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Publication List - Takashi Ishida 2013 (37 / 223 entries)
Journal Paper
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Masahito Ohue,
Yuri Matsuzaki,
Takehiro Shimoda,
Takashi Ishida,
Yutaka Akiyama.
Highly Precise Protein-Protein Interaction Prediction Based on Consensus Between Template-Based and de Novo Docking Methods,
BMC Proceedings,
BioMed Central,
Volume 7,
Supplement 7,
S6,
Dec. 2013.
Official location
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Yuri Matsuzaki,
Nobuyuki Uchikoga,
Masahito Ohue,
Takehiro Shimoda,
Toshiyuki Sato,
Takashi Ishida,
Yutaka Akiyama.
MEGADOCK 3.0: A high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments,
Source Code for Biology and Medicine,
BioMed Central,
Vol. 8,
No. 1,
Sept. 2013.
Official location
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Youhei Namiki,
Takashi Ishida,
Yutaka Akiyama.
Acceleration of sequence clustering using longest common subsequence filtering,
BMC Bioinformatics,
Vol. 14,
Suppl 8,
S7,
May 2013.
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Ren A,
Ishida T,
Akiyama Y.
Assessing statistical reliability of phylogenetic trees via a speedy double bootstrap method,
Mol Phylogenet Evol.,
Vol. 67,
No. 2,
pp. 429-35,
May 2013.
International Conference (Reviewed)
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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.
Official location
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Yasufumi Obata,
Takashi Ishida,
Tohru Natsume,
Yutaka Akiyama.
Acceleration of Tandem Mass Spectrometry Analysis Software CoCoozo using Multi-core CPUs and Graphics Processing Units,
The 2013 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'13) Workshop on Mathematical Modeling and Problem Solving,
Vol. I,
pp. 149-154,
July 2013.
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Aizhen Ren,
Takashi Ishida,
Yutaka Akiyama.
SDBP: An Easy-to-use R Program Package for Assessing Reliability of Estimated Phylogenetic Trees Based on the Speedy Double Bootstrap Method,
The 2013 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'13) Workshop on Mathematical Modeling and Problem Solving,
Vol. I,
pp. 143-148,
July 2013.
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Masahito Ohue,
Yuri Matsuzaki,
Takehiro Shimoda,
Takashi Ishida,
Yutaka Akiyama.
Highly Precise Protein-Protein Interaction Prediction Based on Consensus Between Template-Based and de Novo Docking Methods,
Great Lakes Bioinformatics Conference 2013,
Proceedings of Great Lakes Bioinformatics Conference 2013,
pp. 100-109,
May 2013.
International Conference (Not reviewed / Unknown)
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Takehiro Shimoda,
Masahito Ohue,
Yuri Matsuzaki,
Takayuki Fujiwara,
Nobuyuki Uchikoga,
Takashi Ishida,
Yutaka Akiyama.
The MEGADOCK project: Ultra-high-performance protein-protein interaction prediction tools on supercomputing environments,
ACM Conference on Bioinformatics, Computatioal Biology and Biomedical Informatics (ACM-BCB2013),
p. 668,
Sept. 2013.
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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.
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Masahito Ohue,
Yuri Matsuzaki,
Takehiro Shimoda,
Takashi Ishida,
Yutaka Akiyama.
Highly precise protein-protein interaction prediction by integrating template-based and template-free protein docking,
2nd IIT Madras – Tokyo Tech Joint Symposium on Techniques and Applications of Bioinformatics,
P08,
Sept. 2013.
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Masahito Ohue,
Yuri Matsuzaki,
Takehiro Shimoda,
Takashi Ishida,
Yutaka Akiyama.
Improvement of protein-protein interaction prediction by integrating template-based and template-free protein docking,
ACM Conference on Bioinformatics, Computatioal Biology and Biomedical Informatics (ACM-BCB2013),
p. 667,
Sept. 2013.
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Yuri Matsuzaki,
Masahito Ohue,
Nobuyuki Uchikoga,
Takashi Ishida,
Yutaka Akiyama.
Structure based protein-protein interaction network prediction of EGFR signaling related proteins using MEGADOCK,
2nd IIT Madras – Tokyo Tech Joint Symposium on Techniques and Applications of Bioinformatics,
Sept. 2013.
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Masahito Ohue,
Yuri Matsuzaki,
Nobuyuki Uchikoga,
Kohei Yamamoto,
Takayuki Fujiwara,
Takehiro Shimoda,
Toshiyuki Sato,
Takashi Ishida,
Yutaka Akiyama.
Protein-protein interaction prediction based on rigid-body docking with ultra-high-performance computing technique: applications to affinity prediction on CAPRI round 21 and interactome analyses,
CAPRI 2013 5th Evaluation Meeting,
Apr. 2013.
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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.
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Yuri Matsuzaki,
Nobuyuki Uchikoga,
Masahito Ohue,
Takashi Ishida,
Yutaka Akiyama.
Protein-protein interaction network prediction by using rigid-body docking tool MEGADOCK,
Biophysical Society 57th Annual Meeting,
Feb. 2013.
Domestic Conference (Not reviewed / Unknown)
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Yuki Komatsu,
Takashi Ishida,
Yutaka Akiyama.
拡張されたナイーブベイズを用いたメタゲノム配列の系統分類,
第36回バイオ情報学研究会,
情報処理学会研究報告,
vol. 2013-BIO-36,
no. 21,
pp. 1-6,
Dec. 2013.
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Sho Watanabe,
Shuji Suzuki,
Takashi Ishida,
Yutaka Akiyama.
