Funahashi, Akira

J-GLOBAL         Last updated: Oct 26, 2019 at 02:47
 
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Name
Funahashi, Akira
URL
https://fun.bio.keio.ac.jp/
Affiliation
Keio University
Section
Faculty of Science and Technology Department of Biosciences and Informatics
Job title
Associate Professor
Degree
Ph.D.(Keio University)
Research funding number
70324548
ORCID ID
0000-0003-0605-239X

Research Areas

 
 

Academic & Professional Experience

 
Apr 1997
 - 
Mar 2000
Research Fellow, Japan Society of the Promotion of Science (DC1)
 
May 2000
 - 
Mar 2002
Research Associate, Department of Information Technology, Mie University
 
Apr 2002
 - 
Mar 2007
Researcher, ERATO-SORST Kitano Symbiotic Systems Project, JST
 
Apr 2004
 - 
Mar 2005
Lecturer, Dept. of Electrical Engineering and Bioscience, Waseda University
 
Apr 2004
 - 
Mar 2007
Researcher, The Systems Biology Institute
 
Apr 2004
 - 
Mar 2007
Lecturer, Dept. of Biosciences and Informatics, Keio University
 
Apr 2007
 - 
Mar 2009
慶應義塾大学理工学部生命情報学科専任講師
 
Apr 2009
 - 
Today
Associate Professor, Dept. of Biosciences and Informatics, Keio University
 
Apr 2017
 - 
Today
非常勤講師, 医学系研究科, 山口大学大学院
 

Education

 
Mar 2000
   
 
Dept. of Computer Science, Graduate School, Division of Science and Engineering, Keio University
 
Mar 1997
   
 
Dept. of Computer Science, Graduate School, Division of Science and Engineering, Keio University
 
