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2020 – today
- 2023
[j15]James C. Schaff
, Anuradha Lakshminarayana, Robert F. Murphy, Frank T. Bergmann, Akira Funahashi, Devin P. Sullivan, Lucian P. Smith:
SBML level 3 package: spatial processes, version 1, release 1. J. Integr. Bioinform. 20(1) (2023)- [i3]Mengji Zhang, Yusuke Hiki, Akira Funahashi, Tetsuya J. Kobayashi:
Mol-PECO: a deep learning model to predict human olfactory perception from molecular structures. CoRR abs/2305.12424 (2023) - 2022
- [j14]Hazumi Kubota, Yuta Tokuoka, Takahiro G. Yamada, Akira Funahashi:
Symbolic Integration by Integrating Learning Models With Different Strengths and Weaknesses. IEEE Access 10: 47000-47010 (2022) - [j13]Yuta Tokuoka, Takahiro G. Yamada, Daisuke Mashiko, Zenki Ikeda, Tetsuya J. Kobayashi, Kazuo Yamagata, Akira Funahashi:
An explainable deep learning-based algorithm with an attention mechanism for predicting the live birth potential of mouse embryos. Artif. Intell. Medicine 134: 102432 (2022) - [j12]Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 50(W1): 108-114 (2022) - [i2]Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. CoRR abs/2203.06732 (2022) - 2021
- [i1]Hazumi Kubota, Yuta Tokuoka, Takahiro G. Yamada, Akira Funahashi:
Symbolic integration by integrating learning models with different strengths and weaknesses. CoRR abs/2103.05497 (2021) - 2020
- [j11]Chikahiro Imashiro, Yuta Tokuoka, Kaito Kikuhara, Takahiro G. Yamada, Kenjiro Takemura, Akira Funahashi:
Direct Cell Counting Using Macro-Scale Smartphone Images of Cell Aggregates. IEEE Access 8: 170033-170043 (2020)
2010 – 2019
- 2013
- [j10]Hiromu Takizawa, Kazushige Nakamura, Akito Tabira, Yoichi Chikahara, Tatsuhiro Matsui, Noriko Hiroi, Akira Funahashi:
LibSBMLSim: a reference implementation of fully functional SBML simulator. Bioinform. 29(11): 1474-1476 (2013) - [j9]Roland Keller, Alexander Dörr, Akito Tabira, Akira Funahashi, Michael J. Ziller, Richard R. Adams, Nicolas Rodriguez, Nicolas Le Novère, Noriko Hiroi, Hannes Planatscher, Andreas Zell, Andreas Dräger:
The systems biology simulation core algorithm. BMC Syst. Biol. 7: 55 (2013) - [c22]Noriko Hiroi, Keisuke Iba, Akito Tabira, Takahiro Okuhara, Takeshi Kubojima, Takumi Hiraiwa, Tetsuya J. Kobayashi, Kotaro Oka, Akira Funahashi:
In vivo oriented modeling with consideration of intracellular crowding. EMBC 2013: 2716-2719 - 2012
- [j8]Martijn P. van Iersel, Alice Villéger, Tobias Czauderna, Sarah E. Boyd, Frank T. Bergmann, Augustin Luna, Emek Demir, Anatoly A. Sorokin, Ugur Dogrusöz, Yukiko Matsuoka, Akira Funahashi, Mirit I. Aladjem, Huaiyu Mi, Stuart L. Moodie, Hiroaki Kitano, Nicolas Le Novère, Falk Schreiber:
Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinform. 28(15): 2016-2021 (2012) - [j7]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:
From Microscopy Data to in silico Environments for in vivo Oriented Simulations. EURASIP J. Bioinform. Syst. Biol. 2012: 7 (2012) - 2011
- [j6]Huaiyu Mi, Anushya Muruganujan, Emek Demir, Yukiko Matsuoka, Akira Funahashi, Hiroaki Kitano, Paul D. Thomas:
BioPAX support in CellDesigner. Bioinform. 27(24): 3437-3438 (2011) - 2010
- [j5]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 H. Barboza, Raoul Jean Pierre Bonnal, Richard M. Bruskiewich, Jan Christian Bryne, José María Fernández, Akira Funahashi, Paul M. K. Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard C. G. Holland, Yoshinobu Kano, Edward A. Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R. Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehväslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M. Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew R. Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Lukasz Salwínski, Mark J. Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M. Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A. Vos, Mark D. Wilkinson, William S. York, Christian M. Zmasek, Kiyoshi Asai, Toshihisa Takagi:
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. J. Biomed. Semant. 1: 8 (2010) - [j4]Hideki Yamada, Yui Ogawa, Tomonori Ooya, Tomoya Ishimori, Yasunori Osana, Masato Yoshimi, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Hideharu Amano, Yuichiro Shibata, Kiyoshi Oguri:
Automatic Pipeline Construction Focused on Similarity of Rate Law Functions for an FPGA-based Biochemical Simulator. IPSJ Trans. Syst. LSI Des. Methodol. 3: 244-256 (2010) - [c21]Yui Ogawa, Tomonori Ooya, Yasunori Osana, Masato Yoshimi, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Hideharu Amano, Yuichiro Shibata, Kiyoshi Oguri:
A datapath classification method for FPGA-based scientific application accelerator systems. FPT 2010: 441-444
2000 – 2009
- 2009
- [c20]Tomoya Ishimori, Hideki Yamada, Yuichiro Shibata, Yasunori Osana, Masato Yoshimi, Yuri Nishikawa, Hideharu Amano, Akira Funahashi, Noriko Hiroi, Kiyoshi Oguri:
Pipeline Scheduling with Input Port Constraints for an FPGA-Based Biochemical Simulator. ARC 2009: 368-373 - [c19]Tomonori Ooya, Hideki Yamada, Tomoya Ishimori, Yuichiro Shibata, Yasunori Osana, Kiyoshi Oguri, Masato Yoshimi, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Hideharu Amano:
Configuring area and performance: Empirical evaluation on an FPGA-based biochemical simulator. FPL 2009: 679-682 - [c18]Hideki Yamada, Yasunori Osana, Tomoya Ishimori, Tomonori Ooya, Masato Yoshimi, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Hideharu Amano, Yuichiro Shibata, Kiyoshi Oguri:
A Modular Approach to Heterogeneous Biochemical Model Simulation on an FPGA. ReConFig 2009: 125-130 - 2008
- [j3]Akira Funahashi, Yukiko Matsuoka, Akiya Jouraku, Mineo Morohashi, Norihiro Kikuchi, Hiroaki Kitano:
CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks. Proc. IEEE 96(8): 1254-1265 (2008) - [c17]Masato Yoshimi, Yuri Nishikawa, Yasunori Osana, Akira Funahashi, Yuichiro Shibata, Hideki Yamada, Noriko Hiroi, Hiroaki Kitano, Hideharu Amano:
Practical implementation of a network-based stochastic biochemical simulation system on an FPGA. FPL 2008: 663-666 - 2007
- [j2]Akira Funahashi, Akiya Jouraku, Yukiko Matsuoka, Hiroaki Kitano:
Integration of CellDesigner and SABIO-RK. Silico Biol. 7(6): 81-90 (2007) - [c16]Masato Yoshimi, Yow Iwaoka, Yuri Nishikawa, Toshinori Kojima, Yasunori Osana, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hideki Yamada, Hiroaki Kitano, Hideharu Amano:
FPGA Implementation of a Data-Driven Stochastic Biochemical Simulator with the Next Reaction Method. FPL 2007: 254-259 - [c15]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:
A Combining technique of rate law functions for a cost-effective reconfigurable biological simulator. FPL 2007: 808-811 - [c14]Masato Yoshimi, Yuri Nishikawa, Toshinori Kojima, Yasunori Osana, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Hideki Yamada, Hiroaki Kitano, Hideharu Amano:
A Framework for Implementing a Network-Based Stochastic Biochemical Simulator on an FPGA. FPT 2007: 193-200 - 2006
- [c13]Yasunori Osana, Masato Yoshimi, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, Hideharu Amano:
Performance Evaluation of an Fpga-Based Biochemical Simulator ReCSip. FPL 2006: 1-6 - [c12]Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Yuri Nishikawa, Toshinori Kojima, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, Hideharu Amano:
An FPGA Implementation of High Throughput Stochastic Simulator for Large-Scale Biochemical Systems. FPL 2006: 1-6 - [c11]Akira Funahashi, Yukiko Matsuoka, Akiya Jouraku, Hiroaki Kitano, Norihiro Kikuchi:
CellDesigner: a modeling tool for biochemical networks. WSC 2006: 1707-1712 - 2005
- [c10]Yasunori Osana, Yow Iwaoka, Tomonori Fukushima, Masato Yoshimi, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, Hideharu Amano:
A Framework for ODE-Based Multimodel Biochemical Simulations on an FPGA. FPL 2005: 574-577 - [c9]Naoki Iwanaga, Yuichiro Shibata, Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Tomonori Fukushima, Hideharu Amano, Akira Funahashi, Noriko Hiroi, Hiroaki Kitano, Kiyoshi Oguri:
Efficient Scheduling of Rate Law Functions for ODE-Based Multimodel Biochemical Simulation on an FPGA. FPL 2005: 666-669 - [c8]Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, Hideharu Amano:
The Design of Scalable Stochastic Biochemical Simulator on FPGA. FPT 2005: 339-340 - [c7]Yasunori Osana, Tomonori Fukushima, Masato Yoshimi, Yow Iwaoka, Yuichiro Shibata, Hiroaki Kitano, Akira Funahashi, Noriko Hiroi, Hideharu Amano:
An FPGA-Based, Multi-model Simulation Method for Biochemical Systems. IPDPS 2005 - 2002
- [c6]Akiya Jouraku, Michihiro Koibuchi, Hideharu Amano, Akira Funahashi:
Routing Algorithms Based on 2D Turn Model for Irregular Networks. ISPAN 2002: 289-294 - 2001
- [j1]Yulu Yang, Akira Funahashi, Akiya Jouraku, Hiroaki Nishi, Hideharu Amano, Toshinori Sueyoshi:
Recursive Diagonal Torus: An Interconnection Network for Massively Parallel Computers. IEEE Trans. Parallel Distributed Syst. 12(7): 701-715 (2001) - [c5]Michihiro Koibuchi, Akiya Jouraku, Akira Funahashi, Hideharu Amano:
MMLRU Selection Function: An Output Selection Function on Adaptive Routing. PDCS 2001: 1-6 - [c4]Akira Funahashi, Michihiro Koibuchi, Akiya Jouraku, Hideharu Amano:
The impact of output selection function on adaptive routing. CATA 2001: 241-246 - [c3]Michihiro Koibuchi, Akira Funahashi, Akiya Jouraku, Hideharu Amano:
L-Turn Routing: An Adaptive Routing in Irregular Networks. ICPP 2001: 383-392
1990 – 1999
- 1999
- [c2]Qin Fan, Yulu Yang, Akira Funahashi, Hideharu Amano:
A Torus Assignment for an Interconnection Network Recursive Diagonal Torus. ISPAN 1999: 74-79 - 1997
- [c1]Akira Funahashi, Toshihiro Hanawa, Hideharu Amano, Tomohiro Kudoh:
Adaptive Routing on the Recursive Diagonal Torus. ISHPC 1997: 171-182
Coauthor Index
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