Yasushi Okuno - RankMe

67 papers C 1Journal 58Unranked 8

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Chemical genomics language model toward reliable and explainable compound-protein interaction exploration. J. Cheminformatics Takuto Koyama, Hayato Tsumura, Ryunosuke Okita, Kimihiro Yamazaki, Aki Hasegawa, Keiko Imamura, Takashi Kato, Hiroaki Iwata, Ryosuke Kojima, Haruhisa Inoue, Shigeyuki Matsumoto, Yasushi Okuno
2026	J	`jnl`	ClinDet-Bench: Beyond Abstention, Evaluating Judgment Determinability of LLMs in Clinical Decision-Making. CoRR Yusuke Watanabe, Yohei Kobashi, Takeshi Kojima, Yusuke Iwasawa, Yasushi Okuno, Yutaka Matsuo
2026	J	`jnl`	Elucidating Ligand Charge Effects in MR1 Cell-Surface Translocation Using Molecular Simulations. J. Chem. Inf. Model. Toshiki Fujii, Mitsugu Araki, Shigeyuki Matsumoto, Biao Ma, Takao Otsuka, Gert-Jan Bekker, Narutoshi Kamiya, Hiroaki Ohno, Shinsuke Inuki, Yasushi Okuno
2026	J	`jnl`	Empowering federated learning for robust compound-protein interaction prediction across heterogeneous cross-pharma domains. J. Cheminformatics Takuto Koyama, Hiroaki Iwata, Ryosuke Kojima, Takao Otsuka, Aki Hasegawa, Seungeon Lee, Hiroshi Ueda, Toshiharu Morimoto, Ryoko Sasaki, Nao Torimoto, Sei Murakami, Manabu Tojo, Teruki Honma, Shigeyuki Matsumoto, Yasushi Okuno
2025	J	`jnl`	HELM-BERT: A Transformer for Medium-sized Peptide Property Prediction. CoRR Seungeon Lee, Takuto Koyama, Itsuki Maeda, Shigeyuki Matsumoto, Yasushi Okuno
2025	J	`jnl`	Improving ADME Prediction with Multitask Graph Neural Networks and Assessing Explainability in Lead Optimization. J. Chem. Inf. Model. Shoma Ito, Takuto Koyama, Shigeyuki Matsumoto, Ryosuke Kojima, Yuji Okamoto, Masataka Kuroda, Hitoshi Kawashima, Reiko Watanabe, Tomoki Yonezawa, Takaaki Sumiyoshi, Kazuyoshi Ikeda, Kenji Mizuguchi, Hiroaki Iwata, Yasushi Okuno
2025	J	`jnl`	Supervised Graph Contrastive Learning for Gene Regulatory Network. CoRR Sho Oshima, Yuji Okamoto, Taisei Tosaki, Ryosuke Kojima, Yasushi Okuno
2025	J	`jnl`	kMoL: an open-source machine and federated learning library for drug discovery. J. Cheminformatics Romeo Cozac, Haris Hasic, Jun Jin Choong, Vincent Richard, Loic Beheshti, Cyrille Froehlich, Takuto Koyama, Shigeyuki Matsumoto, Ryosuke Kojima, Hiroaki Iwata, Aki Hasegawa, Takao Otsuka, Yasushi Okuno
2024	J	`jnl`	Binding Mechanism between Platelet Glycoprotein and Cyclic Peptide Elucidated by McMD-Based Dynamic Docking. J. Chem. Inf. Model. Gert-Jan Bekker, Kanji Oshima, Mitsugu Araki, Yasushi Okuno, Narutoshi Kamiya
2024	J	`jnl`	Out-of-distribution Reject Option Method for Dataset Shift Problem in Early Disease Onset Prediction. CoRR Taisei Tosaki, Eiichiro Uchino, Ryosuke Kojima, Yohei Mineharu, Mikio Arita, Nobuyuki Miyai, Yoshinori Tamada, Tatsuya Mikami, Koichi Murashita, Shigeyuki Nakaji, Yasushi Okuno
2024	—	`conf`	Subgrouping Causal Networks of Disease Onset in Large-scale Health and Medical Data using Supercomputer Fugaku. BIBM Taisei Tosaki, Eiichiro Uchino, Yohei Harada, Minoru Sakuragi, Yusuke Koyanagi, Seiji Okajima, Hirofumi Suzuki, Kentaro Kanamori, Masahiro Asaoka, Kouji Kurihara, Takuya Takagi, Koji Maruhashi, Yoshinori Tamada, Tatsuya Mikami, Koichi Murashita, Shigeyuki Nakaji, Yasushi Okuno
