浜田 道昭

研究成果

年別の研究成果 2003 2018 2020 2021 2022

• 1677 被引用数
• 20 h 指数
• 71 Article
• 4 Review article
• 2 Chapter
• 2 Conference contribution
• 3 その他
  • 2 Comment/debate
  • 1 Letter

年別の研究成果

年別の研究成果

検索結果

• Article

  AMAP: A pipeline for whole-genome mutation detection in Arabidopsis thaliana

  Ishii, K., Kazama, Y., Hirano, T., Hamada, M., Ono, Y., Yamada, M. & Abe, T., 2016, In: Genes and Genetic Systems. 91, 4, p. 229-233 5 p.

  研究成果: Article › 査読

  Open Access

  • Arabidopsis 100%
  • Genome 52%
  • Mutation 42%
  • Genetic Phenomena 6%
  • Genetic Translocation 6%
  4 被引用数 (Scopus)

• Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions

  Iwakiri, J., Kameda, T., Asai, K. & Hamada, M., 2013 10月 15, In: Bioinformatics. 29, 20, p. 2524-2528 5 p.

  研究成果: Article › 査読

  • RNA 92%
  • Pairing 83%
  • Protein 80%
  • Base Pairing 78%
  • Molecules 75%
  7 被引用数 (Scopus)

• A non-parametric bayesian approach for predicting rna secondary structures

  Sato, K., Hamada, M., Mituyama, T., Asai, K. & Sakakibara, Y., 2010 8月, In: Journal of Bioinformatics and Computational Biology. 8, 4, p. 727-742 16 p.

  研究成果: Article › 査読

  • Bayes Theorem 100%
  • RNA 98%
  • Secondary Structure 72%
  • Stochastic Processes 62%
  • Context free grammars 54%
  8 被引用数 (Scopus)

• A Novel Method for Assessing the Statistical Significance of RNA-RNA Interactions Between Two Long RNAs

  Fukunaga, T. & Hamada, M., 2018 9月, In: Journal of Computational Biology. 25, 9, p. 976-986 11 p.

  研究成果: Article › 査読

  • Statistical Significance 100%
  • RNA 97%
  • Interaction 58%
  • 5' Untranslated Regions 23%
  • 3' Untranslated Regions 21%

• Antagonistic RNA aptamer specific to a heterodimeric form of human interleukin-17A/F

  Adachi, H., Ishiguro, A., Hamada, M., Sakota, E., Asai, K. & Nakamura, Y., 2011 7月, In: Biochimie. 93, 7, p. 1081-1088 8 p.

  研究成果: Article › 査読

  • human IL17A protein 100%
  • Nucleotide Aptamers 78%
  • Interleukin-17 57%
  • Surface Plasmon Resonance 51%
  • Secondary Structure 47%
  16 被引用数 (Scopus)

• A semi-supervised learning approach for RNA secondary structure prediction

  Yonemoto, H., Asai, K. & Hamada, M., 2015 5月 16, In: Computational Biology and Chemistry. 57, p. 72-79 8 p.

  研究成果: Article › 査読

  • Structure Prediction 100%
  • Supervised Machine Learning 99%
  • Semi-supervised Learning 99%
  • Secondary Structure 74%
  • RNA 43%
  8 被引用数 (Scopus)

• Association analysis of repetitive elements and R-loop formation across species

  Zeng, C., Onoguchi, M. & Hamada, M., 2021 12月, In: Mobile DNA. 12, 1, 3.

  研究成果: Article › 査読

  Open Access

  • R-Loop Structures 100%
  • Diptera 13%
  • Fruit 11%
  • Genome 8%
  • Retroelements 8%
  1 被引用数 (Scopus)

• Beyond similarity assessment: Selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm

  Takeda, T. & Hamada, M., 2018 2月 15, In: Bioinformatics. 34, 4, p. 576-584 9 p.

