Publications

For more details (abstracts and images) click [here] or go to Google Scholar [link].

(051) “Adapting cryogenic correlative light and electron microscopy (cryo-CLEM) for food oxidation studies”, S.Yang, M. Takeuchi, R. Joosten, J.P.M. van Duynhoven*, H. Friedrich*, J. Hohlbein*, Food Structure, 40, 100365, 2024, [link], pre-print on chemRxiv, [link]

(050) Temporal analysis of relative distances (tardis) is a robust, parameter-free alternative to single-particle tracking, K.J.A. Martens, B. Turkowyd, J. Hohlbein, U. Endesfelder, Nature Methods, 2024, [link], preprint on bioRxiv [link]

(049) Response to “Liposome vesicle cannot be formed in non-aqueous phase”, S. Yang, M. Takeuchi, H. Friedrich, J.P.M. van Duynhoven, and J. Hohlbein, Food Chemistry, 439, 138087, 2024, [link]

(048) Open hardware in microscopy, J. Hohlbein and S. Faez, HardwareX, 15, e00473, 2023, [link]

(047) Cooperative action of separate interaction domains promotes high-affinity DNA binding of Arabidopsis thaliana ARF transcription factors, M. Fontana, M. Roosjen, I. Crespo García, W. van den Berg, M. Malfois, R. Boer, D. Weijers, and J. Hohlbein, Proceedings of the National Academy of Science of the United States of America, 120, e2219916120, 2023, [link], preprint on bioRxiv, [link]

(046) Enabling spectrally resolved single-molecule localization microscopy at high emitter densities. K.J.A. Martens, M. Gobes, E. Archontakis, N. Zijlstra, L. Albertazzi, and J. Hohlbein, Nano Letters, 22, 8618, 2022, [link], preprint on bioRxiv, [link]

(045) Unravelling mechanisms of protein and lipid oxidation in mayonnaise at multiple length scales, S. Yang, M. Takeuchi, H. Friedrich, J.P.M. van Duynhoven, and J. Hohlbein, Food Chemistry, 402, 134417, 2023, [link], preprint on chemRxiv, 2022, [link]

(044) Open microscopy in the life sciences: quo vadis? J. Hohlbein, B. Diederich, B. Marsikova, E.G. Reynaud, S. Holden, W. Jahr, R. Haase, and K. Prakash, Nature Methods, 19, 1020, 2022 , [link], preprint on arXiv, [link]

(043) Enabling single-molecule localization microscopy in turbid food emulsions, A. Jabermoradi, S. Yang, M. Gobes, J.P.M. van Duynhoven, and J. Hohlbein, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 380, 20200164, 2022,  [link], preprint on bioRxiv [link]

(042) Single-molecule localization microscopy as an emerging tool to probe multiscale food structures, J. Hohlbein, Food Structure, 30, 100236, 2021, [link]

(041) Integrating engineered point spread functions into the phasor-based single-molecule localization microscopy framework, K.J.A. Martens, A. Jabermoradi, S. Yang, and J. Hohlbein, Methods, 193, 2021, [link]

(040) Probing DNA – transcription factor interactions using single-molecule fluorescence detection in nanofluidic devices, M. Fontana, Š. Ivanovaite , S. Lindhoud, E. van der Wijk, K. Mathwig, W. van den Berg, D. Weijers, and J. Hohlbein, Advanced Biology, 2100953, 2021, [link]

(039) Quantitative spatiotemporal mapping of lipid and protein oxidation in mayonnaise, S. Yang, A.A. Verhoef, D.W.H Merkx, J.P.M. van Duynhoven, and J. Hohlbein, Antioxidants, 9, 1278, 2020, [link]

(038) Extracting transition rates in particle tracking using analytical diffusion distribution analysis, J. Vink, S.J.J. Brouns, and J. Hohlbein, Biophysical Journal, 119, 1970–83, 2020, [link]

