Adaptive Routing on the Recursive Diagonal Torus. - Akira Funahashi; Toshihiro Hanawa; Hideharu Amano; Tomohiro Kudoh (ISHPC, 1997)

A Torus Assignment for an Interconnection Network Recursive Diagonal Torus. - Qin Fan; Yulu Yang; Akira Funahashi; Hideharu Amano (ISPAN, 1999)

MMLRU Selection Function: An Output Selection Function on Adaptive Routing. - Michihiro Koibuchi; Akiya Jouraku; Akira Funahashi; Hideharu Amano (PDCS, 2001)

The impact of output selection function on adaptive routing. - Akira Funahashi; Michihiro Koibuchi; Akiya Jouraku; Hideharu Amano (CATA, 2001)

L-Turn Routing: An Adaptive Routing in Irregular Networks. - Michihiro Koibuchi; Akira Funahashi; Akiya Jouraku; Hideharu Amano (ICPP, 2001)

Recursive Diagonal Torus: An Interconnection Network for Massively Parallel Computers. - Yulu Yang; Akira Funahashi; Akiya Jouraku; Hiroaki Nishi; Hideharu Amano; Toshinori Sueyoshi (IEEE Trans. Parallel Distributed Syst., 2001)

Routing Algorithms Based on 2D Turn Model for Irregular Networks. - Akiya Jouraku; Michihiro Koibuchi; Hideharu Amano; Akira Funahashi (ISPAN, 2002)

Efficient Scheduling of Rate Law Functions for ODE-Based Multimodel Biochemical Simulation on an FPGA. - Naoki Iwanaga; Yuichiro Shibata; Masato Yoshimi; Yasunori Osana; Yow Iwaoka; Tomonori Fukushima; Hideharu Amano; Akira Funahashi; Noriko Hiroi; Hiroaki Kitano; Kiyoshi Oguri (FPL, 2005)

A Framework for ODE-Based Multimodel Biochemical Simulations on an FPGA. - Yasunori Osana; Yow Iwaoka; Tomonori Fukushima; Masato Yoshimi; Akira Funahashi; Noriko Hiroi; Yuichiro Shibata; Naoki Iwanaga; Hiroaki Kitano; Hideharu Amano (FPL, 2005)

The Design of Scalable Stochastic Biochemical Simulator on FPGA. - Masato Yoshimi; Yasunori Osana; Yow Iwaoka; Akira Funahashi; Noriko Hiroi; Yuichiro Shibata; Naoki Iwanaga; Hiroaki Kitano; Hideharu Amano (FPT, 2005)

An FPGA-Based, Multi-model Simulation Method for Biochemical Systems. - Yasunori Osana; Tomonori Fukushima; Masato Yoshimi; Yow Iwaoka; Yuichiro Shibata; Hiroaki Kitano; Akira Funahashi; Noriko Hiroi; Hideharu Amano (IPDPS, 2005)

Performance Evaluation of an Fpga-Based Biochemical Simulator ReCSip. - Yasunori Osana; Masato Yoshimi; Akira Funahashi; Noriko Hiroi; Yuichiro Shibata; Naoki Iwanaga; Hiroaki Kitano; Hideharu Amano (FPL, 2006)

An FPGA Implementation of High Throughput Stochastic Simulator for Large-Scale Biochemical Systems. - Masato Yoshimi; Yasunori Osana; Yow Iwaoka; Yuri Nishikawa; Toshinori Kojima; Akira Funahashi; Noriko Hiroi; Yuichiro Shibata; Naoki Iwanaga; Hiroaki Kitano; Hideharu Amano (FPL, 2006)

CellDesigner: a modeling tool for biochemical networks. - Akira Funahashi; Yukiko Matsuoka; Akiya Jouraku; Hiroaki Kitano; Norihiro Kikuchi (WSC, 2006)

A Combining technique of rate law functions for a cost-effective reconfigurable biological simulator. - Hideki Yamada; Naoki Iwanaga; Yuichiro Shibata; Yasunori Osana; Masato Yoshimi; Yow Iwaoka; Yuri Nishikawa; Toshinori Kojima; Hideharu Amano; Akira Funahashi; Noriko Hiroi; Hiroaki Kitano; et al. (FPL, 2007)

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 (FPL, 2007)

A Framework for Implementing a Network-Based Stochastic Biochemical Simulator on an FPGA. - Masato Yoshimi; Yuri Nishikawa; Toshinori Kojima; Yasunori Osana; Akira Funahashi; Noriko Hiroi; Yuichiro Shibata; Hideki Yamada; Hiroaki Kitano; Hideharu Amano (FPT, 2007)

Integration of CellDesigner and SABIO-RK. - Akira Funahashi; Akiya Jouraku; Yukiko Matsuoka; Hiroaki Kitano (Silico Biol., 2007)

Practical implementation of a network-based stochastic biochemical simulation system on an FPGA. - Masato Yoshimi; Yuri Nishikawa; Yasunori Osana; Akira Funahashi; Yuichiro Shibata; Hideki Yamada; Noriko Hiroi; Hiroaki Kitano; Hideharu Amano (FPL, 2008)

CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks. - Akira Funahashi; Yukiko Matsuoka; Akiya Jouraku; Mineo Morohashi; Norihiro Kikuchi; Hiroaki Kitano (Proc. IEEE, 2008)

Pipeline Scheduling with Input Port Constraints for an FPGA-Based Biochemical Simulator. - Tomoya Ishimori; Hideki Yamada; Yuichiro Shibata; Yasunori Osana; Masato Yoshimi; Yuri Nishikawa; Hideharu Amano; Akira Funahashi; Noriko Hiroi; Kiyoshi Oguri (ARC, 2009)

Configuring area and performance: Empirical evaluation on an FPGA-based biochemical simulator. - Tomonori Ooya; Hideki Yamada; Tomoya Ishimori; Yuichiro Shibata; Yasunori Osana; Kiyoshi Oguri; Masato Yoshimi; Yuri Nishikawa; Akira Funahashi; Noriko Hiroi; Hideharu Amano (FPL, 2009)

A Modular Approach to Heterogeneous Biochemical Model Simulation on an FPGA. - Hideki Yamada; Yasunori Osana; Tomoya Ishimori; Tomonori Ooya; Masato Yoshimi; Yuri Nishikawa; Akira Funahashi; Noriko Hiroi; Hideharu Amano; Yuichiro Shibata; Kiyoshi Oguri (ReConFig, 2009)

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 (FPT, 2010)

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 H. Barboza; et al. (J. Biomed. Semant., 2010)

Automatic Pipeline Construction Focused on Similarity of Rate Law Functions for an FPGA-based Biochemical Simulator. - 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 Trans. Syst. LSI Des. Methodol., 2010)

BioPAX support in CellDesigner. - Huaiyu Mi; Anushya Muruganujan; Emek Demir; Yukiko Matsuoka; Akira Funahashi; Hiroaki Kitano; Paul D. Thomas (Bioinform., 2011)

Software support for SBGN maps: SBGN-ML and LibSBGN. - 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; et al. (Bioinform., 2012)

From Microscopy Data to in silico Environments for in vivo Oriented Simulations. - 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; et al. (EURASIP J. Bioinform. Syst. Biol., 2012)

In vivo oriented modeling with consideration of intracellular crowding. - Noriko Hiroi; Keisuke Iba; Akito Tabira; Takahiro Okuhara; Takeshi Kubojima; Takumi Hiraiwa; Tetsuya J. Kobayashi; Kotaro Oka; Akira Funahashi (EMBC, 2013)

LibSBMLSim: a reference implementation of fully functional SBML simulator. - Hiromu Takizawa; Kazushige Nakamura; Akito Tabira; Yoichi Chikahara; Tatsuhiro Matsui; Noriko Hiroi; Akira Funahashi (Bioinform., 2013)

The systems biology simulation core algorithm. - Roland Keller; Alexander Dörr; Akito Tabira; Akira Funahashi; Michael J. Ziller; Richard R. Adams; Nicolas Rodriguez 001; Nicolas Le Novère; Noriko Hiroi; Hannes Planatscher; Andreas Zell; Andreas Dräger (BMC Syst. Biol., 2013)

Direct Cell Counting Using Macro-Scale Smartphone Images of Cell Aggregates. - Chikahiro Imashiro; Yuta Tokuoka; Kaito Kikuhara; Takahiro G. Yamada; Kenjiro Takemura; Akira Funahashi (IEEE Access, 2020)

Symbolic Integration by Integrating Learning Models With Different Strengths and Weaknesses. - Hazumi Kubota; Yuta Tokuoka; Takahiro G. Yamada; Akira Funahashi (IEEE Access, 2022)

An explainable deep learning-based algorithm with an attention mechanism for predicting the live birth potential of mouse embryos. - Yuta Tokuoka; Takahiro G. Yamada; Daisuke Mashiko; Zenki Ikeda; Tetsuya J. Kobayashi; Kazuo Yamagata; Akira Funahashi (Artif. Intell. Medicine, 2022)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - 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 006; et al. (CoRR, 2022)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - 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 006; et al. (Nucleic Acids Res., 2022)

Mol-PECO: a deep learning model to predict human olfactory perception from molecular structures. - Mengji Zhang; Yusuke Hiki; Akira Funahashi; Tetsuya J. Kobayashi (CoRR, 2023)

SBML level 3 package: spatial processes, version 1, release 1. - James C. Schaff; Anuradha Lakshminarayana; Robert F. Murphy; Frank T. Bergmann; Akira Funahashi; Devin P. Sullivan; Lucian P. Smith (J. Integr. Bioinform., 2023)

Asynchronous Batch Bayesian Optimization with Pipelining Evaluations for Experimental Resource-constrained Conditions. - Yujin Taguchi; Yusuke Shibuya; Yusuke Hiki; Takashi Morikura; Takahiro G. Yamada; Akira Funahashi (CoRR, 2024)

A Cross-Modal Tactile Reproduction Utilizing Tactile and Visual Information Generated by Conditional Generative Adversarial Networks. - Koki Hatori; Takashi Morikura; Akira Funahashi; Kenjiro Takemura (IEEE Access, 2025)