  研究成果: Article › 査読

  Open Access

  • Sequence Alignment 100%
  • Markov Model 74%
  • Similarity 58%
  • Hidden Markov models 55%
  • Simulation 43%

• Binding patterns of RNA-binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements

  Onoguchi, M., Zeng, C., Matsumaru, A. & Hamada, M., 2021 9月 1, In: NAR Genomics and Bioinformatics. 3, 3, lqab055.

  研究成果: Article › 査読

  Open Access

  • Carrier Proteins 100%
  • RNA 75%
  • RNA-Binding Proteins 72%
  • Protein 65%
  • Long Noncoding RNA 27%

• CentroidAlign: Fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score

  Hamada, M., Sato, K., Kiryu, H., Mituyama, T. & Asai, K., 2009 10月 6, In: Bioinformatics. 25, 24, p. 3236-3243 8 p., btp580.

  研究成果: Article › 査読

  • RNA Sequence 100%
  • RNA 88%
  • Alignment 84%
  • Computational Biology 69%
  • Secondary Structure 64%
  36 被引用数 (Scopus)

• CentroidFold: A web server for RNA secondary structure prediction

  Sato, K., Hamada, M., Asai, K. & Mituyama, T., 2009, In: Nucleic acids research. 37, SUPPL. 2, p. W277-W280

  研究成果: Article › 査読

  • RNA 100%
  • Sequence Alignment 58%
  • Ointments 52%
  • Benchmarking 51%
  • Base Pairing 49%
  201 被引用数 (Scopus)

• CentroidHomfold-LAST: Accurate prediction of RNA secondary structure using automatically collected homologous sequences

  Hamada, M., Yamada, K., Sato, K., Frith, M. C. & Asai, K., 2011 7月 1, In: Nucleic acids research. 39, SUPPL. 2, p. W100-W106

  研究成果: Article › 査読

  • Sequence Homology 100%
  • RNA 63%
  • RNA Sequence Analysis 34%
  • Datasets 24%
  17 被引用数 (Scopus)

• Clone decomposition based on mutation signatures provides novel insights into mutational processes

  Matsutani, T. & Hamada, M., 2021 12月 1, In: NAR Genomics and Bioinformatics. 3, 4, lqab093.

  研究成果: Article › 査読

  Open Access

  • Clone 100%
  • Tumors 83%
  • Mutation 81%
  • Tumor 72%
  • Clone Cells 65%

• Comprehensive prediction of lncRNA-RNA interactions in human transcriptome

  Terai, G., Iwakiri, J., Kameda, T., Hamada, M. & Asai, K., 2016 1月 11, In: BMC Genomics. 17, 1, 12.

  研究成果: Article › 査読

  • Long Noncoding RNA 100%
  • Transcriptome 85%
  • RNA 64%
  • Untranslated RNA 23%
  • Catalogs 12%
  43 被引用数 (Scopus)

• Computational approaches for alternative and transient secondary structures of ribonucleic acids

  Fukunaga, T. & Hamada, M., 2018 6月 20, In: Briefings in Functional Genomics. 18, 3, p. 182-191 10 p.

  研究成果: Article › 査読

  • Secondary Structure 69%
  • RNA 54%
  • Kinetics 11%

• DeepM6ASeq: Prediction and characterization of m6A-containing sequences using deep learning

  Zhang, Y. & Hamada, M., 2018 12月 31, In: BMC Bioinformatics. 19, 524.

  研究成果: Article › 査読

  Open Access

  • Deep Learning 100%
  • Methylation 78%
  • Predict 67%
  • Learning 65%
  • Deep learning 64%
  45 被引用数 (Scopus)

• Direct updating of an RNA base-pairing probability matrix with marginal probability constraints

  Hamada, M., 2012 12月 1, In: Journal of Computational Biology. 19, 12, p. 1265-1276 12 p.

