Preprint / プレプリント

1. Takahashi, Zeng, Hamada  (in preparation)

2. Takeda et al. (submitted)

Journal papers  / ジャーナル論文

合計 96報  

* : corresponding author(s);  #: Joint first authors

2024年（令和6年）/ Year 2024 (F:0, C:1, O:1)

1. Tatsuo Adachi, Shigetaka Nakamura, Akiya Michishita, Daiki Kawahara, Mizuki Yamamoto, Michiaki Hamada, Yoshikazu Nakamura, RaptGen-Assisted Generation of an RNA/DNA Hybrid Aptamer against SARS-CoV-2 Spike Protein, Biochemistry, 2024-03-08, https://doi.org/10.1021/acs.biochem.3c00596

2. Shunsuke Sumi, Michiaki Hamada*, Hirohide Saito*, Deep generative design of RNA family sequences, Nat. Methods., 2024-01-18, doi.org/10.1038/s41592-023-02148-8

2023年（令和5年）/ Year 2023 (F:0, C:4, O:5)

1. Kaisei Hara, Natsuki Iwano, Tsukasa Fukunaga,  Michiaki Hamada, DeepRaccess: High-speed RNA accessibility prediction using deep learning, Front. Bioinform., 2023-10-10, vol. 3, doi :10.3389/fbinf.2023.1275787

2. Motoyo Maruyama, Atsushi Sakai, Tsukasa Fukunaga, Yoshitaka Miyagawa, Takashi Okada, Michiaki Hamada,  Hidenori Suzuki, Neat1 lncRNA organizes the inflammatory gene expressions in the dorsal root ganglion in neuropathic pain caused by nerve injury. Front. Immunol. (Sec. Inflammation), Volume 14 (2023). https://www.frontiersin.org/articles/10.3389/fimmu.2023.1185322/abstract

3. Chao Zeng, Takeshi Chujo, Tetsuro Hirose*, Michiaki Hamada*, Landscape of semi-extractable RNAs across five human cell lines. Nucleic Acids Research, gkad567 (2023). https://doi.org/10.1093/nar/gkad567

4. Sekine, K., Onoguchi, M*. & Hamada, M*. Transposons contribute to the acquisition of cell type-specific cis-elements in the brain. Commun Biol 6, 631 (2023). https://doi.org/10.1038/s42003-023-04989-7

5. 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 in Bioinformatics, 25 May 2023, https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbad186/7179751?utm_source=advanceaccess&utm_campaign=bib&utm_medium=email

6. Shohei Kojima, Satoshi Koyama, Mirei Ka, Yuka Saito, Erica H. Parrish, Mikiko Endo, Sadaaki Takata, Misaki Mizukoshi, Keiko Hikino, Atsushi Takeda, Asami F. Gelinas, Steven M. Heaton, Rie Koide, Anselmo J. Kamada, Michiya Noguchi, Michiaki Hamada, Biobank Japan Project Consortium, Yoichiro Kamatani, Yasuhiro Murakawa, Kazuyoshi Ishigaki, Yukio Nakamura, Kaoru Ito, Chikashi Terao, Yukihide Momozawa & Nicholas F. Parrish, Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk, Nature Genetics, 11 May 2023, https://www.nature.com/articles/s41588-023-01390-2

7. Hitoshi Iuchi, Junna Kawasaki, Kento Kubo, Tsukasa Fukunaga, Koki Hokao, Gentaro Yokoyama, Akiko Ichinose, Kanta Suga, Michiaki Hamada, Bioinformatics approaches for unveiling virus-host interactions, Computational and Structural Biotechnology Journal, Volume 21, 27 February 2023, Pages 1774-1784, https://doi.org/10.1016/j.csbj.2023.02.044

8. Tsukasa Fukunaga, Michiaki Hamada, Web Services for RNA-RNA Interaction Prediction, RNA Structure Prediction, Methods in Molecular Biology 2586, Pages 163-173, Springer Protocols, Humana Press, https://link.springer.com/book/10.1007/978-1-0716-2768-6

