"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
"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
"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.
"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","  2022-BIO-74","  38","  1-8",2023,June
"Kengkanna Apakorn,大上 雅史","Enhancing Ligand Property and Activity Prediction and Interpretation Using Multiple Molecular Graph Representations",,"研究報告バイオ情報学（BIO）","情報処理学会","  2023-BIO-73","  35","  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 62","Issue 18","pp. 4549-4560",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.
"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.
"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.
"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.
"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.
"Takafumi Ueki,Masahito Ohue","Improvement of physical properties by redesigning antibody sequences using AfDesign","第6回Tokyo Bioinformatics Meeting",,,,,,2022,Oct.
"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.
"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",,,,,,,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.
"Kairi Furui,Masahito Ohue","Lead optimization through active learning using free energy perturbation","CBI学会2022年大会",,,,,,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.
"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.
"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.
"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.
"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","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.
"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.
"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
"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
"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
"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
"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.
"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.
"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.
"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.
"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.
"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.
"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.
"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.
"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.
"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.
"Yoshio Ri,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.
"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.
"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","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","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.
"Shunya Sugita,Masahito Ohue","Drug-target affinity prediction using applicability domain of feature learning","第5回Tokyo Bioinformatics Meeting",,,,,,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.
"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.
"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.
"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.
"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.
"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.
"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.
"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.
"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.
"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)",,"IEEE",,,,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.
"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",,,,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.
"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.
"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.
"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.
"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.
"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.
"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.
"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",,,,2021,Aug.
"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
"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",,,"pp. 737-746",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
"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
"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
"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.
"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.
"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.
"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",,"情報処理学会研究報告",,"Vol. 2021-BIO-65","No. 8","pp. 1-3",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","  12-13",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.
"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","産総研AIRC 第51回AIセミナー「生命科学系データサイエンスの最前線」",,,,,,2020,Nov.
"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","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.
"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.
"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,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.
"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.
"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
"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.
"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.
"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.
"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.
"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.
"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.
"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.
"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.
"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.
"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.
"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.
"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.
"Max Druyvesteyn,Masahito Ohue,Yutaka Akiyama","Improved protein-protein docking using arbitrary docking-derived protein interface predictions","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.
"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.
"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.
"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.
"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,
"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","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.
"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.
"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.
"Masahito Ohue","Learning-to-rank for ligand-based virtual screening","AHeDD2019/IPAB2019 Joint Symposium",,,,,,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.
"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.
"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.
"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.
"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.
"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.
"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.
"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.
"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.
"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.
"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.
"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.
"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
"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","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
"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",,"IPSJ SIG Technical Report",,"Vol. 2019-MPS-124","No. 3","pp. 1-4",2019,July
"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
"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
"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
"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.
"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.
"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.
"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.
"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.
"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.
"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","High Performance Computing Drug Discovery - Toward Targeting Protein-Protein Interactions","Advances in Neuroinformatics 2018 (AINI2018)",,,,,,2018,Dec.
"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","the 29th International Conference on Genome Informatics (GIW 2018)","BMC Bioinformatics","Springer Nature","Volume 19",,,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","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
"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
"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
"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
"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
"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
"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
"Masahito Ohue","MEGADOCK: a supercomputing bioinformatics application for protein-protein interaction prediction","第1回 RWBC-OIL Workshop",,,,,,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.
"山本悠生,大上雅史,秋山泰","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","情報処理学会研究報告 バイオ情報学（BIO）",,,"  2018-BIO-53(8)",,,2018,Mar.
"大上雅史","出会い系タンパク質を探す旅","情報処理学会第80回全国大会",,,,,,2018,Mar.
"山本悠生,大上雅史,秋山泰.","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","情報処理学会 第53回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2017-BIO-53","  8","  1-8",2018,Mar.
"後藤公太,大上雅史,石田貴士,秋山泰","配列相同性検索ツールGHOSTZ-GPUのMPI環境における高速化","情報処理学会 第53回バイオ情報学研究会","情報処理学会研究報告",,"  2017-BIO-53","  7","  1-8",2018,Mar.
"後藤公太,大上雅史,石田貴士,秋山泰","配列相同性検索ツールGHOSTZ-GPUのMPI環境における高速化","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","  2018-BIO-53","  7","  1-8",2018,Mar.
