Michiaki Hamada

Cited by

	All	Since 2015
Citations	1996	1303
h-index	20	17
i10-index	38	32

320

160

240

200720082009201020112012201320142015201620172018201920206 7 27 47 110 135 116 171 169 197 174 211 248 304

Co-authors

Kiyoshi AsaiProfessor of Computational Biology, University of TokyoVerified email at k.u-tokyo.ac.jp
Kengo SatoKeio University, JapanVerified email at bio.keio.ac.jp
Junichi IwakiriDepartment of Computational Biology and Medical Sciences, the University of TokyoVerified email at cb.k.u-tokyo.ac.jp
Tsukasa FukunagaResearch Associate, Department of Computer Science, The University of TokyoVerified email at is.s.u-tokyo.ac.jp
Martin FrithNational Institute of Advanced Industrial Science and Technology (AIST), University of TokyoVerified email at edu.k.u-tokyo.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
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
Paul HortonNCKU, TaiwanVerified email at iscb.org
Chao ZENGAIST CBBD-OIL / Waseda UniversityVerified email at aoni.waseda.jp
Taku KudoGoogle Inc.Verified email at google.com
Kana ShimizuWaseda University, National Institute of Advanced Industrial Science and TechnologyVerified email at waseda.jp
Edward WijayaStemrim, Inc. & Dept. Stem Cell Therapy Science Osaka UniversityVerified email at stemrim.com
Takatsugu HirokawaMolecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST)Verified email at aist.go.jp
Koji NuidaThe University of TokyoVerified email at mist.i.u-tokyo.ac.jp
Nuttapong AttrapadungAIST, JapanVerified email at aist.go.jp
Jun SakumaProfessor of University of Tsukuba / RIKEN AIPVerified email at cs.tsukuba.ac.jp
shigeo MITSUNARICybozu Labs, Inc.Verified email at nifty.com
Shun SakurabaResearcher, National Institutes for Quantum and Radiological Science and TechnologyVerified email at qst.go.jp
Wataru IwasakiAssociate Professor, Department of Biological Sciences, the University of TokyoVerified email at bs.s.u-tokyo.ac.jp

Michiaki Hamada

Waseda University / AIST CBBD-OIL / Nippon Medical School

Verified email at waseda.jp - Homepage

Bioinformatics Computational Biology Data mining Machine Learning


Title Sort by citations Sort by year Sort by title	Cited by Cited by	Year
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	238	2009
PBSIM: PacBio reads simulator—toward accurate genome assembly Y Ono, K Asai, M Hamada Bioinformatics 29 (1), 119-121, 2013	231	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	205	2009
Parameters for accurate genome alignment MC Frith, M Hamada, P Horton BMC bioinformatics 11 (1), 80, 2010	184	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	171	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	68	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	51	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	50	2009
Mining frequent stem patterns from unaligned RNA sequences M Hamada, K Tsuda, T Kudo, T Kin, K Asai Bioinformatics 22 (20), 2480-2487, 2006	49	2006
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	46	2016
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	46	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	39	2016
Training alignment parameters for arbitrary sequencers with LAST-TRAIN M Hamada, Y Ono, K Asai, MC Frith Bioinformatics 33 (6), 926-928, 2017	36	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	34	2017
Prediction of RNA secondary structure by maximizing pseudo-expected accuracy M Hamada, K Sato, K Asai BMC bioinformatics 11 (1), 586, 2010	27	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	26	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	25	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	23	2012
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	23	2011
CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences M Hamada, K Yamada, K Sato, MC Frith, K Asai Nucleic acids research 39 (suppl_2), W100-W106, 2011	22	2011

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