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ORCIDMichiaki Hamada
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2020 – today
- 2023
[j39]Kengo Sato
, Michiaki Hamada:
Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery. Briefings Bioinform. 24(4) (2023)- [j38]Kaisei Hara, Natsuki Iwano, Tsukasa Fukunaga, Michiaki Hamada:
DeepRaccess: high-speed RNA accessibility prediction using deep learning. Frontiers Bioinform. 3 (2023) - [c2]Takahiro Mimori, Michiaki Hamada:
GeoPhy: Differentiable Phylogenetic Inference via Geometric Gradients of Tree Topologies. NeurIPS 2023 - [i2]Takahiro Mimori, Michiaki Hamada:
GeoPhy: Differentiable Phylogenetic Inference via Geometric Gradients of Tree Topologies. CoRR abs/2307.03675 (2023) - 2022
- [j37]Natsuki Iwano, Tatsuo Adachi, Kazuteru Aoki, Yoshikazu Nakamura, Michiaki Hamada:
Generative aptamer discovery using RaptGen. Nat. Comput. Sci. 2(6): 378-386 (2022) - 2021
- [j36]Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada:
PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores. Bioinform. 37(5): 589-595 (2021) - [j35]Shion Hosoda, Tsukasa Fukunaga, Michiaki Hamada:
Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model. Bioinform. 37(Supplement): 16-24 (2021) - [j34]Shitao Zhao, Michiaki Hamada:
Multi-resBind: a residual network-based multi-label classifier for in vivo RNA binding prediction and preference visualization. BMC Bioinform. 22(1): 554 (2021) - 2020
- [j33]Yiqian Zhang, Michiaki Hamada:
MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq. BMC Bioinform. 21(1): 103 (2020)
2010 – 2019
- 2019
- [j32]Taro Matsutani, Yuki Ueno, Tsukasa Fukunaga, Michiaki Hamada:
Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference. Bioinform. 35(22): 4543-4552 (2019) - [j31]Shimpei Nishida, Shun Sakuraba, Kiyoshi Asai, Michiaki Hamada:
Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data. IEEE ACM Trans. Comput. Biol. Bioinform. 16(5): 1645-1655 (2019) - 2018
- [j30]Taikai Takeda, Michiaki Hamada:
Beyond similarity assessment: selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm. Bioinform. 34(4): 576-584 (2018) - [j29]Yiqian Zhang, Michiaki Hamada:
DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning. BMC Bioinform. 19-S(19): 524:1-524:11 (2018) - [j28]Tsukasa Fukunaga, Michiaki Hamada:
A Novel Method for Assessing the Statistical Significance of RNA-RNA Interactions Between Two Long RNAs. J. Comput. Biol. 25(9): 976-986 (2018) - 2017
- [j27]Michiaki Hamada, Yukiteru Ono, Kiyoshi Asai, Martin C. Frith:
Training alignment parameters for arbitrary sequencers with LAST-TRAIN. Bioinform. 33(6): 926-928 (2017) - [j26]Tsukasa Fukunaga, Michiaki Hamada:
RIblast: an ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach. Bioinform. 33(17): 2666-2674 (2017) - 2016
- [j25]Goro Terai, Junichi Iwakiri, Tomoshi Kameda, Michiaki Hamada, Kiyoshi Asai:
Comprehensive prediction of lncRNA-RNA interactions in human transcriptome. BMC Genom. 17(S-1): 12 (2016) - [j24]Michiaki Hamada, Yukiteru Ono, Hisanori Kiryu, Kengo Sato, Yuki Kato, Tsukasa Fukunaga, Ryota Mori, Kiyoshi Asai:
Rtools: a web server for various secondary structural analyses on single RNA sequences. Nucleic Acids Res. 44(Webserver-Issue): W302-W307 (2016) - 2015
- [j23]Michiaki Hamada, Yukiteru Ono, Ryohei Fujimaki, Kiyoshi Asai:
Learning chromatin states with factorized information criteria. Bioinform. 31(15): 2426-2433 (2015) - [j22]Kana Shimizu, Koji Nuida, Hiromi Arai, Shigeo Mitsunari, Nuttapong Attrapadung, Michiaki Hamada, Koji Tsuda, Takatsugu Hirokawa, Jun Sakuma, Goichiro Hanaoka, Kiyoshi Asai:
Privacy-preserving search for chemical compound databases. BMC Bioinform. 16(S18): S6 (2015) - [j21]Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada:
A semi-supervised learning approach for RNA secondary structure prediction. Comput. Biol. Chem. 57: 72-79 (2015) - 2014