  研究成果: Article › 査読

  • RNA 100%
  • Pairing 89%
  • Base Pairing 84%
  • Structure Prediction 33%
  • Informatics 26%
  8 被引用数 (Scopus)

• Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference

  Matsutani, T., Ueno, Y., Fukunaga, T. & Hamada, M., 2019 11月 1, In: Bioinformatics. 35, 22, p. 4543-4552 10 p.

  研究成果: Article › 査読

  Open Access

  • Mutagens 100%
  • Variational Bayes 82%
  • Genomics 56%
  • Mutation 54%
  • Factorization 54%
  6 被引用数 (Scopus)

• Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

  FANTOM consortium, 2021 12月, In: Nature communications. 12, 1, 3297.

  研究成果: Article › 査読

  Open Access

  • microsatellites 100%
  • Microsatellite Repeats 67%
  • caps 48%
  • gene expression 37%
  • Tandem Repeat Sequences 20%
  3 被引用数 (Scopus)

• Efficient calculation of exact probability distributions of integer features on RNA secondary structures

  Mori, R., Hamada, M. & Asai, K., 2014, In: BMC Genomics. 15, S6.

  研究成果: Article › 査読

  • RNA 100%
  8 被引用数 (Scopus)

• Estimating energy parameters for RNA secondary structure predictions using both experimental and computational data

  Nishida, S., Sakuraba, S., Asai, K. & Hamada, M., 2019 9月, In: IEEE/ACM Transactions on Computational Biology and Bioinformatics. 16, 5, p. 1645-1655 11 p., 3370686.

  研究成果: Article › 査読

  • Structure Prediction 100%
  • RNA 75%
  • Experimental Data 63%
  • Free energy 44%
  • Energy 41%
  2 被引用数 (Scopus)

• Fighting against uncertainty: An essential issue in bioinformatics

  Hamada, M., 2013 5月 7, In: Briefings in Bioinformatics. 15, 5, p. 748-767 20 p.

  研究成果: Article › 査読

  • Bioinformatics 100%
  • Computational Biology 86%
  • Uncertainty 84%
  • Sequence Alignment 36%
  • Data Analysis 22%
  7 被引用数 (Scopus)

• Free-Energy Calculation of Ribonucleic Inosines and Its Application to Nearest-Neighbor Parameters

  Sakuraba, S., Iwakiri, J., Hamada, M., Kameda, T., Tsuji, G., Kimura, Y., Abe, H. & Asai, K., 2020 9月 8, In: Journal of chemical theory and computation. 16, 9, p. 5923-5935 13 p.

  研究成果: Article › 査読

  • ribonucleic acids 100%
  • Inosine 80%
  • RNA 77%
  • Free energy 76%
  • free energy 52%
  1 被引用数 (Scopus)

• G0S2 regulates innate immunity in Kawasaki disease via lncRNA HSD11B1-AS1

  Okabe, M., Takarada, S., Miyao, N., Nakaoka, H., Ibuki, K., Ozawa, S., Watanabe, K., Tsuji, H., Hashimoto, I., Hatasaki, K., Hayakawa, S., Hamaguchi, Y., Hamada, M., Ichida, F. & Hirono, K., 2022, (Accepted/In press) In: Pediatric Research.

  研究成果: Article › 査読

  Open Access

  • Switch Genes 100%
  • Mucocutaneous Lymph Node Syndrome 84%
  • Long Noncoding RNA 71%
  • Innate Immunity 61%
  • Monocytes 13%

• Generalized centroid estimators in bioinformatics

  Hamada, M., Kiryu, H., Iwasaki, W. & Asai, K., 2011, In: PloS one. 6, 2, e16450.

  研究成果: Article › 査読

  • bioinformatics 100%
  • Computational Biology 98%
  12 被引用数 (Scopus)

• HT-SELEX-based identification of binding pre-miRNA hairpin-motif for small molecules

  Mukherjee, S., Murata, A., Ishida, R., Sugai, A., Dohno, C., Hamada, M., Krishna, S. & Nakatani, K., 2022 3月 8, In: Molecular Therapy - Nucleic Acids. 27, p. 165-174 10 p.

