4D Genome Analysis Using PHi-C2.
| Autor: | Shinkai S; Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research (BDR), Hyogo, Kobe, Japan. soya.shinkai@riken.jp., Onami S; Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research (BDR), Hyogo, Kobe, Japan. |
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| Jazyk: | angličtina |
| Zdroj: | Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2025; Vol. 2856, pp. 271-279. |
| DOI: | 10.1007/978-1-0716-4136-1_16 |
| Abstrakt: | Hi-C methods reveal 3D genome features but lack correspondence to dynamic chromatin behavior. PHi-C2, Python software, addresses this gap by transforming Hi-C data into polymer models. After the optimization algorithm, it enables us to calculate 3D conformations and conduct dynamic simulations, providing insights into chromatin dynamics, including the mean-squared displacement and rheological properties. This chapter introduces PHi-C2 usage, offering a tutorial for comprehensive 4D genome analysis. (© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.) |
| Databáze: | MEDLINE |
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