"Haruki Yamane,Takashi Ishida","Helix encoder: a compound-protein interaction prediction model specifically designed for class A GPCRs",,"Frontiers in Bioinformatics","frontiers","Vol. 3",,,2023,May
"Takashi Ishida,Jason Kurniawan","Protein Model Quality Estimation using Molecular Dynamics Simulation",,"ACS OMEGA","American Chemical Society",,,,2022,July
"Yuma Takei,Takashi Ishida","A Benchmark Dataset for Evaluating Practical Performance of Model Quality Assessment of Homology Models",,"Bioengineering",,"Vol. 9","No. 3","p. 118",2022,Mar.
"Toshitaka Tanebe,Takashi Ishida","End-to-end learning for compound activity prediction based on binding pocket information",,"BMC Bioinformatics",,"Vol. 22",,"p. 529",2021,Oct.
"Nobuaki Yasuo,Takashi Ishida,Masakazu Sekijima","Computer aided drug discovery review for infectious diseases with case study of anti-Chagas project",,,,,,,2021,Aug.
"Izawa K,Okamoto-Shibayama K,Kita D,Tomita S,Saito A,Ishida T,Ohue M,Akiyama Y,Ishihara K.","Taxonomic and gene category analyses of subgingival plaques from a group of Japanese individuals with and without periodontitis",,"International Journal of Molecular Sciences","International Journal of Molecular Sciences","Volume 22","Issue 10","  5298",2021,May
"Yuma Takei,Takashi Ishida","P3CMQA: Single-Model Quality Assessment Using 3DCNN with Profile-Based Features",,"Bioengineering","MDPI","Vol. 8","  (3)","Page 40",2021,Mar.
"Haris Hasic,Takashi Ishida","Single-Step Retrosynthesis Prediction Based on the Identification of Potential Disconnection Sites Using Molecular Substructure Fingerprints",,"Journal of Chemical Information and Modeling","American Chemical Society","Vol. 61","Issue 2","pp. 641?652",2021,Feb.
"Haris Hasic,Takashi Ishida","Single-step Retrosynthesis Prediction based on the Identification of Potential Disconnection Sites","The Chem-Bio Informatics Society 2020 Annual Meeting",,,,,,2020,Oct.
"Jason Kurniawan,Takashi Ishida","Quality Assessment of Protein Structure Modelsusing Molecular Dynamics Trajectories","Informatics in Biology, Medicine and Pharmacology （IIBMP2020）",,,,,,2020,Sept.
"Haris Hasic,Takashi Ishida","Singlestep Retrosynthesis Prediction based on the Identification of Potential Disconnection Sites using Molecular Substructure Fingerprints","Informatics in Biology, Medicine and Pharmacology （IIBMP2020）",,,,,,2020,Sept.
"武居佑真,石田 貴士","3DCNNを用いたタンパク質予測構造モデル評価手法の進化的情報の利用による改良","日本バイオインフォマティクス学会2020年年会（IIBMP2020)",,,,,,2020,Sept.
"白石幹,石田貴士","深層学習ネットワーク構造の検討によるタンパク質天然変性領域予測手法の改良","日本バイオインフォマティクス学会2020年年会（IIBMP2020)",,,,,,2020,Sept.
"Aizhen Ren,Takashi Ishida,Yutaka Akiyama","Mathematical proof of the third order accuracy of the speedy double botstrap method",,"Communication in Statistics-Theory and Methods","Taylor & Francis","Vol. 49","issue 16","pp. 3950-3964",2020,Aug.
"Shuichiro Makigaki,Takashi Ishida","Sequence alignment generation using intermediate sequence search for homology modeling",,"Computational and Structural Biotechnology Journal","ELSEVIER","Vol. 18",,"pp. 2043-2050",2020,July
"Shuichiro Makigaki,Takashi Ishida","Sequence alignment using machine learning for accurate template-based protein structure prediction",,"Bioinformatics, btz483","Oxford University Press","Vol. 36","  1","pp. 104-111",2020,Jan.
"Kento Aoyama,Masanori Kakuta,Yuri Matsuzaki,Takashi Ishida,Masahito Ohue,Yutaka Akiyama","Development of computational pipeline software for genome/exome analysis on the K computer",,"Supercomputing Frontiers and Innovations",,"Vol. 7","No. 1","pp. 37-54",2020,
"Shuntaro Chiba,Masahito Ohue,Anastasiia Gryniukova,Petro Borysko,Sergey Zozulya,Nobuaki Yasuo,Ryunosuke Yoshino,Kazuyoshi Ikeda,Woong-Hee Shin,Daisuke Kihara,Mitsuo Iwadate,Hideaki Umeyama,Takaaki Ichikawa,Reiji Teramoto,Kun-Yi Hsin,Vipul Gupta,Hiroaki Kitano,Mika Sakamoto,Akiko Higuchi,Nobuaki Miura,Kei Yura,Masahiro Mochizuki,Chandrasekaran Ramakrishnan,A. Mary Thangakani,D. Velmurugan,M. Michael Gromiha,Itsuo Nakane,Nanako Uchida,Hayase Hakariya,Modong Tan,Hironori Nakamura,Shogo Suzuki,Tomoki Ito,Masahiro Kawatani,Kentaroh Kudoh,Sakurako Takashina,Kazuki Yamamoto,Yoshitaka Moriwaki,Keita Oda,Daisuke Kobayashi,Tatsuya Okuno,Shintaro Minami,George Chikenji,Philip Prathipati,Chioko Nagao,Attayeb Mohsen,Mari Ito,Kenji Mizuguchi,Teruki Honma,Takashi Ishida,Takatsugu Hirokawa,Yutaka Akiyama,Masakazu Sekijima.","A prospective compound screening contest identified broader inhibitors for Sirtuin 1",,"Scientific Reports",,"  9",,,2019,Dec.
"Rin Sato,Takashi Ishida","GCMQA:Graph convolutional neural network for model quality assessment","AHeDD2019/IPAB2019 Joint Symposium  Asia Hub for e-Drug Discovery",,,,,,2019,Nov.
