@book{CTT100848796, author = {木曽良明 and 秋山 泰 and 大上 雅史 and 吉川 寧 and 和久井 直樹}, title = {中分子創薬に適した特性を有する環状ペプチドのインシリコ設計（第8章）}, publisher = {シーエムシー出版}, year = 2019, } @book{CTT100720648, author = {秋山泰}, title = {バイオインフォマティクス入門}, publisher = {慶應義塾大学出版会}, year = 2015, } @book{CTT100507886, author = {秋山泰}, title = {細胞丸ごとRNA解析に向けたバイオインフォマティクス技術}, publisher = {ＣＭＣ出版}, year = 2006, } @book{CTT100507884, author = {秋山 泰}, title = {ポストゲノム－ライフサイエンス最前線}, publisher = {丸善}, year = 2002, } @book{CTT100507882, author = {秋山 泰}, title = {並列タンパク質情報解析(PAPIA)システム}, publisher = {共立出版}, year = 1999, } @book{CTT100507880, author = {秋山 泰}, title = {WWWによる統合データベース環境}, publisher = {共立出版}, year = 1996, } @book{CTT100507879, author = {秋山 泰}, title = {トリッキープログラムの謎を解け－RNA２次構造予測への組合せ最適化的アプローチ}, publisher = {共立出版}, year = 1994, } @book{CTT100507876, author = {秋山 泰}, title = {ボルツマンマシンとその応用}, publisher = {サイエンスフォーラム}, year = 1990, } @book{CTT100507874, author = {秋山 泰}, title = {ニューロチップの開発}, publisher = {三田出版会}, year = 1989, } @book{CTT100507872, author = {秋山 泰}, title = {ニューロチップ}, publisher = {共立出版}, year = 1989, } @article{CTT100920684, author = {Keisuke Yanagisawa and Takuya Fujie and Kazuki Takabatake and Yutaka Akiyama}, title = {QUBO Problem Formulation of Fragment-Based Protein–Ligand Flexible Docking}, journal = {Entropy}, year = 2024, } @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{CTT100883527, author = {Masatake Sugita and Takuya Fujie and Keisuke Yanagisawa and Masahito Ohue and Yutaka Akiyama}, title = {Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations}, journal = {Journal of Chemical Information and Modeling}, year = 2022, } @article{CTT100883528, author = {Keisuke Yanagisawa and Rikuto Kubota and Yasushi Yoshikawa and Masahito Ohue and Yutaka Akiyama}, title = {Effective Protein-Ligand Docking Strategy via Fragment Reuse and a Proof-of-Concept Implementation}, journal = {ACS Omega}, year = 2022, } @article{CTT100863265, author = {Jianan Li and Yanagisawa K and Yoshikawa Y and Ohue M and Akiyama Y.}, title = {Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning}, journal = {Bioinformatics}, year = 2022, } @article{CTT100878409, author = {Takabatake K and Yanagisawa K and Akiyama Y.}, title = {Solving Generalized Polyomino Puzzles Using the Ising Model}, journal = {Entropy}, year = 2022, } @article{CTT100862160, author = {Takabatake K and Izawa K and Akikawa M and Yanagisawa K and Ohue M and Akiyama Y.}, title = {Improved large-scale homology search by two-step seed search using multiple reduced amino acid alphabets}, journal = {Genes}, year = 2021, } @article{CTT100862159, author = {Sugita M and Sugiyama S and Takuya Fujie and Yoshikawa Y and Yanagisawa K and Ohue M and Akiyama Y.}, title = {Large-scale membrane permeability prediction of cyclic peptides crossing a lipid bilayer based on enhanced sampling molecular dynamics simulations}, journal = {Journal of Chemical Information and Modeling}, 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{CTT100848792, author = {Kosuke Fujimoto and Yasumasa Kimura and Jessica R Allegretti and Mako Yamamoto and Yao-zhong Zhang and Kotoe Katayama and Georg Tremmel and Yunosuke Kawaguchi and Masaki Shimohigoshi and Tetsuya Hayashi and Miho Uematsu and Kiyoshi Yamaguchi and Yoichi Furukawa and Yutaka Akiyama and Rui Yamaguchi and Sheila E. Crowe and Peter B. Ernst and Satoru Miyano and Hiroshi Kiyono and Seiya Imoto and Satoshi Uematsu}, title = {Functional Restoration of Bacteriomes and Viromes by Fecal Microbiota Transplantation}, journal = {Gastroenterology}, year = 2021, } @article{CTT100848790, author = {Fujimoto K and Kimura Y and Shimohigoshi M and Satoh T and Sato S and Tremmel G and Uematsu M and Kawaguchi Y and Usui Y and Hayashi T and Kashima K and Yuki Y and Furukawa Y and Kakuta M and Yutaka Akiyama and Yamaguchi R and Crowe SE and Ernst PB and Miyano S and Kiyono H and Imoto S and Uematsu S}, title = {Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts}, journal = {Cell Host & Microbe}, year = 2020, } @article{CTT100848791, author = {Izawa K and Kubosaki A and Kobayashi N and Akiyama Y and Yamazaki A and Hashimoto K and Konuma R and Kamata Y and Hara-Kudo Y and Hasegawa K and Ikaga T and Watanabe M}, title = {Comprehensive Fungal Community Analysis of House Dust Using Next-Generation Sequencing}, journal = {International Journal of Environmental Research and Public Health}, year = 2020, } @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{CTT100839090, author = {Shumpei Matsuno and Masahito Ohue and Yutaka Akiyama}, title = {Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces}, journal = {Biophysics and Physicobiology}, 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{CTT100819246, author = {Ohue M and Shogo Suzuki and Akiyama Y.}, title = {Learning-to-rank technique based on ignoring meaningless ranking orders between compounds}, journal = {Journal of Molecular Graphics and Modelling}, year = 2019, } @article{CTT100810744, author = {Ban T and Ohue M and Akiyama Y.}, title = {NRLMFβ: Bata-distribution-rescored Neighborhood Regularized Logistic Matrix Factorization for Improving Performance of Drug–Target Interaction Prediction}, journal = {Biochemistry and Biophysics Reports}, year = 2019, } @article{CTT100795110, author = {Takashi Tajimi and Naoki Wakui and Keisuke Yanagisawa and Yasushi Yoshikawa and Masahito Ohue and Yutaka Akiyama}, title = {Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques}, journal = {BMC Bioinformatics}, year = 2018, } @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{CTT100776743, author = {Masahiro Mochizuki and Shogo Suzuki and Yanagisawa K and Ohue M and Akiyama Y.}, title = {QEX: target-specific druglikeness filter enhances ligand-based virtual screening}, journal = {Molecular Diversity}, year = 2018, } @article{CTT100766870, author = {Shogo Suzuki and Masahito Ohue and Yutaka Akiyama}, title = {PKRank: a novel learning-to-rank method for ligand-based virtual screening using pairwise kernel and RankSVM}, journal = {Artificial Life and Robotics}, year = 2018, } @article{CTT100766872, author = {Yanagisawa K and Komine S and Kubota R and Ohue M and Akiyama Y.}, title = {Optimization of memory use of fragment extension-based protein–ligand docking with an original fast minimum cost flow algorithm}, journal = {Computational Biology and Chemistry (In Proc. APBC2018)}, year = 2018, } @article{CTT100766873, author = {Hayashi T and Matsuzaki Y and Yanagisawa K and Ohue M and Akiyama Y.}, title = {MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions}, journal = {BMC Bioinformatics (In Proc. APBC2018)}, year = 2018, } @article{CTT100766871, author = {Ban T and Masahito O and Yutaka Akiyama}, title = {Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem}, journal = {Computational Biology and Chemistry}, year = 2018, } @article{CTT100766874, author = {Ramakrishnan C and Thangakani AM and Velmurugan D and Krishnan DA and Sekijima M and Akiyama Y and Gromiha MM.}, title = {Identification of type I and type II inhibitors of c-Yes kinase using in silico and experimental techniques}, journal = {Journal of Biomolecular Structure and Dynamics}, 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{CTT100766869, author = {Yuri Matsuzaki and Nobuyuki Uchikoga and Masahito Ohue and Yutaka Akiyama}, title = {Rigid-Docking Approaches to Explore Protein–Protein Interaction Space}, journal = {Advances in Biochemical Engineering/Biotechnology(Network Biology)}, 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{CTT100714375, author = {Kota Kasahara and Benson Ma and Kota Goto and Bhaskar Dasgupta and Junichi Higo and Ikuo Fukuda and Tadaaki Mashimo and Yutaka Akiyama and Haruki Nakamura}, title = {myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme}, journal = {Biophysics and Physicobiology}, year = 2016, } @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{CTT100715183, author = {Nobuyuki Uchikoga and Yuri Matsuzaki and Masahito Ohue and Yutaka Akiyama}, title = {Specificity of broad protein interaction surfaces for proteins with multiple binding partners}, journal = {Biophysics and Physicobiology}, 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{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{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{CTT100686070, author = {Masahiro Yano and Hiroshi Mori and Yutaka Akiyama and Takuji Yamada and Ken Kurokawa}, title = {CLAST: CUDA implemented large-scale alignment search tool}, journal = {BMC Bioinformatics 2014}, 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{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{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{CTT100676726, author = {Toshimoto K and Wakayama N and Kusama M and Maeda K and Sugiyama Y and Akiyama Y}, title = {In silico prediction of major drug clearance pathways by support vector machines with feature-selected descriptors}, journal = {Drug Metabolism and Disposition}, 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{CTT100805859, author = {石田 貴史 and 秋山泰 and 関嶋 政和 and 大野 一樹 and 折田 正弥}, title = {顧みられない熱帯病に対するIT創薬の現状 (今田治教授退任記念号・兵藤友博教授退任記念号)}, journal = {立命館経営学}, year = 2013, } @article{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{CTT100665992, author = {Hagiwara Y and Ohno K and Orita M and Koga R and Endo T and Akiyama Y and Sekijima M.}, title = {Accelerating quantum chemistry calculations with graphical processing units - toward in high-density (HD) silico drug discovery}, journal = {Curr Comput Aided Drug Des. 2013}, year = 2013, } @article{CTT100666831, author = {Nobuyuki Uchikoga and Yuri Matsuzaki and Masahito Ohue and Takatsugu Hirokawa and Yutaka Akiyama}, title = {Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints}, journal = {PLOS ONE}, year = 2013, } @article{CTT100666829, author = {Yuri Matsuzaki and Masahito Ohue and Nobuyuki Uchikoga and Yutaka Akiyama}, title = {Protein-protein interaction network prediction by using rigid-body docking tools: application to bacterial chemotaxis}, journal = {Protein and Peptide Letters}, year = 2013, } @article{CTT100669378, author = {Ren A and Ishida T and Akiyama Y}, title = {Assessing statistical reliability of phylogenetic trees via a speedy double bootstrap method}, journal = {Mol Phylogenet Evol.}, year = 2013, } @article{CTT100669379, author = {Youhei Namiki and Takashi Ishida and Yutaka Akiyama}, title = {Acceleration of sequence clustering using longest common subsequence filtering}, journal = {BMC Bioinformatics}, year = 2013, } @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{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{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{CTT100631869, author = {Masahito Ohue and Yuri Matsuzaki and Yutaka Akiyama}, title = {Docking-calculation-based Method for Predicting Protein-RNA Interactions}, journal = {Genome Informatics}, year = 2011, } @article{CTT100622415, author = {Kusama M and Toshimoto K and Maeda K and Hirai Y and Imai S and Chiba K and Akiyama Y and Sugiyama Y}, title = {In silico classification of major clearance pathways of drugs with their physiochemical parameters.}, journal = {Drug Metabolism and Disposition}, year = 2010, } @article{CTT100596607, author = {Yuri Matsuzaki and Yusuke Matsuzaki and Toshiyuki Sato and Yutaka Akiyama}, title = {In silico screening of protein-protein interactions with all-to-all rigid docking and clustering: an application to pathway analysis}, journal = {Journal of Bioinformatics and Computational Biology}, year = 2009, } @article{CTT100575032, author = {Tsukamoto K and Yoshikawa T and Hourai Y and Fukui K and Akiyama Y.}, title = {Development of an affinity evaluation and prediction system by using the shape complementarity characteristic between proteins}, journal = {Journal of bioinformatics and computational biology}, year = 2008, } @article{CTT100571673, author = {Daisuke Tominaga and Yutaka Akiyama}, title = {High-throughput automated image processing system for cell array observations}, journal = {Information and Media Technologies}, year = 2008, } @article{CTT100571521, author = {Masakazu Sekijima and Yutaka Akiyama}, title = {Free energy landscape analysis system based on parallel molecular dynamics simulation.}, journal = {IPSJ Transaction on Bioinformatics}, year = 2007, } @article{CTT100507765, author = {Tsukamoto, K. and Shimizu, H. and Ishida, T. and Akiyama, Y. and Nukina, N.