Yasushi Okuno

Publication Activity (10 Years)

Years Active: 2002-2024
Publications (10 Years): 39

Top Topics

Negative Samples

Molecular Dynamics

Machine Learning

Top Venues

J. Chem. Inf. Model.

J. Comput. Chem.

Publications

Gert-Jan Bekker, Kanji Oshima, Mitsugu Araki, Yasushi Okuno, Narutoshi Kamiya
Binding Mechanism between Platelet Glycoprotein and Cyclic Peptide Elucidated by McMD-Based Dynamic Docking. J. Chem. Inf. Model. 64 (10) (2024)
Taisei Tosaki, Eiichiro Uchino, Ryosuke Kojima, Yohei Mineharu, Mikio Arita, Nobuyuki Miyai, Yoshinori Tamada, Tatsuya Mikami, Koichi Murashita, Shigeyuki Nakaji, Yasushi Okuno
Out-of-distribution Reject Option Method for Dataset Shift Problem in Early Disease Onset Prediction. CoRR (2024)
Aya Nakamura, Ryosuke Kojima, Yuji Okamoto, Eiichiro Uchino, Yohei Mineharu, Yohei Harada, Mayumi Kamada, Manabu Muto, Motoko Yanagita, Yasushi Okuno
A New Deep State-Space Analysis Framework for Patient Latent State Estimation and Classification from EHR Time Series Data. CoRR (2023)
Kazuki Nakamura, Eiichiro Uchino, Noriaki Sato, Ayano Araki, Kei Terayama, Ryosuke Kojima, Koichi Murashita, Ken Itoh, Tatsuya Mikami, Yoshinori Tamada, Yasushi Okuno
Individual health-disease phase diagrams for disease prevention based on machine learning. J. Biomed. Informatics 144 (2023)
Hiroaki Iwata, Taichi Nakai, Takuto Koyama, Shigeyuki Matsumoto, Ryosuke Kojima, Yasushi Okuno
VGAE-MCTS: A New Molecular Generative Model Combining the Variational Graph Auto-Encoder and Monte Carlo Tree Search. J. Chem. Inf. Model. 63 (23) (2023)
Takuto Koyama, Shigeyuki Matsumoto, Hiroaki Iwata, Ryosuke Kojima, Yasushi Okuno
Improving Compound-Protein Interaction Prediction by Self-Training with Augmenting Negative Samples. J. Chem. Inf. Model. 63 (15) (2023)
Kazuma Inoue, Ryosuke Kojima, Mayumi Kamada, Yasushi Okuno
An end-to-end framework for gene expression classification by integrating a background knowledge graph: application to cancer prognosis prediction. CoRR (2023)
Kimihiro Yamazaki, Yuichiro Wada, Atsushi Tokuhisa, Mutsuyo Wada, Takashi Katoh, Yuhei Umeda, Yasushi Okuno, Akira Nakagawa
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) (2023)
Tomoaki Mimoto, Hiroyuki Yokoyama, Toru Nakamura, Takamasa Isohara, Masayuki Hashimoto, Ryosuke Kojima, Aki Hasegawa, Yasushi Okuno
Privacy-Preserving Correlation Coefficient. IEICE Trans. Inf. Syst. 106 (5) (2023)
Narumi Hatano, Mayumi Kamada, Ryosuke Kojima, Yasushi Okuno
Network-based prediction approach for cancer-specific driver missense mutations using a graph neural network. BMC Bioinform. 24 (1) (2023)
Kazuki Nakamura, Eiichiro Uchino, Noriaki Sato, Ayano Araki, Kei Terayama, Ryosuke Kojima, Koichi Murashita, Ken Itoh, Tatsuya Mikami, Yoshinori Tamada, Yasushi Okuno
Individual health-disease phase diagrams for disease prevention based on machine learning. CoRR (2022)
Shoichi Ishida, Kei Terayama, Ryosuke Kojima, Kiyosei Takasu, Yasushi Okuno
AI-Driven Synthetic Route Design Incorporated with Retrosynthesis Knowledge. J. Chem. Inf. Model. 62 (6) (2022)
Noriaki Sato, Yoshinori Tamada, Guangchuang Yu, Yasushi Okuno