Mar 1995
   
 
電気工学科, Faculty of Science and Engineering, Keio University
 

Committee Memberships

 
May 2019
 - 
Aug 2019
Google Summer of Code 2019  Google Summer of Code Mentors
 
May 2017
 - 
Aug 2017
Google Summer of Code 2017  Google Summer of Code Mentors
 
Apr 2016
 - 
Aug 2016
Google Summer of Code 2016  Google Summer of Code Mentors
 
Jul 2014
 - 
Aug 2014
Google Summer of Code 2014  Google Summer of Code Mentors
 

Awards & Honors

 
Oct 2015
平成27年度科学研究費審査委員表彰, Japan Society for the Promotion of Science
 

Published Papers

 
Novère Nicolas Le, Hucka Michael, Mi Huaiyu, Moodie Stuart, Schreiber Falk, Sorokin Anatoly, Demir Emek, Wegner Katja, Aladjem Mirit I, Wimalaratne Sarala M, Bergman Frank T, Gauges Ralph, Ghazal Peter, Kawaji Hideya, Li Lu, Matsuoka Yukiko, Villéger Alice, Boyd Sarah E, Calzone Laurence, Courtot Melanie, Dogrusoz Ugur, Freeman Tom C, FUNAHASHI AKIRA, Ghosh Samik, Jouraku Akiya, Kim Sohyoung, Kolpakov Fedor, Luna Augustin, Sahle Sven, Schmidt Esther, Watterson Steven, Wu Guanming, Goryanin Igor, Kell Douglas B, Sander Chris, Sauro Herbert, Snoep Jacky, L Kohn Kurt, Kitano Hiroaki
Nature Biotechnology   27(8) 735-741-741   Aug 2009   [Refereed]
Using process diagrams for the graphical representation of biological networks.
Kitano, H., Funahashi, A., Matsuoka, Y., and Oda, K.
Nature Biotechnology   23(8) 961-966   Aug 2005   [Refereed]
Oda, K., Matsuoka, Y., Funahashi, A., and Kitano, H.
Nature Molecular Systems Biology   1(1) 1-17   May 2005   [Refereed]
Karr Jonathan R., Takahashi Koichi, Funahashi Akira
Current Opinion in Microbiology   27 18-24   Oct 2015   [Refereed]
<p>Whole-cell models which comprehensively predict how phenotypes emerge from genotype promise to enable rational bioengineering and precision medicine. Here, we outline the key principles of whole-cell modeling which have emerged from our work de...
Sumiyoshi, Kei, Hirata, Kazuki, Hiroi, Noriko, Funahashi, Akira
FRONTIERS IN PHYSIOLOGY   6 155-169   Feb 2015   [Refereed]
Yuichiro Nakai; Mitsunori Ozeki; Takumi Hiraiwa; Ryuichi Tanimoto; Akira Funahashi; Noriko Hiroi; Atsushi Taniguchi; Shigenori Nonaka; Viviane Boilot; Roshan Shrestha; Joanna Clark; Naoka Tamura; Viji M. Draviam; Hiromasa Oku
Review of Scientific Instruments   86(1) 013707   Jan 2015   [Refereed]
Tanimoto, Ryuichi, Hiraiwa, Takumi, Nakai, Yuichiro, Shindo, Yutaka, Oka, Kotaro, Hiroi, Noriko, Funahashi, Akira
SCIENTIFIC REPORTS   6 22071   Mar 2016   [Refereed]
Hiraiwa T., Yamada T., Miki N., Funahashi A., Hiroi N.
Journal of the Royal Society, Interface   16(152) 20180934   Mar 2019   [Refereed]
Neuroblastoma is the most common solid tumour of childhood, and it metastasizes to distant organs. However, the mechanism of metastasis, which generally depends on the cell motility of the neuroblastoma, remains unclear. In many solid tumours, it ...
S Nishimoto, Y Tokuoka, TG Yamada, NF Hiroi, A Funahashi
PloS one 14 (9), e0221245   14(9) e0221245   2019   [Refereed]
© 2019 Nishimoto et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source a...
XitoSBML: a modeling tool for creating spatial SBML models from microscopic images
K Ii, K Mashimo, M Ozeki, TG Yamada, NF Hiroi, A Funahashi
Frontiers in Genetics 10, 1027      2019   [Refereed]
Yamada T., Suetsugu Y., Deviatiiarov R., Gusev O., Cornette R., Nesmelov A., Hiroi N., Kikawada T., Funahashi A.
Scientific Reports   8(1) 17941   Dec 2018   [Refereed]
© 2018, The Author(s). The larvae of the African midge, Polypedilum vanderplanki, can enter an ametabolic state called anhydrobiosis to overcome fatal desiccation stress. The Pv11 cell line, derived from P. vanderplanki embryo, shows desiccation t...
Hiraiwa T., Nakai Y., Yamada T., Tanimoto R., Kimura H., Matsumoto Y., Miki N., Hiroi N., Funahashi A.
FEBS Open Bio   8(12) 1920-1935   Dec 2018   [Refereed]
© 2018 The Authors. Published by FEBS Press and John Wiley & Sons Ltd. Proper determination of the cell division axis is essential during development. Wnt3a is a known regulator of the cell division axis; however, the sensitivity of cells to Wnt...
N Hiroi, R Tanimoto, K Ii, M Ozeki, K Mashimo, A Funahashi
Biomedical Imaging and Sensing Conference 10251, 102510Q   10251    2017   [Refereed]
Hiroi, Noriko, Draviam, Viji M., Funahashi, Akira
FRONTIERS IN PHYSIOLOGY   7 196   Jun 2016   [Refereed]
FUNAHASHI Akira, HIROI Noriko
Folia pharmacologica Japonica   147(2) 101-106   Feb 2016   [Refereed][Invited]
Funahashi Akira, Hiroi Noriko
Folia Pharmacologica Japonica   147(2) 101-106   2016
KOBAYASHI Tetsuya, OZEKI Mitsunori, YAMAGATA Kazuo, Funahashi Akira
IEICE technical report.   114(482) 1-6   Mar 2015   [Refereed]
Reconstruction of developmental dynamics of mammalian preimplantation embryos from bioimaging data by using image analysis is now becoming an important challenge in the fields of basic science and assisted reproductive technology. In this work, we...
Tamura, Naoka, Simon, Judith E., Nayak, Arnab, Shenoy, Rajesh, Hiroi, Noriko, Boilot, Viviane, Funahashi, Akira, Draviam, Viji M.
BIOLOGY OPEN   4(2) 155-169   Feb 2015   [Refereed]
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 27th International Conference on Micro Electro Mechanical Systems (MEMS)      Jan 2014   [Refereed]
Matsuoka Yukiko, Funahashi Akira, Ghosh Samik, Kitano Hiroaki
Methods in molecular biology (Clifton, N.J.)   1164 121-145   2014   [Refereed]
<p>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...
Noriko Hiroi, Maciej Swat, Akira Funahashi
Frontiers in physiology   5 128   2014   [Refereed]