2023	J	`jnl`	A New Deep State-Space Analysis Framework for Patient Latent State Estimation and Classification from EHR Time Series Data. CoRR Aya Nakamura, Ryosuke Kojima, Yuji Okamoto, Eiichiro Uchino, Yohei Mineharu, Yohei Harada, Mayumi Kamada, Manabu Muto, Motoko Yanagita, Yasushi Okuno
2023	—	`conf`	An Auto-Encoder to Reconstruct Structure with Cryo-EM Images via Theoretically Guaranteed Isometric Latent Space, and Its Application for Automatically Computing the Conformational Pathway. MICCAI (1) Kimihiro Yamazaki, Yuichiro Wada, Atsushi Tokuhisa, Mutsuyo Wada, Takashi Katoh, Yuhei Umeda, Yasushi Okuno, Akira Nakagawa
2023	J	`jnl`	An end-to-end framework for gene expression classification by integrating a background knowledge graph: application to cancer prognosis prediction. CoRR Kazuma Inoue, Ryosuke Kojima, Mayumi Kamada, Yasushi Okuno
2023	J	`jnl`	Improving Compound-Protein Interaction Prediction by Self-Training with Augmenting Negative Samples. J. Chem. Inf. Model. Takuto Koyama, Shigeyuki Matsumoto, Hiroaki Iwata, Ryosuke Kojima, Yasushi Okuno
2023	J	`jnl`	Individual health-disease phase diagrams for disease prevention based on machine learning. J. Biomed. Informatics Kazuki Nakamura, Eiichiro Uchino, Noriaki Sato, Ayano Araki, Kei Terayama, Ryosuke Kojima, Koichi Murashita, Ken Itoh, Tatsuya Mikami, Yoshinori Tamada, Yasushi Okuno
2023	J	`jnl`	Network-based prediction approach for cancer-specific driver missense mutations using a graph neural network. BMC Bioinform. Narumi Hatano, Mayumi Kamada, Ryosuke Kojima, Yasushi Okuno
2023	J	`jnl`	Privacy-Preserving Correlation Coefficient. IEICE Trans. Inf. Syst. Tomoaki Mimoto, Hiroyuki Yokoyama, Toru Nakamura, Takamasa Isohara, Masayuki Hashimoto, Ryosuke Kojima, Aki Hasegawa, Yasushi Okuno
2023	J	`jnl`	VGAE-MCTS: A New Molecular Generative Model Combining the Variational Graph Auto-Encoder and Monte Carlo Tree Search. J. Chem. Inf. Model. Hiroaki Iwata, Taichi Nakai, Takuto Koyama, Shigeyuki Matsumoto, Ryosuke Kojima, Yasushi Okuno
2022	J	`jnl`	AI-Driven Synthetic Route Design Incorporated with Retrosynthesis Knowledge. J. Chem. Inf. Model. Shoichi Ishida, Kei Terayama, Ryosuke Kojima, Kiyosei Takasu, Yasushi Okuno
2022	—	`conf`	Differential Privacy under Incalculable Sensitivity. CSP Tomoaki Mimoto, Masayuki Hashimoto, Hiroyuki Yokoyama, Toru Nakamura, Takamasa Isohara, Ryosuke Kojima, Aki Hasegawa, Yasushi Okuno
2022	J	`jnl`	GraphIX: Graph-based In silico XAI(explainable artificial intelligence) for drug repositioning from biopharmaceutical network. CoRR Atsuko Takagi, Mayumi Kamada, Eri Hamatani, Ryosuke Kojima, Yasushi Okuno
2022	J	`jnl`	Individual health-disease phase diagrams for disease prevention based on machine learning. CoRR Kazuki Nakamura, Eiichiro Uchino, Noriaki Sato, Ayano Araki, Kei Terayama, Ryosuke Kojima, Koichi Murashita, Ken Itoh, Tatsuya Mikami, Yoshinori Tamada, Yasushi Okuno
