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Journal of Chemical Theory and Computation|August 6, 2016
Improved Accuracy in RNA-Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring FunctionJunichi Iwakiri, Michiaki Hamada, Kiyoshi Asai, et al.
Bioinformatics (Oxford, England)|September 10, 2024
Prediction of antibiotic resistance mechanisms using a protein language modelKanami Yagimoto, Shion Hosoda, Miwa Sato, et al.
Nucleic Acids Research|July 18, 2023
Landscape of semi-extractable RNAs across five human cell linesChao Zeng, Takeshi Chujo, Tetsuro Hirose, et al.
Plos One|March 3, 2011
Generalized centroid estimators in bioinformaticsMichiaki Hamada, Hisanori Kiryu, Wataru Iwasaki, et al.
Bioinformatics (Oxford, England)|August 13, 2013
Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactionsJunichi Iwakiri, Tomoshi Kameda, Kiyoshi Asai, et al.
Bioinformatics Advances|July 11, 2025
RaptGen-UI: an integrated platform for exploring and analyzing the sequence landscape of HT-SELEX experimentsRyota Nakano, Natsuki Iwano, Akiko Ichinose, et al.
RSC Chemical Biology|September 12, 2025
Fitness landscapes and thermodynamic approaches to development of nucleic acids enzymes: from classical methods to AI integrationShuntaro Takahashi, Michiaki Hamada, Hisae Tateishi-Karimata, et al.
Bioinformatics (Oxford, England)|October 7, 2011
Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detectionMichiaki Hamada, Edward Wijaya, Martin C Frith, et al.
Bioinformatics (Oxford, England)|January 1, 2017
Training alignment parameters for arbitrary sequencers with LAST-TRAINMichiaki Hamada, Yukiteru Ono, Kiyoshi Asai, et al.
Computational and Structural Biotechnology Journal|November 13, 2023
Probiotic responder identification in cross-over trials for constipation using a Bayesian statistical model considering lags between intake and effect periodsShion Hosoda, Yuichiro Nishimoto, Yohsuke Yamauchi, et al.
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