Akira Funahashi

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Hiroaki KitanoThe Systems Biology Institute, Director / Sony Computer Science Laboratories, Inc., President and CEO / Okinawa Institute of Science and Technology, ProfessorVerified email at sbi.jp
Noriko F Hiroi, 広井賀子Professor, Kanagawa Institute of Technology/Visiting Researcher, Keio UniversityVerified email at bio.keio.ac.jp
Hideharu AmanoKeio UniversityVerified email at am.ics.keio.ac.jp
Yasunori OsanaUniversity of the RyukyusVerified email at eee.u-ryukyu.ac.jp
Masato YoshimiVerified email at minilab.biz
Yuri NishikawaNational Institute of Advanced Science and Technology (AIST)Verified email at aist.go.jp
Takahiro G. YamadaKeio UniversityVerified email at bio.keio.ac.jp
Emek DemirOHSUVerified email at ohsu.edu
Falk SchreiberProfessor, University of Konstanz and Monash UniversityVerified email at uni-konstanz.de
Yuta TokuokaPreferred Networks Inc., Keio UniversityVerified email at fun.bio.keio.ac.jp
Huaiyu MiPreventive Medicine, University of Southern CaliforniaVerified email at usc.edu
Michael HuckaCalifornia Institute of TechnologyVerified email at caltech.edu
Bruce E. ShapiroCalifornia State University, Northridge, RetiredVerified email at csun.edu
Maria SchilstraPrincipal Laboratory ScientistVerified email at crick.ac.uk
Andreas DrägerJuniorprofessor for Computational Systems Biology of Infection and Antimicrobial-ResistanceVerified email at uni-tuebingen.de
Viji Mythily DraviamQueen Mary University of LondonVerified email at qmul.ac.uk
Tetsuya J. KobayashiInstitute of Industrial Science, the University of TokyoVerified email at mail.crmind.net
Mirit AladjemNCIVerified email at mail.nih.gov
Augustin LunaResearch Associate | Dept. of Data Science, Dana-Farber Cancer Institute, Harvard Medical SchoolVerified email at mail.nih.gov
Anatoly SorokinOkinawa Institute of Science and TechnologyVerified email at oist.jp

Akira Funahashi

Professor of Systems Biology, Keio University

Verified email at bio.keio.ac.jp - Homepage

Systems Biology Quantitative Biology Computational Biology Parallel Processing Machine Learning


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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	1391	2005
The systems biology graphical notation NL Novère, M Hucka, H Mi, S Moodie, F Schreiber, A Sorokin, E Demir, ... Nature biotechnology 27 (8), 735-741, 2009	988	2009
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	736	2003
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	567	2005
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	544	2008
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, ... Systems biology 1 (1), 41-53, 2004	319	2004
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	126	2020
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), 136, 2020	126	2020
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), 22071, 2016	106	2016
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	105	2012
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	105	2001
Integration of CellDesigner and SABIO-RK A Funahashi, A Jouraku, Y Matsuoka, H Kitano In silico biology 7 (2 Supplement), 81-90, 2007	77	2007
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	77	2001
The principles of whole-cell modeling JR Karr, K Takahashi, A Funahashi Current opinion in microbiology 27, 18-24, 2015	69	2015
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	69	2004
Modeling and simulation using CellDesigner Y Matsuoka, A Funahashi, S Ghosh, H Kitano Transcription factor regulatory networks: Methods and protocols, 121-145, 2014	67	2014
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	55	2015
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, 1-19, 2010	54	2010
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	51	2006
COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms M Ostaszewski, A Niarakis, A Mazein, I Kuperstein, R Phair, ... Molecular systems biology 17 (10), e10387, 2021	45	2021

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