"Wexing Hu,Masahito Ohue","SpatialPPI:three-dimensional space protein-protein interaction prediction with AlphaFold Multimer",,"Computational and Structural Biotechnology Journal","ELSEVIER","Volume 23",,"page 1214-1225",2024,Dec.
"大上雅史","PROTAC Linker Design Using Structural Information","MOE Forum 2024",,,,,,2024,Sept.
"大上雅史","AIで創薬はラクになったのか?","Laboratory Automation Developers Conference 2024 (LADEC 2024)",,,,,,2024,Sept.
"大上雅史","AIとシミュレーション計算が駆動する分子設計","情報処理学会第79回バイオ情報学研究会",,,,,,2024,Sept.
"Taisuke Boku,Masatake Sugita,Ryohei Kobayashi,Shinnosuke Furuya,Takuya Fujie,Masahito Ohue,Yutaka Akiyama","Improving Performance on Replica-Exchange Molecular Dynamics Simulations by Optimizing GPU Core Utilization","53rd International Conference on Parallel Processing (ICPP2024)","Proceedings of the 53rd International Conference on Parallel Processing (ICPP2024)","Association for Computing Machinery",,,"Page 1082-1091",2024,Aug.
"大上雅史","アンテナを広げて?インターネット世代の研究とSNS","生物物理夏の学校2024",,,,,,2024,Aug.
"大上雅史","AIとシミュレーション計算が駆動する分子設計",,"研究報告バイオ情報学（BIO）","情報処理学会","  2024-BIO-79","  7","  1-1",2024,Aug.
"大上雅史","AIで広がる分子設計の可能性","学術変革領域研究(A)潜在空間分子設計第１回領域シンポジウム",,,,,,2024,Aug.
"大上雅史","AIで広がる分子設計の可能性","第12回 CBI若手の会講演会 ?若手の眼差しで迫る創薬研究の最先端 ?",,,,,,2024,Aug.
"大上雅史","AIによるペプチドデザイン","第56回若手ペプチド夏の勉強会",,,,,,2024,Aug.
"大上雅史","AIによるタンパク質構造予測と創薬支援計算","第458回CBI学会講演会「創薬の多様化に対応するタ ンパク質構造観察技術の進化」",,,,,,2024,Aug.
"大上雅史","AIで広がる分子設計の可能性","第76回日本細胞生物学会大会, WS1 シンポジウム 「創る」が織りな す未来の細胞生物学者と若手研究者へのメッセージ",,,,,,2024,July
"大上雅史","AIとシミュレーションが駆動する分子設計","令和4?8年度 学術変革領域研究(A) 生体反応の集積・ 予知・創出を基盤としたシステム生物合成科学「予知生合成科学」 第4回公開シンポジウム",,,,,,2024,July
"大上雅史","Beyond Rule-of-Five空間のAI分子設計","学術変革領域研究(A)天然物が織り成す化合物潜在空間が 拓く生物活性分子デザイン第2回公開シンポジウム",,,,,,2024,June
"大上雅史","AlphaFoldによる標的結合型直鎖／環状ペプチドの計算設計","第24回日本蛋白質科学会年会 WS3 ペ プチド設計の現在と未来",,,,,,2024,June
"Masatake Sugita,Takuya Fujie,Yudai Noso,Keisuke Yanagisawa,Masahito Ohue,Yutaka Akiyama","Development and Application of a Protocol for Predicting Membrane Permeability of Cyclic Peptides Based on Molecular Dynamics Simulations","21st IUPAB and 62nd BSJ joint congress 2024",,"American Chemical Society",,,,2024,June
"杉田 昌岳,藤江 拓哉,能祖 雄大,柳澤 渓甫,大上 雅史,秋山 泰","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","第24回日本蛋白質科学会年会",,,,,,2024,June
"大上雅史","AlphaFold3で何ができる？",,"現代化学 2024年7月号","東京化学同人",,"No. 640","page 18",2024,June
"安光夕輝,大上雅史","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",,"研究報告バイオ情報学（BIO）","情報処理学会","  2024-BIO-78","  17","  1-3",2024,June
"内河慶輔,古井海里,大上雅史","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",,"研究報告バイオ情報学（BIO）","情報処理学会","  2024-BIO-78","  16","  1-7",2024,June
"青木滉志郎,Apakorn Kengkanna,大上雅史","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",,"研究報告バイオ情報学（BIO）","情報処理学会","  2024-BIO-78","  15","  1-7",2024,June
"坂野晃,古井海里,大上雅史","化学言語モデルに基づく天然物様化合物生成",,"研究報告バイオ情報学（BIO）","情報処理学会","  2024-BIO-78","  14","  1-8",2024,June
"大上雅史","AlphaFoldで探る分子間相互作用","日本プロテオーム学会2024年大会・第20回日本臨床プロテオゲ ノミクス学会合同大会",,,,,,2024,June
"大上雅史","創薬情報研究の最前線","2024年第1回IPABセミナー",,,,,,2024,May
"Apakorn Kengkanna,Masahito Ohue","Enhancing property and activity prediction and interpretation using multiple molecular graph representations with MMGX",,"Communications Chemistry",,"Vol. 7",,"p. 1-14",2024,Apr.
"Takafumi Ueki,Masahito Ohue","Antibody Complementarity-Determining Region Sequence Design using AlphaFold2 and Binding Affinity Prediction Model","29th International Conference on Parallel & Distributed Processing Techniques and Applications (PDPTA’23)","In Proceedings of The 29th International Conference on Parallel & Distributed Processing Techniques and Applications (PDPTA’23)","IEEE",,,"page 2133-2139",2024,Apr.
"坂野晃,古井海里,大上雅史","天然物様化合物を生成する化学言語モデルの開発","情報処理学会第86回全国大会",,,,,,2024,Mar.
"青木滉志郎,大上雅史,Kengkanna Apakorn","対照学習を用いたGNNによる化合物特性予測","情報処理学会第 86回全国大会",,,,,,2024,Mar.
"Masahito Ohue,Kotoyu Sasayama,Masami Takata","Mathematical Modeling and Problem Solving: From Fundamentals to Applications",,"The Journal of Supercomputing",,"Volume 80",,"page 14116-14119",2024,Mar.
"大上雅史","Beyond Rule-of-Five化合物空間を探る情報科学","日本薬学会第144年会",,,,,,2024,Mar.
"Masahito Ohue,Kairi Furui","FastLomap: Faster Lead Optimization Mapper Algorithm for Large- Scale Relative Free Energy Perturbation",,"The Journal of Supercomputing",,"Volume 80",,"page 14417-14432",2024,Mar.
"大上雅史","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","日本農芸化学会2024年度大会",,,,,,2024,Mar.
"冨樫慧乃辰,小杉孝嗣,大上雅史","AlphaFoldを用いたタンパク質-特殊環状ペプチド複合体予測",,"研究報告バイオ情報学（BIO）","情報処理学会","  2024-BIO-77","  14","  1-8",2024,Feb.
"大上雅史","AIで広がる分子設計の可能性","生命と情報の新たなる融和：超階層生物学とＡＩ・数理ワークショッ プ",,,,,,2024,Feb.