(037) Architecture of DNA elements mediating ARF transcription factor binding and auxin-responsive gene expression in Arabidopsis, A. Freire-Rios, K. Tanaka, I. Crespo, E. van der Wijk, Y. Sizentsova, V. Levitsky, S. Lindhoud, M. Fontana, J. Hohlbein, D.R. Boer, V. Mironova, and D. Weijers, Proceedings of the National Academy of Science of the United States of America, 117 (39), 24557, 2020, [link]

(036) Design principles of a minimal auxin response system, H. Kato, S.K. Mutte, H. Suzuki, I. Crespo, S. Das, T. Radoeva, M. Fontana, Y. Yoshitake, E. Hainiwa, W. van den Berg, S. Lindhoud, L. Ishizaki, J. Hohlbein, J.W. Borst, D.R. Boer, R. Nishihama, T. Kohchi, D. Weijers, Nature Plants, 6, 472, 2020, [link]

(035) Using single-molecule FRET to probe the nucleotide-dependent conformational landscape of Pol β-DNA complexes, C. Fijen, M. Kronenberg, R. Kaup, M. Fontana, J. Towle-Weicksel, J. Sweasy, J. Hohlbein, Journal of Biological Chemistry, 295, 9012–20, 2020, [link]

(034) Spatiotemporal heterogeneity of κ-carrageenan gels investigated via single-particle-tracking fluorescence microscopy, K.J.A. Martens, J. van Duynhoven, and J. Hohlbein, Langmuir, 36, 5502, 2020, [link]

(033) Direct visualization of native CRISPR target search in live bacteria reveals Cascade DNA surveillance mechanism, J.N.A. Vink, K.J.A. Martens, M. Vlot, R.E. McKenzie, C. Almendros, B. Estrada Bonilla, D.J.W. Brocken, J. Hohlbein, S.J.J. Brouns, Molecular Cell, 77, 39-50.e10, 2020, [link]

(032) Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase. T.D. Craggs, M. Sustarsic, A. Plochowietz, M. Mosayebi, H. Kaju, A. Cuthbert, J. Hohlbein, L. Domicevica, P.C. Biggin, J.P. K. Doye, A.N. Kapanidis, Nucleic Acid Research, 47, 10788, 2019, [link]

(031) Visualisation of dCas9 target search in vivo using an open-microscopy framework. K.J.A. Martens, S. van Beljouw, S. van der Els, J.N.A. Vink, S. Baas, G.A. Vogelaar, S.J.J. Brouns, P. van Baarlen, M. Kleerebezem, J. Hohlbein, Nature Communications, 10, 3552, 2019, [link]

(030) Evaluating single-particle tracking by photo-activation localization microscopy (sptPALM) in Lactococcus lactis. S.P.B. van Beljouw, S. van der Els, K.J. A. Martens, M. Kleerebezem, P.A. Bron, J. Hohlbein, Physical Biology, 16, 035001, 2019, [link]

(029) High-throughput, non-equilibrium studies of single biomolecules using glass made nanofluidic devices. M. Fontana, C. Fijen, S. G. Lemay, K. Mathwig and J. Hohlbein, Lab on a Chip, 19, 79, 2019. [link]

(028) Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study. B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M.E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C.A. Hanke, A. Hartmann, J. Hendrix, L.L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B.g Hua, C.G. Hübner, E. Kallis, A.N. Kapanidis, J.Y. Kim, G. Krainer, D.C. Lamb, N.K. Lee, E.A. Lemke, B. Levesque, M. Levitus, J.J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N.C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. Manuel Vera, K.R. Weninger, B. Wünsch, I.S. Yanez-Orozco, J. Michaelis, C.A.M. Seidel, T.D. Craggs, T. Hugel, Nature Methods, 15, 669, 2018, [link], preprint on arXiv: [link]

(027) Phasor based single-molecule localization microscopy in 3D (pSMLM-3D): An algorithm for MHz localization rates using standard CPUs, K.J.A. Martens, A.N. Bader, S. Baas, B. Rieger, J. Hohlbein, The Journal of Chemical Physics, 148, 123311, 2018, [link]