"Rin Sato,Takashi Ishida","GCMQA: Graph convolutional neural network for model quality assessment","Informatics in Biology, Medicine and Pharmacology(IIBMP2019)",,,,,,2019,Sept.
"多治見隆志,石田貴士","分子特徴ベクトルと学習アルゴリズムのアンサンブルによるリガンドベース活性予測精度の向上","日本バイオインフォマティクス学会２０１９年年会 第八回生命医薬情報学連合会",,,,,,2019,Sept.
"Rin Sato,Takashi Ishida","Protein model accuracy estimation based on local structure quality assessment using 3D convolutional neural network",,"PLOS ONE","Public Library of Science","Vol. 14","Issue 9","  e0221347",2019,Sept.
"Shuichiro Makigaki,Takashi Ishida","Remote protein homolog detetction based on sequence similarity networks","Informatics In Biology, Medicine and Pharmacology 2019 (IIBMP2019)",,,,,,2019,Sept.
"Masataka Irokawa,Takashi Ishida","Improvement of deep learning model for reraking predicted protein complex structures","Informatics In Biology, Medicine and Pharmacology 2019 (IIBMP2019)",,,,,,2019,Sept.
"松村真里,石田貴士","タンパク質配列情報と薬剤結合部位構造情報を用いた新規タンパク質に対する深層学習リガンド結合予測","日本バイオインフォマティクス学会２０１９年年会 第八回生命医薬情報学連合会",,,,,,2019,Sept.
"Hasic,Takashi Ishida","Predicting Chemical Reaction Routes with Artificial Intelligence-based Retrosynthesis","Informatics In Biology, Medicine and Pharmacology 2019 (IIBMP2019)",,,,,,2019,Sept.
"Toshitaka Tanebe,Takashi Ishida","End-to-end learning based compound activity prediction using binding pocket information","2019 International Conference on Intelligent Computing",,"Springer, Cham",,,"  226-234",2019,Aug.
"成井政人,石田貴士,牧垣秀一朗","機械学習を用いたホモロジーモデリングのための配列アラインメント生成手法の高速化",,"研究報告数理モデル化と問題解決（MPS）",,"  2019-MPS-124","  4","pp. 1-4",2019,July
"Masato Narui,Takashi Ishida,Shuichiro Makigaki","Acceleration of Machine Learning-based Sequence Alignment Generation","The 25th Int'l Conf on Parallel and Distributed Processing Techniques and Applications(PDPTA2019) CSCE'19","Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA)","The Steering Committee of The World Congress in Computer Science, Computer Engineering and Applied Computing (WorldComp)",,,"pp. 129-134",2019,July
"成井政人,石田貴士,牧垣秀一朗","k最近傍法を用いた構造予測向け配列アラインメント生成手法の高速化","情報処理学会 第 58 回バイオ情報学(SIGBIO)研究会",,,,,,2019,June
"色川雅崇,石田貴士","深層学習を用いたタンパク質複合体予測構造に対するリランキングシステムの開発","第58 回バイオ情報学(SIGBIO)研究会",,,,,,2019,June
"牧垣秀一朗,石田貴士","配列類似性ネットワークに基づく高感度な遠縁タンパク質検索","第 58 回バイオ情報学(SIGBIO)研究会",,,,,,2019,June
"賀来智博,石田貴士","深層学習を用いたスコアマトリクス推定","第23回オープンバイオ研究会",,,,,,2019,Mar.
"牧垣秀一朗,石田貴士","機械学習を用いたホモロジーモデリングのための配列アライメント手法","第57 回バイオ情報学(SIGBIO)研究会",,,,,,2019,Mar.
"種部俊孝,石田貴士","タンパク質ポケット構造情報を考慮したエンドツーエンド表現学習によるリガンド結合 予想","情報処理学会第57回バイオ情報学研究会（SIGB IO)",,,,,,2019,Mar.
"佐藤倫,石田貴士","Graph Convolution を用いたタンパク質予測立体構造の評価手法の開発","情報処理学会第57回バイオ情報学研究会（SIGB IO)",,,,,,2019,Mar.
"Naomi Wakayama,Kota Toshimoto,Kazuya Maeda,Shun Hotta,Takashi Ishida,Yutaka Akiyama,Yuichi Sugiyama","In Silico Prediction of Major Clearance Pathways of Drugs among 9 Routes with Two-Step Support Vector Machines",,"Pharmaceutical Research","Springer US","  35:197","  10","pp. 1-21",2018,Oct.
"Wakayama N,Toshimoto K,Maeda K,Hotta S,Ishida T,Akiyama Y,Sugiyama Y.","In Silico Prediction of Major Clearance Pathways of Drugs among 9 Routes with Two-Step Support Vector Machines",,"Pharmaceutical Research",,,,,2018,Aug.
"Yusuke Matsuyama,Takashi Ishida","Stacking Multiple Molecular Fingerprints for Improving Ligand-Based Virtual Screening","International Conference on Intelligent Computing(ICIC2018)","Lecture Notes in Computer Science book series (LNCS, volume 10955)","Springer, Cham","vol. 10955",,"pp. 279-288",2018,July
"Ruoming He,Takashi Ishida","Prediction of drug-target interactions with 3D structure information of target binding sites","14th International Conference on Intelligent Computing, ICIC 2018",,,,,,2018,July
"佐藤倫,石田貴士","深層学習を用いたタンパク質予測立体構造モデルの評価","第 54 回バイオ情報学(SIGBIO)研究会",,,,,,2018,June
"池田光,石田貴士","3次元畳み込みニューラルネットワークを用いた局所的相互作用に基づくタンパク質複合体予測構造評価","第 54 回バイオ情報学(SIGBIO)研究会",,,,,,2018,June
"Toshitaka Tanebe,Takashi Ishida","Machine learning based compound activity prediction using binding pocket information","The 1st RWBC-OIL Workshop",,,,,,2018,May
"曽我 光瑛,石田 貴士","適合性フィードバックを用いたトリパノソーマ原虫症薬剤標的タンパク質選定の改良","情報処理学会 第53回バイオ情報学研究会",,,,,,2018,Mar.