9. Tsukasa Fukunaga, Junichi Iwakiri, Michiaki Hamada, Fast RNA-RNA Interaction Prediction Methods for Interaction Analysis of Transcriptome-Scale Large Datasets, RNA Structure Prediction, Methods in Molecular Biology 2586, Pages 175-195, Springer Protocols, Humana Press, https://link.springer.com/book/10.1007/978-1-0716-2768-6

2022年（令和4年）/ Year 2022 (F:0, C:4, O:4)

1. Yukiteru Ono, Michiaki Hamada, Kiyoshi Asai, PBSIM3: a simulator for all types of PacBio and ONT long reads, NAR Genomics and Bioinformatics, Volume 4, Issue 4, December 2022, lqac092, https://doi.org/10.1093/nargab/lqac092

2. Yu Ono, Kenta Katayama, Tomoki Onuma, ☆Kento Kubo, Hayato Tsuyuzaki, Michiaki Hamada, Masamitsu Sato, Structure-based screening for functional non-coding RNAs in fission yeast identifies a factor repressing untimely initiation of sexual differentiation, Nucleic Acids Research, Volume 50, Issue 19, 28 October 2022, Pages 11229-11242, https://doi.org/10.1093/nar/gkac825

3. Tsukasa Fukunaga*, Michiaki Hamada, LinAliFold and CentroidLinAliFold: Fast RNA consensus secondary structure prediction for aligned sequences using beam search methods, Bioinformatics Advances, vbac078, https://doi.org/10.1093/bioadv/vbac078 Published: 22 October 2022

4. Chao Zeng*, Atsushi Takeda, Kotaro Sekine, Naoki Osato, Tsukasa Fukunaga, Michiaki Hamada*, Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs, Methods in Molecular Biology, 2509:315-340, 2022. doi: 10.1007/978-1-0716-2380-0_19

5. Natsuki Iwano, Tatsuo Adachi, Kazuteru Aoki, Yoshikazu Nakamura & Michiaki Hamada*, Generative aptamer discovery using RaptGen, Nature Computational Science (2022)

6. Keisuke Yamada, Michiaki Hamada*, Prediction of RNA-protein interactions using a nucleotide language model, Bioinformatics Advances, Volume 2, Issue 1, 2022, vbac023, https://doi.org/10.1093/bioadv/vbac023

7. Mako Okabe, Shinya Takarada, Nariaki Miyao, Hideyuki Nakaoka, Keijiro Ibuki, Sayaka Ozawa, Kazuhiro Watanabe, Harue Tsuji, Ikuo Hashimoto, Kiyoshi Hatasaki, Shotaro Hayakawa, Yu Hamaguchi, Michiaki Hamada, Fukiko Ichida & Keiichi Hirono, G0S2 regulates innate immunity in Kawasaki disease via lncRNA HSD11B1-AS1, Pediatric Research, 15 March 2022. https://doi.org/10.1038/s41390-022-01999-9

8. Mukherjee, S.; Murata, A.; Ishida, R.; Sugai, A.; Dohno, C.; Hamada, M.; Krishna, S.; Nakatani, HT-SELEX based identification of binding pre-miRNA hairpin-motif for small molecule, Mol. Ther. Nucleic Acids, Volume 27, 8 March 2022, Pages 165-174. https://doi.org/10.1016/j.omtn.2021.11.021

2021年（令和3年）/ Year 2020 (F:0, C:7, O:2)

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

2. Yu Hamaguchi*, Chao Zeng, Michiaki Hamada*, Impact of human gene annotations on RNA-seq differential expression analysis, BMC Genomics, 22:730, 2021. doi: 10.1186/s12864-021-08038-7

3. Taro Matsutani, Michiaki Hamada, Clone decomposition based on mutation signatures provides novel insights into mutational processes, NAR Genomics and Bioinformatics, 2021 (in press)

4. Masahiro Onoguchi, Chao Zeng, Ayako Matsumaru, Michiaki Hamada*, Binding patterns of RNA binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements, NAR Genomics and Bioinformatics, 2021 (in press, bioRxiv)

5. Hitoshi Iuchi*, Taro Matsutani, Keisuke Yamada, Natsuki Iwano, Shunsuke Sumi, Shion Hosoda, Shitao Zhao, Tsukasa Fukunaga, Michiaki Hamada*, Representation learning applications in biological sequence analysis, Computational and Structural Biotechnology Journal (in press)