}, title = {Evaluation for Interaction Energy between Glutamine and various Chemical Compounds for Developing the Virtual Screening System using DFT Quantum Chemical Calculations}, journal = {WSEAS Transactions on Computers}, year = 2007, } @article{CTT100507741, author = {Nagano, N. and Noguchi, T. and Akiyama, Y.}, title = {Systematic Comparison of Catalytic Mechanisms of Hydrolysis and Transfer Reactions Classified in the EzCatDB Database}, journal = {PROTEINS: Structure, Function, and Bioinformatics}, year = 2007, } @article{CTT100571524, author = {Yuri Mukai and Takatsugu Hirokawa and Kentaro Tomii and Kiyoshi Asai and Yutaka Akiyama and Makiko Suwa}, title = {Identification of glycosyltransferases focusing on golgi transmembrane region.}, journal = {Trends in Glycoscience and Glycotechnology}, year = 2007, } @article{CTT100571522, author = {Koki Tsukamoto and Hideaki Shimizu and Takashi Ishida and Yutaka Akiyama and Nobuyuki Nukina}, title = {Evaluation for interaction energy between glutamine and glutamine and various chemical compounds for developing the virtual screening system using quantum chemical calculations and molecular dynamics simulations}, journal = {WSEAS Transactions on Computers}, year = 2007, } @article{CTT100507764, author = {Tsukamoto, K. and Shimizu, H. and Ishida, T. and Akiyama, Y. and Nukina, N.}, title = {Aggrigation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations}, journal = {Journal of Molecular Structure: THEOCHEM}, year = 2006, } @article{CTT100507762, author = {Tsukamoto, K. and Akiyama, Y.}, title = {Automated Docking of NADH to the Active Site of Nitric Oxide Reductase from Fusarium Oxysporum and Semi-empirical Calculations of the Electron Transfer Mechanism and the Hydrogen-bonding Network}, journal = {WSEAS Transactions on Computers}, year = 2006, } @article{CTT100507763, author = {Fukui, K. and Akiyama, Y. and Takahashi, K.}, title = {Fragmentation Studies of Peptide and Oligosaccharide using a Mid-IR Free Electron Laser}, journal = {Journal of Japan Society for Laser Surgery and Medicine}, year = 2006, } @article{CTT100507761, author = {Fukui, K. and Kameyama, A. and Mukai, Y. and Takahashi, K. and Ikeda, N. and Akiyama, Y. and Narimatsu H.}, title = {A computational study of structure-reactivity relationships in Na-adduct oligosaccharides in collision-induced dissociation reactions}, journal = {Carbohydrate Research}, year = 2006, } @article{CTT100768755, author = {Tsukamoto, K. and Toshio Watanabe and Nagashima, U. and Akiyama, Y.}, title = {Hartree-Fock and density functional theory calculations for the reaction mechanism of nitric oxide reductase cytochrome P450nor from Fusarium oxysporum}, journal = {Journal of Molecular Structure-Theochem}, year = 2005, } @article{CTT100507759, author = {Sekijima, M. and Motono, C. and Noguchi, T. and Kaneko, K. and Akiyama, Y.}, title = {Structural Changes in flexible region of the Prion Protein induced by P102L Substitution: Investigation through Molecular Dynamics Simulations}, journal = {Protein Science}, year = 2004, } @article{CTT100507740, author = {Shiozawa and K. Maita, N. and Tomii, K and Seto, A. and Goda, N. and Akiyama, Y. and Shimizu, T. and Shirakawa, M. and Hiroaki, H.}, title = {Structure of the N-terminal domain of PEX1 AAA-ATPase: characterization of a putative adaptor-binding domain}, journal = {Journal of Biological Chemistry, Vol.279, Issue 48, pp.50060-50068, 2004.}, year = 2004, } @article{CTT100507739, author = {Hourai, Y. and Akutsu T. and Akiyama Y.}, title = {Optimizing Substitution Matrices by Separating Score Distributions}, journal = {Bioinformatics}, year = 2004, } @article{CTT100507757, author = {Fukui, K. and Naito, Y. and Akiyama, Y. and Takahashi, K.}, title = {Fragmentation study of peptides using Fourier transform ion cyclotron resonance with infrared multiphoton dissociation: experiment and simulation}, journal = {European Journal of Mass Spectrometry}, year = 2004, } @article{CTT100507738, author = {Tomii, K. and Akiyama Y.}, title = {FORTE: a profile-profile comparison tool for protein fold recognition}, journal = {Bioinformatics}, year = 2004, } @article{CTT100507758, author = {Fukui, K. and Naito, Y. and Akiyama, Y. and Takahashi K.}, title = {Charge State Selective Fragmentation Analysis for Protonated Peptides in Infrared Multiphoton Dissociation and Collision Induced Dissociation}, journal = {International Journal of Mass Spectrometry}, year = 2004, } @article{CTT100507722, author = {Tominaga, D. and Takahashi, K. and Akiyama, Y.}, title = {Distributed Genetic Algorithm for Inference of Biological Scale-Free Network Structure}, journal = {Lecture Notes in Computer Science}, year = 2003, } @article{CTT100507756, author = {Sekijima, M. and Motono, C. and Yamasaki, S. and Kaneko, K. and Akiyama, Y.}, title = {Molecular Dynamics Simulation of Prion Protein by Large Scale Cluster Computing}, journal = {Lecture Notes in Computer Science}, year = 2003, } @article{CTT100507723, author = {Kikuchi, S. and Tominaga, D. and Arita, M. and Takahashi, K. and Akiyama, Y.}, title = {Dynamic modeling of genetic networks using genetic algorithm and S-system}, journal = {Bioinformatics}, year = 2003, } @article{CTT100507755, author = {Sekijima, M. and Motono, C. and Yamasaki, S. and Kaneko, K. and Akiyama, Y.}, title = {Molecular dynamics simulation of dimeric and monomeric forms of human prion protein (HuPrP): Insight into dynamics and properties}, journal = {}, year = 2003, } @article{CTT100507735, author = {Noguchi, T. and Akiyama, Y.}, title = {PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003}, journal = {Nucleic Acids Research}, year = 2003, } @article{CTT100507737, author = {Suwa, M. and Sato, T. and Okouchi, I. and Arita, M. and Matsumoto, S. and Tsutsumi, S. and Aburatani, H. and Asai, K. and Akiyama, Y.}, title = {SEVENS: The Comprehensive Collection of Seven Transmembrane Helix Receptors, hunted from Human genome}, journal = {Nucleic Acid Research}, year = 2003, } @article{CTT100507736, author = {Kadota, K. and Tominaga, D. and Akiyama, Y. and Takahashi, K.}, title = {A critical assessment of the effect of outliers on sample classifications}, journal = {Chem-Bio Informatics Journal}, year = 2003, } @article{CTT100507734, author = {Onizuka, K. and Noguchi, T. and Akiyama, Y. and Matsuda, H.}, title = {Using　Data　Compression for Multidimensional Distribution Analysis}, journal = {IEEE Intelligent Systems}, year = 2002, } @article{CTT100507754, author = {Nakano, T. and Kaminuma, T. and Sato, T. and Fukuzawa, K. and Akiyama, Y. and Uebayashi, M. and Kitaura, K.}, title = {Fragment Molecular Orbital Method: use of approximate electrostatic potential}, journal = {Chemical Physics Letters}, year = 2002, } @article{CTT100507752, author = {安藤 誠 and 秋山 泰 and 松田秀雄}, title = {階層的な大規模並列木探索によるタンパク質立体配座解析システムESCAPE/Hi}, journal = {情報処理学会論文誌}, year = 2001, } @article{CTT100507733, author = {Noguchi, T. and Ito, M. and Matsuda, H. and Akiyama, Y. and Nishikawa, K.}, title = {Prediction of Protein Secondary Structure Using the Threading Algorithm and Local Sequence Similarity}, journal = {Research Communications in Biochemistry, Cell and Molecular Biology}, year = 2001, } @article{CTT100507753, author = {Ando, M. and Akiyama, Y. and Matsuda, H.}, title = {Peptide Conformation　Prediction by High-Speed Parallel Tree Search on a Massively Parallel Computer}, journal = {Research Communications in Biochemistry, Cell and Molecular Biology}, year = 2001, } @article{CTT100507732, author = {Noguchi, T. and Matsuda, H. and Akiyama, Y.}, title = {PDB-REPRDB: a database of representative protein chains from the Protein Data Bank(PDB)}, journal = {Nucleic Acids Research}, year = 2001, } @article{CTT100507750, author = {佐藤智之 and 秋山 泰 and 中野達也 and 上林正巳 and 北浦和夫}, title = {Ab initioペア近似法による並列分子軌道計算プログラムABINIT-MPの作成と性能評価}, journal = {情報処理学会論文誌}, year = 2000, } @article{CTT100507731, author = {Noguchi, T. and Onizuka, K. and Ando, M. and Matsuda, H. and Akiyama, Y.}, title = {Quick Selection of Representative Protein Chain Sets Based on Customizable Requirements}, journal = {Bioinformatics}, year = 2000, } @article{CTT100507747, author = {三十尾潔高 and 志澤由久 and 秋山 泰 and 斎藤 稔}, title = {並列化Barnes-Hut tree codeを用いた高精度なタンパク質分子動力学法プログラムの開発}, journal = {情報処理学会論文誌}, year = 2000, } @article{CTT100507751, author = {Nakano, T. and Kaminuma, T. and Sato, T. and Akiyama, Y. and Uebayashi, M. and Kitaura, K.}, title = {Fragment　molecular orbital method: application to polypeptides}, journal = {Chemical Physics Letters}, year = 2000, } @article{CTT100507721, author = {秋山 泰}, title = {エントロピー項の導入によるバックプロパゲーション学習則の拡張と学習効率の向上}, journal = {情報処理学会論文誌}, year = 1999, } @article{CTT100507749, author = {十時 泰 and 秋山 泰 and 鬼塚健太郎 and 野口 保 and 斎藤 稔 and 安藤 誠}, title = {アミノ酸配列のマルチプルアラインメントにおける反復改善過程の並列化とA*アルゴリズムの適用}, journal = {情報処理学会論文誌}, year = 1999, } @article{CTT100507748, author = {斎藤 稔 and 三十尾潔高 and 志澤由久 and 丸川一志 and 秋山 泰 and 野口 保 and 鬼塚健太郎}, title = {分子動学法プログラムAMBERとBarnes-Hut tree codeの並列化による高速化}, journal = {情報処理学会論文誌}, year = 1999, } @article{CTT100507744, author = {Akiyama, Y. and Onizuka, K. and Noguchi, T. and Ando, M.}, title = {Biological- and Chemical- Parallel 　Applications on a PC Cluster}, journal = {Lecture Notes on Computer Science}, year = 1999, } @article{CTT100507730, author = {野口 保 and 秋山 泰 and 鬼塚健太郎 and 安藤 誠}, title = {タンパク質立体構造の配列および原子間距離による分類と非冗長化されたPDB代表タンパク質チェインデータベース(PDB-REPRDB)の作成}, journal = {情報処理学会論文誌}, year = 1999, } @article{CTT100507745, author = {安藤 誠 and 秋山 泰 and 鬼塚健太郎 and 野口 保}, title = {木探索アプローチによるタンパク質立体配座解析と大規模並列計算機上での高速解析システムの構築}, journal = {情報処理学会論文誌, Vol.40, No.SIG02, pp.91-104, 1999}, year = 1999, } @article{CTT100507729, author = {鬼塚健太郎 and 野口 保 and 安藤 誠 and 秋山 泰}, title = {多次元分布の線形変換による圧縮表現のタンパク質立体構造認識問題への応用}, journal = {情報処理学会論文誌}, year = 1999, } @article{CTT100507727, author = {Onizuka, K. and Noguchi, T. and Akiyama, Y.}, title = {Parallel PDB Data Retriever 'PDB Diving Booster'}, journal = {Lecture Notes on Computer Science}, year = 1997, } @article{CTT100507720, author = {Ogata, H. and Akiyama, Y. and Kanehisa, M.}, title = {A genetic algorithm based molecular modeling technique for RNA stem-loop structures}, journal = {Nucleic Acids Research}, year = 1995, } @article{CTT100507719, author = {新田 徹 and 赤穂昭太郎 and 秋山 泰 and 古谷立美}, title = {複素バックプロパゲーション・ネットワークにおける重みパラメータと決定表面の構造}, journal = {情報処理学会論文誌}, year = 1992, } @article{CTT100507716, author = {古谷立美 and 秋山 泰 and 田中敏夫 and 新田 徹}, title = {フィードバック付き多層ニューラルネットワーク}, journal = {情報処理学会論文誌}, year = 1991, } @article{CTT100507715, author = {Akiyama, Y. and Yamashita, A. and Kajiura, M. and Anzai, Y. and Aiso, H.}, title = {The Gaussian Machine: A Stochastic Neural Network for Solving Assignment Problems}, journal = {Journal of Neural Network Computing}, year = 1991, } @inproceedings{CTT100925880, author = {Taisuke Boku and Masatake Sugita and Ryohei Kobayashi and Shinnosuke Furuya and Takuya Fujie and Masahito Ohue and Yutaka Akiyama}, title = {Improving Performance on Replica-Exchange Molecular Dynamics Simulations by Optimizing GPU Core Utilization}, booktitle = {Proceedings of the 53rd International Conference on Parallel Processing (ICPP2024)}, year = 2024, } @inproceedings{CTT100920689, author = {Masatake Sugita and Takuya Fujie and Yudai Noso and Keisuke Yanagisawa and Masahito Ohue and Yutaka Akiyama}, title = {Development and Application of a Protocol for Predicting Membrane Permeability of Cyclic Peptides Based on Molecular Dynamics Simulations}, booktitle = {}, year = 2024, } @inproceedings{CTT100920693, author = {杉田 昌岳 and 藤江 拓哉 and 能祖 雄大 and 柳澤 渓甫 and 大上 雅史 and 秋山 泰}, title = {拡張アンサンブル分子動力学シミュレーションに基づいた環状ペプチドの膜透過性予測技術の開発と応用}, booktitle = {}, year = 2024, } @inproceedings{CTT100920696, author = {李 佳男 and 柳澤 渓甫 and 秋山 泰}, title = {CycPeptMP：マルチレベルの分子特徴とデータ拡張による環状ペプチドの膜透過性予測手法の開発}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2024, } @inproceedings{CTT100920700, author = {Masatake Sugita and Takuya Fujie and Keisuke Yanagisawa and Masahito Ohue and Yutaka Akiyama}, title = {Development of a Protocol for Predicting Membrane Permeability of Cyclic Peptides Based on Molecular Dynamics Simulations}, booktitle = {}, year = 2023, } @inproceedings{CTT100893467, author = {李 佳男 and 柳澤 渓甫 and 杉田 昌岳 and 藤江 拓哉 and 大上 雅史 and 秋山 泰}, title = {CycPeptMPDB：包括的な環状ペプチド膜透過率データベースの開発}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2023, } @inproceedings{CTT100876315, author = {津嶋佑旗 and 柳澤渓甫 and 大上雅史 and 秋山泰}, title = {新たなデータセットによる長距離フラグメントリンキング手法の再評価}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2022, } @inproceedings{CTT100876286, author = {稲垣雅也 and 柳澤渓甫 and 大上雅史 and 秋山泰}, title = {フラグメント化された化合物立体構造データベースの構築}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2022, } @inproceedings{CTT100876290, author = {山崎眞拓 and 伊澤和輝 and 平田稜 and 柳澤渓甫 and 大上雅史 and 秋山泰}, title = {結合エネルギーを考慮したゲノムワイドな高速短鎖核酸配列検索手法の開発}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2022, } @inproceedings{CTT100876300, author = {玉野史結 and 伊澤和輝 and 柳澤渓甫 and 大上雅史 and 秋山泰}, title = {Gapmer型ASOにおけるオフターゲット効果のリスク評価手法の提案}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2022, } @inproceedings{CTT100876344, author = {杉田昌岳 and 杉山聡 and 藤江拓哉 and 吉川寧 and 柳澤渓甫 and 大上雅史 and 秋山泰}, title = {分子動力学シミュレーションに基づいた環状ペプチドの膜透過率の大規模予測}, booktitle = {}, year = 2021, } @inproceedings{CTT100876345, author = {杉田昌岳 and 杉山聡 and 藤江拓哉 and 吉川寧 and 柳澤渓甫 and 大上雅史 and 秋山泰}, title = {分子動力学シミュレーションに基づいた環状ペプチドの膜透過率の大規模予測}, booktitle = {}, year = 2021, } @inproceedings{CTT100876239, author = {Kazuki Takabatake and Kazuki Izawa and Motohiro Akikawa and Keisuke Yanagisawa and Masahito Ohue and Yutaka Akiyama}, title = {Improved Homology Search for Metagenomic Analysis by Two-Step Seed Search with Reduced Amino Acid Alphabets}, booktitle = {}, year = 2021, } @inproceedings{CTT100876383, author = {Sugita M and Sugiyama S and Takuya Fujie and Yoshikawa Y and Yanagisawa K and Ohue M and Akiyama Y.