"松山 祐輔,石田 貴士","多様な活性化合物発見のための化合物Fingerprintアンサンブル手法の開発","報処理学会 第53回バイオ情報学研究会",,,,,,2018,Mar.
"Shuichiro Makigaki,Takashi Ishida","Improvement of template-based protein structure prediction by using chimera alignment","8th International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB)","Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics","ACM",,,"pp. 32-37",2018,Jan.
"Takashi Ishida","Ensembling multiple molecular fingerprint-based predictions for improvement of ligand-based drug discovery","4th IITM-Tokyo Tech Joint Symposium on Frontiers in Bioinformatics",,,,,,2017,Nov.
"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",2017,Oct.
"松山 祐輔,石田 貴士","Using multiple molecular fingerprints for improvement of drug activity prediction","CBI学会2017年大会",,,,,,2017,Oct.
"Yusuke Matsuyama,Takashi Ishida","Ensemble multiple molecular fingerprints for improvement of ligand based drug discovery","Informatics In Biology, Medicine and Pharmacology 2017",,,,,,2017,Sept.
"Shuntaro Chiba,Takashi Ishida,Kazuyoshi Ikeda,Masahiro Mochizuki,Reiji Teramoto,Y-h. Taguchi,Mitsuo Iwadate,Hideaki Umeyama,Chandrasekaran Ramakrishnan,A. Mary Thangakani,D. Velmurugan,M. Michael Gromiha,Tatsuya Okuno,Koya Kato,Shintaro Minami,George Chikenji,Shogo D. Suzuki,Keisuke Yanagisawa,Woong-Hee Shin,Daisuke Kihara,Kazuki Z. Yamamoto,Yoshitaka Moriwaki,Nobuaki Yasuo,Ryunosuke Yoshino,Sergey Zozulya,Petro Borysko,Roman Stavniichuk,Teruki Honma,Takatsugu Hirokawa,Yutaka Akiyama,Masakazu Sekijima","An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes",,"Scientific Reports","Nature Publishing Group","Vol. 7","No. 12038","pp. 1-13",2017,Sept.
"石田 貴士","深層学習技術が加速するIT創薬技術の深化","Japan Analytical & Scientific Instruments Show (JASIS) 2017",,,,,,2017,Sept.
"Ryunosuke Yoshino,Nobuaki Yasuo,Yohsuke Hagiwara,Takashi Ishida,Daniel Ken Inaoka,Yasushi Amano,Yukihiro Tateishi,Kazuki Ohno,Ichiji Namatame,Tatsuya Niimi,Masaya Orita,Kiyoshi Kita,Yutaka Akiyama,Masakazu Sekijima","In silico, in vitro, X-ray crystallography, and integrated strategies for discovering spermidine synthase inhibitors for Chagas disease",,"Scientific Reports","Springer Nature","  7",,,2017,July
"大石智博,石田貴士","薬剤標的タンパク質選定支援に向けた立体構造上での株間変異情報表示システムの開発","情報処理学会 第50回バイオ情報学研究会",,,,,,2017,June
"賀来智博,石田貴士","配列プロファイル生成の改良によるタンパク質天然変性領域予測の高速化","情報処理学会 第50回バイオ情報学研究会","情報処理学会研究報告",,,,,2017,June
"伊澤 和輝,山澤 まりな,大上 雅史,石田 貴士,秋山 泰","歯周病の発症要因の特定に向けた口腔内細菌叢解析","情報処理学会 第50回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2017-BIO-50","  40","  1-6",2017,June
"山澤 まりな,伊澤 和輝,大上 雅史,石田 貴士,Kazuyuki Ishihara,秋山 泰","高速相同性解析ツールGHOSTXを用いた口腔内メタゲノム解析","情報処理学会 第50回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2017-BIO-50","  41","  1-7",2017,June
"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",2017,Apr.
"松山祐輔,石田貴士","薬剤活性予測の改良のための、化合物フィンガープリントの比較解析","情報処理学会 第49回バイオ情報学研究会","情報処理学会研究報告",,,,,2017,Mar.
"Yanagisawa K,Komine S,Shogo Suzuki,Ohue M,Ishida T,Akiyama Y.","Spresso: an ultrafast compound pre-screening method based on compound decomposition",,"Bioinformatics","OXFORD Academic","Volume 33","Issue 23","Page 3836-3843",2017,Mar.
"Keisuke Yanagisawa,Shunta Komine,Shogo Suzuki,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","ESPRESSO: An ultrafast compound pre-screening method based on compound decomposition","The 27th International Conference on Genome Informatics (GIW 2016)",,,,,,2016,Oct.
"Keisuke Yanagisawa,Shunta Komine,Shogo Suzuki,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","ESPRESSO: An ultrafast compound pre-screening method with segmented compounds","Chem-Bio Informatics Society(CBI) Annual Meeting 2016",,,,,,2016,Oct.
"石田貴士","機械学習の進展と生命科学研究への応用","近畿化学協会コンピュータ化学部会  公開講演会（第97回例会）",,,,,,2016,Oct.
"Marina Yamasawa,Tomoya Fujii,Kota Goto,Masahito Ohue,Takashi Ishida,Kazuyuki Ishihara,Yutaka Akiyama","GPU/MPI Parallelization of Metagenomic Sequence Homology Search Tool and Its Application to Oral Metagenomics","Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)",,,,,,2016,Sept.
"Keisuke Yanagisawa,Shunta Komine,Shogo Suzuki,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","ESPRESSO: An ultrafast compound pre-screening method based on compound segmentation","Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)",,,,,,2016,Sept.
"Mitsuaki Soga,Takashi Ishida","Improvement of NTDs drug target protein selection by learning to rank","Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)",,,,,,2016,Sept.
"Yusuke Matsuyama,Takashi Ishida","Improvement of ligand-based virtual screening by introducing pharmacophore fingerprint","Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)",,,,,,2016,Sept.