2022	J	`jnl`	Protein-ligand binding affinity prediction of cyclin-dependent kinase-2 inhibitors by dynamically averaged fragment molecular orbital-based interaction energy. J. Comput. Chem. Kenichiro Takaba, Chiduru Watanabe, Atsushi Tokuhisa, Yoshinobu Akinaga, Biao Ma, Ryo Kanada, Mitsugu Araki, Yasushi Okuno, Yusuke Kawashima, Hirotomo Moriwaki, Norihito Kawashita, Teruki Honma, Kaori Fukuzawa, Shigenori Tanaka
2022	J	`jnl`	Single-Image Super-Resolution Improvement of X-ray Single-Particle Diffraction Images Using a Convolutional Neural Network. J. Chem. Inf. Model. Atsushi Tokuhisa, Yoshinobu Akinaga, Kei Terayama, Yuji Okamoto, Yasushi Okuno
2022	J	`jnl`	Using incomplete Cholesky factorization to increase the time step in molecular dynamics simulations. J. Comput. Appl. Math. Takumi Washio, Xiaoke Cui, Ryo Kanada, Jun-ichi Okada, Seiryo Sugiura, Yasushi Okuno, Shoji Takada, Toshiaki Hisada
2021	J	`jnl`	Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking. J. Chem. Inf. Model. Gert-Jan Bekker, Mitsugu Araki, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya
2021	J	`jnl`	Complex network prediction using deep learning. CoRR Yoshihisa Tanaka, Ryosuke Kojima, Shoichi Ishida, Fumiyoshi Yamashita, Yasushi Okuno
2021	J	`jnl`	Extraction of protein dynamics information from cryo-EM maps using deep learning. Nat. Mach. Intell. Shigeyuki Matsumoto, Shoichi Ishida, Mitsugu Araki, Takayuki Kato, Kei Terayama, Yasushi Okuno
2021	J	`jnl`	Prediction and visualization of acute kidney injury in intensive care unit using one-dimensional convolutional neural networks based on routinely collected data. Comput. Methods Programs Biomed. Noriaki Sato, Eiichiro Uchino, Ryosuke Kojima, Shusuke Hiragi, Motoko Yanagita, Yasushi Okuno
2021	J	`jnl`	Structure-Based de Novo Molecular Generator Combined with Artificial Intelligence and Docking Simulations. J. Chem. Inf. Model. Biao Ma, Kei Terayama, Shigeyuki Matsumoto, Yuta Isaka, Yoko Sasakura, Hiroaki Iwata, Mitsugu Araki, Yasushi Okuno
2021	J	`jnl`	eSkip-Finder: a machine learning-based web application and database to identify the optimal sequences of antisense oligonucleotides for exon skipping. Nucleic Acids Res. Shuntaro Chiba, Kenji Rowel Q. Lim, Narin Sheri, Saeed Anwar, Esra Erkut, Md Nur Ahad Shah, Tejal Aslesh, Stanley Woo, Omar Sheikh, Rika Maruyama, Hiroaki Takano, Katsuhiko Kunitake, William Duddy, Yasushi Okuno, Yoshitsugu Aoki, Toshifumi Yokota
2020	J	`jnl`	Classification of glomerular pathological findings using deep learning and nephrologist-AI collective intelligence approach. Int. J. Medical Informatics Eiichiro Uchino, Kanata Suzuki, Noriaki Sato, Ryosuke Kojima, Yoshinori Tamada, Shusuke Hiragi, Hideki Yokoi, Nobuhiro Yugami, Sachiko Minamiguchi, Hironori Haga, Motoko Yanagita, Yasushi Okuno
2020	J	`jnl`	Coarse-Grained Diffraction Template Matching Model to Retrieve Multiconformational Models for Biomolecule Structures from Noisy Diffraction Patterns. J. Chem. Inf. Model. Atsushi Tokuhisa, Ryo Kanada, Shuntaro Chiba, Kei Terayama, Yuta Isaka, Biao Ma, Narutoshi Kamiya, Yasushi Okuno
2020	J	`jnl`	CompRet: a comprehensive recommendation framework for chemical synthesis planning with algorithmic enumeration. J. Cheminformatics Ryosuke Shibukawa, Shoichi Ishida, Kazuki Yoshizoe, Kunihiro Wasa, Kiyosei Takasu, Yasushi Okuno, Kei Terayama, Koji Tsuda