"Takafumi Ueki,Masahito Ohue","Antibody Complementarity-Determining Region Design using AlphaFold2 and DDG Predictor",,"The Journal of Supercomputing",,"Volume 80",,"page 11989-12002",2024,Feb.
"石沢涼太,大上雅史","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",,"研究報告バイオ情報学（BIO）","情報処理学会","  2024-BIO-77","  32","  1-8",2024,Feb.
"Midori Arai,Yoshinori Makita,Shun Saito,Shiina Suzuki,Yuki Narushima,Nanoha Izawa,Yuki Tanaka,Kairi Furui,Masahito Ohue,Masami Ishibashi","The Indole Rocaglamide Induces S and G2/M Phase Cell Cycle Arrest in Small Cell Lung Cancer Cells Through ASCL1 Translation Inhibition",,,"SSRN preprint",,,,2024,
"Koh Sakano,Kairi Furui,Masahito Ohue","Natural Product-like Compound Generation with Chemical Language Models","30th International Conference on Parallel & Distributed Processing Techniques and Applications (PDPTA’24)","In Proceedings of The 30th International Conference on Parallel & Distributed Processing Techniques and Applications (PDPTA’24)","Springer Nature",,,,2024,
"大上雅史","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","日本化学会第104春季年会 併催シンポジウム",,,,,,2024,
"Kairi Furui,Masahito Ohue","Active learning for energy-based antibody optimization and enhanced screening",,,"arXiv preprint",,,,2024,
"大上雅史","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?","日本学術会 議公開シンポジウム「第13回計算力学シンポジウム」",,,,,,2023,Dec.
"内河 慶輔,古井 海里,大上 雅史","ハ?ーチャルスクリーニンク?に適した AlphaFold2 タンハ?ク質立体構造モテ?ルの選択","第61回日本生物物理学会年会",,,,,,2023,Nov.
"石沢 涼太,大上 雅史","PROTAC molecular linker design using fragment linking method","第61回日本生物物理学会年会",,,,,,2023,Nov.
"冨樫 慧乃辰,小杉 孝嗣,大上 雅史","Docking prediction of cyclic peptide- protein complex by AlphaFold Multimer with cyclic offset","第61回日本生物物理学会年会",,,,,,2023,Nov.
"古井 海里,大上 雅史","Study of efficient perturbation map construction for large-scale free energy perturbation calculations","第61回日本生物物理学会年会",,,,,,2023,Nov.
"大上雅史","AIが加速する創薬・生命科学?AlphaFold2の衝撃とTransformerアルゴリズム?","第92回関西CAE懇話会",,,,,,2023,Nov.
"Toshiki Ochiai,Tensei Inukai,Manato Akiyama,Kairi Furui,Masahito Ohue,Nobuaki Matsumori,Shinsuke Inuki,Motonari Uesugi,Toshiaki Sunazuka,Kazuya Kikuchi,Hideaki Kakeya,Yasubumi Sakakibara","Variational autoencoder-based chemical latent space for large molecular structures with 3D complexity",,"Communications Chemistry","nature","Vol. 6",,,2023,Nov.
"大上雅史","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",,"PHARMSTAGE 2023年11月号","技術情報協会","  23","  8","  24-28",2023,Nov.
"Masatake Sugita,Takuya Fujie,Keisuke Yanagisawa,Masahito Ohue,Yutaka Akiyama","Development of a Protocol for Predicting Membrane Permeability of Cyclic Peptides Based on Molecular Dynamics Simulations","The 61st Annual Meeting of The Biophysical Society of Japan",,,,,,2023,Nov.
"古井 海里,大上 雅史","Design of scalable perturbation maps for relative binding free energy calculations","CBI学会2023年大会",,,,,,2023,Oct.
"Kengkanna Apakorn,大上 雅史","Enhancing Model Learning and Interpretation Using Multiple Molecular Graph Representations for Compound Property and Activity Prediction","CBI学会2023年大会",,,,,,2023,Oct.
"内河 慶輔,古井 海里,大上 雅史","Identifying suitable AlphaFold2 protein structure models for improved structure-based virtual screening","CBI学会2023年大会",,,,,,2023,Oct.
"冨樫 慧乃辰,小杉 孝嗣,大上 雅史","Docking prediction of cyclic peptide- protein complex by AlphaFold Multimer with cyclic offset","CBI学会2023年大会",,,,,,2023,Oct.
"大上雅史","AlphaFold2を活用した分子設計","CBI学会2023年大会",,,,,,2023,Oct.
"小杉 孝嗣,大上 雅史","Design of Cyclic Peptides Targeting Protein-Protein Interactions using AlphaFold","CBI学会2023年大会",,,,,,2023,Oct.
"石沢 涼太,大上 雅史","PROTAC molecular linker design using fragment linking method","CBI学会2023年大会",,,,,,2023,Oct.
"Kusuri Murakumo,Naruki Yoshikawa,Kentaro Rikimaru,Shogo Nakamura,Kairi Furui,Takamasa Suzuki,Hiroyuki Yamasaki,Yuki Nishigaya,Yuzo Takagi,Masahito Ohue","LLM Drug Discovery Challenge: A Contest as a Feasibility Study on the Utilization of Large Language Models in Medicinal Chemistry","AI for Accelerated Materials Design (AI4Mat) NeurIPS 2023 Workshop","In Proceedings of AI for Accelerated Materials Design (AI4Mat) NeurIPS 2023 Workshop","Openview.net",,,"Page 8",2023,Oct.
"HU Wenxing,大上 雅史","Spatial Predictions of Protein-Protein Interaction with AlphaFold Multimer","CBI学会2023年大会",,,,,,2023,Oct.
"大上雅史","AIが加速する創薬・生命科学","蔵前工業会 第46回蔵前科学技術セミナー",,,,,,2023,Oct.
"Masahito Ohue","MEGADOCK-on-Colab: an easy-to-use protein-protein docking tool on Google Colaboratory",,"BMC Research Notes","SPRINGERNATURE","  16","  1",,2023,Sept.
"大上雅史","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","第12回生命医薬情報学連合大会 (IIBMP2023)",,,,,,2023,Sept.
"Takatsugu Kosugi,Masahito Ohue","Design of cyclic peptides targeting protein?protein interactions using AlphaFold",,"International Journal of Molecular Sciences","MDPI","  24","  17",,2023,Aug.
"大上雅史","AlphaFoldによるタンパク質立体構造予測（実践編）",,"生物工学会誌 2023年8月号","日本生物工学会","  101","  8","  443-446",2023,Aug.
"Apakorn Kengkanna,Masahito Ohue","Enhancing Model Learning and Interpretation Using Multiple Molecular Graph Representations for Compound Property and Activity Prediction","20th IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2023)","In Proceedings of The 20th IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2023)","IEEE",,,,2023,Aug.
