Publications may also be found on Google Scholar.

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Effective in vivo binding energy landscape illustrates kinetic stability of RBPJ-DNA binding
D. Huynh, P. Hoffmeister, T. Friedrich, K. Zhang, M. Bartkuhn, F. Ferrante, B.D. Giaimo, R. Kovall, T. Borggrefe, F. Oswald, and J.C.M. Gebhardt
bioRxiv (2024), https://doi.org/10.1101/2023.12.19.572376

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Increasingly efficient chromatin binding of cohesin and CTCF supports chromatin architecture formation during zebrafish embryogenesis
J. Coßmann, P.I. Kos, V. Varamogianni-Mamatsi, D. Assenheimer, T. Bischof, T. Kuhn, T. Vomhof, A. Papantonis, L. Giorgetti, and J.C.M. Gebhardt
bioRxiv (2023), https://doi.org/10.1101/2023.12.08.570809

A multimorphic mutation in IRF4 causes human autosomal dominant combined immunodeficiency
IRF4 International Consortium, O. Fornes, A. Jia, H.S. Kuehn, Q. Min, U. Pannicke, N. Schleussner, R. Thouenon, Z. Yu, M. De Los Angeles Astbury, C.M. Biggs, M. Galicchio, J.A. Garcia-Campos, S. Gismondi, G. Gonzalez Villarreal, K.J. Hildebrand, M. Hönig, J. Hou, D. Moshous, S. Pittaluga, X. Qian, J. Rozmus, A.S. Schulz, A.T. Staines-Boone, B. Sun, J. Sun, S. Uwe, E. Venegas-Montoya, W. Wang, X. Wang, W. Ying, X. Zhai, Q. Zhou, A. Akalin, I. André, T.F.E. Barth, B. Baumann, A. Brüstle, G. Burgio, J.C. Bustamante, J.-L. Casanova, M.G. Casarotto, M. Cavazzana, L. Chentout, I.A. Cockburn, M. Costanza, C. Cui, O. Daumke, K.L. Del Bel, H. Eibel, X. Feng, V. Franke, J.C.M. Gebhardt, A. Götz, S. Grunwald, B. Hoareau, T.R. Hughes, E.-M. Jacobsen, M. Janz, A. Jolma, C. Lagresle-Peyrou, N. Lai, Y. Li, S. Lin, H.Y. Lu, S.O. Lugo-Reyes, X. Meng, P. Möller, N. Moreno-Corona, J.E. Niemela, G. Novakovsky, J.J. Perez-Caraballo, C. Picard, L. Poggi, M.-E. Puig-Lombardi, K.L. Randall, A. Reisser, Y. Schmitt, S. Seneviratne, M. Sharma, J. Stoddard, S. Sundararaj, H. Sutton, L.Q. Tran, Y. Wang, W.W. Wasserman, Z. Wen, W. Winkler, E. Xiong, A.W.H. Yang, M. Yu, L. Zhang, H. Zhang, Q. Zhao, X. Zhen, A. Enders, S. Kracker, R. Martinez-Barricarte, S. Mathas, S.D. Rosenzweig, K. Schwarz, S.E. Turvey, and J.-Y. Wang
Science Immunology 8, eade7953 (2023), https://doi.org/10.1126/sciimmunol.ade7953

Transcriptional reprogramming by mutated IRF4 in lymphoma
N. Schleussner, P. Cauchy, V. Franke, M. Giefing, O. Fornes, N. Vankadari, S.A. Assi, M. Costanza, M.A. Weniger, A. Akalin, I. Anagnostopoulos, T. Bukur, M.G. Casarotto, F. Damm, O. Daumke, B. Edginton-White, J.C.M. Gebhardt, M. Grau, S. Grunwald, M.-L. Hansmann, S. Hartmann, L. Huber, E. Kärgel, S. Lusatis, D. Noerenberg, N. Obier, U. Pannicke, A. Fischer, A. Reisser, A. Rosenwald, K. Schwarz, S. Sundararaj, A. Weilemann, W. Winkler, W. Xu, G. Lenz, K. Rajewsky, W.W. Wasserman, P.N. Cockerill, C. Scheidereit, R. Siebert, R. Küppers, R. Grosschedl, M. Janz, C. Bonifer, and S. Mathas
Nature Communications 14, 6947 (2023), https://doi.org/10.1038/s41467-023-41954-8

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Single-molecule tracking of Nodal and Lefty in live zebrafish embryos supports hindered diffusion model
T. Kuhn, A.N. Landge, D. Mörsdorf, J. Coßmann, J. Gerstenecker, D. Čapek, P. Müller, and J.C.M. Gebhardt
Nature Communications 13, 6101 (2022), https://doi.org/10.1038/s41467-022-33704-z

Stress induced TDP-43 mobility loss independent of stress granules
L. Streit, T. Kuhn, T. Vomhof, V. Bopp, A.C. Ludolph, J.H. Weishaupt, J.C.M. Gebhardt, J. Michaelis, and K.M. Danzer
Nature Communications 13, 5480 (2022), https://doi.org/10.1038/s41467-022-32939-0

