浜田 道昭

研究成果

年別の研究成果 2003 2021

• 1301 被引用数
• 16 h-index
• 65 Article
• 3 Chapter
• 2 Conference contribution
• 2 Review article
• 2 その他
  • 1 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

  • Arabidopsis
  • Genome
  • Mutation
  • Genetic Phenomena
  • Genetic Translocation
  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 15, In: Bioinformatics. 29, 20, p. 2524-2528 5 p.

  研究成果: Article › 査読

  • RNA Secondary Structure
  • RNA
  • Pairing
  • Protein
  • Molecules
  5 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 1, In: Journal of Bioinformatics and Computational Biology. 8, 4, p. 727-742 16 p.

  研究成果: Article › 査読

  • Bayes Theorem
  • RNA
  • Stochastic Processes
  • Context free grammars
  • Bioinformatics
  7 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, In: Journal of Computational Biology. 25, 9, p. 976-986 11 p.

  研究成果: Article › 査読

  • Statistical Significance
  • RNA
  • Interaction
  • 5' Untranslated Regions
  • 3' Untranslated Regions

• 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 1, In: Biochimie. 93, 7, p. 1081-1088 8 p.

  研究成果: Article › 査読

  • human IL17A protein
  • Nucleotide Aptamers
  • Interleukin-17
  15 被引用数 (Scopus)

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

  Yonemoto, H., Asai, K. & Hamada, M., 2015 1 2, In: Computational Biology and Chemistry. 57, p. 72-79 8 p.

  研究成果: Article › 査読

  • Supervised Machine Learning
  • Semi-supervised Learning
  • Structure Prediction
  • RNA Secondary Structure
  • RNA
  7 被引用数 (Scopus)

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

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

  研究成果: Article › 査読

  Open Access

  • Diptera
  • Fruit
  • Genome
  • Retroelements
  • Arabidopsis

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

  Zeng, C., Onoguchi, M. & Hamada, M., 2020 11 10, In: Unknown Journal.

  研究成果: Article › 査読

  • Fruits
  • Diptera
  • fruit flies
  • Fruit
  • Arabidopsis

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

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

  研究成果: Article › 査読

  • Sequence Alignment
  • Markov Model
  • Similarity
  • Hidden Markov models
  • Bioinformatics

• Beyond similarity assessment: Selecting the optimal model for sequence alignment via the factorized asymptotic Bayesian algorithm

  Takeda, T. & Hamada, M., 2017 5 19, In: Unknown Journal.

  研究成果: Article › 査読

  • alignment
  • deletion
  • insertion
  • deoxyribonucleic acid

• 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 6, In: Bioinformatics. 25, 24, p. 3236-3243 8 p., btp580.

  研究成果: Article › 査読

  • RNA
  • Alignment
  • Computational Biology
  • Untranslated RNA
  • Benchmarking
  35 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
  • Sequence Alignment
  • Benchmarking
  • Ointments
  • Software
  174 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 1, In: Nucleic acids research. 39, SUPPL. 2, p. W100-W106

  研究成果: Article › 査読

  • Sequence Homology
  • RNA
  • RNA Sequence Analysis
  • Datasets
  15 被引用数 (Scopus)

• Comprehensive prediction of lncRNA-RNA interactions in human transcriptome

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

  研究成果: Article › 査読

  • Long Noncoding RNA
  • Transcriptome
  • RNA
  • Untranslated RNA
  • Catalogs
  36 被引用数 (Scopus)

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

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

  研究成果: Article › 査読

  • RNA
  • Computational methods
  • Cells
  • Kinetics

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

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

  研究成果: Article › 査読

  • Deep Learning
  • Methylation
  • Deep learning
  • Predict
  • Learning
  16 被引用数 (Scopus)

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

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

  研究成果: Article › 査読

  • RNA
  • Updating
  • Pairing
  • RNA Secondary Structure
  • Structure Prediction
  7 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 1, In: Bioinformatics. 35, 22, p. 4543-4552 10 p.

  研究成果: Article › 査読

  Open Access

  • Mutagens
  • Variational Bayes
  • Factorization
  • Mutation
  • Signature
  4 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
  6 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., 2018 3 9, (Accepted/In press) In: IEEE/ACM Transactions on Computational Biology and Bioinformatics.