}, title = {Large-scale membrane permeability prediction of cyclic peptides crossing a lipid bilayer based on enhanced sampling molecular dynamics simulations}, booktitle = {}, year = 2021, } @inproceedings{CTT100876380, author = {杉田昌岳 and 杉山聡 and 藤江拓哉 and 吉川寧 and 柳澤渓甫 and 大上雅史 and 秋山泰}, title = {分子動力学シミュレーションに基づいた環状ペプチドの膜透過率の大規模予測}, booktitle = {}, year = 2021, } @inproceedings{CTT100839093, author = {Masahito Ohue and Kento Aoyama and Yutaka Akiyama}, title = {High-performance cloud computing for exhaustive protein-protein docking}, booktitle = {Advances in Parallel & Distributed Processing, and Applications}, year = 2021, } @inproceedings{CTT100863267, author = {津嶋佑旗 and 柳澤渓甫 and 大上雅史 and 秋山泰.}, title = {タンパク質表面との結合親和性を考慮した長距離フラグメントリンキング手法の開発}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2021, } @inproceedings{CTT100851553, author = {Masahito Ohue and Hiroki Watanabe and Yutaka Akiyama}, title = {MEGADOCK-Web-Mito: human mitochondrial protein-protein interaction prediction database}, booktitle = {Advances in Parallel & Distributed Processing, and Applications(Accepted)}, year = 2021, } @inproceedings{CTT100862146, author = {Isawa Kazuya and Yanagisawa Keisuke and Ohue Masahito and Akiyama Yutaka}, title = {Antisense oligonucleotide activity analysis based on opening and binding energies to targets}, booktitle = {Advances in Parallel & Distributed Processing and Applications}, year = 2021, } @inproceedings{CTT100851550, author = {Masahito Ohue and Yutaka Akiyama}, title = {MEGADOCK-GUI: a GUI-based complete cross-docking tool for exploring protein-protein interactions}, booktitle = {Advances in Parallel & Distributed Processing, and Applications(Accepted)}, year = 2021, } @inproceedings{CTT100848794, author = {井澤和也 and 柳澤渓甫 and 大上雅史 and 秋山泰}, title = {標的配列との結合・開放エネルギー推定に基づくアンチセンス核酸の阻害活性モデルの研究}, booktitle = {情報処理学会研究報告}, year = 2021, } @inproceedings{CTT100851835, author = {大上雅史 and 青山建人 and 秋山泰}, title = {GPUスパコンによる細胞スケールのタンパク質間相互作用予測}, booktitle = {}, year = 2020, } @inproceedings{CTT100839077, author = {Masahito Ohue and Kento Aoyama and Yutaka Akiyama}, title = {High-performance cloud computing for exhaustive protein-protein docking}, booktitle = {IPSJ Technical Report}, year = 2020, } @inproceedings{CTT100839094, author = {Kento Aoyama and Hiroki Watanabe and Masahito Ohue and Yutaka Akiyama}, title = {Multiple HPC environments-aware container image configuration workflow for large-scale all-to-all protein-protein docking calculations}, booktitle = {Lecture Notes in Computer Science}, year = 2020, } @inproceedings{CTT100851627, author = {Takuya Fujie and Masatake Sugita and Satoshi Sugiyama and Yasushi Yoshikawa and Masahito Ohue and Yutaka Akiyama}, title = {Conformational Sampling with Molecular Dynamics Simulation for Prediction of Membrane Permeability of Cyclic Peptide}, booktitle = {}, year = 2020, } @inproceedings{CTT100839081, author = {高畠和輝 and 伊澤和輝 and 秋川元宏 and 大上雅史 and 秋山泰}, title = {圧縮アミノ酸を利用した二段階のシード探索によるメタゲノム配列相同性検索の改良}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2020, } @inproceedings{CTT100839080, author = {村田翔太朗 and 山田雄太 and 吉川寧 and 大上雅史 and 秋山泰}, title = {二次元分子記述子を用いた機械学習による環状ペプチドの細胞膜透過性予測}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2020, } @inproceedings{CTT100839079, author = {久保田陸人 and 柳澤渓甫 and 吉川寧 and 大上雅史 and 秋山泰}, title = {共通な部分構造の再利用による高速なタンパク質リガンドドッキング手法の開発}, booktitle = {情報処理学会研究報告}, year = 2020, } @inproceedings{CTT100839078, author = {渡辺紘生 and 大上雅史 and 秋山泰}, title = {マルチノード・マルチGPU上での網羅的なタンパク質間相互作用予測の高速化}, booktitle = {情報処理学会研究報告}, year = 2020, } @inproceedings{CTT100851626, author = {Masaya Inagaki and Masahito Ohue and Yutaka Akiyama}, title = {Fragment Linking with DQN}, booktitle = {}, year = 2020, } @inproceedings{CTT100851612, author = {Kazuki Izawa and K Shibayama and Masahito Ohue and Takashi Ishida and Kazuyuki Ishihara and Yutaka Akiyama}, title = {The shifts in bacterial community and gene category composition between healthy sites and periodontal disease sites}, booktitle = {}, year = 2020, } @inproceedings{CTT100851625, author = {Yuki Tsushima and Masahito Ohue and Yutaka Akiyama}, title = {Development of fragment linking method for beyond rule of five}, booktitle = {}, year = 2020, } @inproceedings{CTT100839075, author = {Masahito Ohue and Shogo D. Suzuki and Yutaka Akiyama}, title = {PKRank & SPDRank - Learning-to-rank methods for machine-learning-based drug discovery}, booktitle = {}, year = 2020, } @inproceedings{CTT100851638, author = {Max Druyvesteyn and Masahito Ohue and Yutaka Akiyama}, title = {Improved protein-protein docking using arbitrary docking-derived protein interface predictions}, booktitle = {}, year = 2020, } @inproceedings{CTT100851641, author = {Shunpei Matsuno and Masahito Ohue and Yutaka Akiyama}, title = {Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces}, booktitle = {}, year = 2020, } @inproceedings{CTT100851639, author = {Satoshi Sugiyama and Yasushi Yoshikawa and Masahito Ohue and Yutaka Akiyama}, title = {Development of Membrane Permeability Prediction System for Cyclic Peptide: Large-Scale Molecular Dynamics Simulations}, booktitle = {}, year = 2020, } @inproceedings{CTT100851637, author = {Li Jianan and Yasushi Yoshikawa and Masahito Ohue and Yutaka Akiyama}, title = {Prediction of plasma protein binding for cyclic peptides by deep learning and molecular docking}, booktitle = {}, year = 2020, } @inproceedings{CTT100851634, author = {Kento Aoyama and Hiroki Watanabe and Masahito Ohue and Yutaka Akiyama}, title = {Multiple HPC Environments-Aware Container Image Configuration Workflow for Large-Scale All-to-All Protein-Protein Docking Calculations}, booktitle = {}, year = 2020, } @inproceedings{CTT100851630, author = {Hiroki Watanabe and Masahito Ohue and Yutaka Akiyama}, title = {Exhaustive protein-protein interaction prediction using MEGADOCK on a large-scale HPC environment}, booktitle = {}, year = 2020, } @inproceedings{CTT100810747, author = {Keren Jiang and Di Zhang and Tsubasa Iino and Risa Kimura and Tatsuo Nakajima and Kana Shimizu and Masahito Ohue and Yutaka Akiyama.}, title = {A playful tool for predicting protein-protein docking}, booktitle = {In Proceedings of the 18th International Conference on Mobile and Ubiquitous Multimedia (MUM 2019)}, year = 2019, } @inproceedings{CTT100839076, author = {Kento Aoyama and Hiroki Watanabe and Masahito Ohue and Yutaka Akiyama}, title = {Multiple HPC Environments-Aware Container Image Configuration for Bioinformatics Application}, booktitle = {}, year = 2019, } @inproceedings{CTT100851841, author = {大上雅史 and 鈴木翔吾 and 秋山泰}, title = {PKRank & SPDRank 化合物選別のためのランク学習法}, booktitle = {}, year = 2019, } @inproceedings{CTT100851868, author = {Hiroki Watanabe and Masahito Ohue and Yutaka Akiyama}, title = {Accelerating MEGADOCK: protein-protein interaction prediction software on multiple nodes and multiple GPUs environment}, booktitle = {}, year = 2019, } @inproceedings{CTT100851843, author = {Masahito Ohue and Hiroki Watanabe and Kento Aoyama and Yutaka Akiyama}, title = {Acceleration and virtualization of parallel protein-protein interaction prediction system MEGADOCK}, booktitle = {}, year = 2019, } @inproceedings{CTT100851861, author = {Masahito Ohue and Shogo D. Suzuki and Yutaka Akiyama}, title = {PKRank & SPDRank: Learning-to-rank methods for ligand-based virtual screening}, booktitle = {}, year = 2019, } @inproceedings{CTT100851864, author = {Kento Aoyama and Hiroki Watanabe and Masahito Ohue and Yutaka Akiyama}, title = {Multiple HPC Environments-Aware Container Image Configuration for Bioinformatics Application}, booktitle = {}, year = 2019, } @inproceedings{CTT100851873, author = {Yuta Yamada and Yasushi Yoshikawa and Naoki Wakui and Masahito Ohue and Yutaka Akiyama}, title = {Development of Membrane Permeability Prediction Method for Cyclic Peptids with Machine Learning}, booktitle = {}, year = 2019, } @inproceedings{CTT100851878, author = {Kazuki Izawa and Kazuki Shibayama and Masahito Ohue and Kazuyuki Ishihara and Yutaka Akiyama}, title = {Bacterial community and gene category composition analysis with high-speed homology search tool suggests the difference between periodontal disease and healthy sites}, booktitle = {}, year = 2019, } @inproceedings{CTT100851883, author = {Shumpei Matsuno and Masahito Ohue and Yutaka Akiyama}, title = {Multidomain protein structure prediction using multimeric interaction residue pair information}, booktitle = {}, year = 2019, } @inproceedings{CTT100810748, author = {Masahito Ohue and Marina Yamasawa and Kazuki Izawa and Yutaka Akiyama}, title = {Parallelized pipeline for whole genome shotgun metagenomics with GHOSTZ-GPU and MEGAN}, booktitle = {}, year = 2019, } @inproceedings{CTT100851739, author = {Ohue M and Ii R and Yanagisawa K and Akiyama Y.}, title = {Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graph}, booktitle = {IPSJ SIG Technical Report}, year = 2019, } @inproceedings{CTT100810741, author = {Aoyama K and Yamamoto Y and Ohue M and Akiyama Y.}, title = {Performance evaluation of MEGADOCK protein–protein interaction prediction system implemented with distributed containers on a cloud computing environment}, booktitle = {In Proceedings of the 2019 International Conference on Parallel and Distributed Processing Techniques & Applications (PDPTA'19)}, year = 2019, } @inproceedings{CTT100851740, author = {Aoyama K and Yamamoto Y and Ohue M and Akiyama Y.}, title = {Performance evaluation of MEGADOCK protein–protein interaction prediction system implemented with distributed containers on a cloud computing environment}, booktitle = {IPSJ SIG Technical Report}, year = 2019, } @inproceedings{CTT100810742, author = {Ohue M and Ii R and Yanagisawa K and Akiyama Y.}, title = {Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graph}, booktitle = {In Proceedings of the 2019 International Conference on Parallel and Distributed Processing Techniques & Applications (PDPTA'19)}, year = 2019, } @inproceedings{CTT100810739, author = {松野駿平 and 大上雅史 and 秋山泰.}, title = {マルチドメインタンパク質の相互作用残基ペア予測を用いた立体構造予測手法の改良}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2019, } @inproceedings{CTT100810740, author = {李佳男 and 吉川寧 and 大上雅史 and 秋山泰.}, title = {機械学習を用いた環状ペプチドの体内安定性予測手法の改良}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2019, } @inproceedings{CTT100809992, author = {Masahito Ohue and Takanori Hayashi and Yuri Matsuzaki and Keisuke Yanagisawa and Yutaka Akiyama}, title = {Megadock-Web: An Integrated Database of High-Throughput Structure-Based Protein-Protein Interaction Predictions}, booktitle = {}, year = 2019, } @inproceedings{CTT100823269, author = {黄毅聰 and 吉川寧 and 和久井直樹 and 大上雅史 and 秋山泰.}, title = {拡張サンプリング法による環状ペプチドの膜透過性予測システムの構築}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2019, } @inproceedings{CTT100810736, author = {伊井 良太 and 柳澤 渓甫 and 大上 雅史 and 秋山 泰}, title = {分子グラフ上の距離を考慮したグラフ畳込みニューラルネットワークによる化合物活性予測}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2019, } @inproceedings{CTT100810733, author = {林 孝紀 and 大上 雅史 and 秋山 泰.