Quantum Optical Microphone in the Audio Band
R. Nold, C. Babin, J. Schmidt, T. Linkewitz, M.T.P. Zaballos, R. Stöhr, R. Kolesov, V. Vorobyov, D.M. Lukin, R. Boppert, S. Barz, J. Vučković, J.C.M. Gebhardt, F. Kaiser, and J. Wrachtrup
PRX Quantum 3, 020358 (2022), https://doi.org/10.1103/PRXQuantum.3.020358

A guide to changing paradigms of glucocorticoid receptor function—a model system for genome regulation and physiology
S. Vettorazzi, D. Nalbantoglu, J.C.M. Gebhardt, and J. Tuckermann
The FEBS Journal 289, 5718–5743 (2022), https://doi.org/10.1111/febs.16100

Single-molecule tracking (SMT) and localization of SRF and MRTF transcription factors during neuronal stimulation and differentiation
O. Kuchler, J. Gerlach, T. Vomhof, J. Hettich, J. Steinmetz, J.C.M. Gebhardt, J. Michaelis, and B. Knöll
Open Biology 12, 210383 (2022), https://doi.org/10.1098/rsob.210383

Myosin VI regulates the spatial organisation of mammalian transcription initiation
Y. Hari-Gupta, N. Fili, Á. Dos Santos, A.W. Cook, R.E. Gough, H.C.W. Reed, L. Wang, J. Aaron, T. Venit, E. Wait, A. Grosse-Berkenbusch, J.C.M. Gebhardt, P. Percipalle, T.-L. Chew, M. Martin-Fernandez, and C.P. Toseland
Nature Communications 13, 1346 (2022), https://doi.org/10.1038/s41467-022-28962-w

Periodic synchronization of isolated network elements facilitates simulating and inferring gene regulatory networks including stochastic molecular kinetics
J. Hettich and J.C.M. Gebhardt
BMC Bioinformatics 23, 1–30 (2022), https://doi.org/10.1186/s12859-021-04541-6

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Transcription Factor RBPJL Is Able to Repress Notch Target Gene Expression but Is Non-Responsive to Notch Activation
L. Pan, P. Hoffmeister, A. Turkiewicz, N.N.D. Huynh, A. Große-Berkenbusch, U. Knippschild, J.C.M. Gebhardt, B. Baumann, T. Borggrefe, and F. Oswald
Cancers 13, 5027 (2021), https://doi.org/10.3390/cancers13195027

A Fibrinogen Alpha Fragment Mitigates Chemotherapy-Induced MLL Rearrangements
J. Eberle, R.S. Wiehe, B. Gole, L.J. Mattis, A. Palmer, L. Ständker, W.-G. Forssmann, J. Münch, J.C.M. Gebhardt, and L. Wiesmüller
Frontiers in Oncology 11, 689063 (2021), https://doi.org/10.3389/fonc.2021.689063

Altering transcription factor binding reveals comprehensive transcriptional kinetics of a basic gene
A.P. Popp, J. Hettich, and J.C.M. Gebhardt
Nucleic Acids Research 49, 6249–6266 (2021), https://doi.org/10.1093/nar/gkab443

Single molecule tracking and analysis framework including theory-predicted parameter settings
T. Kuhn, J. Hettich, R. Davtyan, and J.C.M. Gebhardt
Scientific Reports 11, 9465 (2021), https://doi.org/10.1038/s41598-021-88802-7

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Myosin VI moves on nuclear actin filaments and supports long-range chromatin rearrangements
A. Große-Berkenbusch, J. Hettich, T. Kuhn, N. Fili, A. Cook, Y. Hari-Gupta, A. Palmer, L. Streit, P. Ellis, C. Toseland, and J.C.M. Gebhardt
bioRxiv (2020), https://doi.org/10.1101/2020.04.03.023614

Inferring quantity and qualities of superimposed reaction rates from single molecule survival time distributions
M. Reisser, J. Hettich, T. Kuhn, A.P. Popp, A. Große-Berkenbusch, and J.C.M. Gebhardt
Scientific Reports 10, 1758 (2020), https://doi.org/10.1038/s41598-020-58634-y

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Mitotic chromosome binding predicts transcription factor properties in interphase
M. Raccaud, E.T. Friman, A.B. Alber, H. Agarwal, C. Deluz, T. Kuhn, J.C.M. Gebhardt, and D.M. Suter
Nature Communications 10, 487 (2019), https://doi.org/10.1038/s41467-019-08417-5

Single-molecule imaging of the transcription factor SRF reveals prolonged chromatin-binding kinetics upon cell stimulation
L. Hipp, J. Beer, O. Kuchler, M. Reisser, D. Sinske, J. Michaelis, J.C.M. Gebhardt, and B. Knöll
PNAS 116, 880–889 (2019), https://doi.org/10.1073/pnas.1812734116