"Wakui, N.,Yoshino, R.,Yasuo, N.,Ohue, M.,Sekijima, M.","Exploring the selectivity of inhibitor complexes with Bcl-2 and Bcl-XL: A molecular dynamics simulation approach",,"Journal of Molecular Graphics and Modelling",,"Vol. 79",,"pp. 166-174",2018,Jan.
"Naoki Wakui,Ryunosuke Yoshino,Nobuaki Yasuo,Masahito Ohue,Masakazu Sekijima","Exploring the selectivity of inhibitor complexes with Bcl-2 and Bcl-XL: a molecular dynamics simiulation approach","4th IIT Madras-Tokyo Tech Joint Symposium on Frontiers in Bioinformatics: Large Scale Data Analysis, Resources and Drug Design",,,,,,2017,Nov.
"Masahito Ohue,Yuki Yamamoto,Kento Aoyama,Yutaka Akiyama","MEGADOCK-Azure: high-performance protein-protein docking on Microsoft Azure HPC","4th IIT Madras-Tokyo Tech Joint Symposium on Frontiers in Bioinformatics: Large Scale Data Analysis, Resources and Drug Design",,,,,,2017,Nov.
"Masahito Ohue","Prediction of Protein-Protein Interactions with MEGADOCK: Parallelization, Application, and Open Database","4th IIT Madras-Tokyo Tech Joint Symposium on Frontiers in Bioinformatics: Large Scale Data Analysis, Resources and Drug Design",,,,,,2017,Nov.
"Ban T,Ohue M,Akiyama Y","Efficient Hyperparameter Optimization by Using Bayesian Optimization for Drug-Target Interaction Prediction","In Proceedings of the 7th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2017)",,"IEEE",,,,2017,Oct.
"Ohue M,Yamazaki T,Ban T,Akiyama Y","Link Mining for Kernel-based Compound-Protein Interaction Predictions Using a Chemogenomics Approach","Intelligent Computing Theories and Application (In Proceedings of ICIC2017, Lecture Notes in Computer Science)","Lecture Notes in Computer Science","Springer, Cham","Vol. 10362",,"pp. 549-558",2017,Aug.
"山澤 まりな,伊澤 和輝,大上 雅史,石田 貴士,Kazuyuki Ishihara,秋山 泰","高速相同性解析ツールGHOSTXを用いた口腔内メタゲノム解析","情報処理学会 第50回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2017-BIO-50","  41","  1-7",2017,June
"伊澤 和輝,山澤 まりな,大上 雅史,石田 貴士,秋山 泰","歯周病の発症要因の特定に向けた口腔内細菌叢解析","情報処理学会 第50回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2017-BIO-50","  40","  1-6",2017,June
"柳澤渓甫,小峰駿汰,久保田陸人,大上雅史,秋山泰","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","情報処理学会 第50回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2017-BIO-50","  38","  1-8",2017,June
"林孝紀,山本悠生,松崎由理,大上雅史,秋山泰","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","情報処理学会 第50回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2017-BIO-50","  39","  1-8",2017,June
"Yuri Matsuzaki,Nobuyuki Uchikoga,Masahito Ohue,Yutaka Akiyama","Rigid-Docking Approaches to Explore Protein?Protein Interaction Space",,"Advances in Biochemical Engineering/Biotechnology(Network Biology)","Springer, Cham","volume 160",,"pp. 33-35",2017,May
"Shuji Suzuki,Takashi Ishida,Masahito Ohue,Masanori Kakuta,Yutaka Akiyama","GHOSTX: A Fast Sequence Homology Search Tool for Functional Annotation of Metagenomic Data",,"Methods in Molecular Biology(Protein Function Prediction)","Springer","Volume 1611",,"pp. 15-25",2017,Apr.
"柳澤渓甫,大上雅史,石田貴士,秋山泰","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","情報処理学会 第49回バイオ情報学研究会","研究報告バイオ情報学（BIO）",,"  2017-BIO-49","  6","  1-7",2017,Mar.
"Yanagisawa K,Komine S,Shogo Suzuki,Ohue M,Ishida T,Akiyama Y.","Spresso: an ultrafast compound pre-screening method based on compound decomposition",,"Bioinformatics","OXFORD Academic","Volume 33","Issue 23","Page 3836-3843",2017,Mar.