6. Shion Hosoda*, Tsukasa Fukunaga, Michiaki Hamada*,  Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model (accepted in ISMB/ECCB2022 to be published in Bioinformatics)

7. Satoshi Takahashi, Rintaro Noro, Masahiro Seike*, Chao Zeng, Masaru Matsumoto, Akiko Yoshikawa, Shinji Nakamichi, Teppei Sugano, Mariko Hirao, Kuniko Matsuda, Michiaki Hamada, Akihiko Gemma, Long Non-Coding RNA CRNDE is Involved in Resistance to EGFR Tyrosine Kinase Inhibitor in EGFR-Mutant Lung Cancer via eIF4A3/MUC1/EGFR Signaling, International Journal of Molecular Sciences, 22(8):4005, 2021. doi: 10.3390/ijms22084005 

8. Morteza M. Saber, Marziyeh Karimiavargani, Takanori Uzawa, Nilmini Hettiarachchi, Michiaki Hamada, Yoshihiro Ito, Naruya Saitou*, Possible roles for the hominoid-specific DSCR4 gene in human cells, Genes & Genetic Systems, Article ID: 20-00012, https://doi.org/10.1266/ggs.20-00012

9. Hitoshi Iuchi* and Michiaki Hamada*, Jonckheere-Terpstra-Kendall-based nonparametric analysis of temporal differential gene expression, NAR Genomics and Bioinformatics (in press)

10. Yiqian Zhang, Michiaki Hamada*, Identification of m6A-associated RNA binding proteins using an integrative computational framework,  Frontiers in Genetics, 12:625797, 2021. doi: 10.3389/fgene.2021.625797

11. Chao Zeng*, Masahiro Onoguchi, Michiaki Hamada*, Association analysis of repetitive elements and R-loop formation across species, Mobile DNA 2021 (in press) [bioRxiv] [preLights]

12. Chao Zeng, Michiaki Hamada*, Detection and characterization of ribosome-associated lncRNA, Methods in Molecular Biology. 2021, 2254:179-194. doi: 10.1007/978-1-0716-1158-6_11. [URL]

2020年（令和2年）/ Year 2020 (F:0, C:６, O:3)

1. Taro Matsutani, Michiaki Hamada*, Parallelized latent Dirichlet allocation provides a novel interpretability of mutation signatures in cancer genomes, Genes (Basel). 2020 Sep 25;11(10):E1127. doi: 10.3390/genes11101127.

2. Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada*, PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores, Bioinformatics. 2020 Sep 25:btaa835. doi: 10.1093/bioinformatics/btaa835.

3. Shun Sakuraba, Junichi Iwakiri,  Michiaki Hamada,  Tomoshi Kameda, Genichiro Tsuji, Yasuaki Kimura, Hiroshi Abe,  Kiyoshi Asai*, Nearest-neighbor parameter for inosine-cytosine pairs through a combined experimental and computational approach, J Chem Theory Comput. 2020 Sep 8;16(9):5923-5935. doi: 10.1021/acs.jctc.0c00270. 

4. Chao Zeng*, Michiaki Hamada*, RNA-seq analysis reveals localization-associated alternative splicing across 13 cell lines, Genes (Basel). 2020 Jul 18;11(7):820. doi: 10.3390/genes11070820.

5. Ryoga Ishida, Tatsuo Adachi, Aya Yokota, Hidehito Yoshihara, Kazuteru Aoki, Yoshikazu Nakamura, Michiaki Hamada*, RaptRanker: in silico RNA aptamer selection from HT-SELEX experiment based on local sequence and structure information, Nucleic Acids Res. 2020 Aug 20;48(14):e82. doi: 10.1093/nar/gkaa484.

6. Shion Hosoda, Suguru Nishijima, Tsukasa Fukunaga, Masahira Hattori, Michiaki Hamada*, Revealing microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation, Microbiome. 2020 Jun 23;8(1):95. doi: 10.1186/s40168-020-00864-3.

