Yasushi Okuno 研究室

主宰者：Yasushi Okuno

京都大学・Kyoto University Hospital

兼任：理化学研究所・RIKEN Center for Computational Science

AI 要約（直近 5 年の研究成果）

奥野恭史研究室は、医学や薬学における複雑な現象を計算機科学で解き明かす研究を進めています。主な関心は、医薬品開発における物質の体内動態予測、タンパク質と化合物の相互作用メカニズム、そして患者データから病態パターンを抽出することにあります。これらの課題に対し、機械学習やグラフニューラルネットワークといった人工知能手法、および分子動力学シミュレーションを用いた原子レベルの解析を組み合わせています。特に注目される研究の方向性は三つあります。第一に、限られたデータから医薬品の吸収・分布・代謝・排泄特性をより正確に予測する方法の開発と、その予測根拠を明示することです。第二に、数千規模の分子対について大規模シミュレーションを実施し、タンパク質と化合物がどのように認識・結合するかという普遍的な原理を明らかにすることです。第三に、電子カルテや健康診断データといった実臨床データから統計的因果関係を抽出し、患者ごとに異なる疾患発症のメカニズムを解明することです。これらの研究は、超高速計算機や多機関データの活用を通じ、創薬効率化および精密医療の実現に貢献することを目指しています。

※ AI（Claude）が、公開されている論文要旨から研究の問い・手法・主要な発見を事実情報として抽出・再構成して自動生成しています。誤りを含む可能性があるため、正確性は研究室公式情報でご確認ください。

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研究成果（101 件）

[2026] Digital twin of biomacromolecular thermodynamics in cryo-EM data
DOI: https://doi.org/10.1038/s42004-026-02077-5
[2025] Mutation of CMTR2 in Lung Adenocarcinoma Alters RNA Alternative Splicing and Reveals Therapeutic Vulnerabilities
DOI: https://doi.org/10.1038/s41467-025-64821-0
[2025] BPS2025 – Deep-learning approaches for protein dynamics extraction from cryo-EM maps and structure-based de novo molecular generation
DOI: https://doi.org/10.1016/j.bpj.2024.11.1865
[2025] Predictors of Bleeding Complications After Extracorporeal Cardiopulmonary Resuscitation
DOI: https://doi.org/10.1016/j.jacasi.2025.09.027
[2025] Molecular recognition of natural compounds by MR1 and their implication in MAIT cell activation elucidated through McMD-based dynamic docking simulations
DOI: https://doi.org/10.1038/s41598-025-28682-3
[2025] Predicting measurement continuity in home blood pressure monitoring using machine learning
DOI: https://doi.org/10.1038/s41440-025-02444-0
[2025] Empowering Federated Learning for Robust Compound-Protein Interaction Prediction across Heterogeneous Cross-Pharma Domains
DOI: https://doi.org/10.26434/chemrxiv-2025-nj6jd
[2025] Predicting mortality dynamics in cancer patients: A machine learning approach to pre-death events
DOI: https://doi.org/10.1371/journal.pone.0331650
[2025] Network analysis reveals causal relationships among individual background risk factors leading to influenza susceptibility
DOI: https://doi.org/10.1038/s41598-025-15131-4
[2025] Conversion of an agonistic anti-TNFR2 biparatopic antibody into an antagonist by insertion of peptide linkers into the hinge region
DOI: https://doi.org/10.1016/j.jbc.2025.110548

