Books - FUNAHASHI Akira

Cell Biology by the Numbers

Ron Milo, Rob Phillips, 舟橋 啓, 羊土社, 2020.03,  Page： 320

Scope: 監訳

機械学習を生命科学に使う! シークエンスや画像データをどう解析し、新たな生物学的発見につなげるか?

小林徹也, 杉村薫, 舟橋啓, 羊土社, 2020.12,  Page： 240

Scope: 編集; 寄稿

機械学習を生命科学に使う! : シークエンスや画像データをどう解析し、新たな生物学的発見につなげるか?

小林 徹也, 杉村 薫, 舟橋 啓, 羊土社, 2020

組織としての生命

荒金 直人, 堀田 耕司, 坂内健一, 鳥海 崇, 山尾 佐智子, 舟橋 啓, 林 良信, 河野 礼子, 大宮 勘一郎, 黒沢 文貴, 田上 雅徳, 斎藤 慶典, 慶應義塾大学出版会, 2019.05,  Page： 240

Scope: 生命現象を組織として理解する

バイオインフォマティクス入門

秋山 泰, 中井 謙太, 冨田 勝, 向井 有理, 長崎 英樹, 中村 保一, 池田 修己, 向井 友花, 越中谷 賢治, 飯田 泰広, 濱田 康太, 榊原 康文, 舟橋 啓, 鎌田 真由美, 小森 隆, 佐藤 健吾, 浜田 道昭, 内山 郁夫, 阿部 貴志, 野口 英樹, 白井 剛, 土方 敦司, 諏訪 牧子, 有田 正規, 後藤 修, 櫻井 望, 慶應義塾大学出版会, 2015.08,  Page： 176

Scope: 第2章 計算科学

Modeling and Simulation Using CellDesigner

MATSUOKA Yukiko, FUNAHASHI Akira, GHOSH Samik, KITANO Hiroaki, Springer, 2014.06

Scope: 121-145

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In silico modeling and simulation are effective means to understand how the regulatory systems function in life. In this chapter, we explain how to build a model and run the simulation using CellDesigner, adopting the standards such as SBML and SBGN.

Fabrication Method to A High Resolution Control in the Space of Cell Culturing Environment with Microfluidic System

Takumi Hiraiwa, Tadamasa Kimura, Yuma Takenaka, Ryo Tanamoto, Hiroki Ota, Hiroshi Kimura, Yoshihiro Taguchi, Norihisa Miki, Yoshinori Matsumoto, Kotaro Oka, Akira Funahashi, Noriko Hiroi, IEEE, 2014.01

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This paper describes the fabrication and the evaluation of a reusable Cell Culturing Device, designed for a single cell and cellular networks analysis. This is the first success of combination of Microcontact Printing (mCP) and Vacuum Device. This combination has following advantages; (1) cells stay within the micropatterns for long enough duration to achieve local activation of cells or cellular networks (more than 24 h), (2) the displacement distance of laminar flow from the interface of two fluids in Cell Culturing Device keeps smaller than the diameter of a cell, (3) all components of our device except micropatterned substrate are reusable for further analyses. The success of the combination of above techniques provides a controllable environment for the local activation of a single cell and cellular networks. Our device allows to exhibit the different responses induced with the various conditions in a single observation sight at exactly the same time point.

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Introduction to Systems Biology

Shapiro, B., Finney, A., Hucka, M., Bornstein, B., Funahashi, A., Jouraku, A., Keating, S., Novere, N., Matthews, J., and Schilstra, M., Humana Press, 2007.07

Scope: 395-421

Introduction to Systems Biology

FUNAHASHI Akira, Humana Press, 2007.07

Scope: 422-434

Introduction to Systems Biology

Hiroi, N. and Funahashi, A., Humana Press, 2007.07

Scope: 261-281

CellDesigner: A graphical biological network editor and workbench interfacing simulator

Funahashi, A., Morohashi, M., Matsuoka, Y., Jouraku, A., Kitano, H., Introduction to Systems Biology, 2007

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<p>Understanding the logic and dynamics of gene-regulatory and biochemical networks is a major challenge of systems biology. To facilitate this research topic, we have developed CellDesigner, a modeling tool of gene-regulatory and biochemical networks. CellDesigner supports users to easily create such networks, using solidly defined and comprehensive graphical representation (SBGN, systems biology graphical notation). CellDesigner is systems biology markup language (SBML) compliant, and has Systems Biology Workbench(SBW)-enabled software so that it can import/export SBML-described documents and integrate with other SBW-enabled simulation/analysis software packages. CellDesigner also supports simulation and parameter search, which is supported by integration with SBML ordinary differential equation (ODE) Solver, enabling us to simulate through our sophisticated graphical user interface. We can also browse and modify existing SBML models with references to existing databases. CellDesigner is implemented in Java; thus, it runs on various platforms such as Windows, Linux, and MacOS X. CellDesigner is freely available from our Web site at http://celldesigner.org/. © 2007 Humana Press I

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Kinetics of dimension-restricted conditions

N Hiroi, A Funahashi, 2007

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SBML models and MathSBML

BE Shapiro, A Finney, M Hucka, B Bornstein, A Funahashi, A Jouraku, ..., 2007

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Software infrastructure for effective communication and reuse of computational models

A Finney, M Hucka, BJ Bornstein, SM Keating, BE Shapiro, J Matthews, ..., 2006.03

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System Modeling in Cellular Biology: From Concepts to Nuts and Bolts

Finney, A., Hucka, M., Bornstein, B., Keating, S., Shapiro, B., Matthews, J., Kovitz, B., Schilstra, M., FUNAHASHI Akira, Doyle, J., and Kitano, H., MIT Press, 2006.03

入門FreeBSD : Beginner's course

舟橋 啓, 西本 隆之助, 秀和システム, 1998.08