: Bayesian network plots for enrichment analysis. Bioinform. 38 (10) (2022)
Atsuko Takagi, Mayumi Kamada, Eri Hamatani, Ryosuke Kojima, Yasushi Okuno
GraphIX: Graph-based In silico XAI(explainable artificial intelligence) for drug repositioning from biopharmaceutical network. CoRR (2022)
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
Protein-ligand binding affinity prediction of cyclin-dependent kinase-2 inhibitors by dynamically averaged fragment molecular orbital-based interaction energy. J. Comput. Chem. 43 (20) (2022)
Takumi Washio, Xiaoke Cui, Ryo Kanada, Jun-ichi Okada, Seiryo Sugiura, Yasushi Okuno, Shoji Takada, Toshiaki Hisada
Using incomplete Cholesky factorization to increase the time step in molecular dynamics simulations. J. Comput. Appl. Math. 415 (2022)
Tomoaki Mimoto, Masayuki Hashimoto, Hiroyuki Yokoyama, Toru Nakamura, Takamasa Isohara, Ryosuke Kojima, Aki Hasegawa, Yasushi Okuno
Differential Privacy under Incalculable Sensitivity. CSP (2022)
Atsushi Tokuhisa, Yoshinobu Akinaga, Kei Terayama, Yuji Okamoto, Yasushi Okuno
Single-Image Super-Resolution Improvement of X-ray Single-Particle Diffraction Images Using a Convolutional Neural Network. J. Chem. Inf. Model. 62 (14) (2022)
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
eSkip-Finder: a machine learning-based web application and database to identify the optimal sequences of antisense oligonucleotides for exon skipping. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
Gert-Jan Bekker, Mitsugu Araki, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya
Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking. J. Chem. Inf. Model. 61 (10) (2021)
Noriaki Sato, Eiichiro Uchino, Ryosuke Kojima, Shusuke Hiragi, Motoko Yanagita, Yasushi Okuno
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. 206 (2021)
Yoshihisa Tanaka, Ryosuke Kojima, Shoichi Ishida, Fumiyoshi Yamashita, Yasushi Okuno
Complex network prediction using deep learning. CoRR (2021)
Biao Ma, Kei Terayama, Shigeyuki Matsumoto, Yuta Isaka, Yoko Sasakura, Hiroaki Iwata, Mitsugu Araki, Yasushi Okuno
Structure-Based de Novo Molecular Generator Combined with Artificial Intelligence and Docking Simulations. J. Chem. Inf. Model. 61 (7) (2021)
Shigeyuki Matsumoto, Shoichi Ishida, Mitsugu Araki, Takayuki Kato, Kei Terayama, Yasushi Okuno
Extraction of protein dynamics information from cryo-EM maps using deep learning. Nat. Mach. Intell. 3 (2) (2021)
Gert-Jan Bekker, Mitsugu Araki, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya
Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking. J. Comput. Chem. 41 (17) (2020)
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
High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning. J. Chem. Inf. Model. 60 (7) (2020)
Kazuki Nakamura, Ryosuke Kojima, Eiichiro Uchino, Koichi Murashita, Ken Itoh, Shigeyuki Nakaji, Yasushi Okuno
Health improvement framework for planning actionable treatment process using surrogate Bayesian model. CoRR (2020)
Atsushi Tokuhisa, Ryo Kanada, Shuntaro Chiba, Kei Terayama, Yuta Isaka, Biao Ma, Narutoshi Kamiya, Yasushi Okuno