2020	J	`jnl`	Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking. J. Comput. Chem. Gert-Jan Bekker, Mitsugu Araki, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya
2020	J	`jnl`	Health improvement framework for planning actionable treatment process using surrogate Bayesian model. CoRR Kazuki Nakamura, Ryosuke Kojima, Eiichiro Uchino, Koichi Murashita, Ken Itoh, Shigeyuki Nakaji, Yasushi Okuno
2020	J	`jnl`	High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning. J. Chem. Inf. Model. Koichiro Kato, Tomohide Masuda, Chiduru Watanabe, Naoki Miyagawa, Hideo Mizouchi, Shumpei Nagase, Kikuko Kamisaka, Kanji Oshima, Satoshi Ono, Hiroshi Ueda, Atsushi Tokuhisa, Ryo Kanada, Masateru Ohta, Mitsunori Ikeguchi, Yasushi Okuno, Kaori Fukuzawa, Teruki Honma
2020	J	`jnl`	Prediction of blood pressure variability using deep neural networks. Int. J. Medical Informatics Hiroshi Koshimizu, Ryosuke Kojima, Kazuomi Kario, Yasushi Okuno
2020	J	`jnl`	kGCN: a graph-based deep learning framework for chemical structures. J. Cheminformatics Ryosuke Kojima, Shoichi Ishida, Masateru Ohta, Hiroaki Iwata, Teruki Honma, Yasushi Okuno
2019	J	`jnl`	Force-field parametrization based on radial and energy distribution functions. J. Comput. Chem. Shuntaro Chiba, Yasushi Okuno, Teruki Honma, Mitsunori Ikeguchi
2019	—	`conf`	Med2RDF: Semantic Biomedical Knowledge-base and APIs for the Clinical Genome Medicine. SWAT4HCLS Mayumi Kamada, Toshiaki Katayama, Shuichi Kawashima, Ryosuke Kojima, Masahiko Nakatsui, Yasushi Okuno
2019	J	`jnl`	Prediction and Interpretable Visualization of Retrosynthetic Reactions Using Graph Convolutional Networks. J. Chem. Inf. Model. Shoichi Ishida, Kei Terayama, Ryosuke Kojima, Kiyosei Takasu, Yasushi Okuno
2018	J	`jnl`	Improving the Accuracy of Protein-Ligand Binding Mode Prediction Using a Molecular Dynamics-Based Pocket Generation Approach. J. Comput. Chem. Mitsugu Araki, Hiroaki Iwata, Biao Ma, Atsuto Fujita, Kei Terayama, Yukari Sagae, Fumie Ono, Koji Tsuda, Narutoshi Kamiya, Yasushi Okuno
2018	J	`jnl`	Machine learning accelerates MD-based binding pose prediction between ligands and proteins. Bioinform. Kei Terayama, Hiroaki Iwata, Mitsugu Araki, Yasushi Okuno, Koji Tsuda
2017	—	`conf`	Construction of Knowledge-Base for Clinical Interpretation of Genomic Variants. SWAT4LS Mayumi Kamada, Toshiaki Katayama, Shuichi Kawashima, Ryosuke Kojima, Masahiko Nakatsui, Yasushi Okuno
2016	J	`jnl`	The Effect of Conformational Flexibility on Binding Free Energy Estimation between Kinases and Their Inhibitors. J. Chem. Inf. Model. Mitsugu Araki, Narutoshi Kamiya, Miwa Sato, Masahiko Nakatsui, Takatsugu Hirokawa, Yasushi Okuno
2014	J	`jnl`	Computational chemogenomics: Is it more than inductive transfer? J. Comput. Aided Mol. Des. J. B. Brown, Yasushi Okuno, Gilles Marcou, Alexandre Varnek, Dragos Horvath
2013	J	`jnl`	Chemical Genomics Approach for GPCR-Ligand Interaction Prediction and Extraction of Ligand Binding Determinants. J. Chem. Inf. Model. Akira Shiraishi, Satoshi Niijima, J. B. Brown, Masahiko Nakatsui, Yasushi Okuno