}, title = {代表タンパク質構造群との構造アラインメントスコアプロファイルに基づくタンパク質間相互作用予測の高速化}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2019, } @inproceedings{CTT100810731, author = {山田 雄太 and 吉川 寧 and 和久井 直樹 and 大上 雅史 and 秋山 泰}, title = {機械学習を用いた環状ペプチドの膜透過性予測手法の開発}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2019, } @inproceedings{CTT100851460, author = {Takashi Tajimi and Naoki Wakui and Keisuke Yanagisawa and Yasushi Yoshikawa and Masahito Ohue and Yutaka Akiyama}, title = {Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques}, booktitle = {BMC Bioinformatics}, year = 2018, } @inproceedings{CTT100809993, author = {Masahito Ohue and Takanori Hayashi and Hiroki Watanabe and Yuri Matsuzaki and Nobuyuki Uchikoga and Yutaka Akiyama}, title = {Supercomputing-based exhaustive protein-protein interaction prediction and its open database.}, booktitle = {}, year = 2018, } @inproceedings{CTT100776748, author = {久保田陸人 and 柳澤渓甫 and 大上雅史 and 秋山泰}, title = {共通な部分構造の再利用アルゴリズムを用いたタンパク質リガンドドッキング手法の開発}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2018, } @inproceedings{CTT100776756, author = {青山健人 and 大上雅史 and 秋山泰}, title = {生命情報解析分野におけるコンテナ型仮想化技術の動向と性能検証}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2018, } @inproceedings{CTT100776751, author = {渡辺紘生 and 林孝紀 and 大上雅史 and 秋山泰}, title = {ミトコンドリアに関連したヒトタンパク質間相互作用予測データベースMEGADOCK-Web-Mitoの開発}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2018, } @inproceedings{CTT100776749, author = {多治見隆志 and 和久井直樹 and 大上雅史 and 秋山泰}, title = {複数のLasso回帰解に基づく解釈性の良い予測モデルを目指した環状ペプチド医薬品の体内安定性予測}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2018, } @inproceedings{CTT100766887, author = {山本悠生 and 大上雅史 and 秋山泰.}, title = {クラウド上の分散GPU環境におけるタンパク質間相互作用予測計算フレームワークの開発}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2018, } @inproceedings{CTT100766886, author = {後藤公太 and 大上雅史 and 石田貴士 and 秋山泰}, title = {配列相同性検索ツールGHOSTZ-GPUのMPI環境における高速化}, booktitle = {情報処理学会研究報告}, year = 2018, } @inproceedings{CTT100776753, author = {後藤公太 and 大上雅史 and 石田貴士 and 秋山泰}, title = {配列相同性検索ツールGHOSTZ-GPUのMPI環境における高速化}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2018, } @inproceedings{CTT100776754, author = {山本悠生 and 大上雅史 and 秋山泰}, title = {クラウド上の分散GPU環境におけるタンパク質間相互作用予測計算フレームワークの開発}, booktitle = {}, year = 2018, } @inproceedings{CTT100783055, author = {Masahito Ohue and Yuki Yamamoto and Kento Aoyama and Yutaka Akiyama}, title = {MEGADOCK-Azure: high-performance protein-protein docking on Microsoft Azure HPC}, booktitle = {}, year = 2017, } @inproceedings{CTT100776727, author = {Ban T and Ohue M and Akiyama Y}, title = {Efficient Hyperparameter Optimization by Using Bayesian Optimization for Drug-Target Interaction Prediction}, booktitle = {}, year = 2017, } @inproceedings{CTT100776726, author = {Ohue M and Yamazaki T and Ban T and Akiyama Y}, title = {Link Mining for Kernel-based Compound-Protein Interaction Predictions Using a Chemogenomics Approach}, booktitle = {Lecture Notes in Computer Science}, 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{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{CTT100766884, author = {林孝紀 and 山本悠生 and 松崎由理 and 大上雅史 and 秋山泰}, title = {タンパク質間相互作用予測統合データベースMEGADOCK-WEBの改良とクラウド計算環境との連携}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2017, } @inproceedings{CTT100766885, author = {柳澤渓甫 and 小峰駿汰 and 久保田陸人 and 大上雅史 and 秋山泰}, title = {フラグメント伸長型化合物ドッキング計算のための重み付きオフラインキャッシュ問題の厳密解アルゴリズム}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2017, } @inproceedings{CTT100766880, author = {大上 雅史 and 山本 悠生 and 秋山 泰}, title = {Microsoft Azure上でのタンパク質間相互作用予測システムの並列計算と性能評価}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2017, } @inproceedings{CTT100766882, author = {青山 健人 and 山本 悠生 and 大上 雅史 and 秋山 泰}, title = {コンテナ型仮想化による分散計算環境におけるタンパク質間相互作用予測システムの性能評価}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2017, } @inproceedings{CTT100766879, author = {柳澤渓甫 and 大上雅史 and 石田貴士 and 秋山泰}, title = {標的タンパク質の立体構造を用いたリガンド候補化合物の上限サイズの推定による化合物フィルタリング}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2017, } @inproceedings{CTT100806049, author = {Masahito Ohue and Yamamoto, Yuki and Hayashi, Takanori and Yuri Matsuzaki and Yutaka Akiyama}, title = {Cloud Computing for All-To-All Protein-Protein Docking on Azure HPC}, booktitle = {BIOPHYSICAL JOURNAL}, year = 2017, } @inproceedings{CTT100806075, author = {Yuri Matsuzaki and Simm, Jaak and Uchikoga, Nobuyuki and Yutaka Akiyama}, title = {A Docking Based Approach to Analyze Interaction Surfaces of Virus-Host Protein-Protein Interactions}, booktitle = {BIOPHYSICAL JOURNAL}, year = 2017, } @inproceedings{CTT100805974, author = {Uchikoga, Nobuyuki and Yuri Matsuzaki and Masahito Ohue and Yutaka Akiyama}, title = {Interaction Surfaces of Proteins Involved in Bacterial Chemotaxis with Rigid-Body Docking Decoys}, booktitle = {BIOPHYSICAL JOURNAL}, year = 2017, } @inproceedings{CTT100851563, author = {Shogo Suzuki and Masahito Ohue and Yutaka Akiyama}, title = {Learning-to-rank based compound virtual screening by using pairwise kernel with multiple heterogeneous experimental data}, booktitle = {}, 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{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{CTT100715195, author = {Takanori Hayashi and Kazuki Nagasawa and Yuri Matsuzaki and Masahito Ohue and Yutaka Akiyama}, title = {MEGADOCK-WEB: a database of predicted protein-protein interactions and its web interface}, booktitle = {}, year = 2016, } @inproceedings{CTT100715197, author = {Kota Goto and Kota Kasahara and Masahito Ohue and Haruki Nakamura and Yutaka Akiyama}, title = {Accelerating SHAKE Calculation of myPresto/omegagene Molecular Dynamics Simulation on CPU/GPU heterogeneous environment}, 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{CTT100715194, author = {Shogo Suzuki and Masahito Ohue and Yutaka Akiyama}, title = {Learning to Rank with Ignoring Meaningless Order and Its Application to Virtual Screening for Drug Discovery}, booktitle = {}, year = 2016, } @inproceedings{CTT100715192, author = {Masahito Ohue and Yuki Yamamoto and Hiroyuki Sato and Takashi Matsushita and Yutaka Akiyama}, title = {MEGADOCK-Azure: High-performance protein-protein interaction prediction system on Microsoft Azure HPC}, 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{CTT100722736, author = {秋山 泰}, title = {アミノ酸配列に対する高速な配列相同性検索（GHOSTXおよび並列版GHOST-MP）}, booktitle = {}, year = 2016, } @inproceedings{CTT100722732, author = {Yutaka Akiyama}, title = {Massively parallel bioinformatics computing on K-computer, TSUBAME, and Azure: Metagenome analysis and exhaustive protein-protein interaction prediction}, booktitle = {}, year = 2016, } @inproceedings{CTT100710861, author = {後藤 公太 and 笠原 浩太 and 大上 雅史 and 中村 春木 and 秋山 泰}, title = {SHAKE法に着目した分子動力学ソフトウェアmyPresto/OmegageneのCPU・GPU混在環境における高速化}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2016, } @inproceedings{CTT100710863, author = {鈴木 翔吾 and 大上 雅史 and 秋山 泰}, title = {活性値情報のグループ化とランク学習による化合物スクリーニング}, booktitle = {研究報告バイオ情報学（BIO）}, 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{CTT100722730, author = {秋山 泰}, title = {Azure上での1000コア級並列計算 ～生命情報解析の共通基盤を目指して}, booktitle = {http://www.nii.ac.jp/csi/openforum2016/track/day2_5.html#period1}, 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{CTT100701949, author = {長澤一輝 and 松崎由理 and 大上雅史 and 秋山泰}, title = {タンパク質間相互作用予測結果データベース及び表示系の構築}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2016, } @inproceedings{CTT100703203, author = {山崎卓朗 and 大上雅史 and 秋山泰}, title = {タンパク質-化合物相互作用ネットワークのリンクマイニング}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2016, } @inproceedings{CTT100715115, author = {Nobuyuki Uchikoga and Yuri Matsuzaki and Masahito Ohue and Yutaka Akiyama}, title = {Analysis of Physico-Chemical Properties of Protein Docking Decoys Generated by Rigid-Body Docking}, booktitle = {}, 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{CTT100715117, author = {Masahito Ohue and Yutaka Akiyama}, title = {A rescoring method of protein-peptide docking prediction with amino acid profiles of rigid-body search results}, booktitle = {}, year = 2016, } @inproceedings{CTT100722733, author = {Yutaka Akiyama}, title = {GHOST-MP: an ultra-fast and high-sensitive homology search tool for metagenome analysis}, booktitle = {}, year = 2016, } @inproceedings{CTT100715163, author = {大上雅史 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システムMEGADOCKによるEGFRパスウェイ解析}, 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{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{CTT100715121, author = {Tomohiro Ban and Masahito Ohue and Yutaka Akiyama}, title = {Improving protein-ligand docking and inverse docking prediction by deepening conformation search on multiple grids}, 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{CTT100715131, author = {Nobuyuki Uchikoga and Yuri Matsuzaki and Masahito Ohue and Takatsugu Hirokawa and Yutaka Akiyama}, title = {Analysis of protein docking decoys in terms of physicochemical properties of protein surfaces using rigid-body docking process}, 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{CTT100715167, author = {鈴木翔吾 and 大上雅史 and 秋山泰}, title = {活性値情報のグループ化とランク学習による活性化合物予測}, booktitle = {}, year = 2015, } @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{CTT100715165, author = {鈴木翔吾 and 大上雅史 and 秋山泰}, title = {活性値情報のグループ化を用いたランク学習による化合物スクリーニング}, booktitle = {}, year = 2015, } @inproceedings{CTT100715164, author = {伴 兼弘 and 大上 雅史 and 秋山 泰}, title = {Multiple Grids Arrangement for Improving Conformational Search of Protein-Ligand Docking and Its Application to Inverse Docking Problem}, booktitle = {}, year = 2015, } @inproceedings{CTT100806093, author = {Uchikoga, Nobuyuki and Masahito Ohue and Yuri Matsuzaki and Yutaka Akiyama}, title = {Post-docking analysis by physicochemical properties of protein-protein interactions generated from rigid-body docking processes}, booktitle = {PROTEIN SCIENCE}, year = 2015, } @inproceedings{CTT100722735, author = {秋山 泰}, title = {次世代シークエンサデータ解析のための情報処理システムの開発}, booktitle = {}, year = 2015, } @inproceedings{CTT100715185, author = {Tomohiro Ban and Masahito Ohue and Yutaka Akiyama}, title = {Multiple Grids Arrangement for Ligand Docking and Its Application to Inverse Docking Problem}, 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{CTT100715170, author = {内古閑伸之 and 松崎由理 and 大上雅史 and 秋山泰}, title = {剛体アンサンブルドッキングによって得られた候補構造群における相互作用残基ペアの特徴の解析}, booktitle = {}, year = 2015, } @inproceedings{CTT100715168, author = {大上雅史 and 内古閑伸之 and 松崎由理 and 秋山泰}, title = {アミノ酸プロファイルによるタンパク質ペプチド複合体のポストドッキング解析}, booktitle = {}, year = 2015, } @inproceedings{CTT100715173, author = {大上雅史 and 内古閑伸之 and 松崎由理 and 秋山泰}, title = {タンパク質間相互作用残基の物理化学的性質による単純化プロファイルを用いたポストドッキング解析}, booktitle = {}, 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{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{CTT100715213, author = {Yutaka Akiyama and Takashi Ishida}, title = {iNTRODB and its Applicationin anti-Trypanosome Drug Discovery}, 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{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{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{CTT100715136, author = {Nobuyuki Uchikoga and Yuri Matsuzaki and Masahito Ohue and Takatsugu Hirokawa and Yutaka Akiyama}, title = {Analysis of amino acid properties in interaction surfaces of decoys generated by re-docking}, booktitle = {}, year = 2015, } @inproceedings{CTT100715140, author = {Yuri Matsuzaki and Nobuyuki Uchikoga and Masahito Ohue and Yutaka Akiyama}, title = {Prediction of human-virus protein-protein interactions by exhaustive rigid docking.