Coarse-Grained Diffraction Template Matching Model to Retrieve Multiconformational Models for Biomolecule Structures from Noisy Diffraction Patterns. J. Chem. Inf. Model. 60 (6) (2020)
Ryosuke Shibukawa, Shoichi Ishida, Kazuki Yoshizoe, Kunihiro Wasa, Kiyosei Takasu, Yasushi Okuno, Kei Terayama, Koji Tsuda
CompRet: a comprehensive recommendation framework for chemical synthesis planning with algorithmic enumeration. J. Cheminformatics 12 (1) (2020)
Hiroshi Koshimizu, Ryosuke Kojima, Kazuomi Kario, Yasushi Okuno
Prediction of blood pressure variability using deep neural networks. Int. J. Medical Informatics 136 (2020)
Ryosuke Kojima, Shoichi Ishida, Masateru Ohta, Hiroaki Iwata, Teruki Honma, Yasushi Okuno
kGCN: a graph-based deep learning framework for chemical structures. J. Cheminformatics 12 (1) (2020)
Eiichiro Uchino, Kanata Suzuki, Noriaki Sato, Ryosuke Kojima, Yoshinori Tamada, Shusuke Hiragi, Hideki Yokoi, Nobuhiro Yugami, Sachiko Minamiguchi, Hironori Haga, Motoko Yanagita, Yasushi Okuno
Classification of glomerular pathological findings using deep learning and nephrologist-AI collective intelligence approach. Int. J. Medical Informatics 141 (2020)
Shoichi Ishida, Kei Terayama, Ryosuke Kojima, Kiyosei Takasu, Yasushi Okuno
Prediction and Interpretable Visualization of Retrosynthetic Reactions Using Graph Convolutional Networks. J. Chem. Inf. Model. 59 (12) (2019)
Shuntaro Chiba, Yasushi Okuno, Teruki Honma, Mitsunori Ikeguchi
Force-field parametrization based on radial and energy distribution functions. J. Comput. Chem. 40 (29) (2019)
Mayumi Kamada, Toshiaki Katayama, Shuichi Kawashima, Ryosuke Kojima, Masahiko Nakatsui, Yasushi Okuno
Med2RDF: Semantic Biomedical Knowledge-base and APIs for the Clinical Genome Medicine. SWAT4HCLS (2019)
Kei Terayama, Hiroaki Iwata, Mitsugu Araki, Yasushi Okuno, Koji Tsuda
Machine learning accelerates MD-based binding pose prediction between ligands and proteins. Bioinform. 34 (5) (2018)
Mitsugu Araki, Hiroaki Iwata, Biao Ma, Atsuto Fujita, Kei Terayama, Yukari Sagae, Fumie Ono, Koji Tsuda, Narutoshi Kamiya, Yasushi Okuno
Improving the Accuracy of Protein-Ligand Binding Mode Prediction Using a Molecular Dynamics-Based Pocket Generation Approach. J. Comput. Chem. 39 (32) (2018)
Mayumi Kamada, Toshiaki Katayama, Shuichi Kawashima, Ryosuke Kojima, Masahiko Nakatsui, Yasushi Okuno
Construction of Knowledge-Base for Clinical Interpretation of Genomic Variants. SWAT4LS (2017)
Mitsugu Araki, Narutoshi Kamiya, Miwa Sato, Masahiko Nakatsui, Takatsugu Hirokawa, Yasushi Okuno
The Effect of Conformational Flexibility on Binding Free Energy Estimation between Kinases and Their Inhibitors. J. Chem. Inf. Model. 56 (12) (2016)
J. B. Brown, Yasushi Okuno, Gilles Marcou, Alexandre Varnek, Dragos Horvath
Computational chemogenomics: Is it more than inductive transfer? J. Comput. Aided Mol. Des. 28 (6) (2014)
Shinnosuke Seki, Yasushi Okuno
On the Behavior of Tile Assembly System at High Temperatures. Comput. 2 (2) (2013)
Akira Shiraishi, Satoshi Niijima, J. B. Brown, Masahiko Nakatsui, Yasushi Okuno