2013	J	`jnl`	On computational complexity of graph inference from counting. Nat. Comput. Szilárd Zsolt Fazekas, Hiro Ito, Yasushi Okuno, Shinnosuke Seki, Kei Taneishi
2013	J	`jnl`	On the Behavior of Tile Assembly System at High Temperatures. Comput. Shinnosuke Seki, Yasushi Okuno
2012	—	`conf`	Chemogenomic approach to comprehensive predictions of ligand-target interactions: A comparative study. BIBM Workshops J. B. Brown, Satoshi Niijima, Akira Shiraishi, Masahiko Nakatsui, Yasushi Okuno
2012	J	`jnl`	Dissecting Kinase Profiling Data to Predict Activity and Understand Cross-Reactivity of Kinase Inhibitors. J. Chem. Inf. Model. Satoshi Niijima, Akira Shiraishi, Yasushi Okuno
2012	C	`conf`	On the Behavior of Tile Assembly System at High Temperatures. CiE Shinnosuke Seki, Yasushi Okuno
2012	J	`jnl`	On the behavior of tile assembly system at high temperatures CoRR Shinnosuke Seki, Yasushi Okuno
2011	J	`jnl`	Cross-Target View to Feature Selection: Identification of Molecular Interaction Features in Ligand-Target Space. J. Chem. Inf. Model. Satoshi Niijima, Hiroaki Yabuuchi, Yasushi Okuno
2010	J	`jnl`	A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. BMC Bioinform. Eelke van der Horst, Julio E. Peironcely, Adriaan P. IJzerman, Margot W. Beukers, Jonathan Robert Lane, Herman W. T. van Vlijmen, Michael T. M. Emmerich, Yasushi Okuno, Andreas Bender
2009	J	`jnl`	Laplacian Linear Discriminant Analysis Approach to Unsupervised Feature Selection. IEEE ACM Trans. Comput. Biol. Bioinform. Satoshi Niijima, Yasushi Okuno
2009	J	`jnl`	Substructure Mining of GPCR Ligands Reveals Activity-Class Specific Functional Groups in an Unbiased Manner. J. Chem. Inf. Model. Eelke van der Horst, Yasushi Okuno, Andreas Bender, Adriaan P. IJzerman
2008	J	`jnl`	GLIDA: GPCR - ligand database for chemical genomics drug discovery - database and tools update. Nucleic Acids Res. Yasushi Okuno, Akiko Tamon, Hiroaki Yabuuchi, Satoshi Niijima, Yohsuke Minowa, Koichiro Tonomura, Ryo Kunimoto, Chunlai Feng
2007	J	`jnl`	Predicting implicit associated cancer genes from OMIM and MEDLINE by a new probabilistic model. BMC Syst. Biol. Shanfeng Zhu, Yasushi Okuno, Gozoh Tsujimoto, Hiroshi Mamitsuka
2006	J	`jnl`	GLIDA: GPCR-ligand database for chemical genomic drug discovery. Nucleic Acids Res. Yasushi Okuno, Jiyoon Yang, Kei Taneishi, Hiroaki Yabuuchi, Gozoh Tsujimoto
2005	—	`conf`	A probabilistic model for mining implicit 'chemical compound-gene' relations from literature. ECCB/JBI Shanfeng Zhu, Yasushi Okuno, Gozoh Tsujimoto, Hiroshi Mamitsuka
2004	—	`conf`	A Hierarchical Mixture of Markov Models for Finding Biologically Active Metabolic Paths Using Gene Expression and Protein Classes. CSB Hiroshi Mamitsuka, Yasushi Okuno
2004	J	`jnl`	The KEGG resource for deciphering the genome. Nucleic Acids Res. Minoru Kanehisa, Susumu Goto, Shuichi Kawashima, Yasushi Okuno, Masahiro Hattori
2003	J	`jnl`	Mining biologically active patterns in metabolic pathways using microarray expression profiles. SIGKDD Explor. Hiroshi Mamitsuka, Yasushi Okuno, Atsuko Yamaguchi
2002	J	`jnl`	LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res. Susumu Goto, Yasushi Okuno, Masahiro Hattori, Takaaki Nishioka, Minoru Kanehisa