2021)
- Bekker G, Araki M, Oshima K, Okuno Y, Kamiya N., “Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking” Journal of Chemical Information and Modeling, 61(10), p5161-5171, 2021, https://doi.org/10.1021/acs.jcim.1c00712
- Sato N, Uchino E, Kojima R, Sakuragi M, Hiragi S, Minamiguchi S, Haga H, Yokoi H, Yanagita M, Okuno Y , Evaluation of Kidney Histological Images Using Unsupervised Deep Learning. Kidney international reports ,6(9), 2445－2454 , 2021/9 , DOI: 10.1016/j.ekir.2021.06.008
- Miyaguchi I,Sato M,Kashima A,Nakagawa H,Kokabu Y, M Biao,Matsumoto S,Tokuhisa A, Ohta M& Ikeguchi M, Machine learning to estimate the local quality of protein crystal structures,Scientific Report,11, 23599 , 2021,https://doi.org/10.1038/s41598-021-02948-y
- Mai Adachi Nakazawa, Yoshinori Tamada, Yoshihisa Tanaka, Marie Ikeguchi, Kako Higashihara & Yasushi Okuno,Novel cancer subtyping method based on patient-specific gene regulatory network,Scientific Reports volume 11, Article number: 23653, 2021, DOI:https://doi.org/10.1038/s41598-021-02394-w
- Nakamura H, Takami H, Yanagisawa T, Kumabe T, Fujimaki T, Arakawa Y, Karasawa K, Terashima K, Yokoo H, Fukuoka K, Sonoda Y, Sakurada K, Mineharu Y, Soejima T, Fujii M, Shinojima N, Hara J, Yamasaki K, Fujimura J, Takahashi M, Suzuki T, Sato I, Nishikawa R, Sugiyama K, guideline committee in The Japan Society for Neuro-Oncology (JSNO) Task Force on Central Nervous System Germ Cell Tumors. The Japan Society for Neuro-Oncology Guideline on the Diagnosis and Treatment of Central Nervous System Germ Cell Tumors. Neuro. Oncol. noab242 , 2021, https://doi.org/10.1093/neuonc/noab242
- Arakawa Y, Sasaki K, Mineharu Y, Uto M, Mizowaki T, Mizusawa J, Sekino Y, Ono T, Aoyama H, Satomi K, et al. A randomized phase III study of short-course radiotherapy combined with Temozolomide in elderly patients with newly diagnosed glioblastoma; Japan clinical oncology group study JCOG1910 (AgedGlio-PIII). BMC Cancer. 21:1105., 2021, https://doi.org/10.1186/s12885-021-08834-0
- Makino Y, Arakawa Y, Yoshioka E, Shofuda T, Minamiguchi S, Kawauchi T, Tanji M, Kanematsu D, Nonaka M, Okita Y, Kodama Y, Mano M, Hirose T, Mineharu Y, Miyamoto S, Kanemura Y. Infrequent RAS mutation is not associated with specific histological phenotype in gliomas. BMC Cancer. ,21:1025. , 2021,https://doi.org/10.1186/s12885-021-08733-4
- Mineharu Y, Takagi Y, Koizumi A, Morimoto T, Funaki T, Hishikawa T, Araki Y, Hasegawa H, Takahashi JC, Kuroda S, Houkin K, and Miyamoto S: on behalf of the SUPRA Japan Study Group. Genetic and non-genetic factors for contralateral progression of unilateral moyamoya disease: the first report from the SUPRA Japan Study Group, J Neurosurg, 2021,https://doi.org/10.3171/2021.3.JNS203913
- Terayama K, Sumita M, Katouda M, Tsuda K, Okuno Y, Efficient Search for Energetically Favorable Molecular Conformations against Metastable States via Gray-Box Optimization. Journal of Chemical Theory and Computation, 17:5419–5427, 2021,DOI:https://doi.org/10.1021/acs.jctc.1c00301
- Matsumoto S, Taniguchi-Tamura H, Araki M, Kawamura T, Miyamoto R, Tsuda C, Shima F, Kumasaka T, Okuno Y*, Kataoka T*, Oncogenic mutations Q61L and Q61H confer active form-like structural features to the inactive state (state 1) conformation of H-Ras protein. Biochemical and Biophysical Research Communications. 565:85-90, 2021,https://doi.org/10.1016/j.bbrc.2021.05.084
- Iwata H, Kojima R, Okuno Y*, AIM in Pharmacology and Drug Discovery. Artificial Intelligence in Medicine. 1-9, 2021,https://doi.org/10.1007/978-3-030-58080-3_145-1
- Uchino E,Sato N, Okuno Y, Artificial Intelligence in Predicting Kidney Function and Acute Kidney Injury, Artificial Intelligence in Medicine,pp 1-17,2021/8,https://doi.org/10.1007/978-3-030-58080-3_270-1
- Sato N,Uchino E,Okuno Y. Artificial Intelligence in Kidney Pathology. In: Lidströmer N., Ashrafian H. (eds) Artificial Intelligence in Medicine. Springer, Cham.pp 1-11,2021, https://doi.org/10.1007/978-3-030-58080-3_181-1
- Tsutsui T, Arakawa Y*, Makino Y, Kataoka H, Mineharu Y, Minamiguchi S, Hirose T, Nobusawa S, Nakano Y, Ichimura K, Haga H, Miyamoto S. Spinal cord astroblastoma with EWSR1-BEND2 fusion classified as HGNET-MN1 by methylation classification: a case report Brain Tumor Pathology volume 38, pages283–289 ,2021,https://doi.org/10.1007/s10014-021-00412-3
