Michiaki Hamada
Michiaki Hamada
Waseda University / AIST CBBD-OIL / Nippon Medical School
Verified email at waseda.jp - Homepage
Cited by
Cited by
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
PBSIM: PacBio reads simulator—toward accurate genome assembly
Y Ono, K Asai, M Hamada
Bioinformatics 29 (1), 119-121, 2013
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), 1-14, 2010
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
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
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
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
Comprehensive prediction of lncRNA–RNA interactions in human transcriptome
G Terai, J Iwakiri, T Kameda, M Hamada, K Asai
BMC genomics 17 (1), 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
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
Bioinformatics tools for lncRNA research
J Iwakiri, M Hamada, K Asai
Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1859 (1), 23-30, 2016
Training alignment parameters for arbitrary sequencers with LAST-TRAIN
M Hamada, Y Ono, K Asai, MC Frith
Bioinformatics 33 (6), 926-928, 2017
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
Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data
C Zeng, T Fukunaga, M Hamada
BMC genomics 19 (1), 1-14, 2018
Prediction of RNA secondary structure by maximizing pseudo-expected accuracy
M Hamada, K Sato, K Asai
BMC bioinformatics 11 (1), 1-10, 2010
Computational prediction of lncRNA-mRNA interactions by integrating tissue specificity in human transcriptome
J Iwakiri, G Terai, M Hamada
Biology direct 12 (1), 1-8, 2017
Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection
M Hamada, E Wijaya, MC Frith, K Asai
Bioinformatics 27 (22), 3085-3092, 2011
DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning
Y Zhang, M Hamada
BMC bioinformatics 19 (19), 1-11, 2018
A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA)
M Hamada, K Asai
Journal of Computational Biology 19 (5), 532-549, 2012
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