Corrigan, Adam M., Shrestha, Roshan L., Zulkipli, Ihsan, Hiroi, Noriko, Liu, Yingjun, Tamura, Naoka, Yang, Bing, Patel, Jessica, Funahashi, Akira, Donald, Athene, Draviam, Viji M.
CELL CYCLE   12(16) 2643-2655   Aug 2013   [Refereed]
in vivo oriented modeling with consideration of intracellular crowding
N Hiroi, K Iba, A Tabira, T Okuhara, T Kubojima, T Hiraiwa, T J Kobayashi, K Oka, A Funahashi
35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)      Jul 2013   [Refereed][Invited]
Keller, Roland, Doerr, Alexander, Tabira, Akito, Funahashi, Akira, Ziller, Michael J., Adams, Richard, Rodriguez, Nicolas, Le Novere, Nicolas, Hiroi, Noriko, Planatscher, Hannes, Zell, Andreas, Draeger, Andreas
BMC SYSTEMS BIOLOGY   7 2643-2655   Jul 2013   [Refereed]
TAKIZAWA Hiromu, NAKAMURA Kazushige, TABIRA Akito, CHIKAHARA Yoichi, MATSUI Tatsuhiro, HIROI Noriko, FUNAHASHI Akira
BIOINFORMATICS   29(11) 1474-1476   Jun 2013   [Refereed]
Viji M Draviam, Akira Funahashi, Noriko Hiroi, Akatsuki Kimura, Tetsuya J Kobayashi
Frontiers in physiology   3 479   Jan 2013   [Refereed]
TAKIZAWA Hiromu, HIROI Noriko, FUNAHASHI Akira
PLOS ONE   7(12) e51000   Dec 2012   [Refereed]
van Iersel, Martijn P., Villeger, Alice C., Czauderna, Tobias, Boyd, Sarah E., Bergmann, Frank T., Luna, Augustin, Demir, Emek, Sorokin, Anatoly, Dogrusoz, Ugur, Matsuoka, Yukiko, Funahashi, Akira, Aladjem, Mirit I., Mi, Huaiyu, Moodie, Stuart L., Kitano, Hiroaki, Le Novere, Nicolas, Schreiber, Falk
BIOINFORMATICS   28(15) 2016-2021   Aug 2012   [Refereed]
Noriko Hiroi, Takahiro Okuhara, Takeshi Kubojima, Keisuke Iba, Akito Tabira, Shuji Yamashita, Yasunori Okada, Tetsuya J Kobayashi, Akira Funahashi
Frontiers in physiology   3 293   Jul 2012   [Refereed]
Noriko Hiroi, Michael Klann, Keisuke Iba, Pablo de Heras Ciechomski, Shuji Yamashita, Akito Tabira, Takahiro Okuhara, Takeshi Kubojima, Yasunori Okada, Kotaro Oka, Robin Mange, Michael Unger, Akira Funahashi, Heinz Koeppl
EURASIP Journal on Bioinformatics and Systems Biology   2012(1) 7   2012   [Refereed]
Mi, Huaiyu, Muruganujan, Anushya, Demir, Emek, Matsuoka, Yukiko, Funahashi, Akira, Kitano, Hiroaki, Thomas, Paul D.
BIOINFORMATICS   27(24) 3437-3438   Dec 2011   [Refereed]
Physiological environment induces quick response–slow exhaustion reactions
Noriko Hiroi, James Lu, Keisuke Iba, Akito Tabira, Shuji Yamashita, Yasunori Okada, Christoph Flamm, Kotaro Oka, Gottfried Köhler, Akira Funahashi
Frontiers in physiology   2 50   Sep 2011   [Refereed]
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows.
Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong-Woo Chun, Jan Aerts, Bruno Aranda, Lord Hendrix Barboza, Raoul JP Bonnal, Richard Bruskiewich, Jan C Bryne, José M Fernández, Akira Funahashi, Paul MK Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard Holland, Yoshinobu Kano, Edward A Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehvaslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Lukasz Salwinski, Mark Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A Vos, Mark D Wilkinson, William York, Christian M Zmasek, Kiyoshi Asai, Toshihisa Takagi
Journal of biomedical semantics   1(1) 1-19   Dec 2010   [Refereed]
A datapath classification method for FPGA-based scientific application accelerator systems
Yui Ogawa, Tomonori Ooya, Yasunori Osana, Masato Yoshimi, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Hideharu Amano, Yuichiro Shibata, Kiyoshi Oguri
International Conference on Field-Programmable Technology (FPT)   441-444   Dec 2010   [Refereed]
Hideki Yamada, Yui Ogawa, Tomonori Ooya, Tomoya Ishimori, Yasunori Osana, Masato Yoshimi, Yuri Nishikawa,Akira Funahashi, Noriko Hiroi, Hideharu Amano, Yuichiro Shibata, Kiyoshi Oguri
IPSJ Transactions on System LSI Design Methodology   3 244-256   Aug 2010   [Refereed]
For FPGA-based scientific simulation systems, hardware design technique that can reduce required amount of hardware resources is a key issue, since the size of simulation target is often limited by the size of the FPGA. Focusing on FPGA-based bioc...
Hideki Yamada, Yasunori Osana, Tomoya Ishimori, Tomonori Ooya, Masato Yoshimi, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Hideharu Amano, Yuichiro Shibata, Kiyoshi Oguri
International Conference on Reconfigurable Computing and FPGAs, 2009. ReConFig'09.   125-130   Dec 2009   [Refereed]
Tomonori Ooya, Hideki Yamada, Tomoya Ishimori, Yuichiro Shibata, Yasunori Osana, Kiyoshi Oguri, Masato Yoshimi, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Hideharu Amano
International Conference on Field Programmable Logic and Applications, 2009. FPL 2009   679-682   Aug 2009   [Refereed]
Tomoya Ishimori, Hideki Yamada, Yuichiro Shibata, Yasunori Osana, Masato Yoshimi, Yuri Nishikawa, Hideharu Amano, Akira Funahashi, Noriko Hiroi, Kiyoshi Oguri
5th International Workshop, ARC 2009, Proceedings   5453(2009) 368-373   Mar 2009   [Refereed]
FPGAを用いた高スループット確率モデル生化学シミュレータの設計と評価
YOSHIMI Masato, NISHIKAWA Yuri, OSANA Yasunori, FUNAHASHI Akira, HIROI Noriko, SHIBATA Yuuichirou, YAMADA Hideki, KITANO Hiroaki, AMANO Hideharu
IPSJ Transactions on Advanced Computing System   1(3) 120-135   Dec 2008   [Refereed]
Masato Yoshimi, Yuri Nishikawa, Yasunori Osana, Akira Funahashi, Yuichiro Shibata, Hideki Yamada, Noriko Hiroi, Hiroaki Kitano, Hideharu Amano
International Conference on Field Programmable Logic and Applications, 2008. FPL 2008   663-666   Sep 2008   [Refereed]
FPGA上でのシミュレーションに向けた生化学コンパイラの実装
IWAOKA Yo, OSANA Yasunori, YOSHIMI Masato, NISHIKAWA Yuri, KOJIMA Toshinori, FUNAHASHI Akira, HIROI Noriko, SHIBATA Yuuichirou, IWANAGA Naoki, KITANO Hiroaki, AMANO Hideharu
