論文

• Masanori Kakuta, Shuji Suzuki, Kazuki Izawa, Takashi Ishida, Yutaka Akiyama. A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data, International Journal of Molecular Sciences, Multidisciplinary Digital Publishing Institute, Vol. 18, No. 10, pp. 2124, Oct. 2017.
• Shuji Suzuki, Takashi Ishida, Masahito Ohue, Masanori Kakuta, Yutaka Akiyama. GHOSTX: A Fast Sequence Homology Search Tool for Functional Annotation of Metagenomic Data, Methods in Molecular Biology(Protein Function Prediction), Springer, Volume 1611, pp. 15-25, Apr. 2017.  公式リンク  
  
• Shuji Suzuki, Masanori Kakuta, Takashi Ishida, Yutaka Akiyama. GPU-Acceleration of Sequence Homology Searches with Database Subsequence Clustering, PLOS ONE, Vol. 11, No. 8, e0157338, Aug. 2016.
• Suzuki S, Kakuta M, Ishida T, Akiyama Y.. Faster sequence homology searches by clustering subsequences, Bioinformatics, 31, 8, 1183-90, Apr. 2015.  公式リンク  
  
• Takehiro Shimoda, Shuji Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama.. Protein-Protein Docking on Hardware Accelerators : Comparison of GPU and MIC Architectures, The Thirteenth Asia-Pacific Bioinformatics Conference (APBC2015), BMC Systems Biology, BioMed Central, Vol. 9, No. Suppl 1, Jan. 2015.  公式リンク  
  
• Ohue, M., Shimoda, T., Suzuki, S., Matsuzaki, Y., Ishida, T., Akiyama, Y.. MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers, Bioinformatics, Oxford University Press, Vol. 30, No. 22, pp. 3281-3283, Aug. 2014.  公式リンク  
  
• Suzuki, S, Ishida, T, Akiyama, Y. GHOSTX: An improved sequence homology search algorithm using a query suffix array and a database suffix array, PLoS ONE, Vol. 6, No. 9, e103833, Aug. 2014.
• Satoshi Matsuoka, Hitoshi Sato, Osamu Tatebe, Michihiro Koibuchi, Ikki Fujiwara, Shuji Suzuki, Masanori Kakuta, Takashi Ishida, Yutaka Akiyama, Toyotaro Suzumura, Koji Ueno, Hiroki Kanezashi, Takemasa Miyoshi.. Extreme Big Data (EBD): Next Generation Big Data Infrastructure Technologies Towards Yottabyte/Year, Supercomputing frontiers and innovations, Vol. 1, No. 2, pp. 89-107, 2014.
• Shuji Suzuki, Takashi Ishida, Ken Kurokawa, Yutaka Akiyama. GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics, PLoS ONE, Vol. 7, No. 5, Page e36060, May 2012.

国際会議発表 (査読有り)

• Kakuta, M., Suzuki, S., Ishida, T., Akiyama, Y.. GHOST-MP: A Massively Parallel Biological Sequence Similarity Search for Metagenomics using OpenMP and MPI, Annual Meeting on Advanced Computing System and Infrastructure (ACSI) 2015, Jan. 2015.
• Takehiro Shimoda, Takashi Ishida, Shuji Suzuki, Masahito Ohue, Yutaka Akiyama. MEGADOCK-GPU: Acceleration of Protein-Protein Docking Calculation on GPUs, ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2013 (ACM-BCB 2013), 2nd International Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio2013), Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2013 (ACM-BCB 2013), Association for Computing Machinery, pp. 883-889, Sept. 2013.  公式リンク  
  
• Hiroya Nagao, Shuji Suzuki, Kazuyuki Shudo. A 3D Visualization System for Structured Overlays, 11th IEEE Int'l Conference on Peer-to-Peer Computing (IEEE P2P'11), Proc. 11th IEEE Int'l Conference on Peer-to-Peer Computing (IEEE P2P'11), pp. 168-169, Aug. 2011.

国内会議発表 (査読有り)

• Zhang Chaojie, Koichi Shirahata, Shuji Suzuki, Yutaka Akiyama, Satoshi Matsuoka. Performance Analysis of MapReduce Implementations for High Performance Homology Search, HPCS2015, 2015.  公式リンク  
  
• 鈴木脩司, 石田貴士, 秋山泰. GPUによるDNA断片配列の高速マッピング, 先進的計算基盤システムシンポジウムSACSIS2010, 先進的計算基盤システムシンポジウムSACSIS2010論文集, pp. 137-138, May 2010.

国際会議発表 (査読なし・不明)

• Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Takashi Ishida, Yutaka Akiyama. A comparative study of GPU and MIC accelerations in fast Fourier transform-based protein-protein docking, 3nd IIT Madras – Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics, Nov. 2015.
• Shuji Suzuki, Masanori Kakuta, Takashi Ishida, Yutaka Akiyama. GHOSTZ-GPU: Fast Protein Sequence Homology Search on GPUs, GPU Technology Conference 2015 (GTC2015), No. P5273, Mar. 2015.
• Masahito Ohue, Takehiro Shimoda, Shuji suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama. MEGADOCK 4.0: an ultra–high-performance protein-protein docking software for heterogeneous supercomputers, APBC 2015: The Thirteenth Asia Pacific Bioinformatics Conference, Jan. 2015.
• Masahito Ohue, Takehiro Shimoda, Shuji suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama. MEGADOCK 4.0: an ultra–high-performance protein-protein docking software for heterogeneous supercomputers, GIW/ISCB-Asia 2014, Dec. 2014.
• Shuji Suzuki, Takashi Ishida, Yutaka Akiyama. Accelerating identification of frequent k-mers in DNA sequences with GPU, GPU Technology Conference 2014 (GTC2014), No. P4190, Mar. 2014.
• Takehiro Shimoda, Takashi Ishida, Shuji Suzuki, Masahito Ohue, Yutaka Akiyama. MEGADOCK-GPU: Acceleration of Protein-Protein Docking Calculation on GPUs, 2nd IIT Madras – Tokyo Tech Joint Symposium on Techniques and Applications of Bioinformatics, P13, Sept. 2013.
• Shuji Suzuki, Takashi Ishida, Yutaka Akiyama. An Ultra-fast Computing Pipeline for Metagenome Analysis with GPUs, GPU Technology Conference 2013 (GTC2013), No. P0192, Mar. 2013.
• Shuji Suzuki, Takashi Ishida, Yutaka Akiyama. Improvement of a fast homology search tool on GPUs with suffix array, The 9th International Workshop on Advanced Genomics, July 2011.
• Shuji Suzuki, Yutaka Akiyama. Ultra fast short sequence alignment on GPU, BIOINFO 2009 CBI-KSBSB Joint Conference, Proc. BIOINFO 2009 CBI-KSBSB Joint Conference, P3-22, Nov. 2009.

国内会議発表 (査読なし・不明)

• Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama. The MEGADOCK Project: high-performance protein-protein interaction prediction tools on supercomputing environments, The Asia hub for e-drug discovery symposium 2014 (AHeDD' 2014), Nov. 2014.
• Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama. MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers, IIBMP2014, Bioinformatics, Volume 30, Issue 22, page 3281-3283, Nov. 2014.  公式リンク  
  
• Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama. The MEGADOCK Project: high-performance protein-protein interaction prediction tools on supercomputing environments, Biophysical Society Thematic Meeting Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations, Sept. 2014.
• 大上雅史, 下田雄大, 松崎由理, 内古閑伸之, 鈴木脩司, 石田貴士, 秋山泰. MEGADOCK 4.0: mega-dock per dayへの道のり, 生命情報科学若手の会 第5回研究会, Feb. 2014.
• 渡部翔, 鈴木脩司, 石田貴士, 秋山泰. GPGPUを用いた高速な配列相同性検索の圧縮アミノ酸を用いたアルゴリズム改良, 第36回バイオ情報学研究会, 情報処理学会研究報告, vol. 2013, no. 20, pp. 1-7, Dec. 2013.
• 下田雄大, 石田貴士, 鈴木脩司, 大上雅史, 秋山泰. MEGADOCK-GPU: GPUによるタンパク質間ドッキング計算の高速化, GTC Workshop Japan 2013, No. 1, July 2013.
• 渡部翔, 鈴木脩司, 石田貴士, 秋山泰. GPUを用いた配列相同性検索ツールGHOSTMの圧縮アミノ酸による高速化, GTC Workshop Japan 2013, July 2013.
• 鈴木脩司, 石田貴士, 秋山泰. データベースの部分文字列クラスタリングによるアミノ酸配列相同性検索の高速化, 第34回バイオ情報学研究会, 情報処理学会研究報告, vol. 2013-BIO-34, no. 14, pp. 1-7, June 2013.
• 鈴木脩司, 石田貴士, 秋山 泰. Suffix arrayを用いた高速な配列相同性検索の改良とエピゲノム解析への対応, 第29回バイオ情報学研究会, 情報処理学会研究報告, Vol. 2012-BIO-29, No. 24, pp. 1-7, June 2012.
• 坂田幸佑, 鈴木脩司, 石田貴士, 秋山泰. GPU を用いた配列相同性検索ツールの マルチGPU 向け最適化, 情報処理学会研究報告バイオ情報学(BIO), vol. 2011-BIO-26(2), pp. 1-7, Oct. 2011.
• 鈴木 脩司, 石田 貴士, 秋山 泰. マルチCPUコアとGPUを用いた高速な配列相同性検索, GTC Workshop Japan 2011, July 2011.
• 鈴木脩司, 石田貴士, 秋山 泰. GPUを用いた高速な配列相同性検索のsuffix arrayによる改良, 情報処理学会 第25回バイオ情報学研究会, vol. 2011-BIO-25, pp. 1-8, June 2011.
• 坂田幸佑, 鈴木脩司, 石田貴士, 秋山 泰. GPU配列相同性検索ツールのマルチGPU向け最適化と長断片への対応, 情報処理学会 第73回全国大会, Mar. 2011.
• 鈴木 脩司, 石田 貴士, 秋山 泰. FM-indexを用いた高速な配列相同性検索ツールの開発, 情報処理学会研究報告バイオ情報学(BIO), vol. 2010-BIO-23(20), pp. 1-6, Dec. 2010.
• 鈴木脩司, 石田貴士, 秋山泰. GPUによるDNA断片配列の高速マッピング, 情報処理学会研究報告バイオ情報学(BIO), vol. 2010-BIO-21(23), pp. 1-6, June 2010.

その他の論文・著書など

• 秋山 泰, 石田 貴士, 角田将典, 鈴木脩司. 次世代ＤＮＡシークエンサデータの超高速解析, BioSupercomputing Newsletter, Vol. 5, pp. 13, Nov. 2011.

学位論文

• 大量メタゲノム情報に対するアミノ酸配列相同性検索の高速化,  論文要旨,  博士（工学）,  東京工業大学,  2015/03/26,   
• Faster Protein Sequence Homology Searches for Large-scale Metagenomic Data,  Thesis,  博士（工学）,  Tokyo Institute of Technology,  2015/03/26,   
• Faster Protein Sequence Homology Searches for Large-scale Metagenomic Data,  Exam Summary,  博士（工学）,  Tokyo Institute of Technology,  2015/03/26,   

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