- Mineharu Y, Miyamoto S. RNF213 and GUCY1A3 in Moyamoya Disease: Key Regulators of Metabolism, Inflammation, and Vascular Stability. Front Neurol ,12:1–12. ,2021,https://doi.org/10.3389/fneur.2021.687088
- Yamawaki R*, Nankaku M, Umaba C, Ueda M, Liang N, Mineharu Y, Yamao Y, Ikeguchi R, Matsuda S, Miyamoto S, et al. Assessment of neurocognitive function in association with WHO grades in gliomas. Clin Neurol Neurosurg ,208:106824. ,2021,https://doi.org/10.1016/j.clineuro.2021.106824
- Kamada M, Takagi A, KojimaR, TanakaY, Nakatsui M, Tanabe N, Hirata M, Yoshida T, Okuno Y , Network-based pathogenicity prediction for variants of uncertain significance. bioRxiv, 2021 ,https://doi.org/10.1016/j.bbrc.2021.05.084
- Makino Y, Arakawa Y, Yoshioka E, Shofuda T, Kawauchi T, Terada Y, Tanji M, Kanematsu D, Mineharu Y, Miyamoto S, et al. Prognostic stratification for IDH wild type lower grade astrocytoma by Sanger sequencing and copy number alteration analysis with MLPA. Sci Rep volume 11, Article number: 14408,1–12., 2021 , https://doi.org/10.1038/s41598-021-93937-8
- Kamada M, Okuno Y*, AIM in genomic basis of medicine: applications. Artificial Intelligence in Medicine. 1-10, 2021 , https://doi.org/10.1007/978-3-030-58080-3_145-1
- Ma B, Terayama K*, Matsumoto S, Isaka Y, Sasakura Y, Iwata H, Araki M, Okuno Y*, Structure-Based de Novo Molecular Generator Combined with Artificial Intelligence and Docking Simulations. Journal of Chemical Information and Modeling. 61(7): 3304–3313, 2021,doi.org/10.1021/acs.jcim.1c00679
- Shinno K, Arakawa Y, Minamiguchi S, Terada Y, Tanji M, Mineharu Y, Kikuchi T, Haga H, Miyamoto S. Papillary glioneuronal tumor growing slowly for 26 years: illustrative case. J Neurosurg Case Lessons 2:5–8. https://doi.org/10.3171/CASE21266
- Sato N, Uchino E, Kojima R, Hiragi S, Yanagita M, Okuno Y*, Prediction and visualization of acute kidney injury in intensive care unit using one-dimensional convolutional neural networks based on routinely collected data. Computer Methods and Programs in Biomedicine. 206:106129, 2021,https://doi.org/10.1016/j.cmpb.2021.106129
- Chiba S, Lim KRQ, Sheri N, Anwar S, Erkut E, Shah MH, Aslesh T, Woo S, Sheikh O, Maruyama R, Takano H, Kunitake K, Duddy W, Okuno Y*, Aoki Y*, Yokota T*, eSkip-Finder: a machine learning-based web application and database to identify the optimal sequences of antisense oligonucleotides for exon skipping. Nucleic Acids Research. gkab442, 2021,https://doi.org/10.1093/nar/gkab442
- Mizota T, Hamada M, Shiraki A, Kikuchi T, Mineharu Y, Yamao Y, Hattori EY, Yonezawa A, Furukawa K, Arakawa Y. Factors associated with somnolence during brain function mapping in awake craniotomy. J. Clin. Neurosci. ,89:349–353., 2021, https://doi.org/10.1016/j.jocn.2021.05.050
- Tanaka Y, Higashihara K, Nakazawa M.A, Yamashita F, Tamada Y & Okuno Y. “Dynamic changes in gene-to-gene regulatory networks in response to SARS-CoV-2 infection” Sci Rep. ,11:11241. , 2021,https://doi.org/10.1038/s41598-021-90556-1
- Nojima S, Terayama K, Shimoura S, Hijiki S, Nonomura N, Morii E, Okuno Y , Fujita K* A deep learning system to diagnose the malignant potential of urothelial carcinoma cells in cytology specimens. Cancer Cytopathology ,6(9), 2445－2454 , 2021/9 , DOI: 10.1002/cncy.22443
- Nakamura K, Kojima R, Uchino E, Ono K, Yanagita M, Murashita K, Itoh K, Nakaji S & Okuno Y. “Health improvement framework for actionable treatment planning using a surrogate Bayesian model” Nat Commun. ,12:3088. , 2021, https://doi.org/10.1038/s41467-021-23319-1
- Araki M, Matsumoto S, Bekker GJ, Isaka Y, Sagae Y, Kamiya N & Okuno Y. “Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics” Nat Commun. .12:2793. , 2021,https://doi.org/10.1038/s41467-021-23157-1
- Matsumoto S, Ishida S, Araki M, Kato T, Terayama K, Okuno Y. “Extraction of protein dynamics information from cryo-EM maps using deep learning” Nat Mach Intell. ,3:153-160. , 2021,https://doi.org/10.1038/s42256-020-00290-y
- Iwata H, Matsuo T, Mamada H, Motomura T, Matsushita M, Fujiwara T, Maeda K, Handa K. “Prediction of Total Drug Clearance in Humans Using Animal Data: Proposal of a Multimodal Learning Method Based on Deep Learning” Journal of Pharmaceutical Sciences. , 2021,https://doi.org/10.1016/j.xphs.2021.01.020
