@book{CTT100851593,
  author = {大上雅史},
  title = {学振申請書の書き方とコツ DC/PD獲得を目指す若者へ 改訂第２版},
  publisher = {講談社},
  year = 2021,
}

@book{CTT100851594,
  author = {生化学若い研究者の会 and 大上雅史},
  title = {核酸の生化学（第8章）},
  publisher = {秀和システム},
  year = 2021,
}

@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{CTT100715107,
  author = {大上雅史},
  title = {学振申請書の書き方とコツ DC/PD獲得を目指す若者へ},
  publisher = {講談社},
  year = 2016,
}

@book{CTT100715109,
  author = {生化学若い研究者の会 and 大上雅史},
  title = {核酸の生化学（第8章）},
  publisher = {秀和システム},
  year = 2014,
}

@article{CTT100925857,
  author = {Wexing Hu and Masahito Ohue},
  title = {SpatialPPI:three-dimensional space protein-protein interaction prediction with AlphaFold Multimer},
  journal = {Computational and Structural Biotechnology Journal},
  year = 2024,
}

@article{CTT100925850,
  author = {Apakorn Kengkanna and Masahito Ohue},
  title = {Enhancing property and activity prediction and interpretation using multiple molecular graph representations with MMGX},
  journal = {Communications Chemistry},
  year = 2024,
}

@article{CTT100925852,
  author = {Masahito Ohue and Kotoyu Sasayama and Masami Takata},
  title = {Mathematical Modeling and Problem Solving: From Fundamentals to Applications},
  journal = {The Journal of Supercomputing},
  year = 2024,
}

@article{CTT100925853,
  author = {Masahito Ohue and Kairi Furui},
  title = {FastLomap: Faster Lead Optimization Mapper Algorithm for Large- Scale Relative Free Energy Perturbation},
  journal = {The Journal of Supercomputing},
  year = 2024,
}

@article{CTT100925854,
  author = {Takafumi Ueki and Masahito Ohue},
  title = {Antibody Complementarity-Determining Region Design using AlphaFold2 and DDG Predictor},
  journal = {The Journal of Supercomputing},
  year = 2024,
}

@article{CTT100925860,
  author = {Toshiki Ochiai and Tensei Inukai and Manato Akiyama and Kairi Furui and Masahito Ohue and Nobuaki Matsumori and Shinsuke Inuki and Motonari Uesugi and Toshiaki Sunazuka and Kazuya Kikuchi and Hideaki Kakeya and Yasubumi Sakakibara},
  title = {Variational autoencoder-based chemical latent space for large molecular structures with 3D complexity},
  journal = {Communications Chemistry},
  year = 2023,
}

@article{CTT100925861,
  author = {Masahito Ohue},
  title = {MEGADOCK-on-Colab: an easy-to-use protein-protein docking tool on Google Colaboratory},
  journal = {BMC Research Notes},
  year = 2023,
}

@article{CTT100925862,
  author = {Takatsugu Kosugi and Masahito Ohue},
  title = {Design of cyclic peptides targeting protein–protein interactions using AlphaFold},
  journal = {International Journal of Molecular Sciences},
  year = 2023,
}

@article{CTT100925863,
  author = {Masahito Ohue and Yuki Kojima and Takatsugu Kosugi},
  title = {Generating potential protein-protein interaction inhibitor molecules based on physicochemical properties},
  journal = {Molecules},
  year = 2023,
}

@article{CTT100925864,
  author = {Jessica Andreani and Brain Jiménez-García and Masahito Ohue},
  title = {Web Tools for Modeling and Analysis of Biomolecular Interactions Volume II},
  journal = {Frontiers in Molecular Biosciences},
  year = 2023,
}

@article{CTT100925870,
  author = {Jianan Li and Keisuke Yanagisawa and Masatake Sugita and Takuya Fujie and Masahito Ohue and Yutaka Akiyama},
  title = {CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides},
  journal = {Journal of Chemical Information and Modeling},
  year = 2023,
}

@article{CTT100893464,
  author = {Jianan Li and Keisuke Yanagisawa and Masatake Sugita and Takuya Fujie and Masahito Ohue and Yutaka Akiyama},
  title = {CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides},
  journal = {Journal of Chemical Information and Modeling},
  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{CTT100883503,
  author = {Takatsugu Kosugi and Masahito Ohue},
  title = {Solubility-aware protein binding peptide design using AlphaFold},
  journal = {Biomedicines},
  year = 2022,
}

@article{CTT100925878,
  author = {Jessica Andreani and Masahito Ohue and Brain Jiménez-García},
  title = {Web Tools for Modeling and Analysis of Biomolecular Interactions},
  journal = {Frontiers in Molecular Biosciences},
  year = 2022,
}

@article{CTT100863265,
  author = {Yoshio Ri 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{CTT100876137,
  author = {Takatsugu Kosugi and Masahito Ohue},
  title = {Quantitative Estimate Index for Early-Stage Screening of Compounds Targeting Protein-Protein Interactions},
  journal = {International Journal of Molecular Sciences},
  year = 2021,
}

@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{CTT100839065,
  author = {Sho Ito and Akinobu Senoo and Satoru Nagatoishi and Masahito Ohue and Masaki Yamamoto and Kouhei Tsumoto and Naoki Wakui},
  title = {Structural basis for binding mechanism of human serum albumin complexed with cyclic peptide dalbavancin},
  journal = {Journal of Medicinal Chemistry},
  year = 2020,
}