続きを表示（残り 91 件）

[2025] Quantitative Assessment of Microsurgical Skill in Intrascleral Fixation Surgery Using Wearable Strain Sensors: A Pilot Study
DOI: https://doi.org/10.1167/tvst.14.7.7
[2025] Out-of-distribution reject option method for dataset shift problem in early disease onset prediction
DOI: https://doi.org/10.1038/s41598-025-01811-8
[2025] Diverse, Stable, and Efficient All-Atom Structure Sampling Based on Parallelized Coarse-Grained Elastic Network Model
DOI: https://doi.org/10.1109/ccgrid64434.2025.00026
[2025] Peripheral blood GATA2 expression impacts RNF213 mutation penetrance and clinical severity in moyamoya disease
DOI: https://doi.org/10.1136/svn-2024-003970
[2025] Precision spatiotemporal analysis of large-scale compound–protein interactions through molecular dynamics simulation
DOI: https://doi.org/10.1093/pnasnexus/pgaf094
[2025] kMoL: an open-source machine and federated learning library for drug discovery
DOI: https://doi.org/10.1186/s13321-025-00967-9
[2025] BPS2025 - Deep learning approaches for protein dynamics extraction from cryo-EM maps and structure-based de novo molecular generation
DOI: https://doi.org/10.1016/j.bpj.2024.11.1790
[2025] Abstract TP359: Peripheral blood GATA2 expression increases RNF213 mutation penetrance and clinical severity in moyamoya disease
DOI: https://doi.org/10.1161/str.56.suppl_1.tp359
[2025] In Silico Prediction and Selection of Exon-Skipping Antisense Oligonucleotide Sequences Using eSkip-Finder
DOI: https://doi.org/10.1007/978-1-0716-4730-1_6
[2025] Gut Microbiota and Viral Infections in Moyamoya Disease: Association with Type 2 Inflammation
DOI: https://doi.org/10.2335/scs.53.96
[2025] RWD155 Real-World Evidence of Atezolizumab in Unresectable Recurrent NSCLC: Insights From Japan's Next-Generation Medical Infrastructure Act
DOI: https://doi.org/10.1016/j.jval.2025.09.2905
[2025] Improving ADME Prediction with Multitask Graph Neural Networks and Assessing Explainability in Lead Optimization
DOI: https://doi.org/10.1021/acs.jcim.5c00758
[2025] Improving ADME Prediction with Multitask Graph Neural Networks and Assessing Explainability in Lead Optimization
DOI: https://doi.org/10.26434/chemrxiv-2025-ls77r-v2
[2024] Developing a GNN-based AI model to predict mitochondrial toxicity using the bagging method
DOI: https://doi.org/10.2131/jts.49.117
[2024] Interpretable machine learning-based individual analysis of acute kidney injury in immune checkpoint inhibitor therapy
DOI: https://doi.org/10.1371/journal.pone.0298673
[2024] 3) Prediction and Prevention Strategies for Non-communicable Diseases Using AI
DOI: https://doi.org/10.2169/naika.113.368
[2024] Feature extraction of particle morphologies of pharmaceutical excipients from scanning electron microscope images using convolutional neural networks
DOI: https://doi.org/10.1016/j.ijpharm.2024.123873
[2024] A multiscale molecular simulation approach for assessing the effects of mutation on protein activity and drug sensitivity of oncogenic kinases
DOI: https://doi.org/10.1016/j.bpj.2023.11.1972
[2024] Idiopathic pulmonary fibrosis-specific Bayesian network integrating extracellular vesicle proteome and clinical information
DOI: https://doi.org/10.1038/s41598-023-50905-8
[2024] Recent developments in machine learning modeling methods for hypertension treatment
DOI: https://doi.org/10.1038/s41440-023-01547-w
[2024] Receptor-independent regulation of Gα13 by alpha-1-antitrypsin C-terminal peptides
DOI: https://doi.org/10.1016/j.jbc.2024.108136
[2024] A macrocyclic kinase inhibitor overcomes triple resistant mutations in EGFR-positive lung cancer
DOI: https://doi.org/10.1038/s41698-024-00542-9
[2024] Constructing a graph neural network-based artificial intelligence model to predict drug-induced phospholipidosis potential
