Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations. - Toru Niina; Giovanni B. Brandani; Cheng Tan 004; Shoji Takada (PLoS Comput. Biol., 2017)

Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA. - Giovanni B. Brandani; Shoji Takada (PLoS Comput. Biol., 2018)

The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study. - Giovanni B. Brandani; Cheng Tan 004; Shoji Takada (PLoS Comput. Biol., 2021)

Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion. - Chenyang Gu; Shoji Takada; Giovanni B. Brandani; Tsuyoshi Terakawa (PLoS Comput. Biol., 2025)