[[https://researchmap.jp/yoichi|ResearchMap]]\\
===== 学術論文(査読あり) =====
  * 有澤文太, 村上洋一, 小早川睦貴, 布広永示, (2023), "喫煙画像刺激時の喫煙者の脳波に有意に変化する周波数成分と喫煙経験との関係性に関する研究", 東京情報大学研究論集, vol.27, no.2, pp.1-11. (2024年3月末発行予定）
  * Murakami, Y. and Mizuguchi, K. (2022), "Recent developments of sequence-based prediction of protein–protein interactions", Biophysical Reviews. vol.14, no.6, pp.1393-1411.
  * 水野芳子, 西村あをい, 村上洋一, 前田はる香, 山浦那津子, (2022),"多様な施設で行う小児看護学実習の学びの特徴", 東京情報大学研究論集, vol.25, no.2, pp.45-54.
  * Saito, A. Tsuchiya, D. Sato, S. Okamoto, A. Murakami, Y. Mizuguchi, K. Toh, H. Nemoto, W. (2020), "Update of the GRIP web service", Journal of Receptors and Signal Transduction, vol.40, no.4, pp.348-356.
  * 中野心太, 早稲田篤志, 村上洋一, 岸本頼紀, 花田真樹, 関口竜也, 折田彰, 布広永示, (2020), "不正アクセスの痕跡情報を用いたタイムライン型イベントログ可視化機能の開発", 東京情報大学研究論集, vol.24, no.1, pp.1-10.
  * Murakami Y, (2019), "Study of Characterization of Promiscuous Binding Sites in Protein-Small Molecule Complexes", Proceedings of the 2019 6th International Conference on Bioinformatics Research and Applications, pp.67–72, https://doi.org/10.1145/3383783.3383794
  * Tripathi, L.P. Chen, Y.A. Mizuguchi, K. Murakami, Y. (2019), "Network-Based Analysis for Biological Discovery" , Encyclopedia of Bioinformatics and Computational Biology, vol.3, pp.283-291.
  * Murakami, Y. and Mizuguchi, K. (2017), “Making protein-protein interaction prediction more reliable with a large-scale dataset at the proteome level”, Journal of Bioinformatics and Neuroscience, vol.3, issue.3, pp.91-98.
  * Murakami, Y. and Mizuguchi, K. (2017), “PSOPIA: Toward more reliable protein-protein interactions prediction from sequence information”, Intelligent Informatics and Biomedical Sciences (ICIIBMS), 2017 International Conference on, doi: 10.1109/ICIIBMS.2017.8279749.
  * Murakami, Y et al. (2017), “Network analysis and in silico prediciton of protein-protein interactions with applications in drug discovery”, Current Opinion in Structural Biology, vol.44, pp.134-142, doi: 10.1016/j.sbi.2017.02.005.
  * Murakami, Y et al. (2017), “Network analysis and in silico prediciton of protein-protein interactions with applications in drug discovery”, Current Opinion in Structural Biology, (in press).
  * Murakami, Y et al. (2016), “NLDB: a database for 3D protein–ligand interactions in enzymatic reactions”, Journal of Structural and Functional Genomics, vol.17, issue.4. pp.101-110, doi:10.1007/s10969-016-9206-0.
  * Chen, Y.A et al. (2014), “Brefeldin A-inhibited guanine nucleotide-exchange protein 3 (BIG3) is predicted to interact with its partner through an ARM-type alpha helical structure”, BMC Research Notes, 7:435, doi:10.1186/1756-0500-7-435.
  * Murakami, Y et al. (2014), “Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators”, BMC Bioinformatics, 15:213, doi:10.1186/1471-2105-15-213.
  * Lensink, M.F et al., (2013), “Blind Prediction of Interfacial Water Positions in CAPRI”, Proteins: Structure, Function and Bioinformaces, 82(4), pp.620-632, doi:10.1002/prot.24439.
  * Yoshimaru, T et al. (2013), “Targeting BIG3-PHB2 interaction to overcome tamoxifen resistance in breast cancer cells”, Nature Communication, 4:2443, doi:10.1038/ncomms3443.
  * Murakami, Y et al. (2013), “Exhaustive comparison and classification of ligand-binding surfaces in proteins”, Protein Science, 22(10), pp.1379-1391, doi:10.1002/pro.2329
  * Kanamori et al. (2013), “Biomolecular Forms and Functions”, in Bansal,M. and Srlnlvasan,N. (eds.), World Scientific, Singapore, pp.160-172.
  * Murakami, Y. and Mizuguchi, K. (2010), “Applying the Naive Byes classifier with kernel density estimation to the prediction of protein-protein interaction sites”, Bioinformatics, 26(15), pp.1841-1848, doi:10.1093/bioinformatics/btq302.
  * Murakami, Y et al. (2010), “Sequence-based prediction of protein-protein interaction sites using a Naïve Bayes classifier with kernel density estimation”, The proceedings of the 2010 Annual Conference of the Japanese Society for Bioinformatics, pp.1379-1391.
  * Murakami, Y.* and Spriggs, R.V* et al. (2010), “PiRaNhA: A server for the computational prediction of RNA-binding residues in protein sequences”, Nucleic Acid Research, 38(Web Server Issue): W412-W416, doi:10.1093/nar/gkq474. * 共同筆頭著者
  * Spriggs, R.V.* and Murakami, Y* et al. (2009), “Protein Function annotation from sequence: prediction of specific RNA-binding residues”, Bioinformatics, 25(12), pp.1492-1497, doi:10.1093/bioinformatics/btp257. * 共同筆頭著者
  * Murakami, Y et al. (2008), “Development of a fast similarity search method for the molecular surface database”, The proceedings of the 2008 Annual Conference of the Japanese Society for Bioinformatics, pp.026.1-026.2.
  * Kanamori, K et al. (2007), “Docking of protein molecular surfaces with evolutionary trace analysis”, Proteins: Structural, Function, and Bioinformatics, vol.69, issue.4, pp.832-838, doi:10.1002/prot.21737.
  * Kinoshita, K et al. (2007), “eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape”, Nucleic Acid Research, 35(Web Server Issue), W398-W402, doi:10.1093/nar/gkm351.
  * Jones, S. and Murakami, Y. (2007), “Bioinformatics Research and Development, Lecture Notes in Computer Science, Volume 4414”, in Hochreiter,S. and Wangner,S. (eds.), Springer, pp.303-313.
  * Murakami, Y et al. (2006), “SHARP2: protein-protein interaction predictions using patch analysis”, Bioinformatics, 22(14), pp.1794-1795, doi:10.1093/bioinformatics/btl171.

