D3M: detection of differential distributions of methylation levels. - Yusuke Matsui 002; Masahiro Mizuta; Satoshi Ito; Satoru Miyano; Teppei Shimamura (Bioinform., 2016)

Tumor Subclonal Progression Model for Cancer Hallmark Acquisition. - Yusuke Matsui 002; Satoru Miyano; Teppei Shimamura (CIBB, 2017)

GIMLET: Identifying Biological Modulators in Context-Specific Gene Regulation Using Local Energy Statistics. - Teppei Shimamura; Yusuke Matsui 002; Taisuke Kajino; Satoshi Ito; Takashi Takahashi; Satoru Miyano (CIBB, 2017)

phyC: Clustering cancer evolutionary trees. - Yusuke Matsui 002; Atsushi Niida; Ryutaro Uchi; Koshi Mimori; Satoru Miyano; Teppei Shimamura (PLoS Comput. Biol., 2017)

A network of networks approach for modeling interconnected brain tissue-specific networks. - Hideko Kawakubo; Yusuke Matsui 002; Itaru Kushima; Norio Ozaki; Teppei Shimamura (Bioinform., 2019)

RoDiCE: robust differential protein co-expression analysis for cancer complexome. - Yusuke Matsui 002; Yuichi Abe; Kohei Uno; Satoru Miyano (Bioinform., 2022)

Types of anomalies in two-dimensional video-based gait analysis in uncontrolled environments. - Yuki Sugiyama; Kohei Uno; Yusuke Matsui 002 (PLoS Comput. Biol., 2023)

GlycanGT: a pretrained graph transformer framework for glycan graph representation and generative learning. - Akihiro Kitani; Bingyuan Zhang; Koichi Himori; Yusuke Matsui 002 (Bioinform., 2026)