Mining frequent stem patterns from unaligned RNA sequences. - Michiaki Hamada; Koji Tsuda; Taku Kudo; Taishin Kin; Kiyoshi Asai (Bioinform., 2006)

Software.ncrna.org: web servers for analyses of RNA sequences. - Kiyoshi Asai; Hisanori Kiryu; Michiaki Hamada; Yasuo Tabei; Kengo Sato; Hiroshi Matsui; Yasubumi Sakakibara; Goro Terai; Toutai Mituyama (Nucleic Acids Res., 2008)

Prediction of RNA secondary structure using generalized centroid estimators. - Michiaki Hamada; Hisanori Kiryu; Kengo Sato; Toutai Mituyama; Kiyoshi Asai (Bioinform., 2009)

Predictions of RNA secondary structure by combining homologous sequence information. - Michiaki Hamada; Kengo Sato; Hisanori Kiryu; Toutai Mituyama; Kiyoshi Asai (Bioinform., 2009)

CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score. - Michiaki Hamada; Kengo Sato; Hisanori Kiryu; Toutai Mituyama; Kiyoshi Asai (Bioinform., 2009)

CENTROIDFOLD: a web server for RNA secondary structure prediction. - Kengo Sato; Michiaki Hamada; Kiyoshi Asai; Toutai Mituyama (Nucleic Acids Res., 2009)

RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. - Yuki Kato; Kengo Sato; Michiaki Hamada; Yoshihide Watanabe; Kiyoshi Asai; Tatsuya Akutsu (Bioinform., 2010)

Parameters for accurate genome alignment. - Martin C. Frith; Michiaki Hamada; Paul Horton (BMC Bioinform., 2010)

Prediction of RNA secondary structure by maximizing pseudo-expected accuracy. - Michiaki Hamada; Kengo Sato; Kiyoshi Asai (BMC Bioinform., 2010)

A Non-Parametric Bayesian Approach for Predicting RNA Secondary Structures. - Kengo Sato; Michiaki Hamada; Toutai Mituyama; Kiyoshi Asai; Yasubumi Sakakibara (J. Bioinform. Comput. Biol., 2010)

Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection. - Michiaki Hamada; Edward Wijaya; Martin C. Frith; Kiyoshi Asai (Bioinform., 2011)

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. - Kengo Sato; Yuki Kato; Michiaki Hamada; Tatsuya Akutsu; Kiyoshi Asai (Bioinform., 2011)

Improving the accuracy of predicting secondary structure for aligned RNA sequences. - Michiaki Hamada; Kengo Sato; Kiyoshi Asai (Nucleic Acids Res., 2011)

CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences. - Michiaki Hamada; Koichiro Yamada; Kengo Sato; Martin C. Frith; Kiyoshi Asai (Nucleic Acids Res., 2011)

Direct Updating of an RNA Base-Pairing Probability Matrix with Marginal Probability Constraints. - Michiaki Hamada (J. Comput. Biol., 2012)

A Classification of Bioinformatics Algorithms from the Viewpoint of Maximizing Expected Accuracy (MEA). - Michiaki Hamada; Kiyoshi Asai (J. Comput. Biol., 2012)

Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions. - Junichi Iwakiri; Tomoshi Kameda; Kiyoshi Asai; Michiaki Hamada (Bioinform., 2013)

PBSIM: PacBio reads simulator - toward accurate genome assembly. - Yukiteru Ono; Kiyoshi Asai; Michiaki Hamada (Bioinform., 2013)

Generalized Centroid Estimators in Bioinformatics - Michiaki Hamada; Hisanori Kiryu; Wataru Iwasaki 001; Kiyoshi Asai (CoRR, 2013)

Fighting against uncertainty: an essential issue in bioinformatics. - Michiaki Hamada (Briefings Bioinform., 2014)

Reference-free prediction of rearrangement breakpoint reads. - Edward Wijaya; Kana Shimizu; Kiyoshi Asai; Michiaki Hamada (Bioinform., 2014)

Learning chromatin states with factorized information criteria. - Michiaki Hamada; Yukiteru Ono; Ryohei Fujimaki; Kiyoshi Asai (Bioinform., 2015)

