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Single Molecule Mechanisms of Spatio-Temporal Chromatin Architecture

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Single-molecule tracking of Nodal and Lefty in live zebrafish embryos supports hindered diffusion model

Author(s): Timo Kuhn, Amit N. Landge, David Mörsdorf, Jonas Coßmann, Johanna Gerstenecker, Patrick Müller, J. Christof M. Gebhardt
Published in: bioRxiv, 2022
Publisher: CSHL
DOI: 10.1101/2022.04.05.487143

Periodic synchronization of isolated network elements facilitates simulating and inferring gene regulatory networks including stochastic molecular kinetics

Author(s): Johannes Hettich, J. Christof M. Gebhardt
Published in: BMC Bioinformatics, 23, 2022, Page(s) 13
Publisher: Springer Nature
DOI: 10.1186/s12859-021-04541-6

Myosin VI moves on nuclear actin filaments and supports long-range chromatin rearrangements

Author(s): A. Große-Berkenbusch, J. Hettich, T. Kuhn, N. Fili, A.W. Cook, Y. Hari-Gupta, A. Palmer, L. Streit, P.J.I. Ellis, C.P. Toseland* and J.C.M. Gebhardt
Published in: bioRxiv, 2020
Publisher: CSHL
DOI: 10.1101/2020.04.03.023614

Transcription Factor RBPJL Is Able to Repress Notch Target Gene Expression but Is Non-Responsive to Notch Activation

Author(s): Leiling Pan, Philipp Hoffmeister, Aleksandra Turkiewicz, N. N. Duyen Huynh, Andreas Große-Berkenbusch, Uwe Knippschild, J. Christof M. Gebhardt, Bernd Baumann, Tilman Borggrefe, Franz Oswald
Published in: Cancers, 13/19, 2021, Page(s) 5027, ISSN 2072-6694
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers13195027

Single molecule tracking and analysis framework including theory-predicted parameter settings

Author(s): Timo Kuhn, Johannes Hettich, Rubina Davtyan, J. Christof M. Gebhardt
Published in: Scientific Reports, 11/1, 2021, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-88802-7

Altering transcription factor binding reveals comprehensive transcriptional kinetics of a basic gene

Author(s): Achim P Popp, Johannes Hettich, J Christof M Gebhardt
Published in: Nucleic Acids Research, 2021, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab443

A guide to changing paradigms of glucocorticoid receptor function—a model system for genome regulation and physiology

Author(s): Sabine Vettorazzi, Denis Nalbantoglu, J. Christof M. Gebhardt, Jan Tuckermann
Published in: The FEBS Journal, 2021, ISSN 1742-464X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/febs.16100

Single-molecule imaging correlates decreasing nuclear volume with increasing TF-chromatin associations during zebrafish development

Author(s): Matthias Reisser, Anja Palmer, Achim P. Popp, Christopher Jahn, Gilbert Weidinger, J. Christof M. Gebhardt
Published in: Nature Communications, 9/1, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-07731-8

DNA residence time is a regulatory factor of transcription repression

Author(s): Karen Clauß, Achim P. Popp, Lena Schulze, Johannes Hettich, Matthias Reisser, Laura Escoter Torres, N. Henriette Uhlenhaut, J. Christof M. Gebhardt
Published in: Nucleic Acids Research, 45/19, 2017, Page(s) 11121-11130, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkx728

Transcription factor target site search and gene regulation in a background of unspecific binding sites

Author(s): J. Hettich, J.C.M. Gebhardt
Published in: Journal of Theoretical Biology, 2018, ISSN 0022-5193
Publisher: Academic Press
DOI: 10.1016/j.jtbi.2018.05.037

Correction: Endonuclease G promotes mitochondrial genome cleavage and replication

Author(s): Rahel Stefanie Wiehe, Boris Gole, Laurent Chatre, Paul Walther, Enrico Calzia, Anja Palmer, J. Christof M. Gebhardt, Miria Ricchetti, Lisa Wiesmüller
Published in: Oncotarget, 9/45, 2018, ISSN 1949-2553
Publisher: Impact Journals
DOI: 10.18632/oncotarget.25645

Mitotic chromosome binding predicts transcription factor properties in interphase

Author(s): Mahé Raccaud, Elias T. Friman, Andrea B. Alber, Harsha Agarwal, Cédric Deluz, Timo Kuhn, J. Christof M. Gebhardt, David M. Suter
Published in: Nature Communications, 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-08417-5

Single-molecule imaging of the transcription factor SRF reveals prolonged chromatin-binding kinetics upon cell stimulation

Author(s): Lisa Hipp, Judith Beer, Oliver Kuchler, Matthias Reisser, Daniela Sinske, Jens Michaelis, J. Christof M. Gebhardt, Bernd Knöll
Published in: Proceedings of the National Academy of Sciences, 2018, Page(s) 201812734, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1812734116

Inferring quantity and qualities of superimposed reaction rates from single molecule survival time distributions

Author(s): Matthias Reisser, Johannes Hettich, Timo Kuhn, Achim P. Popp, Andreas Große-Berkenbusch, J. Christof M. Gebhardt
Published in: Scientific Reports, 10/1, 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-020-58634-y

Myosin VI regulates the spatial organization of mammalian transcription initiation

Author(s): Yukti Hari-Gupta, Natalia Fili, Ália dos Santos, Alexander W. Cook, Rosemarie E. Gough, Hannah C. W. Reed, Lin Wang, Jesse Aaron, Tomas Venit, Eric Wait, Andreas Grosse-Berkenbusch, J. Christof M. Gebhardt, Piergiorgio Percipalle, Teng-Leong Chew, Marisa Martin-Fernandez, Christopher P. Toseland
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-28962-w

Direct Observation of Cell-Cycle-Dependent Interactions between CTCF and Chromatin

Author(s): Harsha Agarwal, Matthias Reisser, Celina Wortmann, J. Christof M. Gebhardt
Published in: Biophysical Journal, 112/10, 2017, Page(s) 2051-2055, ISSN 0006-3495
Publisher: Biophysical Society
DOI: 10.1016/j.bpj.2017.04.018