===== 研究論文(査読なし) ====
  * 上田さつき, 村上洋一. (2023) "タンパク質の分散表現とその配列・構造的特徴の関係性に関する解析", 情報処理学会研究報 IPSJ SIG Technical Report, vol.2023-MPS-142,no.20,pp.1-3.
  * 林子易, 鈴木優介, 井関文一, 村上洋一. (2022) "Jupyter を使用したリアルタイム学習進捗監視システムの実装 - プログラミングを効率的に教えるための新しいツール -", 電子情報通信学会技術研究報告 (Web), vol.122, no.191, pp.42-47.
  * 鈴木優介, 林子易, 井関文一, 村上洋一. (2022) "JupyterLab 上での実行ログのリアルタイム取得と学習状況の可視化", 電子情報通信学会技術研究報告 (Web), vol.121, no.406, pp.54-58.

===== その他、著書など =====
  * 村上洋一、長尾知生子、水口賢司 (2023) 「ケモインフォマティクスにおけるデータ収集の最適化と解析手法」 『第8章・5節 創薬研究に有用なデータベースとその活用のポイント)』 技術情報協会 (ISBN: 9784861049446)
  * 村上洋一、水口賢司 （2018）「in silicoを用いたタンパク質間相互作用(PPI)の網羅的解析と創薬応用」 『In silico創薬におけるスクリーニングの高速化・高精度化技術』 技術情報協会
  * Kanamori et al. (2013), “Biomolecular Forms and Functions”, in Bansal,M. and Srlnlvasan,N. (eds.), World Scientific, Singapore, pp.160-172.
  * Murakami, Y et al. (2010), “Sequence-based prediction of protein-protein interaction sites using a Naïve Bayes classifier with kernel density estimation”, The proceedings of the 2010 Annual Conference of the Japanese Society for Bioinformatics, pp.1379-1391.
  * Murakami, Y et al. (2008), “Development of a fast similarity search method for the molecular surface database”, The proceedings of the 2008 Annual Conference of the Japanese Society for Bioinformatics, pp.026.1-026.2.
  * Jones, S. and Murakami, Y. (2007), “Bioinformatics Research and Development, Lecture Notes in Computer Science, Volume 4414”, in Hochreiter,S. and Wangner,S. (eds.), Springer, pp.303-313.

===== 主な学会発表・講演など =====
  * 「PSOPIA: Toward more reliable protein-protein interactions prediction from sequence information」International Conference on Intelligent Informatics and Biomedical Sciences (ICIIBMS)（於沖縄科学技術大学院大学）, 2017.11
  * 「A machine learning approach for predicting protein-protein interactions」 大阪大学蛋白質研究所セミナー (於大阪大学 蛋白質研究所), 2015.3
  * 「Exhaustive comparison of representative partial surfaces of ligand binding sites in proteins」 2011年日本バイオインフォマティクス学会年会 (於神戸国際会議場）, 2011.11
  * 「PiRaNhA: a server for the prediction of RNA-binding residues in protein sequences」 日英シンポジウム（於千里ライフサイエンスセンター), 2008.9
  * 「An application of genetic algorithm to a backward evolution of cellular automata」 1999 International Symposium on Nonlinear Theory and its Applications NOLTA’99 （於ハワイ島,アメリカ）, 1999.11