A case study of instant workbench for InterProScan by Knoppix high throughput computing edition. - Fumikazu Konishi; Shingo Ohki; Yusuke Hamano; Manabu Ishii (HPDC, 2005)

Improving the Research Environment of High Performance Computing for Non-cluster Experts Based on Knoppix Instant Computing Technology. - Fumikazu Konishi; Manabu Ishii; Shingo Ohki; Yusuke Hamano; Shuichi Fukuda; Akihiko Konagaya (Euro-Par, 2006)

RABC: A Conceptual Design of Pervasive Infrastructure for Browser Computing based on Ajax technologies. - Fumikazu Konishi; Manabu Ishii; Shingo Ohki; Ryo Umetsu; Akihiko Konagaya (CCGRID, 2007)

A Secure Data Repository Integrating Huge Volumes of Digital Contents as a Semantic Web. - Norio Kobayashi; Yuko Makita; Eli Kaminuma; Shuji Kawaguchi; Yuko Yoshida; Yoshiki Mochizuki; Akihiro Matsushima; Manabu Ishii; Ryo Umetsu; Satomi Asano; Naohiko Heida; Tetsuya Sakurai; et al. (SWAT4LS, 2008)

OmicBrowse: a Flash-based high-performance graphics interface for genomic resources. - Akihiro Matsushima; Norio Kobayashi; Yoshiki Mochizuki; Manabu Ishii; Shuji Kawaguchi; Takaho A. Endo; Ryo Umetsu; Yuko Makita; Tetsuro Toyoda (Nucleic Acids Res., 2009)

PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning. - Yuko Yoshida; Yuko Makita; Naohiko Heida; Satomi Asano; Akihiro Matsushima; Manabu Ishii; Yoshiki Mochizuki; Hiroshi Masuya; Shigeharu Wakana; Norio Kobayashi; Tetsuro Toyoda (Nucleic Acids Res., 2009)

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases. - Norio Kobayashi; Manabu Ishii; Satoshi Takahashi; Yoshiki Mochizuki; Akihiro Matsushima; Tetsuro Toyoda (Nucleic Acids Res., 2011)

The RIKEN integrated database of mammals. - Hiroshi Masuya; Yuko Makita; Norio Kobayashi; Koro Nishikata; Yuko Yoshida; Yoshiki Mochizuki; Koji Doi; Terue Takatsuki; Kazunori Waki; Nobuhiko Tanaka; Manabu Ishii; Akihiro Matsushima; et al. (Nucleic Acids Res., 2011)

PosMed: A Biomedical Entity Prioritisation Tool Based on Statistical Inference over Literature and the Semantic Web. - Norio Kobayashi; Yuko Makita; Manabu Ishii; Akihiro Matsushima; Yoshiki Mochizuki; Koji Doi; Koro Nishikata; David Gifford 002; Terue Takatsuki; Hiroshi Masuya; Tetsuro Toyoda (SWAT4LS, 2013)

PosMed: ranking genes and bioresources based on Semantic Web Association Study. - Yuko Makita; Norio Kobayashi; Yuko Yoshida; Koji Doi; Yoshiki Mochizuki; Koro Nishikata; Akihiro Matsushima; Satoshi Takahashi; Manabu Ishii; Terue Takatsuki; Rinki Bhatia; Zolzaya Khadbaatar; et al. (Nucleic Acids Res., 2013)

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)

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