@article{CTT100839067,
  author = {Guillaume Launay and Masahito Ohue and Julia Prieto Santero and Yuri Matsuzaki and Cécile Hilpert and Nobuyuki Uchikoga and Takanori Hayashi and Juliette Martin},
  title = {Evaluation of CONSRANK-like scoring functions for rescoring ensembles of protein-protein docking poses},
  journal = {Frontiers in Molecular Biosciences},
  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{CTT100851458,
  author = {Koki Yamamoto and Yasushi Yoshikawa and Masahito Ohue and Shinsuke Inuki and Hiroaki Ohno and Shinya Oishi},
  title = {Synthesis of Triazolo- and Oxadiazolopiperazines by Gold(I)-Catalyzed Domino Cyclization: Application to the Design of a Mitogen Activated Protein (MAP) Kinase Inhibitor},
  journal = {Organic Letters},
  year = 2018,
}

@article{CTT100851475,
  author = {Daisuke Kami and Tomoya Kitani and Akihiro Nakamura and Naoki Wakui and Rena Mizutani and Masahito Ohue and Fuyuki Kametani and Nobuyoshi Akimitsu and Satoshi Gojo},
  title = {The DEAD-box RNA-binding protein DDX6 regulates parental RNA decay for cellular reprogramming to pluripotency},
  journal = {PLOS ONE},
  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{CTT100783049,
  author = {Wakui, N. and Yoshino, R. and Yasuo, N. and Ohue, M. and Sekijima, M.},
  title = {Exploring the selectivity of inhibitor complexes with Bcl-2 and Bcl-XL: A molecular dynamics simulation approach},
  journal = {Journal of Molecular Graphics and Modelling},
  year = 2018,
}

@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{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{CTT100715180,
  author = {根岸瑠美 and 大上雅史},
  title = {そもそも「ポスドク問題」ってなんだろう？男女共同参画・若手支援シンポジウム報告},
  journal = {生物物理},
  year = 2016,
}

@article{CTT100715181,
  author = {大上雅史 and 根岸瑠美},
  title = {「鍵はダイバーシティ」男女共同参画・若手支援シンポジウム報告},
  journal = {生物物理},
  year = 2015,
}

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

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

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

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

@article{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{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,
}

@inproceedings{CTT100925966,
  author = {大上雅史},
  title = {PROTAC Linker Design Using Structural Information},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100925965,
  author = {大上雅史},
  title = {AIで創薬はラクになったのか?},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100925945,
  author = {大上雅史},
  title = {AIとシミュレーション計算が駆動する分子設計},
  booktitle = {},
  year = 2024,
}

@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{CTT100925967,
  author = {大上雅史},
  title = {アンテナを広げて～インターネット世代の研究とSNS},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100925952,
  author = {大上雅史},
  title = {AIとシミュレーション計算が駆動する分子設計},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2024,
}

@inproceedings{CTT100925997,
  author = {大上雅史},
  title = {AIで広がる分子設計の可能性},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100925970,
  author = {大上雅史},
  title = {AIで広がる分子設計の可能性},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100925946,
  author = {大上雅史},
  title = {AIによるペプチドデザイン},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100925968,
  author = {大上雅史},
  title = {AIによるタンパク質構造予測と創薬支援計算},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100925971,
  author = {大上雅史},
  title = {AIで広がる分子設計の可能性},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100925947,
  author = {大上雅史},
  title = {AIとシミュレーションが駆動する分子設計},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100925973,
  author = {大上雅史},
  title = {Beyond Rule-of-Five空間のAI分子設計},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100925974,
  author = {大上雅史},
  title = {AlphaFoldによる標的結合型直鎖／環状ペプチドの計算設計},
  booktitle = {},
  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{CTT100925953,
  author = {安光夕輝 and 大上雅史},
  title = {タンパク質立体構造予測モデルの転移学習によるバーチャルスクリーニング至適構造の生成},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2024,
}

@inproceedings{CTT100925954,
  author = {内河慶輔 and 古井海里 and 大上雅史},
  title = {構造ベーススクリーニングに適したAlphaFoldタンパク質構造生成の最適化},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2024,
}

@inproceedings{CTT100925955,
  author = {青木滉志郎 and Apakorn Kengkanna and 大上雅史},
  title = {対照学習を用いたグラフニューラルネットワークによる化合物 の特性予測の最適化},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2024,
}

@inproceedings{CTT100925956,
  author = {坂野晃 and 古井海里 and 大上雅史},
  title = {化学言語モデルに基づく天然物様化合物生成},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2024,
}

@inproceedings{CTT100925972,
  author = {大上雅史},
  title = {AlphaFoldで探る分子間相互作用},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100925975,
  author = {大上雅史},
  title = {創薬情報研究の最前線},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100925930,
  author = {Takafumi Ueki and Masahito Ohue},
  title = {Antibody Complementarity-Determining Region Sequence Design using AlphaFold2 and Binding Affinity Prediction Model},
  booktitle = {In Proceedings of The 29th International Conference on Parallel & Distributed Processing Techniques and Applications (PDPTA’23)},
  year = 2024,
}

@inproceedings{CTT100925979,
  author = {坂野晃 and 古井海里 and 大上雅史},
  title = {天然物様化合物を生成する化学言語モデルの開発},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100925980,
  author = {青木滉志郎 and 大上雅史 and Kengkanna Apakorn},
  title = {対照学習を用いたGNNによる化合物特性予測},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100925976,
  author = {大上雅史},
  title = {Beyond Rule-of-Five化合物空間を探る情報科学},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100925977,
  author = {大上雅史},
  title = {天然物ケミカルバイオロジーを加速する深層学習技術基盤},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100925957,
  author = {冨樫慧乃辰 and 小杉孝嗣 and 大上雅史},
  title = {AlphaFoldを用いたタンパク質-特殊環状ペプチド複合体予測},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2024,
}

