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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
100%
Genome
52%
Mutation
42%
Genetic Phenomena
6%
Genetic Translocation
6%
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%
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%
Statistical Significance
100%
RNA
97%
Interaction
58%
5' Untranslated Regions
23%
3' Untranslated Regions
21%
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%
Structure Prediction
100%
Supervised Machine Learning
99%
Semi-supervised Learning
99%
Secondary Structure
74%
RNA
43%
R-Loop Structures
100%
Diptera
13%
Fruit
11%
Genome
8%
Retroelements
8%
Sequence Alignment
100%
Markov Model
74%
Similarity
58%
Hidden Markov models
55%
Simulation
43%
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
Carrier Proteins
100%
RNA
75%
RNA-Binding Proteins
72%
Protein
65%
Long Noncoding RNA
27%
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%
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%
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%
Clone
100%
Tumors
83%
Mutation
81%
Tumor
72%
Clone Cells
65%
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%
Secondary Structure
69%
RNA
54%
Kinetics
11%
Deep Learning
100%
Methylation
78%
Predict
67%
Learning
65%
Deep learning
64%
RNA
100%
Pairing
89%
Base Pairing
84%
Structure Prediction
33%
Informatics
26%
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
Mutagens
100%
Variational Bayes
82%
Genomics
56%
Mutation
54%
Factorization
54%
microsatellites
100%
Microsatellite Repeats
67%
caps
48%
gene expression
37%
Tandem Repeat Sequences
20%
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%
Bioinformatics
100%
Computational Biology
86%
Uncertainty
84%
Sequence Alignment
36%
Data Analysis
22%
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%
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
Switch Genes
100%
Mucocutaneous Lymph Node Syndrome
84%
Long Noncoding RNA
71%
Innate Immunity
61%
Monocytes
13%
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%
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
MicroRNA
100%
MicroRNAs
68%
Surface Plasmon Resonance Spectroscopy
56%
Nucleotide Aptamers
39%
RNA-Binding Motifs
37%
Long Noncoding RNA
100%
Ribosomes
96%
Catalogs
9%
Cytoplasm
6%
Proteins
5%
RNA-Binding Proteins
100%
Protein Binding
21%
N(6)-methyladenosine
11%
RNA
10%
Protein Domains
7%
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%
Chishima, T. ,
Iwakiri, J. &
Hamada, M. ,
2018 1月 ,
In: Genes. 9 ,
1 , 23.
研究成果: Article › 査読
DNA Transposable Elements
100%
Long Noncoding RNA
84%
Organ Specificity
27%
Human Embryonic Stem Cells
17%
Endogenous Retroviruses
9%
Biological Science Disciplines
100%
Long Noncoding RNA
86%
Ribosomes
31%
RNA
13%
RNA Splicing
13%
Molecular Sequence Annotation
100%
RNA-Seq
88%
Human Genome
8%
Technology
5%
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%
Untranslated RNA
100%
Computational Biology
83%
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%
Gene Expression
100%
Differential Expression
98%
Gene expression
87%
Gene
77%
Genes
75%
RNA Sequence
100%
RNA
88%
Untranslated RNA
82%
Secondary Structure
64%
Gradient-Accelerated Spectroscopy
29%
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%
Fukunaga, T. ,
Iwakiri, J. ,
Ono, Y. &
Hamada, M. ,
2019 ,
In: Frontiers in Genetics. 10 ,
MAY , 462.
研究成果: Article › 査読
Long Noncoding RNA
100%
RNA
64%
Biological Phenomena
8%
Messenger RNA
5%
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
Eukaryotic Initiation Factor-4A
100%
Epidermal Growth Factor
96%
tyrosine
78%
Tyrosine Kinase Inhibitor
77%
Eukaryotic Initiation Factors
75%
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%
RNA Sequencing
100%
RNA
72%
Sequencing
71%
RNA Sequence Analysis
67%
Immunoprecipitation
58%
Classifier
100%
RNA
88%
Visualization
79%
RNA-Binding Proteins
63%
Labels
61%
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
Nuclear RNA
100%
nucleosomes
90%
Nucleosomes
86%
non-coding RNA
85%
Untranslated RNA
83%
Matsutani, T. &
Hamada, M. ,
2020 10月 ,
In: Genes. 11 ,
10 1 ,
p. 20 1 p. , 1127.
研究成果: Article › 査読
Genome
100%
Mutation
82%
Catalogs
81%
Neoplasms
47%
APOBEC Deaminases
28%
Alignment
100%
Genomics
89%
Genome
58%
Protein
35%
Fungal Genome
24%
Simulator
100%
Normal Distribution
92%
Genomics
80%
Libraries
69%
Sequencing
62%
Nanopores
100%
Generative Models
91%
Simulator
82%
Error
48%
Simulators
46%
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
Down Syndrome Critical Region
100%
Down Syndrome
34%
Genes
23%
Chromosomes, Human, Pair 21
21%
Immune System
19%
RNA
79%
Secondary Structure
58%
Prediction
52%
Base Pairing
45%
RNA Sequence
35%