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Researcher Information

last modified:2019/02/15

Assistant Professor HIROSE, Osamu

Laboratory Website

Faculty, Affiliation

Faculty of Biological Science and Technology,Institute of Science and Engineering
Assistant professor

College and School Educational Field

Division of Electrical Engineering and Computer Science, Graduate School of Natural Science and Technology


Academic Background

【Academic background(Doctoral/Master's Degree)】
The University of Tokyo 200803 Completed
【Academic background(Bachelor's Degree)】
Kyushu University Faculty of Physics 200303
Ph.D. (Information Science and Technology)


Year & Month of Birth

Academic Society

Institute of Electrical and Electronics Engineers (IEEE)
Information Processing Society of Japan



Statistical science、ゲノム生物学

Speciality Keywords

Bioimage informatics, Object tracking, Particle filter, State space model, Markov random field, High-dimensional data, Clustering, Time-series analysis, RNA-seq, NGS, Bioinfomatics, Bayesian statistics.

Research Themes



  •  SPF-CellTracker: Tracking multiple cells with strongly-correlated moves using a spatial particle filter Osamu Hirose, Shotaro Kawaguchi, Terumasa Tokunaga, Yu Toyoshima, Takayuki Teramoto, Sayuri Kuge, Takeshi Ishihara, Yuichi Iino, Ryo Yoshida IEEE/ACM Transactions on Computational Biology and Bioinformatics 2017/12/11
  •  The RB-IL-6 axis controls self-renewal and endocrine therapy resistance by fine-tuning mitochondrial activity Kitajima S, Yoshida A, Kohno S, Li F, Suzuki S, Nagatani N, Nishimoto Y, Sasaki N, Muranaka H, Wan Y, Thai T C, Okahashi N, Matsuda F, Shimizu H, Nishiuchi T, Suzuki Y, Tominaga K, Gotoh N, Suzuki M, Ewen M E, Barbie D A, Hirose O, Tanaka T and Takahashi C.  Oncogene  36 5145--5157 2017/05/08
  •  MicroRNA-140 mediates RB tumor suppressor function to control stem cell-like activity through interleukin-6 Yoshida A, Kitajima S, Li F, Cheng C, Takegami Y, Kohno S, Wan YS, Hayashi N, Muranaka H, Nishimoto Y, Nagatani N, Nishiuchi T, Thai TC, Suzuki S, Nakao S, Tanaka T, Hirose O, Barbie DA, Takahashi C Oncotarget 8 8 13872-13885 2017/02/21
  •  Accurate automatic detection of densely distributed cell nuclei in 3D space Yu Toyoshima, Terumasa Tokunaga, Osamu Hirose, Manami Kanamori, Takayuki Teramoto, Moon Sun Jang, Sayuri Kuge, Takeshi Ishihara, Ryo Yoshida and Yuichi Iino PLoS Computational Biology 12 6 1-20 2016/06/06
  •   Inflammation in gastric cancer: Interplay of the COX-2/prostaglandin E2 and Toll-like receptor/MyD88 pathways Kanae Echizen, Osamu Hirose, Yusuke Maeda and Masanobu Oshima Cancer Science 107 4 391-397 2016/03/18