  研究成果: Article › 査読

  • Structure Prediction
  • RNA Secondary Structure
  • RNA
  • Experimental Data
  • Free energy
  1 被引用数 (Scopus)

• Fighting against uncertainty: An essential issue in bioinformatics

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

  研究成果: Article › 査読

  • Bioinformatics
  • Computational Biology
  • Uncertainty
  • Sequence Alignment
  • Data Analysis
  4 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 8, In: Journal of chemical theory and computation. 16, 9, p. 5923-5935 13 p.

  研究成果: Article › 査読

  • ribonucleic acids
  • Inosine
  • RNA
  • Free energy
  • free energy

• 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
  • bioinformatics
  • Computational Biology
  11 被引用数 (Scopus)

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

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

  研究成果: Article › 査読

  • Long Noncoding RNA
  • Ribosomes
  • Catalogs
  • Cytoplasm
  • Proteins
  19 被引用数 (Scopus)

• 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., 2018 1 1, (Accepted/In press) In: Biochemical and Biophysical Research Communications.

  研究成果: Article › 査読

  • Chemical Safety
  • Stem cells
  • Biomarkers
  • Mouse Embryonic Stem Cells
  • RNA Sequence Analysis
  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, In: Genes. 9, 1, 23.

  研究成果: Article › 査読

  • DNA Transposable Elements
  • Long Noncoding RNA
  • Organ Specificity
  • Human Embryonic Stem Cells
  • Endogenous Retroviruses
  15 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 31, In: BMC Genomics. 19, 906.

  研究成果: Article › 査読

  • Biological Science Disciplines
  • Long Noncoding RNA
  • Ribosomes
  • RNA
  • RNA Splicing
  4 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 13, In: Journal of Chemical Theory and Computation. 12, 9, p. 4688-4697 10 p.

  研究成果: Article › 査読

  • scoring
  • RNA
  • rigid structures
  • Molecular dynamics
  • field theory (physics)
  15 被引用数 (Scopus)

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

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

  研究成果: Article › 査読

  • Untranslated RNA
  • Computational Biology
  34 被引用数 (Scopus)

• In silico approaches to RNA aptamer design

  Hamada, M., 2017, (Accepted/In press) In: Biochimie.

  研究成果: Article › 査読

  • Nucleotide Aptamers
  • Computer Simulation
  • Costs and Cost Analysis
  • Pharmaceutical Preparations
  • Computational methods
  8 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, In: Bioinformatics. 27, 13, p. i85-i93 btr215.

  研究成果: Article › 査読

  • RNA Secondary Structure
  • RNA
  • Integer Programming
  • Integer programming
  • Prediction
  117 被引用数 (Scopus)

• 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
  • Untranslated RNA
  • Combinatorial optimization
  • Sequence Analysis
  • Experiments
  1 被引用数 (Scopus)

• Learning chromatin states with factorized information criteria

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

  研究成果: Article › 査読

  • Chromatin
  • Information Criterion
  • Learning
  • Genes
  • Acetylation
  6 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
  • RNA
  • Biological Phenomena
  10 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, In: Bioinformatics. 22, 20, p. 2480-2487 8 p.

  研究成果: Article › 査読

  • Mining
  • RNA
  • Secondary Structure
  • Graph Mining
  • Directed graphs
  36 被引用数 (Scopus)

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

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

  研究成果: Article › 査読

  Open Access

  • RNA
  • Sequencing
  • RNA Sequence Analysis
  • Immunoprecipitation
  • Model-based
  2 被引用数 (Scopus)

• Nearest-neighbor parameter for inosine-cytosine pairs through a combined experimental and computational approach

  Sakuraba, S., Iwakiri, J., Hamada, M., Kameda, T., Tsuji, G., Kimura, Y., Abe, H. & Asai, K., 2018 10 26, In: Unknown Journal.

  研究成果: Article › 査読

  • Inosine
  • inosine
  • Cytosine
  • cytosine
  • RNA

• 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 1, In: Communications Biology. 3, 1, 60.

  研究成果: Article › 査読

  Open Access

  • Nuclear RNA
  • nucleosomes
  • non-coding RNA
  • Nucleosomes
  • Untranslated RNA
  3 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, In: Genes. 11, 10 1, p. 20 1 p., 1127.