DOI: https://doi.org/10.2131/fts.11.279
[2024] Subgrouping Causal Networks of Disease Onset in Large-scale Health and Medical Data using Supercomputer Fugaku
DOI: https://doi.org/10.1109/bibm62325.2024.10822105
[2024] Postoperative Karnofsky performance status prediction in patients with IDH wild-type glioblastoma: A multimodal approach integrating clinical and deep imaging features
DOI: https://doi.org/10.1371/journal.pone.0303002
[2024] Synergistic involvement of the NZF domains of the LUBAC accessory subunits HOIL-1L and SHARPIN in the regulation of LUBAC function
DOI: https://doi.org/10.1038/s41419-024-07199-z
[2024] Molecular Dynamics Unveils Multiple-Site Binding of Inhibitors with Reduced Activity on the Surface of Dihydrofolate Reductase
DOI: https://doi.org/10.1021/jacs.4c04648
[2024] Artificial Intelligence-Based Histopathological Subtyping of High-Grade Serous Ovarian Cancer
DOI: https://doi.org/10.1016/j.ajpath.2024.06.010
[2024] Binding Mechanism between Platelet Glycoprotein and Cyclic Peptide Elucidated by McMD-Based Dynamic Docking
DOI: https://doi.org/10.1021/acs.jcim.4c00100
[2024] Development of Interpretable Machine Learning Models to Predict in-Hospital Prognosis of Acute Heart Failure Patients
DOI: https://doi.org/10.1002/ehf2.14834
[2024] LTK mutations responsible for resistance to lorlatinib in non-small cell lung cancer harboring CLIP1-LTK fusion
DOI: https://doi.org/10.1038/s42003-024-06116-6
[2023] S-47-1: THE POTENTIAL OF AI IN HYPERTENSION TREATMENT
DOI: https://doi.org/10.1097/01.hjh.0000913744.21565.69
[2023] Exploring the mechanism of BK polyomavirus-associated nephropathy through consensus gene network approach
DOI: https://doi.org/10.1371/journal.pone.0282534
[2023] Enhanced Coarse-Grained Molecular Dynamics Simulation with a Smoothed Hybrid Potential Using a Neural Network Model
DOI: https://doi.org/10.1021/acs.jctc.3c00889
[2023] 10075-CO-3 PREDICTION OF KPS DETERIORATION IN GLIOBLASTOMA USING MULTIMODAL LEARNING WITH PRE- AND POST-OPERATIVE MRI IMAGES AND CLINICAL INFORMATION
DOI: https://doi.org/10.1093/noajnl/vdad141.034
[2023] VGAE-MCTS: A New Molecular Generative Model Combining the Variational Graph Auto-Encoder and Monte Carlo Tree Search
DOI: https://doi.org/10.1021/acs.jcim.3c01220
[2023] Abstract 16400: Development of Deep Neural Network Models for Identification of Pulmonary Vein Potentials From Body Surface Electrocardiograms of Patients With Atrial Fibrillation
DOI: https://doi.org/10.1161/circ.148.suppl_1.16400
[2023] Interpretable Machine Learning-Based Individual Analysis of AKI in Immune Checkpoint Inhibitor Therapy
DOI: https://doi.org/10.1681/asn.20233411s1411d
[2023] Network-based prediction approach for cancer-specific driver missense mutations using a graph neural network
DOI: https://doi.org/10.1186/s12859-023-05507-6
[2023] Establishment of an MR1 Presentation Reporter Screening System and Identification of Phenylpropanoid Derivatives as MR1 Ligands
DOI: https://doi.org/10.1021/acs.jmedchem.3c01122
[2023] Deep Learning-Based Differential Diagnosis of Follicular Thyroid Tumors Using Histopathological Images
DOI: https://doi.org/10.1016/j.modpat.2023.100296
[2023] Individual health-disease phase diagrams for disease prevention based on machine learning
DOI: https://doi.org/10.1016/j.jbi.2023.104448
[2023] Improving Compound–Protein Interaction Prediction by Self-Training with Augmenting Negative Samples
DOI: https://doi.org/10.1021/acs.jcim.3c00269
[2023] Inhibition of the bone morphogenetic protein pathway suppresses tumor growth through downregulation of epidermal growth factor receptor in <scp>MEK</scp>/<scp>ERK</scp>‐dependent colorectal cancer
DOI: https://doi.org/10.1111/cas.15882