7. Yiqian Zhang and Michiaki Hamada*, MoAIMS: Efficient Software for Detection of Enriched Regions of MeRIP-Seq, BMC Bioinformatics. 2020 Mar 14;21(1):103. doi: 10.1186/s12859-020-3430-0.

8. Risa Fujita#, Tatsuro Yamamoto#, Yasuhiro Arimura, Saori Fujiwara, Hiroaki Tachiwana, Yuichi Ichikawa, Yuka Sakata, Liying Yang, Reo Maruyama, Michiaki Hamada, Mitsuyoshi Nakao, Noriko Saitoh* and Hitoshi Kurumizaka*, Nucleosome destabilization by nuclear-RNA, Commun Biol. 2020 Feb 11;3(1):60. doi: 10.1038/s42003-020-0784-9.

9. Chawnshang Chang, Hangchuan Shi, Yin Sun, Miao He, Xiong Yang, Michiaki Hamada, Tsukasa Fukunaga, and Xiaoping Zhang*, Targeting the TR4 nuclear receptor-mediated lncTASR/AXL signaling with Tretinoin increases the Sunitinib sensitivity to better suppress the RCC progression, Oncogene. 2020 Jan;39(3):530-545. doi: 10.1038/s41388-019-0962-8. 

2019年（令和元年）/ Year 2019 (F:0, C:3, O:2)

1. Taro Matsutani, Yuki Ueno, Tsukasa Fukunaga, Michiaki Hamada*, Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference, Bioinformatics. 2019 Nov 1;35(22):4543-4552. doi: 10.1093/bioinformatics/btz266.

2. Yuko Matsumura, Yasuhiko Ito, Yoshihiro Mezawa, Kaidiliayi Sulidan, Yataro Daigo, Toru Hiraga, Kaoru Mogushi, Nadila Wali, Urszula Polanska, Hiromu Suzuki, Takumi Itoh, Yohei Miyagi, Tomoyuki Yokose, Satoru Shimizu, Atsushi Takano, Yasuhisa Terao, Harumi Saeki, Masayuki Ozawa, Masaaki Abe, Satoru Takeda, Ko Okumura, Sonoko Habu, O Hino, Kazuyoshi Takeda, Michiaki Hamada, and Akira Orimo, Stromal fibroblasts induce metastatic tumor cell clusters via epithelial-mesenchymal plasticity, Life Sci Alliance. 2019 Jul 22;2(4). pii: e201900425. doi: 10.26508/lsa.201900425. 

3. Shimpei Nishida, Shun Sakuraba, Kiyoshi Asai, and Michiaki Hamada*, Estimating energy parameters for RNA secondary structure predictions using both experimental and computational data, IEEE/ACM Trans Comput Biol Bioinform. 2019 Sep-Oct;16(5):1645-1655. doi: 10.1109/TCBB.2018.2813388. 

4. Tsukasa Fukunaga, Junichi Iwakiri, Yukiteru Ono, Michiaki Hamada*, LncRRIsearch: a web server for lncRNA-RNA interaction prediction integrated with tissue-specific expression and subcellular localization data, Front Genet. 2019 May 28;10:462. doi: 10.3389/fgene.2019.00462. 

5. Tani H*, Matsutani T, Aoki H, Nakamura K, Hamaguchi Y, Nakazato T, Hamada M., Identification of RNA biomarkers for chemical safety screening in neural cells derived from mouse embryonic stem cells using RNA deep sequencing analysis. Biochem Biophys Res Commun. 2019 May 14;512(4):641-646. doi: 10.1016/j.bbrc.2018.11.141. 

2018年（平成30年）/ Year 2018 (F:1,C:7,O:0)

1. Tsukasa Fukunaga, Michiaki Hamada*, Computational approaches for alternative and transient secondary structures of ribonucleic acids, Brief Funct Genomics. 2018 Jun 20;18(3):182-191. doi: 10.1093/bfgp/ely042. Review.

2. Chao Zeng*, Michiaki Hamada*, Identifying sequence features that drive ribosomal association for lncRNA, BMC Genomics. 2018 Dec 31;19(Suppl 10):906. doi: 10.1186/s12864-018-5275-8.