}, booktitle = {}, 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{CTT100677921, author = {Zhang Chaojie and Koichi Shirahata and Shuji Suzuki and Yutaka Akiyama and Satoshi Matsuoka}, title = {Performance Analysis of MapReduce Implementations for High Performance Homology Search}, 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{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{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{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{CTT100715216, author = {Takashi Ishida and Kozue Hasumi and Yutaka Akiyama}, title = {iNTRODB: database for NTDs drug target protein selection}, 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{CTT100715174, author = {大上雅史 and 松崎由理 and 石田貴士 and 秋山泰}, title = {タンパク質とペプチドのドッキング計算}, 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{CTT100715176, 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: a high-performance protein-protein interaction prediction tool on supercomputing environments}, booktitle = {}, year = 2014, } @inproceedings{CTT100715177, author = {内古閑伸之 and 松崎由理 and 大上雅史 and 広川貴次 and 秋山泰}, title = {Analysis of properties of protein-protein interaction surface areas involved in more near-native conmplexes by Re-docking scheme}, 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{CTT100805483, 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 (情報論的学習理論と機械学習)}, 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{CTT100805952, 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 (情報論的学習理論と機械学習)}, 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{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{CTT100805061, 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 = {研究報告数理モデル化と問題解決（MPS）}, 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{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{CTT100722740, author = {Yutaka Akiyama}, title = {Development of an Ultra-Fast Computing Pipeline for Metagenome Analysis on Supercomputers}, booktitle = {}, year = 2014, } @inproceedings{CTT100805086, 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 = {研究報告数理モデル化と問題解決（MPS）}, year = 2014, } @inproceedings{CTT100722747, author = {秋山 泰}, title = {大規模メタゲノム解析向け超並列相同性検索パイプラインの構築}, booktitle = {}, 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{CTT100722748, author = {Yutaka Akiyama}, title = {Development of an Ultra-Fast Computing Pipeline for Metagenome Analysis on Supercomputers}, booktitle = {}, year = 2014, } @inproceedings{CTT100722743, author = {Yutaka Akiyama}, title = {Development of an Ultra-Fast Computing Pipeline for Metagenome Analysis on TSUBAME2.5 and K-computer}, booktitle = {}, year = 2014, } @inproceedings{CTT100666898, author = {Nobuyuki Uchikoga and Yuri Matsuzaki and Masahito Ohue and Takatsugu Hirokawa and Yutaka Akiyama}, title = {Re-docking scheme to explore docking search space by using interaction profiles}, 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{CTT100669689, author = {杉浦典和 and 石田貴士 and 秋山泰 and 関嶋政和}, title = {de Bruijn Graphの分割によるVelvetの消費メモリの低減}, booktitle = {情報処理学会研究報告}, year = 2013, } @inproceedings{CTT100669691, author = {小松祐城 and 石田貴士 and 秋山泰}, title = {拡張されたナイーブベイズを用いたメタゲノム配列の系統分類}, booktitle = {情報処理学会研究報告}, year = 2013, } @inproceedings{CTT100666834, author = {Masahito Ohue and Yuri Matsuzaki and Takehiro Shimoda and Takashi Ishida and Yutaka Akiyama}, title = {Highly precise protein-protein interaction prediction by integrating template-based and template-free protein docking}, booktitle = {}, year = 2013, } @inproceedings{CTT100722750, author = {Yutaka Akiyama}, title = {Development of GPU-accelerated Bioinformatics Application Tools for supporting Drug Discovery: A Case Study in “Drugs for NTDs” Project}, booktitle = {}, year = 2013, } @inproceedings{CTT100669649, author = {石田貴士 and 蓮実梢 and 伴兼弘 and 秋山泰}, title = {NTDs創薬ターゲットタンパク質選択のためのデータベースiNTRODBの開発}, booktitle = {}, year = 2013, } @inproceedings{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{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{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{CTT100876463, author = {Nobuyuki Uchikoga and Yuri Matsuzaki and Masahito Ohue and Takatsugu Hirokawa and Yutaka Akiyama}, title = {Re-docking scheme of protein-protein interactions for generating near-native interaction patterns in difficult docking cases}, booktitle = {}, year = 2013, } @inproceedings{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{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{CTT100666836, author = {Masahito Ohue and Yuri Matsuzaki and Takehiro Shimoda and Takashi Ishida and Yutaka Akiyama}, title = {Highly precise protein-protein interaction prediction by integrating template-based and template-free protein docking}, booktitle = {}, year = 2013, } @inproceedings{CTT100801989, author = {小幡 康文 and 石田貴士 and 夏目 徹 and 秋山泰}, title = {タンデム質量分析ソフトウェアCoCoozoのマルチコアCPUとGPUを用いた高速化}, booktitle = {研究報告数理モデル化と問題解決（MPS）}, year = 2013, } @inproceedings{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{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{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{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{CTT100802049, author = {任 愛珍 and 石田貴士 and 秋山泰}, title = {SDBP: スピーディー・ダブルブートストラップ法に基づいた系統樹の信頼性評価のためのRパッケージ}, booktitle = {研究報告数理モデル化と問題解決（MPS）}, year = 2013, } @inproceedings{CTT100802226, author = {齊藤 有紀 and 石田貴士 and 関嶋 政和 and 秋山泰}, title = {結合自由エネルギー計算を用いた薬物クリアランス経路予測の改善 (ニューロコンピューティング)}, booktitle = {電子情報通信学会技術研究報告 = IEICE technical report : 信学技報}, year = 2013, } @inproceedings{CTT100669693, author = {吉川舜亮 and 石田貴士 and 関嶋政和 and 秋山泰}, title = {Sparse k-mer graphアルゴリズムの評価とVelvetへの実装}, booktitle = {情報処理学会研究報告}, year = 2013, } @inproceedings{CTT100669694, author = {小幡康文 and 石田貴士 and 夏目徹 and 秋山泰}, title = {GPGPUによるタンパク質タンデム質量分析の高速化}, booktitle = {情報処理学会研究報告}, year = 2013, } @inproceedings{CTT100669695, author = {齊藤有紀 and 石田貴士 and 関嶋政和 and 秋山泰}, title = {結合自由エネルギー予測を用いたクリアランス経路予測の改善に関する研究}, booktitle = {情報処理学会研究報告}, year = 2013, } @inproceedings{CTT100666851, author = {大上雅史 and 松崎由理 and 内古閑伸之 and 石田貴士 and 秋山泰}, title = {MEGADOCK：構造ドッキング計算を用いたタンパク質間相互作用の大規模予測}, booktitle = {第13回日本蛋白質科学会年会}, year = 2013, } @inproceedings{CTT100669692, author = {鈴木脩司 and 石田貴士 and 秋山泰}, title = {データベースの部分文字列クラスタリングによるアミノ酸配列相同性検索の高速化}, booktitle = {情報処理学会研究報告}, year = 2013, } @inproceedings{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{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{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{CTT100666852, author = {大上雅史 and 松崎由理 and 内古閑伸之 and 山本航平 and 下田雄大 and 藤原隆之 and 石田貴士 and 秋山泰}, title = {MEGADOCK 3.0：超並列タンパク質間相互作用予測システム}, booktitle = {生命情報科学若手の会 第4回研究会}, year = 2013, } @inproceedings{CTT100658081, author = {Yuri Matsuzaki and Nobuyuki Uchikoga and Masahito Ohue and Takashi Ishida and Yutaka Akiyama}, title = {Protein-protein interaction network prediction by using rigid-body docking tool MEGADOCK}, booktitle = {}, year = 2013, } @inproceedings{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{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{CTT100658550, author = {Yutaka Akiyama}, title = {Large-scale protein-protein interaction network prediction by an exhaustive rigid docking system MEGADOCK}, booktitle = {}, year = 2013, } @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{CTT100722752, author = {秋山 泰}, title = {世界最深度のメタゲノム解析を可能にする超並列パイプラインの開発}, 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{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{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{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{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{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{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{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{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{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{CTT100634030, author = {松崎 由理 and 内古閑 伸之 and 大上 雅史 and 秋山 泰}, 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 = 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{CTT100633809, author = {秋山泰}, title = {スーパーコンピュータが解き明かす生命の不思議}, booktitle = {}, year = 2012, } @inproceedings{CTT100633786, author = {N. Uchikoga and T. Hirokawa and Y. Akiyama}, title = {Post-docking process by using representative interaction fingerprints}, booktitle = {}, 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{CTT100633808, author = {秋山泰}, title = {網羅的タンパク質間相互作用予測ソフトウェア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{CTT100633796, author = {Yutaka Akiyama}, title = {An Ultra-fast Computing Pipeline for Metagenome Analysis on Tsubame 2.0}, booktitle = {}, year = 2011, } @inproceedings{CTT100633798, author = {秋山泰}, title = {機械学習を用いた薬物のクリアランス経路予測}, 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{CTT100633807, author = {秋山泰}, title = {次世代DNAシークエンサデータの超高速解析}, 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{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{CTT100633787, author = {内古閑 伸之 and 松崎 由理 and 大上 雅史 and 広川 貴次 and 秋山 泰}, title = {相互作用プロファイルを用いたタンパク質間ドッキングの代表相互作用の探索}, 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{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{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{CTT100633790, author = {Wisnu Ananta Kusuma and Takashi Ishida and Yutaka Akiyama}, title = {De novo sequence assembly and metagenomic fragments binning}, booktitle = {}, year = 2011, } @inproceedings{CTT100633797, author = {Yutaka Akiyama}, title = {Supercomputing experiences in bioinformatics}, booktitle = {}, year = 2011, } @inproceedings{CTT100633806, author = {秋山泰}, title = {「京」がひらく生命情報解析の扉}, booktitle = {}, year = 2011, } @inproceedings{CTT100625008, author = {池田和史 and 前田和哉 and 尾瀬 淳 and 杉山雄一 and 秋山 泰}, title = {特徴選択とサポートベクターマシンを用いた薬物トランスポーター予測システムの構築}, 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{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{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{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{CTT100806043, author = {Wakayama, Naomi and Toshimoto, Kouta and Hotta, Shun and Maeda, Kazuya and Kusama, Makiko and Imai, Satoki and Yutaka Akiyama and Sugiyama, Yuichi}, title = {Evaluation of a novel in silico prediction method of drug clearance pathways from simple physicochemical parameters}, booktitle = {DRUG METABOLISM REVIEWS}, 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{CTT100622417, author = {Wisnu Ananta Kusuma and Yutaka Akiyama}, title = {Metagenome Fragment Binning Based on Characterization Vectors}, 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{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{CTT100625009, author = {大上雅史 and 松崎由理 and 秋山 泰}, title = {立体構造情報を用いたドッキング計算による大規模タンパク質-RNA間相互作用予測手法}, booktitle = {}, year = 2011, } @inproceedings{CTT100625007, author = {尾渡裕成 and 関嶋政和 and 秋山 泰}, title = {タンパク質-リガンド間の結合性解析の自動パイプライン化}, 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{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{CTT100633804, author = {Yutaka Akiyama}, title = {Exhaustive Protein-Protein Interaction Network Prediction by MEGADOCK}, booktitle = {}, year = 2011, } @inproceedings{CTT100622420, author = {並木洋平 and 秋山泰}, title = {最長共通部分列に基づくDNA配列の高速クラスタリング}, booktitle = {情報処理学会研究報告バイオ情報学(BIO)}, year = 2010, } @inproceedings{CTT100631872, author = {Masahito Ohue and Yuri Matsuzaki and Yutaka Akiyama}, title = {Development of a Protein-RNA Interaction Prediction Method Based on a Docking Calculation}, booktitle = {}, year = 2010, } @inproceedings{CTT100624988, author = {Nobuyuki Uchikoga and Takatsugu Hirokawa and Yutaka Akiyama}, title = {Post-Doking Analysis with Interaction FingerPrint}, booktitle = {}, year = 2010, } @inproceedings{CTT100633803, author = {Yutaka Akiyama}, title = {Exhaustive Protein-Protein Interaction Network Prediction by MEGADOCK}, booktitle = {}, year = 2010, } @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{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{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{CTT100633802, author = {秋山泰}, title = {MEGADOCK: Ultra Fast Structure Based Protein-Protein Interaction Prediction System}, booktitle = {}, year = 2010, } @inproceedings{CTT100624985, author = {Shun Hotta and Kouta Toshimoto and Kazushi Ikeda and Makiko Kusama and Kazuya Maeda and Yuichi Sugiyama and Yutaka Akiyama}, title = {Construction of a web-based system for the prediction of major clearance pathway of drugs from their physicochemical properties}, booktitle = {}, year = 2010, } @inproceedings{CTT100633801, author = {秋山泰}, title = {Large-scale Bioinformatics Applications on Multi-node GPU}, booktitle = {}, year = 2010, } @inproceedings{CTT100624987, author = {Kazushi Ikeda and Kazuya Maeda and Atsushi Ose and Yuichi Sugiyama and Yutaka Akiyama}, title = {In silico prediction of substrates of drug transporters based on support vector machine and feature selection}, booktitle = {}, year = 2010, } @inproceedings{CTT100624984, author = {Naomi Wakayama and Kouta Toshimoto and Shun Hotta and Kazuya Maeda and Makiko Kusama and Satashi Imai and Yutaka Akiyama}, title = {Evaluation of in silico prediction method of drug clearance pathways from simple physicochemical parameters}, booktitle = {}, year = 2010, } @inproceedings{CTT100619146, author = {Matsuzaki Yuri. and Ohue Masahito. and Matsuzaki Yusuke. and Sato Toshuyuki and Akiyama Yutaka}, title = {A computational screening system of protein-protein interactions: connecting protein structural information to biological pathway estimation}, booktitle = {}, year = 2010, } @inproceedings{CTT100876222, author = {大上雅史 and 松崎由理 and 松崎裕介 and 佐藤智之 and 秋山泰}, title = {MEGADOCK：立体構造情報からの網羅的タンパク質間相互作用予測とそのシステム生物学への応用}, booktitle = {情報処理学会論文誌数理モデル化と応用（TOM）}, year = 2010, } @inproceedings{CTT100876469, author = {Masahito Ohue and Yuri Matsuzaki and Yusuke Matsuzaki and Toshiyuki Sato and Yutaka Akiyama}, title = {n silico prediction of PPI network with structure-based all-to-all docking}, booktitle = {}, year = 2010, } @inproceedings{CTT100622418, author = {Wisnu Ananta Kusuma and Yutaka Akiyama}, title = {Design and simulation of hybrid de novo DNA sequence assembly for large eukaryotic genome}, booktitle = {}, 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{CTT100622654, author = {堀田駿 and 年本広太 and 池田和史 and 草間真紀子 and 前田和哉 and 杉山雄一 and 秋山泰}, title = {ウェブアプリケーションによるクリアランス経路予測}, booktitle = {情報処理学会研究報告}, 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{CTT100605237, author = {大上雅史 and 松崎由理 and 松崎裕介 and 佐藤智之 and 秋山泰}, title = {MEGADOCK：立体構造情報からの網羅的タンパク質間相互作用予測とそのシステム生物学への応用}, booktitle = {研究報告数理モデル化と問題解決（MPS）}, 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{CTT100624983, author = {年本 広太 and 草間 真紀子 and 池田 和史 and 堀田 駿 and 前田 和哉 and 杉山 雄一 and 秋山 泰}, title = {SVMを用いた薬物クリアランス経路予測システムの開発―複数経路予測への拡張と外部データによる評価―}, booktitle = {}, year = 2010, } @inproceedings{CTT100604323, author = {秋山 泰}, title = {MEGADOCKの新機能と開発状況}, booktitle = {}, year = 2010, } @inproceedings{CTT100604306, author = {Masahito Ohue and Yusuke Matsuzaki and Yuri Matsuzaki and Toshiyuki Sato and Yutaka Akiyama}, title = {MEGADOCK: An all-to-all protein-protein interaction prediction system -- Improving the accuracy using boosting and binding energy reranking.