@article{CTT100922720,
  author = {Jason Kurniawan and Takashi Ishida},
  title = {Comparing Supervised Learning and Rigorous Approach for Predicting Protein Stability upon Point Mutations in Difficult Targets},
  journal = {Journal of Chemical Information and Modeling},
  year = 2023,
}

@article{CTT100922719,
  author = {Ryunosuke Yoshino and Nobuaki Yasuo and Yohsuke Hagiwara and Takashi Ishida and Daniel Ken Inaoka and Yasushi Amano and Yukihiro Tateishi and Kazuki Ohno and Ichiji Namatame and Tatsuya Niimi and Masaya Orita and Kiyoshi Kita and Yutaka Akiyama and Masakazu Sekijima},
  title = {Discovery of a Hidden Trypanosoma cruzi Spermidine Synthase Binding Site and Inhibitors through In Silico, In Vitro, and X-ray Crystallography},
  journal = {ACS omega},
  year = 2023,
}

@article{CTT100907404,
  author = {Haruki Yamane and Takashi Ishida},
  title = {Helix encoder: a compound-protein interaction prediction model specifically designed for class A GPCRs},
  journal = {Frontiers in Bioinformatics},
  year = 2023,
}

@article{CTT100882508,
  author = {Takashi Ishida and Jason Kurniawan},
  title = {Protein Model Quality Estimation using Molecular Dynamics Simulation},
  journal = {ACS OMEGA},
  year = 2022,
}

@article{CTT100876905,
  author = {Yuma Takei and Takashi Ishida},
  title = {A Benchmark Dataset for Evaluating Practical Performance of Model Quality Assessment of Homology Models},
  journal = {Bioengineering},
  year = 2022,
}

@article{CTT100876903,
  author = {Toshitaka Tanebe and Takashi Ishida},
  title = {End-to-end learning for compound activity prediction based on binding pocket information},
  journal = {BMC Bioinformatics},
  year = 2021,
}

@article{CTT100876904,
  author = {Nobuaki Yasuo and Takashi Ishida and Masakazu Sekijima},
  title = {Computer aided drug discovery review for infectious diseases with case study of anti-Chagas project},
  journal = {},
  year = 2021,
}

@article{CTT100848793,
  author = {Izawa K and Okamoto-Shibayama K and Kita D and Tomita S and Saito A and Ishida T and Ohue M and Akiyama Y and Ishihara K.},
  title = {Taxonomic and gene category analyses of subgingival plaques from a group of Japanese individuals with and without periodontitis},
  journal = {International Journal of Molecular Sciences},
  year = 2021,
}

@article{CTT100847049,
  author = {Yuma Takei and Takashi Ishida},
  title = {P3CMQA: Single-Model Quality Assessment Using 3DCNN with Profile-Based Features},
  journal = {Bioengineering},
  year = 2021,
}

@article{CTT100846988,
  author = {Haris Hasic and Takashi Ishida},
  title = {Single-Step Retrosynthesis Prediction Based on the Identification of Potential Disconnection Sites Using Molecular Substructure Fingerprints},
  journal = {Journal of Chemical Information and Modeling},
  year = 2021,
}

@article{CTT100847538,
  author = {Aizhen Ren and Takashi Ishida and Yutaka Akiyama},
  title = {Mathematical proof of the third order accuracy of the speedy double botstrap method},
  journal = {Communication in Statistics-Theory and Methods},
  year = 2020,
}

@article{CTT100846987,
  author = {Shuichiro Makigaki and Takashi Ishida},
  title = {Sequence alignment generation using intermediate sequence search for homology modeling},
  journal = {Computational and Structural Biotechnology Journal},
  year = 2020,
}

@article{CTT100800913,
  author = {Shuichiro Makigaki and Takashi Ishida},
  title = {Sequence alignment using machine learning for accurate template-based protein structure prediction},
  journal = {Bioinformatics, btz483},
  year = 2020,
}

@article{CTT100839089,
  author = {Kento Aoyama and Masanori Kakuta and Yuri Matsuzaki and Takashi Ishida and Masahito Ohue and Yutaka Akiyama},
  title = {Development of computational pipeline software for genome/exome analysis on the K computer},
  journal = {Supercomputing Frontiers and Innovations},
  year = 2020,
}

@article{CTT100810746,
  author = {Shuntaro Chiba and Masahito Ohue and Anastasiia Gryniukova and Petro Borysko and Sergey Zozulya and Nobuaki Yasuo and Ryunosuke Yoshino and Kazuyoshi Ikeda and Woong-Hee Shin and Daisuke Kihara and Mitsuo Iwadate and Hideaki Umeyama and Takaaki Ichikawa and Reiji Teramoto and Kun-Yi Hsin and Vipul Gupta and Hiroaki Kitano and Mika Sakamoto and Akiko Higuchi and Nobuaki Miura and Kei Yura and Masahiro Mochizuki and Chandrasekaran Ramakrishnan and A. Mary Thangakani and D. Velmurugan and M. Michael Gromiha and Itsuo Nakane and Nanako Uchida and Hayase Hakariya and Modong Tan and Hironori Nakamura and Shogo Suzuki and Tomoki Ito and Masahiro Kawatani and Kentaroh Kudoh and Sakurako Takashina and Kazuki Yamamoto and Yoshitaka Moriwaki and Keita Oda and Daisuke Kobayashi and Tatsuya Okuno and Shintaro Minami and George Chikenji and Philip Prathipati and Chioko Nagao and Attayeb Mohsen and Mari Ito and Kenji Mizuguchi and Teruki Honma and Takashi Ishida and Takatsugu Hirokawa and Yutaka Akiyama and Masakazu Sekijima.},
  title = {A prospective compound screening contest identified broader inhibitors for Sirtuin 1},
  journal = {Scientific Reports},
  year = 2019,
}

@article{CTT100804160,
  author = {Rin Sato and Takashi Ishida},
  title = {Protein model accuracy estimation based on local structure quality assessment using 3D convolutional neural network},
  journal = {PLOS ONE},
  year = 2019,
}

@article{CTT100847542,
  author = {成井政人 and 石田貴士 and 牧垣秀一朗},
  title = {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},
  journal = {研究報告数理モデル化と問題解決（MPS）},
  year = 2019,
}