@inproceedings{CTT100925948,
  author = {大上雅史},
  title = {AIで広がる分子設計の可能性},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100925958,
  author = {石沢涼太 and 大上雅史},
  title = {複合体構造予測とフラグメントリンキングによるPROTAC設計手法の開発},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2024,
}

@inproceedings{CTT100925886,
  author = {Koh Sakano and Kairi Furui and Masahito Ohue},
  title = {Active learning for energy-based antibody optimization and enhanced screening},
  booktitle = {In Proceedings of The 30th International Conference on Parallel & Distributed Processing Techniques and Applications (PDPTA’24)},
  year = 2024,
}

@inproceedings{CTT100925978,
  author = {大上雅史},
  title = {beyond Rule-of-Five化合物の潜在空間学習と分子設計を支えるAI技術},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100925949,
  author = {大上雅史},
  title = {生成AIが加速する創薬・生命科学～AlphaFold2の衝撃とTransformerアルゴリズム～},
  booktitle = {},
  year = 2023,
}

@inproceedings{CTT100925982,
  author = {内河 慶輔 and 古井 海里 and 大上 雅史},
  title = {バーチャルスクリーニングに適した AlphaFold2 タンパク質立体構造モデルの選択},
  booktitle = {},
  year = 2023,
}

@inproceedings{CTT100925983,
  author = {石沢 涼太 and 大上 雅史},
  title = {PROTAC molecular linker design using fragment linking method},
  booktitle = {},
  year = 2023,
}

@inproceedings{CTT100925984,
  author = {冨樫 慧乃辰 and 小杉 孝嗣 and 大上 雅史},
  title = {Docking prediction of cyclic peptide- protein complex by AlphaFold Multimer with cyclic offset},
  booktitle = {},
  year = 2023,
}

@inproceedings{CTT100925981,
  author = {古井 海里 and 大上 雅史},
  title = {Study of efficient perturbation map construction for large-scale free energy perturbation calculations},
  booktitle = {},
  year = 2023,
}

@inproceedings{CTT100925950,
  author = {大上雅史},
  title = {AIが加速する創薬・生命科学～AlphaFold2の衝撃とTransformerアルゴリズム～},
  booktitle = {},
  year = 2023,
}

@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{CTT100925987,
  author = {古井 海里 and 大上 雅史},
  title = {Design of scalable perturbation maps for relative binding free energy calculations},
  booktitle = {},
  year = 2023,
}

@inproceedings{CTT100925990,
  author = {Kengkanna Apakorn and 大上 雅史},
  title = {Enhancing Model Learning and Interpretation Using Multiple Molecular Graph Representations for Compound Property and Activity Prediction},
  booktitle = {},
  year = 2023,
}

@inproceedings{CTT100925992,
  author = {内河 慶輔 and 古井 海里 and 大上 雅史},
  title = {Identifying suitable AlphaFold2 protein structure models for improved structure-based virtual screening},
  booktitle = {},
  year = 2023,
}

@inproceedings{CTT100925993,
  author = {冨樫 慧乃辰 and 小杉 孝嗣 and 大上 雅史},
  title = {Docking prediction of cyclic peptide- protein complex by AlphaFold Multimer with cyclic offset},
  booktitle = {},
  year = 2023,
}

@inproceedings{CTT100925994,
  author = {大上雅史},
  title = {AlphaFold2を活用した分子設計},
  booktitle = {},
  year = 2023,
}

@inproceedings{CTT100925985,
  author = {小杉 孝嗣 and 大上 雅史},
  title = {Design of Cyclic Peptides Targeting Protein-Protein Interactions using AlphaFold},
  booktitle = {},
  year = 2023,
}

@inproceedings{CTT100925988,
  author = {石沢 涼太 and 大上 雅史},
  title = {PROTAC molecular linker design using fragment linking method},
  booktitle = {},
  year = 2023,
}

@inproceedings{CTT100925890,
  author = {Kusuri Murakumo and Naruki Yoshikawa and Kentaro Rikimaru and Shogo Nakamura and Kairi Furui and Takamasa Suzuki and Hiroyuki Yamasaki and Yuki Nishigaya and Yuzo Takagi and Masahito Ohue},
  title = {LLM Drug Discovery Challenge: A Contest as a Feasibility Study on the Utilization of Large Language Models in Medicinal Chemistry},
  booktitle = {In Proceedings of AI for Accelerated Materials Design (AI4Mat) NeurIPS 2023 Workshop},
  year = 2023,
}

@inproceedings{CTT100925986,
  author = {HU Wenxing and 大上 雅史},
  title = {Spatial Predictions of Protein-Protein Interaction with AlphaFold Multimer},
  booktitle = {},
  year = 2023,
}

@inproceedings{CTT100925995,
  author = {大上雅史},
  title = {AIが加速する創薬・生命科学},
  booktitle = {},
  year = 2023,
}

@inproceedings{CTT100925996,
  author = {大上雅史},
  title = {計算創薬・バイオインフォマティクスを支える情報技術とGPU},
  booktitle = {},
  year = 2023,
}

@inproceedings{CTT100925928,
  author = {Apakorn Kengkanna and Masahito Ohue},
  title = {Enhancing Model Learning and Interpretation Using Multiple Molecular Graph Representations for Compound Property and Activity Prediction},
  booktitle = {In Proceedings of The 20th IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2023)},
  year = 2023,
}

@inproceedings{CTT100925951,
  author = {大上雅史},
  title = {AIで広がる分子設計の可能性},
  booktitle = {},
  year = 2023,
}