}, booktitle = {}, year = 2010, } @inproceedings{CTT100604304, author = {Yuri Matsuzaki and Yusuke Matsuzaki and Masahito Ohue and Toshiyuki Sato and Yutaka Akiyama}, title = {A computational screening system of protein-protein interactions: connecting structural information to pathway estimation.}, booktitle = {}, year = 2010, } @inproceedings{CTT100600835, author = {大上雅史 and 松崎裕介 and 松崎由理 and 佐藤智之 and 秋山 泰}, title = {エネルギー計算に基づくリランキングとクラスタリングを用いた網羅的タンパク質間相互作用予測手法の提案}, booktitle = {第2回データ工学と情報マネジメントに関するフォーラム(DEIM2010)}, year = 2010, } @inproceedings{CTT100619307, author = {Takashi Ishida and Yutaka Akiyama}, title = {GPU-Acceleration of de novo Protein Tertiary Structure Prediction}, booktitle = {}, year = 2010, } @inproceedings{CTT100600836, author = {大上雅史 and 松崎裕介 and 松崎由理 and 佐藤智之 and 秋山泰}, title = {リランキングを用いたタンパク質ドッキングの精度向上と網羅的タンパク質間相互作用予測への応用}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2010, } @inproceedings{CTT100604322, author = {松崎裕介 and 大上雅史 and 松崎由理 and 佐藤智之 and 関嶋政和 and 秋山泰}, title = {タンパク質の特性に基づくunboundドッキングのための剛体予測手法の改良}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2010, } @inproceedings{CTT100805951, author = {池田 和史 and 前田 和哉 and 尾瀬 淳 and 杉山 雄一 and 秋山泰}, title = {計算機によるサポートベクターマシンと特徴選択を用いた薬物トランスポーター基質予測}, booktitle = {日本薬物動態学会年会講演要旨集}, year = 2010, } @inproceedings{CTT100805611, author = {若山 直美 and 年本 広太 and 堀田 駿 and 前田 和哉 and 草間 真紀子 and 今井 覚 and 秋山泰 and 杉山 雄一}, title = {薬物排泄経路予測法の評価}, booktitle = {日本薬物動態学会年会講演要旨集}, year = 2010, } @inproceedings{CTT100593788, author = {Masahito Ohue and Yusuke Matsuzaki and Yuri Matsuzaki and Yutaka Akiyama}, title = {Improvement of all-to-all protein-protein interaction prediction system MEGADOCK}, booktitle = {The 20th International Conference on Genome Informatics Workshop Poster Proceedings}, year = 2009, } @inproceedings{CTT100593486, author = {Masahito Ohue and Yusuke Matsuzaki and Yuri Matsuzaki and Yutaka Akiyama}, title = {Improvement of all-to-all protein-protein interaction prediction system MEGADOCK}, booktitle = {Proc. BIOINFO 2009 CBI-KSBSB Joint Conference}, year = 2009, } @inproceedings{CTT100593481, author = {Yusuke Matsuzaki and Yuri Matsuzaki and Masakazu Sekijima and Yutaka Akiyama}, title = {Protein structure sampling based on molecular dynamics and improvement of docking prediction}, booktitle = {Proc. BIOINFO 2009 CBI-KSBSB Joint Conference}, year = 2009, } @inproceedings{CTT100593479, author = {Wisnu Ananta Kusuma and Yutaka Akiyama}, title = {Preliminary Study on de novo Sequence Assembly for Very Short Reads}, booktitle = {Proc. BIOINFO 2009 CBI-KSBSB Joint Conference}, year = 2009, } @inproceedings{CTT100593478, author = {Yuri Matsuzaki and Yusuke Matsuzaki and Masahito Ohue and Toshiyuki Sato and Yutaka Akiyama}, title = {A computational screening system of protein-protein interactions using tertiary structure data: an application to signaling pathway analysis.}, booktitle = {Proc. BIOINFO 2009 CBI-KSBSB Joint Conference}, year = 2009, } @inproceedings{CTT100592858, author = {Kouta Toshimoto and Makiko Kusama and Kazuya Maeda and Yuichi Sugiyama and Yutaka Akiyama}, title = {In Silico Prediction System of Major Drug Clearance Pathways by Feature Selection and Support Vector Machines}, booktitle = {Proc. BIOINFO 2009 CBI-KSBSB Joint Conference}, year = 2009, } @inproceedings{CTT100593490, author = {Kazushi Ikeda and Kouta Toshimoto and Makiko Kusama and Kazuya Maeda and Yuichi Sugiyama and Yutaka Akiyama}, title = {Prediction of Drug Clearance Pathway by Boosting Algorithm}, booktitle = {Proc. BIOINFO 2009 CBI-KSBSB Joint Conference}, year = 2009, } @inproceedings{CTT100593491, author = {Yusei Owatari and Masakazu Sekijima and Yutaka Akiyama}, title = {Binding analysis of neuraminidase inhibitors by fragment MO calculation}, booktitle = {Proc. BIOINFO 2009 CBI-KSBSB Joint Conference}, year = 2009, } @inproceedings{CTT100593493, author = {Shuji Suzuki and Yutaka Akiyama}, title = {Ultra fast short sequence alignment on GPU}, booktitle = {Proc. BIOINFO 2009 CBI-KSBSB Joint Conference}, year = 2009, } @inproceedings{CTT100593494, author = {Shun Hotta and Kouta Toshimoto and Kazushi Ikeda and Makiko Kusama and Kazuya Maeda and Yuichi Sugiyama and Yutaka Akiyama}, title = {A web-based system for clearance pathway prediction}, booktitle = {Proc. BIOINFO 2009 CBI-KSBSB Joint Conference}, year = 2009, } @inproceedings{CTT100593489, author = {Youhei Namiki and Yutaka Akiyama}, title = {Correcting read errors on DNA sequences determined by Pyrosequencing}, booktitle = {Proc. BIOINFO 2009 CBI-KSBSB Joint Conference}, year = 2009, } @inproceedings{CTT100590384, author = {松崎裕介 and 松崎由理 and 関嶋政和 and 秋山泰}, title = {分子動力学法に基づくタンパク質構造サンプリングとドッキング予測の改良}, booktitle = {情報処理学会研究報告}, year = 2009, } @inproceedings{CTT100590410, author = {尾渡裕成 and 関嶋政和 and 秋山泰}, title = {フラグメントMO法によるノイラミニダーゼ阻害薬の結合性解析}, booktitle = {情報処理学会研究報告}, year = 2009, } @inproceedings{CTT100589920, author = {大上雅史 and 松崎裕介 and 松崎由理 and 秋山泰}, title = {網羅的タンパク質間相互作用予測システムにおける判別精度の改良}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2009, } @inproceedings{CTT100589560, author = {Yuri Matsuzaki and Yusuke Matsuzaki and Masahito Ohue and Toshiyuki Sato and Yutaka Akiyama}, title = {In silico screening of protein-protein interactions with all-to-all rigid docking and clustering: an application to pathway analysis}, booktitle = {}, year = 2009, } @inproceedings{CTT100590837, author = {秋山泰}, title = {バイオインフォマティクスは複雑系を説明する}, booktitle = {第61回日本生物工業学会大会講演要旨集}, year = 2009, } @inproceedings{CTT100586434, author = {Yuri Matsuzaki and Yusuke Matsuzaki and Masahito Ohue and Toshiyuki Sato and Yutaka Akiyama}, title = {A computational screening system of protein-protein interactions using tertiary structure data: with application to pathway analysis}, booktitle = {}, year = 2009, } @inproceedings{CTT100723080, author = {秋山 泰}, title = {HPCに支えられてきたバイオインフォマティクス研究}, booktitle = {}, year = 2009, } @inproceedings{CTT100576892, author = {大上雅史 and 松崎裕介 and 松崎由理 and 佐藤智之 and 秋山泰}, title = {物理化学的相互作用の導入による網羅的タンパク質間相互作用予測システムの高精度化}, booktitle = {研究報告バイオ情報学（BIO）}, year = 2009, } @inproceedings{CTT100581870, author = {並木洋平 and 秋山泰}, title = {パイロシーケンシング法で決定されたDNA配列の読み取り誤差の訂正}, booktitle = {情報処理学会バイオ情報学研究会研究報告}, year = 2009, } @inproceedings{CTT100581866, author = {池田和史 and 年本広太 and 草間真紀子 and 前田和哉 and 杉山雄一 and 秋山泰}, title = {ブースティングによる薬物クリアランス経路予測}, booktitle = {情報処理学会バイオ情報学研究会研究報告}, year = 2009, } @inproceedings{CTT100572627, author = {秋山泰}, title = {GPUによる超高速処理～配列マッピングとタンパク質ドッキングへの応用～}, booktitle = {}, year = 2009, } @inproceedings{CTT100572568, author = {松崎 由理 and 松崎 裕介 and 大上雅史 and 佐藤 智之 and 秋山 泰}, title = {ドッキング後処理によるPPI検出システムの応用と評価～EGFRシグナル伝達系への適用にむけて}, booktitle = {}, year = 2009, } @inproceedings{CTT100572628, author = {秋山泰}, title = {バイオインフォマティクスの最新動向 －生物情報解析と音響学の隠れたハーモニー－}, booktitle = {}, year = 2009, } @inproceedings{CTT100571799, author = {Yutaka Akiyama and Toshiyuki Sato and Yusuke Matsuzaki and Yuri Matsuzaki}, title = {Megadock - a rapid screening system for all-to-all protein docking analysis with precalculated fourier library of protein structures}, booktitle = {}, year = 2008, } @inproceedings{CTT100576738, author = {Yuri Matsuzaki and Yusuke Matsuzaki and Toshiyuki Sato and Yutaka Akiyama}, title = {In silico screening method of protein-protein interactions using all-to-all rigid docking and clustering: with application to pathway analysis}, booktitle = {}, year = 2008, } @inproceedings{CTT100575985, author = {Yutaka Akiyama and Takahiro Ide and Fumikazu Konishi}, title = {A GPGPU-based ultra fast computer system for mapping short DNA fragments onto human/mouse full genome sequence}, booktitle = {}, year = 2008, } @inproceedings{CTT100576744, author = {Yutaka Akiyama and Toshiyuki Sato and Yusuke Matsuzaki and Yuri Matsuzaki}, title = {MEGADOCK - A massively parallel software system for all-to-all protein docking analysis with pre-calculated Fourier library of protein structures}, booktitle = {}, year = 2008, } @inproceedings{CTT100571806, author = {Kouta Toshimoto and Kazuya Maeda and Yuichi Sugiyama and Yutaka Akiyama}, title = {Drug clearance pathways prediction system based on machine learning techniques}, booktitle = {}, year = 2008, } @inproceedings{CTT100571802, author = {Yuri Matsuzaki and Yusuke Matsuzaki and Toshiyuki Sato and Yutaka Akiyama}, title = {Virtual screening of protein-protein interactions: an application to known signal transduction systems}, booktitle = {}, year = 2008, } @inproceedings{CTT100571690, author = {Yutaka Akiyama}, title = {Predicting protein-protein interactions with a peta-flops computer: Techniques and potential applications to systems biology research}, booktitle = {}, year = 2008, } @inproceedings{CTT100571810, author = {Kazuya Maeda and Makiko Kusama and Kouta Toshimoto and Yuka Hirai and Satoki Imai and Koji Chiba and Yutaka Akiyama and Yuichi Sugiyama}, title = {Classification of major clearance pathways of drugs based on their physicochemical parameters}, booktitle = {}, year = 2008, } @inproceedings{CTT100571814, author = {Kouta Toshimoto and Makiko Kusama and Kazuya Maeda and Yuichi Sugiyama and Yutaka Akiyama}, title = {In silico prediction of major drug clearance pathways by machine learning techniques}, booktitle = {}, year = 2008, } @inproceedings{CTT100571813, author = {Satoshi Matsuoka and Yutaka Akiyama and Akira Nukada and Toshio Endo and Yasuhiko Ogata and Fumikazu Konishi}, title = {HPC-GPGPU: Large-scale commodity accelerated clusters and its application to advanced structural proteomics}, booktitle = {}, year = 2008, } @inproceedings{CTT100571811, author = {Kouta Toshimoto and Makiko Kusama and Kazuya Maeda and Yuichi Sugiyama and Yutaka Akiyama}, title = {In silico prediction of major drug clearance pathways by machine learning techniques}, booktitle = {}, year = 2008, } @inproceedings{CTT100571727, author = {Makiko Kusama and Kouta Toshimoto and Kazuya Maeda and Yuka Hirai and Satoki Imai and Koji Chiba and Yutaka Akiyama and Yuichi Sugiyama}, title = {Classification of major clearance pathways of drugs based on physicochemical parameters}, booktitle = {}, year = 2008, } @inproceedings{CTT100571812, author = {Yutaka Akiyama and Takahiro Ide and Fumikazu Konishi}, title = {A GPGPU-based ultra fast sequence comparison system for mapping short DNA fragments onto human/mouse full genome sequence}, booktitle = {}, year = 2008, } @inproceedings{CTT100571729, author = {Kouta Toshimoto and Makiko Kusama and Kazuya Maeda and Yuichi Sugiyama and Yutaka Akiyama}, title = {In silico prediction of major drug clearance pathways by machine learning techniques}, booktitle = {}, year = 2008, } @inproceedings{CTT100571732, author = {Makiko Kusama and Kouta Toshimoto and Kazuya Maeda and Yuka Hirai and Satoki Imai and Koji Chiba and Yutaka Akiyama and Yuichi Sugiyama}, title = {Classification of major clearance pathways of drugs based on physicochemical parameters}, booktitle = {}, year = 2008, } @inproceedings{CTT100571816, author = {Yutaka Akiyama and Takahiro Ide and Fumikazu Konishi}, title = {A GPGPU-based ultra fast computer system for mapping short DNA fragments onto