3. Yiqian Zhang, Michiaki Hamada*, DeepM6ASeq: Prediction and Characterization of m6A-containing Sequences using Deep Learning, BMC Bioinformatics. 2018 Dec 31;19(Suppl 19):524. doi: 10.1186/s12859-018-2516-4.

4. Tsukasa Fukunaga*, Michiaki Hamada*, A novel method for assessing the statistical significance of RNA-RNA interactions between two long RNAs, J Comput Biol. 2018 Sep;25(9):976-986. doi: 10.1089/cmb.2017.0260. 

5. Chao Zeng, Tsukasa Fukunaga, Michiaki Hamada*, Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data, BMC Genomics. 2018 May 29;19(1):414. doi: 10.1186/s12864-018-4765-z.

6. Taikai Takeda and Michiaki Hamada*, Beyond similarity assessment: Selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm, Bioinformatics. 2018 Feb 15;34(4):576-584. doi: 10.1093/bioinformatics/btx643

7. Michiaki Hamada*, In silico approaches to RNA aptamer design, Biochimie. 2018 Feb;145:8-14. doi: 10.1016/j.biochi.2017.10.005. 

8. Takafumi Chishima, Junichi Iwakiri, Michiaki Hamada*, Identification of transposable elements contributing to tissue-specific expression of long non-coding RNAs, Genes (Basel). 2018 Jan 9;9(1). pii: E23. doi: 10.3390/genes9010023

2017年（平成29年）/ Year 2017 (F:1, C:1, O:2)

1. Junichi Iwakiri*, Goro Terai, Michiaki Hamada, Computational prediction of lncRNA-mRNA interactions by integrating tissue specificity in human transcriptome, Biol Direct. 2017 Jun 8;12(1):15. doi: 10.1186/s13062-017-0183-4.

2. Tsukasa Fukunaga*, Michiaki Hamada*, RIblast: An ultrafast RNA-RNA interaction prediction system for comprehensive lncRNA interaction analysis, Bioinformatics. 2017 Sep 1;33(17):2666-2674. doi: 10.1093/bioinformatics/btx287.

3. Michiaki Hamada*, Yukiteru Ono, Kiyoshi Asai, Martin C. Frith*, Training alignment parameters for arbitrary sequencers with last-train, Bioinformatics. 2017 Mar 15;33(6):926-928. doi: 10.1093/bioinformatics/btw742.

4. Kotaro Ishii, Yusuke Kazama, Tomonari Hirano, Michiaki Hamada, Yukiteru Ono, Mieko Yamada, Tomoko Abe, AMAP: A pipeline for whole-genome mutation detection in Arabidopsis thaliana, Genes & Genetic Systems (2017) Mar 17;91(4):229-233. doi: 10.1266/ggs.15-00078.

2016年（平成28年）/ Year 2016 (F:2, C:1, O:1)

1. Junichi Iwakiri, Michiaki Hamada, Kiyoshi Asai, Tomoshi Kameda*, Improved accuracy in RNA-protein rigid body docking by incorporating force field for molecular dynamics simulation into the scoring function, J. Chem. Theory Comput. (2016), 12 (9), pp 4688–4697. DOI: 10.1021/acs.jctc.6b00254. Publication Date (Web): August 5, 2016.

2. 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. 2016 Jul 8;44(W1):W302-7. doi: 10.1093/nar/gkw337. 

3. Goro Terai#, Junichi Iwakiri#, Tomoshi Kameda, Michiaki Hamada*, Kiyoshi Asai*, Comprehensive prediction of lncRNA–RNA interactions in human transcriptome, BMC Genomics. 2016 Jan 11;17 Suppl 1:12. doi: 10.1186/s12864-015-2307-5.

4. Junichi Iwakiri#, Michiaki Hamada#, Kiyoshi Asai*, Bioinformatics tools for lncRNA research, Biochim Biophys Acta. 2016 Jan;1859(1):23-30. doi: 10.1016/j.bbagrm.2015.07.014. 

2015年（平成27年）/ Year 2015 (F:2, C:1, O:1)

1. 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 Bioinformatics (2015)16 Suppl 18:S6. 

2. Michiaki Hamada*, Yukiteru Ono, Ryohei Fujimaki, Kiyoshi Asai, Learning chromatin states with factorized information criteria, Bioinformatics (2015) 31 (15): 2426-2433.

3. Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada*, A semi-supervised learning approach for RNA secondary structure prediction, Computational Biology and Chemistry (2015) 57: 72–79.

4. Michiaki Hamada*, RNA secondary structure prediction from multi-aligned sequences, RNA Bioinformatics, Methods Mol Biol. 2015;1269:17-38. doi: 10.1007/978-1-4939-2291-8_2.

2014年（平成26年）/ Year 2014 (F:1, C:1, O:2)

1. Ryota Mori*, Michiaki Hamada, Kiyoshi Asai, Efficient calculation of exact probability distributions of integer features on RNA secondary structures, BMC Genomics (2014) 15(Suppl 10):S6

2. Edward Wijaya*, Kana Shimizu, Kiyoshi Asai, Michiaki Hamada*, Reference-free Prediction of Rearrangement Breakpoint Reads, Bioinformatics (2014) 30(18):2559-67. 

3. Michiaki Hamada*, Fighting against uncertainty: An essential issue in bioinformatics, Briefings in Bioinformatics (2014) 15 (5): 748-767. doi: 10.1093/bib/bbt038 First published online: June 26, 2013. [Preprint version in arXiv]

4. Kiyoshi Asai* and Michiaki Hamada, Structural alignments, Part II: "Non-Sankoff approaches for Structural alignments", in Chapter 14 of "RNA sequence, structure and function: computational and bioinformatic methods"  Methods Mol Biol. 2014;1097:291-301. doi: 10.1007/978-1-62703-709-9_14.

2013年（平成25年）/ Year 2013 (F:0 C:3, O:0)

1. Junichi Iwakiri*, Tomoshi Kameda, Kiyoshi Asai, Michiaki Hamada*, Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions, Bioinformatics (2013) 29 (20): 2524-2528.

2. Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada*, CentroidAlign-Web: a fast and accurate multiple aligner for long non-coding RNAs, Int. J. Mol. Sci. (2013) 14(3), 6144-6156; doi:10.3390/ijms14036144 (special issue: Non-Coding RNAs 2012).

3. Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada*, PBSIM: PacBio reads simulator--toward accurate genome assembly, Bioinformatics (2013) 29 (1): 119-121. 

2012年（平成24年）/ Year 2012 (F:2, C:1, O:0)

1. Michiaki Hamada*. Direct updating of an RNA base-pairing probability matrix with marginal probability constraints, Journal of Computational Biology (2012) 19(12): 1265-1276. 

2. Hiroki Asida*, Kiyoshi Asai, Michiaki Hamada*. Shape-based Alignment of Genomic Landscapes in Multi-scale Resolution, Nucleic Acids Research, 40 (14): 6435-6448, 2012. 

3. Michiaki Hamada*, Kiyoshi Asai. A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA), Journal of Computational Biology 19(5): 532-549,  May 2012. 

2011年（平成23年）/ Year 2011 (F:3, C:0, O:2)

1. 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, Bioinformatics 27 (22): 3085-3092, 2011.

2. 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 Research 39(Web Server issue):W100-6, 2011

3. Hironori Adachi, Akira Ishiguro, Michiaki Hamada, Eri Sakota, Kiyoshi Asai, Yoshikazu Nakamura*, Antagonistic RNA aptamer specific to a heterodimeric form of human interleukin-17A/F, Biochimie 93(7):1081-1088, 2011. 

4. Kengo Sato*, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai, IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming, Bioinformatics 27(13):i85-i93, 2011. (This paper was presented at ISMB/ECCB2011) 

5. Michiaki Hamada*, Hisanori Kiryu, Wataru Iwasaki, Kiyoshi Asai, Generalized Centroid Estimators in Bioinformatics, PLoS ONE 6(2):e16450, 2011. A corrected version is available from arXiv.

2010年（平成22年）/ Year 2010 (F:2, C:0, O:3)

1. Michiaki Hamada*, Kengo Sato, Kiyoshi Asai, Prediction of RNA secondary structure by maximizing pseudo-expected accuracy, BMC Bioinformatics 11:586, 2010. 