@article{CTT100776745,
  author = {Naomi Wakayama and Kota Toshimoto and Kazuya Maeda and Shun Hotta and Takashi Ishida and Yutaka Akiyama and Yuichi Sugiyama},
  title = {In Silico Prediction of Major Clearance Pathways of Drugs among 9 Routes with Two-Step Support Vector Machines},
  journal = {Pharmaceutical Research},
  year = 2018,
}

@article{CTT100795121,
  author = {Wakayama N and Toshimoto K and Maeda K and Hotta S and Ishida T and Akiyama Y and Sugiyama Y.},
  title = {In Silico Prediction of Major Clearance Pathways of Drugs among 9 Routes with Two-Step Support Vector Machines},
  journal = {Pharmaceutical Research},
  year = 2018,
}

@article{CTT100766243,
  author = {Masanori Kakuta and Shuji Suzuki and Kazuki Izawa and Takashi Ishida and Yutaka Akiyama},
  title = {A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data},
  journal = {International Journal of Molecular Sciences},
  year = 2017,
}

@article{CTT100766244,
  author = {Shuntaro Chiba and Takashi Ishida and Kazuyoshi Ikeda and Masahiro Mochizuki and Reiji Teramoto and Y-h. Taguchi and Mitsuo Iwadate and Hideaki Umeyama and Chandrasekaran Ramakrishnan and A. Mary Thangakani and D. Velmurugan and M. Michael Gromiha and Tatsuya Okuno and Koya Kato and Shintaro Minami and George Chikenji and Shogo D. Suzuki and Keisuke Yanagisawa and Woong-Hee Shin and Daisuke Kihara and Kazuki Z. Yamamoto and Yoshitaka Moriwaki and Nobuaki Yasuo and Ryunosuke Yoshino and Sergey Zozulya and Petro Borysko and Roman Stavniichuk and Teruki Honma and Takatsugu Hirokawa and Yutaka Akiyama and Masakazu Sekijima},
  title = {An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes},
  journal = {Scientific Reports},
  year = 2017,
}

@article{CTT100766242,
  author = {Ryunosuke Yoshino and Nobuaki Yasuo and Yohsuke Hagiwara and Takashi Ishida and Daniel Ken Inaoka and Yasushi Amano and Yukihiro Tateishi and Kazuki Ohno and Ichiji Namatame and Tatsuya Niimi and Masaya Orita and Kiyoshi Kita and Yutaka Akiyama and Masakazu Sekijima},
  title = {In silico, in vitro, X-ray crystallography, and integrated strategies for discovering spermidine synthase inhibitors for Chagas disease},
  journal = {Scientific Reports},
  year = 2017,
}

@article{CTT100766245,
  author = {Shuji Suzuki and Takashi Ishida and Masahito Ohue and Masanori Kakuta and Yutaka Akiyama},
  title = {GHOSTX: A Fast Sequence Homology Search Tool for Functional Annotation of Metagenomic Data},
  journal = {Methods in Molecular Biology(Protein Function Prediction)},
  year = 2017,
}

@article{CTT100776729,
  author = {Yanagisawa K and Komine S and Shogo Suzuki and Ohue M and Ishida T and Akiyama Y.},
  title = {Spresso: an ultrafast compound pre-screening method based on compound decomposition},
  journal = {Bioinformatics},
  year = 2017,
}

@article{CTT100738036,
  author = {Shuji Suzuki and Masanori Kakuta and Takashi Ishida and Yutaka Akiyama},
  title = {GPU-Acceleration of Sequence Homology Searches with Database Subsequence Clustering},
  journal = {PLOS ONE},
  year = 2016,
}

@article{CTT100738049,
  author = {青山 健人 and 角田 将典 and 松崎 由理 and 石田 貴士 and 秋山 泰},
  title = {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},
  journal = {情報処理学会論文誌コンピューティングシステム（ACS）},
  year = 2016,
}

@article{CTT100738031,
  author = {Atsushi Ose and Kota Toshimoto and Kazushi Ikeda and Kazuya Maeda and Shuya Yoshida and Fumiyoshi Yamashita and Mitsuru Hashida and Takashi Ishida and Yutaka Akiyama and Yuichi Sugiyama},
  title = {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 = {Journal of Pharmaceutical Sciences},
  year = 2016,
}

@article{CTT100709036,
  author = {Shuntaro Chiba and Kazuyoshi Ikeda and Takashi Ishida and M. Michael Gromiha and Y-h. Taguchi and Mitsuo Iwadate and Hideaki Umeyama and Kun-Yi Hsin and Hiroaki Kitano and Kazuki Yamamoto and Nobuyoshi Sugaya and Koya Kato and Tatsuya Okuno and George Chikenji and Masahiro Mochizuki and Nobuaki Yasuo and Ryunosuke Yoshino and Keisuke Yanagisawa and Tomohiro Ban and Reiji Teramoto and Chandrasekaran Ramakrishnan and A. Mary Thangakani and D. Velmurugan and Philip Prathipati and Junichi Ito and Yuko Tsuchiya and Kenji Mizuguchi and Teruki Honma and Takatsugu Hirokawa and Yutaka Akiyama and Masakazu Sekijima},
  title = {Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target},
  journal = {Scientific Reports},
  year = 2015,
}

@article{CTT100695528,
  author = {Keisuke Yanagisawa and Takashi Ishida and Yutaka Akiyama},
  title = {Drug Clearance Pathway Prediction Based on Semi-supervised Learning},
  journal = {IPSJ Transactions on Bioinformatics},
  year = 2015,
}

@article{CTT100684743,
  author = {Suzuki S and Kakuta M and Ishida T and Akiyama Y.},
  title = {Faster sequence homology searches by clustering subsequences},
  journal = {Bioinformatics},
  year = 2015,
}

@article{CTT100677438,
  author = {Takehiro Shimoda and Shuji Suzuki and Masahito Ohue and Takashi Ishida and Yutaka Akiyama.},
  title = {Protein-Protein Docking on Hardware Accelerators : Comparison of GPU and MIC Architectures},
  journal = {BMC Systems Biology},
  year = 2015,
}

