Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data. - Michiel J. L. de Hoon; Yuko Makita; Seiya Imoto; Kazuo Kobayashi; Naotake Ogasawara; Kenta Nakai; Satoru Miyano (ISMB/ECCB (Supplement of Bioinformatics), 2004)

BTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. - Yuko Makita; Mitsuteru Nakao; Naotake Ogasawara; Kenta Nakai (Nucleic Acids Res., 2004)

Bayesian Joint Prediction of Associated Transcription Factors in Bacillus subtilis. - Yuko Makita; Michiel J. L. de Hoon; Naotake Ogasawara; Satoru Miyano; Kenta Nakai (Pacific Symposium on Biocomputing, 2005)

Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species. - Michiel J. L. de Hoon; Yuko Makita; Kenta Nakai; Satoru Miyano (PLoS Comput. Biol., 2005)

Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes. - Yuko Makita; Michiel J. L. de Hoon; Antoine Danchin (BMC Bioinform., 2007)

Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions. - Toshiyuki Okumura; Hiroki Makiguchi; Yuko Makita; Riu Yamashita; Kenta Nakai (Nucleic Acids Res., 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)

DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. - Nicolas Sierro; Yuko Makita; Michiel J. L. de Hoon; Kenta Nakai (Nucleic Acids Res., 2008)

Amino-Acid Residue Association Models for Large Scale Protein-Protein Interaction Prediction. - K. Rao Raghuraj; Kyaw Tun; Yuko Makita; Samavedham Lakshminarayanan; Pawan K. Dhar (Silico Biol., 2009)

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)

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)

Development of Linked Open Data for Bioresources. - Hiroshi Masuya; Terue Takatsuki; Yuko Makita; Yuko Yoshida; Yoshiki Mochizuki; Norio Kobayashi; Atsushi Yoshiki; Yukio Nakamura; Tetsuro Toyoda; Yuichi Obata (JIST, 2012)

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)

PromoterCAD: data-driven design of plant regulatory DNA. - Robert Sidney Cox III; Koro Nishikata; Sayoko Shimoyama; Yuko Yoshida; Minami Matsui; Yuko Makita; Tetsuro Toyoda (Nucleic Acids Res., 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)