"大上雅史","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",,"タンパク質の構造解析手法とIn silicoスクリーニングへの応用事例","技術情報協会",,,"  402-410",2023,July
"Masahito Ohue,Yuki Kojima,Takatsugu Kosugi","Generating potential protein-protein interaction inhibitor molecules based on physicochemical properties",,"Molecules","MDPI","  28","  15",,2023,July
"大上雅史","AIで広がる分子設計の可能性","Visionary 農芸化学100シンポジウム / 第50回 農芸化学「化学と生 物」シンポジウム",,,,,,2023,July
"Kairi Furui,Masahito Ohue","Faster Lead Optimization Mapper Algorithm for Large-Scale Relative Free Energy Perturbation","29th International Conference on Parallel & Distributed Processing Techniques and Applications (PDPTA’23)","In Proceedings of The 29th International Conference on Parallel & Distributed Processing Techniques and Applications (PDPTA’23)","IEEE",,,"page 2126-2132",2023,July
"大上雅史","AIによって変わる生命科学",,"現代化学 2023年8月号","東京化学同人",,,"  28-30",2023,July
"冨樫慧乃辰,小杉孝嗣,大上雅史","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",,"研究報告バイオ情報学（BIO）","情報処理学会","  2023-BIO-74","  41","  1-6",2023,June
"内河慶輔,古井海里,大上雅史","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",,"研究報告バイオ情報学（BIO）","情報処理学会","  2023-BIO-74","  40","  1-7",2023,June
"石沢涼太,大上雅史","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",,"研究報告バイオ情報学（BIO）","情報処理学会","  2023-BIO-74","  42","  1-6",2023,June
"Jessica Andreani,Brain Jim?nez-Garc?a,Masahito Ohue","Web Tools for Modeling and Analysis of Biomolecular Interactions Volume II",,"Frontiers in Molecular Biosciences",,"Volume 10",,,2023,June
"李 佳男,柳澤 渓甫,杉田 昌岳,藤江 拓哉,大上 雅史,秋山 泰","CycPeptMPDB：包括的な環状ペプチド膜透過率データベースの開発","情報処理学会 第143回MPS・第74回BIO合同研究発表会","研究報告バイオ情報学（BIO）","情報処理学会","  2023-BIO-74","  38","  1-8",2023,June
"古井海里,大上雅史","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",,"研究報告バイオ情報学（BIO）","情報処理学会","  2023-BIO-74","  39","  1-7",2023,June
"植木 孝史,大上 雅史","AlphaFold2を用いた抗体配列設計の評価",,"研究報告バイオ情報学（BIO）","情報処理学会","  2023-BIO-73","  21","  1-4",2023,Mar.
"Jianan Li,Keisuke Yanagisawa,Masatake Sugita,Takuya Fujie,Masahito Ohue,Yutaka Akiyama","CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides",,"Journal of Chemical Information and Modeling","American Chemical Society","Volume 63","Issue 7","pp. 2240-2250",2023,Mar.
"Apakorn Kengkanna,Masahito Ohue","Enhancing Ligand Property and Activity Prediction and Interpretation Using Multiple Molecular Graph Representations",,"研究報告バイオ情報学（BIO）","ISPJ","  2023-BIO-73","  35","  1-4",2023,Mar.
"植木孝史,大上雅史","AlphaFoldを用いた抗体配列の設計性能の検証","情報処理学会第85回全国大会",,,,,,2023,Mar.
"内河慶輔,古井海里,大上雅史.","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","情報処理学会第85回全国大会",,,,,,2023,Mar.
"杉田駿也,大上雅史","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",,"研究報告バイオ情報学（BIO）","情報処理学会","  2023-BIO-73","  16","  1-6",2023,Mar.
"古井 海里,大上 雅史","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",,"研究報告バイオ情報学（BIO）","情報処理学会","  2023-BIO-73","  19","  1-3",2023,Mar.
"大上雅史","中分子ペプチド創薬のインフォマティクス",,"実験医学2023年1月号","羊土社","  41","  1","  20-26",2022,Dec.
"Keisuke Uchikawa,Kairi Furui,Masahito Ohue","Investigation of AlphaFold2 predictive structure generation method suitable for structure-based virtual screening","第6回Tokyo Bioinformatics Meeting",,,,,,2022,Oct.
"Apakorn Kengkanna,大上雅史","Multiple Molecular Graph Representation Learning and Interpretation for Molecular Property/Activity Prediction in Drug Discovery","第6回Tokyo Bioinformatics Meeting",,,,,,2022,Oct.
"兒嶋佑季,小杉孝嗣,大上雅史","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","第6回Tokyo Bioinformatics Meeting",,,,,,2022,Oct.
"Takafumi Ueki,Masahito Ohue","Improvement of physical properties by redesigning antibody sequences using AfDesign","第6回Tokyo Bioinformatics Meeting",,,,,,2022,Oct.
"冨樫慧乃辰,大上雅史","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","第6回Tokyo Bioinformatics Meeting",,,,,,2022,Oct.
"杉田駿也,大上雅史","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","第6回Tokyo Bioinformatics Meeting",,,,,,2022,Oct.
"石沢涼太,大上雅史","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","第6回Tokyo Bioinformatics Meeting",,,,,,2022,Oct.
"Kairi Furui,Masahito Ohue","Compound virtual screening by learning-to-rank with gradient boosting decision tree and enrichment-based cumulative gain","第6回Tokyo Bioinformatics Meeting",,,,,,2022,Oct.
"大上雅史","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","CBI学会2022年大会",,,,,,2022,Oct.
"Yuki Kojima,Takatsugu Kosugi,Masahito Ohue","Molecular Generation for Protein-Protein Interaction Inhibitor Design focusing on Physicochemical Properties","CBI学会2022年大会",,,,,,2022,Oct.
"大上雅史","創薬研究におけるAI技術","名古屋大学Online Sience Club",,,,,,2022,Oct.
"Kairi Furui,Masahito Ohue","Lead optimization through active learning using free energy perturbation","CBI学会2022年大会",,,,,,2022,Oct.
"大上雅史","タンパク質間相互作用を狙う創薬インフォマティクス","筑波大学計算科学研究センター 計算メディカルサイエンスワークショップ2022",,,,,,2022,Oct.
"Wenxing Hu,Masahito Ohue","Protein-Protein Interaction Prediction Based On Atomic Volume Distributions With AlphaFold Multimer","IIBMP2022",,,,,,2022,Sept.
"Shunya Sugita,Masahito Ohue","Drug-target affinity prediction using applicability domain considering the characteristics of the prediction model","IIBMP2022",,,,,,2022,Sept.
"Takatsugu Kosugi,Masahito Ohue","Solubility-Aware Protein Binding Peptide Design Using AlphaFold","IIBMP2022",,,,,,2022,Sept.
"Masatake Sugita,Takuya Fujie,Keisuke Yanagisawa,Masahito Ohue,Yutaka Akiyama","Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations",,"Journal of Chemical Information and Modeling","American Chemical Society","Volume 62","Issue 18","pp. 4549-4560",2022,Sept.
"大上雅史","情報学で挑むバイオ・創薬イノベーション","生物物理夏の学校2022",,,,,,2022,Sept.
"大上 雅史","博士人材の多様なキャリアパス","第11回生命医薬情報学連合大会",,,,,,2022,Sept.
