A critical role of the periplasm in copper homeostasis in Gram-negative bacteria - Jun-ichi Ishihara; Tomohiro Mekubo; Chikako Kusaka; Suguru Kondo; Ryotaro Oiko; Kensuke Igarashi; Hirofumi Aiba; Shu Ishikawa; Naotake Ogasawara; Taku Oshima; Hiroki Takahashi (Biosyst., 2023)

AMDORAP: Non-targeted metabolic profiling based on high-resolution LC-MS - Hiroki Takahashi; Takuya Morimoto; Naotake Ogasawara; Shigehiko Kanaya (BMC Bioinform., 2011)

Genome-wide binding profiles of the Bacillus subtilis transition state regulator AbrB and its homolog Abh reveals their interactive role in transcriptional regulation - Onuma Chumsakul; Hiroki Takahashi; Taku Oshima; Takahiro Hishimoto; Shigehiko Kanaya; Naotake Ogasawara; Shu Ishikawa (Nucleic Acids Res., 2011)

A Constrained Gaussian Mixture Model for Correlation-Based Cluster Analysis of Gene Expression Data - Naoto Yukinawa; Taku Yoshioka; Kazuo Kobayashi; Naotake Ogasawara; Shin Ishii (Inf. Media Technol., 2009)

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)

Elucidating Conservation of Genes in Multiple Genomes Based on Graphs Configured by Bidirectional Best-Hit Relationships - Hijiri Maeno; Md. Altaf-Ul-Amin; Yoko Shinbo; Ken Kurokawa; Naotake Ogasawara; Shigehiko Kanaya (Inf. Media Technol., 2007)

Bayesian Joint Prediction of Associated Transcription Factors in Bacillus subtilis - Yuko Makita; Michiel J. L. de Hoon; Naotake Ogasawara; Satoru Miyano; Kenta Nakai (Biocomputing 2005, Proceedings of the Pacific Symposium, Hawaii, USA, 4-8 January 2005, 2005)

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)

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 (Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, Glasgow, UK, July 31-August 4, 2004, 2004)

Predicting the Operon Structure of Bacillus subtilis Using Operon Length, Intergene Distance, and Gene Expression Information - Michiel J. L. de Hoon; Seiya Imoto; Kazuo Kobayashi; Naotake Ogasawara; Satoru Miyano (Biocomputing 2004, Proceedings of the Pacific Symposium, Hawaii, USA, 6-10 January 2004, 2004)

Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data of Bacillus Subtilis Using Differential Equations - Michiel J. L. de Hoon; Seiya Imoto; Kazuo Kobayashi; Naotake Ogasawara; Satoru Miyano (Proceedings of the 8th Pacific Symposium on Biocomputing, PSB 2003, Lihue, Hawaii, USA, January 3-7, 2003, 2003)

Clustering of Gene Expression Data by Mixture of PCA Models - Taku Yoshioka; Ryouko Morioka; Kazuo Kobayashi; Shigeyuki Oba; Naotake Ogasawara; Shin Ishii (Artificial Neural Networks - ICANN 2002, International Conference, Madrid, Spain, August 28-30, 2002, Proceedings, 2002)