EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes. - Itoshi Nikaido; Chika Saito; Akiko Wakamoto; Yasuhiro Tomaru; Takahiro Arakawa; Yoshihide Hayashizaki; Yasushi Okazaki (Nucleic Acids Res., 2004)

MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis. - Koki Tsuyuzaki; Gota Morota; Manabu Ishii; Takeru Nakazato; Satoru Miyazaki; Itoshi Nikaido (BMC Bioinform., 2015)

SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation. - Hirotaka Matsumoto; Hisanori Kiryu; Chikara Furusawa; Minoru S. H. Ko; Shigeru B. H. Ko; Norio Gouda; Tetsutaro Hayashi; Itoshi Nikaido (Bioinform., 2017)

Biological Systems as Heterogeneous Information Networks: A Mini-review and Perspectives. - Koki Tsuyuzaki; Itoshi Nikaido (CoRR, 2017)

nnTensor: An R package for non-negative matrix/tensor decomposition. - Koki Tsuyuzaki; Itoshi Nikaido (J. Open Source Softw., 2023)

Sctensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data. - Koki Tsuyuzaki; Manabu Ishii; Itoshi Nikaido (BMC Bioinform., 2023)

WormTensor: a clustering method for time-series whole-brain activity data from C. elegans. - Koki Tsuyuzaki; Kentaro Yamamoto; Yu Toyoshima; Hirofumi Sato; Manami Kanamori; Takayuki Teramoto; Takeshi Ishihara; Yuichi Iino; Itoshi Nikaido (BMC Bioinform., 2023)