  研究成果: Article › 査読

  Open Access

  • MicroRNA 100%
  • MicroRNAs 68%
  • Surface Plasmon Resonance Spectroscopy 56%
  • Nucleotide Aptamers 39%
  • RNA-Binding Motifs 37%

• Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

  Zeng, C., Fukunaga, T. & Hamada, M., 2018 5月 29, In: BMC Genomics. 19, 1, 414.

  研究成果: Article › 査読

  • Long Noncoding RNA 100%
  • Ribosomes 96%
  • Catalogs 9%
  • Cytoplasm 6%
  • Proteins 5%
  33 被引用数 (Scopus)

• Identification of m⁶A-Associated RNA Binding Proteins Using an Integrative Computational Framework

  Zhang, Y. & Hamada, M., 2021 3月 1, In: Frontiers in Genetics. 12, 625797.

  研究成果: Article › 査読

  Open Access

  • RNA-Binding Proteins 100%
  • Protein Binding 21%
  • N(6)-methyladenosine 11%
  • RNA 10%
  • Protein Domains 7%

• Identification of RNA biomarkers for chemical safety screening in neural cells derived from mouse embryonic stem cells using RNA deep sequencing analysis

  Tani, H., Matsutani, T., Aoki, H., Nakamura, K., Hamaguchi, Y., Nakazato, T. & Hamada, M., 2019 5月 14, In: Biochemical and Biophysical Research Communications. 512, 4, p. 641-646 6 p.

  研究成果: Article › 査読

  • Chemical Safety 100%
  • Mouse Embryonic Stem Cells 78%
  • Untranslated RNA 71%
  • RNA Sequence Analysis 71%
  • High-Throughput Nucleotide Sequencing 60%
  1 被引用数 (Scopus)

• Identification of transposable elements contributing to tissue-specific expression of long non-coding RNAs

  Chishima, T., Iwakiri, J. & Hamada, M., 2018 1月, In: Genes. 9, 1, 23.

  研究成果: Article › 査読

  Open Access

  • DNA Transposable Elements 100%
  • Long Noncoding RNA 84%
  • Organ Specificity 27%
  • Human Embryonic Stem Cells 17%
  • Endogenous Retroviruses 9%
  25 被引用数 (Scopus)

• Identifying sequence features that drive ribosomal association for lncRNA 06 Biological Sciences 0604 Genetics

  Zeng, C. & Hamada, M., 2018 12月 31, In: BMC Genomics. 19, 906.

  研究成果: Article › 査読

  Open Access

  • Biological Science Disciplines 100%
  • Long Noncoding RNA 86%
  • Ribosomes 31%
  • RNA 13%
  • RNA Splicing 13%
  11 被引用数 (Scopus)

• Impact of human gene annotations on RNA-seq differential expression analysis

  Hamaguchi, Y., Zeng, C. & Hamada, M., 2021 12月, In: BMC Genomics. 22, 1, 730.

  研究成果: Article › 査読

  Open Access

  • Molecular Sequence Annotation 100%
  • RNA-Seq 88%
  • Human Genome 8%
  • Technology 5%
  1 被引用数 (Scopus)

• Improved Accuracy in RNA-Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring Function

  Iwakiri, J., Hamada, M., Asai, K. & Kameda, T., 2016 9月 13, In: Journal of chemical theory and computation. 12, 9, p. 4688-4697 10 p.

  研究成果: Article › 査読

  • scoring 100%
  • RNA 91%
  • rigid structures 85%
  • Molecular dynamics 85%
  • field theory (physics) 76%
  18 被引用数 (Scopus)

• Improving the accuracy of predicting secondary structure for aligned RNA sequences

  Hamada, M., Sato, K. & Asai, K., 2011 1月, In: Nucleic acids research. 39, 2, p. 393-402 10 p.