human/mouse full genome sequence}, booktitle = {}, year = 2008, } @inproceedings{CTT100571815, author = {Yutaka Akiyama and Toshiyuki Sato and Yusuke Matsuzaki and Yuri Matsuzaki}, title = {Megadock - a rapid screening system for all-to-all protein docking analysis with pre-calculated fourier library of protein structures}, booktitle = {}, year = 2008, } @inproceedings{CTT100571819, author = {Yuri Matsuzaki and Yusuke Matsuzaki and Toshiyuki Sato and Yutaka Akiyama}, title = {Analysis of protein-protein interactions of signal transduction pathways using a docking prediction program}, booktitle = {}, year = 2008, } @inproceedings{CTT100571817, author = {Yusuke Matsuzaki and Yuri Matsuzaki and Toshiyuki Sato and Yutaka Akiyama}, title = {Development of post-docking system for protein-protein interaction prediction}, booktitle = {}, year = 2008, } @inproceedings{CTT100571742, author = {松崎 裕介 and 松崎 由理 and 佐藤 智之 and 秋山 泰}, title = {タンパク質間相互作用予測のためのドッキング後処理システムの開発}, booktitle = {情報処理学会 研究報告}, year = 2008, } @inproceedings{CTT100571821, author = {秋山 泰}, title = {パイロシーケンシング法における読み取りエラー発生シミュレータとその応用}, booktitle = {}, year = 2008, } @inproceedings{CTT100571738, author = {年本 広太 and 草間 真紀子 and 前田 和哉 and 杉山 雄一 and 秋山 泰}, title = {医薬品の物理化学的特性に基づいた薬物動態プロファイリング (II)}, booktitle = {}, year = 2008, } @inproceedings{CTT100575984, author = {小西史一 and 竹本千重 and 赤坂領吾 and 行木信一 and 秋山泰 and 横山茂之 and 豊田哲郎 and 村山和隆}, title = {結晶スクリーニング結果を活用した機械学習による結晶化条件の予測モデルアレイ}, booktitle = {情報処理学会 研究報告}, year = 2008, } @inproceedings{CTT100571734, author = {草間 真紀子 and 平井 由香 and 前田 和哉 and 今井 覚己 and 千葉 康司 and 年本 広太 and 秋山 泰 and 杉山 雄一}, title = {医薬品の物理化学的特性に基づいた薬物動態プロファイリング (I)}, booktitle = {}, year = 2008, } @inproceedings{CTT100571756, author = {年本 広太 and 草間 真紀子 and 前田 和哉 and 杉山 雄一 and 秋山 泰}, title = {機械学習を用いた薬物のクリアランス経路予測}, booktitle = {情報処理学会 研究報告}, year = 2008, } @inproceedings{CTT100571745, author = {松崎 由理 and 松崎 裕介 and 佐藤 智之 and 秋山 泰}, title = {タンパク質ドッキング予測プログラムによるシグナル伝達系のタンパク質間相互作用解析}, booktitle = {情報処理学会 研究報告}, year = 2008, } @inproceedings{CTT100571692, author = {Yutaka Akiyama}, title = {Large scale computing for bioinformatics}, booktitle = {}, year = 2008, } @inproceedings{CTT100571822, author = {Satoshi Matsuoka and Yutaka Akiyama}, title = {HPC-GPGPU: Large-scale commodity accelerated clusters and its application to advanced structural proteomics}, booktitle = {}, year = 2008, } @inproceedings{CTT100571760, author = {松崎 由理 and 松崎 裕介 and 佐藤 智之 and 秋山 泰}, title = {細菌の走化性系への適用によるタンパク質間相互作用予測プログラムの評価}, booktitle = {}, year = 2008, } @inproceedings{CTT100571759, author = {Priyantha Wijayatunga and Yutaka Akiyama}, title = {On protein-protein interaction prediction with yeast two-hybrid experiment data and protein domain associations}, booktitle = {}, year = 2008, } @inproceedings{CTT100571758, author = {秋山 泰 and 松崎 裕介 and 佐藤 智之 and 藤原 康広 and 松崎 由理 and 小西 史一}, title = {形状相補性に基づくタンパク質間相互作用予測ソフトウェアと大規模並列計算機上での網羅的な予測環境の開発}, booktitle = {}, year = 2008, } @inproceedings{CTT100571699, author = {秋山泰}, title = {バイオインフォマティクスと大規模並列処理}, booktitle = {}, year = 2008, } @inproceedings{CTT100571823, author = {秋山 泰}, title = {パイロシーケンシング法における読み取りエラー発生シミュレータとその応用}, booktitle = {}, year = 2008, } @inproceedings{CTT100571829, author = {Yutaka Akiyama}, title = {SimPyro: Pyrosequencing simulation software for analyzing random process with millions of reactions}, booktitle = {}, year = 2007, } @inproceedings{CTT100571826, author = {K Tsukamoto and H Shimizu and T Ishida and Y Akiyama and N Nukina}, title = {Aggregation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations}, booktitle = {}, year = 2007, } @inproceedings{CTT100571828, author = {C Motono and T Hirokawa and Y Sato and K Fujiwara and N Misoo and N Sakaya and K Tomii and Y Akiyama}, title = {An exhaustive modeling and evaluation system in protein 3d structure prediction pipeline FORTE-SUITE}, booktitle = {}, year = 2007, } @inproceedings{CTT100571718, author = {秋山 泰}, title = {バイオインフォマティクスの概要}, booktitle = {}, year = 2007, } @inproceedings{CTT100571762, author = {Masakazu Sekijima and Chie Motono and Yutaka Akiyama and Tamotsu Noguchi}, title = {Free energy landscape analysis of prion protein}, booktitle = {}, year = 2007, } @inproceedings{CTT100571674, author = {Akira Nukada and Yutaka Akiyama}, title = {High performance 3D convolution for protein docking on IBM Blue Gene}, booktitle = {Proc. of the Fifth International Symposium on Parallel and Distributed Processing and Applications (ISPA07)}, year = 2007, } @inproceedings{CTT100571765, author = {秋山 泰}, title = {バイオインフォマティクスとは何か？}, booktitle = {}, year = 2007, } @inproceedings{CTT100571761, author = {秋山 泰}, title = {大規模計算を用いた網羅的なタンパク質相互作用予測への試み}, booktitle = {}, year = 2007, } @inproceedings{CTT100571830, author = {富永 大介 and 油谷 幸代 and 中川 康二 and 孫 富艶 and 堀本 勝久 and 秋山 泰 and 吉田 寛 and 阿久津 達也}, title = {細胞アレイによる時系列データの処理および解析砲の開発}, booktitle = {}, year = 2007, } @inproceedings{CTT100571679, author = {Daisuke Tominaga and Fukumi Iguchi and Yutaka Akiyama and Katsuhisa Horimoto}, title = {Development of automated image processing procedure for cell-arrays}, booktitle = {Proc. of the 11th World Multi-Conference on Systemics, Cybernetics and Informatics}, year = 2007, } @inproceedings{CTT100571768, author = {関嶋 政和 and 土井 淳 and 本田 真也 and 野口 保 and 清水 茂則 and 秋山 泰}, title = {大規模分子動力学シミュレーションによる自由エネルギー地形解析システムの開発タンパク質間相互作用予測のためのドッキング後処理システムの開発}, booktitle = {情報処理学会 研究報告}, year = 2007, } @inproceedings{CTT100571779, author = {秋山 泰 and 堀本 勝久 and 富永 大介 and 油谷 幸代 and 中川 康二 and 孫 富艶}, title = {細胞アレイ計測に基づくアポトーシス関連ネットワーク解析}, booktitle = {}, year = 2007, } @inproceedings{CTT100571714, author = {秋山 泰}, title = {システム生物学と創薬}, booktitle = {}, year = 2007, } @inproceedings{CTT100571706, author = {Yutaka Akiyama and Koki Tsukamoto and Yuichiro Hourai and Tatsuya Yoshikawa}, title = {PPPDock: a parallelized protein-protein docking software toward a challenge to all-to-all protein docking study}, booktitle = {}, year = 2007, } @inproceedings{CTT100571702, author = {Yutaka Akiyama}, title = {Protein structure prediction and compound docking study on massively parallel computers}, booktitle = {}, year = 2007, } @inproceedings{CTT100571785, author = {富永 大介 and 井口 富久美 and 堀本 勝久 and 秋山 泰}, title = {細胞アレイのための大規模画像処理システムの開発}, booktitle = {情報処理学会 研究報告}, year = 2007, } @inproceedings{CTT100571791, author = {Masakazu Sekijima and Chie Motono and Yutaka Akiyama and Tamotsu Noguchi}, title = {Free energy landscape analysis of prion protein}, booktitle = {}, year = 2007, } @inproceedings{CTT100507849, author = {Sekijima, M. and Doi, J. and Noguchi, T. and Akiyama, Y. and Shimizu, S.}, title = {Optimization and Evaluation of Parallel Molecular Dynamics Simulation on Blue Gene/L}, booktitle = {Proc. the IASTED Int'l Conf. on Parallel and Distributed Computing and Networks (PDCN2007)}, year = 2007, } @inproceedings{CTT100507950, author = {関嶋政和 and 本田真也 and 本野千恵 and 秋山 泰 and 野口 保}, title = {大規模分子動力学シミュレーションによる生体分子の自由エネルギー地形解析}, booktitle = {平成18年度ライフサイエンス分野融合会議 生命工学部会バイオテクノロジー研究会 合同研究発表会・講演会予稿集}, year = 2007, } @inproceedings{CTT100507949, author = {吉川達也 and 塚本弘毅 and 蓬来祐一郎 and 藤原康広 and 秋山 泰}, title = {PPPDock: Protein-Protein docking system using a high-performance FFT algorithm on BlueGene (BlueProtein),}, booktitle = {平成18年度ライフサイエンス分野融合会議 生命工学部会バイオテクノロジー研究会 合同研究発表会・講演会要旨集}, year = 2007, } @inproceedings{CTT100507948, author = {本野千恵 and 藤原康広 and 佐藤美和 and 酒谷尚文 and 富井健太郎 and 広川貴次 and 秋山 泰}, title = {タンパク質立体構造予測における網羅的モデリング・構造評価システムの並列化}, booktitle = {平成18年度ライフサイエンス分野融合会議 生命工学部会バイオテクノロジー研究会 合同研究発表会・講演会予稿集}, year = 2007, } @inproceedings{CTT100507947, author = {秋山 泰 and 堀本勝久 and 富永大介 and 油谷幸代 and 中川康二 and 孫 富艶}, title = {トランスフェクション・マイクロアレイによる生細胞観察のための大規模全自動画像処理システムの開発}, booktitle = {平成18年度ライフサイエンス分野融合会議 生命工学部会バイオテクノロジー研究会 合同研究発表会・講演会予稿集}, year = 2007, } @inproceedings{CTT100571684, author = {Masakazu Sekijima and Jun Doi and Tamotsu Noguchi and Yutaka Akiyama and Shigenori Shimizu}, title = {Optimization and evaluation of parallel molecular dynamics simulation on blue gene/l}, booktitle = {Proc. of the IASTED International Conference on Parallel and Distributed Computer and Networks (PDCN2007)}, year = 2007, } @inproceedings{CTT100507946, author = {秋山泰}, title = {大規模計算によるタンパク質立体構造解析と創薬支援}, booktitle = {第3回未来ソリューション・フォーラム予稿集}, year = 2006, } @inproceedings{CTT100507945, author = {Tomii, K. and Motono, C. and Sato, M. and Ota, M. and Hirokawa, T. and Horton, P. and Akiyama, Y.}, title = {Andante - Tertiary Structure Prediction of CASP7 Targets Using Exhaustive Modeling and Evaluation}, booktitle = {Proc. of Critical Assesment of Techniques for Protein Structure Prediction Seventh Meeting (CASP7)}, year = 2006, } @inproceedings{CTT100507943, author = {Akiyama, Y. and Tsukamoto, K. and Yoshikawa, T.}, title = {A New Protein-Protein Docking Algorithm and a Challenge for All-to-All Protein Docking Study}, booktitle = {Proc. 2nd Taiwan-Japan Bilateral Symposium on Bioinformatics}, year = 2006, } @inproceedings{CTT100507954, author = {Yutaka Akiyama}, title = {OdaibaDock: Protein-Protein Docking System using a high-performance FFT algorithm on BlueGene/L}, booktitle = {Proc. Fifth East Asian Biophysics Symposium & Fourty-Fourth Annual Meeting of the Biophysical Society of Japan (EABS & BSJ2006), 2P447}, year = 2006, } @inproceedings{CTT100507942, author = {福井一彦 and 高橋勝利 and 秋山 泰}, title = {実験とシミュレーションによる中赤外自由電子レーザーを用いたフラグメント解析}, booktitle = {CBRC 2006予稿集　G6}, year = 2006, } @inproceedings{CTT100507941, author = {塚本弘毅 and 清水英明 and 石田貴士 and 秋山 泰 and 貫名信行}, title = {CAGリピート病におけるポリグルタミン領域のアグリゲーションメカニズムの解析}, booktitle = {CBRC 2006 予稿集 G5}, year = 2006, } @inproceedings{CTT100507940, author = {吉川達也 and 塚本弘毅 and 蓬来祐一郎 and 真下忠彰 and 秋山 泰}, title = {超並列計算機BlueGene(BlueProtein)を用いた大規模タンパク質ドッキングシステムの開発}, booktitle = {CBRC 2006 予稿集 G3}, year = 2006, } @inproceedings{CTT100507939, author = {本野千恵 and 藤原康広 and 三十尾潔高 and 佐藤美和 and 酒谷尚文 and 富井健太郎 and 広川貴次 and 秋山 泰}, title = {タンパク質立体構造予測システムFORTE-SUITEの自動化・並列化}, booktitle = {CBRC 2006 予稿集 G2}, year = 2006, } @inproceedings{CTT100507936, author = {富井健太郎 and 本野千恵 and 佐藤美和 and 太田元規 and 酒谷尚文 and 藤原康広 and 三十尾潔高 and 広川貴次 and Paul Horton and 秋山 泰}, title = {立体構造予測実験CASP7に対するとり組み}, booktitle = {CBRC 2006 予稿集 B5}, year = 2006, } @inproceedings{CTT100507935, author = {秋山 泰}, title = {タンパク質立体構造およびタンパク質間ドッキングの計算機予測へ向けて}, booktitle = {}, year = 2006, } @inproceedings{CTT100507925, author = {秋山 泰}, title = {バイオインフォマティクスによる大規模情報解析の最前線}, booktitle = {}, year = 2006, } @inproceedings{CTT100507926, author = {秋山泰}, title = {生命の謎と算数パズル}, booktitle = {}, year = 2006, } @inproceedings{CTT100507867, author = {Akiyama, Y.}, title = {Computer prediction of protein tertiary structures and protein-protein interactions}, booktitle = {Prof. of Third International Conference on Genomics, Proteomics, Bioinformatics and Nanotechnologies for Medicine}, year = 2006, } @inproceedings{CTT100507933, author = {秋山 泰 and 藤渕 航}, title = {mRNAの網羅的発現データを対象としたバイオインフォマティクス解析プラットフォームの構築}, booktitle = {}, year = 2006, } @inproceedings{CTT100507866, author = {Akiyama, Y.}, title = {Building a Supercomputing Pipeline from Genome Sequence to Protein Structure and Drug Design}, booktitle = {Proc. of the Eleventh "Science in Japan" Forum}, year = 2006, } @inproceedings{CTT100507934, author = {Akiyama, Y. and Fujibuchi, W.}, title = {Sequence identification and expression pattern analysis system for single cell mRNA analysis}, booktitle = {Proc. The 1st International Workshop on Approaches to Single-Cell Analysis}, year = 2006, } @inproceedings{CTT100507932, author = {秋山 泰}, title = {細胞内mRNAの網羅的計測を支援するデータ処理ソフトウェアの開発}, booktitle = {第３回ライフサーベイヤシンポジウム講演予稿集}, year = 2006, } @inproceedings{CTT100507930, author = {Akiyama, Y.}, title = {Life Sciences at AIST: Achievements and Outlook - Building a Supercomputing Pipeline from Genome Sequences to Drug Discovery}, booktitle = {Global Grid Form GGF17}, year = 2006, } @inproceedings{CTT100507931, author = {秋山 泰}, title = {並列バイオインフォマティクス：オームワイドな網羅計算への挑戦}, booktitle = {}, year = 2006, } @inproceedings{CTT100507928, author = {Akiyama, Y.}, title = {Toward a Computational Pipeline from Genome Sequence to Protein Structures and Molecular Docking Study}, booktitle = {Proc. The First Japan-Taiwan Bilateral Symposium on Bioinformatics}, year = 2006, } @inproceedings{CTT100507957, author = {秋山 泰 and 藤原康広 and 中山 洋 and 夏目 徹}, title = {大規模プロテオミクス研究向け質量分析エンジンCoCoozoの改良}, booktitle = {平成17年度ライフサイエンス分野融合会議 生命工学部会バイオテクノロジー研究会 合同研究発表会・講演会要旨集}, year = 2006, } @inproceedings{CTT100507955, author = {福井一彦 and 秋山 泰 and 高橋勝利}, title = {波長可変レーザーを用いた糖鎖・糖ペプチドの赤外多光子励起}, booktitle = {平成17年度ライフサイエンス分野融合会議 生命工学部会バイオテクノロジー研究会 合同研究発表会・講演会要旨集}, year = 2006, } @inproceedings{CTT100507956, author = {向井有理 and 広川貴次 and 富井健太郎 and 浅井 潔 and 秋山 泰 and 諏訪牧子}, title = {GGtraP:ゴルジ膜貫通領域に注目した糖転移酵素検出ツール}, booktitle = {平成17年度ライフサイエンス分野融合会議 生命工学部会バイオテクノロジー研究会 合同研究発表会・講演会要旨集}, year = 2006, } @inproceedings{CTT100507863, author = {Akiyama, Y.