@article{CTT100684742,
  author = {Ohue, M. and Shimoda, T. and Suzuki, S. and Matsuzaki, Y. and Ishida, T. and Akiyama, Y.},
  title = {MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers},
  journal = {Bioinformatics},
  year = 2014,
}

@article{CTT100684741,
  author = {Suzuki, S and Ishida, T and Akiyama, Y},
  title = {GHOSTX: An improved sequence homology search algorithm using a query suffix array and a database suffix array},
  journal = {PLoS ONE},
  year = 2014,
}

@article{CTT100666828,
  author = {Masahito Ohue and Yuri Matsuzaki and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK: An all-to-all protein-protein interaction prediction system using tertiary structure data},
  journal = {Protein and Peptide Letters},
  year = 2014,
}

@article{CTT100669382,
  author = {You H and Kim GE and Na CH and Lee S and Lee CJ and Cho KH and Akiyama Y and Ishida T and No KT.},
  title = {An empirical model for gas phase acidity and basicity estimation},
  journal = {SAR and QSAR in Environmental Research},
  year = 2014,
}

@article{CTT100676869,
  author = {Satoshi Matsuoka and Hitoshi Sato and Osamu Tatebe and Michihiro Koibuchi and Ikki Fujiwara and Shuji Suzuki and Masanori Kakuta and Takashi Ishida and Yutaka Akiyama and Toyotaro Suzumura and Koji Ueno and Hiroki Kanezashi and Takemasa Miyoshi.},
  title = {Extreme Big Data (EBD): Next Generation Big Data Infrastructure Technologies Towards Yottabyte/Year},
  journal = {Supercomputing frontiers and innovations},
  year = 2014,
}

@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{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{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,
}

@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{CTT100647888,
  author = {Oates ME and Romero P and Ishida T and Ghalwash M and Mizianty MJ and Dosztányi Z and Uversky VN and Obradovic Z and Kurgan L and Dunker AK and Gough J.},
  title = {D2P2: database of disordered protein predictions.},
  journal = {Nucleic Acids Res.},
  year = 2012,
}

@article{CTT100636180,
  author = {Shuji Suzuki and Takashi Ishida and Ken Kurokawa and Yutaka Akiyama},
  title = {GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics},
  journal = {PLoS ONE},
  year = 2012,
}

@article{CTT100631867,
  author = {Sarel J. Fleishman and Timothy A. Whitehead and Eva-Maria Strauch and Jacob E. Corn and Sanbo Qin and Huan-Xiang Zhou and Julie C. Mitchell and Omar N. A. Demerdash and Mayuko Takeda-Shitaka and Genki Terashi and Iain H. Moal and Xiaofan Li and Paul A. Bates and Martin Zacharias and Hahnbeom Park and Jun-su Ko and Hasup Lee and Chaok Seok and Thomas Bourquard and Julie Bernauer and Anne Poupon and Jerome Aze and Seren Soner and Sefik Kerem Oval. and Pemra Ozbek and Nir Ben Tal and Turkan Haliloglu and Howook Hwang and Thom Vreven and Brian G. Pierce and Zhiping Weng and Laura Perez-Cano and Carles Pons and Juan Fernandez-Recio and Fan Jiang and Feng Yang and Xinqi Gong and Libin Cao and Xianjin Xu and Bin Liu and Panwen Wang and Chunhua Li and Cunxin Wang and Charles H. Robert and Mainak Guharoy and Shiyong Liu and Yangyu Huang and Lin Li and Dachuan Guo and Ying Chen and Yi Xiao and Nir London and Zohar Itzhaki and Ora Schueler-Furman and Yuval Inbar and Vladimir Patapov and Mati Cohen and Gideon Schreiber and Yuko Tsuchiya and Eiji Kanamori and Daron M. Standley and Haruki Nakamura and Kengo Kinoshita and Camden M. Driggers and Robert G. Hall and Jessica L. Morgan and Victor L. Hsu and Jian Zhan and Yuedong Yang and Yaoqi Zhou and Panagiotis L. Kastritis and Alexandre M. J. J. Bonvin and Weiyi Zhang and Carlos J. Camacho and Krishna P. Kilambi and Aroop Sircar and Jeffrey J. Gray and Masahito Ohue and Nobuyuki Uchikoga and Yuri Matsuzaki and Takashi Ishida and Yutaka Akiyama and Raed Khashan and Stephen Bush and Denis Fouches and Alexander Tropsha and Juan Esquivel-Rodriguez and Daisuke Kihara and P. Benjamin Stranges and Ron Jacak and Brian Kuhlman and Sheng-You Huang and Xiaoqin Zou and Shoshana J. Wodak and Joel Janin and David Baker},
  title = {Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology},
  journal = {Journal of Molecular Biology},
  year = 2011,
}

@article{CTT100633773,
  author = {W.A. Kusuma and T. Ishida and Y. Akiyama},
  title = {A combined approach for de novo DNA assembly of very short reads},
  journal = {IPSJ Transaction on Bioinformatics},
  year = 2011,
}

@article{CTT100619311,
  author = {Matsuyuki Shirota and Takashi Ishida and Kengo Kinoshita},
  title = {Absolute quality evaluation of protein model structures using statistical potentials with respect to the native and reference states},
  journal = {Proteins},
  year = 2011,
}

@article{CTT100619306,
  author = {Matsuyuki Shirota and Takashi Ishida and Kengo Kinoshita},
  title = {Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials},
  journal = {Protein science},
  year = 2009,
}

@article{CTT100619305,
  author = {Miho Higurashi and Takashi Ishida and Kengo},
  title = {PiSite: a database of protein interaction sites using multiple binding states in the PDB.},
  journal = {Nucleic Acid Research},
  year = 2009,
}

@inproceedings{CTT100846986,
  author = {Haris Hasic and Takashi Ishida},
  title = {Single-step Retrosynthesis Prediction based on the Identification of Potential Disconnection Sites},
  booktitle = {},
  year = 2020,
}

@inproceedings{CTT100846983,
  author = {Jason Kurniawan and Takashi Ishida},
  title = {Quality Assessment of Protein Structure Modelsusing Molecular Dynamics Trajectories},
  booktitle = {},
  year = 2020,
}