"Naoto Kakami,Takashi Ishida","Prediction of Protein-Ligand Binding Sites Using 3D Convolutional Neural Networks","Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)",,,,,,2016,Sept.
"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",2016,Aug.
"曽我光瑛,石田貴士","ランク学習を用いたNTDs薬剤標的タンパク質候補選択の改良","情報処理学会 第46回バイオ情報学研究会","情報処理学会研究報告",,"  2016-BIO-46",,,2016,July
"青山 健人,角田 将典,松崎 由理,石田 貴士,秋山 泰","スーパーコンピュータ「京」上でのエクソーム解析パイプラインの開発",,"情報処理学会論文誌コンピューティングシステム（ACS）",,"Vol. 9","No. 2","p. 15-33",2016,July
"Atsushi Ose,Kota Toshimoto,Kazushi Ikeda,Kazuya Maeda,Shuya Yoshida,Fumiyoshi Yamashita,Mitsuru Hashida,Takashi Ishida,Yutaka Akiyama,Yuichi Sugiyama","Development of a Support Vector Machine-Based System to Predict Whether a Compound Is a Substrate of a Given Drug Transporter Using Its Chemical Structure",,"Journal of Pharmaceutical Sciences",,"Vol. 105","No. 77","p. 2222-2230",2016,July
"石田貴士","顧みられない熱帯病創薬に向けた薬剤標的タンパク質選定補助システム iNTRODB","第374回CBI学会講演会「感染症研究の将来?グローバルヘルスに貢献する創薬?」",,,,,,2016,July
"松山祐輔,石田貴士","ファーマコフォアフィンガープリントを利用した薬剤活性予測の改良","情報処理学会 第46回バイオ情報学研究会","情報処理学会研究報告",,"  2016-BIO-46",,,2016,July
"各務直人,石田貴士","3次元畳み込みニューラルネットワークを用いたタンパク質リガンド結合ポケットの予測","情報処理学会 第46回バイオ情報学研究会","情報処理学会研究報告",,"  2016-BIO-46",,,2016,July
"柳澤 渓甫,小峰 駿汰,鈴木 翔吾,大上 雅史,石田 貴士,秋山 泰","フラグメント分割に基づく超高速化合物プレスクリーニング手法ESPRESSO","情報処理学会 第46回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2016-BIO-46","  18","  1-7",2016,June
"藤井智也,角田将典,大上雅史,石田貴士,石原和幸,秋山泰","GPUを用いたメタゲノム配列相同性解析ツールのMPI並列化と応用",,"研究報告バイオ情報学（BIO）","情報処理学会","  2016-BIO-45","  3","  1-4",2016,Mar.
"Masahito Ohue,Yuri Matsuzaki,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers","Biophysical Society 60th Annual Meeting",,,,,,2016,Feb.
"柳澤 渓甫,小峰 駿汰,大上 雅史,石田 貴士,秋山 泰","Fast pre-filtering for virtual screening based on ligand decomposition","第21回創剤フォーラム若手研究会",,,,,,2015,Nov.
"年本広太,尾瀬淳,池田和史,前田和哉,石田貴士,秋山泰,杉山 雄一","機械学習を用いた薬物トランスポーター基質のin silico予測","第21回創剤フォーラム若手研究会",,,,,,2015,Nov.
"Takashi Ishida","Protein structure prediction based on machine learning","3nd IIT Madras ? Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics",,,,,,2015,Nov.
"Yuri Matsuzaki,Masahito Ohue,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK: A high-performance protein-protein interaction prediction software for petascale supercomputing environments","3nd IIT Madras ? Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics",,,,,,2015,Nov.
"Keisuke Yanagisawa,Shunta Komine,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","Fast pre-filtering for virtual screening based on compound fragmentation","3nd IIT Madras ? Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics",,,,,,2015,Nov.
"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",,,,,,2015,Nov.
"Shuntaro Chiba,Kazuyoshi Ikeda,Takashi Ishida,M. Michael Gromiha,Y-h. Taguchi,Mitsuo Iwadate,Hideaki Umeyama,Kun-Yi Hsin,Hiroaki Kitano,Kazuki Yamamoto,Nobuyoshi Sugaya,Koya Kato,Tatsuya Okuno,George Chikenji,Masahiro Mochizuki,Nobuaki Yasuo,Ryunosuke Yoshino,Keisuke Yanagisawa,Tomohiro Ban,Reiji Teramoto,Chandrasekaran Ramakrishnan,A. Mary Thangakani,D. Velmurugan,Philip Prathipati,Junichi Ito,Yuko Tsuchiya,Kenji Mizuguchi,Teruki Honma,Takatsugu Hirokawa,Yutaka Akiyama,Masakazu Sekijima","Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target",,"Scientific Reports",,"Vol. 5","No. 17209",,2015,Nov.
"Keisuke Yanagisawa,Shunta Komine,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","Fast pre-filtering for virtual screening based on compound decomposition","IIBMP2015",,,,,,2015,Oct.
"Keisuke Yanagisawa,Takashi Ishida,Yutaka Akiyama","Drug Clearance Pathway Prediction Based on Semi-supervised Learning",,"IPSJ Transactions on Bioinformatics",,"Vol. 8",,"pp. 21-27",2015,Aug.
"年本広太,尾瀬淳,池田和史,前田和哉,石田貴士,秋山泰,杉山雄一","機械学習を用いた薬物トランスポーター基質のin silico予測","第10回トランスポーター研究会年会","トランスポーター研究会年会抄録集",,"Vol. 10",,"pp. 78",2015,June
"和久井直樹,大上雅史,千葉峻太朗,石田貴士,岩?博史,秋山泰","既知の活性／非活性化合物のドッキング解析によるバーチャルスクリーニングに適したタンパク質立体構造モデルの選択","情報処理学会 第42回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2015-BIO-42","  60","  1-4",2015,June
"鈴木翔吾,柳澤渓甫,大上雅史,石田貴士,秋山泰","SVMとDeep Learningに基づくヒトc-Yesキナーゼ阻害化合物の予測","情報処理学会 第42回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2015-BIO-42","  36","  1-7",2015,June
"Yutaka Akiyama,Takashi Ishida","iNTRODB and its Applicationin anti-Trypanosome Drug Discovery","ISNTD d3 2015",,,,,,2015,May
"Suzuki S,Kakuta M,Ishida T,Akiyama Y.","Faster sequence homology searches by clustering subsequences",,"Bioinformatics",,"  31","  8","  1183-90",2015,Apr.
