Michiaki Hamada

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Citations	4112	2464
h-index	31	27
i10-index	62	48

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Kiyoshi AsaiProfessor of Computational Biology, University of TokyoVerified email at k.u-tokyo.ac.jp
Kengo SatoProfessor, Institute of Science Tokyo, JapanVerified email at m.isct.ac.jp
Tsukasa FukunagaAssociate Professor, Waseda Institute for Advanced Study, Waseda UniversityVerified email at aoni.waseda.jp
yukiteru onoUniversity of TokyoVerified email at edu.k.u-tokyo.ac.jp
Junichi IwakiriDepartment of Computational Biology and Medical Sciences, the University of TokyoVerified email at cb.k.u-tokyo.ac.jp
Chao ZengWaseda UniversityVerified email at aoni.waseda.jp
Yuki KatoAssociate Professor, Osaka UniversityVerified email at rna.med.osaka-u.ac.jp
Tomoshi Kameda産業技術総合研究所　人工知能研究センターVerified email at aist.go.jp
Martin FrithUniversity of Tokyo, National Institute of Advanced Industrial Science and Technology (AIST)Verified email at edu.k.u-tokyo.ac.jp
Shion HosodaWaseda UniversityVerified email at hamadalab.com
taro matsutaniWaseda UniversityVerified email at hamadalab.com
Tatsuya AkutsuProfessor, Bioinformatics Center, Institute for Chemical Research, Kyoto UniversityVerified email at kuicr.kyoto-u.ac.jp
Koji TsudaProfessor, GSFS, The University of TokyoVerified email at k.u-tokyo.ac.jp
Hitoshi IuchiWaseda UniversityVerified email at hamadalab.com
Paul HortonNCKU, TaiwanVerified email at iscb.org
Keisuke YamadaUniversity of PennsylvaniaVerified email at seas.upenn.edu
Shunsuke SumiThe University of TokyoVerified email at iqb.u-tokyo.ac.jp
Takatsugu HirokawaMolecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST)Verified email at aist.go.jp
Jun SakumaInstitute of Science Tokyo (Tokyo Institute of Technology), School of ComputingVerified email at c.titech.ac.jp
Koji NuidaKyushu UniversityVerified email at imi.kyushu-u.ac.jp

Michiaki Hamada

Waseda University / AIST / Nippon Medical School

Verified email at waseda.jp - Homepage

Bioinformatics Computational Biology Data mining Machine Learning


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PBSIM: PacBio reads simulator—toward accurate genome assembly Y Ono, K Asai, M Hamada Bioinformatics 29 (1), 119-121, 2013	375	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	350	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	323	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	270	2009
Parameters for accurate genome alignment MC Frith, M Hamada, P Horton BMC bioinformatics 11, 1-14, 2010	248	2010
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	132	2021
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	129	2019
DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning Y Zhang, M Hamada BMC bioinformatics 19, 1-11, 2018	121	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	103	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	99	2021
Training alignment parameters for arbitrary sequencers with LAST-TRAIN M Hamada, Y Ono, K Asai, MC Frith Bioinformatics 33 (6), 926-928, 2017	89	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
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	72	2011
Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data C Zeng, T Fukunaga, M Hamada BMC genomics 19, 1-14, 2018	70	2018
Bioinformatics tools for lncRNA research J Iwakiri, M Hamada, K Asai Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1859 (1), 23-30, 2016	68	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	64	2016
RaptRanker: in silico RNA aptamer selection from HT-SELEX experiment based on local sequence and structure information R Ishida, T Adachi, A Yokota, H Yoshihara, K Aoki, Y Nakamura, ... Nucleic acids research 48 (14), e82-e82, 2020	59	2020
Mining frequent stem patterns from unaligned RNA sequences M Hamada, K Tsuda, T Kudo, T Kin, K Asai Bioinformatics 22 (20), 2480-2487, 2006	59	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	58	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	58	2009

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