"Yuki Kojima,Takatsugu Kosugi,Masahito Ohue","Molecular Generation for Protein-Protein Interaction Inhibitor Design focusing on Physicochemical Properties","IIBMP2022",,,,,,2022,Sept.
"Kairi Furui,Masahito Ohue","Evaluation of Compound Virtual Screening Performance Using Learning-to-Rank in Diverse Experimental Scenarios","IIBMP2022",,,,,,2022,Sept.
"Keisuke Yanagisawa,Rikuto Kubota,Yasushi Yoshikawa,Masahito Ohue,Yutaka Akiyama","Effective Protein-Ligand Docking Strategy via Fragment Reuse and a Proof-of-Concept Implementation",,"ACS Omega","American Chemical Society","Volume 7","Issue 34","pp. 30265-30274",2022,Aug.
"Kairi Furui,Masahito Ohue","Compound virtual screening by learning-to-rank with gradient boosting decision tree and enrichment-based cumulative gain","19th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology(IEEE CIBCB2022)","In Proceedings of The 19th IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2022)","IEEE",,,,2022,Aug.
"大上雅史","AIが加速する創薬・生命科学","NVIDIA/湘南アイパーク共催 メンバーシップ入会記念オンラインセミナー 「NVIDIA AI Colloquim」",,,,,,2022,Aug.
"Takatsugu Kosugi,Masahito Ohue","Solubility-aware protein binding peptide design using AlphaFold",,"Biomedicines","MDPI","Volume 10","Issue 7",,2022,July
"大上雅史","AlphaFold2の登場と創薬への影響",,"革新的AI創薬?医療ビッグデータ、人工知能がもたらす創薬研究の未来像?","株式会社エヌ・ティー・エス",,,,2022,July
"古井海里,大上雅史","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",,"研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-70","  49","  1-6",2022,June
"大上雅史","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","第65回日本腎臓学会学術総会",,,,,,2022,June
"能祖雄大,杉田昌岳,藤江拓哉,柳澤渓甫,大上雅史,秋山泰","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",,"研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-70","  50","  1-8",2022,June
"兒嶋佑季,小杉孝嗣,大上雅史","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",,"研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-70","  48","  1-6",2022,June
"大上雅史","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","第32回バイオメディカル研究会「最先端構造解析の現状と課題」",,,,,,2022,May
"大上雅史","AlphaFoldの計算創薬への応用と今後","第434回CBI学会講演会 「タンパク質立体構造予測の最前線?AlphaFold2は創薬に真のブレークスルーをもたらすのか?」",,,,,,2022,May
"Jessica Andreani,Masahito Ohue,Brain Jim?nez-Garc?a","Web Tools for Modeling and Analysis of Biomolecular Interactions",,"Frontiers in Molecular Biosciences","Frontiers Media S.A.","Volume 9",,,2022,Apr.
"兒嶋佑季,小杉孝嗣,大上雅史","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","第26回オープンバイオ研究会",,,,,,2022,Mar.
"兒嶋佑季,小杉孝嗣,大上雅史","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","情報処理学会第84回全国大会",,,,,,2022,Mar.
"古井海里,大上雅史","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","情報処理学会第84回全国大会",,,,,,2022,Mar.
"古井海里,大上雅史","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","第26回オープンバイオ研究会",,,,,,2022,Mar.
"大上雅史","AI・計算科学が加速する生命科学","「機能タンパク質の構造と機能のダイナミクスと、それに基づく細胞・生体システム作動機構の研究拠点の形成」最終成果報告会",,,,,,2022,Mar.
"津嶋佑旗,柳澤渓甫,大上雅史,秋山泰","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",,"研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-69","  16","  1-8",2022,Mar.
"玉野史結,伊澤和輝,柳澤渓甫,大上雅史,秋山泰","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",,"研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-69","  7","  1-7",2022,Mar.
"山崎眞拓,伊澤和輝,平田稜,柳澤渓甫,大上雅史,秋山泰","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",,"研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-69","  8","  1-8",2022,Mar.
"稲垣雅也,柳澤渓甫,大上雅史,秋山泰","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",,"研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-69","  15","  1-8",2022,Mar.
"杉田駿也,大上雅史","適用領域を考慮した薬剤標的親和性予測",,"研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-69","  4","  1-6",2022,Mar.
"杉田駿也,大上雅史","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",,"研究報告数理モデル化と問題解決（MPS）","情報処理学会","  2022-MPS-137","  12","  1-6",2022,Feb.
"Jianan Li,Yanagisawa K,Yoshikawa Y,Ohue M,Akiyama Y.","Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning",,"Bioinformatics",,"Volume 38","Issue 4","  1110-1117",2022,Feb.
"大上雅史","AI・計算科学が加速する生命科学","日本農芸化学会 産学官若手交流会 第37回さんわかセミナー「生命科学のDX：農化系ラボのデジタル展開を探る」",,,,,,2022,Jan.
"大上雅史","AlphaFold利用のすすめ",,"実験医学2022年2月号","羊土社","Vol. 40","No. 2","pp. 433-438",2022,Jan.
"大上雅史","AlphaFoldのタンパク質立体構造予測の性能",,"実験医学2022年2月号","羊土社","Vol. 40","No. 2","pp. 427-430",2022,Jan.
"大上雅史","タンパク質構造予測法AlphaFold2の可能性","中分子創薬に関わる次世代産業研究会(IMD2) 第3回基礎講座",,,,,,2021,Dec.
"大上雅史","バイオインフォマティクス分野のAI事情","ACLSガンマクラブ2021年度総会",,,,,,2021,Dec.
"Takatsugu Kosugi,Masahito Ohue","Quantitative Estimate Index for Early-Stage Screening of Compounds Targeting Protein-Protein Interactions","第5回Tokyo Bioinformatics Meeting",,,,,,2021,Nov.
"Shunya Sugita,Masahito Ohue","Drug-target affinity prediction using applicability domain of feature learning","第5回Tokyo Bioinformatics Meeting",,,,,,2021,Nov.
"大上雅史","情報技術による低分子・中分子創薬SX","Tokyo Tech Research Festival（TTRF）2021",,,,,,2021,Nov.
"杉田昌岳,杉山聡,藤江拓哉,吉川寧,柳澤渓甫,大上雅史,秋山泰","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","第58回日本生物物理学会年会",,,,,,2021,Nov.
"杉田昌岳,杉山聡,藤江拓哉,吉川寧,柳澤渓甫,大上雅史,秋山泰","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","第58回日本生物物理学会年会",,,,,,2021,Nov.
"Kairi Furi,Masahito Ohue","Improvement of learning-to-rank for ligand-based virtual screening using gradient boosting technique with relevance refinement","第5回Tokyo Bioinformatics Meeting",,,,,,2021,Nov.
"杉田昌岳,杉山聡,藤江拓哉,吉川寧,柳澤渓甫,大上雅史,秋山泰","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","第43回溶液化学シンポジウム",,,,,,2021,Oct.