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  •  Myeloid differentiation factor 88 signaling in bone marrow-derived cells promotes gastric tumorigenesis by generation of inflammatory microenvironment Yusuke Maeda, Kanae Echizen, Hiroko Oshima, Liang Yu, Natthiya Sakulsak, Osamu Hirose, Yoichi Yamada, Tadatsugu Taniguchi, Brendan J. Jenkins, Hideyuki Saya and Masanobu Oshima Cancer Prevention Research 9 3 253-263 2016/03/09
  •  Factors to preserve CpG-rich sequences in methylated CpG islands Hiroki Miyahara, Osamu Hirose, Kenji Satou, and Yoichi Yamada 16 1 1-15 2015/02/28
  •  Automated detection and tracking of many cells by using 4D live-cell imaging data T. Tokunaga, O. Hirose, S. Kawaguchi, Y. Toyoshima, T. Teramoto, H. Ikebata, S. Kuge, T. Ishihara, Y. Iino and R. Yoshida BIOINFORMATICS 30 43-51 2014/06
  •  TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference Naoki Nariai, Osamu Hirose, Kaname Kojima, Masao Nagasaki BIOINFORMATICS 2013/08
  •  EpicCapo: Epitope Prediction using Combined Information of Amino Acid Pairwise Contact Potentials and HLA-Peptide Contact Site Information Thammakorn Saethang, Osamu Hirose, Ingorn Kimkong, Vu Anh Tran, Xuan Tho Dang, Lan Anh T. Nguyen, Tu Kien T. Le, Mamoru Kubo, Yoichi Yamada and Kenji Satou BMC Bioinformatics 2012/11
  •  SiGN-SSM: open source parallel software for estimating gene networks with state space models. Yoshinori Tamada, Rui Yamaguchi, Seiya Imoto, Osamu Hirose, Ryo Yoshida, Masao Nagasaki, Satoru Miyano Bioinformatics 2011/02
  •  PAAQD: Predicting immunogenicity of MHC class I binding peptides using amino acid pairwise contact potentials and quantum topological molecular similarity descriptors. Saethang T,Hirose O,Kimkong I,Tran VA,Dang XT,Nguyen LA,Le TK,Kubo M,Yamada Y,Satou K J Immunol Methods 387 1-2 293-302
  •  Prediction of Carbohydrate-Binding Proteins from Sequences Using Support Vector Machines Seizi Someya, Masanori Kakuta, Mizuki Morita, Kazuya Sumikoshi, Cao Wei, Ge Zhenyi, Osamu Hirose, Shugo Nakamura, Tohru Terada, Kentaro Shimizu Advances in Bioinformatics 2010/01
  •  A Self-organizing State Space Approach to Inferring Time-Varying Causalities between Regulatory Proteins Osamu Hirose, Kentaro Shimizu Lecture Notes in Computer Science 6266 158-171 2010/09
  •  Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. Bioinformatics 24 7 932--942 2008/05
  •  Analyzing Time Course Gene Expression Data with Biological and Technical Replicates to Estimate Gene Networks by State Space Models. Osamu Hirose, Ryo Yoshida, Rui Yamaguchi, Seiya Imoto, Tomoyuki Higuchi, Satoru Miyano AMS 2008 2008/01
  •  Clustering samples characterized by time course gene expression profiles using the mixture of state space models. Osamu Hirose, Ryo Yoshida, Rui Yamaguchi, Seiya Imoto, Tomoyuki Higuchi, Satoru Miyano Genome Informatics 18 258-266 2007/02
  •  Estimating Gene Networks from Expression Data and Binding Location Data via Boolean Networks. Osamu Hirose, Naoki Nariai, Yoshinori Tamada, Hideo Bannai, Seiya Imoto, Satoru Miyano Lecture in Computer Science 2005/05

Conference Presentations

  • Robust point set registration using prior shape information(2018/01/28)
  • 変位場の滑らかさを前提としない頑健な点群マッチング手法の開発(conference:The 31st Annual Conference of the Japanese Society for Artificial Intelligence, 2017)(2017/05/24)
  • SPF-CellTracker: Tracking multiple cells with strongly-correlated moves using a spatial particle filter(conference:Bioimage informatics conference 2015)(2015/10/14)
  • SPF-CellTracker: Tracking multiple cells with strongly-correlated moves using a spatial particle filter(conference:GIW/InCoB 2015)
  • Tracking multiple cells with a spatial particle filter (conference:IBISML)(2015/06/23)

Arts and Fieldwork


Theme to the desired joint research

Grant-in-Aid for Scientific Research


Classes (Bachelors)

○Information and Computer System Engineering Laboratory 1(2018)
○Genome Informatics(2018)
○Freshman Seminar I(2018)
○Presentation and Debate (Freshman Seminar II)(2018)
○Freshman Seminar I(2017)
○Genome Informatics(2017)
○Information and Computer System Engineering Laboratory 1(2017)
○Presentation and Debate (Freshman Seminar II)(2017)
○Freshman Seminar I(2016)
○Presentation and Debate (Freshman Seminar II)(2016)
○Genome Informatics(2016)
○Information and Computer System Engineering Laboratory 1(2016)

Classes (Graduate Schools)

International Project

International Students

Lecture themes

Others (Social Activities)

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