@inproceedings{CTT100846982,
  author = {Haris Hasic and Takashi Ishida},
  title = {Singlestep Retrosynthesis Prediction based on the Identification of Potential Disconnection Sites using Molecular Substructure Fingerprints},
  booktitle = {},
  year = 2020,
}

@inproceedings{CTT100846984,
  author = {武居佑真 and 石田 貴士},
  title = {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},
  booktitle = {},
  year = 2020,
}

@inproceedings{CTT100846985,
  author = {白石幹 and 石田貴士},
  title = {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},
  booktitle = {},
  year = 2020,
}

@inproceedings{CTT100829240,
  author = {Rin Sato and Takashi Ishida},
  title = {GCMQA:Graph convolutional neural network for model quality assessment},
  booktitle = {},
  year = 2019,
}

@inproceedings{CTT100823437,
  author = {Rin Sato and Takashi Ishida},
  title = {GCMQA: Graph convolutional neural network for model quality assessment},
  booktitle = {},
  year = 2019,
}

@inproceedings{CTT100808023,
  author = {多治見隆志 and 石田貴士},
  title = {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},
  booktitle = {},
  year = 2019,
}

@inproceedings{CTT100808022,
  author = {松村真里 and 石田貴士},
  title = {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},
  booktitle = {},
  year = 2019,
}

@inproceedings{CTT100808016,
  author = {Masataka Irokawa and Takashi Ishida},
  title = {Improvement of deep learning model for reraking predicted protein complex structures},
  booktitle = {},
  year = 2019,
}

@inproceedings{CTT100808015,
  author = {Shuichiro Makigaki and Takashi Ishida},
  title = {Remote protein homolog detetction based on sequence similarity networks},
  booktitle = {},
  year = 2019,
}

@inproceedings{CTT100808014,
  author = {Hasic and Takashi Ishida},
  title = {Predicting Chemical Reaction Routes with Artificial Intelligence-based Retrosynthesis},
  booktitle = {},
  year = 2019,
}

@inproceedings{CTT100808026,
  author = {Toshitaka Tanebe and Takashi Ishida},
  title = {End-to-end learning based compound activity prediction using binding pocket information},
  booktitle = {},
  year = 2019,
}

@inproceedings{CTT100821931,
  author = {Masato Narui and Takashi Ishida and Shuichiro Makigaki},
  title = {Acceleration of Machine Learning-based Sequence Alignment Generation},
  booktitle = {Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA)},
  year = 2019,
}

@inproceedings{CTT100822153,
  author = {色川雅崇 and 石田貴士},
  title = {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},
  booktitle = {},
  year = 2019,
}

@inproceedings{CTT100822152,
  author = {牧垣秀一朗 and 石田貴士},
  title = {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},
  booktitle = {},
  year = 2019,
}

@inproceedings{CTT100822154,
  author = {成井政人 and 石田貴士 and 牧垣秀一朗},
  title = {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},
  booktitle = {},
  year = 2019,
}

@inproceedings{CTT100822127,
  author = {賀来智博 and 石田貴士},
  title = {深層学習を用いたスコアマトリクス推定},
  booktitle = {},
  year = 2019,
}

@inproceedings{CTT100806641,
  author = {佐藤倫 and 石田貴士},
  title = {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},
  booktitle = {},
  year = 2019,
}

@inproceedings{CTT100806642,
  author = {種部俊孝 and 石田貴士},
  title = {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},
  booktitle = {},
  year = 2019,
}

@inproceedings{CTT100822126,
  author = {牧垣秀一朗 and 石田貴士},
  title = {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},
  booktitle = {},
  year = 2019,
}

@inproceedings{CTT100781323,
  author = {Ruoming He and Takashi Ishida},
  title = {Prediction of drug-target interactions with 3D structure information of target binding sites},
  booktitle = {},
  year = 2018,
}

@inproceedings{CTT100781308,
  author = {Yusuke Matsuyama and Takashi Ishida},
  title = {Stacking Multiple Molecular Fingerprints for Improving Ligand-Based Virtual Screening},
  booktitle = {Lecture Notes in Computer Science book series (LNCS, volume 10955)},
  year = 2018,
}

@inproceedings{CTT100822124,
  author = {池田光 and 石田貴士},
  title = {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},
  booktitle = {},
  year = 2018,
}

@inproceedings{CTT100822123,
  author = {佐藤倫 and 石田貴士},
  title = {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},
  booktitle = {},
  year = 2018,
}

@inproceedings{CTT100822125,
  author = {Toshitaka Tanebe and Takashi Ishida},
  title = {Machine learning based compound activity prediction using binding pocket information},
  booktitle = {},
  year = 2018,
}

@inproceedings{CTT100781324,
  author = {曽我 光瑛 and 石田 貴士},
  title = {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},
  booktitle = {},
  year = 2018,
}

@inproceedings{CTT100781322,
  author = {松山 祐輔 and 石田 貴士},
  title = {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},
  booktitle = {},
  year = 2018,
}

@inproceedings{CTT100766246,
  author = {Shuichiro Makigaki and Takashi Ishida},
  title = {Improvement of template-based protein structure prediction by using chimera alignment},
  booktitle = {Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics},
  year = 2018,
}

@inproceedings{CTT100781318,
  author = {Takashi Ishida},
  title = {Ensembling multiple molecular fingerprint-based predictions for improvement of ligand-based drug discovery},
  booktitle = {},
  year = 2017,
}

@inproceedings{CTT100781312,
  author = {松山 祐輔 and 石田 貴士},
  title = {Using multiple molecular fingerprints for improvement of drug activity prediction},
  booktitle = {},
  year = 2017,
}

@inproceedings{CTT100781317,
  author = {石田 貴士},
  title = {深層学習技術が加速するIT創薬技術の深化},
  booktitle = {},
  year = 2017,
}

@inproceedings{CTT100781311,
  author = {Yusuke Matsuyama and Takashi Ishida},
  title = {Ensemble multiple molecular fingerprints for improvement of ligand based drug discovery},
  booktitle = {},
  year = 2017,
}

@inproceedings{CTT100781309,
  author = {賀来智博 and 石田貴士},
  title = {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},
  booktitle = {情報処理学会研究報告},
  year = 2017,
}

@inproceedings{CTT100766878,
  author = {山澤 まりな and 伊澤 和輝 and 大上 雅史 and 石田 貴士 and Kazuyuki Ishihara and 秋山 泰},
  title = {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},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2017,
}