電子情報通信学会論文誌 D   J91-D(9) 2205-2216   Sep 2008   [Refereed]
FUNAHASHI Akira, MATSUOKA Yukiko, JOURAKU Akiya, MOROHASHI Mineo, KIKUCHI Norihiro, KITANO Hiroaki
IEEE Special Issue: Computational Systems Biology   96(8) 1254-1265-1265   Aug 2008   [Refereed]
Masato Yoshimi, Yuri Nishikawa, Toshinori Kojima, Yasunori Osana, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Hideki Yamada, Hiroaki Kitano, Hideharu Amano
International Conference on Field-Programmable Technology, 2007. ICFPT 2007.   193-200   Dec 2007   [Refereed]
FPGA implementation of a data-driven stochastic biochemical simulator with the next reaction method
Masato Yoshimi, Yow Iwaoka, Yuri Nishikawa, Toshinori Kojima, Yasunori Osana, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hideki Yamada, Hiroaki Kitano, Hideharu Amano
International Conference on Field Programmable Logic and Applications, 2007. FPL 2007   254-259   Aug 2007   [Refereed]
Hideki Yamada, Naoki Iwanaga, Yuichiro Shibata, Yasunori Osana, Masato Yoshimi, Yow Iwaoka, Yuri Nishikawa, Toshinori Kojima, Hideharu Amano, Akira Funahashi, Noriko Hiroi, Hiroaki Kitano, Kiyoshi Oguri
International Conference on Field Programmable Logic and Applications, 2007. FPL 2007   808-811   Aug 2007   [Refereed]
Deduction of intracellular sub-systems from a topological description of the network.
NORDLING Torbjorn, HIROI, Noriko, FUNAHASHI Akira and KITANO Hiroaki
Molecular Biosystems   3(8) 523-529   Aug 2007   [Refereed]
ReCSiP: An FPGA-Based Biochemical Simulator
Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H
Electronics and Communications in Japan (Part II: Electronics)   90(7) 1-10   Jul 2007   [Refereed]
An integration of CellDesigner and SABIO-RK
FUNAHASHI Akira, JOURAKU Akiya, MATSUOKA Yukiko, KITANO Hiroaki
In Silico Biology   7(2) S81-S90.   Mar 2007   [Refereed]
FPGA-Based Stochastic Biochemical Simulator
Yoshimi, M., Osana, Y., Iwaoka, Y., Nishikawa, Y., Kojima, T., Shibata, Y., Iwanaga, N., Funahashi, A., Hiroi, N., Kitano, H., and Amano, H.
IPSJ Transactions on Advanced Computing System   48(SIG 3 (ACS 17)) 45-58   Feb 2007   [Refereed]
Funahashi Akira, Morohashi Mineo, Matsuoka Yukiko, Jouraku Akiya, Kitano Hiroaki
422-434   2007
<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 netw...
Nordling Torbjörn E M, Hiroi Noriko, Funahashi Akira, Kitano Hiroaki
Molecular BioSystems   3(8) 523-529   2007
<p>Non-linear behaviour of biochemical networks, such as intracellular gene, protein or metabolic networks, is commonly represented using graphs of the underlying topology. Nodes represent abundance of molecules and edges interactions between pair...
Hiroi Noriko, Funahashi Akira
261-281   2007
<p>The intracellular environment is crowded with skeletal proteins, organelle membranes, ribosomes, and so on. When molecular movement is restricted by such environments, some biochemical reaction processes cannot be represented by classical model...
Shapiro Bruce E., Finney Andrew, Hucka Michael, Bornstein Benjamin, Funahashi Akira, Jouraku Akiya, Keating Sarah M., Le Novère Nicolas, Matthews Joanne, Schilstra Maria J.
395-421   2007
<p>MathSBML is an open-source, freely downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a tool-neutral, computer-readable format for representing models of biochemical reaction ne...
Integration of cell designer and SABIO-RK
Funahashi Akira, Jouraku Akiya, Matsuoka Yukiko, Kitano Hiroaki
In Silico Biology   7(SUPPL. 2) 81-90   2007   [Refereed]
<p>Understanding the logic and dynamics of gene-regulatory and biochemical networks is a major challenge for systems biology. To facilitate this research topic, we have developed CellDesigner to visualize, model and simulate biochemical networks. ...
Introduction to systems biology
S Choi
Humana press      2007   [Refereed]
CellDesigner: a modeling tool for biochemical networks
Akira Funahashi, Yukiko Matsuoka, Akiya Jouraku, Hiroaki Kitano, Norihiro Kikuchi
Proceedings of the 38th conference on Winter simulation conference (WSC'06)   1707-1712   Dec 2006   [Refereed][Invited]
Yasunori Osana, Masato Yoshimi, Yow Iwaoka, Toshinori Kojima, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, N Kitano, Hideharu Amano
International Conference on Field Programmable Logic and Applications, 2006. FPL'06.   1-6   Aug 2006   [Refereed]
Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Yuri Nishikawa, Toshinori Kojima, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, Hideharu Amano
International Conference on Field Programmable Logic and Applications, 2006. FPL'06.   1-6   Aug 2006   [Refereed]
OSANA Yasunori, YOSHIMI Masato, IWAOKA Yow, KOJIMA Toshinori, NISHIKAWA Yuri, FUNAHASHI Akira, HIROI Noriko, SHIBATA Yuichiro, IWANAGA Naoki, KITANO Hiroaki, AMANO Hideharu
The IEICE transactions on information and systems   89(6) 1163-1172   Jun 2006   [Refereed]
細胞内部の生化学反応を数理モデルとして記述し,シミュレーションを行うことで生命現象をシステムとして理解しようとする試みが盛んになっている.しかしながら,汎用のマイクロプロセッサで得られる処理能力は決して十分とはいえず,シミュレーションを高速に実行できる計算基盤が求められている.本論文では,FPGAを用いて常微分方程式を用いた生化学モデルのシミュレーションを高速に実行するシステムであるReCSiPの構成とハードウェアの実装について述べる.評価の結果,最大スループットはXilinx社のFPGA...
Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H.
IEICE Transactions on Information and Systems   J89-D(6) 1163-1172-10   Jun 2006   [Refereed]
Hiroi, N., Funahashi, A., and Kitano, H.
Cancer Gene Therapy   13(1) 7-12-12   Jan 2006   [Refereed]
Analysis for Dimension-Restricted Kinetics with Bacterial Endonuclease Movement.
Hiroi, N., Funahashi, A., and Kitano, H.
