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. 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)
  2. 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)
  3. 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)
  4. 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).
  5. 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).
  6. 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).
  7. 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).
  8. 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).