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Researcher Information

last modified：2024/04/12

Associate Professor　HIROSE, Osamu

Laboratory Website

Faculty, Affiliation

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

College and School Educational Field

Division of Electrical Engineering and Computer Science, Graduate School of Natural Science and Technology
Course in Bioengineering, School of Biological Science and Technology, College of Science and Engineering

Laboratory

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
【Degree】
Ph.D. (Information Science and Technology)

Career

Year & Month of Birth

Academic Society

Institute of Electrical and Electronics Engineers (IEEE)

Award

Specialities

Statistics、Bioinformatics

Speciality Keywords

Shape analysis, Bayesian statistics, Bioimage informatics

Research Themes

Books

Papers

  • 　Geodesic-Based Bayesian Coherent Point Drift　Osamu Hirose　IEEE Transactions on Pattern Analysis and Machine Intelligence　45　5　5816 - 5832　2022/10/13　
  • 　Acceleration of non-rigid point set registration with downsampling and Gaussian process regression　Osamu Hirose　IEEE Transactions on Pattern Analysis and Machine Intelligence　43　8　2858 - 2865　2020/12/11　
  • 　A Bayesian formulation of coherent point drift　Osamu Hirose 　IEEE Transactions on Pattern Analysis and Machine Intelligence　43　7　2269 - 2286.　2020/02/06　
  • 　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　15　6　1822-1831　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

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  • 　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
  • 　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

  • Generalization of Coherent Point Drift and Its Acceleration(conference： IEICE-[ML/IE/SIP/BioX], IST, ME )(2020/05/28)
  • Fast point set registration using prior shape information(conference：The 32nd Annual Conference of the Japanese Society for Artificial Intelligence, 2018)(2018/06/05)
  • 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)

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  • 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)

Others

Arts and Fieldwork

Patent

Theme to the desired joint research

Grant-in-Aid for Scientific Research

○「高品質な3次元形状を自動作成するための基盤技術開発」(2022-2025)　
○「線虫の神経細胞に対する細胞核自動アノテーションのための人工知能技術の開発」(2017-2021)　
○「4Dライブセルイメージングデータ内の非常に多数の細胞の自動追跡手法の開発」(2015-2016)　
○「レクチン・複合糖鎖結合予測のための統計的方法論の開発」(2012-2013)　

Competitive research funding,Contribution

Collaborative research,Consignment study

Classes (Bachelors)

○Data Science A(2020)
○Bioinformatics B(2020)
○Programming for Biology C(2020)
○Introduction to Researches in Bioengineering(2020)
○Bioinformatics D(2020)
○Programming for Biology D(2020)
○Bioinformatics A(2020)
○Bioinformatics C(2020)
○Data Science B(2020)
○Fundamentals of Bioengineering A(2020)
○Guide to Biology and Bioengineering B(2020)
○Fundamentals of Bioengineering B(2020)
○Data Science B(2019)
○Fundamentals of Bioengineering B(2019)
○Data Science A(2019)
○Genome Informatics(2019)
○Fundamentals of Bioengineering A(2019)
○Presentation and Debate (Freshman Seminar II)(2019)
○Guide to Biology and Bioengineering B(2019)
○Genome Informatics(2018)
○Information and Computer System Engineering Laboratory 1(2018)
○Guide to Biology and Bioengineering B(2018)
○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)
○Presentation and Debate (Freshman Seminar II)(2017)
○Genome Informatics(2017)
○Information and Computer System Engineering Laboratory 1(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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