(026) A Nanofluidic Mixing Device for High-Throughput Fluorescence Sensing of Single Molecules, K. Mathwig, C. Fijen, M. Fontana, S. G. Lemay and J. Hohlbein, Procedia Technology, 27, 141,  2017, [link]

(025) A single-molecule FRET sensor for monitoring DNA synthesis in real time, C. Fijen, A. Montón Silva, A. Hochkoeppler and J. Hohlbein, Physical Chemistry Chemical Physics, 19, 4222-4230, 2017, [link]

(024) Visualization of BRI1 and SERK3/BAK1 Nanoclusters in Arabidopsis Roots, S.J. Hutten, D.S. Hamers, M.A. an den Toorn, W. van Esse, A. Nolles, C.A. Bücherl, S.C. de Vries, J. Hohlbein, J.W. Borst, PLoS ONE 12(1): e0169905, 2017, [link]

(023) Probing the conformational landscape of DNA polymerases using diffusion-based single-molecule FRET, J. Hohlbein and A.N. Kapanidis, Methods in Enzymology: Single-molecule enzymology Part A & B, 581, 353-378, 2016, [link]

(022) Fluorescence resonance energy transfer and protein-induced fluorescence enhancement as synergetic multi-scale molecular rulers, E. Ploetz, E. Lerner, F. Husada, M. Roelfs, S. Chung, J. Hohlbein, S. Weiss, T. Cordes, Scientific Reports,6, 33257 , 2016, [link]

(021) A Quantitative Theoretical Framework For PIFE-FRET, E. Lerner, E. Ploetz, J. Hohlbein, T. Cordes, S. Weiss, The Journal of Physical Chemistry B,120, 6401–6410, 2016, [link]

(020) Single Molecule 3D Orientation in Time and Space: A 6D Dynamic Study on Fluorescently Labeled Lipid Membranes, R. Börner, N. Ehrlich, J. Hohlbein, C.G. Hübner, Journal of Fluorescence, 26, 963-975,  2016 [link]

(019) Complex coacervate core micelles with spectroscopic labels for diffusometric probing of biopolymer networks, N. Bourouina, D. de Kort, F. Hoeben, H. Janssen, H. Van As, J. Hohlbein, J. van Duynhoven, J.M. Kleijn, Langmuir, 31, 12635-12643, 2015, [link]

(018) New technologies for DNA analysis – a review of the READNA Project, S. McGinn, D. Bauer, T. Brefort, L. Dong, A. El-Sagheer, A. Elsharawy, G. Evans, E. Falk-Sörqvist, M. Forster, S. Fredriksson, P. Freeman, C. Freitag, J. Fritzsche, S. Gibson, M. Gullberg, M. Gut, S. Heath, I. Heath-Brun, A.J. Heron, J. Hohlbein, R. Ke, O. Lancaster, L. Le Reste, G. Maglia, R. Marie, F. Mauger, F. Mertes, M. Mignardi, L. Moens, J. Oostmeijer, R. Out, J. Nyvold Pedersen, F. Persson, V. Picaud, D. Rotem, N. Schracke, J. Sengenes, P.F. Stähler, B. Stade, D. Stoddart, X. Teng, C.D. Veal, N. Zahra, H. Bayley, M. Beier, T. Brown, C. Dekker, B. Ekström, H. Flyvbjerg, A. Franke, S. Guenther, A.N. Kapanidis, J. Kaye, A. Kristensen, H. Lehrach, J. Mangion, S. Sauer, E. Schyns, J. Tost, J.M.L.M. van Helvoort, P.J. van der Zaag, J. O. Tegenfeldt, A.J. Brookes, K.Mir, M. Nilsson, S. Willcocks, I.G. Gut, New Biotechnology, 33, 310-330, 2016, [link]

(017) Camera-based single-molecule FRET detection with improved time resolution, S. Farooq and J. Hohlbein, Physical Chemistry Chemical Physics, 17, 27862, 2015, [link], open access

(016) Real-time single-molecule studies of the motions of DNA polymerase fingers illuminate DNA synthesis mechanisms, G.W. Evans, J. Hohlbein, T. Craggs, L. Aigrain and A.N. Kapanidis, Nucleic Acids Research, 43, 5998-6008, 2015, [link], open access

