出版物

査読付き論文等

引用数100以上は赤字、引用数20以上は(著者名から)太字にしています。(引用数の詳細や論文のダウンロード等はGoogle Scholar Citations から。)

1. Yachie N, Robotic Biology Consortium (including Takahashi K), and Natsume T: Robotic crowd biology with Maholo LabDroids. Nature Biotechnology 2017, 35:310–312.

2. Arjunan SN, Takahashi K: Multi-algorithm particle simulations with spatiocyte. Methods in Molecular Biology. Accepted.

3. Itaya K, Takahashi K, Nakamura M, Koizumi M, Arakawa N, Tomita M, Yamakawa H: BriCA: A modular software platform for whole brain architecture. In Neural information processing – 23rd international conference, ICONIP 2016, kyoto, japan, october 16-21, 2016, proceedings, part I; 2016:334–341.

4.  Iwamoto K, Shindo Y, Takahashi K: Modeling cellular noise underlying heterogeneous cell responses in the epidermal growth factor signaling pathway. PLOS Computational Biology 2016, 12:1–18.

5. Shindo Y, Iwamoto K, Mouri K, Hibino K, Tomita M, Kosako H, Sako Y, Takahashi K: Conversion of graded phosphorylation into switch-like nuclear translocation via autoregulatory mechanisms in ERK signalling. Nature communications 2016, 7.

6. Takahashi K, Itaya K, Nakamura M, Koizumi M, Arakawa N, Tomita M, Yamakawa H: A generic software platform for brain-inspired cognitive computing. Proc Comput Sci 2015.

7. Karr JR, Takahashi K, Funahashi A: The principles of whole-cell modeling. Current opinion in microbiology 2015, 27:18–24.

8. Watabe M, Arjunan SNV, Fukushima S, Iwamoto K, Kozuka J, Matsuoka S, Shindo Y, Ueda M, Takahashi K: A computational framework for bioimaging simulation. PLOS ONE 2015, 10:e0130089.

9. Shimo H, Arjunan SNV, Machiyama H, Nishino T, Suematsu M, Fujita H, Tomita M, Takahashi K: Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes. PLoS computational biology 2015, 11:e1004210.

10. Feig M, Harada R, Mori T, Yu I, Takahashi K, Sugita Y: Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology. Journal of Molecular Graphics and Modelling 2015, 58:1–9.

11. Maeshima K, Kaizu K, Tamura S, Nozaki T, Kokubo T, Takahashi K: The physical size of transcription factors is key to transcriptional regulation in chromatin domains. Journal of Physics: Condensed Matter 2015, 27:064116.

12. Nishida K, Ono K, Kanaya S, Takahashi K: KEGGscape: A cytoscape app for pathway data integration. F1000Research 2014, 3.

13. Kaizu K, Ronde W de, Paijmans J, Takahashi K, Tostevin F, Wolde PR ten: The berg-purcell limit revisited. Biophysical journal 2014,106:976–985.

14. Hayashi K, Pack C, Sato M, Mouri K, Kaizu K, Takahashi K, Okada Y: Viscosity and drag force involved in organelle transport: Investigation of the fluctuation dissipation theorem. The European Physical Journal E 2013, 36:1–7.

15. Nozaki T, Kaizu K, Pack C-G, Tamura S, Tani T, Hihara S, Nagai T, Takahashi K, Maeshima K: Flexible and dynamic nucleosome fiber in living mammalian cells. Nucleus 2013, 4:349–356.

16. Aoki K, Takahashi K, Kaizu K, Matsuda M: A quantitative model of ERK MAP kinase phosphorylation in crowded media. Scientific reports 2013, 3.

17. Hihara S, Pack C-G, Kaizu K, Tani T, Hanafusa T, Nozaki T, Takemoto S, Yoshimi T, Yokota H, Imamoto N, others: Local nucleosome dynamics facilitate chromatin accessibility in living mammalian cells. Cell reports 2012, 2:1645–1656.

18. Mugler A, Bailey AG, Takahashi K, Wolde PR ten: Membrane clustering and the role of rebinding in biochemical signaling. Biophysical journal 2012, 102:1069–1078.

19. Takahashi K, Tănase-Nicola S, Ten Wolde PR: Spatio-temporal correlations can drastically change the response of a MAPK pathway.Proceedings of the National Academy of Sciences 2010, 107:2473–2478.

20. Takahashi K: An exact brownian dynamics method for cell simulation. In Computational methods in systems biology. Springer; 2008:347–366.

21. Takahashi K: The E-Cell project and challenges in computational systems biology. In Proc NIC workshop. Volume 36; 2007:55–60.

