Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model. - Ryoko Morioka; Shigehiko Kanaya; Masami Y. Hirai; Mitsuru Yano; Naotake Ogasawara; Kazuki Saito (BMC Bioinform., 2007)

PRIMe: A Web Site That Assembles Tools for Metabolomics and Transcriptomics. - Kenji Akiyama; Eisuke Chikayama; Hiroaki Yuasa; Yukihisa Shimada; Takayuki Tohge; Kazuo Shinozaki; Masami Y. Hirai; Tetsuya Sakurai; Jun Kikuchi; Kazuki Saito (Silico Biol., 2008)

A U-system approach for predicting metabolic behaviors and responses based on an alleged metabolic reaction network. - Kansuporn Sriyudthsak; Yuji Sawada; Yukako Chiba; Yui Yamashita; Shigehiko Kanaya; Hitoshi Onouchi; Toru Fujiwara; Satoshi Naito; Eberhard O. Voit; Fumihide Shiraishi; Masami Y. Hirai (BMC Syst. Biol., 2014)

PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems. - Kansuporn Sriyudthsak; Ramon Francisco Pacquiao Mejia; Masanori Arita; Masami Y. Hirai (Nucleic Acids Res., 2016)

Extraction of RNA from an intact single plant cell with cell wall using focused electric field. - Sangamithirai Subramanian Parimalam; Naoyuki Sotta; Takashi Kuromori; Toru Fujiwara; Masami Yokota Hirai; Hirofumi Shintaku (MHS, 2019)

I-SVVS: integrative stochastic variational variable selection to explore joint patterns of multi-omics microbiome data. - Tung Dang; Yushiro Fuji; Kie Kumaishi; Erika Usui; Shungo Kobori; Takumi Sato; Megumi Narukawa; Yusuke Toda; Kengo Sakurai; Yuji Yamasaki; Hisashi Tsujimoto; Masami Yokota Hirai; et al. (Briefings Bioinform., 2025)