@article{CTT100666826,
  author = {Masahito Ohue and Yuri Matsuzaki and Takehiro Shimoda and Takashi Ishida and Yutaka Akiyama},
  title = {Highly Precise Protein-Protein Interaction Prediction Based on Consensus Between Template-Based and de Novo Docking Methods},
  journal = {BMC Proceedings},
  year = 2013,
}

@article{CTT100805859,
  author = {石田 貴史 and 秋山泰 and 関嶋 政和 and 大野 一樹 and 折田 正弥},
  title = {顧みられない熱帯病に対するIT創薬の現状 (今田治教授退任記念号・兵藤友博教授退任記念号)},
  journal = {立命館経営学},
  year = 2013,
}

@article{CTT100665992,
  author = {Hagiwara Y and Ohno K and Orita M and Koga R and Endo T and Akiyama Y and Sekijima M.},
  title = {Accelerating quantum chemistry calculations with graphical processing units - toward in high-density (HD) silico drug discovery},
  journal = {Curr Comput Aided Drug Des. 2013},
  year = 2013,
}

@article{CTT100666827,
  author = {Yuri Matsuzaki and Nobuyuki Uchikoga and Masahito Ohue and Takehiro Shimoda and Toshiyuki Sato and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK 3.0: A high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments},
  journal = {Source Code for Biology and Medicine},
  year = 2013,
}

@article{CTT100666829,
  author = {Yuri Matsuzaki and Masahito Ohue and Nobuyuki Uchikoga and Yutaka Akiyama},
  title = {Protein-protein interaction network prediction by using rigid-body docking tools: application to bacterial chemotaxis},
  journal = {Protein and Peptide Letters},
  year = 2013,
}

@article{CTT100666831,
  author = {Nobuyuki Uchikoga and Yuri Matsuzaki and Masahito Ohue and Takatsugu Hirokawa and Yutaka Akiyama},
  title = {Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints},
  journal = {PLOS ONE},
  year = 2013,
}

@article{CTT100669378,
  author = {Ren A and Ishida T and Akiyama Y},
  title = {Assessing statistical reliability of phylogenetic trees via a speedy double bootstrap method},
  journal = {Mol Phylogenet Evol.},
  year = 2013,
}

@article{CTT100669379,
  author = {Youhei Namiki and Takashi Ishida and Yutaka Akiyama},
  title = {Acceleration of sequence clustering using longest common subsequence filtering},
  journal = {BMC Bioinformatics},
  year = 2013,
}

@inproceedings{CTT100669689,
  author = {杉浦典和 and 石田貴士 and 秋山泰 and 関嶋政和},
  title = {de Bruijn Graphの分割によるVelvetの消費メモリの低減},
  booktitle = {情報処理学会研究報告},
  year = 2013,
}

@inproceedings{CTT100669691,
  author = {小松祐城 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {情報処理学会研究報告},
  year = 2013,
}

@inproceedings{CTT100669690,
  author = {渡部翔 and 鈴木脩司 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {情報処理学会研究報告},
  year = 2013,
}

@inproceedings{CTT100666834,
  author = {Masahito Ohue and Yuri Matsuzaki and Takehiro Shimoda and Takashi Ishida and Yutaka Akiyama},
  title = {Highly precise protein-protein interaction prediction by integrating template-based and template-free protein docking},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100722750,
  author = {Yutaka Akiyama},
  title = {Development of GPU-accelerated Bioinformatics Application Tools for supporting Drug Discovery: A Case Study in “Drugs for NTDs” Project},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100669649,
  author = {石田貴士 and 蓮実梢 and 伴兼弘 and 秋山泰},
  title = {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},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100666838,
  author = {Takehiro Shimoda and Masahito Ohue and Yuri Matsuzaki and Takayuki Fujiwara and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {The MEGADOCK project: Ultra-high-performance protein-protein interaction prediction tools on supercomputing environments},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100666837,
  author = {Masahito Ohue and Yuri Matsuzaki and Takehiro Shimoda and Takashi Ishida and Yutaka Akiyama},
  title = {Improvement of protein-protein interaction prediction by integrating template-based and template-free protein docking},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100876464,
  author = {Yuri Matsuzaki and Masahito Ohue and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {Structure based protein-protein interaction network prediction of EGFR signaling related proteins using MEGADOCK},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100876463,
  author = {Nobuyuki Uchikoga and Yuri Matsuzaki and Masahito Ohue and Takatsugu Hirokawa and Yutaka Akiyama},
  title = {Re-docking scheme of protein-protein interactions for generating near-native interaction patterns in difficult docking cases},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100666832,
  author = {Takehiro Shimoda and Takashi Ishida and Shuji Suzuki and Masahito Ohue and Yutaka Akiyama},
  title = {MEGADOCK-GPU: Acceleration of Protein-Protein Docking Calculation on GPUs},
  booktitle = {Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2013 (ACM-BCB 2013)},
  year = 2013,
}