WSEAS Transactions on Biology and Biomedicine   3(1) 1-6   Jan 2006   [Refereed]
Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, Hideharu Amano
IEEE International Conference on Field-Programmable Technology, 2005.   339-340   Dec 2005   [Refereed]
Kitano Hiroaki, Funahashi Akira, Matsuoka Yukiko, Oda Kanae
Nature Biotechnology   23(8) 961-966   Aug 2005
<p>With the increased interest in understanding biological networks, such as protein-protein interaction networks and gene regulatory networks, methods for representing and communicating such networks in both human- and machine-readable form have ...
Naoki Iwanaga, Yuichiro Shibata, Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Tomonori Fukushima, Hideharu Amano, Akira Funahashi, Noriko Hiroi, Hiroaki Kitano, Kiyoshi Oguri
International Conference on Field Programmable Logic and Applications, 2005.   666-669   Aug 2005   [Refereed]
Yasunori Osana, T Fukushima, M Yoshimi, Y Iwaoka, H Amano, A Funahashi, N Hiroi, H Kitano, Y Shibata, N Iwanaga
International Conference on Field Programmable Logic and Applications, 2005   574-577   Aug 2005   [Refereed]
Yasunori Osana, Tomonori Fukushima, Masato Yoshimi, Yow Iwaoka, A Funahashi, N Hiroi, Y Shibata, H Kitano, Hideharu Amano
Proceedings. 19th IEEE International Parallel and Distributed Processing Symposium, 2005.   4   Apr 2005   [Refereed]
An I/O mechanism on a dynamically reconfigurable processor-which should be moved: data or configuration?
H Amano, S Abe, K Deguchi, Y Hasegawa
International Conference on Field Programmable Logic and Applications, 2005 …      2005   [Refereed]
Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.
Hucka, M., Finney, A., Bornstein, B. J., Keating, S. M., Shapiro, B. E., Matthews, J., Kovitz, B. L., Schilstra, M. J., Funahashi, A., Doyle J. C., and Kitano, H.
IEE Systems Biology   1(1) 41-53   Sep 2004   [Refereed]
Molecular Interaction Map of Macrophage.
Oda, K., Kimura, T, Matsuoka, Y., Funahashi, A., Muramatsu, M., and Kitano, H.
AfCS Report   2(14) 1-12   Aug 2004
CellDesigner: a process diagram editor for gene-regulatory and biochemical networks.
Funahashi, A., Tanimura, N., Morohashi, M., and Kitano, H.
BioSilico   1(5) 159-162   Nov 2003
[The ERATO Systems Biology Workbench and Systems Biology Markup Language: an integrated environment and standardization for systems biology].
Funahashi A
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme   48(7) 810-6   Jun 2003   [Refereed]
The ERATO Systems Biology Workbench and Systems Biology Markup Language
Funahashi Akira
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme   48(7) 810-816   2003
An Output Selection Function based on the characteristic of virtual channel
Sugiyama, S. and Funahashi, A.
IPSJ Journal   43(3) 764-775   Mar 2002   [Refereed]
Z-routing: Adaptive routing on irregular networks
Igawa, Y. and Funahashi, A.
IPSJ Journal   43(3) 754-763   Mar 2002   [Refereed]
The Impact of Output Selection Function on Adaptive Routing.
Funahashi, A., Koibuchi, M., Jouraku, A., and Amano, H.
ISCA Information: An International Journal   4(4) 541-550   Nov 2001   [Refereed]
Koibuchi, M., Funahashi, A., Jouraku, A., and Amano, H.
IPSJ Journal of High Performance Computing System   42(SIG9) 119-134-134   Aug 2001   [Refereed]
Network-based parallel processing using commodity personal computers has been widely developed. Since such systems require high degree of flexibility and scalability of wiring, a high-speed network with an irregular topology is often needed. In tr...
Recursive Diagonal Torus: an interconnection network for massively parallel computers.
Yang, Y., Funahashi, A., Jouraku, A., Nishi, H., Amano, H., and Sueyoshi, T.
IEEE Trans. on Parallel and Distributed Systems   12(7) 701-715-715   Jul 2001   [Refereed]
The Impact of Output Selection Function on Adaptive Routing.
Koibuchi, M., Funahashi, A., Jouraku, A., and Amano, H.
IPSJ Journal   42(4) 704-713   Apr 2001   [Refereed]
Funahashi, A., Jouraku, A., and Amano, H.
IEICE Transactions on Information and Systems   J89-D-I(11) 1143-1153-1153   Nov 2000   [Refereed]
相互結合網RDTは再帰構造をもつTorusの重なりから構成されており, 超並列計算機のプロセッサ間接続を行うために優れた性質を多くもっている.超並列計算機に用いられる相互結合網において, 混雑若しくは故障したノードを回避できるルーチングアルゴリズムは必要不可欠である.既存のベクトルルーチングはシンプルではあるが, 固定ルーチング(deterministic routing)であるためこのようなノードを迂回することはできない.本研究では, Duatoによる必要十分条件を用いることによりRDT...
Torus assignment for an interconnection network recursive diagonal torus
Fan Qin, Yang Yulu, Funahashi Akira, Amano Hideharu
Proceedings of the International Symposium on Parallel Architectures, Algorithms and Networks, I-SPAN   74-79   1999
<p>Recursive Diagonal Torus (RDT) is a class of interconnection network consisting of recursively overlaid two-dimensional square diagonal tori for massively parallel computers with up to 216 nodes. Connection structures of the RDT vary...
A torus assignment for an interconnection network recursive diagonal torus
Q Fan, Y Yang, A Funahashi, H Amano
Proceedings Fourth International Symposium on Parallel Architectures …      1999   [Refereed]
Adaptive routing on the recursive Diagonal torus
A Funahashi, T Hanawa, T Kudoh, H Amano
International Symposium on High Performance Computing, 171-182      1997   [Refereed]
Funahashi, A., Hanawa, T., and Amano, H.
IEICE Transactions on Information and Systems   E79-D(8) 1180-1189-1189   Aug 1996   [Refereed]
Multistage Interconnection Networks (MIN) with multiple outlets are networks which can support higher bandwidth than those of nonblocking networks by passing multiple packets to the same destination. Fault recovery mechanisms are proposed for two ...