}, title = {From Genome Sequence to Protein Structure and Drug Discovery: a computational pipeline with bioinformatics and supercomputing}, booktitle = {}, year = 2005, } @inproceedings{CTT100507864, author = {Akiyama, Y.}, title = {e-Drug Discovery related projects in Japan and CBRC’s strategies for e-Drug Discovery}, booktitle = {}, year = 2005, } @inproceedings{CTT100507862, author = {Akiyama, Y.}, title = {From bioinformatics to computational biology: aligning, clustering, fitting, toward simulating}, booktitle = {}, year = 2005, } @inproceedings{CTT100507861, author = {Akiyama, Y.}, title = {Building a High-Performance Computing Pipeline from Genome Sequence to Protein Structure and Drug Discovery}, booktitle = {}, year = 2005, } @inproceedings{CTT100723081, author = {秋山 泰}, title = {大規模並列計算を利用した遺伝情報解析支援}, booktitle = {}, year = 2004, } @inproceedings{CTT100507860, author = {Akiyama, Y.}, title = {Large-scale Parallel Computing for Bioinformatics}, booktitle = {}, year = 2004, } @inproceedings{CTT100507859, author = {Akiyama, Y.}, title = {Bioinformatics research activity at CBRC - Deep computing with a 1040-CPU PC cluster}, booktitle = {}, year = 2003, } @inproceedings{CTT100507854, author = {Akiyama, Y.}, title = {Large-scale parallel computing for systematic biological analysis}, booktitle = {}, year = 2003, } @inproceedings{CTT100507858, author = {Akiyama, Y.}, title = {Gene Finding and Approaches to Protein Structure Prediction}, booktitle = {}, year = 2002, } @inproceedings{CTT100507850, author = {Akiyama, Y.}, title = {Bioinformatics research project using a 1040-cpu PC cluster and expectation for GRID technology}, booktitle = {}, year = 2002, } @inproceedings{CTT100507853, author = {Akiyama, Y.}, title = {Bioinformatics approaches to Human Genome analysis}, booktitle = {}, year = 2002, } @inproceedings{CTT100507857, author = {Yutaka Akiyama}, title = {Bioinformatics Research at CBRC using a 1040-processors PC Cluster}, booktitle = {}, year = 2001, } @inproceedings{CTT100507847, author = {Ando, M. and Akiyama Y. and Matsuda, H.}, title = {ESCAPE 2.0: Parallel Exhaustive Conformational Search System of Peptides with Conformational Libraries as Building Blocks}, booktitle = {Proc. the Fourth International Conference on High-Performance Computing in Asia-Pacific Region (HPC-Asia 2000)}, year = 2000, } @inproceedings{CTT100507848, author = {Misoo, K. and Akiyama, Y. and Shizawa Y. and Saito, M.}, title = {Development of Molecular Dynamics Programs for Protein with a Parallelized Barnes-Hut Code}, booktitle = {Proc. the Fourth International Conference on High-Performance Computing in Asia-Pacific Region (HPC-Asia 2000)}, year = 2000, } @inproceedings{CTT100507846, author = {Akiyama, Y. and Onizuka, K. and Noguchi, T. and Ando, M.}, title = {Parallel Protein Information Analysis (PAPIA) system running on a 64-node PC Cluster}, booktitle = {Proc. of 5th Int'l Conf. on Artificial Life and Robotics}, year = 2000, } @inproceedings{CTT100507845, author = {Ando, M. and Akiyama, Y. and Onizuka, K. and Noguchi, T.}, title = {ESCAPE: Parallel Tree Search System for Conformational Analysis of Peptides}, booktitle = {Proc. the 1999 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'99)}, year = 1999, } @inproceedings{CTT100507746, author = {三十尾潔高 and 志澤由久 and 秋山 泰 and 斎藤 稔}, title = {並列化Barnes-Hut tree codeを用いた高精度なタンパク質分子動力学法プログラムの開発}, booktitle = {並列処理シンポジウムJSPP'99 論文集}, year = 1999, } @inproceedings{CTT100507728, author = {Akiyama, Y. and Onizuka, K. and Noguchi, T and Ando, M.}, title = {Parallel Protein Information Analysis (PAPIA) system running on a 64-node PC Cluster}, booktitle = {Genome Informatics}, year = 1998, } @inproceedings{CTT100507743, author = {斉藤 稔 and 三十尾潔高 and 志澤由久 and 丸川一志 and 秋山 泰 and 野口 保 and 鬼塚健太郎}, title = {分子動力学法プログラムAMBERとBarnes-Hut tree codeの並列化による高速化}, booktitle = {並列処理シンポジウム JSPP'98論文集}, year = 1998, } @inproceedings{CTT100507844, author = {Akiyama Y.}, title = {Development of Biological and Chemical Applications on a 64-node PC Cluster}, booktitle = {Proc. Int'l Workshop on Innovative Architectures (IWIA'98)}, year = 1998, } @inproceedings{CTT100507843, author = {Ando, M. and Tanaka, Y. and Kubota, K. and Matsuda, M. and Akiyama, Y. and Sato, M.}, title = {Performance Characterization of Shared- and Distributed-Memory Multiprocessors on a Tree Search Problem}, booktitle = {Proc. 3rd High Performance Computing Asia (HPC-Asia’98)}, year = 1998, } @inproceedings{CTT100507841, author = {Fujibuchi, W. and Goto, S. and Migimatsu, H. and Uchiyama, I. and Ogiwara, A. and Akiyama, Y. and Kanehisa, M.}, title = {DBGET/LinkDB: an Integrated Database Retrieval System}, booktitle = {Proc. of PSB'98}, year = 1998, } @inproceedings{CTT100507742, author = {Akiyama, Y. and Misoo, K. and Omura, Y. and Matsumoto, H. and Saito, M. and Noguchi, T. and Onizuka, K.}, title = {Parallelization of Space Plasma Particle Simulation}, booktitle = {Lecture Notes on Computer Science}, year = 1997, } @inproceedings{CTT100507839, author = {Noguchi, T. and Onizuka, K. and Akiyama, Y. and Saito, M.}, title = {PDB-REPRDB: A Database of Representative Protein Chains in PDB (Protein Data Bank)}, booktitle = {Proc. the fifth Int'l Conf. on Intelligent Systems for Molecular Biology (ISMB’97), pp.214-217}, year = 1997, } @inproceedings{CTT100507855, author = {Akiyama, Y. and Goto, S. and Uchiyama, I. and Kanehisa, M.}, title = {WebDBGET: An Integrated Database Retrieval System which provides HyperLinks among Related Entries}, booktitle = {}, year = 1995, } @inproceedings{CTT100507725, author = {Araki, S. and Goshima, M. and Mori, S. and Nakashima, H. and Akiyama, Y. and Kanehisa, M.}, title = {Application of Parallelized DP and A* Algorithm to Multiple Sequence Alignment}, booktitle = {Genome Informatics}, year = 1993, } @inproceedings{CTT100507724, author = {Akiyama, Y. and Mori, H. and Kuhara, S. and Ogasawara, N. and Miyajima, N. and Furukawa, T. and Sato, K. and Murakami, Y.}, title = {Genomatica: an Integrated Data Management and Analysis Tool for Genome Sequencing Projects}, booktitle = {Genome Informatics}, year = 1993, } @inproceedings{CTT100507717, author = {秋山 泰 and 古谷立美}, title = {ホップフィールド型ニューラルネットにおける制約の動的な制御の効果}, booktitle = {並列処理シンポジウムJSPP'91 論文集}, year = 1991, } @inproceedings{CTT100507837, author = {Kajiura, M. and Akiyama, Y. and Anzai, Y.}, title = {Solving Large-scale Puzzles with Neural Networks}, booktitle = {Proc. of IEEE Int'l Workshop on Tools for Artificial Intelligence (TAI’89)}, year = 1989, } @inproceedings{CTT100507838, author = {Akiyama, Y. and Yamashita, A. and Kajiura, M. and Anzai, Y. and Aiso, H.}, title = {Gaussian Machines: A Stochastic Neural Network Model for Solving Assignment Problems}, booktitle = {Proc. of ACM 5th Aerospace Applications of Artificial Intelligence Conference (AAAIC’89)}, year = 1989, } @inproceedings{CTT100507836, author = {Akiyama, Y. and Yamashita, A. and Kajiura, M. and Aiso, H.}, title = {Combinatorial Optimization with Gaussian Machines}, booktitle = {Proc. of 1989 Int'l Joint Conf. on Neural Networks (IJCNN’89)}, year = 1989, } @inproceedings{CTT100507835, author = {Akiyama, Y. and Takefuji, Y. and Aiso, H.}, title = {Conductance Programmable ‘Neural' Chips Employing Switched Resistors}, booktitle = {Proc. of 1988 Joint Technical Conference on Circuits /Systems, Computers and Communications (JTC-CSCC’88)}, year = 1988, } @misc{CTT100920691, author = {赤木 果歩 and 柳澤 渓甫 and 秋山 泰}, title = {共溶媒分子動力学法による化合物ドッキング向けのバイアス情報の取得}, year = 2024, } @misc{CTT100920690, author = {清水 正義 and 柳澤 渓甫 and 秋山 泰}, title = {有望なフラグメント空間配置対に基づく化合物プレスクリーニング手法の開発}, year = 2024, } @misc{CTT100920694, author = {布部 絢子 and 柳澤 渓甫 and 秋山 泰}, title = {フラグメントに基づくバーチャルスクリーニングへの利用などを目指したフラグメント集合の選定}, year = 2024, } @misc{CTT100893466, author = {齋藤那哉 and 柳澤渓甫 and 秋山 泰}, title = {フラグメント対の相対位置から検索可能な化合物立体配座データベースの構築}, year = 2023, } @misc{CTT100893465, author = {渡辺銀河 and 柳澤渓甫 and 秋山 泰}, title = {標的RNAの高次構造予測に基づく低活性ASO候補配列の推測}, year = 2023, } @misc{CTT100851590, author = {大上雅史 and 林孝紀 and 秋山泰}, title = {タンパク質間相互作用と複合体構造の予測結果を検索できるウェブサイト「MEGADOCK-Web」}, year = 2019, } @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{CTT100619147, author = {Yutaka Akiyama and Yuri Matsuzaki and Nobuyuki Uchikoga and Masahito Ohue}, title = {Exhaustive protein-protein interaction network prediction by using MEGADOCK}, year = 2010, } @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, } @misc{CTT100571687, author = {秋山泰}, title = {バイオインフォマティクス}, year = 2007, } @misc{CTT100507923, author = {阿久津達也 and 秋山 泰}, title = {バイオインフォマティクスと人工知能の相互作用}, year = 2007, } @misc{CTT100507921, author = {向井有理 and 広川貴次 and 富井健太郎 and 諏訪牧子 and 浅井潔 and 成松久 and 秋山 泰}, title = {バイオインフォマティクスによる糖転移酵素遺伝子の発見}, year = 2006, } @misc{CTT100507920, author = {秋山 泰}, title = {Erwin Schroedinger: What is Life?}, year = 2006, } @misc{CTT100507915, author = {秋山 泰}, title = {生命科学と超高速コンピュータシステム}, year = 2005, } @misc{CTT100507919, author = {秋山 泰}, title = {バイオインフォマティクス研究者スキル}, year = 2005, } @misc{CTT100507918, author = {秋山 泰}, title = {バイオインフォマティクス―生物学と情報科学の学際分野にて}, year = 2005, } @misc{CTT100507914, author = {秋山 泰}, title = {超高速計算機で分子シミュレーションの壁を砕く}, year = 2004, } @misc{CTT100507911, author = {秋山 泰}, title = {バイオインフォマティクスが必要とする計算機環境}, year = 2003, } @misc{CTT100507909, author = {秋山 泰}, title = {生命情報科学研究センターとバイオインフォマティクス研究}, year = 2002, } @misc{CTT100507906, author = {秋山 泰}, title = {生命情報科学と大規模PCクラスタ －Pentium系で世界一の654GFlopsを達成－}, year = 2001, } @misc{CTT100507905, author = {秋山 泰}, title = {日本初のコンピューテーショナルバイオロジー研究施設　お台場に始動}, year = 2001, } @misc{CTT100507908, author = {秋山 泰}, title = {バイオインフォマティクス}, year = 2001, } @misc{CTT100507894, author = {秋山 泰}, title = {ニューラルネットワークによる最適化計算}, year = 2000, } @misc{CTT100507904, author = {秋山 泰}, title = {大規模並列計算機によるタンパク質情報解析}, year = 2000, } @misc{CTT100507903, author = {秋山 泰}, title = {バイオインフォマティクス～情報システムとしての生命現象の理解へ～}, year = 1999, } @misc{CTT100507901, author = {秋山 泰}, title = {パソコンクラスタを用いた超高速タンパク質情報解析システム}, year = 1998, } @misc{CTT100507902, author = {秋山 泰}, title = {並列タンパク質情報解析(PAPIA)システム}, year = 1998, } @misc{CTT100507900, author = {秋山 泰}, title = {ＷＷＷによる研究支援}, year = 1996, } @misc{CTT100507899, author = {秋山 泰 and 金久 實}, title = {ゲノムネットのデータベース・サービス}, year = 1995, } @misc{CTT100507897, author = {秋山 泰}, title = {RNAの二次構造予測}, year = 1993, } @misc{CTT100507726, author = {秋山 泰}, title = {二次構造を予測する}, year = 1993, } @misc{CTT100507895, author = {秋山 泰}, title = {ボルツマンマシン}, year = 1991, } @misc{CTT100507718, author = {秋山泰}, title = {ニューラルネットワークのハードウェア}, year = 1991, } @misc{CTT100507893, author = {秋山 泰}, title = {ガウシアンマシンと巡回セールスマン問題}, year = 1990, } @misc{CTT100507892, author = {梶浦正浩 and 秋山 泰}, title = {ボルツマンマシンとNクイーン問題}, year = 1990, } @misc{CTT100507890, author = {秋山 泰}, title = {ニューラルネットの新モデルを構築－重みづけを自由にかえられるニューロチップも開発}, year = 1988, } @misc{CTT100596480, author = {Yutaka Akiyama}, title = {The Gaussian Machine: A Stochastic, Continuous Neural Network Model}, year = 1990, } @misc{CTT100507958, author = {Yutaka Akiyama}, title = {The Gaussian Machine: A Stochastic, Continuous Neural Network Model}, year = 1990, } @misc{CTT100880495, author = {秋山泰 and 大上雅史 and 柳澤渓甫 and 吉川寧 and 李佳男}, title = {予測装置、学習済みモデルの生成装置、予測方法、学習済みモデルの生成方法、予測プログラム、及び学習済みモデルの生成プログラム}, howpublished = {登録特許}, year = 2022, month = {}, note = {特願2021-035648(2021/03/05), 特許第7057004号(2022/04/11)} } @misc{CTT100881800, author = {秋山泰 and 大上雅史 and 柳澤渓甫 and 吉川寧}, title = {情報処理装置、情報処理方法、情報処理プログラム、及び情報処理システム}, howpublished = {登録特許}, year = 2022, month = {}, note = {特願2021-023750(2021/02/17), 特開2022-078924(2022/05/25), 特許第7125575号(2022/08/17)} } @misc{CTT100880496, author = {秋山泰 and 大上雅史 and 柳澤渓甫 and 吉川寧 and 杉田昌岳 and 藤江　拓哉 and 杉山聡 and 村田翔太朗}, title = {予測装置、学習済みモデルの生成装置、予測方法、学習済みモデルの生成方法、予測プログラム、及び学習済みモデルの生成プログラム}, howpublished = {登録特許}, year = 2022, month = {}, note = {特願2021-031234(2021/02/26), 特許第7057003号(2022/04/11)} } @phdthesis{CTT100596480, author = {Yutaka Akiyama}, title = {The Gaussian Machine: A Stochastic, Continuous Neural Network Model}, school = {慶應義塾大学}, year = 1990, } @phdthesis{CTT100507958, author = {Yutaka Akiyama}, title = {The Gaussian Machine: A Stochastic, Continuous Neural Network Model}, school = {}, year = 1990, }