@inproceedings{CTT100925933,
  author = {Kairi Furui and Masahito Ohue},
  title = {Faster Lead Optimization Mapper Algorithm for Large-Scale Relative Free Energy Perturbation},
  booktitle = {In Proceedings of The 29th International Conference on Parallel & Distributed Processing Techniques and Applications (PDPTA’23)},
  year = 2023,
}

@inproceedings{CTT100925960,
  author = {内河慶輔 and 古井海里 and 大上雅史},
  title = {バーチャルスクリーニングに適したAlphaFold2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 = 2023,
}

@inproceedings{CTT100925959,
  author = {古井海里 and 大上雅史},
  title = {大規模自由エネルギー摂動法計算のための摂動マップ構築アルゴリズムの高速化},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2023,
}

@inproceedings{CTT100925961,
  author = {冨樫慧乃辰 and 小杉孝嗣 and 大上雅史},
  title = {Cyclic offsetを導入したAlphaFold multimerによる環状ペプチド複合体構造予測},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2023,
}

@inproceedings{CTT100925962,
  author = {石沢涼太 and 大上雅史},
  title = {フラグメントリンキング法に基づくタンパク質分解誘導キメラ分子のリンカー設計},
  booktitle = {研究報告バイオ情報学（BIO）},
  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{CTT100895561,
  author = {植木 孝史 and 大上 雅史},
  title = {AlphaFold2を用いた抗体配列設計の評価},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2023,
}

@inproceedings{CTT100895559,
  author = {Apakorn Kengkanna and Masahito Ohue},
  title = {Enhancing Ligand Property and Activity Prediction and Interpretation Using Multiple Molecular Graph Representations},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2023,
}

@inproceedings{CTT100895567,
  author = {植木孝史 and 大上雅史},
  title = {AlphaFoldを用いた抗体配列の設計性能の検証},
  booktitle = {},
  year = 2023,
}

@inproceedings{CTT100895566,
  author = {内河慶輔 and 古井海里 and 大上雅史.},
  title = {バーチャルスクリーニングに適したAlphaFoldタンパク質立体構造モデルの選択},
  booktitle = {},
  year = 2023,
}

@inproceedings{CTT100895563,
  author = {杉田駿也 and 大上雅史},
  title = {親和性閾値を考慮した適用領域による薬剤標的親和性予測},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2023,
}

@inproceedings{CTT100895562,
  author = {古井 海里 and 大上 雅史},
  title = {2種類の言語モデルを用いたタンパク質-化合物相互作用予測手法の開発},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2023,
}

@inproceedings{CTT100883620,
  author = {Keisuke Uchikawa and Kairi Furui and Masahito Ohue},
  title = {Investigation of AlphaFold2 predictive structure generation method suitable for structure-based virtual screening},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100883626,
  author = {Apakorn Kengkanna and 大上雅史},
  title = {Multiple Molecular Graph Representation Learning and Interpretation for Molecular Property/Activity Prediction in Drug Discovery},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100883625,
  author = {兒嶋佑季 and 小杉孝嗣 and 大上雅史},
  title = {タンパク質間相互作用阻害化合物ライブラリ構築のための分子生成手法の開発},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100883623,
  author = {Takafumi Ueki and Masahito Ohue},
  title = {Improvement of physical properties by redesigning antibody sequences using AfDesign},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100883622,
  author = {冨樫慧乃辰 and 大上雅史},
  title = {環状ペプチド複合体の構造データベース構築と相互作用解析},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100883617,
  author = {杉田駿也 and 大上雅史},
  title = {予測モデルの性質を考慮した適用領域による薬剤標的親和性予測},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100883616,
  author = {石沢涼太 and 大上雅史},
  title = {フラグメントリンキング法に基づくPROTAC分子リンカー設計},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100883615,
  author = {Kairi Furui and Masahito Ohue},
  title = {Compound virtual screening by learning-to-rank with gradient boosting decision tree and enrichment-based cumulative gain},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100883613,
  author = {大上雅史},
  title = {AI創薬・生命科学関連技術の進展とそれを支えるGPUソリューション},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100883612,
  author = {Yuki Kojima and Takatsugu Kosugi and Masahito Ohue},
  title = {Molecular Generation for Protein-Protein Interaction Inhibitor Design focusing on Physicochemical Properties},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100883611,
  author = {大上雅史},
  title = {創薬研究におけるAI技術},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100883610,
  author = {Kairi Furui and Masahito Ohue},
  title = {Lead optimization through active learning using free energy perturbation},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100883609,
  author = {大上雅史},
  title = {タンパク質間相互作用を狙う創薬インフォマティクス},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100883629,
  author = {Wenxing Hu and Masahito Ohue},
  title = {Protein-Protein Interaction Prediction Based On Atomic Volume Distributions With AlphaFold Multimer},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100883628,
  author = {Shunya Sugita and Masahito Ohue},
  title = {Drug-target affinity prediction using applicability domain considering the characteristics of the prediction model},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100883627,
  author = {Takatsugu Kosugi and Masahito Ohue},
  title = {Solubility-Aware Protein Binding Peptide Design Using AlphaFold},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100883633,
  author = {大上雅史},
  title = {情報学で挑むバイオ・創薬イノベーション},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100883632,
  author = {大上 雅史},
  title = {博士人材の多様なキャリアパス},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100883631,
  author = {Yuki Kojima and Takatsugu Kosugi and Masahito Ohue},
  title = {Molecular Generation for Protein-Protein Interaction Inhibitor Design focusing on Physicochemical Properties},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100883630,
  author = {Kairi Furui and Masahito Ohue},
  title = {Evaluation of Compound Virtual Screening Performance Using Learning-to-Rank in Diverse Experimental Scenarios},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100876237,
  author = {Kairi Furui and Masahito Ohue},
  title = {Compound virtual screening by learning-to-rank with gradient boosting decision tree and enrichment-based cumulative gain},
  booktitle = {In Proceedings of The 19th IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2022)},
  year = 2022,
}