Misc

 
【病理形態学の新技術】画像解析と深層学習を用いた診断の基礎
舟橋 啓, 徳岡 雄大, 大岡 麻耶, 西本 勝利, 山田 貴大, 広井 賀子
病理と臨床   37(7) 631-635   Jul 2019   [Refereed][Invited]
Funahashi Akira, Hiroi Noriko
Folia Pharmacologica Japonica   147(2) 101-106   Feb 2016   [Refereed][Invited]
生命現象の理解には個別のコンポーネントについての理解に加え、それらの統合されたふるまいを知る必要がある。このような様々な分子のダイナミクスの背景にあるメカニズムを理解する上で強力なツールとなるのが数理モデルである。システムバイオロジーでは、数理モデルを用いて生命現象を司るメカニズムを理解する手法を頻用する。歴史的には解析的に解くことが可能なモデルが用いられたが、コンピュータの発達により、常微分方程式モデル、偏微分方程式モデル、確率モデル、これらのハイブリッドモデルなど多岐に渡る形式で記述さ...
【バイオイメージング】定量的生命科学のためのバイオ画像解析とその哺乳類発生動態への応用
小林 徹也, バシャール・カイルル , 舟橋 啓, 藤森 俊彦, 山縣 一夫
MEDICAL IMAGING TECHNOLOGY   33(3) 84-89   May 2015   [Refereed][Invited]
バイオイメージング技術の発展と普及とともに、顕微鏡イメージから生命システムの動態に関する情報を定量的に取得する方法としてバイオ画像解析技術は大きく注目されている。本稿では、イメージングデータへの画像解析の応用事例について概説するとともに、哺乳類着床前胚の発生動態と細胞系譜の再構成を目的とするわれわれの研究の進展について紹介する。(著者抄録)
【生命動態システム科学】定量生物学 分子・細胞の計測 基本技術 生命現象のシステムレベルでの理解に向けた基盤技術開発
舟橋 啓
生体の科学   65(5) 388-389   Oct 2014   [Refereed][Invited]
FPGAを用いた汎用生化学シミュレータReCSiP
長名 保範, 吉見 真聡, 岩岡 洋, 小嶋 利紀, 西川 由理, 舟橋 啓, 広井 賀子, 柴田 裕一郎, 岩永 直樹, 北野 宏明, 天野 英晴
電子情報通信学会論文誌D: 情報・システム   89(6) 1163-1172   Jun 2006   [Refereed][Invited]
細胞内部の生化学反応を数理モデルとして記述し,シミュレーションを行うことで生命現象をシステムとして理解しようとする試みが盛んになっている.しかしながら,汎用のマイクロプロセッサで得られる処理能力は決して十分とはいえず,シミュレーションを高速に実行できる計算基盤が求められている.本論文では,FPGAを用いて常微分方程式を用いた生化学モデルのシミュレーションを高速に実行するシステムであるReCSiPの構成とハードウェアの実装について述べる.評価の結果,最大スループットはXilinx社のFPGA...