"大上 雅史,山本 悠生,秋山 泰","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","情報処理学会 第49回バイオ情報学研究会","研究報告バイオ情報学（BIO）",,"  2017-BIO-49","  4","  1-3",2017,Mar.
"青山 健人,山本 悠生,大上 雅史,秋山 泰","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","情報処理学会 第49回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2017-BIO-49","  3","  1-8",2017,Mar.
"Uchikoga, Nobuyuki,Yuri Matsuzaki,Masahito Ohue,Yutaka Akiyama","Interaction Surfaces of Proteins Involved in Bacterial Chemotaxis with Rigid-Body Docking Decoys","58th Annual Meeting of the Biophysical-Society","BIOPHYSICAL JOURNAL","CELL PRESS","Vol. 112","No. 3","pp. 290A-290A",2017,Feb.
"Masahito Ohue,Yamamoto, Yuki,Hayashi, Takanori,Yuri Matsuzaki,Yutaka Akiyama","Cloud Computing for All-To-All Protein-Protein Docking on Azure HPC","58th Annual Meeting of the Biophysical-Society","BIOPHYSICAL JOURNAL","CELL PRESS","Vol. 112","No. 3","pp. 451A-451A",2017,Feb.
"Shogo Suzuki,Masahito Ohue,Yutaka Akiyama","Learning-to-rank based compound virtual screening by using pairwise kernel with multiple heterogeneous experimental data","22nd International Symposium on Artifical Life and Robotics",,,,,"  114-119",2017,Jan.
"高橋 聡,新井 宗仁,大上雅史,広瀬 恵子","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",,"生物物理","一般社団法人 日本生物物理学会","Vol. 57","No. 3","pp. 159-160",2017,
"Keisuke Yanagisawa,Shunta Komine,Shogo Suzuki,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","ESPRESSO: An ultrafast compound pre-screening method with segmented compounds","Chem-Bio Informatics Society(CBI) Annual Meeting 2016",,,,,,2016,Oct.
"Kazuki Yamamoto,Yoshitaka Moriwaki,Keita Oda,Masahito Ohue,Itsuo Nakane,Ryunosuke Yoshino,Hayase Hakariya,Tadaaki Mashimo,Mitsuhito Wada,Yoshifumi Fukunishi","Human insight in drug discovery: docking pose selection in protein-ligand docking and hit-compounds selection in structure-based virtual screening","Chem-Bio Informatics Society(CBI) Annual Meeting 2016",,,,,,2016,Oct.
"Keisuke Yanagisawa,Shunta Komine,Shogo Suzuki,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","ESPRESSO: An ultrafast compound pre-screening method based on compound decomposition","The 27th International Conference on Genome Informatics (GIW 2016)",,,,,,2016,Oct.
"大上雅史","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","CBI学会2016年大会",,,,,,2016,Oct.
"Shogo Suzuki,Masahito Ohue,Yutaka Akiyama","Learning to Rank with Ignoring Meaningless Order and Its Application to Virtual Screening for Drug Discovery","Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)",,,,,,2016,Sept.
"Masahito Ohue,Yuki Yamamoto,Hiroyuki Sato,Takashi Matsushita,Yutaka Akiyama","MEGADOCK-Azure: High-performance protein-protein interaction prediction system on Microsoft Azure HPC","Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)",,,,,,2016,Sept.
"Keisuke Yanagisawa,Shunta Komine,Shogo Suzuki,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","ESPRESSO: An ultrafast compound pre-screening method based on compound segmentation","Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)",,,,,,2016,Sept.
"Kazuki Yamamoto,Yoshitaka Moriwaki,Keita Oda,Masahito Ohue,Itsuo Nakane,Ryunosuke Yoshino,Hayase Hakariya,Tadaaki Mashimo,Mitsuhito Wada,Yoshifumi Fukunishi","Human insight in drug discovery: docking pose selection in protein-ligand docking and hit-compounds selection in structure-based virtual screening","Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)",,,,,,2016,Sept.
"大上雅史","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","FIT2016 第15回情報科学技術フォーラム",,,,,,2016,Sept.
"大上雅史","薬のタネ発見のための計算技術と創薬知BoF","第5回生命医薬情報学連合大会",,,,,,2016,Sept.