[2023] Ensemble-Learning and Feature Selection Techniques for Enhanced Antisense Oligonucleotide Efficacy Prediction in Exon Skipping
DOI: https://doi.org/10.3390/pharmaceutics15071808
[2023] Privacy-Preserving Correlation Coefficient
DOI: https://doi.org/10.1587/transinf.2022dap0014
[2023] Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL
DOI: https://doi.org/10.1038/s42003-023-04720-6
[2023] Hypersound-perturbed molecular dynamics simulation for accelerating slow biomolecular interaction processes
DOI: https://doi.org/10.1016/j.bpj.2022.11.2278
[2023] Development of a GCN-based model to predict in vitro phototoxicity from the chemical structure and HOMO-LUMO gap
DOI: https://doi.org/10.2131/jts.48.243
[2023] Development and validation of ischemic heart disease and stroke prognostic models using large-scale real-world data from Japan
DOI: https://doi.org/10.1265/ehpm.22-00106
[2023] Quantitative analysis of protein dynamics using a deep learning technique combined with experimental cryo-EM density data and MD simulations
DOI: https://doi.org/10.2142/biophysico.bppb-v20.0022
[2022] Everolimus reduces BK polyomavirus infection by suppressing its replication and spread of infection
DOI: https://doi.org/10.1016/j.antiviral.2022.105456
[2022] Increased abundance of Ruminococcus gnavus in gut microbiota is associated with moyamoya disease and non-moyamoya intracranial large artery disease
DOI: https://doi.org/10.1038/s41598-022-24496-9
[2022] Structure-Based Affinity Maturation of Antibody Based on Double-Point Mutations
DOI: https://doi.org/10.1007/978-1-0716-2609-2_18
[2022] GCN-Based Structure-Activity Relationship and DFT Studies of Staphylococcus aureus FabI Inhibitors
DOI: https://doi.org/10.4018/ijqspr.313627
[2022] Robust prognostic prediction model developed with integrated biological markers for acute myocardial infarction
DOI: https://doi.org/10.1371/journal.pone.0277260
[2022] Classification of scanning electron microscope images of pharmaceutical excipients using deep convolutional neural networks with transfer learning
DOI: https://doi.org/10.1016/j.ijpx.2022.100135
[2022] Novel Calcium-Binding Ablating Mutations Induce Constitutive RET Activity and Drive Tumorigenesis
DOI: https://doi.org/10.1158/0008-5472.can-22-0834
[2022] Characterizing eye-gaze positions of people with severe motor dysfunction: Novel scoring metrics using eye-tracking and video analysis
DOI: https://doi.org/10.1371/journal.pone.0265623
[2022] Using incomplete Cholesky factorization to increase the time step in molecular dynamics simulations
DOI: https://doi.org/10.1016/j.cam.2022.114519
[2022] Protein–ligand binding affinity prediction of cyclin‐dependent kinase‐2 inhibitors by dynamically averaged fragment molecular orbital‐based interaction energy
DOI: https://doi.org/10.1002/jcc.26940
[2022] Sensitivity to dabrafenib and trametinib treatments in patients with non-small-cell cancer harboring BRAF compound mutations: A pooled analysis of BRAF p.V600E-positive advanced non-small-cell lung cancer
DOI: https://doi.org/10.1016/j.cancergen.2022.05.001
[2022] CBNplot: Bayesian network plots for enrichment analysis
DOI: https://doi.org/10.1093/bioinformatics/btac175
[2022] Enhanced Conformational Sampling with an Adaptive Coarse-Grained Elastic Network Model Using Short-Time All-Atom Molecular Dynamics
DOI: https://doi.org/10.1021/acs.jctc.1c01074
[2022] AI-Driven Synthetic Route Design Incorporated with Retrosynthesis Knowledge
DOI: https://doi.org/10.1021/acs.jcim.1c01074
[2022] A multiscale molecular simulation approach for assessing the effects of mutations on functional activity and drug sensitivity in kinases
DOI: https://doi.org/10.1016/j.bpj.2021.11.553
[2022] Integrated approach to functional analysis of an ERBB2 variant of unknown significance detected by a cancer gene panel test