  研究成果: Article › 査読

  • Untranslated RNA 100%
  • Computational Biology 83%
  41 被引用数 (Scopus)

• IPknot: Fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming

  Sato, K., Kato, Y., Hamada, M., Akutsu, T. & Asai, K., 2011 7月, In: Bioinformatics. 27, 13, p. i85-i93 btr215.

  研究成果: Article › 査読

  • RNA 79%
  • Integer Programming 71%
  • Integer programming 70%
  • Secondary Structure 58%
  • Prediction 52%
  144 被引用数 (Scopus)

• Jonckheere-Terpstra-Kendall-based non-parametric analysis of temporal differential gene expression

  Iuchi, H. & Hamada, M., 2021 3月 1, In: NAR Genomics and Bioinformatics. 3, 1, lqab021.

  研究成果: Article › 査読

  Open Access

  • Gene Expression 100%
  • Differential Expression 98%
  • Gene expression 87%
  • Gene 77%
  • Genes 75%

• Large scale similarity search for locally stable secondary structures among RNA sequences

  Hamada, M., Mituyama, T. & Asai, K., 2009, In: IPSJ Transactions on Bioinformatics. 2, p. 36-46 11 p.

  研究成果: Article › 査読

  • RNA Sequence 100%
  • RNA 88%
  • Untranslated RNA 82%
  • Secondary Structure 64%
  • Gradient-Accelerated Spectroscopy 29%
  1 被引用数 (Scopus)

• Learning chromatin states with factorized information criteria

  Hamada, M., Ono, Y., Fujimaki, R. & Asai, K., 2015 8月 1, In: Bioinformatics. 31, 15, p. 2426-2433 8 p.

  研究成果: Article › 査読

  • Chromatin 100%
  • Information Criterion 72%
  • Genomics 60%
  • Learning 52%
  • Acetylation 33%
  8 被引用数 (Scopus)

• Lncrrisearch: A web server for lncRNA-RNA interaction prediction integrated with tissue-specific expression and subcellular localization data

  Fukunaga, T., Iwakiri, J., Ono, Y. & Hamada, M., 2019, In: Frontiers in Genetics. 10, MAY, 462.

  研究成果: Article › 査読

  Open Access

  • Long Noncoding RNA 100%
  • RNA 64%
  • Biological Phenomena 8%
  • Messenger RNA 5%
  35 被引用数 (Scopus)

• Long non-coding RNA CRNDE is involved in resistance to EGFR tyrosine kinase inhibitor in EGFR-mutant lung cancer via eIF4A3/MUC1/EGFR signaling

  Takahashi, S., Noro, R., Seike, M., Zeng, C., Matsumoto, M., Yoshikawa, A., Nakamichi, S., Sugano, T., Hirao, M., Matsuda, K., Hamada, M. & Gemma, A., 2021 4月 2, In: International journal of molecular sciences. 22, 8, 4005.

  研究成果: Article › 査読

  Open Access

  • Eukaryotic Initiation Factor-4A 100%
  • Epidermal Growth Factor 96%
  • tyrosine 78%
  • Tyrosine Kinase Inhibitor 77%
  • Eukaryotic Initiation Factors 75%
  4 被引用数 (Scopus)

• Mining frequent stem patterns from unaligned RNA sequences

  Hamada, M., Tsuda, K., Kudo, T., Kin, T. & Asai, K., 2006 10月, In: Bioinformatics. 22, 20, p. 2480-2487 8 p.

  研究成果: Article › 査読

  • RNA Sequence 100%
  • Mining 91%
  • RNA 88%
  • Secondary Structure 69%
  • Graph Mining 42%
  36 被引用数 (Scopus)

• MoAIMS: Efficient software for detection of enriched regions of MeRIP-Seq

  Zhang, Y. & Hamada, M., 2020 3月 14, In: BMC Bioinformatics. 21, 1, 103.