  研究成果: Article › 査読

  Open Access

  • Genome
  • Mutation
  • Catalogs
  • Neoplasms
  • APOBEC Deaminases

• Parameters for accurate genome alignment

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

  研究成果: Article › 査読

  • Alignment
  • Genome
  • Genes
  • Fungal Genome
  • Plant Genome
  122 被引用数 (Scopus)

• PBSIM: PacBio reads simulator - Toward accurate genome assembly

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

  研究成果: Article › 査読

  • Simulator
  • Normal Distribution
  • Genome
  • Genes
  • Libraries
  127 被引用数 (Scopus)

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

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

  研究成果: Article › 査読

  • RNA Secondary Structure
  • RNA
  • Prediction
  • Secondary Structure
  • Structure Prediction
  19 被引用数 (Scopus)

• Prediction of RNA secondary structure using generalized centroid estimators

  Hamada, M., Kiryu, H., Sato, K., Mituyama, T. & Asai, K., 2009 2, In: Bioinformatics. 25, 4, p. 465-473 9 p.

  研究成果: Article › 査読

  • RNA Secondary Structure
  • RNA
  • Centroid
  • Secondary Structure
  • Prediction
  145 被引用数 (Scopus)

• Predictions of RNA secondary structure by combining homologous sequence information

  Hamada, M., Sato, K., Kiryu, H., Mituyama, T. & Asai, K., 2009, In: Bioinformatics. 25, 12, p. i330-i338

  研究成果: Article › 査読

  • RNA Secondary Structure
  • RNA
  • Sequence Homology
  • Prediction
  • Secondary Structure
  31 被引用数 (Scopus)

• Privacy-preserving search for chemical compound databases

  Shimizu, K., Nuida, K., Arai, H., Mitsunari, S., Attrapadung, N., Hamada, M., Tsuda, K., Hirokawa, T., Sakuma, J., Hanaoka, G. & Asai, K., 2015 12 9, In: BMC Bioinformatics. 16, 18, S6.

  研究成果: Article › 査読

  • Privacy Preserving
  • Chemical Databases
  • Chemical compounds
  • Privacy
  • Databases
  7 被引用数 (Scopus)

• Probabilistic alignments with quality scores: An application to short-read mapping toward accurate SNP/indel detection

  Hamada, M., Wijaya, E., Frith, M. C. & Asai, K., 2011 11, In: Bioinformatics. 27, 22, p. 3085-3092 8 p., btr537.

  研究成果: Article › 査読

  • Alignment
  • Single Nucleotide Polymorphism
  • hydrogen sulfite
  • Statistical Models
  • Probabilistic Model
  12 被引用数 (Scopus)

• RactIP: Fast and accurate prediction of RNA-RNA interaction using integer programming

  Kato, Y., Sato, K., Hamada, M., Watanabe, Y., Asai, K. & Akutsu, T., 2010 9 4, In: Bioinformatics. 26, 18, p. i460-i466 btq372.

  研究成果: Article › 査読

  • RNA
  • Integer Programming
  • Integer programming
  • Prediction
  • Interaction
  49 被引用数 (Scopus)

• RaptRanker: In silico RNA aptamer selection from HT-SELEX experiment based on local sequence and structure information

  Ishida, R., Adachi, T., Yokota, A., Yoshihara, H., Aoki, K., Nakamura, Y. & Hamada, M., 2019 12 31, In: Unknown Journal.

  研究成果: Article › 査読

  • Leptosols
  • systematic evolution of ligands by exponential enrichment
  • SELEX Aptamer Technique
  • nucleotide aptamers
  • Nucleotide Aptamers

• RaptRanker: In silico RNA aptamer selection from HT-SELEX experiment based on local sequence and structure information

  Ishida, R., Adachi, T., Yokota, A., Yoshihara, H., Aoki, K., Nakamura, Y. & Hamada, M., 2020 8 20, In: Nucleic acids research. 48, 14, e82.

  研究成果: Article › 査読

  Open Access

  • SELEX Aptamer Technique
  • Nucleotide Aptamers
  • Computer Simulation
  • Datasets
  • Single-Stranded DNA
  1 被引用数 (Scopus)

• Reference-free prediction of rearrangement breakpoint reads

  Wijaya, E., Shimizu, K., Asai, K. & Hamada, M., 2014 9 15, In: Bioinformatics. 30, 18, p. 2559-2567 9 p.

  研究成果: Article › 査読

  • Genome
  • Rearrangement
  • Genes
  • Sequencing
  • Prediction
  5 被引用数 (Scopus)