"Shuji Suzuki,Masanori Kakuta,Takashi Ishida,Yutaka Akiyama","GHOSTZ-GPU: Fast Protein Sequence Homology Search on GPUs","GPU Technology Conference 2015 (GTC2015)",,,,"No. P5273",,2015,Mar.
"相澤 洋輔,石田貴士,秋山泰","ディープラーニングを利用したタンパク質天然変性領域予測",,"研究報告バイオ情報学（BIO）","一般社団法人情報処理学会","Vol. 2015","No. 13","pp. 1-6",2015,Mar.
"小幡 康文,石田貴士,秋山泰","タンパク質ドッキングと配列情報特徴解析の融合によるタンパク質間相互作用予測の高精度化",,"研究報告バイオ情報学（BIO）","一般社団法人情報処理学会","Vol. 2015","No. 14","pp. 1-6",2015,Mar.
"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",,,,,,2015,Jan.
"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",,,,,,2015,Jan.
"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",,2015,Jan.
"杉原舜,石田貴士,秋山泰","低分子化合物二次元構造比較システムの改良","情報処理学会 第42回バイオ情報学研究会","情報処理学会研究報告",,,,,2015,
"小峰駿汰,石田貴士,秋山泰","フラグメント伸長型タンパク質-化合物ドッキングのビームサーチによる高速化","情報処理学会 第42回バイオ情報学研究会","情報処理学会研究報告",,,,,2015,
"年本 広太,若山 直美,堀田駿,前田 和哉,石田 貴士,秋山 泰,杉山 雄一","機械学習を用いた 9 つの主要な in vivo 薬物クリアランス経路の in silico 予測","日本動物実験代替法学会 第27回大会",,,,,,2014,Dec.
"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",,,,,,2014,Dec.
"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",2014,Nov.
"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)",,,,,,2014,Nov.
"Takashi Ishida,Kozue Hasumi,Yutaka Akiyama","iNTRODB: database for NTDs drug target protein selection","The Asia hub for e-drug discovery symposium 2014 (AHeDD' 2014)",,,,,,2014,Nov.
"石田貴士","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","第55回日本熱帯医学会大会・第29回日本国際保健医療学会学術大会合同大会",,,,,,2014,Nov.
"石田貴士","スーパーコンピュータが実現する大規模メタゲノム機能解析","生命医薬情報学連合大会2014",,,,,,2014,Oct.
"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",,,,,,2014,Sept.
"Yuki Komatsu,Takashi Ishida,Yutaka Akiyama","Metagenomic Phylogenetic Classification Using Improved Na?ve Bayes","the Tenth International Conference on Intelligent Computing (ICIC 2014)",,,,,,2014,Aug.
"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",2014,Aug.
"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",2014,Aug.
"Ban, T.,Ishida, T.,Akiyama, Y.","Improvement of a conformational search on protein-ligand docking based on optimal arrangement of multiple small search grids","The 2014 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'14)",,,,,,2014,July
"青山 健人,角田 将典,松崎 由理,石田 貴士,秋山 泰","エクソーム解析パイプラインの京コンピュータ上での大規模並列化","情報処理学会第38回バイオ情報学研究会","情報処理学会研究報告",,"  2014-BIO-38",,,2014,June
"蓮実 梢,石田 貴士,秋山 泰","パスウェイ情報を用いた顧みられない熱帯病 創薬支援のための統合データベースiNTRODBの改良","情報処理学会 第38回バイオ情報学研究会","情報処理学会研究報告",,"  2014-BIO-38",,,2014,June
"Masahito Ohue,Yuri Matsuzaki,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK: An all-to-all protein-protein interaction prediction system using tertiary structure data",,"Protein and Peptide Letters","Bentham Science","Volume 21","Issue 8","Page 766-778",2014,June
"柳澤 渓甫,石田貴士,秋山泰","半教師付き学習を用いた薬物クリアランス経路予測 (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. 114","No. 104","pp. 55-60",2014,June
"大上雅史,下田 雄大,松崎由理,石田貴士,秋山泰","大規模GPUクラスタによるタンパク質ドッキング計算システム",,"研究報告バイオ情報学（BIO）","一般社団法人情報処理学会","Vol. 2014-BIO-38","No. 32","pp. 1-4",2014,June
"大上 雅史,下田 雄大,松崎由理,石田貴士,秋山泰","大規模GPUクラスタによるタンパク質ドッキング計算システム (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. 114","No. 104","pp. 173-176",2014,June
"柳澤 渓甫,石田貴士,秋山泰","半教師付き学習を用いた薬物クリアランス経路予測",,"研究報告バイオ情報学（BIO）","一般社団法人情報処理学会","Vol. 2014","No. 10","pp. 1-6",2014,June
"Shuji Suzuki,Takashi Ishida,Yutaka Akiyama","Accelerating identification of frequent k-mers in DNA sequences with GPU","GPU Technology Conference 2014 (GTC2014)",,,,"No. P4190",,2014,Mar.
"伴兼弘,石田貴士,秋山泰","蛋白質-化合物ドッキングにおけるグリッドの分散配置による配座探索の改良","第37回バイオ情報学研究会","情報処理学会研究報告",,"vol. 2014-BIO-37","no. 4","pp. 1-7",2014,Mar.
"You H,Kim GE,Na CH,Lee S,Lee CJ,Cho KH,Akiyama Y,Ishida T,No KT.","An empirical model for gas phase acidity and basicity estimation",,"SAR and QSAR in Environmental Research",,"Vol. 25","No. 2","pp. 91-115",2014,Feb.