@inproceedings{CTT100666835,
  author = {Takehiro Shimoda and Takashi Ishida and Shuji Suzuki and Masahito Ohue and Yutaka Akiyama},
  title = {MEGADOCK-GPU: Acceleration of Protein-Protein Docking Calculation on GPUs},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100666836,
  author = {Masahito Ohue and Yuri Matsuzaki and Takehiro Shimoda and Takashi Ishida and Yutaka Akiyama},
  title = {Highly precise protein-protein interaction prediction by integrating template-based and template-free protein docking},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100801989,
  author = {小幡 康文 and 石田貴士 and 夏目 徹 and 秋山泰},
  title = {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},
  booktitle = {研究報告数理モデル化と問題解決（MPS）},
  year = 2013,
}

@inproceedings{CTT100666850,
  author = {下田雄大 and 石田貴士 and 鈴木脩司 and 大上雅史 and 秋山泰},
  title = {MEGADOCK-GPU: GPUによるタンパク質間ドッキング計算の高速化},
  booktitle = {GTC Workshop Japan 2013},
  year = 2013,
}

@inproceedings{CTT100669380,
  author = {Aizhen Ren and Takashi Ishida and Yutaka Akiyama},
  title = {SDBP: An Easy-to-use R Program Package for Assessing Reliability of                   Estimated Phylogenetic Trees Based on the Speedy Double Bootstrap Method},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100669381,
  author = {Yasufumi Obata and Takashi Ishida and Tohru Natsume and Yutaka Akiyama},
  title = {Acceleration of Tandem Mass Spectrometry Analysis Software CoCoozo                   using Multi-core CPUs and Graphics Processing Units},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100669650,
  author = {渡部翔 and 鈴木脩司 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100802049,
  author = {任 愛珍 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {研究報告数理モデル化と問題解決（MPS）},
  year = 2013,
}

@inproceedings{CTT100802226,
  author = {齊藤 有紀 and 石田貴士 and 関嶋 政和 and 秋山泰},
  title = {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)},
  booktitle = {電子情報通信学会技術研究報告 = IEICE technical report : 信学技報},
  year = 2013,
}

@inproceedings{CTT100666851,
  author = {大上雅史 and 松崎由理 and 内古閑伸之 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {第13回日本蛋白質科学会年会},
  year = 2013,
}

@inproceedings{CTT100669692,
  author = {鈴木脩司 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {情報処理学会研究報告},
  year = 2013,
}

@inproceedings{CTT100669693,
  author = {吉川舜亮 and 石田貴士 and 関嶋政和 and 秋山泰},
  title = {Sparse k-mer graphアルゴリズムの評価とVelvetへの実装},
  booktitle = {情報処理学会研究報告},
  year = 2013,
}

@inproceedings{CTT100669694,
  author = {小幡康文 and 石田貴士 and 夏目徹 and 秋山泰},
  title = {GPGPUによるタンパク質タンデム質量分析の高速化},
  booktitle = {情報処理学会研究報告},
  year = 2013,
}

@inproceedings{CTT100669695,
  author = {齊藤有紀 and 石田貴士 and 関嶋政和 and 秋山泰},
  title = {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},
  booktitle = {情報処理学会研究報告},
  year = 2013,
}

@inproceedings{CTT100666833,
  author = {Masahito Ohue and Yuri Matsuzaki and Takehiro Shimoda and Takashi Ishida and Yutaka Akiyama},
  title = {Highly Precise Protein-Protein Interaction Prediction Based on Consensus Between Template-Based and de Novo Docking Methods},
  booktitle = {Proceedings of Great Lakes Bioinformatics Conference 2013},
  year = 2013,
}

@inproceedings{CTT100666845,
  author = {Masahito Ohue and Yuri Matsuzaki and Nobuyuki Uchikoga and Kohei Yamamoto and Takayuki Fujiwara and Takehiro Shimoda and Toshiyuki Sato and Takashi Ishida and Yutaka Akiyama},
  title = {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},
  booktitle = {CAPRI 2013 5th Evaluation Meeting},
  year = 2013,
}

@inproceedings{CTT100669651,
  author = {Shuji Suzuki and Takashi Ishida and Yutaka Akiyama},
  title = {An Ultra-fast Computing Pipeline for Metagenome Analysis with GPUs},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100658089,
  author = {松崎由理 and 大上雅史 and 石田貴士 and 内古閑伸之 and 秋山泰},
  title = {大規模タンパク質間ネットワーク推定に関する研究},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100658033,
  author = {秋山泰 and 松崎由理 and 石田貴士 and 大上雅史 and 内古閑 伸之},
  title = {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},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100666852,
  author = {大上雅史 and 松崎由理 and 内古閑伸之 and 山本航平 and 下田雄大 and 藤原隆之 and 石田貴士 and 秋山泰},
  title = {MEGADOCK 3.0：超並列タンパク質間相互作用予測システム},
  booktitle = {生命情報科学若手の会 第4回研究会},
  year = 2013,
}

@inproceedings{CTT100658081,
  author = {Yuri Matsuzaki and Nobuyuki Uchikoga and Masahito Ohue and Takashi Ishida and Yutaka Akiyama},
  title = {Protein-protein interaction network prediction by using rigid-body docking tool MEGADOCK},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100658027,
  author = {秋山泰 and 松崎由理 and 大上雅史 and 石田貴士 and 内古閑伸之},
  title = {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},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100658028,
  author = {大上雅史 and 松崎由理 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100658550,
  author = {Yutaka Akiyama},
  title = {Large-scale protein-protein interaction network prediction by an exhaustive rigid docking system MEGADOCK},
  booktitle = {},
  year = 2013,
}