"Kota Goto,Kota Kasahara,Masahito Ohue,Haruki Nakamura,Yutaka Akiyama","Accelerating SHAKE Calculation of myPresto/omegagene Molecular Dynamics Simulation on CPU/GPU heterogeneous environment","Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)",,,,,,2016,Sept.
"Marina Yamasawa,Tomoya Fujii,Kota Goto,Masahito Ohue,Takashi Ishida,Kazuyuki Ishihara,Yutaka Akiyama","GPU/MPI Parallelization of Metagenomic Sequence Homology Search Tool and Its Application to Oral Metagenomics","Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)",,,,,,2016,Sept.
"Takanori Hayashi,Kazuki Nagasawa,Yuri Matsuzaki,Masahito Ohue,Yutaka Akiyama","MEGADOCK-WEB: a database of predicted protein-protein interactions and its web interface","Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)",,,,,,2016,Sept.
"Nobuyuki Uchikoga,Yuri Matsuzaki,Masahito Ohue,Yutaka Akiyama","Specificity of broad protein interaction surfaces for proteins with multiple binding partners",,"Biophysics and Physicobiology","THE BIOPHYSICAL SOCIETY OF JAPAN","Vol. 13",,"pp. 105-115",2016,July
"内古閑伸之,松崎由理,大上雅史,秋山泰","細菌走化性におけるタンパク質間相互作用面の解析","第16回日本蛋白質科学会年会",,,,,,2016,June
"鈴木 翔吾,大上 雅史,秋山 泰","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","情報処理学会 第46回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2016-BIO-46","  26","  1-7",2016,June
"柳澤 渓甫,小峰 駿汰,鈴木 翔吾,大上 雅史,石田 貴士,秋山 泰","フラグメント分割に基づく超高速化合物プレスクリーニング手法ESPRESSO","情報処理学会 第46回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2016-BIO-46","  18","  1-7",2016,June
"後藤 公太,笠原 浩太,大上 雅史,中村 春木,秋山 泰","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","情報処理学会 第46回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2016-BIO-46","  17","  1-7",2016,June
"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",,"学振申請書の書き方とコツ DC/PD獲得を目指す若者へ","講談社",,,,2016,Apr.
"根岸瑠美,大上雅史","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",,"生物物理","一般社団法人生物物理学会","Vol. 56","No. 2","pp. 126-127",2016,Mar.
"山崎卓朗,大上雅史,秋山泰","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","情報処理学会 第45回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2016-BIO-45","  9","  1-7",2016,Mar.
"藤井智也,角田将典,大上雅史,石田貴士,石原和幸,秋山泰","GPUを用いたメタゲノム配列相同性解析ツールのMPI並列化と応用",,"研究報告バイオ情報学（BIO）","情報処理学会","  2016-BIO-45","  3","  1-4",2016,Mar.
"長澤一輝,松崎由理,大上雅史,秋山泰","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","情報処理学会 第45回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2016-BIO-45","  2","  1-4",2016,Mar.
"Nobuyuki Uchikoga,Yuri Matsuzaki,Masahito Ohue,Yutaka Akiyama","Analysis of Physico-Chemical Properties of Protein Docking Decoys Generated by Rigid-Body Docking","Biophysical Society 60th Annual Meeting",,,,,,2016,Feb.
"Masahito Ohue,Yuri Matsuzaki,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers","Biophysical Society 60th Annual Meeting",,,,,,2016,Feb.
"Masahito Ohue,Yutaka Akiyama","A rescoring method of protein-peptide docking prediction with amino acid profiles of rigid-body search results","The Fourteenth Asia Pacific Bioinformatics Conference (APBC2016)",,,,,,2016,Jan.
"Tomohiro Ban,Masahito Ohue,Yutaka Akiyama","Improving protein-ligand docking and inverse docking prediction by deepening conformation search on multiple grids","3nd IIT Madras ? Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics",,,,,,2015,Nov.
"柳澤 渓甫,小峰 駿汰,大上 雅史,石田 貴士,秋山 泰","Fast pre-filtering for virtual screening based on ligand decomposition","第21回創剤フォーラム若手研究会",,,,,,2015,Nov.