@inproceedings{CTT100883634,
  author = {大上雅史},
  title = {AIが加速する創薬・生命科学},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100876271,
  author = {古井海里 and 大上雅史},
  title = {多様な実験設定におけるランク学習を用いた化合物スクリーニングの性能評価},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2022,
}

@inproceedings{CTT100876322,
  author = {大上雅史},
  title = {タンパク質の理解と制御のための構造インフォマティクス},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100876279,
  author = {能祖雄大 and 杉田昌岳 and 藤江拓哉 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軌跡データからの環状ペプチドの膜透過性と相関が高い特徴量の抽出},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2022,
}

@inproceedings{CTT100876264,
  author = {兒嶋佑季 and 小杉孝嗣 and 大上雅史},
  title = {物理化学的特性に着目したタンパク質間相互作用阻害候補化合物の生成},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2022,
}

@inproceedings{CTT100876324,
  author = {大上雅史},
  title = {AlphaFoldの計算創薬への応用と今後},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100876326,
  author = {大上雅史},
  title = {タンパク質間相互作用の理解と制御のための構造インフォマティクス},
  booktitle = {},
  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{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{CTT100876284,
  author = {杉田駿也 and 大上雅史},
  title = {適用領域を考慮した薬剤標的親和性予測},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2022,
}

@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{CTT100876327,
  author = {大上雅史},
  title = {AI・計算科学が加速する生命科学},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100876328,
  author = {古井海里 and 大上雅史},
  title = {ランク学習を用いた化合物スクリーニングにおける多様なアッセイデータの統合戦略},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100876335,
  author = {古井海里 and 大上雅史},
  title = {ランク学習を用いた化合物スクリーニングにおける多様なアッセイデータの統合戦略},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100876330,
  author = {兒嶋佑季 and 小杉孝嗣 and 大上雅史},
  title = {タンパク質間相互作用阻害剤設計のための分子生成手法の開発},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100876337,
  author = {兒嶋佑季 and 小杉孝嗣 and 大上雅史},
  title = {タンパク質間相互作用阻害剤設計のための分子生成手法の開発},
  booktitle = {},
  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{CTT100876318,
  author = {杉田駿也 and 大上雅史},
  title = {自由エネルギー摂動法計算における化合物ネットワーク構造の効率化},
  booktitle = {研究報告数理モデル化と問題解決（MPS）},
  year = 2022,
}

@inproceedings{CTT100876339,
  author = {大上雅史},
  title = {AI・計算科学が加速する生命科学},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100926048,
  author = {大上雅史},
  title = {バイオインフォマティクス分野のAI事情},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100876341,
  author = {大上雅史},
  title = {タンパク質構造予測法AlphaFold2の可能性},
  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{CTT100876348,
  author = {Shunya Sugita and Masahito Ohue},
  title = {Drug-target affinity prediction using applicability domain of feature learning},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100876349,
  author = {Takatsugu Kosugi and Masahito Ohue},
  title = {Quantitative Estimate Index for Early-Stage Screening of Compounds Targeting Protein-Protein Interactions},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100876379,
  author = {Kairi Furi and Masahito Ohue},
  title = {Improvement of learning-to-rank for ligand-based virtual screening using gradient boosting technique with relevance refinement},
  booktitle = {},
  year = 2021,
}

@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{CTT100876342,
  author = {大上雅史},
  title = {情報技術による低分子・中分子創薬SX},
  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{CTT100876382,
  author = {大上雅史},
  title = {TSUBAME 3.0 による Cresset Flare FEP 計算の展開},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100876381,
  author = {大上雅史},
  title = {情報学で挑むバイオ・創薬イノベーション},
  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{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{CTT100862955,
  author = {Takatsugu Kosugi and Masahito Ohue},
  title = {Quantitative estimate of protein-protein interaction targeting drug-likeness},
  booktitle = {In Proceedings of The 18th IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2021)},
  year = 2021,
}

@inproceedings{CTT100876387,
  author = {大上雅史},
  title = {AlphaFold2の登場とオープンサイエンス},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100876386,
  author = {Shunya Sugita and Masahito Ohue},
  title = {Drug-target affinity prediction using applicability domain of feature learning},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100876384,
  author = {Takatsugu Kosugi and Masahito Ohue},
  title = {Development of a Quantitative Estimate Index for Early-Stage Screening of Compounds Targeting Protein-Protein Interactions},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100876385,
  author = {Kairi Furi and Masahito Ohue},
  title = {Improvement of learning-to-rank for ligand-based virtual screening using gradient boosting technique with relevance refinement},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100876409,
  author = {大上雅史},
  title = {計算によるタンパク質間相互作用予測と複合体構造予測},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100876238,
  author = {Shunya Sugita and Masahito Ohue},
  title = {Drug-target affinity prediction using applicability domain based on data density},
  booktitle = {In Proceedings of The 18th IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2021)},
  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{CTT100839092,
  author = {Masahito Ohue},
  title = {Re-ranking of computational protein–peptide docking solutions with amino acid profiles of rigid-body docking results},
  booktitle = {Advances in Computer Vision and Computational Biology},
  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{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{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{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{CTT100851817,
  author = {杉田駿也 and 大上雅史},
  title = {適用領域を考慮した薬剤標的親和性予測},
  booktitle = {},
  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{CTT100851688,
  author = {大上雅史 and 古井海里},
  title = {GBDTによる化合物の血液胎盤関門透過性予測},
  booktitle = {情報処理学会研究報告},
  year = 2021,
}