DOI: https://doi.org/10.1007/s13402-021-00656-3
[2022] A Novel Three-Dimensional Imaging System Based on Polysaccharide Staining for Accurate Histopathological Diagnosis of Inflammatory Bowel Diseases
DOI: https://doi.org/10.1016/j.jcmgh.2022.07.001
[2022] Extraction of Protein Dynamics Hidden in Cryo-EM Maps Using Deep Learning
DOI: https://doi.org/10.2142/biophys.62.193
[2022] Drug screening for COVID-19 using supercomputer “Fugaku”
DOI: https://doi.org/10.1254/fpj.21085
[2022] Differential Privacy under Incalculable Sensitivity
DOI: https://doi.org/10.1109/csp55486.2022.00013
[2021] Drug Screening for COVID-19 using Supercomputer "Fugaku"
DOI: https://doi.org/10.1254/jpssuppl.94.0_1-s01-1
[2021] Author Correction: Structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis
DOI: https://doi.org/10.1038/s41598-021-97892-2
[2021] Novel cancer subtyping method based on patient-specific gene regulatory network
DOI: https://doi.org/10.1038/s41598-021-02394-w
[2021] PD42-10 DEVELOPMENT OF A DEEP-LEARNING–BASED SYSTEM TO DIAGNOSE UROTHELIAL CARCINOMA CELLS IN CYTOLOGY SPECIMENS
DOI: https://doi.org/10.1097/ju.0000000000002056.10
[2021] Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking
DOI: https://doi.org/10.1021/acs.jcim.1c00712
[2021] Efficient Search for Energetically Favorable Molecular Conformations against Metastable States via Gray-Box Optimization
DOI: https://doi.org/10.1021/acs.jctc.1c00301
[2021] Structure-Based de Novo Molecular Generator Combined with Artificial Intelligence and Docking Simulations
DOI: https://doi.org/10.1021/acs.jcim.1c00679
[2021] Evaluation of Kidney Histological Images Using Unsupervised Deep Learning
DOI: https://doi.org/10.1016/j.ekir.2021.06.008
[2021] Oncogenic mutations Q61L and Q61H confer active form-like structural features to the inactive state (state 1) conformation of H-Ras protein
DOI: https://doi.org/10.1016/j.bbrc.2021.05.084
[2021] Dynamic changes in gene-to-gene regulatory networks in response to SARS-CoV-2 infection
DOI: https://doi.org/10.1038/s41598-021-90556-1
[2021] Health improvement framework for actionable treatment planning using a surrogate Bayesian model
DOI: https://doi.org/10.1038/s41467-021-23319-1
[2021] Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics
DOI: https://doi.org/10.1038/s41467-021-23157-1
[2021] eSkip-Finder: a machine learning-based web application and database to identify the optimal sequences of antisense oligonucleotides for exon skipping
DOI: https://doi.org/10.1093/nar/gkab442
[2021] A deep learning system to diagnose the malignant potential of urothelial carcinoma cells in cytology specimens
DOI: https://doi.org/10.1002/cncy.22443
[2021] Prediction and visualization of acute kidney injury in intensive care unit using one-dimensional convolutional neural networks based on routinely collected data
DOI: https://doi.org/10.1016/j.cmpb.2021.106129
[2021] Microsecond-timescale MD simulation of EGFR minor mutation predicts the structural flexibility of EGFR kinase core that reflects EGFR inhibitor sensitivity
DOI: https://doi.org/10.1038/s41698-021-00170-7
[2021] Gilteritinib overcomes lorlatinib resistance in ALK-rearranged cancer
DOI: https://doi.org/10.1038/s41467-021-21396-w
[2021] Extraction of protein dynamics information from cryo-EM maps using deep learning
DOI: https://doi.org/10.1038/s42256-020-00290-y
[2021] Challenges in AI-based drug development revealed from activities of Life Intelligence Consortium "LINC"
[2021] Today and future of AI-based drug development
DOI: https://doi.org/10.1254/jpssuppl.94.0_1-sl3

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AI 要約（直近 5 年の研究成果）

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研究成果（101 件）

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