@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{CTT100869173,
  author = {Keisuke Yanagisawa and Ryunosuke Yoshino and Genki Kudo and Takatsugu Hirokawa},
  title = {Inverse Mixed-Solvent Molecular Dynamics for Visualization of the Residue Interaction Profile of Molecular Probes},
  journal = {International Journal of Molecular Sciences},
  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{CTT100878409,
  author = {Takabatake K and Yanagisawa K and Akiyama Y.},
  title = {Solving Generalized Polyomino Puzzles Using the Ising Model},
  journal = {Entropy},
  year = 2022,
}

@article{CTT100862160,
  author = {Takabatake K and Izawa K and Akikawa M and Yanagisawa K and Ohue M and Akiyama Y.},
  title = {Improved large-scale homology search by two-step seed search using multiple reduced amino acid alphabets},
  journal = {Genes},
  year = 2021,
}

@article{CTT100876596,
  author = {柳澤渓甫},
  title = {タンパク質立体構造情報を用いた薬剤バーチャルスクリーニング},
  journal = {JSBi Bioinformatics Review},
  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{CTT100857382,
  author = {Keisuke Yanagisawa and Yoshitaka Moriwaki and Tohru Terada and Kentaro Shimizu},
  title = {EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation},
  journal = {},
  year = 2021,
}

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

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

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

@inproceedings{CTT100876344,
  author = {杉田昌岳 and 杉山聡 and 藤江拓哉 and 吉川寧 and 柳澤渓甫 and 大上雅史 and 秋山泰},
  title = {分子動力学シミュレーションに基づいた環状ペプチドの膜透過率の大規模予測},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100876345,
  author = {杉田昌岳 and 杉山聡 and 藤江拓哉 and 吉川寧 and 柳澤渓甫 and 大上雅史 and 秋山泰},
  title = {分子動力学シミュレーションに基づいた環状ペプチドの膜透過率の大規模予測},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100876239,
  author = {Kazuki Takabatake and Kazuki Izawa and Motohiro Akikawa and Keisuke Yanagisawa and Masahito Ohue and Yutaka Akiyama},
  title = {Improved Homology Search for Metagenomic Analysis by Two-Step Seed Search with Reduced Amino Acid Alphabets},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100876383,
  author = {Sugita M and Sugiyama S and Takuya Fujie and Yoshikawa Y and Yanagisawa K and Ohue M and Akiyama Y.},
  title = {Large-scale membrane permeability prediction of cyclic peptides crossing a lipid bilayer based on enhanced sampling molecular dynamics simulations},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100876380,
  author = {杉田昌岳 and 杉山聡 and 藤江拓哉 and 吉川寧 and 柳澤渓甫 and 大上雅史 and 秋山泰},
  title = {分子動力学シミュレーションに基づいた環状ペプチドの膜透過率の大規模予測},
  booktitle = {},
  year = 2021,
}

@inproceedings{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{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{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{CTT100849183,
  author = {柳澤 渓甫},
  title = {共溶媒分子動力学シミュレーションにおける創薬向け共溶媒セットの構築},
  booktitle = {},
  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{CTT100849419,
  author = {Keisuke Yanagisawa and Yoshitaka Moriwaki and Tohru Terada and Kentaro Shimizu},
  title = {Systematic construction of the cosolvents sets for cosolvent MD (CMD) with the large-scale simulation},
  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{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{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{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{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{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{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{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{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{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{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{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{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{CTT100715186,
  author = {Keisuke Yanagisawa and Shunta Komine and Masahito Ohue and Takashi Ishida and Yutaka Akiyama},
  title = {Fast pre-filtering for virtual screening based on compound decomposition},
  booktitle = {},
  year = 2015,
}

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

@misc{CTT100893466,
  author = {齋藤那哉 and 柳澤渓甫 and 秋山 泰},
  title = {フラグメント対の相対位置から検索可能な化合物立体配座データベースの構築},
  year = 2023,
}

@misc{CTT100893465,
  author = {渡辺銀河 and 柳澤渓甫 and 秋山 泰},
  title = {標的RNAの高次構造予測に基づく低活性ASO候補配列の推測},
  year = 2023,
}

@misc{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},
  year = 2023,
}

@misc{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},
  year = 2022,
}

@misc{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},
  year = 2022,
}

@misc{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},
  year = 2022,
}

@misc{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},
  year = 2022,
}

@misc{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},
  year = 2022,
}

@misc{CTT100792339,
  author = {Keisuke Yanagisawa},
  title = {Fast structure-based virtual screening with commonality of compound substructure},
  year = 2019,
}

@misc{CTT100792348,
  author = {柳澤渓甫},
  title = {化合物群の部分構造の共通性に着目した高速バーチャルスクリーニング手法の開発},
  year = 2019,
}

@misc{CTT100826664,
  author = {Keisuke Yanagisawa},
  title = {Fast structure-based virtual screening with commonality of compound substructure},
  year = 2019,
}

@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{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)}
}


@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)}
}




@phdthesis{CTT100792339,
  author = {Keisuke Yanagisawa},
  title = {Fast structure-based virtual screening with commonality of compound substructure},
  school = {東京工業大学},
  year = 2019,
}

@phdthesis{CTT100792348,
  author = {柳澤渓甫},
  title = {化合物群の部分構造の共通性に着目した高速バーチャルスクリーニング手法の開発},
  school = {東京工業大学},
  year = 2019,
}

@phdthesis{CTT100826664,
  author = {Keisuke Yanagisawa},
  title = {Fast structure-based virtual screening with commonality of compound substructure},
  school = {東京工業大学},
  year = 2019,
}