"Masahito Ohue,Kento Aoyama,Yutaka Akiyama","High-performance cloud computing for exhaustive protein-protein docking","The 26th International Conference on Parallel & Distributed Processing (PDPTA’20)","Advances in Parallel & Distributed Processing, and Applications","Springer,cham",,,"pp. 737-746",2021,Oct.
"大上雅史","TSUBAME 3.0 による Cresset Flare FEP 計算の展開","CBI学会2021年大会",,,,,,2021,Oct.
"Takatsugu Kosugi,Masahito Ohue","Quantitative estimate of protein-protein interaction targeting drug-likeness","2021 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","In Proceedings of The 18th IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2021)","IEEE",,,"pp. 1-8",2021,Oct.
"Sugita M,Sugiyama S,Takuya Fujie,Yoshikawa Y,Yanagisawa K,Ohue M,Akiyama Y.","Large-scale membrane permeability prediction of cyclic peptides crossing a lipid bilayer based on enhanced sampling molecular dynamics simulations","CBI学会2021年大会",,,,,,2021,Oct.
"Shunya Sugita,Masahito Ohue","Drug-target affinity prediction using applicability domain based on data density","18th IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology(IEEE CIBCB2021)","In Proceedings of The 18th IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2021)","IEEE",,,"Page 1-6",2021,Oct.
"Kazuki Takabatake,Kazuki Izawa,Motohiro Akikawa,Keisuke Yanagisawa,Masahito Ohue,Yutaka Akiyama","Improved Homology Search for Metagenomic Analysis by Two-Step Seed Search with Reduced Amino Acid Alphabets","The 10th International Conference on Bioinformatics and Biomedical Science (ICBBS2021)",,,,,,2021,Oct.
"Takatsugu Kosugi,Masahito Ohue","Quantitative Estimate Index for Early-Stage Screening of Compounds Targeting Protein-Protein Interactions",,"International Journal of Molecular Sciences","MDPI","Volume 22","Issue 20",,2021,Oct.
"大上雅史","情報学で挑むバイオ・創薬イノベーション","ヒューマンネットワーク高専(HNK) 月例会(2021年10月度)",,,,,,2021,Oct.
"Shunya Sugita,Masahito Ohue","Drug-target affinity prediction using applicability domain of feature learning","第10回生命医薬情報学連合大会（IIBMP2021）",,,,,,2021,Sept.
"Takatsugu Kosugi,Masahito Ohue","Development of a Quantitative Estimate Index for Early-Stage Screening of Compounds Targeting Protein-Protein Interactions","第10回生命医薬情報学連合大会（IIBMP2021）",,,,,,2021,Sept.
"津嶋佑旗,柳澤渓甫,大上雅史,秋山泰.","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","第67回BIO研究発表会","研究報告バイオ情報学（BIO）","情報処理学会","  2021-BIO-67","  1","Page 1-8",2021,Sept.
"Takabatake K,Izawa K,Akikawa M,Yanagisawa K,Ohue M,Akiyama Y.","Improved large-scale homology search by two-step seed search using multiple reduced amino acid alphabets",,"Genes",,"  12","  9","  1455",2021,Sept.
"大上雅史","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","MED BINDS 長浜バイオ大学におけるBINDSユニット連携講習会 創薬のためのタンパク質構造インフォマティクス２",,,,,,2021,Sept.
"大上雅史","AlphaFold2の登場とオープンサイエンス","第10回生命医薬情報学連合大会（IIBMP2021）",,,,,,2021,Sept.
"Kairi Furi,Masahito Ohue","Improvement of learning-to-rank for ligand-based virtual screening using gradient boosting technique with relevance refinement","第10回生命医薬情報学連合大会（IIBMP2021）",,,,,,2021,Sept.
"Isawa Kazuya,Yanagisawa Keisuke,Ohue Masahito,Akiyama Yutaka","Antisense oligonucleotide activity analysis based on opening and binding energies to targets","Proceedings of The 27th International Conference on Parallel & Distributed Processing Techniques and Applications (PDPTA’21)","Advances in Parallel & Distributed Processing and Applications",,,,,2021,July
"Masahito Ohue,Yutaka Akiyama","MEGADOCK-GUI: a GUI-based complete cross-docking tool for exploring protein-protein interactions","27th International Conference on Parallel & Distributed Processing (PDPTA’21)","Advances in Parallel & Distributed Processing, and Applications(Accepted)","Springer",,,,2021,July
"Masahito Ohue,Hiroki Watanabe,Yutaka Akiyama","MEGADOCK-Web-Mito: human mitochondrial protein-protein interaction prediction database","27th International Conference on Parallel & Distributed Processing (PDPTA’21)","Advances in Parallel & Distributed Processing, and Applications(Accepted)","Springer",,,,2021,July
"Sugita M,Sugiyama S,Takuya Fujie,Yoshikawa Y,Yanagisawa K,Ohue M,Akiyama Y.","Large-scale membrane permeability prediction of cyclic peptides crossing a lipid bilayer based on enhanced sampling molecular dynamics simulations",,"Journal of Chemical Information and Modeling",,"  61","  7","  3681-3695",2021,July
"Izawa K,Okamoto-Shibayama K,Kita D,Tomita S,Saito A,Ishida T,Ohue M,Akiyama Y,Ishihara K.","Taxonomic and gene category analyses of subgingival plaques from a group of Japanese individuals with and without periodontitis",,"International Journal of Molecular Sciences","International Journal of Molecular Sciences","Volume 22","Issue 10","  5298",2021,May
"大上雅史","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",,"学振申請書の書き方とコツ 改訂第２版","講談社",,,,2021,Mar.
"大上雅史","Oxford Journals-JSBi Prize受賞報告",,"日本バイオインフォマティクス学会ニュースレター","特定非営利活動法人日本ハ?イオインフォマティクス学会",,"  39","pp. 12-13",2021,Mar.
"杉田駿也,大上雅史","適用領域を考慮した薬剤標的親和性予測","情報処理学会第83回全国大会",,,,,,2021,Mar.
"Masahito Ohue","Re-ranking of computational protein?peptide docking solutions with amino acid profiles of rigid-body docking results","The 21st International Conference on Bioinformatics & Computational Biology (BIOCOMP'20)","Advances in Computer Vision and Computational Biology","Springer,cham",,,"pp. 749-758",2021,Mar.
"大上雅史,古井海里","GBDTによる化合物の血液胎盤関門透過性予測",,"研究報告バイオ情報学（BIO)",,"Vol. 2021-BIO-65","No. 8","pp. 1-3",2021,Mar.
"井澤和也,柳澤渓甫,大上雅史,秋山泰","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",,"情報処理学会研究報告",,"Vol. 2021-BIO-65","No. 7","pp. 1-7",2021,Mar.
"生化学若い研究者の会,大上雅史","核酸の生化学（第8章）",,"これだけ!生化学 第２版","秀和システム",,,,2021,Feb.
"大上雅史","並列計算を駆使したタンパク質間相互作用予測","第43回日本分子生物学会年会",,,,,,2020,Dec.
"大上雅史,山本一樹","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","第43回日本分子生物学会年会",,,,,,2020,Dec.