@inproceedings{CTT100781310,
  author = {大石智博 and 石田貴士},
  title = {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},
  booktitle = {},
  year = 2017,
}

@inproceedings{CTT100766883,
  author = {伊澤 和輝 and 山澤 まりな and 大上 雅史 and 石田 貴士 and 秋山 泰},
  title = {歯周病の発症要因の特定に向けた口腔内細菌叢解析},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2017,
}

@inproceedings{CTT100738048,
  author = {松山祐輔 and 石田貴士},
  title = {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},
  booktitle = {情報処理学会研究報告},
  year = 2017,
}

@inproceedings{CTT100715720,
  author = {Keisuke Yanagisawa and Shunta Komine and Shogo Suzuki and Masahito Ohue and Takashi Ishida and Yutaka Akiyama},
  title = {ESPRESSO: An ultrafast compound pre-screening method with segmented compounds},
  booktitle = {},
  year = 2016,
}

@inproceedings{CTT100738050,
  author = {石田貴士},
  title = {機械学習の進展と生命科学研究への応用},
  booktitle = {},
  year = 2016,
}

@inproceedings{CTT100715200,
  author = {Keisuke Yanagisawa and Shunta Komine and Shogo Suzuki and Masahito Ohue and Takashi Ishida and Yutaka Akiyama},
  title = {ESPRESSO: An ultrafast compound pre-screening method based on compound decomposition},
  booktitle = {},
  year = 2016,
}

@inproceedings{CTT100738045,
  author = {Naoto Kakami and Takashi Ishida},
  title = {Prediction of Protein-Ligand Binding Sites Using 3D Convolutional Neural Networks},
  booktitle = {},
  year = 2016,
}

@inproceedings{CTT100715191,
  author = {Keisuke Yanagisawa and Shunta Komine and Shogo Suzuki and Masahito Ohue and Takashi Ishida and Yutaka Akiyama},
  title = {ESPRESSO: An ultrafast compound pre-screening method based on compound segmentation},
  booktitle = {},
  year = 2016,
}

@inproceedings{CTT100738046,
  author = {Yusuke Matsuyama and Takashi Ishida},
  title = {Improvement of ligand-based virtual screening by introducing pharmacophore fingerprint},
  booktitle = {},
  year = 2016,
}

@inproceedings{CTT100738047,
  author = {Mitsuaki Soga and Takashi Ishida},
  title = {Improvement of NTDs drug target protein selection by learning to rank},
  booktitle = {},
  year = 2016,
}

@inproceedings{CTT100715196,
  author = {Marina Yamasawa and Tomoya Fujii and Kota Goto and Masahito Ohue and Takashi Ishida and Kazuyuki Ishihara and Yutaka Akiyama},
  title = {GPU/MPI Parallelization of Metagenomic Sequence Homology Search Tool and Its Application to Oral Metagenomics},
  booktitle = {},
  year = 2016,
}

@inproceedings{CTT100715217,
  author = {石田貴士},
  title = {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},
  booktitle = {},
  year = 2016,
}

@inproceedings{CTT100715209,
  author = {松山祐輔 and 石田貴士},
  title = {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},
  booktitle = {情報処理学会研究報告},
  year = 2016,
}

@inproceedings{CTT100715208,
  author = {各務直人 and 石田貴士},
  title = {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},
  booktitle = {情報処理学会研究報告},
  year = 2016,
}

@inproceedings{CTT100715206,
  author = {曽我光瑛 and 石田貴士},
  title = {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},
  booktitle = {情報処理学会研究報告},
  year = 2016,
}

@inproceedings{CTT100710862,
  author = {柳澤 渓甫 and 小峰 駿汰 and 鈴木 翔吾 and 大上 雅史 and 石田 貴士 and 秋山 泰},
  title = {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},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2016,
}

@inproceedings{CTT100701948,
  author = {藤井智也 and 角田将典 and 大上雅史 and 石田貴士 and 石原和幸 and 秋山泰},
  title = {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},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2016,
}

@inproceedings{CTT100715113,
  author = {Masahito Ohue and Yuri Matsuzaki and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers},
  booktitle = {},
  year = 2016,
}

@inproceedings{CTT100715166,
  author = {柳澤 渓甫 and 小峰 駿汰 and 大上 雅史 and 石田 貴士 and 秋山 泰},
  title = {Fast pre-filtering for virtual screening based on ligand decomposition},
  booktitle = {},
  year = 2015,
}

@inproceedings{CTT100715133,
  author = {Yuri Matsuzaki and Masahito Ohue and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK: A high-performance protein-protein interaction prediction software for petascale supercomputing environments},
  booktitle = {},
  year = 2015,
}

@inproceedings{CTT100715119,
  author = {Masahito Ohue and Takehiro Shimoda and Shuji Suzuki and Takashi Ishida and Yutaka Akiyama},
  title = {A comparative study of GPU and MIC accelerations in fast Fourier transform-based protein-protein docking},
  booktitle = {},
  year = 2015,
}

@inproceedings{CTT100715125,
  author = {Keisuke Yanagisawa and Shunta Komine and Masahito Ohue and Takashi Ishida and Yutaka Akiyama},
  title = {Fast pre-filtering for virtual screening based on compound fragmentation},
  booktitle = {},
  year = 2015,
}

@inproceedings{CTT100715205,
  author = {Takashi Ishida},
  title = {Protein structure prediction based on machine learning},
  booktitle = {},
  year = 2015,
}

@inproceedings{CTT100715211,
  author = {年本広太 and 尾瀬淳 and 池田和史 and 前田和哉 and 石田貴士 and 秋山泰 and 杉山 雄一},
  title = {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},
  booktitle = {},
  year = 2015,
}

@inproceedings{CTT100715186,
  author = {Keisuke Yanagisawa and Shunta Komine and Masahito Ohue and Takashi Ishida and Yutaka Akiyama},
  title = {Fast pre-filtering for virtual screening based on compound decomposition},
  booktitle = {},
  year = 2015,
}

@inproceedings{CTT100703207,
  author = {鈴木翔吾 and 柳澤渓甫 and 大上雅史 and 石田貴士 and 秋山泰},
  title = {SVMとDeep Learningに基づくヒトc-Yesキナーゼ阻害化合物の予測},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2015,
}

