Computational methods and modeling to decipher organelle nanophysiology

Project Information

OrganellenanoComp

Grant agreement ID: 882673

DOI

10.3030/882673

EC signature date 20 October 2020

Start date 1 March 2021

End date 28 February 2027

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 374 698,00

EU contribution

€ 2 374 698,00

Coordinated by

CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
France

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Book chapters (1)

Analyzing Photoactivation with Diffusion Models to Study Transport in the Endoplasmic Reticulum Network

Author(s): Matteo Dora, Frédéric Paquin-Lefebvre, David Holcman
Published in: Methods in Molecular Biology, The Plant Endoplasmic Reticulum, 2024, Page(s) 407-432
Publisher: Springer US
DOI: 10.1007/978-1-0716-3710-4_31

Peer reviewed articles (9)

Diversity of dynamic voltage patterns in neuronal dendrites revealed by nanopipette electrophysiology

Author(s): Jeffrey Mc Hugh, Stanislaw Makarchuk, Daria Mozheiko, Ana Fernandez-Villegas, Gabriele S. Kaminski Schierle, Clemens F. Kaminski, Ulrich F. Keyser, David Holcman, Nathalie Rouach
Published in: Nanoscale, Issue 15, 2024, Page(s) 12245-12254, ISSN 2040-3364
Publisher: Royal Society of Chemistry
DOI: 10.1039/d2nr03475a

Computational methods and diffusion theory in triangulation sensing to model neuronal navigation

Author(s): Ulrich Dobramysl, David Holcman
Published in: Reports on Progress in Physics, Issue 85, 2022, Page(s) 104601, ISSN 0034-4885
Publisher: Institute of Physics Publishing
DOI: 10.1088/1361-6633/ac906b

Voltage mapping in subcellular nanodomains using electro-diffusion modeling

Author(s): Frédéric Paquin-Lefebvre, David Holcman
Published in: The Journal of Chemical Physics, Issue 161, 2024, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/5.0215900

Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries

Author(s): Li-Hsin Chang, Sourav Ghosh, Andrea Papale, Jennifer M. Luppino, Mélanie Miranda, Vincent Piras, Jéril Degrouard, Joanne Edouard, Mallory Poncelet, Nathan Lecouvreur, Sébastien Bloyer, Amélie Leforestier, Eric F. Joyce, David Holcman, Daan Noordermeer
Published in: Nature Communications, Issue 14, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-41265-y

Chromatin phase separated nanoregions explored by polymer cross-linker models and reconstructed from single particle trajectories

Author(s): Andrea Papale, David Holcman
Published in: PLOS Computational Biology, Issue 20, 2024, Page(s) e1011794, ISSN 1553-7358
Publisher: plos CB
DOI: 10.1371/journal.pcbi.1011794

Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD

Author(s): S. Basu, O. Shukron, D. Hall, P. Parutto, A. Ponjavic, D. Shah, W. Boucher, D. Lando, W. Zhang, N. Reynolds, L. H. Sober, A. Jartseva, R. Ragheb, X. Ma, J. Cramard, R. Floyd, J. Balmer, T. A. Drury, A. R. Carr, L.-M. Needham, A. Aubert, G. Communie, K. Gor, M. Steindel, L. Morey, E. Blanco, T. Bartke, L. Di Croce, I. Berger, C. Schaffitzel, S. F. Lee, T. J. Stevens, D. Klenerman, B. D. Hendrich, D
Published in: Nature Structural & Molecular Biology, Issue 30, 2023, Page(s) 1628-1639, ISSN 1545-9993
Publisher: Nature Publishing Group
DOI: 10.1038/s41594-023-01095-4

High-throughput super-resolution single-particle trajectory analysis reconstructs organelle dynamics and membrane reorganization

Author(s): Pierre Parutto, Jennifer Heck, Meng Lu, Clemens Kaminski, Edward Avezov, Martin Heine, David Holcman
Published in: Cell Reports Methods, Issue 2, 2022, Page(s) 100277, ISSN 2667-2375
Publisher: Cell
DOI: 10.1016/j.crmeth.2022.100277

Synapsin 2a tetramerisation selectively controls the presynaptic nanoscale organisation of reserve synaptic vesicles

Author(s): Shanley F. Longfield, Rachel S. Gormal, Matis Feller, Pierre Parutto, Jürgen Reingruber, Tristan P. Wallis, Merja Joensuu, George J. Augustine, Ramón Martínez-Mármol, David Holcman, Frédéric A. Meunier
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-46256-1

Interactive nanocluster compaction of the ELKS scaffold and Cacophony Ca ²⁺ channels drives sustained active zone potentiation

Author(s): Tina Ghelani, Marc Escher, Ulrich Thomas, Klara Esch, Janine Lützkendorf, Harald Depner, Marta Maglione, Pierre Parutto, Scott Gratz, Tanja Matkovic-Rachid, Stefanie Ryglewski, Alexander M. Walter, David Holcman, Kate O‘Connor Giles, Martin Heine, Stephan J. Sigrist
Published in: Science Advances, Issue 9, 2024, ISSN 2375-2548
Publisher: Nature
DOI: 10.1126/sciadv.ade7804

Other (2)

Exit versus escape in a stochastic dynamical system of neuronal networks explains heterogenous bursting intervals

Author(s): Zonca, Lou; Holcman, David
Published in: 2020, 2020
Publisher: arxiv
DOI: 10.48550/arxiv.2010.06699

Escape from an attractor generated by recurrent exit

Author(s): Lou Zonca; Lou Zonca; David Holcman
Published in: 2020, 2021
Publisher: arxiv
DOI: 10.48550/arxiv.2009.06745