"鈴木翔吾,大上雅史,秋山泰","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","第21回創剤フォーラム若手研究会",,,,,,2015,Nov.
"伴 兼弘,大上 雅史,秋山 泰","Multiple Grids Arrangement for Improving Conformational Search of Protein-Ligand Docking and Its Application to Inverse Docking Problem","第21回創剤フォーラム若手研究会",,,,,,2015,Nov.
"大上雅史,松崎由理,石田貴士,秋山泰","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","第21回創剤フォーラム若手研究会",,,,,,2015,Nov.
"大上雅史","数学と計算で探るタンパク質の出会いとネットワーク","サイエンスアゴラ2015 数学協働プログラム",,,,,,2015,Nov.
"Yuri Matsuzaki,Masahito Ohue,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK: A high-performance protein-protein interaction prediction software for petascale supercomputing environments","3nd IIT Madras ? Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics",,,,,,2015,Nov.
"Nobuyuki Uchikoga,Yuri Matsuzaki,Masahito Ohue,Takatsugu Hirokawa,Yutaka Akiyama","Analysis of protein docking decoys in terms of physicochemical properties of protein surfaces using rigid-body docking process","3nd IIT Madras ? Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics",,,,,,2015,Nov.
"Keisuke Yanagisawa,Shunta Komine,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","Fast pre-filtering for virtual screening based on compound fragmentation","3nd IIT Madras ? Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics",,,,,,2015,Nov.
"Masahito Ohue,Takehiro Shimoda,Shuji Suzuki,Takashi Ishida,Yutaka Akiyama","A comparative study of GPU and MIC accelerations in fast Fourier transform-based protein-protein docking","3nd IIT Madras ? Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics",,,,,,2015,Nov.
"鈴木翔吾,大上雅史,秋山泰","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","第18回情報論的学習理論ワークショップ (IBIS2015)",,,,,,2015,Nov.
"Uchikoga, Nobuyuki,Masahito Ohue,Yuri Matsuzaki,Yutaka Akiyama","Post-docking analysis by physicochemical properties of protein-protein interactions generated from rigid-body docking processes","29th Annual Symposium of the Protein-Society","PROTEIN SCIENCE","WILEY-BLACKWELL","Vol. 24",,"pp. 253-253",2015,Oct.
"Tomohiro Ban,Masahito Ohue,Yutaka Akiyama","Multiple Grids Arrangement for Ligand Docking and Its Application to Inverse Docking Problem","IIBMP2015",,,,,,2015,Oct.
"Keisuke Yanagisawa,Shunta Komine,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","Fast pre-filtering for virtual screening based on compound decomposition","IIBMP2015",,,,,,2015,Oct.
"内古閑伸之,松崎由理,大上雅史,秋山泰","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","第53回日本生物物理学会年会",,,,,,2015,Sept.
"大上雅史,内古閑伸之,松崎由理,秋山泰","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","第53回日本生物物理学会年会",,,,,,2015,Sept.
"大上雅史","大規模タンパク質間相互作用予測によるEGFR系解析","第4回育志賞研究発表会",,,,,,2015,Aug.
"大上雅史,内古閑伸之,松崎由理,秋山泰","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","第15回日本蛋白質科学会年会",,,,,,2015,June
"鈴木翔吾,柳澤渓甫,大上雅史,石田貴士,秋山泰","SVMとDeep Learningに基づくヒトc-Yesキナーゼ阻害化合物の予測","情報処理学会 第42回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2015-BIO-42","  36","  1-7",2015,June
"和久井直樹,大上雅史,千葉峻太朗,石田貴士,岩?博史,秋山泰","既知の活性／非活性化合物のドッキング解析によるバーチャルスクリーニングに適したタンパク質立体構造モデルの選択","情報処理学会 第42回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2015-BIO-42","  60","  1-4",2015,June
"大上雅史,根岸瑠美","「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",,"生物物理","一般社団法人生物物理学会","Vol. 55","No. 2","pp. 108-110",2015,Mar.
"Nobuyuki Uchikoga,Yuri Matsuzaki,Masahito Ohue,Takatsugu Hirokawa,Yutaka Akiyama","Analysis of amino acid properties in interaction surfaces of decoys generated by re-docking","Biophysical Society 59th Annual Meeting",,,,,,2015,Feb.