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Single-molecule imaging correlates decreasing nuclear volume with increasing TF-chromatin associations during zebrafish development
M. Reisser, A. Palmer, A.P. Popp, C. Jahn, G. Weidinger, and J.C.M. Gebhardt
Nature Communications 9, 5218 (2018), https://doi.org/10.1038/s41467-018-07731-8

Endonuclease G promotes mitochondrial genome cleavage and replication
R.S. Wiehe, B. Gole, L. Chatre, P. Walther, E. Calzia, A. Palmer, J.C.M. Gebhardt, M. Ricchetti, and L. Wiesmüller
Oncotarget 9, 89081 (2018), https://doi.org/10.18632/oncotarget.25645

Transcription factor target site search and gene regulation in a background of unspecific binding sites
J. Hettich and J.C.M. Gebhardt
Journal of Theoretical Biology 454, 91–101 (2018), https://doi.org/10.1016/j.jtbi.2018.05.037

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DNA residence time is a regulatory factor of transcription repression
K. Clauß, A.P. Popp, L. Schulze, J. Hettich, M. Reisser, L.E. Torres, N.H. Uhlenhaut, and J.C.M. Gebhardt
Nucleic Acids Research 45, 11121–11130 (2017), https://doi.org/10.1093/nar/gkx728

Direct Observation of Cell-Cycle-Dependent Interactions between CTCF and Chromatin
H. Agarwal, M. Reisser, C. Wortmann, and J.C.M. Gebhardt
Biophysical Journal 112, 2051–2055 (2017), https://doi.org/10.1016/j.bpj.2017.04.018

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Spatial organization of RNA polymerase II insidea mammalian cell nucleus revealed by reflectedlight-sheet superresolution microscopy
Z.W. Zhao, R. Roy, J.C.M. Gebhardt, D.M. Suter, A.R. Chapman, and X.S. Xie
PNAS 111, 681–686 (2014), https://doi.org/10.1073/pnas.1318496111

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From mechanical folding trajectories to intrinsic energy landscapes of biopolymers
M. Hinczewski, C.M. Gebhardt, M. Rief, and D. Thirumalai
PNAS 110, 4500–4505 (2013), https://doi.org/10.1073/pnas.1214051110

Reply to “convergence of chromatin binding estimates in live cells”
Z.W. Zhao, J.C.M. Gebhardt, D.M. Suter, and X.S. Xie
Nature Methods 10, 692 (2013), https://doi.org/10.1038/nmeth.2574

Single-molecule imaging of transcription factor binding to DNA in live mammalian cells
J.C.M. Gebhardt, D.M. Suter, R. Roy, Z.W. Zhao, A.R. Chapman, S. Basu, T. Maniatis, and X.S. Xie
Nature Methods 10, 421–426 (2013), https://doi.org/10.1038/nmeth.2411

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The complex folding network of single calmodulin molecules
J. Stigler, F. Ziegler, A. Gieseke, J.C.M. Gebhardt, and M. Rief
Science 334, 512–516 (2011), https://doi.org/10.1126/science.1207598

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Regulation of a heterodimeric kinesin-2 through an unprocessive motor domain that is turned processive by its partner
M. Brunnbauer, F. Mueller-Planitz, S. Kösem, T.H. Ho, R. Dombi, J.C.M. Gebhardt, M. Rief, and Z. Ökten
PNAS 107, 10460–10465 (2010), https://doi.org/10.1073/pnas.1005177107

Full distance-resolved folding energy landscape of one single protein molecule
J.C.M. Gebhardt, T. Bornschlögl, and M. Rief
PNAS 107, 2013–2018 (2010), https://doi.org/10.1073/pnas.0909854107

The lever arm effects a mechanical asymmetry of the myosin-V-actin bond
J.C.M. Gebhardt, Z. Ökten, and M. Rief
Biophysical Journal 98, 277–281 (2010), https://doi.org/10.1016/j.bpj.2009.10.017

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Designing the folding mechanics of coiled coils
T. Bornschlögl, J. Christof M Gebhardt, and M. Rief
ChemPhysChem 10, 2800–2804 (2009), https://doi.org/10.1002/cphc.200900575

Force signaling in biology
J.C.M. Gebhardt, and M. Rief
Science 324, 1278–1280 (2009), https://doi.org/10.1126/science.1175874

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Myosin V stepping mechanism
G. Cappello, P. Pierobon, C. Symonds, L. Busoni, J.C.M. Gebhardt, M. Rief, and J. Prost
PNAS 104, 15328–15333 (2007), https://doi.org/10.1073/pnas.0706653104

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Myosin-V is a mechanical ratchet
J.C.M. Gebhardt, A.E.M. Clemen, J. Jaud, and M. Rief
PNAS 103, 8680–8685 (2006), https://doi.org/10.1073/pnas.0510191103

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The smallest possible nanocrystals of semiionic oxides
P. Persson, J.C.M. Gebhardt, and S. Lunell
Journal of Physical Chemistry B 107, 3336–3339 (2003), https://doi.org/10.1021/jp022036e

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