@inproceedings{CTT100851821,
  author = {大上雅史 and 山本一樹},
  title = {フォーラム2F-11/インシリコ創薬を支える最先端情報科学},
  booktitle = {},
  year = 2020,
}

@inproceedings{CTT100851824,
  author = {大上雅史},
  title = {並列計算を駆使したタンパク質間相互作用予測},
  booktitle = {},
  year = 2020,
}

@inproceedings{CTT100876346,
  author = {大上雅史},
  title = {超並列計算と機械学習による創薬支援インフォマティクス},
  booktitle = {},
  year = 2020,
}

@inproceedings{CTT100839083,
  author = {大上雅史},
  title = {超並列計算と機械学習による創薬支援インフォマティクス},
  booktitle = {},
  year = 2020,
}

@inproceedings{CTT100839084,
  author = {大上雅史},
  title = {創薬・生命科学研究を加速するインフォマティクス技術},
  booktitle = {},
  year = 2020,
}

@inproceedings{CTT100839082,
  author = {杉田駿也 and 大上雅史},
  title = {自由エネルギー計算を利用した薬剤標的相互作用予測手法の検討},
  booktitle = {},
  year = 2020,
}

@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{CTT100839085,
  author = {大上雅史},
  title = {薬のタネを探すインフォマティクス技術},
  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{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{CTT100839070,
  author = {Masahito Ohue},
  title = {Supercomputing-based exhaustive protein-protein interaction prediction with MEGADOCK},
  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{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{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{CTT100851626,
  author = {Masaya Inagaki and Masahito Ohue and Yutaka Akiyama},
  title = {Fragment Linking with DQN},
  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{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{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{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{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{CTT100839086,
  author = {大上雅史},
  title = {薬のタネ探しを支援する計算技術},
  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{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{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{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{CTT100839087,
  author = {大上雅史},
  title = {薬のタネを探すインフォマティクス技術},
  booktitle = {},
  year = 2019,
}

@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{CTT100839074,
  author = {Masahito Ohue},
  title = {Learning-to-rank for ligand-based virtual screening},
  booktitle = {},
  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{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{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{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{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{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{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{CTT100839088,
  author = {大上雅史},
  title = {バイオデ―タと戦う情報学},
  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{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{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{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{CTT100851898,
  author = {大上雅史},
  title = {ペプチド創薬時代を支える大規模分子シミュレーション技術および機械学習技術の最新動向},
  booktitle = {},
  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{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{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{CTT100851911,
  author = {大上雅史},
  title = {知的創薬基盤：創薬支援のためのタンパク質結合予測システム「ペプチド創薬支援システム」の開発},
  booktitle = {},
  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{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{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{CTT100839072,
  author = {Masahito Ohue},
  title = {High Performance Computing Drug Discovery - Toward Targeting Protein-Protein Interactions},
  booktitle = {},
  year = 2018,
}

@inproceedings{CTT100883537,
  author = {Masahito Ohue},
  title = {Exploring Protein-Protein Interactions with MEGADOCK: Parallelization, Application, and Open Database},
  booktitle = {},
  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{CTT100876868,
  author = {Masahito Ohue},
  title = {Prediction of Protein-Protein Interactions with MEGADOCK: Parallelization, Application, and Open Database},
  booktitle = {},
  year = 2018,
}

@inproceedings{CTT100876865,
  author = {Masahito Ohue},
  title = {Supercomputing-based exhaustive protein-protein interaction prediction and its open database},
  booktitle = {},
  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{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{CTT100876460,
  author = {Masahito Ohue},
  title = {MEGADOCK: a supercomputing bioinformatics application for protein-protein interaction prediction},
  booktitle = {},
  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{CTT100783050,
  author = {大上雅史},
  title = {出会い系タンパク質を探す旅},
  booktitle = {},
  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{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{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{CTT100783052,
  author = {Masahito Ohue},
  title = {Prediction of Protein-Protein Interactions with MEGADOCK: Parallelization, Application, and Open Database},
  booktitle = {},
  year = 2017,
}

@inproceedings{CTT100783054,
  author = {Naoki Wakui and Ryunosuke Yoshino and Nobuaki Yasuo and Masahito Ohue and Masakazu Sekijima},
  title = {Exploring the selectivity of inhibitor complexes with Bcl-2 and Bcl-XL: a molecular dynamics simiulation approach},
  booktitle = {},
  year = 2017,
}

@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{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{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{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{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{CTT100715199,
  author = {大上雅史},
  title = {構造情報に基づくタンパク質間相互作用予測システムMEGADOCK},
  booktitle = {},
  year = 2016,
}

@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{CTT100715719,
  author = {Kazuki Yamamoto and Yoshitaka Moriwaki and Keita Oda and Masahito Ohue and Itsuo Nakane and Ryunosuke Yoshino and Hayase Hakariya and Tadaaki Mashimo and Mitsuhito Wada and Yoshifumi Fukunishi},
  title = {Human insight in drug discovery: docking pose selection in protein-ligand docking and hit-compounds selection in structure-based virtual screening},
  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{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{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{CTT100715189,
  author = {Kazuki Yamamoto and Yoshitaka Moriwaki and Keita Oda and Masahito Ohue and Itsuo Nakane and Ryunosuke Yoshino and Hayase Hakariya and Tadaaki Mashimo and Mitsuhito Wada and Yoshifumi Fukunishi},
  title = {Human insight in drug discovery: docking pose selection in protein-ligand docking and hit-compounds selection in structure-based virtual screening},
  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{CTT100715198,
  author = {大上雅史},
  title = {薬のタネ発見のための計算技術と創薬知BoF},
  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{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{CTT100715160,
  author = {大上雅史},
  title = {計算で明らかにするタンパク質の出会いとネットワーク},
  booktitle = {},
  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{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{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{CTT100715161,
  author = {内古閑伸之 and 松崎由理 and 大上雅史 and 秋山泰},
  title = {細菌走化性におけるタンパク質間相互作用面の解析},
  booktitle = {},
  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{CTT100701948,
  author = {藤井智也 and 角田将典 and 大上雅史 and 石田貴士 and 石原和幸 and 秋山泰},
  title = {GPUを用いたメタゲノム配列相同性解析ツールのMPI並列化と応用},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2016,
}