"Sho Ito,Akinobu Senoo,Satoru Nagatoishi,Masahito Ohue,Masaki Yamamoto,Kouhei Tsumoto,Naoki Wakui","Structural basis for binding mechanism of human serum albumin complexed with cyclic peptide dalbavancin",,"Journal of Medicinal Chemistry",,"vol. 63","issue 22","pp. 14045-14053",2020,Nov.
"大上雅史","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","第418回CBI学会講演会",,,,,,2020,Nov.
"大上雅史","構造情報に基づくタンパク質間相互作用の計算予測",,"ファインケミカル2020年10月号","シーエムシー出版","Vol. 49","No. 10","pp. 25-31",2020,Oct.
"Guillaume Launay,Masahito Ohue,Julia Prieto Santero,Yuri Matsuzaki,C?cile Hilpert,Nobuyuki Uchikoga,Takanori Hayashi,Juliette Martin","Evaluation of CONSRANK-like scoring functions for rescoring ensembles of protein-protein docking poses",,"Frontiers in Molecular Biosciences",,"vol. 7",,,2020,Oct.
"大上雅史","創薬・生命科学研究を加速するインフォマティクス技術","第1回 先端生物物理学セミナー",,,,,,2020,Oct.
"杉田駿也,大上雅史","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","第9回生命医薬情報学連合大会（IIBMP2020）",,,,,,2020,Sept.
"大上雅史","薬のタネを探すインフォマティクス技術","生物工学フォーラム「情報解析が切り拓く創薬・生物工学研究の新展開」",,,,,,2020,Aug.
"大上雅史,青山建人,秋山泰","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","生命情報科学若手の会第12回研究会",,,,,,2020,Aug.
"Masahito Ohue,Kento Aoyama,Yutaka Akiyama","High-performance cloud computing for exhaustive protein-protein docking",,"IPSJ Technical Report",,"Vol. 2020-MPS-129","No. 6","pp. 1-4",2020,July
"Kento Aoyama,Hiroki Watanabe,Masahito Ohue,Yutaka Akiyama","Multiple HPC environments-aware container image configuration workflow for large-scale all-to-all protein-protein docking calculations","The 6th Asian Conference on Supercomputing Frontiers (SCFA2020)","Lecture Notes in Computer Science","Springer","Vol. 12082",,"pp. 23-39",2020,June
"Masaya Inagaki,Masahito Ohue,Yutaka Akiyama","Fragment Linking with DQN","The 5th IITM-Tokyo Tech Joint Symposium-Current trends in Bioinformatics: Big data analysis, machine learning and drug design",,,,,,2020,Mar.
"Masahito Ohue","Supercomputing-based exhaustive protein-protein interaction prediction with MEGADOCK","The 5th IITM-Tokyo Tech Joint Symposium-Current trends in bioinformatics: Big data analysis, machine learning and drug design",,,,,,2020,Mar.
"高畠和輝,伊澤和輝,秋川元宏,大上雅史,秋山泰","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",,"研究報告バイオ情報学（BIO）",,"Vol. 2020-BIO-61","No. 10","pp. 1-6",2020,Mar.
"村田翔太朗,山田雄太,吉川寧,大上雅史,秋山泰","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",,"研究報告バイオ情報学（BIO）","情報処理学会","Vol. 2020-BIO-61","No. 5","pp. 1-7",2020,Mar.
"久保田陸人,柳澤渓甫,吉川寧,大上雅史,秋山泰","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",,"情報処理学会研究報告",,"Vol. 2020-BIO-61","No. 4","pp. 1-8",2020,Mar.
"渡辺紘生,大上雅史,秋山泰","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",,"情報処理学会研究報告","情報処理学会","Vol. 2020-BIO-61","No. 3","pp. 1-8",2020,Mar.
"Kazuki Izawa,K Shibayama,Masahito Ohue,Takashi Ishida,Kazuyuki Ishihara,Yutaka Akiyama","The shifts in bacterial community and gene category composition between healthy sites and periodontal disease sites","The 5th IITM-Tokyo Tech Joint Symposium-Current trends in Bioinformatics: Big data analysis, machine learning and drug design",,,,,,2020,Mar.
"Yuki Tsushima,Masahito Ohue,Yutaka Akiyama","Development of fragment linking method for beyond rule of five","The 5th IITM-Tokyo Tech Joint Symposium-Current trends in Bioinformatics: Big data analysis, machine learning and drug design",,,,,,2020,Mar.
"Takuya Fujie,Masatake Sugita,Satoshi Sugiyama,Yasushi Yoshikawa,Masahito Ohue,Yutaka Akiyama","Conformational Sampling with Molecular Dynamics Simulation for Prediction of Membrane Permeability of Cyclic Peptide","The 5th IITM-Tokyo Tech Joint Symposium-Current trends in Bioinformatics: Big data analysis, machine learning and drug design",,,,,,2020,Mar.
"Masahito Ohue,Shogo D. Suzuki,Yutaka Akiyama","PKRank & SPDRank - Learning-to-rank methods for machine-learning-based drug discovery","Biophysical Society 64th Annual Meeting",,,,,,2020,Feb.
"Max Druyvesteyn,Masahito Ohue,Yutaka Akiyama","Improved protein-protein docking using arbitrary docking-derived protein interface predictions","2nd RWBC-OIL Workshop",,,,,,2020,Jan.
"Shunpei Matsuno,Masahito Ohue,Yutaka Akiyama","Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces","2nd RWBC-OIL Workshop",,,,,,2020,Jan.
"Satoshi Sugiyama,Yasushi Yoshikawa,Masahito Ohue,Yutaka Akiyama","Development of Membrane Permeability Prediction System for Cyclic Peptide: Large-Scale Molecular Dynamics Simulations","2nd RWBC-OIL Workshop",,,,,,2020,Jan.
"大上雅史","薬のタネ探しを支援する計算技術","LiHub創薬技術革新グループ ワークショップ 異分野融合による創薬研究",,,,,,2020,Jan.
"Shumpei Matsuno,Masahito Ohue,Yutaka Akiyama","Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces",,"Biophysics and Physicobiology",,"Vol. 17",,"pp. 2-13",2020,Jan.
"Li Jianan,Yasushi Yoshikawa,Masahito Ohue,Yutaka Akiyama","Prediction of plasma protein binding for cyclic peptides by deep learning and molecular docking","2nd RWBC-OIL Workshop",,,,,,2020,Jan.
"Hiroki Watanabe,Masahito Ohue,Yutaka Akiyama","Exhaustive protein-protein interaction prediction using MEGADOCK on a large-scale HPC environment","2nd RWBC-OIL Workshop",,,,,,2020,Jan.
"Kento Aoyama,Hiroki Watanabe,Masahito Ohue,Yutaka Akiyama","Multiple HPC Environments-Aware Container Image Configuration Workflow for Large-Scale All-to-All Protein-Protein Docking Calculations","2nd RWBC-OIL Workshop",,,,,,2020,Jan.