22. Takahashi K, Arjunan SNV, Tomita M: Space in systems biology of signaling pathways–towards intracellular molecular crowding in silico. FEBS letters 2005, 579:1783–1788.

23. Sugimoto M, Takahashi K, Kitayama T, Ito D, Tomita M: Distributed cell biology simulations with E-Cell system. In Grid computing in life science. Springer; 2005:20–31.

24. Takahashi K, Kaizu K, Hu B, Tomita M: A multi-algorithm, multi-timescale method for cell simulation. Bioinformatics 2004, 20:538–546.

25. Takahashi K, Ishikawa N, Sadamoto Y, Sasamoto H, Ohta S, Shiozawa A, Miyoshi F, Naito Y, Nakayama Y, Tomita M: E-Cell 2: Multi-platform E-Cell simulation system. Bioinformatics 2003, 19:1727–1729.

26. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, others: The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 2003,19:524–531.

27. Takahashi K, Yugi K, Hashimoto K, Yamada Y, Pickett CJ, Tomita M: Computational challenges in cell simulation: A software engineering approach. Intelligent Systems, IEEE 2002, 17:64–71.

28. Tomita M, Hashimoto K, Takahashi K, Matsuzaki Y, Matsushima R, Saito K, Yugi K, Miyoshi F, Nakano H, Tanida S, Saito Y, Kawase A, Watanabe N, Simizu T, Nakayama Y: The E-CELL project: Towards integrative simulation of cellular processes. New Generation Computing 2000, 18:1–12.

29. Tomita M, Hashimoto K, Takahashi K, Shimizu TS, Matsuzaki Y, Miyoshi F, Saito K, Tanida S, Yugi K, Venter JC, others: E-CELL: Software environment for whole-cell simulation. Bioinformatics 1999, 15:72–84.

30. Tomita M, Shimizu T, Saito K, Venter JC, Hashimoto K, Matsuzaki Y, Tanida S, Hutchison CA, Takahashi K, Miyoshi F, others: E-CELL: Software environment for whole cell simulation. Genome Informatics 1997, 8:147–155.

31. Shimizu TS, Takahashi K, Tomita M: CpG distribution patterns in methylated and non-methylated species. Gene 1997, 205:103–107.

その他論文等

1. 渡部匡己, 都築拓, 海津一成, 高橋恒一: 人工知能による科学研究の加速. 人工知能学会全国大会論文集 2016, 30:1–4.

2. 高橋恒一, 板谷琴音, 中村政義: 認知コンピューティングのための汎用ソフトウエアプラットフォームの設計と開発. 人工知能学会全国大会論文集 2015, 29:1–4.

著書等

  1. Hibino K, Kaizu K, Takahashi K, and Maeshima K, A Combination Approach Based on Live-Cell Imaging and Computational Modeling to Further Our Understanding of Chromatin, Epigenetics, and the Genome, In Epigenetics and Systems Biology, Eds. Ringrose L, Academic Press  (2017)
  2. 高橋恒一 「学際的な知見の融合・共創による人工知能技術開発」 赤門マネジメント・レビュー 15巻12号 (2016)
  3. 今井亮輔、海津一成、野崎慎、前島一博、高橋恒一 「定量的1分子蛍光イメージングと計算機シミュレーションを用いたゲノムダイナミクスの解析」生化学 Vol.86 No.2 pp.192-200 (2014)
  4. 岩本一成、海津一成、高橋恒一 「生化学反応ネットワークのシミュレーション」 生体の科学 Vol.65 No.5 pp.446-447 (2014)
  5. Addy N, and Takahashi K, Foundations of E-Cell Simulation Environment Architecture, In E-Cell System – Basic Concepts and Applications, Eds. Arjunan S.N.V., Dhar P, and Tomita M, Landes Biosciences (2013).
  6. 高橋恒一  「1分子粒度細胞シミュレーション」 シミュレーション辞典、 Eds. 日本シミュレーション学会 (コロナ社) (2012).
  7. 高橋恒一、 海津一成 「細胞シミュレーション – 計算機上での細胞機能の再構成」 実験医学増刊 Vol.29 No.7 「細胞を創る・生命システムを創る」、 Eds.上田泰己、竹内昌治 (羊土社) (2011).
  8. 高橋恒一 「システム生物学」 計算力学シミュレーションハンドブック – 超ペタスケールコンピューティングの描像、Eds. 小柳義夫、土居範久、松田卓也、矢川元基、(丸善) (2009).
  9. Dhar P, Takahashi K, Nakayama Y, and Tomita M. Computer Simulation of the Cell, In Encyclopedia of Molecular Cell Biology and Molecular Medicine, Wiley VCH, (2003).