Akira Funahashi
Akira Funahashi
Associate Professor of Systems Biology, Keio University
Verified email at bio.keio.ac.jp - Homepage
Title
Cited by
Cited by
Year
A comprehensive pathway map of epidermal growth factor receptor signaling
K Oda, Y Matsuoka, A Funahashi, H Kitano
Molecular systems biology 1 (1), 2005.0010, 2005
12732005
The systems biology graphical notation
N Le Novere, M Hucka, H Mi, S Moodie, F Schreiber, A Sorokin, E Demir, ...
Nature biotechnology 27 (8), 735-741, 2009
9192009
CellDesigner: a process diagram editor for gene-regulatory and biochemical networks
A Funahashi, M Morohashi, H Kitano, N Tanimura
Biosilico 1 (5), 159-162, 2003
7062003
Using process diagrams for the graphical representation of biological networks
H Kitano, A Funahashi, Y Matsuoka, K Oda
Nature biotechnology 23 (8), 961-966, 2005
5392005
CellDesigner 3.5: a versatile modeling tool for biochemical networks
A Funahashi, Y Matsuoka, A Jouraku, M Morohashi, N Kikuchi, H Kitano
Proceedings of the IEEE 96 (8), 1254-1265, 2008
5122008
Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project
M Hucka, A Finney, BJ Bornstein, SM Keating, BE Shapiro, J Matthews, ...
IEE Proceedings-Systems Biology 1 (1), 41-53, 2004
3032004
Recursive diagonal torus: an interconnection network for massively parallel computers
Y Yang, A Funahashi, A Jouraku, H Nishi, H Amano, T Sueyoshi
IEEE Transactions on Parallel and Distributed Systems 12 (7), 701-715, 2001
1042001
COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms
M Ostaszewski, A Mazein, ME Gillespie, I Kuperstein, A Niarakis, ...
Scientific data 7 (1), 1-4, 2020
932020
Software support for SBGN maps: SBGN-ML and LibSBGN
MP Van Iersel, AC Villéger, T Czauderna, SE Boyd, FT Bergmann, A Luna, ...
Bioinformatics 28 (15), 2016-2021, 2012
922012
Detection of temperature difference in neuronal cells
R Tanimoto, T Hiraiwa, Y Nakai, Y Shindo, K Oka, N Hiroi, A Funahashi
Scientific reports 6 (1), 1-10, 2016
802016
Integration of CellDesigner and SABIO-RK
A Funahashi, A Jouraku, Y Matsuoka, H Kitano
In silico biology 7 (2 Supplement), 81-90, 2007
742007
L-turn routing: An adaptive routing in irregular networks
M Koibuchi, A Funahashi, A Jouraku, H Amano
International Conference on Parallel Processing, 2001., 383-392, 2001
742001
Molecular interaction map of a macrophage
K Oda, T Kimura, Y Matsuoka, A Funahashi, M Muramatsu, H Kitano
AfCS Research Reports 2 (14), 1-12, 2004
652004
The principles of whole-cell modeling
JR Karr, K Takahashi, A Funahashi
Current opinion in microbiology 27, 18-24, 2015
582015
SBML Level 3: an extensible format for the exchange and reuse of biological models
SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ...
Molecular systems biology 16 (8), e9110, 2020
552020
Modeling and simulation using CellDesigner
Y Matsuoka, A Funahashi, S Ghosh, H Kitano
Transcription Factor Regulatory Networks, 121-145, 2014
552014
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows
T Katayama, K Arakawa, M Nakao, K Ono, KF Aoki-Kinoshita, ...
Journal of biomedical semantics 1 (1), 1-19, 2010
502010
High-speed microscopy with an electrically tunable lens to image the dynamics of in vivo molecular complexes
Y Nakai, M Ozeki, T Hiraiwa, R Tanimoto, A Funahashi, N Hiroi, ...
Review of Scientific Instruments 86 (1), 013707, 2015
492015
CellDesigner: a modeling tool for biochemical networks
A Funahashi, Y Matsuoka, A Jouraku, H Kitano, N Kikuchi
Proceedings of the 2006 Winter Simulation Conference, 1707-1712, 2006
462006
The systems biology simulation core algorithm
R Keller, A Dörr, A Tabira, A Funahashi, MJ Ziller, R Adams, N Rodriguez, ...
BMC systems biology 7 (1), 1-16, 2013
412013
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Articles 1–20