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.
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Norikazu Sugiura,
Takashi Ishida,
Yutaka Akiyama,
Masakazu Sekijima.
de Bruijn Graphの分割によるVelvetの消費メモリの低減,
第36回バイオ情報学研究会,
情報処理学会研究報告,
vol. 2013-BIO-36,
no. 6,
pp. 1-7,
Dec. 2013.
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Masahito Ohue,
Yuri Matsuzaki,
Takehiro Shimoda,
Takashi Ishida,
Yutaka Akiyama.
Highly precise protein-protein interaction prediction by integrating template-based and template-free protein docking,
The 2013 Annual Conference of the Japanese Society for Bioinformatics (JSBi2013),
P077,
Nov. 2013.
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Takashi Ishida,
Kozue Hasumi,
Tomohiro Ban,
Yutaka Akiyama.
NTDs創薬ターゲットタンパク質選択のためのデータベースiNTRODBの開発,
第54回日本熱帯医学会大会,
No. p2-53,
Oct. 2013.
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任 愛珍,
Takashi Ishida,
Yutaka Akiyama.
SDBP: スピーディー・ダブルブートストラップ法に基づいた系統樹の信頼性評価のためのRパッケージ,
研究報告数理モデル化と問題解決(MPS),
一般社団法人情報処理学会,
Vol. 2013,
No. 4,
pp. 1-4,
July 2013.
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Takehiro Shimoda,
Takashi Ishida,
Shuji Suzuki,
Masahito Ohue,
Yutaka Akiyama.
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.
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Sho Watanabe,
Shuji Suzuki,
Takashi Ishida,
Yutaka Akiyama.
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.
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小幡 康文,
Takashi Ishida,
夏目 徹,
Yutaka Akiyama.
タンデム質量分析ソフトウェアCoCoozoのマルチコアCPUとGPUを用いた高速化,
研究報告数理モデル化と問題解決(MPS),
一般社団法人情報処理学会,
Vol. 2013,
No. 5,
pp. 1-4,
July 2013.
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Yuuki Saitou,
Takashi Ishida,
Masakazu Sekijima,
Yutaka Akiyama.
結合自由エネルギー予測を用いたクリアランス経路予測の改善に関する研究,
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. 15,
pp. 1-6,
June 2013.
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Shuji Suzuki,
Takashi Ishida,
Yutaka Akiyama.
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.
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Masahito Ohue,
Yuri Matsuzaki,
Nobuyuki Uchikoga,
Takashi Ishida,
Yutaka Akiyama.
MEGADOCK:構造ドッキング計算を用いたタンパク質間相互作用の大規模予測,
第13回日本蛋白質科学会年会,
1P-059,
June 2013.
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齊藤 有紀,
Takashi Ishida,
関嶋 政和,
Yutaka Akiyama.
結合自由エネルギー計算を用いた薬物クリアランス経路予測の改善 (ニューロコンピューティング),
電子情報通信学会技術研究報告 = IEICE technical report : 信学技報,
一般社団法人電子情報通信学会,
Vol. 113,
No. 111,
pp. 83-88,
June 2013.
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Shunsuke Yoshikawa,
Takashi Ishida,
Masakazu Sekijima,
Yutaka Akiyama.
Sparse k-mer graphアルゴリズムの評価とVelvetへの実装,
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. 1,
pp. 1-7,
June 2013.
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Yasufumi Obata,
Takashi Ishida,
Tohru Natsume,
Yutaka Akiyama.
GPGPUによるタンパク質タンデム質量分析の高速化,
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. 13,
pp. 1-8,
June 2013.
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Masahito Ohue,
Yuri Matsuzaki,
Nobuyuki Uchikoga,
Kohei Yamamoto,
Takehiro Shimoda,
Takayuki Fujiwara,
Takashi Ishida,
Yutaka Akiyama.
MEGADOCK 3.0:超並列タンパク質間相互作用予測システム,
生命情報科学若手の会 第4回研究会,
Mar. 2013.
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Yutaka Akiyama,
Yuri Matsuzaki,
Takashi Ishida,
Masahito Ohue,
Nobuyuki Uchikoga.
網羅的タンパク質ドッキング予測プログラムMEGADOCKの開発と応用,
文部科学省「革新的ハイパフォーマンス・コンピューティング・インフラ (HPCI) の構築」HPCI戦略プログラム「グランドチャレンジ・アプリケーションの研究開発」公開シンポジウム,
Mar. 2013.
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Yuri Matsuzaki,
Masahito Ohue,
Takashi Ishida,
Nobuyuki Uchikoga,
Yutaka Akiyama.
大規模タンパク質間ネットワーク推定に関する研究,
平成24年度「京」を中核とするHPCIシステム利用研究課題中間報告会,
Mar. 2013.
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Takashi Ishida.
天然変性蛋白質領域予測 PrDOS-CNF & metaPrDOS2,
Frontier of Protein Structure Prediction,
Feb. 2013.
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Masahito Ohue,
Yuri Matsuzaki,
Takashi Ishida,
Yutaka Akiyama.
MEGADOCK: 大規模タンパク質間相互作用予測システムとその応用,
HPCS2013 ハイパフォーマンスコンピューティングと計算科学シンポジウム,
Jan. 2013.
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Yutaka Akiyama,
Yuri Matsuzaki,
Masahito Ohue,
Takashi Ishida,
内古閑伸之.
網羅的タンパク質ドッキング解析プログラムMEGADOCKの開発と応用,
ISLiMソフトウェア研究開発報告会,
Jan. 2013.
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