Michiaki Hamada
Michiaki Hamada
Waseda University / AIST / Nippon Medical School
Verified email at - Homepage
Cited by
Cited by
PBSIM: PacBio reads simulator—toward accurate genome assembly
Y Ono, K Asai, M Hamada
Bioinformatics 29 (1), 119-121, 2013
CentroidFold: a web server for RNA secondary structure prediction
K Sato, M Hamada, K Asai, T Mituyama
Nucleic acids research 37 (suppl_2), W277-W280, 2009
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
K Sato, Y Kato, M Hamada, T Akutsu, K Asai
Bioinformatics 27 (13), i85-i93, 2011
Prediction of RNA secondary structure using generalized centroid estimators
M Hamada, H Kiryu, K Sato, T Mituyama, K Asai
Bioinformatics 25 (4), 465-473, 2009
Parameters for accurate genome alignment
MC Frith, M Hamada, P Horton
BMC bioinformatics 11, 1-14, 2010
LncRRIsearch: a web server for lncRNA-RNA interaction prediction integrated with tissue-specific expression and subcellular localization data
T Fukunaga, J Iwakiri, Y Ono, M Hamada
Frontiers in genetics 10, 462, 2019
PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores
Y Ono, K Asai, M Hamada
Bioinformatics 37 (5), 589-595, 2021
DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning
Y Zhang, M Hamada
BMC bioinformatics 19, 1-11, 2018
RIblast: an ultrafast RNA–RNA interaction prediction system based on a seed-and-extension approach
T Fukunaga, M Hamada
Bioinformatics 33 (17), 2666-2674, 2017
RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming
Y Kato, K Sato, M Hamada, Y Watanabe, K Asai, T Akutsu
Bioinformatics 26 (18), i460-i466, 2010
Training alignment parameters for arbitrary sequencers with LAST-TRAIN
M Hamada, Y Ono, K Asai, MC Frith
Bioinformatics 33 (6), 926-928, 2017
Representation learning applications in biological sequence analysis
H Iuchi, T Matsutani, K Yamada, N Iwano, S Sumi, S Hosoda, S Zhao, ...
Computational and Structural Biotechnology Journal 19, 3198-3208, 2021
Improving the accuracy of predicting secondary structure for aligned RNA sequences
M Hamada, K Sato, K Asai
Nucleic acids research 39 (2), 393-402, 2011
Bioinformatics tools for lncRNA research
J Iwakiri, M Hamada, K Asai
Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1859 (1), 23-30, 2016
Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data
C Zeng, T Fukunaga, M Hamada
BMC genomics 19, 1-14, 2018
Comprehensive prediction of lncRNA–RNA interactions in human transcriptome
G Terai, J Iwakiri, T Kameda, M Hamada, K Asai
BMC genomics 17, 153-164, 2016
Mining frequent stem patterns from unaligned RNA sequences
M Hamada, K Tsuda, T Kudo, T Kin, K Asai
Bioinformatics 22 (20), 2480-2487, 2006
Stromal fibroblasts induce metastatic tumor cell clusters via epithelial–mesenchymal plasticity
Y Matsumura, Y Ito, Y Mezawa, K Sulidan, Y Daigo, T Hiraga, K Mogushi, ...
Life science alliance 2 (4), 2019
Predictions of RNA secondary structure by combining homologous sequence information
M Hamada, K Sato, H Kiryu, T Mituyama, K Asai
Bioinformatics 25 (12), i330-i338, 2009
CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score
M Hamada, K Sato, H Kiryu, T Mituyama, K Asai
Bioinformatics 25 (24), 3236-3243, 2009
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