"Yuri Matsuzaki,Nobuyuki Uchikoga,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","Prediction of protein-protein interactions based on tertiary structures and transcription information","Biophysical Society 58th Annual Meeting",,,,,,2014,Feb.
"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",,,,,2014,Feb.
"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,
"小松祐城,石田貴士,秋山泰","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",2013,Dec.
"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",2013,Dec.
"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",2013,Dec.
"杉浦典和,石田貴士,秋山泰,関嶋政和","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",2013,Dec.
"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",2013,Nov.
"石田貴士,蓮実梢,伴兼弘,秋山泰","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",,2013,Oct.
"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",,,,,,2013,Sept.
"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",2013,Sept.
"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",2013,Sept.
"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",2013,Sept.
"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",2013,Sept.
"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",,2013,Sept.
"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",2013,Sept.
"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",,,,,,2013,July
"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",2013,July
"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",2013,July
"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",,2013,July
"小幡 康文,石田貴士,夏目 徹,秋山泰","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",2013,July
"任 愛珍,石田貴士,秋山泰","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",2013,July
"齊藤 有紀,石田貴士,関嶋 政和,秋山泰","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",2013,June
"齊藤有紀,石田貴士,関嶋政和,秋山泰","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",2013,June
"吉川舜亮,石田貴士,関嶋政和,秋山泰","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",2013,June
"大上雅史,松崎由理,内古閑伸之,石田貴士,秋山泰","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",2013,June
"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",2013,June
"小幡康文,石田貴士,夏目徹,秋山泰","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",2013,June
"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",2013,May
"Youhei Namiki,Takashi Ishida,Yutaka Akiyama","Acceleration of sequence clustering using longest common subsequence filtering",,"BMC Bioinformatics",,"Vol. 14","  Suppl 8","  S7",2013,May
"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",2013,May
"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",,,,,2013,Apr.
"Shuji Suzuki,Takashi Ishida,Yutaka Akiyama","An Ultra-fast Computing Pipeline for Metagenome Analysis with GPUs","GPU Technology Conference 2013 (GTC2013)",,,,"No. P0192",,2013,Mar.
"大上雅史,松崎由理,内古閑伸之,山本航平,下田雄大,藤原隆之,石田貴士,秋山泰","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",,,,,2013,Mar.
"松崎由理,大上雅史,石田貴士,内古閑伸之,秋山泰","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",,,,,,2013,Mar.
"秋山泰,松崎由理,石田貴士,大上雅史,内古閑 伸之","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",,,,,,2013,Mar.
"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",,,,,,2013,Feb.
"石田貴士","天然変性蛋白質領域予測 PrDOS-CNF & metaPrDOS2","タンパク質立体構造予測の最前線",,,,,,2013,Feb.
"秋山泰,松崎由理,大上雅史,石田貴士,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",,,,,,2013,Jan.
"大上雅史,松崎由理,石田貴士,秋山泰","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",,,,,,2013,Jan.
"Takashi Ishida","Prediction of protein disordered region based on conditional neural fields","CASP10 meeting",,,,,,2012,Dec.
"Masahito Ohue,Yuri Matsuzaki,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK: A rapid screening system of protein-protein interactions with all-to-all physical docking.","International Society for Computational Biology, ISCB-Asia 2012",,,,,,2012,Dec.
"石田貴士","ゲノムサイエンスを支えるビッグデータ解析","第18回 ビジュアリゼーションカンファレンス",,,,,,2012,Dec.
"Yuri Matsuzaki,Masahito Ohue,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","Application of exhaustive protein-protein interaction prediction system by using protein docking to signal transduction pathways.","International Society for Computational Biology, ISCB-Asia 2012",,,,,,2012,Dec.
"山本航平,大上雅史,石田貴士,秋山泰","構造情報に基づくタンパク質間相互作用ネットワーク予測精度の改善","第32回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","vol. 2012-BIO-32","no. 14","pp. 1-7",2012,Nov.
"Masahito Ohue,Yuri Matsuzaki,Takashi Ishida,Yutaka Akiyama","Improvement of the protein-protein docking prediction by introducing a simple hydrophobic interaction model: an application to interaction pathway analysis.","The 7th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB2012)","Lecture Notes in Bioinformatics","Springer Heidelberg","Vol. 7632",,"Page 178-187",2012,Nov.
"Oates ME,Romero P,Ishida T,Ghalwash M,Mizianty MJ,Doszt?nyi Z,Uversky VN,Obradovic Z,Kurgan L,Dunker AK,Gough J.","D2P2: database of disordered protein predictions.",,"Nucleic Acids Res.",,"Vol. 41",,"pp. D508-D516",2012,Nov.
"大上雅史,松崎由理,石田貴士,秋山泰","MEGADOCKを用いたタンパク質間相互作用予測のヒトアポトーシスパスウェイ解析への応用","第32回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","Vol. 2012-BIO-32","No. 13","pp. 1-8",2012,Nov.
"石田貴士","GHOST-MP：「京」を用いた超高速メタゲノム解析パイプライン","生命医薬情報学連合大会 (2012年 日本バイオインフォマティクス学会年会、情報計算化学生物学会年次大会、オミックス医療研究会年会)",,,,,,2012,Oct.