(015) Studying DNA-protein interactions with single-molecule Förster resonance energy transfer, S. Farooq, C. Fijen, J. Hohlbein, Protoplasma, SPECIAL ISSUE: NEW/EMERGING TECHNIQUES IN BIOLOGICAL MICROSCOPY, 251, 317-332, 2014 [link]

(014) Alternating-laser excitation: single-molecule FRET and beyond, J. Hohlbein, T.D. Craggs, T. Cordes, Chemical Society Reviews, 43, 1156-1171, 2014, [link]

(013)  A Novel Parallel Nanomixer for High-Throughput Single-Molecule Fluorescence Detection, K. Mathwig, S. Schlautmann, S. G. Lemay, J. Hohlbein,, Proceedings of the 17th International Conference on Miniaturized Systems for Chemistry and Life Science, Freiburg, Germany, Oct. 27 – 31 (2013) 1385,  [link]

(012) Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion, J. Hohlbein, L. Aigrain, T.D. Craggs, O. Bermek, O. Potapova, P. Shoolizadeh, N.D.F. Grindley, C.M. Joyce, A.N. Kapanidis, Nature Communications, 4,  2131, 2013, [link]

(011) Characterization of dark quencher chromophores as non-fluorescent acceptors for single-molecule FRET, L. Le Reste, J. Hohlbein, K. Gryte, A.N. Kapanidis, Biophysical Journal, 102, 2658-2668, 2012, [link]

(010) Identifying molecular dynamics in single-molecule FRET experiments with Burst Variance Analysis, J.P. Torella, S.J. Holden, Y. Santoso, J. Hohlbein, A.N. Kapanidis, Biophysical Journal, 100, 1568-1577, 2011, [link]

(009) Defining the limits of single-molecule FRET resolution in TIRF microscopy, S.J. Holden, S. Uphoff, J. Hohlbein, D. Yadin, L. Le Reste, O.J. Britton, A.N. Kapanidis, Biophysical Journal, 99, Issue 9, 2011, 3102-3111 [link]

(008) Surfing on a new wave of single-molecule methods, J. Hohlbein, K. Gryte, M. Heilemann, A.N. Kapanidis, Physical Biology, 7, 031001, 2010, [link]

(007) Conformational transitions in DNA polymerase I revealed by single-molecule FRET, Y. Santoso, C.M. Joyce, O. Potapova, L. Le Reste, J. Hohlbein, J.P. Torella, N.D.F. Grindley, and A.N. Kapanidis, Proceedings of the National Academy of Sciences of the USA, 107, 715, 2010, [link]

(006) Single-Molecule FRET: Methods and Biological Applications in Handbook of Single-molecule Biophysics, L.C. Hwang, J. Hohlbein, S.J. Holden, and A.N. Kapanidis. Springer-Verlag New York Inc., edit. P. Hinterdorfer and A. Van Oijen, 2009

(005) Three-dimensional orientation determination of the emission dipoles of single molecules: The shot noise limit, J. Hohlbein, and C.G. Huebner, Journal of Chemical Physics, 129, 094703, 2008, [link]

(004) Confined diffusion in ordered nanoporous alumina membranes, J. Hohlbein, M. Steinhart, C. Schiene-Fischer, A. Benda, M. Hof and C.G. Hübner, Small, 3, 380, 2007, [link]

(003) A simple scheme for rapid three-dimensional orientation determination of the emission dipole of single molecules, J. Hohlbein and C.G. Hübner, Applied Physics Letters, 86, 121104, 2005, [link]

(002) Recurrence and photon statistics in fluorescence fluctuation spectroscopy, G. Zumofen, J. Hohlbein, and C.G. Hübner, Physical Review Letters, 93, 260601, 2004, [link]

(001) In-situ optical characterisation of porous alumina, J. Hohlbein, U. Rehn, and R. B. Wehrspohn, Physica Status Solidi (a), 204, 803, 2004, [link]