Michiaki Hamada

Publication Activity (10 Years)

Years Active: 2006-2023
Publications (10 Years): 18

Top Topics

Statistical Significance

Latent Dirichlet Allocation

Rna Secondary Structure Prediction

Top Venues

Briefings Bioinform.

Publications

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)
Kaisei Hara, Natsuki Iwano, Tsukasa Fukunaga, Michiaki Hamada
DeepRaccess: high-speed RNA accessibility prediction using deep learning. Frontiers Bioinform. 3 (2023)
Takahiro Mimori, Michiaki Hamada
GeoPhy: Differentiable Phylogenetic Inference via Geometric Gradients of Tree Topologies. NeurIPS (2023)
Takahiro Mimori, Michiaki Hamada
GeoPhy: Differentiable Phylogenetic Inference via Geometric Gradients of Tree Topologies. CoRR (2023)
Natsuki Iwano, Tatsuo Adachi, Kazuteru Aoki, Yoshikazu Nakamura, Michiaki Hamada
Generative aptamer discovery using RaptGen. Nat. Comput. Sci. 2 (6) (2022)
Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada
PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores. Bioinform. 37 (5) (2021)
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) (2021)
Shion Hosoda, Tsukasa Fukunaga, Michiaki Hamada
Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model. Bioinform. 37 (Supplement) (2021)
Yiqian Zhang, Michiaki Hamada
MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq. BMC Bioinform. 21 (1) (2020)
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) (2019)
Taro Matsutani, Yuki Ueno, Tsukasa Fukunaga, Michiaki Hamada
Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference. Bioinform. 35 (22) (2019)
Taikai Takeda, Michiaki Hamada
Beyond similarity assessment: selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm. Bioinform. 34 (4) (2018)
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) (2018)
Yiqian Zhang, Michiaki Hamada
DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning. BMC Bioinform. (19) (2018)
Tsukasa Fukunaga, Michiaki Hamada
RIblast: an ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach. Bioinform. 33 (17) (2017)
Michiaki Hamada, Yukiteru Ono, Kiyoshi Asai, Martin C. Frith
Training alignment parameters for arbitrary sequencers with LAST-TRAIN. Bioinform. 33 (6) (2017)
Goro Terai, Junichi Iwakiri, Tomoshi Kameda, Michiaki Hamada, Kiyoshi Asai
Comprehensive prediction of lncRNA-RNA interactions in human transcriptome. BMC Genom. 17 (S-1) (2016)
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) (2016)
Michiaki Hamada, Yukiteru Ono, Ryohei Fujimaki, Kiyoshi Asai
Learning chromatin states with factorized information criteria. Bioinform. 31 (15) (2015)
Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada
A semi-supervised learning approach for RNA secondary structure prediction. Comput. Biol. Chem. 57 (2015)
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) (2015)
Michiaki Hamada
Fighting against uncertainty: an essential issue in bioinformatics. Briefings Bioinform. 15 (5) (2014)
Edward Wijaya, Kana Shimizu, Kiyoshi Asai, Michiaki Hamada
Reference-free prediction of rearrangement breakpoint reads. Bioinform. 30 (18) (2014)
Junichi Iwakiri, Tomoshi Kameda, Kiyoshi Asai, Michiaki Hamada
Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions. Bioinform. 29 (20) (2013)
Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada
PBSIM: PacBio reads simulator - toward accurate genome assembly. Bioinform. 29 (1) (2013)
Michiaki Hamada, Hisanori Kiryu, Wataru Iwasaki, Kiyoshi Asai
Generalized Centroid Estimators in Bioinformatics CoRR (2013)
Michiaki Hamada, Kiyoshi Asai
A Classification of Bioinformatics Algorithms from the Viewpoint of Maximizing Expected Accuracy (MEA). J. Comput. Biol. 19 (5) (2012)
Michiaki Hamada
Direct Updating of an RNA Base-Pairing Probability Matrix with Marginal Probability Constraints. J. Comput. Biol. 19 (12) (2012)
Michiaki Hamada, Kengo Sato, Kiyoshi Asai
Improving the accuracy of predicting secondary structure for aligned RNA sequences. Nucleic Acids Res. 39 (2) (2011)
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) (2011)
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) (2011)
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) (2011)
Martin C. Frith, Michiaki Hamada, Paul Horton
Parameters for accurate genome alignment. BMC Bioinform. 11 (2010)
Michiaki Hamada, Kengo Sato, Kiyoshi Asai
Prediction of RNA secondary structure by maximizing pseudo-expected accuracy. BMC Bioinform. 11 (2010)
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)
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) (2010)
Michiaki Hamada, Hisanori Kiryu, Kengo Sato, Toutai Mituyama, Kiyoshi Asai
Prediction of RNA secondary structure using generalized centroid estimators. Bioinform. 25 (4) (2009)
Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara
A Non-parametric Bayesian Approach for Predicting RNA Secondary Structures. WABI (2009)
Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai
Predictions of RNA secondary structure by combining homologous sequence information. Bioinform. 25 (12) (2009)
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) (2009)
Kengo Sato, Michiaki Hamada, Kiyoshi Asai, Toutai Mituyama
CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
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) (2008)
Michiaki Hamada, Koji Tsuda, Taku Kudo, Taishin Kin, Kiyoshi Asai
Mining frequent stem patterns from unaligned RNA sequences. Bioinform. 22 (20) (2006)