciting developments in fundamental research and real-world applications. Detecting and studying biological phenomena on the<br/>single molecule level requires a unique synergy between researchers working on instrumentation, physics, and the life sciences. In the...journal article 2021
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Lerner, Eitan (author), Barth, A. (author), Hendrix, Jelle (author), Ambrose, Benjamin (author), Birkedal, Victoria (author), Blanchard, Scott C. (author), Börner, Richard (author), Joo, C. (author), Lee, Tae Hee (author)Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever- increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs...review 2021
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de Lannoy, C.V. (author), Filius, M. (author), Kim, S.H. (author), Joo, C. (author), de Ridder, Dick (author)Förster resonance energy transfer (FRET) is a useful phenomenon in biomolecular investigations, as it can be leveraged for nanoscale measurements. The optical signals produced by such experiments can be analyzed by fitting a statistical model. Several software tools exist to fit such models in an unsupervised manner but lack the flexibility...journal article 2021
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de Lannoy, C.V. (author), Filius, M. (author), van Wee, R.G. (author), Joo, C. (author), de Ridder, Dick (author)Single-molecule protein identification is an unrealized concept with potentially ground-breaking applications in biological research. We propose a method called FRET X (Förster Resonance Energy Transfer via DNA eXchange) fingerprinting, in which the FRET efficiency is read out between exchangeable dyes on protein-bound DNA docking strands and...journal article 2021
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Patrick, Samantha C. (author), Assink, Jelle D. (author), Basille, Mathieu (author), Clusella-Trullas, Susana (author), Clay, Thomas A. (author), den Ouden, O.F.C. (author), Joo, Rocío (author), Evers, L.G. (author), Smets, P.S.M. (author)Seabirds are amongst the most mobile of all animal species and spend large amounts of their lives at sea. They cross vast areas of ocean that appear superficially featureless, and our understanding of the mechanisms that they use for navigation remains incomplete, especially in terms of available cues. In particular, several large-scale...journal article 2021
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Cnossen, J.P. (author), Cui, Tao Ju (author), Joo, C. (author), Smith, C.S. (author)Localization microscopy offers resolutions down to a single nanometer but currently requires additional dedicated hardware or fiducial markers to reduce resolution loss from the drift of the sample. Drift estimation without fiducial markers is typically implemented using redundant cross correlation (RCC). We show that RCC has sub-optimal...journal article 2021
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Bohländer, P.R. (author), Filius, M. (author), van Kooten, Xander F. (author), Pomorski, A.K. (author), Schmid, S. (author), Dekker, C. (author), Eelkema, R. (author), Kim, S.H. (author), Joo, C. (author)Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside...review 2021
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Loeff, L. (author), Kerssemakers, J.W.J. (author), Joo, C. (author), Dekker, C. (author)Single-molecule techniques allow the visualization of the molecular dynamics of nucleic acids and proteins with high spatiotemporal resolution. Valuable kinetic information of biomolecules can be obtained when the discrete states within single-molecule time trajectories are determined. Here, we present a fast, automated, and bias-free step...journal article 2021
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Filius, M. (author), Kim, S.H. (author), Severins, I.W.H. (author), Joo, C. (author)Single-molecule FRET is a versatile tool to study nucleic acids and proteins at the nanometer scale. However, currently, only a couple of FRET pairs can be reliably measured on a single object, which makes it difficult to apply single-molecule FRET for structural analysis of biomolecules. Here, we present an approach that allows for the...journal article 2021
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van Wee, R.G. (author), Filius, M. (author), Joo, C. (author)Single-molecule localization microscopy (SMLM) is a potent tool to examine biological systems with unprecedented resolution, enabling the investigation of increasingly smaller structures. At the forefront of these developments is DNA-based point accumulation for imaging in nanoscale topography (DNA-PAINT), which exploits the stochastic and...review 2021
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Bastiaanssen, C.K.J.M.L. (author), Joo, C. (author)Transposable elements have both detrimental and beneficial effects on their host genome. Tetrahymena is a unicellular eukaryote that deals with transposable elements in a unique way. It has a separate somatic and germline genome in two nuclei in a single cell. During sexual reproduction, a small RNA directed system compares the germline and...review 2021
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Balci, Hamza (author), Globyte, V. (author), Joo, C. (author)Clustered regularly interspaced palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins, particularly Cas9, have provided unprecedented control on targeting and editing specific DNA sequences. If the target sequences are prone to folding into noncanonical secondary structures, such as G-quadruplex (GQ), the conformational states and...journal article 2021
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Clay, Thomas A. (author), Joo, Rocío (author), Weimerskirch, Henri (author), Phillips, Richard A. (author), den Ouden, O.F.C. (author), Basille, Mathieu (author), Clusella-Trullas, Susana (author), Assink, Jelle D. (author), Patrick, Samantha C. (author)In a highly dynamic airspace, flying animals are predicted to adjust foraging behaviour to variable wind conditions to minimize movement costs. Sexual size dimorphism is widespread in wild animal populations, and for large soaring birds which rely on favourable winds for energy-efficient flight, differences in morphology, wing loading and...journal article 2020