Idiographica: a general-purpose web application to build idiograms on-demand for human, mouse and rat. - Taishin Kin; Yukiteru Ono (Bioinform., 2007)

fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. - Taishin Kin; Kouichirou Yamada; Goro Terai; Hiroaki Okida; Yasuhiko Yoshinari; Yukiteru Ono; Aya Kojima; Yuki Kimura; Takashi Komori; Kiyoshi Asai (Nucleic Acids Res., 2007)

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs. - Toutai Mituyama; Kouichirou Yamada; Emi Hattori; Hiroaki Okida; Yukiteru Ono; Goro Terai; Aya Yoshizawa; Takashi Komori; Kiyoshi Asai (Nucleic Acids Res., 2009)

PBSIM: PacBio reads simulator - toward accurate genome assembly. - Yukiteru Ono; Kiyoshi Asai; Michiaki Hamada (Bioinform., 2013)

Learning chromatin states with factorized information criteria. - Michiaki Hamada; Yukiteru Ono; Ryohei Fujimaki; Kiyoshi Asai (Bioinform., 2015)

Rtools: a web server for various secondary structural analyses on single RNA sequences. - Michiaki Hamada; Yukiteru Ono; Hisanori Kiryu; Kengo Sato; Yuki Kato; Tsukasa Fukunaga; Ryota Mori; Kiyoshi Asai (Nucleic Acids Res., 2016)

Training alignment parameters for arbitrary sequencers with LAST-TRAIN. - Michiaki Hamada; Yukiteru Ono; Kiyoshi Asai; Martin C. Frith (Bioinform., 2017)

PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores. - Yukiteru Ono; Kiyoshi Asai; Michiaki Hamada (Bioinform., 2021)