"Kento Aoyama,Masanori Kakuta,Yuri Matsuzaki,Takashi Ishida,Masahito Ohue,Yutaka Akiyama","Development of computational pipeline software for genome/exome analysis on the K computer",,"Supercomputing Frontiers and Innovations",,"Vol. 7","No. 1","pp. 37-54",2020,
"大上雅史","ほにゃららインフォマティクスの未来",,"バイオサイエンスとインダストリー（Ｂ＆Ｉ）",,"Vol. 78","No. 2","p. 132",2020,
"Shuntaro Chiba,Masahito Ohue,Anastasiia Gryniukova,Petro Borysko,Sergey Zozulya,Nobuaki Yasuo,Ryunosuke Yoshino,Kazuyoshi Ikeda,Woong-Hee Shin,Daisuke Kihara,Mitsuo Iwadate,Hideaki Umeyama,Takaaki Ichikawa,Reiji Teramoto,Kun-Yi Hsin,Vipul Gupta,Hiroaki Kitano,Mika Sakamoto,Akiko Higuchi,Nobuaki Miura,Kei Yura,Masahiro Mochizuki,Chandrasekaran Ramakrishnan,A. Mary Thangakani,D. Velmurugan,M. Michael Gromiha,Itsuo Nakane,Nanako Uchida,Hayase Hakariya,Modong Tan,Hironori Nakamura,Shogo Suzuki,Tomoki Ito,Masahiro Kawatani,Kentaroh Kudoh,Sakurako Takashina,Kazuki Yamamoto,Yoshitaka Moriwaki,Keita Oda,Daisuke Kobayashi,Tatsuya Okuno,Shintaro Minami,George Chikenji,Philip Prathipati,Chioko Nagao,Attayeb Mohsen,Mari Ito,Kenji Mizuguchi,Teruki Honma,Takashi Ishida,Takatsugu Hirokawa,Yutaka Akiyama,Masakazu Sekijima.","A prospective compound screening contest identified broader inhibitors for Sirtuin 1",,"Scientific Reports",,"  9",,,2019,Dec.
"大上雅史","薬のタネを探すインフォマティクス技術","第42回日本分子生物学会年会, [1F-06]フォーラム 薬効評価・予測技術の進歩による創薬研究の加速",,,,,,2019,Dec.
"Masahito Ohue","Learning-to-rank for ligand-based virtual screening","AHeDD2019/IPAB2019 Joint Symposium",,,,,,2019,Nov.
"Kento Aoyama,Hiroki Watanabe,Masahito Ohue,Yutaka Akiyama","Multiple HPC Environments-Aware Container Image Configuration for Bioinformatics Application","International Conference for High Performance Computing, Networking, Storage, and Analysis (SC'19)",,,,,,2019,Nov.
"Keren Jiang,Di Zhang,Tsubasa Iino,Risa Kimura,Tatsuo Nakajima,Kana Shimizu,Masahito Ohue,Yutaka Akiyama.","A playful tool for predicting protein-protein docking","Mobile and Ubiquitous Multimedia (MUM 2019)","In Proceedings of the 18th International Conference on Mobile and Ubiquitous Multimedia (MUM 2019)","ACM",,"No. 40","Page 1-5",2019,Nov.
"Ohue M,Shogo Suzuki,Akiyama Y.","Learning-to-rank technique based on ignoring meaningless ranking orders between compounds",,"Journal of Molecular Graphics and Modelling","Elsevier","Volume 92",,"pp. 192-200",2019,Nov.
"大上雅史,鈴木翔吾,秋山泰","PKRank & SPDRank 化合物選別のためのランク学習法","生命情報科学若手の会第11回研究会",,,,,,2019,Oct.
"Kento Aoyama,Hiroki Watanabe,Masahito Ohue,Yutaka Akiyama","Multiple HPC Environments-Aware Container Image Configuration for Bioinformatics Application","第8回生命医薬情報学連合大会 (IIBMP2019)",,,,,,2019,Sept.
"Kazuki Izawa,Kazuki Shibayama,Masahito Ohue,Kazuyuki Ishihara,Yutaka Akiyama","Bacterial community and gene category composition analysis with high-speed homology search tool suggests the difference between periodontal disease and healthy sites","第8回生命医薬情報学連合大会 (IIBMP2019)",,,,,,2019,Sept.
"Shumpei Matsuno,Masahito Ohue,Yutaka Akiyama","Multidomain protein structure prediction using multimeric interaction residue pair information","第8回生命医薬情報学連合大会 (IIBMP2019)",,,,,,2019,Sept.
"Yuta Yamada,Yasushi Yoshikawa,Naoki Wakui,Masahito Ohue,Yutaka Akiyama","Development of Membrane Permeability Prediction Method for Cyclic Peptids with Machine Learning","第8回生命医薬情報学連合大会 (IIBMP2019)",,,,,,2019,Sept.
"Masahito Ohue,Hiroki Watanabe,Kento Aoyama,Yutaka Akiyama","Acceleration and virtualization of parallel protein-protein interaction prediction system MEGADOCK","The 57th Annual Meeting of the Biophysical Society of Japan",,,,,,2019,Sept.
"Masahito Ohue,Shogo D. Suzuki,Yutaka Akiyama","PKRank & SPDRank: Learning-to-rank methods for ligand-based virtual screening","第8回生命医薬情報学連合大会 (IIBMP2019)",,,,,,2019,Sept.
"Hiroki Watanabe,Masahito Ohue,Yutaka Akiyama","Accelerating MEGADOCK: protein-protein interaction prediction software on multiple nodes and multiple GPUs environment","第8回生命医薬情報学連合大会 (IIBMP2019)",,,,,,2019,Sept.
"大上雅史","バイオデ―タと戦う情報学","情報学の次世代検討会?",,,,,,2019,Aug.
"Masahito Ohue,Marina Yamasawa,Kazuki Izawa,Yutaka Akiyama","Parallelized pipeline for whole genome shotgun metagenomics with GHOSTZ-GPU and MEGAN","In Proceedings of the 19th annual IEEE International Conference on Bioinformatics and Bioengineering (IEEE BIBE 2019)",,"IEEE",,,"  152-156",2019,Aug.