@inproceedings{CTT100703206,
  author = {和久井直樹 and 大上雅史 and 千葉峻太朗 and 石田貴士 and 岩﨑博史 and 秋山泰},
  title = {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},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2015,
}

@inproceedings{CTT100715212,
  author = {年本広太 and 尾瀬淳 and 池田和史 and 前田和哉 and 石田貴士 and 秋山泰 and 杉山雄一},
  title = {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},
  booktitle = {トランスポーター研究会年会抄録集},
  year = 2015,
}

@inproceedings{CTT100715213,
  author = {Yutaka Akiyama and Takashi Ishida},
  title = {iNTRODB and its Applicationin anti-Trypanosome Drug Discovery},
  booktitle = {},
  year = 2015,
}

@inproceedings{CTT100684652,
  author = {Shuji Suzuki and Masanori Kakuta and Takashi Ishida and Yutaka Akiyama},
  title = {GHOSTZ-GPU: Fast Protein Sequence Homology Search on GPUs},
  booktitle = {},
  year = 2015,
}

@inproceedings{CTT100802239,
  author = {小幡 康文 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2015,
}

@inproceedings{CTT100801954,
  author = {相澤 洋輔 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2015,
}

@inproceedings{CTT100715151,
  author = {Masahito Ohue and Takehiro Shimoda and Shuji suzuki and Yuri Matsuzaki and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK 4.0: an ultra–high-performance protein-protein docking software for heterogeneous supercomputers},
  booktitle = {},
  year = 2015,
}

@inproceedings{CTT100684746,
  author = {Kakuta, M. and Suzuki, S. and Ishida, T. and Akiyama, Y.},
  title = {GHOST-MP: A Massively Parallel Biological Sequence Similarity Search for Metagenomics using OpenMP and MPI},
  booktitle = {},
  year = 2015,
}

@inproceedings{CTT100703209,
  author = {小峰駿汰 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {情報処理学会研究報告},
  year = 2015,
}

@inproceedings{CTT100703208,
  author = {杉原舜 and 石田貴士 and 秋山泰},
  title = {低分子化合物二次元構造比較システムの改良},
  booktitle = {情報処理学会研究報告},
  year = 2015,
}

@inproceedings{CTT100715153,
  author = {Masahito Ohue and Takehiro Shimoda and Shuji suzuki and Yuri Matsuzaki and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK 4.0: an ultra–high-performance protein-protein docking software for heterogeneous supercomputers},
  booktitle = {},
  year = 2014,
}

@inproceedings{CTT100715215,
  author = {年本 広太 and 若山 直美 and 堀田駿 and 前田 和哉 and 石田 貴士 and 秋山 泰 and 杉山 雄一},
  title = {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},
  booktitle = {},
  year = 2014,
}

@inproceedings{CTT100715216,
  author = {Takashi Ishida and Kozue Hasumi and Yutaka Akiyama},
  title = {iNTRODB: database for NTDs drug target protein selection},
  booktitle = {},
  year = 2014,
}

@inproceedings{CTT100684745,
  author = {石田貴士},
  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},
  booktitle = {},
  year = 2014,
}

@inproceedings{CTT100715154,
  author = {Masahito Ohue and Takehiro Shimoda and Shuji Suzuki and Yuri Matsuzaki and Takashi Ishida and Yutaka Akiyama},
  title = {The MEGADOCK Project: high-performance protein-protein interaction prediction tools on supercomputing environments},
  booktitle = {},
  year = 2014,
}

@inproceedings{CTT100715175,
  author = {Masahito Ohue and Takehiro Shimoda and Shuji Suzuki and Yuri Matsuzaki and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers},
  booktitle = {Bioinformatics},
  year = 2014,
}

@inproceedings{CTT100684747,
  author = {石田貴士},
  title = {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},
  booktitle = {},
  year = 2014,
}

@inproceedings{CTT100715157,
  author = {Masahito Ohue and Takehiro Shimoda and Shuji Suzuki and Yuri Matsuzaki and Takashi Ishida and Yutaka Akiyama},
  title = {The MEGADOCK Project: high-performance protein-protein interaction prediction tools on supercomputing environments},
  booktitle = {},
  year = 2014,
}

@inproceedings{CTT100677439,
  author = {Yuki Komatsu and Takashi Ishida and Yutaka Akiyama},
  title = {Metagenomic Phylogenetic Classification Using Improved Naïve Bayes},
  booktitle = {},
  year = 2014,
}

@inproceedings{CTT100684744,
  author = {Ban, T. and Ishida, T. and Akiyama, Y.},
  title = {Improvement of a conformational search on protein-ligand docking based on optimal arrangement of multiple small search grids},
  booktitle = {},
  year = 2014,
}

@inproceedings{CTT100715219,
  author = {青山 健人 and 角田 将典 and 松崎 由理 and 石田 貴士 and 秋山 泰},
  title = {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},
  booktitle = {情報処理学会研究報告},
  year = 2014,
}

@inproceedings{CTT100715218,
  author = {蓮実 梢 and 石田 貴士 and 秋山 泰},
  title = {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},
  booktitle = {情報処理学会研究報告},
  year = 2014,
}

@inproceedings{CTT100801894,
  author = {柳澤 渓甫 and 石田貴士 and 秋山泰},
  title = {半教師付き学習を用いた薬物クリアランス経路予測},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2014,
}

@inproceedings{CTT100801935,
  author = {大上 雅史 and 下田 雄大 and 松崎由理 and 石田貴士 and 秋山泰},
  title = {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)},
  booktitle = {電子情報通信学会技術研究報告 = IEICE technical report : 信学技報},
  year = 2014,
}

@inproceedings{CTT100801959,
  author = {大上雅史 and 下田 雄大 and 松崎由理 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2014,
}

@inproceedings{CTT100802163,
  author = {柳澤 渓甫 and 石田貴士 and 秋山泰},
  title = {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)},
  booktitle = {電子情報通信学会技術研究報告 = IEICE technical report : 信学技報},
  year = 2014,
}

@inproceedings{CTT100669688,
  author = {伴兼弘 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {情報処理学会研究報告},
  year = 2014,
}