A semi-supervised learning approach for RNA secondary structure prediction. - Haruka Yonemoto; Kiyoshi Asai; Michiaki Hamada (Comput. Biol. Chem., 2015)

Privacy-preserving search for chemical compound databases. - Kana Shimizu; Koji Nuida; Hiromi Arai; Shigeo Mitsunari; Nuttapong Attrapadung; Michiaki Hamada; Koji Tsuda; Takatsugu Hirokawa; Jun Sakuma; Goichiro Hanaoka; Kiyoshi Asai (BMC Bioinform., 2015)

Comprehensive prediction of lncRNA-RNA interactions in human transcriptome. - Goro Terai; Junichi Iwakiri; Tomoshi Kameda; Michiaki Hamada; Kiyoshi Asai (BMC Genom., 2016)

Rtools: a web server for various secondary structural analyses on single RNA sequences. - Michiaki Hamada; Yukiteru Ono; Hisanori Kiryu; Kengo Sato; Yuki Kato; Tsukasa Fukunaga; Ryota Mori; Kiyoshi Asai (Nucleic Acids Res., 2016)

RIblast: an ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach. - Tsukasa Fukunaga; Michiaki Hamada (Bioinform., 2017)

Training alignment parameters for arbitrary sequencers with LAST-TRAIN. - Michiaki Hamada; Yukiteru Ono; Kiyoshi Asai; Martin C. Frith (Bioinform., 2017)

Beyond similarity assessment: selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm. - Taikai Takeda; Michiaki Hamada (Bioinform., 2018)

DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning. - Yiqian Zhang; Michiaki Hamada (BMC Bioinform., 2018)

A Novel Method for Assessing the Statistical Significance of RNA-RNA Interactions Between Two Long RNAs. - Tsukasa Fukunaga; Michiaki Hamada (J. Comput. Biol., 2018)

Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference. - Taro Matsutani; Yuki Ueno; Tsukasa Fukunaga; Michiaki Hamada (Bioinform., 2019)

Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data. - Shimpei Nishida; Shun Sakuraba; Kiyoshi Asai; Michiaki Hamada (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq. - Yiqian Zhang; Michiaki Hamada (BMC Bioinform., 2020)

Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model. - Shion Hosoda; Tsukasa Fukunaga; Michiaki Hamada (Bioinform., 2021)

PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores. - Yukiteru Ono; Kiyoshi Asai; Michiaki Hamada (Bioinform., 2021)

Multi-resBind: a residual network-based multi-label classifier for in vivo RNA binding prediction and preference visualization. - Shitao Zhao; Michiaki Hamada (BMC Bioinform., 2021)

Generative aptamer discovery using RaptGen. - Natsuki Iwano; Tatsuo Adachi; Kazuteru Aoki; Yoshikazu Nakamura; Michiaki Hamada (Nat. Comput. Sci., 2022)

GeoPhy: Differentiable Phylogenetic Inference via Geometric Gradients of Tree Topologies. - Takahiro Mimori; Michiaki Hamada (NeurIPS, 2023)

DeepRaccess: high-speed RNA accessibility prediction using deep learning. - Kaisei Hara; Natsuki Iwano; Tsukasa Fukunaga; Michiaki Hamada (Frontiers Bioinform., 2023)

Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery. - Kengo Sato; Michiaki Hamada (Briefings Bioinform., 2023)

Screening of Key Transcripts from Expression Data Using Applied Artificial Intelligence for Cancer Prediction. - Anju Pratap; Michiaki Hamada (Int. J. Comput. Intell. Syst., 2024)

Searching Candidate Sequences for RNA Aptamers Using Quantum Computation. - Sora Tomita; Tatsuhiko Shirai; Michiaki Hamada; Tatsuo Adachi; Nozomu Togawa (ICCE, 2025)

Multi-objective computational optimization of human 5′ UTR sequences. - Keisuke Yamada; Kanta Suga; Naoko Abe; Koji Hashimoto; Susumu Tsutsumi; Masahito Inagaki; Fumitaka Hashiya; Hiroshi Abe; Michiaki Hamada (Briefings Bioinform., 2025)