Books etc

 
Modeling and Simulation Using CellDesigner
MATSUOKA Yukiko, FUNAHASHI Akira, GHOSH Samik, KITANO Hiroaki (Part:Joint Work, 121-145)
Springer   Jun 2014   ISBN:978-1-4939-0804-2
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.
Shapiro, B., Finney, A., Hucka, M., Bornstein, B., Funahashi, A., Jouraku, A., Keating, S., Novere, N., Matthews, J., and Schilstra, M. (Part:Joint Work, 395-421)
Humana Press   Jul 2007   ISBN:1-58829-706-3
Hiroi, N. and Funahashi, A. (Part:Joint Work, 261-281)
Humana Press   Jul 2007   ISBN:1-58829-706-3
FUNAHASHI Akira
Humana Press   Jul 2007   ISBN:1-58829-706-3
Finney, A., Hucka, M., Bornstein, B., Keating, S., Shapiro, B., Matthews, J., Kovitz, B., Schilstra, M., FUNAHASHI Akira, Doyle, J., and Kitano, H. (Part:Joint Work)
MIT Press   Mar 2006   ISBN:0-262-19548-8

Conference Activities & Talks

 
腫瘍内不均一性を考慮した予後の予測に向けた深層学習ベースの組織画像解析 [Invited]
FUNAHASHI Akira
群馬大学数理データ科学教育研究センター主催第1回レギュラトリー サイエンスセミナー   5 Sep 2019   
機械学習による画像分類 [Invited]
FUNAHASHI Akira, Tokuoka, Y.
AIによる生物画像解析トレーニングコース   29 Aug 2019   
Inference of transcriptional regulatory network driven by desiccation and rehydration in Polypedilum vanderplanki [Invited]
Hiki, Y., Yamada, T.G., Kozlova, O., Cornette, R., Gusev, O., Kikawada, T., FUNAHASHI Akira
Moscow Conference on Computational Molecular Biology 2019   28 Jul 2019   
Mathematical Modeling with CellDesigner. [Invited]
FUNAHASHI Akira
Computational and Mathematical Biology Course, Okinawa Institute of Science and Technology   24 Jul 2019   
CellDesigner: A modeling tool for biochemical networks [Invited]
FUNAHASHI Akira
COMBINE 2019   17 Jul 2019   
畳み込みニューラルネットワークを用いた神経分化判別および特徴量解析 [Invited]
FUNAHASHI Akira
山口大学 AIシステム医学医療研究教育センター セミナー   28 May 2019   
不妊治療に資する深層学習を用いた初期胚定量評価手法の開発 [Invited]
FUNAHASHI Akira
Cardiovascular Meeting   20 May 2019   
不妊治療に資する深層学習を用いた初期胚定量評価手法の開発 [Invited]
徳岡 雄大, 山田 貴大, 広井 賀子, 小林 徹也, 山縣 一夫, 舟橋 啓
第18回日本再生医療学会総会   23 Mar 2019   
Convolutional Neural Network-Based Instance Segmentation Algorithm to Acquire Quantitative Criteria of Early Mouse Development [Invited]
FUNAHASHI Akira
Seminar at University of Nottingham   8 Mar 2019   
深層学習が駆動するPv11生存細胞スクリーニング [Invited]
Tokuoka, Y., Yamada, T., Cornette, R., Hiroi, N., Kikawada, T., and FUNAHASHI Akira
エンジニアリングネットワーク・ワークショップ - 生物のもつ耐性機能と工学の融合 -   26 Feb 2019   
深層学習が明らかにする細胞顕微鏡画像解析の新展開 [Invited]
FUNAHASHI Akira
山口大学 AIシステム医学医療研究教育センター セミナー   14 Dec 2018   
Quantitative analysis of sensitivity to Wnt3a gradient in determination of the pole-to-pole axis of mitotic cells by using a microfluidic device. [Invited]
Hiraiwa, T., Yamada, T. G., Miki, N., FUNAHASHI Akira., and Hiroi, N.
Keio University International Symposium on Advanced Technologies for Mechano-biology and Regenerative Medicine   21 Sep 2018   
ディープラーニングを用いたマウス発生過程における定量的指標の獲得 [Invited]
FUNAHASHI Akira
第36回 日本受精着床学会総会・学術講演会   27 Jul 2018   
深層学習が明らかにする細胞顕微鏡画像解析の新展開 [Invited]
FUNAHASHI Akira
関西医科大学大学院セミナー   17 Jul 2018   
Mathematical Modeling with CellDesigner. [Invited]
FUNAHASHI Akira
Computational and Mathematical Biology Course, Okinawa Institute of Science and Technology   22 Jun 2018   
深層学習が明らかにする細胞顕微鏡画像解析の新展開 [Invited]
FUNAHASHI Akira
自然科学研究機構 新分野創成センター合同シンポジウム 「分野横断・分野融合研究による生命創成を探究する新しい科学の創成」   15 Mar 2018   
CellDesigner [Invited]
FUNAHASHI Akira
SYSBIO 2018 Advanced Lecture Course on Systems Biology   1 Mar 2018   
Segmenting Four-dimensional Fluorescence Microscopic Image using Convolutional Neural Network [Invited]
FUNAHASHI Akira
OIST Integrated Open Systems Unit Seminar   5 Dec 2017   
Segmenting four-dimensional fluorescence microscopic image using Convolutional Neural Network. [Invited]
FUNAHASHI Akira
Life of Genomes 2017   1 Sep 2017   
The foundation of Biothermology from the point of view of nano/microscale thermophysical properties of biopolymers. [Invited]
Hiroi, N., Nakamura, T., Saito, T., and FUNAHASHI Akira
EMN Europe Meetings, on Quantum   20 Jun 2017   
Mathematical Modeling with CellDesigner. [Invited]
FUNAHASHI Akira
Computational and Mathematical Biology Course, Okinawa Institute of Science and Technology   9 Aug 2016   
CellDesigner: A process diagram editor for gene-regulatory and biochemical networks [Invited]
FUNAHASHI Akira
Advanced Lecture Course on Systems Biology   29 Feb 2016   
Mathematical Modeling with CellDesigner. [Invited]
FUNAHASHI Akira
Computational and Mathematical Biology Course, Okinawa Institute of Science and Technology   20 Aug 2015   
CellDesignerによる生化学ネットワークのシミュレーション [Invited]
舟橋 啓
第88回日本薬理学会年会・薬理学研究を加速させる数理モデル構築・シミュレーションソフトウェア、名古屋国際会議場   19 Mar 2015   
Cells in Computers [Invited]
FUNAHASHI Akira
Japanese-American Frontiers of Science Symposium (JAFoS)   5 Dec 2014   
Computational Platform for Systems Biology [Invited]
FUNAHASHI Akira
Multiscale Spatial Computational Systems Biology, Dagstuhl Seminar   24 Nov 2014   
Development of Nuclei Identification System from Fluorescent 4D Embryonic Images [Invited]
Ozeki, M., Hori, M., Hiroi, N., Bashar, M. K., Yamagata, K., Kobayashi, T. J., and FUNAHASHI Akira
International Workshop on Quantitative Biology 2014   13 Sep 2014   
CellDesigner: A process diagram editor for gene-regulatory and biochemical networks [Invited]
FUNAHASHI Akira
Advanced Lecture Course on Systems Biology,   3 Mar 2014   
Introduction of Mathematical Modeling. [Invited]
FUNAHASHI Akira and Hiroi, N.
Computational and Mathematical Biology Course, Okinawa Institute of Science and Technology   20 Aug 2013   
CellDesigner: A process diagram editor for gene-regulatory and biochemical networks [Invited]
FUNAHASHI Akira and Hiroi, N.
Computational and Mathematical Biology Course, Okinawa Institute of Science and Technology   20 Aug 2013   
CellDesigner 4.3: A Modeling Tool for Biochemical Networks. [Invited]
FUNAHASHI Akira
The 2nd HD Physiology International Symposium: Integrative Multi-level Systems Biology for In Silico Cardiology and Pharmacokinetics, Marunouchi My Plaza Hall   28 Jun 2013   
CellDesigner: A process diagram editor for gene-regulatory and biochemical networks. [Invited]
FUNAHASHI Akira and Hiroi, N.
CellDesigner Workshop, Monash University   7 May 2013   
SBGN support in CellDesigner. [Invited]
FUNAHASHI Akira
9th SBGN workshop   30 Apr 2013   
CellDesigner: A Modeling Tool for Biochemical Networks. [Invited]
舟橋 啓
CiRA Open Seminar Series、京都大学iPS細胞研究所   6 Dec 2012   
定量生物に効く数値計算 [Invited]
舟橋 啓
定量生物学の会第5回年会・チュートリアル   23 Nov 2012   
バイオイメージの高速画像処理 [Invited]
舟橋 啓
画像科学夏の勉強会、核融合研究所   25 Sep 2012   
CellDesigner plugin [Invited]
FUNAHASHI Akira
Garuda 7 workshop   22 Feb 2012   
CellDesigner 4.2: A Modeling Tool for Biochemical Networks. [Invited]
FUNAHASHI Akira
The 1st HD Physiology International Symposium: Integrative Multi-level Systems Biology for In Silico Cardiology and Pharmacokinetics, The University of Tokyo   20 Jan 2012   
定量生物に効く数値計算 [Invited]
舟橋 啓
定量生物学の会第4回年会・チュートリアル   7 Jan 2012   
CellDesigner 4.2: A Modeling Tool for Biochemical Networks. [Invited]
FUNAHASHI Akira
The 4th Global COE International Symposium on Physiome and Systems Biology for Integrated Life Sciences and Predictive Medicine   22 Nov 2011   
An interactive equation-based biological model builder [Invited]
FUNAHASHI Akira
Garuda 6 workshop   29 Sep 2011   
Implementation of GPU accelerated ODE solver [Invited]
FUNAHASHI Akira
Center for Bioinformatics, University of Tuebingen   2 Sep 2011   
CellDesigner4.1: A process diagram editor for gene-regulatory and biochemical networks. [Invited]
FUNAHASHI Akira
4th FEBS and 1st Systems X Advanced Lecture Course on Systems Biology   27 Feb 2011   
CellDesigner plugin [Invited]
FUNAHASHI Akira
Garuda 4 workshop   24 Feb 2011   
CellDesigner [Invited]
FUNAHASHI Akira
Garuda 4 workshop   23 Feb 2011   
GPGPUを用いたバイオイメージの高速画像処理 [Invited]
舟橋 啓
バイオイメージ・インフォマティクスワークショップ、理研   28 Jan 2011   
CellDesigner [Invited]
FUNAHASHI Akira
Garuda One workshop   23 Feb 2010   
CellDesigner plugin [Invited]
FUNAHASHI Akira
Garuda One workshop   23 Feb 2010   
CellDesigner plugin [Invited]
FUNAHASHI Akira
Winter School on Computational Modeling in Biology   Feb 2010   
CellDesigner [Invited]
FUNAHASHI Akira
Winter School on Computational Modeling in Biology   Feb 2010   
CellDesigner [Invited]
FUNAHASHI Akira
Winter School on Computational Modeling in Biology   6 Dec 2009   
生化学ネットワーク解析環境 CellDesignerの設計と実装 [Invited]
舟橋 啓
第 24 回生体・生理工学シンポジウム、東北大学   25 Sep 2009   
生化学ネットワークエディタ CellDesignerの使い方 [Invited]
舟橋 啓
日本バイオインフォマティクス学会・夏の学校、静岡   13 Sep 2009   
生化学ネットワーク解析環境CellDesignerの設計と実装 [Invited]
FUNAHASHI Akira
第24回生体・生理工学シンポジウム   Sep 2009   日本計測自動学会
Integration of CellDesigner and SABIO-RK [Invited]
FUNAHASHI Akira
SABIO-RK User Meeting   16 Jun 2009   
Integration of CellDesigner and SABIO-RK [Invited]
FUNAHASHI Akira
SABIO-RK User Meeting   Jun 2009   
システムバイオロジーの最前線: 定量生物学から計算生物学まで [Invited]
小林 徹也, and 舟橋 啓
農学生命情報科学特論II、東京大学大学院農学生命科学研究科   23 Oct 2008   
CellDesigner 4.0beta [Invited]
FUNAHASHI Akira
Super-hackathon: Standards and Ontologies for Systems Biology 2008   30 Jan 2008   
CellDesigner 4.0beta [Invited]
FUNAHASHI Akira
Super-hackathon: Standards and Ontologies for Systems Biology   Jan 2008   
An integration of CellDesigner and SABIO-RK [Invited]
FUNAHASHI Akira, Matsuoka, Y., Jouraku, A., Kikuchi, N., and Kitano, H.
Storage and Annotation of Reaction Kinetics Data   22 May 2007   
An integration of CellDesigner and SABIO-RK [Invited]
FUNAHASHI Akira
Storage and Annotation of Reaction Kinetics Data   May 2007   
CellDesigner 4, towards CellDesigner 5 [Invited]
FUNAHASHI Akira
Second BioModels.net training camp   14 Jan 2007   
CellDeisgner 4, towards CellDesigner 5 [Invited]
FUNAHASHI Akira
Second BioModels.net training camp   Jan 2007   
簡単プログラミングでコンピュータを従える [Invited]
舟橋 啓
UNIX講座、東北公益文科大学   22 Feb 2005   
テキスト主義宣言 [Invited]
舟橋 啓
UNIX講座、東北公益文科大学   24 Feb 2004   
ソフトウェアの統合と標準化の基盤, SBMLとSBW [Invited]
舟橋 啓
第1回バイオインフォマティクスセミナー、富士総合研究所   1 Dec 2003   
コンピュータの公益性 [Invited]
舟橋 啓
現代社会進化論、東北公益文科大学   25 Feb 2003   