- [j20]Michiaki Hamada:
Fighting against uncertainty: an essential issue in bioinformatics. Briefings Bioinform. 15(5): 748-767 (2014) - [j19]Edward Wijaya, Kana Shimizu, Kiyoshi Asai, Michiaki Hamada:
Reference-free prediction of rearrangement breakpoint reads. Bioinform. 30(18): 2559-2567 (2014) - 2013
- [j18]Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada:
PBSIM: PacBio reads simulator - toward accurate genome assembly. Bioinform. 29(1): 119-121 (2013) - [j17]Junichi Iwakiri, Tomoshi Kameda, Kiyoshi Asai, Michiaki Hamada:
Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions. Bioinform. 29(20): 2524-2528 (2013) - [i1]Michiaki Hamada, Hisanori Kiryu, Wataru Iwasaki, Kiyoshi Asai:
Generalized Centroid Estimators in Bioinformatics. CoRR abs/1305.4339 (2013) - 2012
- [j16]Michiaki Hamada, Kiyoshi Asai:
A Classification of Bioinformatics Algorithms from the Viewpoint of Maximizing Expected Accuracy (MEA). J. Comput. Biol. 19(5): 532-549 (2012) - [j15]Michiaki Hamada:
Direct Updating of an RNA Base-Pairing Probability Matrix with Marginal Probability Constraints. J. Comput. Biol. 19(12): 1265-1276 (2012) - 2011
- [j14]Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai:
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinform. 27(13): 85-93 (2011) - [j13]Michiaki Hamada, Edward Wijaya, Martin C. Frith, Kiyoshi Asai:
Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection. Bioinform. 27(22): 3085-3092 (2011) - [j12]Michiaki Hamada, Kengo Sato, Kiyoshi Asai:
Improving the accuracy of predicting secondary structure for aligned RNA sequences. Nucleic Acids Res. 39(2): 393-402 (2011) - [j11]Michiaki Hamada, Koichiro Yamada, Kengo Sato, Martin C. Frith, Kiyoshi Asai:
CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences. Nucleic Acids Res. 39(Web-Server-Issue): 100-106 (2011) - 2010
- [j10]Yuki Kato, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, Tatsuya Akutsu:
RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinform. 26(18) (2010) - [j9]Martin C. Frith, Michiaki Hamada, Paul Horton:
Parameters for accurate genome alignment. BMC Bioinform. 11: 80 (2010) - [j8]Michiaki Hamada, Kengo Sato, Kiyoshi Asai:
Prediction of RNA secondary structure by maximizing pseudo-expected accuracy. BMC Bioinform. 11: 586 (2010) - [j7]Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara:
A Non-Parametric Bayesian Approach for Predicting RNA Secondary Structures. J. Bioinform. Comput. Biol. 8(4): 727-742 (2010)
2000 – 2009
- 2009
- [j6]Michiaki Hamada, Hisanori Kiryu, Kengo Sato, Toutai Mituyama, Kiyoshi Asai:
Prediction of RNA secondary structure using generalized centroid estimators. Bioinform. 25(4): 465-473 (2009) - [j5]Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai:
Predictions of RNA secondary structure by combining homologous sequence information. Bioinform. 25(12) (2009) - [j4]Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai:
CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score. Bioinform. 25(24): 3236-3243 (2009) - [j3]Kengo Sato, Michiaki Hamada, Kiyoshi Asai, Toutai Mituyama:
CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res. 37(Web-Server-Issue): 277-280 (2009) - [c1]Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara:
A Non-parametric Bayesian Approach for Predicting RNA Secondary Structures. WABI 2009: 286-297 - 2008
- [j2]Kiyoshi Asai, Hisanori Kiryu, Michiaki Hamada, Yasuo Tabei, Kengo Sato, Hiroshi Matsui, Yasubumi Sakakibara, Goro Terai, Toutai Mituyama:
Software.ncrna.org: web servers for analyses of RNA sequences. Nucleic Acids Res. 36(Web-Server-Issue): 75-78 (2008) - 2006
- [j1]Michiaki Hamada, Koji Tsuda, Taku Kudo, Taishin Kin, Kiyoshi Asai:
Mining frequent stem patterns from unaligned RNA sequences. Bioinform. 22(20): 2480-2487 (2006)
Coauthor Index
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