@inproceedings{CTT100669644,
  author = {Shuji Suzuki and Takashi Ishida and Yutaka Akiyama},
  title = {Accelerating identification of frequent k-mers in DNA sequences with GPU},
  booktitle = {},
  year = 2014,
}

@inproceedings{CTT100666899,
  author = {Yuri Matsuzaki and Nobuyuki Uchikoga and Masahito Ohue and Takashi Ishida and Yutaka Akiyama},
  title = {Prediction of protein-protein interactions based on tertiary structures and transcription information},
  booktitle = {},
  year = 2014,
}

@inproceedings{CTT100666854,
  author = {大上雅史 and 下田雄大 and 松崎由理 and 内古閑伸之 and 鈴木脩司 and 石田貴士 and 秋山泰},
  title = {MEGADOCK 4.0: mega-dock per dayへの道のり},
  booktitle = {生命情報科学若手の会 第5回研究会},
  year = 2014,
}

@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{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{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{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{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{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{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{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{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{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{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{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{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{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{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{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{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{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{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{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{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{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{CTT100649174,
  author = {石田貴士},
  title = {天然変性蛋白質領域予測 PrDOS-CNF & metaPrDOS2},
  booktitle = {},
  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{CTT100649173,
  author = {Takashi Ishida},
  title = {Prediction of protein disordered region based on conditional neural fields},
  booktitle = {},
  year = 2012,
}

@inproceedings{CTT100648452,
  author = {石田貴士},
  title = {ゲノムサイエンスを支えるビッグデータ解析},
  booktitle = {},
  year = 2012,
}

@inproceedings{CTT100658030,
  author = {Yuri Matsuzaki and Masahito Ohue and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {Application of exhaustive protein-protein interaction prediction system by using protein docking to signal transduction pathways.},
  booktitle = {},
  year = 2012,
}

@inproceedings{CTT100658031,
  author = {Masahito Ohue and Yuri Matsuzaki and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK: A rapid screening system of protein-protein interactions with all-to-all physical docking.},
  booktitle = {},
  year = 2012,
}

@inproceedings{CTT100657808,
  author = {Masahito Ohue and Yuri Matsuzaki and Takashi Ishida and Yutaka Akiyama},
  title = {Improvement of the protein-protein docking prediction by introducing a simple hydrophobic interaction model: an application to interaction pathway analysis.},
  booktitle = {Lecture Notes in Bioinformatics},
  year = 2012,
}

@inproceedings{CTT100658083,
  author = {大上雅史 and 松崎由理 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2012,
}

@inproceedings{CTT100658553,
  author = {山本航平 and 大上雅史 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2012,
}

@inproceedings{CTT100648451,
  author = {石田貴士},
  title = {GHOST-MP：「京」を用いた超高速メタゲノム解析パイプライン},
  booktitle = {},
  year = 2012,
}

@inproceedings{CTT100657810,
  author = {Masahito Ohue and Yuri Matsuzaki and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK: A rapid screening system of protein-protein interactions with all-to-all physical docking.},
  booktitle = {},
  year = 2012,
}

@inproceedings{CTT100657809,
  author = {Yuri Matsuzaki and Masahito Ohue and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {Application of exhaustive protein-protein interaction prediction system by using protein docking to signal transduction pathways.},
  booktitle = {},
  year = 2012,
}

@inproceedings{CTT100658026,
  author = {Yuri Matsuzaki and Masahito Ohue and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {Application of exhaustive protein-protein interaction prediction system by using protein docking to signal transduction pathways.},
  booktitle = {},
  year = 2012,
}

@inproceedings{CTT100658029,
  author = {Masahito Ohue and Yuri Matsuzaki and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK: A rapid screening system of protein-protein interactions with all-to-all physical docking.},
  booktitle = {},
  year = 2012,
}

@inproceedings{CTT100658082,
  author = {藤原隆之 and 松崎由理 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {情報処理学会研究報告},
  year = 2012,
}

@inproceedings{CTT100658647,
  author = {下田雄大 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {第29回バイオ情報学研究会},
  year = 2012,
}

@inproceedings{CTT100664759,
  author = {鈴木脩司 and 石田貴士 and 秋山 泰},
  title = {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},
  booktitle = {情報処理学会研究報告},
  year = 2012,
}

@inproceedings{CTT100640046,
  author = {杉浦典和 and 石田貴士 and 関嶋政和 and 秋山泰},
  title = {ハッシュテーブルの分割によるde novoアセンブリの改良},
  booktitle = {情報処理学会研究報告},
  year = 2012,
}

@inproceedings{CTT100647889,
  author = {Y. Namiki and T. Ishida and Y. Akiyama},
  title = {Fast DNA Sequence Clustering Based on Longest Common Subsequence},
  booktitle = {Communications in Computer and Information Science},
  year = 2012,
}

@inproceedings{CTT100802108,
  author = {藤原 隆之 and 松崎由理 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {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},
  year = 2012,
}

@inproceedings{CTT100658646,
  author = {大上雅史 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2012,
}

@inproceedings{CTT100633782,
  author = {Masahito Ohue and Yuri Matsuzaki and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {Protein Complex Structure Prediction with Normal Mode Ensemble and Physical Docking},
  booktitle = {Bioinformatics week in Odaiba 2011 (BiWO2011)},
  year = 2012,
}

@inproceedings{CTT100633781,
  author = {Masahito Ohue and Yuri Matsuzaki and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {Bound state structure estimation of protein-protein complex using rigid-body protein-protein docking method},
  booktitle = {The 10th Asia-Pacific Bioinformatics Conference (APBC2012)},
  year = 2012,
}

@inproceedings{CTT100801558,
  author = {Suzuki, S. and Takashi Ishida and Yutaka Akiyama},
  title = {An ultra-fast computing pipeline for metagenome analysis with next-generation DNA sequencers},
  booktitle = {Proceedings - 2012 SC Companion: High Performance Computing, Networking Storage and Analysis, SCC 2012},
  year = 2012,
}

@inproceedings{CTT100634035,
  author = {秋山 泰 and 松崎 由理 and 内古閑 伸之 and 石田 貴士 and 大上 雅史},
  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 = 2011,
}