Research Grants & Projects

 
深層学習を用いたヒトES,iPS細胞由来心筋細胞の分化、成熟度評価法の開発
Keio University: 
Project Year: Jun 2019 - Mar 2021    Investigator(s): 藤田 淳
申請者は心筋細胞の純化法や大量培養法を確立したが、多能性幹細胞由来の心筋細胞技術の汎用化、産業化のためには大量の心筋細胞の品質を効率よく短時間で評価する方法を確立する必要性がある。画像解析データとオミックスデータを照合することによって心筋細胞の分化誘導効率と成熟度を評価するアルゴリズムを作製することができれば、心筋細胞の品質評価だけでなく、効率的な心筋細胞の分化誘導法や成熟化法を開発するための強力なツールとなる。
本挑戦的技術の開発は病態解明と創薬開発におけるES/iPS細胞研究のブレーク...
力学刺激の知能化によるin vitro3次元組織の超効率的成熟化
Keio University: 
Project Year: Apr 2019 - Mar 2022    Investigator(s): 尾上 弘晃
本研究の目的は,多様な力学刺激条件によって促進されるin vitro 3次元組織の成熟化の条件探索プロセスを,計算機制御された力学刺激培養装置と単一細胞ライブイメージングおよび深層学習,ベイズ的最適化を併用することで,迅速かつ効率的・効果的なin vitro組織成熟化を可能とする新規方法論を創出することである.これにより,金銭的・時間的・人的に多大なコストが必要であった現在の再生医療研究開発の課題を革新的に解決すると同時に,汎用的な組織工学の次世代基盤技術の創出を目指す.
Development of Robust Segmentation Algorithm using Unsupervised Learning
MEXT,JSPS: Grant-in-Aid for Scientific Research
Project Year: Apr 2018 - Mar 2020    Investigator(s): 舟橋 啓
Gene regulatory networks underlying 3-D conformational change in genome associated with anhydrobiosis
National Agriculture and Food Research Organization: 
Project Year: Apr 2017 - Mar 2021    Investigator(s): 黄川田 隆洋
黄川田グループ:平成29年度は、ネムリユスリカ培養細胞の乾燥耐性誘導過程に変動するゲノム高次構造を知る目的で、手始めに水和状態のPv11細胞をコントロールにin situ HiC解析を行った。その結果、染色体のTADとドメイン構造を判別することが可能になった。また、HiCデータの利用により、ネムリユスリカゲノムアッセンブリーのスキャホールドN50の大幅な向上が確認できた。Pv11細胞の乾燥・再水和過程の遺伝子発現変動パターンを知るために、total RNA-seqを実施した。得られたデータ...
Development of Deep Learning-based Nuclear Detection Algorithm for Mouse Embryo
MEXT,JSPS: Grant-in-Aid for Scientific Research
Project Year: Apr 2016 - Mar 2020    Investigator(s): 舟橋 啓
平成29年度は山縣研究室から提供いただいたマウス胚3次元蛍光顕微鏡画像から核のみをセグメンテーションするアルゴリズムの実装を行った。前年度の実装結果を反映し、セグメンテーションアルゴリズムには多層のニューラルネットワークから構成される深層学習を用いた。学習に用いるデータセット作成においては、マウス胚4次元蛍光顕微鏡画像から4細胞期のある 1 time point のみを切り出し、それに伴う正解データ(セグメンテーション画像)を手動で作成した。また、取得された3次元蛍光顕微鏡画像はZ軸方向の...
細胞分裂を再現する力学モデルの構築と検証
National Institute of Genetics: 
Project Year: Jul 2015 - Mar 2019    Investigator(s): 木村 暁
本研究の目的は動物細胞の細胞分裂を再現する力学モデルを構築し、そのモデルの妥当性を実験的に検証することである。実験には線虫C. elegansの初期胚を主に用いる。研究代表者はこれまでに、動物細胞の細胞分裂に伴う空間的に動的な過程である(i)細胞質流動、(ii)細胞核の中央配置、(iii)染色体の分配(紡錘体の伸長)、および(iv)細胞質分裂、に関してそれぞれ力学モデルを提案してきた。本研究では、これらの力学モデルを発展させるとともに、異なる過程を統合する統一的なモデルの構築を目指して研究...
再生医療を目指した神経細胞分化制御における剪断応力の影響
Keio University: 
Project Year: Apr 2015 - Mar 2020    Investigator(s): 広井 賀子
昨年度に続き、流路抵抗生成部を備えたマイクロ流体デバイスを用い、3つのチャネルごとに異なる流量下で培養を行い、流れのSH-SY5Yの神経突起慎重方向の分布への寄与を検討した。SH-SY5Yはレチノイン酸及び脳由来神経栄養因子を用いて分化誘導を行った。準備したSH-SY5Y細胞を培養デバイスに撒種し、静置培養の場合をコントロールとして、流路ごとに神経突起の伸長方向を計数した。取得したデータに対しベイズ統計解析を行うにあたり、神経突起方向の角度分布を説明する仮説として、灌流培養時に神経突起方向...