Chemical Genomics Approach for GPCR-Ligand Interaction Prediction and Extraction of Ligand Binding Determinants. J. Chem. Inf. Model. 53 (6) (2013)
Szilárd Zsolt Fazekas, Hiro Ito, Yasushi Okuno, Shinnosuke Seki, Kei Taneishi
On computational complexity of graph inference from counting. Nat. Comput. 12 (4) (2013)
J. B. Brown, Satoshi Niijima, Akira Shiraishi, Masahiko Nakatsui, Yasushi Okuno
Chemogenomic approach to comprehensive predictions of ligand-target interactions: A comparative study. BIBM Workshops (2012)
Shinnosuke Seki, Yasushi Okuno
On the Behavior of Tile Assembly System at High Temperatures. CiE (2012)
Shinnosuke Seki, Yasushi Okuno
On the behavior of tile assembly system at high temperatures CoRR (2012)
Satoshi Niijima, Akira Shiraishi, Yasushi Okuno
Dissecting Kinase Profiling Data to Predict Activity and Understand Cross-Reactivity of Kinase Inhibitors. J. Chem. Inf. Model. 52 (4) (2012)
Satoshi Niijima, Hiroaki Yabuuchi, Yasushi Okuno
Cross-Target View to Feature Selection: Identification of Molecular Interaction Features in Ligand-Target Space. J. Chem. Inf. Model. 51 (1) (2011)
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
A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. BMC Bioinform. 11 (2010)
Satoshi Niijima, Yasushi Okuno
Laplacian Linear Discriminant Analysis Approach to Unsupervised Feature Selection. IEEE ACM Trans. Comput. Biol. Bioinform. 6 (4) (2009)
Eelke van der Horst, Yasushi Okuno, Andreas Bender, Adriaan P. IJzerman
Substructure Mining of GPCR Ligands Reveals Activity-Class Specific Functional Groups in an Unbiased Manner. J. Chem. Inf. Model. 49 (2) (2009)
Yasushi Okuno, Akiko Tamon, Hiroaki Yabuuchi, Satoshi Niijima, Yohsuke Minowa, Koichiro Tonomura, Ryo Kunimoto, Chunlai Feng
GLIDA: GPCR - ligand database for chemical genomics drug discovery - database and tools update. Nucleic Acids Res. 36 (Database-Issue) (2008)
Shanfeng Zhu, Yasushi Okuno, Gozoh Tsujimoto, Hiroshi Mamitsuka
Predicting implicit associated cancer genes from OMIM and MEDLINE by a new probabilistic model. BMC Syst. Biol. 1 (S-1) (2007)
Yasushi Okuno, Jiyoon Yang, Kei Taneishi, Hiroaki Yabuuchi, Gozoh Tsujimoto
GLIDA: GPCR-ligand database for chemical genomic drug discovery. Nucleic Acids Res. 34 (Database-Issue) (2006)
Shanfeng Zhu, Yasushi Okuno, Gozoh Tsujimoto, Hiroshi Mamitsuka
A probabilistic model for mining implicit 'chemical compound-gene' relations from literature. ECCB/JBI (2005)
Hiroshi Mamitsuka, Yasushi Okuno
A Hierarchical Mixture of Markov Models for Finding Biologically Active Metabolic Paths Using Gene Expression and Protein Classes. CSB (2004)
Minoru Kanehisa, Susumu Goto, Shuichi Kawashima, Yasushi Okuno, Masahiro Hattori
The KEGG resource for deciphering the genome. Nucleic Acids Res. 32 (Database-Issue) (2004)
Hiroshi Mamitsuka, Yasushi Okuno, Atsuko Yamaguchi
Mining biologically active patterns in metabolic pathways using microarray expression profiles. SIGKDD Explor. 5 (2) (2003)
Susumu Goto, Yasushi Okuno, Masahiro Hattori, Takaaki Nishioka, Minoru Kanehisa
LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res. 30 (1) (2002)