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

@inproceedings{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{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{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{CTT100926049,
  author = {大上雅史},
  title = {数学と計算で探るタンパク質の出会いとネットワーク},
  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{CTT100876870,
  author = {大上雅史},
  title = {数学と計算で探るタンパク質の出会いとネットワーク},
  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{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{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{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{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{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{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{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{CTT100715171,
  author = {大上雅史},
  title = {大規模タンパク質間相互作用予測によるEGFR系解析},
  booktitle = {},
  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{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{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{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{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{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{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{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{CTT100715179,
  author = {大上雅史},
  title = {立体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},
  booktitle = {},
  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{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{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{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{CTT100926051,
  author = {大上雅史},
  title = {MEGADOCK：de novoドッキング計算の可能性を探る},
  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{CTT100926050,
  author = {Masahito Ohue},
  title = {MEGADOCK: An all-to-all protein-protein interaction prediction system using tertiary structure data},
  booktitle = {},
  year = 2013,
}

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

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

@inproceedings{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{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{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{CTT100666830,
  author = {中嶋悠介 and 大上雅史 and 越野亮},
  title = {配列情報に基づくタンパク質間相互作用予測の構造情報付加による高精度化},
  booktitle = {FIT2013 第12回情報科学技術フォーラム講演論文集},
  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{CTT100926052,
  author = {大上雅史},
  title = {MEGADOCK：de novoドッキング計算の可能性を探る},
  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{CTT100926054,
  author = {大上雅史},
  title = {MEGADOCK：de novoドッキング計算の可能性を探る},
  booktitle = {},
  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{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{CTT100658089,
  author = {松崎由理 and 大上雅史 and 石田貴士 and 内古閑伸之 and 秋山泰},
  title = {大規模タンパク質間ネットワーク推定に関する研究},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100658033,
  author = {秋山泰 and 松崎由理 and 石田貴士 and 大上雅史 and 内古閑 伸之},
  title = {網羅的タンパク質ドッキング予測プログラムMEGADOCKの開発と応用},
  booktitle = {},
  year = 2013,
}

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

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

@inproceedings{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{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{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{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{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{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{CTT100926055,
  author = {大上雅史},
  title = {MEGADOCK：タンパク質ドッキング予測から相互作用ネットワーク予測へ},
  booktitle = {},
  year = 2012,
}

@inproceedings{CTT100926056,
  author = {大上雅史},
  title = {MEGADOCK：タンパク質剛体ドッキング計算の秘めたる可能性},
  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{CTT100658026,
  author = {Yuri Matsuzaki and Masahito Ohue and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {Application of exhaustive protein-protein interaction prediction system by using protein docking to signal transduction pathways.},
  booktitle = {},
  year = 2012,
}

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

@inproceedings{CTT100926058,
  author = {大上雅史},
  title = {MEGADOCK：タンパク質ドッキング予測から相互作用ネットワーク予測へ},
  booktitle = {},
  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{CTT100926059,
  author = {Masahito Ohue},
  title = {MEGADOCK: An all-to-all protein-protein interaction prediction system using tertiary structures},
  booktitle = {},
  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{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{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{CTT100926060,
  author = {大上雅史},
  title = {MEGADOCK：タンパク質構造から相互作用ネットワーク予測へ},
  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{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{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{CTT100926061,
  author = {大上雅史},
  title = {立体構造情報に基づく網羅的タンパク質間相互作用予測},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100926062,
  author = {大上雅史},
  title = {MEGADOCK：タンパク質構造からネットワーク予測へ},
  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{CTT100633784,
  author = {Masahito Ohue},
  title = {MEGADOCK: An all-to-all protein-protein interaction prediction system based on tertiary structures information},
  booktitle = {Proc. of IIT Madras-Tokyo Tech Joint Workshop on Bioinformatics and Large Scale Data Analysis},
  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{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{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{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{CTT100926066,
  author = {大上雅史},
  title = {ファンド獲得への第一歩を踏み出すために},
  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{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{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{CTT100926063,
  author = {大上雅史},
  title = {サクソフォンカルテットの世界},
  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{CTT100926064,
  author = {大上雅史},
  title = {タンパク質ドッキング計算を利用した網羅的タンパク質間相互作用予測},
  booktitle = {},
  year = 2010,
}

@inproceedings{CTT100926065,
  author = {大上雅史},
  title = {バイオ高専},
  booktitle = {},
  year = 2010,
}

@inproceedings{CTT100926068,
  author = {大上雅史},
  title = {MEGADOCK：立体構造情報からの網羅的PPI予測},
  booktitle = {},
  year = 2010,
}

@inproceedings{CTT100926067,
  author = {大上雅史},
  title = {立体構造情報に基づく網羅的タンパク質間相互作用予測},
  booktitle = {},
  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{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{CTT100604324,
  author = {大上雅史},
  title = {MEGADOCKにおける評価関数の改良とリランキングの導入},
  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{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{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{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{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{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{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{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{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{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{CTT100575034,
  author = {大上雅史},
  title = {物理化学的相互作用の導入によるタンパク質間相互作用予測システムの高精度化},
  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{CTT100589269,
  author = {大上雅史 and 越野亮},
  title = {遺伝子発現データ解析のための新しい属性選択手法の提案},
  booktitle = {},
  year = 2007,
}

