PBSIM: PacBio reads simulator—toward accurate genome assembly Y Ono, K Asai, M Hamada Bioinformatics 29 (1), 119-121, 2013 | 359 | 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 | 323 | 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 | 297 | 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 | 264 | 2009 |
Parameters for accurate genome alignment MC Frith, M Hamada, P Horton BMC bioinformatics 11, 1-14, 2010 | 232 | 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 | 114 | 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 | 105 | 2021 |
DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning Y Zhang, M Hamada BMC bioinformatics 19, 1-11, 2018 | 105 | 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 | 95 | 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 | 85 | 2010 |
Training alignment parameters for arbitrary sequencers with LAST-TRAIN M Hamada, Y Ono, K Asai, MC Frith Bioinformatics 33 (6), 926-928, 2017 | 82 | 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 | 76 | 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 | 71 | 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 | 65 | 2016 |
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 | 63 | 2016 |
Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data C Zeng, T Fukunaga, M Hamada BMC genomics 19, 1-14, 2018 | 62 | 2018 |
Mining frequent stem patterns from unaligned RNA sequences M Hamada, K Tsuda, T Kudo, T Kin, K Asai Bioinformatics 22 (20), 2480-2487, 2006 | 58 | 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 | 57 | 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 | 57 | 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 | 56 | 2009 |