@inproceedings{CTT100631870,
  author = {Masahito Ohue and Yuri Matsuzaki and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {Binding Conformation Prediction of a Protein Complex Using Physical Docking},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100630509,
  author = {坂田幸佑 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の マルチGPU 向け最適化},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100631871,
  author = {Yuri Matsuzaki and Masahito Ohue and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK: a Fast Protein-protein Interaction Prediction System by Exhaustive Docking},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100634038,
  author = {松崎由理 and 内古閑伸之 and 大上雅史 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100633792,
  author = {Yuri Matsuzaki and Masahito Ohue and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK: A fast protein-protein interaction prediction system by exhaustive docking},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100633790,
  author = {Wisnu Ananta Kusuma and Takashi Ishida and Yutaka Akiyama},
  title = {De novo sequence assembly and metagenomic fragments binning},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100633791,
  author = {Shuji Suzuki and Takashi Ishida and Yutaka Akiyama},
  title = {Improvement of a fast homology search tool on GPUs with suffix array},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100633794,
  author = {Takashi Ishida},
  title = {Disordered Protein Region Prediction by Using Naive Bayse Classifier},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100633793,
  author = {鈴木 脩司 and 石田 貴士 and 秋山 泰},
  title = {マルチCPUコアとGPUを用いた高速な配列相同性検索},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100624994,
  author = {山本航平 and 大上雅史 and 内古閑伸之 and 松崎由理 and 石田貴士 and 秋山 泰},
  title = {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},
  booktitle = {研究報告 バイオ情報学（BIO）},
  year = 2011,
}

@inproceedings{CTT100624995,
  author = {鈴木脩司 and 石田貴士 and 秋山 泰},
  title = {GPUを用いた高速な配列相同性検索のsuffix arrayによる改良},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100624993,
  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 = {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},
  booktitle = {研究報告 バイオ情報学（BIO）},
  year = 2011,
}

@inproceedings{CTT100624991,
  author = {稲吉一馬 and 石田貴士 and 前田和哉 and 杉山雄一 and 秋山 泰},
  title = {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},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100625002,
  author = {坂田幸佑 and 鈴木脩司 and 石田貴士 and 秋山 泰},
  title = {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},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100625006,
  author = {山本航平 and 大上雅史 and 松崎由理 and 石田貴士 and 秋山 泰},
  title = {タンパク質ドッキング計算結果の可視化とその解析},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100625003,
  author = {並木洋平 and 石田貴士 and 秋山 泰},
  title = {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},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100622419,
  author = {Wisnu Ananta Kusuma and Takashi Ishida and Yutaka Akiyama},
  title = {An Effective Approach for Assembling Very Short Reads from Next Genaration Sequencer},
  booktitle = {情報処理学会研究報告バイオ情報学(BIO)},
  year = 2011,
}

@inproceedings{CTT100619144,
  author = {松崎由理 and 内古閑伸之 and 大上雅史 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100619309,
  author = {Takashi Ishida and Yutaka Akiyama},
  title = {GPU-Acceleration of Protein Tertiary Structure Prediction based on a Fragment Assembly Simulation},
  booktitle = {},
  year = 2010,
}

@inproceedings{CTT100622421,
  author = {鈴木 脩司 and 石田 貴士 and 秋山 泰},
  title = {FM-indexを用いた高速な配列相同性検索ツールの開発},
  booktitle = {情報処理学会研究報告バイオ情報学(BIO)},
  year = 2010,
}

@inproceedings{CTT100619145,
  author = {Matsuzaki Yuri. and Uchikoga Nobuyuki. and Ohue Masahito. and Ishida Takashi. and Akiyama Yutaka},
  title = {Exhaustive protein-protein interaction prediction with MEGADOCK and its application to signaling pathway estimation},
  booktitle = {},
  year = 2010,
}

@inproceedings{CTT100619310,
  author = {Takashi Ishida},
  title = {Protein disorder prediction based on the evolutionary conservation},
  booktitle = {},
  year = 2010,
}

@inproceedings{CTT100622652,
  author = {鈴木脩司 and 石田貴士 and 秋山泰},
  title = {GPUによるDNA断片配列の高速マッピング},
  booktitle = {情報処理学会研究報告バイオ情報学(BIO)},
  year = 2010,
}

@inproceedings{CTT100619312,
  author = {石田貴士 and 秋山泰},
  title = {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},
  booktitle = {情報処理学会研究報告バイオ情報学(BIO)},
  year = 2010,
}

@inproceedings{CTT100619308,
  author = {Takashi Ishida},
  title = {GPU Acceleration of de Novo Protein Tertiary Structure Prediction},
  booktitle = {GPU Acceleration of de Novo Protein Tertiary Structure Prediction},
  year = 2010,
}

@inproceedings{CTT100622653,
  author = {鈴木脩司 and 石田貴士 and 秋山泰},
  title = {GPUによるDNA断片配列の高速マッピング},
  booktitle = {先進的計算基盤システムシンポジウムSACSIS2010論文集},
  year = 2010,
}

@inproceedings{CTT100619307,
  author = {Takashi Ishida and Yutaka Akiyama},
  title = {GPU-Acceleration of de novo Protein Tertiary Structure Prediction},
  booktitle = {},
  year = 2010,
}

@inproceedings{CTT100600381,
  author = {Matsuyuki Shirota and Takashi Ishida and Kengo Kinoshita},
  title = {Development of a New Meta-Score for Protein Structure Prediction from Seven All-Atom Distance Dependent Potentials Using Support Vector Regression},
  booktitle = {Genome Informatics},
  year = 2009,
}

@inproceedings{CTT100600486,
  author = {Takashi Ishida and Kengo Kinoshita},
  title = {Development of prediction servers for protein disorder},
  booktitle = {Proc. BIOINFO 2009 CBI-KSBSB Joint Conference},
  year = 2009,
}

@misc{CTT100633795,
  author = {秋山 泰 and 石田 貴士 and 角田将典 and 鈴木脩司},
  title = {次世代ＤＮＡシークエンサデータの超高速解析},
  year = 2011,
}

@misc{CTT100633789,
  author = {松崎由理 and 大上雅史 and 内古閑伸之 and 石田貴士 and 秋山 泰},
  title = {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～},
  year = 2010,
}