  研究成果: Article › 査読

  Open Access

  • RNA Sequencing 100%
  • RNA 72%
  • Sequencing 71%
  • RNA Sequence Analysis 67%
  • Immunoprecipitation 58%
  6 被引用数 (Scopus)

• Multi-resBind: a residual network-based multi-label classifier for in vivo RNA binding prediction and preference visualization

  Zhao, S. & Hamada, M., 2021 12月, In: BMC Bioinformatics. 22, 1, 554.

  研究成果: Article › 査読

  Open Access

  • Classifier 100%
  • RNA 88%
  • Visualization 79%
  • RNA-Binding Proteins 63%
  • Labels 61%

• Nucleosome destabilization by nuclear non-coding RNAs

  Fujita, R., Yamamoto, T., Arimura, Y., Fujiwara, S., Tachiwana, H., Ichikawa, Y., Sakata, Y., Yang, L., Maruyama, R., Hamada, M., Nakao, M., Saitoh, N. & Kurumizaka, H., 2020 12月 1, In: Communications Biology. 3, 1, 60.

  研究成果: Article › 査読

  Open Access

  • Nuclear RNA 100%
  • nucleosomes 90%
  • Nucleosomes 86%
  • non-coding RNA 85%
  • Untranslated RNA 83%
  5 被引用数 (Scopus)

• Parallelized latent dirichlet allocation provides a novel interpretability of mutation signatures in cancer genomes

  Matsutani, T. & Hamada, M., 2020 10月, In: Genes. 11, 10 1, p. 20 1 p., 1127.

  研究成果: Article › 査読

  Open Access

  • Genome 100%
  • Mutation 82%
  • Catalogs 81%
  • Neoplasms 47%
  • APOBEC Deaminases 28%
  1 被引用数 (Scopus)

• Parameters for accurate genome alignment

  Frith, M. C., Hamada, M. & Horton, P., 2010 2月 9, In: BMC Bioinformatics. 11, 80.

  研究成果: Article › 査読

  • Alignment 100%
  • Genomics 89%
  • Genome 58%
  • Protein 35%
  • Fungal Genome 24%
  134 被引用数 (Scopus)

• PBSIM: PacBio reads simulator - Toward accurate genome assembly

  Ono, Y., Asai, K. & Hamada, M., 2013 1月, In: Bioinformatics. 29, 1, p. 119-121 3 p.

  研究成果: Article › 査読

  • Simulator 100%
  • Normal Distribution 92%
  • Genomics 80%
  • Libraries 69%
  • Sequencing 62%
  157 被引用数 (Scopus)

• PBSIM2: A simulator for long-read sequencers with a novel generative model of quality scores

  Ono, Y., Asai, K. & Hamada, M., 2021 3月 1, In: Bioinformatics. 37, 5, p. 589-595 7 p.

  研究成果: Article › 査読

  Open Access

  • Nanopores 100%
  • Generative Models 91%
  • Simulator 82%
  • Error 48%
  • Simulators 46%
  5 被引用数 (Scopus)

• Possible roles for the hominoid-specific dscr4 gene in human cells

  Saber, M. M., Karimiavargani, M., Uzawa, T., Hettiarachchi, N., Hamada, M., Ito, Y. & Saitou, N., 2021, In: Genes and Genetic Systems. 96, 1, p. 1-11 11 p.

  研究成果: Article › 査読

  Open Access

  • Down Syndrome Critical Region 100%
  • Down Syndrome 34%
  • Genes 23%
  • Chromosomes, Human, Pair 21 21%
  • Immune System 19%
  1 被引用数 (Scopus)

• Prediction of RNA secondary structure by maximizing pseudo-expected accuracy

  Hamada, M., Sato, K. & Asai, K., 2010 11月 30, In: BMC Bioinformatics. 11, 586.

  研究成果: Article › 査読

  • RNA 79%
  • Secondary Structure 58%
  • Prediction 52%
  • Base Pairing 45%
  • RNA Sequence 35%
  20 被引用数 (Scopus)