"Yuri Matsuzaki,Masahito Ohue,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","Application of exhaustive protein-protein interaction prediction system by using protein docking to signal transduction pathways.","20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2012)",,,,,,2012,July
"Masahito Ohue,Yuri Matsuzaki,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK: A rapid screening system of protein-protein interactions with all-to-all physical docking.","20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2012)",,,,,,2012,July
"Yuri Matsuzaki,Masahito Ohue,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","Application of exhaustive protein-protein interaction prediction system by using protein docking to signal transduction pathways.","3DSIG: The 8th structural bioinformatics and computational biophysics meeting",,,,,,2012,July
"Masahito Ohue,Yuri Matsuzaki,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK: A rapid screening system of protein-protein interactions with all-to-all physical docking.","3DSIG: The 8th structural bioinformatics and computational biophysics meeting",,,,,,2012,July
"下田雄大,石田貴士,秋山泰","タンパク質間ドッキング予測における実空間での効率的な評価スコア計算方法の研究","情報処理学会研究報告","第29回バイオ情報学研究会",,"vol. 2012-BIO-29","no. 20","p. 1-3",2012,June
"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",2012,June
"大上雅史,石田貴士,秋山泰","簡易疎水性相互作用モデルによるタンパク質間ドッキング予測の高精度化","第29回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","vol. 2012-BIO-29","no. 21","p. 1-3",2012,June
"藤原隆之,松崎由理,石田貴士,秋山泰","タンパク質間ドッキング予測における機械学習を用いた目的関数の動的調整","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. 19","pp. 1-3",2012,June
"Y. Namiki,T. Ishida,Y. Akiyama","Fast DNA Sequence Clustering Based on Longest Common Subsequence","ICIC2012","Communications in Computer and Information Science",,,"No. 304","pp. 453-460",2012,June
"杉浦典和,石田貴士,関嶋政和,秋山泰","ハッシュテーブルの分割によるde novoアセンブリの改良","情報処理学会第29回バイオ情報学研究発表会","情報処理学会研究報告","情報処理学会","  2012-BIO-29",,,2012,June
"藤原 隆之,松崎由理,石田貴士,秋山泰","タンパク質間ドッキング予測における目的関数の機械学習を用いた動的調整",,"電子情報通信学会技術研究報告. NC, ニューロコンピューティング","一般社団法人電子情報通信学会","Vol. 112","No. 108","pp. 101-103",2012,June
"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",2012,May
"Masahito Ohue,Yuri Matsuzaki,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","Bound state structure estimation of protein-protein complex using rigid-body protein-protein docking method","The 10th Asia-Pacific Bioinformatics Conference (APBC2012)","The 10th Asia-Pacific Bioinformatics Conference (APBC2012)",,,,"  P-50",2012,Jan.
"Masahito Ohue,Yuri Matsuzaki,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","Protein Complex Structure Prediction with Normal Mode Ensemble and Physical Docking","Bioinformatics week in Odaiba 2011 (BiWO2011)","Bioinformatics week in Odaiba 2011 (BiWO2011)",,,,"  P-01",2012,Jan.
"Suzuki, S.,Takashi Ishida,Yutaka Akiyama","An ultra-fast computing pipeline for metagenome analysis with next-generation DNA sequencers",,"Proceedings - 2012 SC Companion: High Performance Computing, Networking Storage and Analysis, SCC 2012",,,,"pp. 1549-1551",2012,
"秋山 泰,松崎 由理,内古閑 伸之,石田 貴士,大上 雅史","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","次世代生命体統合シミュレーションソフトウェアの研究開発成果報告会 ISLiM成果報告会2011",,,,,,2011,Dec.
"Masahito Ohue,Yuri Matsuzaki,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","Binding Conformation Prediction of a Protein Complex Using Physical Docking","GCOE Compview Final Symposium (Preliminary event of ISAAC 2011)",,,,,,2011,Dec.
"Sarel J. Fleishman,Timothy A. Whitehead,Eva-Maria Strauch,Jacob E. Corn,Sanbo Qin,Huan-Xiang Zhou,Julie C. Mitchell,Omar N. A. Demerdash,Mayuko Takeda-Shitaka,Genki Terashi,Iain H. Moal,Xiaofan Li,Paul A. Bates,Martin Zacharias,Hahnbeom Park,Jun-su Ko,Hasup Lee,Chaok Seok,Thomas Bourquard,Julie Bernauer,Anne Poupon,Jerome Aze,Seren Soner,Sefik Kerem Oval.,Pemra Ozbek,Nir Ben Tal,Turkan Haliloglu,Howook Hwang,Thom Vreven,Brian G. Pierce,Zhiping Weng,Laura Perez-Cano,Carles Pons,Juan Fernandez-Recio,Fan Jiang,Feng Yang,Xinqi Gong,Libin Cao,Xianjin Xu,Bin Liu,Panwen Wang,Chunhua Li,Cunxin Wang,Charles H. Robert,Mainak Guharoy,Shiyong Liu,Yangyu Huang,Lin Li,Dachuan Guo,Ying Chen,Yi Xiao,Nir London,Zohar Itzhaki,Ora Schueler-Furman,Yuval Inbar,Vladimir Patapov,Mati Cohen,Gideon Schreiber,Yuko Tsuchiya,Eiji Kanamori,Daron M. Standley,Haruki Nakamura,Kengo Kinoshita,Camden M. Driggers,Robert G. Hall,Jessica L. Morgan,Victor L. Hsu,Jian Zhan,Yuedong Yang,Yaoqi Zhou,Panagiotis L. Kastritis,Alexandre M. J. J. Bonvin,Weiyi Zhang,Carlos J. Camacho,Krishna P. Kilambi,Aroop Sircar,Jeffrey J. Gray,Masahito Ohue,Nobuyuki Uchikoga,Yuri Matsuzaki,Takashi Ishida,Yutaka Akiyama,Raed Khashan,Stephen Bush,Denis Fouches,Alexander Tropsha,Juan Esquivel-Rodriguez,Daisuke Kihara,P. Benjamin Stranges,Ron Jacak,Brian Kuhlman,Sheng-You Huang,Xiaoqin Zou,Shoshana J. Wodak,Joel Janin,David Baker","Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology",,"Journal of Molecular Biology","ScienceDirect","Volume 414","Issue 2","pp. 289-302",2011,Nov.
"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",2011,Nov.
"W.A. Kusuma,T. Ishida,Y. Akiyama","A combined approach for de novo DNA assembly of very short reads",,"IPSJ Transaction on Bioinformatics",,"vol. 4","no. 10","pp. 21-33",2011,Nov.
"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",2011,Oct.
"Yuri Matsuzaki,Masahito Ohue,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK: a Fast Protein-protein Interaction Prediction System by Exhaustive Docking","12th International Conference on Systems Biology (ICSB 2011)",,,,,,2011,Sept.