"Aoyama K,Yamamoto Y,Ohue M,Akiyama Y.","Performance evaluation of MEGADOCK protein?protein interaction prediction system implemented with distributed containers on a cloud computing environment",,"IPSJ SIG Technical Report",,"Vol. 2019-MPS-124","No. 13","pp. 1-4",2019,July
"Ban T,Ohue M,Akiyama Y.","NRLMFβ: Bata-distribution-rescored Neighborhood Regularized Logistic Matrix Factorization for Improving Performance of Drug?Target Interaction Prediction",,"Biochemistry and Biophysics Reports","Elsevier","Volume 18",,,2019,July
"Ohue M,Ii R,Yanagisawa K,Akiyama Y.","Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graph","Parallel and Distributed Processing Techniques and Applications （PDPTA'19）","In Proceedings of the 2019 International Conference on Parallel and Distributed Processing Techniques & Applications (PDPTA'19)",,,,"Page 122-128",2019,July
"Aoyama K,Yamamoto Y,Ohue M,Akiyama Y.","Performance evaluation of MEGADOCK protein?protein interaction prediction system implemented with distributed containers on a cloud computing environment","Parallel and Distributed Processing Techniques and Applications （PDPTA'19）","In Proceedings of the 2019 International Conference on Parallel and Distributed Processing Techniques & Applications (PDPTA'19)",,,,"pp. 175-181",2019,July
"Ohue M,Ii R,Yanagisawa K,Akiyama Y.","Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graph",,"IPSJ SIG Technical Report",,"Vol. 2019-MPS-124","No. 3","pp. 1-4",2019,July
"李佳男,吉川寧,大上雅史,秋山泰.","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","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）",,"Vol. 2019-BIO-58","No. 52","pp. 1-8",2019,June
"松野駿平,大上雅史,秋山泰.","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","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","Vol. 2019-BIO-58","No. 53","pp. 1-7",2019,June
"木曽良明,秋山 泰,大上 雅史,吉川 寧,和久井 直樹","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）",,"木曽良明監修「ペプチド創薬の最前線」","シーエムシー出版",,,"pp. 70-78",2019,May
"大上雅史,林孝紀,秋山泰","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」",,"実験医学 2019年6月号","羊土社","Vol. 37","No. 9","pp. 1469-1474",2019,May
"林 孝紀,大上 雅史,秋山 泰.","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","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","Vol. 2019-BIO-57","No. 12","pp. 1-8",2019,Mar.
"大上雅史","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","ファーマIT&デジタルヘルスエキスポ2019",,,,,,2019,Mar.
"黄毅聰,吉川寧,和久井直樹,大上雅史,秋山泰.","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","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","Vol. 2019-BIO-57","No. 10","pp. 1-8",2019,Mar.
"伊井 良太,柳澤 渓甫,大上 雅史,秋山 泰","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","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","Vol. 2019-BIO-57","No. 11","pp. 1-8",2019,Mar.
"Masahito Ohue,Takanori Hayashi,Yuri Matsuzaki,Keisuke Yanagisawa,Yutaka Akiyama","Megadock-Web: An Integrated Database of High-Throughput Structure-Based Protein-Protein Interaction Predictions","Biophysical Society 63rd Annual Meeting",,,,,,2019,Mar.
"山田 雄太,吉川 寧,和久井 直樹,大上 雅史,秋山 泰","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","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","Vol. 2019-BIO-57","No. 13","pp. 1-8",2019,Mar.
"大上雅史","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","2018年度リサーチコンプレックス融合研究報告会",,,,,,2019,Mar.
"Koki Yamamoto,Yasushi Yoshikawa,Masahito Ohue,Shinsuke Inuki,Hiroaki Ohno,Shinya Oishi","Synthesis of Triazolo- and Oxadiazolopiperazines by Gold(I)-Catalyzed Domino Cyclization: Application to the Design of a Mitogen Activated Protein (MAP) Kinase Inhibitor",,"Organic Letters","American Chemical Society","Volume 21","Issue 2","Page 373-377",2018,Dec.
"Takashi Tajimi,Naoki Wakui,Keisuke Yanagisawa,Yasushi Yoshikawa,Masahito Ohue,Yutaka Akiyama","Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques",,"BMC Bioinformatics","Springer Nature","Volume 19",,,2018,Dec.
"Masahito Ohue","High Performance Computing Drug Discovery - Toward Targeting Protein-Protein Interactions","Advances in Neuroinformatics 2018 (AINI2018)",,,,,,2018,Dec.
"Takashi Tajimi,Naoki Wakui,Keisuke Yanagisawa,Yasushi Yoshikawa,Masahito Ohue,Yutaka Akiyama","Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques","the 29th International Conference on Genome Informatics (GIW 2018)","BMC Bioinformatics","Springer Nature","Volume 19",,,2018,Dec.
"Masahito Ohue","Exploring Protein-Protein Interactions with MEGADOCK: Parallelization, Application, and Open Database","KAUST CBRC Seminar",,,,,,2018,Nov.
"Daisuke Kami,Tomoya Kitani,Akihiro Nakamura,Naoki Wakui,Rena Mizutani,Masahito Ohue,Fuyuki Kametani,Nobuyoshi Akimitsu,Satoshi Gojo","The DEAD-box RNA-binding protein DDX6 regulates parental RNA decay for cellular reprogramming to pluripotency",,"PLOS ONE",,"Volume 13","Issue 10",,2018,Oct.
"Masahito Ohue","Supercomputing-based exhaustive protein-protein interaction prediction and its open database","The 56th Annual Meeting of the Biophysical Society of Japan",,,,,,2018,Sept.
"Masahito Ohue","Prediction of Protein-Protein Interactions with MEGADOCK: Parallelization, Application, and Open Database","Asia Hub e-Drug Discovery Symposium (AHeDD2018)",,,,,,2018,Sept.
"Masahito Ohue,Takanori Hayashi,Hiroki Watanabe,Yuri Matsuzaki,Nobuyuki Uchikoga,Yutaka Akiyama","Supercomputing-based exhaustive protein-protein interaction prediction and its open database.","The 56th Annual Meeting of the Biophysical Society of Japan",,,,,,2018,Sept.
"Masahiro Mochizuki,Shogo Suzuki,Yanagisawa K,Ohue M,Akiyama Y.","QEX: target-specific druglikeness filter enhances ligand-based virtual screening",,"Molecular Diversity","Springer","Volume 23","issue 1","pp. 11-18",2018,July
"青山健人,大上雅史,秋山泰","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","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","  2018-BIO-54","  47","  1-7",2018,June
"渡辺紘生,林孝紀,大上雅史,秋山泰","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","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","  2018-BIO-54","  46","  1-8",2018,June
"多治見隆志,和久井直樹,大上雅史,秋山泰","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","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","  2018-BIO-54","  45","  1-8",2018,June
"Shogo Suzuki,Masahito Ohue,Yutaka Akiyama","PKRank: a novel learning-to-rank method for ligand-based virtual screening using pairwise kernel and RankSVM",,"Artificial Life and Robotics","Springer Japan","  23","  2","  205-212",2018,June
"Yanagisawa K,Komine S,Kubota R,Ohue M,Akiyama Y.","Optimization of memory use of fragment extension-based protein?ligand docking with an original fast minimum cost flow algorithm",,"Computational Biology and Chemistry (In Proc. APBC2018)",,"Volume 74",,"Page 399-406",2018,June
"久保田陸人,柳澤渓甫,大上雅史,秋山泰","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","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","  2018-BIO-54(42)",,"  1-8",2018,June
"Masahito Ohue","MEGADOCK: a supercomputing bioinformatics application for protein-protein interaction prediction","第1回 RWBC-OIL Workshop",,,,,,2018,May
"Hayashi T,Matsuzaki Y,Yanagisawa K,Ohue M,Akiyama Y.","MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions",,"BMC Bioinformatics (In Proc. APBC2018)",,"  19","  (Suppl 4)","  62",2018,May
"Ban T,Masahito O,Yutaka Akiyama","Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem",,"Computational Biology and Chemistry",,"Volume 73",,"Page 139-146",2018,Apr.