Michiaki Hamada

48 papers A* 1C 2Journal 45

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Differentiation of RNA-protein docking structures through molecular dynamics simulation and machine learning methods. Briefings Bioinform. Bui Tien Thanh, Yoichi Kurumida, Kaito Kobayashi, Michiaki Hamada, Tomoshi Kameda
2025	J	`jnl`	Multi-objective computational optimization of human 5′ UTR sequences. Briefings Bioinform. Keisuke Yamada, Kanta Suga, Naoko Abe, Koji Hashimoto, Susumu Tsutsumi, Masahito Inagaki, Fumitaka Hashiya, Hiroshi Abe, Michiaki Hamada
2025	C	`conf`	Searching Candidate Sequences for RNA Aptamers Using Quantum Computation. ICCE Sora Tomita, Tatsuhiko Shirai, Michiaki Hamada, Tatsuo Adachi, Nozomu Togawa
2024	J	`jnl`	Prediction of antibiotic resistance mechanisms using a protein language model. Bioinform. Kanami Yagimoto, Shion Hosoda, Miwa Sato, Michiaki Hamada
2024	J	`jnl`	Screening of Key Transcripts from Expression Data Using Applied Artificial Intelligence for Cancer Prediction. Int. J. Comput. Intell. Syst. Anju Pratap, Michiaki Hamada
2023	J	`jnl`	DeepRaccess: high-speed RNA accessibility prediction using deep learning. Frontiers Bioinform. Kaisei Hara, Natsuki Iwano, Tsukasa Fukunaga, Michiaki Hamada
2023	A*	`conf`	GeoPhy: Differentiable Phylogenetic Inference via Geometric Gradients of Tree Topologies. NeurIPS Takahiro Mimori, Michiaki Hamada
2023	J	`jnl`	GeoPhy: Differentiable Phylogenetic Inference via Geometric Gradients of Tree Topologies. CoRR Takahiro Mimori, Michiaki Hamada
2023	J	`jnl`	Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery. Briefings Bioinform. Kengo Sato, Michiaki Hamada
2022	J	`jnl`	Generative aptamer discovery using RaptGen. Nat. Comput. Sci. Natsuki Iwano, Tatsuo Adachi, Kazuteru Aoki, Yoshikazu Nakamura, Michiaki Hamada
2021	J	`jnl`	Multi-resBind: a residual network-based multi-label classifier for in vivo RNA binding prediction and preference visualization. BMC Bioinform. Shitao Zhao, Michiaki Hamada
2021	J	`jnl`	PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores. Bioinform. Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada
2021	J	`jnl`	Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model. Bioinform. Shion Hosoda, Tsukasa Fukunaga, Michiaki Hamada
2020	J	`jnl`	MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq. BMC Bioinform. Yiqian Zhang, Michiaki Hamada
2019	J	`jnl`	Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference. Bioinform. Taro Matsutani, Yuki Ueno, Tsukasa Fukunaga, Michiaki Hamada
2019	J	`jnl`	Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data. IEEE ACM Trans. Comput. Biol. Bioinform. Shimpei Nishida, Shun Sakuraba, Kiyoshi Asai, Michiaki Hamada
2018	J	`jnl`	A Novel Method for Assessing the Statistical Significance of RNA-RNA Interactions Between Two Long RNAs. J. Comput. Biol. Tsukasa Fukunaga, Michiaki Hamada
2018	J	`jnl`	Beyond similarity assessment: selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm. Bioinform. Taikai Takeda, Michiaki Hamada
2018	J	`jnl`	DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning. BMC Bioinform. Yiqian Zhang, Michiaki Hamada
2017	J	`jnl`	RIblast: an ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach. Bioinform. Tsukasa Fukunaga, Michiaki Hamada
2017	J	`jnl`	Training alignment parameters for arbitrary sequencers with LAST-TRAIN. Bioinform. Michiaki Hamada, Yukiteru Ono, Kiyoshi Asai, Martin C. Frith
2016	J	`jnl`	Comprehensive prediction of lncRNA-RNA interactions in human transcriptome. BMC Genom. Goro Terai, Junichi Iwakiri, Tomoshi Kameda, Michiaki Hamada, Kiyoshi Asai
2016	J	`jnl`	Rtools: a web server for various secondary structural analyses on single RNA sequences. Nucleic Acids Res. Michiaki Hamada, Yukiteru Ono, Hisanori Kiryu, Kengo Sato, Yuki Kato, Tsukasa Fukunaga, Ryota Mori, Kiyoshi Asai