@inproceedings{CTT100589270,
  author = {大上雅史 and 越野亮},
  title = {遺伝子発現データ解析における遺伝子偏差を用いた前処理方法の提案},
  booktitle = {第69回情報処理学会全国大会講演論文集},
  year = 2007,
}

@inproceedings{CTT100589271,
  author = {大上雅史 and 越野亮},
  title = {決定木による白血病遺伝子の自動分類ルールの抽出},
  booktitle = {平成18年度電気関係学会北陸支部連合大会講演論文集},
  year = 2006,
}

@misc{CTT100925935,
  author = {大上雅史},
  title = {AlphaFold3で何ができる？},
  year = 2024,
}

@misc{CTT100926005,
  author = {Midori Arai and Yoshinori Makita and Shun Saito and Shiina Suzuki and Yuki Narushima and Nanoha Izawa and Yuki Tanaka and Kairi Furui and Masahito Ohue and Masami Ishibashi},
  title = {The Indole Rocaglamide Induces S and G2/M Phase Cell Cycle Arrest in Small Cell Lung Cancer Cells Through ASCL1 Translation Inhibition},
  year = 2024,
}

@misc{CTT100926004,
  author = {Kairi Furui and Masahito Ohue},
  title = {Active learning for energy-based antibody optimization and enhanced screening},
  year = 2024,
}

@misc{CTT100925939,
  author = {大上雅史},
  title = {AlphaFoldによる高精度なタンパク質立体構造予測と創薬への活用},
  year = 2023,
}

@misc{CTT100925940,
  author = {大上雅史},
  title = {AlphaFoldによるタンパク質立体構造予測（実践編）},
  year = 2023,
}

@misc{CTT100925941,
  author = {大上雅史},
  title = {AIによって変わる生命科学},
  year = 2023,
}

@misc{CTT100925942,
  author = {大上雅史},
  title = {PPI（タンパク質間相互作用）を標的とするドラッグデザイン},
  year = 2023,
}

@misc{CTT100925943,
  author = {大上雅史},
  title = {中分子ペプチド創薬のインフォマティクス},
  year = 2022,
}

@misc{CTT100876247,
  author = {大上雅史},
  title = {AlphaFold2の登場と創薬への影響},
  year = 2022,
}

@misc{CTT100876250,
  author = {大上雅史},
  title = {AlphaFoldのタンパク質立体構造予測の性能},
  year = 2022,
}

@misc{CTT100876253,
  author = {大上雅史},
  title = {AlphaFold利用のすすめ},
  year = 2022,
}

@misc{CTT100852320,
  author = {大上雅史},
  title = {Oxford Journals-JSBi Prize受賞報告},
  year = 2021,
}

@misc{CTT100839069,
  author = {大上雅史},
  title = {構造情報に基づくタンパク質間相互作用の計算予測},
  year = 2020,
}

@misc{CTT100839091,
  author = {大上雅史},
  title = {ほにゃららインフォマティクスの未来},
  year = 2020,
}

@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{CTT100805142,
  author = {高橋 聡 and 新井 宗仁 and 大上雅史 and 広瀬 恵子},
  title = {日本生物物理学会第54回年会報告　日本生物物理学会学生発表賞},
  year = 2017,
}

@misc{CTT100666856,
  author = {大上雅史},
  title = {凄い生命情報科学研究を目指して－特集:次世代の生命情報科学に向けて - 若手研究者からの視点・論点},
  year = 2012,
}

@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{CTT100633788,
  author = {大上雅史},
  title = {日本のバイオインフォマティクス研究室},
  year = 2010,
}

@misc{CTT100687164,
  author = {Masahito Ohue},
  title = {Protein-Protein Interaction Network Prediction Based on Tertiary Structure Data},
  year = 2014,
}

@misc{CTT100666824,
  author = {Masahito Ohue},
  title = {Protein-Protein Interaction Network Prediction Based on Tertiary Structure Data},
  year = 2014,
}

@misc{CTT100687305,
  author = {Masahito Ohue},
  title = {Protein-Protein Interaction Network Prediction Based on Tertiary Structure Data},
  year = 2014,
}

@misc{CTT100633783,
  author = {大上雅史},
  title = {立体構造情報に基づく網羅的タンパク質間相互作用予測に関する研究},
  year = 2011,
}

@misc{CTT100633785,
  author = {大上雅史},
  title = {物理化学的相互作用の導入によるタンパク質間相互作用予測の高精度化},
  year = 2009,
}

@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{CTT100687164,
  author = {Masahito Ohue},
  title = {Protein-Protein Interaction Network Prediction Based on Tertiary Structure Data},
  school = {東京工業大学},
  year = 2014,
}

@phdthesis{CTT100666824,
  author = {Masahito Ohue},
  title = {Protein-Protein Interaction Network Prediction Based on Tertiary Structure Data},
  school = {東京工業大学},
  year = 2014,
}

@phdthesis{CTT100687305,
  author = {Masahito Ohue},
  title = {Protein-Protein Interaction Network Prediction Based on Tertiary Structure Data},
  school = {東京工業大学},
  year = 2014,
}

@mastersthesis{CTT100633783,
  author = {大上雅史},
  title = {立体構造情報に基づく網羅的タンパク質間相互作用予測に関する研究},
  school = {東京工業大学},
  year = 2011,
}

@misc{CTT100633785,
  author = {大上雅史},
  title = {物理化学的相互作用の導入によるタンパク質間相互作用予測の高精度化},
  school = {東京工業大学},
  year = 2009,
  note = {undergraduate thesis},
}