"松崎由理,内古閑伸之,大上雅史,石田貴士,秋山泰","MEGADOCK: 網羅的な立体構造のドッキングによるタンパク質間相互作用予測アプリケーション","バイオスーパーコンピューティング サマースクール2011バイオスーパーコンピューティング",,,,,,2011,Sept.
"Takashi Ishida","Disordered Protein Region Prediction by Using Naive Bayse Classifier","IIT Madras ? Tokyo Tech joint Workshop on  Bioinformatics and Large-scale data analysis",,,,,,2011,July
"Wisnu Ananta Kusuma,Takashi Ishida,Yutaka Akiyama","De novo sequence assembly and metagenomic fragments binning","The 9th International Workshop on Advanced Genomics",,,,,,2011,July
"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",,,,,,2011,July
"Yuri Matsuzaki,Masahito Ohue,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK: A fast protein-protein interaction prediction system by exhaustive docking","The 9th International Workshop on Advanced Genomics",,,,,,2011,July
"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",,,,,,2011,July
"山本航平,大上雅史,内古閑伸之,松崎由理,石田貴士,秋山 泰","タンパク質間相互作用予測における可視化手法の開発および予測精度の改善","情報処理学会 第25回バイオ情報学研究会","研究報告 バイオ情報学（BIO）","情報処理学会","vol. 2011-BIO-25","  31","pp. 1-7",2011,June
"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",2011,June
"大上雅史,松崎由理,内古閑伸之,石田貴士,秋山 泰","ドッキング計算に基づく網羅的タンパク質-RNA間相互作用予測","情報処理学会 第25回バイオ情報学研究会","研究報告 バイオ情報学（BIO）","情報処理学会","vol. 2011-BIO-25","  30","pp. 1-8",2011,June
"稲吉一馬,石田貴士,前田和哉,杉山雄一,秋山 泰","能動学習法を利用した薬物クリアランス経路予測の改良","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",2011,June
"Matsuyuki Shirota,Takashi Ishida,Kengo Kinoshita","Absolute quality evaluation of protein model structures using statistical potentials with respect to the native and reference states",,"Proteins",,"Vol. 79",,"p. 1550-63",2011,May
"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",,,,,,2011,Mar.
"Wisnu Ananta Kusuma,Takashi Ishida,Yutaka Akiyama","An Effective Approach for Assembling Very Short Reads from Next Genaration Sequencer",,"情報処理学会研究報告バイオ情報学(BIO)",,"vol. 2011-BIO-24","no. 4","pp. 1-7",2011,Mar.
"並木洋平,石田貴士,秋山 泰","次世代シーケンサーから得られたDNA配列の高速クラスタリングに関する研究","情報処理学会 第73回全国大会",,,,,,2011,Mar.
"山本航平,大上雅史,松崎由理,石田貴士,秋山 泰","タンパク質ドッキング計算結果の可視化とその解析","情報処理学会 第73回全国大会",,,,,,2011,Mar.
"松崎由理,内古閑伸之,大上雅史,石田貴士,秋山泰","MEGADOCKを用いたタンパク質間相互作用予測のシグナル伝達系への応用","第3回 バイオスーパーコンピューティングシンポジウム",,,,,,2011,Feb.
"Matsuzaki Yuri.,Uchikoga Nobuyuki.,Ohue Masahito.,Ishida Takashi.,Akiyama Yutaka","Exhaustive protein-protein interaction prediction with MEGADOCK and its application to signaling pathway estimation","Asia Hub for e-Drug Discovery (AHeDD) Symoposium 2010",,,,,,2010,Dec.
"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",2010,Dec.
"Takashi Ishida,Yutaka Akiyama","GPU-Acceleration of Protein Tertiary Structure Prediction based on a Fragment Assembly Simulation","CASP9 meeting",,,,,,2010,Dec.
"松崎由理,大上雅史,内古閑伸之,石田貴士,秋山 泰","MEGADOCKによるタンパク質間相互作用予測?システム生物学への応用?",,"TSUBAME e-Science Journal","東京工業大学 学術国際情報センター","vol. 2","No. 2","pp. 14-18",2010,Nov.
"Takashi Ishida","Protein disorder prediction based on the evolutionary conservation","Gordon Research Conference "Intrinsically Disordered Proteins"",,,,,,2010,July
"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",2010,June
"石田貴士,秋山泰","単純ベイズ確率モデルの導入による天然変性蛋白質領域予測の改良",,"情報処理学会研究報告バイオ情報学(BIO)",,"Vol. 21","No. 34","pp. 1-6",2010,June
"Takashi Ishida","GPU Acceleration of de Novo Protein Tertiary Structure Prediction","ETHZ - Tokyo Tech Workshop : Computing with GPUs, Cells, and Multicores","GPU Acceleration of de Novo Protein Tertiary Structure Prediction",,,,,2010,May
"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",2010,May
"Takashi Ishida,Yutaka Akiyama","GPU-Acceleration of de novo Protein Tertiary Structure Prediction","The 2nd Biosupercomputing Symposium",,,,,,2010,Mar.
"Matsuyuki Shirota,Takashi Ishida,Kengo Kinoshita","Development of a New Meta-Score for Protein Structure Prediction from Seven All-Atom Distance Dependent Potentials Using Support Vector Regression",,"Genome Informatics",,"Vol. 23",,"pp. 149-158",2009,Dec.
"Takashi Ishida,Kengo Kinoshita","Development of prediction servers for protein disorder","BIOINFO 2009 CBI-KSBSB Joint Conference","Proc. BIOINFO 2009 CBI-KSBSB Joint Conference",,,,,2009,Nov.
"Miho Higurashi,Takashi Ishida,Kengo","PiSite: a database of protein interaction sites using multiple binding states in the PDB.",,"Nucleic Acid Research",,"Vol. 37",,"Page 360-364",2009,
"Matsuyuki Shirota,Takashi Ishida,Kengo Kinoshita","Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials",,"Protein science",,"Vol. 18",,"Page 1906-15",2009,