2015	J	`jnl`	A semi-supervised learning approach for RNA secondary structure prediction. Comput. Biol. Chem. Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada
2015	J	`jnl`	Learning chromatin states with factorized information criteria. Bioinform. Michiaki Hamada, Yukiteru Ono, Ryohei Fujimaki, Kiyoshi Asai
2015	J	`jnl`	Privacy-preserving search for chemical compound databases. BMC Bioinform. Kana Shimizu, Koji Nuida, Hiromi Arai, Shigeo Mitsunari, Nuttapong Attrapadung, Michiaki Hamada, Koji Tsuda, Takatsugu Hirokawa, Jun Sakuma, Goichiro Hanaoka, Kiyoshi Asai
2014	J	`jnl`	Fighting against uncertainty: an essential issue in bioinformatics. Briefings Bioinform. Michiaki Hamada
2014	J	`jnl`	Reference-free prediction of rearrangement breakpoint reads. Bioinform. Edward Wijaya, Kana Shimizu, Kiyoshi Asai, Michiaki Hamada
2013	J	`jnl`	Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions. Bioinform. Junichi Iwakiri, Tomoshi Kameda, Kiyoshi Asai, Michiaki Hamada
2013	J	`jnl`	Generalized Centroid Estimators in Bioinformatics CoRR Michiaki Hamada, Hisanori Kiryu, Wataru Iwasaki, Kiyoshi Asai
2013	J	`jnl`	PBSIM: PacBio reads simulator - toward accurate genome assembly. Bioinform. Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada
2012	J	`jnl`	A Classification of Bioinformatics Algorithms from the Viewpoint of Maximizing Expected Accuracy (MEA). J. Comput. Biol. Michiaki Hamada, Kiyoshi Asai
2012	J	`jnl`	Direct Updating of an RNA Base-Pairing Probability Matrix with Marginal Probability Constraints. J. Comput. Biol. Michiaki Hamada
2011	J	`jnl`	CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences. Nucleic Acids Res. Michiaki Hamada, Koichiro Yamada, Kengo Sato, Martin C. Frith, Kiyoshi Asai
2011	J	`jnl`	IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinform. Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai
2011	J	`jnl`	Improving the accuracy of predicting secondary structure for aligned RNA sequences. Nucleic Acids Res. Michiaki Hamada, Kengo Sato, Kiyoshi Asai
2011	J	`jnl`	Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection. Bioinform. Michiaki Hamada, Edward Wijaya, Martin C. Frith, Kiyoshi Asai
2010	J	`jnl`	A Non-Parametric Bayesian Approach for Predicting RNA Secondary Structures. J. Bioinform. Comput. Biol. Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara
2010	J	`jnl`	Parameters for accurate genome alignment. BMC Bioinform. Martin C. Frith, Michiaki Hamada, Paul Horton
2010	J	`jnl`	Prediction of RNA secondary structure by maximizing pseudo-expected accuracy. BMC Bioinform. Michiaki Hamada, Kengo Sato, Kiyoshi Asai
2010	J	`jnl`	RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinform. Yuki Kato, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, Tatsuya Akutsu
2009	C	`conf`	A Non-parametric Bayesian Approach for Predicting RNA Secondary Structures. WABI Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara
2009	J	`jnl`	CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res. Kengo Sato, Michiaki Hamada, Kiyoshi Asai, Toutai Mituyama
2009	J	`jnl`	CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score. Bioinform. Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai
2009	J	`jnl`	Prediction of RNA secondary structure using generalized centroid estimators. Bioinform. Michiaki Hamada, Hisanori Kiryu, Kengo Sato, Toutai Mituyama, Kiyoshi Asai
2009	J	`jnl`	Predictions of RNA secondary structure by combining homologous sequence information. Bioinform. Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai
2008	J	`jnl`	Software.ncrna.org: web servers for analyses of RNA sequences. Nucleic Acids Res. Kiyoshi Asai, Hisanori Kiryu, Michiaki Hamada, Yasuo Tabei, Kengo Sato, Hiroshi Matsui, Yasubumi Sakakibara, Goro Terai, Toutai Mituyama
2006	J	`jnl`	Mining frequent stem patterns from unaligned RNA sequences. Bioinform. Michiaki Hamada, Koji Tsuda, Taku Kudo, Taishin Kin, Kiyoshi Asai