2. Michiaki Hamada*, Kengo Sato, Kiyoshi Asai, Improving the accuracy of predicting secondary structure for aligned RNA sequences, Nucleic Acids Research 39(2):393-402, 2011. 

3. Yuki Kato*, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, Tatsuya Akutsu, RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming, Bioinformatics 26(18): i460-i466, 2010. (This paper was presented at ECCB2010) 

4. Kengo Sato*, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasufumi Sakakibara, A non-parametric Bayesian approach for predicting RNA secondary structures, Journal of Bioinformatics and Computational Biology 8(4): 727-742, 2010. 

5. Martin C Frith*, Michiaki Hamada, Paul Horton, Parameters for accurate genome alignment, BMC Bioinformatics 11:80, 2010. 

2009年（平成21年）/ Year 2009 (F:4, C:0, O:1)

1. 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, Bioinformatics 25: 3236-3243, 2009. 

2. Kengo Sato*, Michiaki Hamada, Kiyoshi Asai, Toutai Mituyama, CentroidFold: a web application for RNA secondary structure prediction, Nucleic Acids Research 37(suppl2):W277-280, 2009. 

3. Michiaki Hamada*, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai, Predictions of RNA secondary structure by combining homologous sequence information, Bioinformatics 25(12): i330-i338, 2009. 

4. Michiaki Hamada*, Hisanori Kiryu, Kengo Sato, Toutai Mituyama, Kiyoshi Asai, Predictions of RNA secondary structure using generalized centroid estimators, Bioinformatics 25(4):465-473, 2009.  (2011 impact factor: 5.468) 

5. Michiaki Hamada*, Mituyama Toutai, Kiyoshi Asai, Large Scale Similarity Search for Locally Stable Secondary Structures among RNA Sequences, IPSJ transaction on Bioinformatics (TBIO) 2. 36-46, 2009. (2008-2009 SIGBIO Best Paper Award was given to this paper) 

2008年以前 / Before Year 2008 (F:3, C:0, O:2)

1. Kiyoshi Asai*, Hisanori Kiryu, Michiaki Hamada, Yasuo Tabei, Kengo Sato, Hiroshi Matsui, Yasubumi Sakakibara, Goro Terai, Totai Mituyama, Software.ncrna.org: web servers for analyses of RNA sequences, Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W75-8. doi: 10.1093/nar/gkn222. 

2. Michiaki Hamada*, Koji Tsuda, Taku Kudo, Taishin Kin, Kiyoshi Asai, Mining frequent stem patterns from unaligned RNA sequences, Bioinformatics. 2006 Oct 15;22(20):2480-7. doi: 10.1093/bioinformatics/btl431. 

3. Hitoshi Goto*, Sigeaki Obata, Toshiyuki Kamakura, Naofumi Nakayama, Mitsuhisa Sato, Yoshihiro Nakajima, Umpei Nagashima, Toshio Watanabe, Yuichi Inadomi, Masakatsu Ito, Takeshi Nishikawa, Tatsuya Nakano, Lennart Nilsson, Shigenori Tanaka, Kaori Fukuzawa, Yuichiro Inagaki, Michiaki Hamada, Hiroshi Chuman, “Drug Discovery Using Grid Technology”, in ”Modern Methods for Theoretical Physical Chemistry of Biopolymers”, edited by E.B. Starikov, J.P. Lewis and S. Tanaka (Elsevier B.V., Amsterdam, The Netherlands, 2006) pp 227-248. 

4. Michiaki Hamada*, Cheng Feng, Yuichiro Inagaki, Unpei Nagashima, Kazuaki Murakami, Hiroshi Chuman, A High Performance Computing Environments for Prediction of Activity and function of Biomolecules : An Application to Analysis of HIV Protease Inhibitors(超高速計算環境での生体関連分子の活性・機能予測システムの構築 : HIVプロテアーゼ阻害剤の解析への応用), Transactions of the Japan Society for Industrial and Applied Mathematics(応用数理学会論文誌) 14(4):267-288, 2004.

5. Michiaki Hamada*, Remark on application of distribution function inequality for Toeplitz and Hankel operators, Hokkaido Mathematical Journal 32(1):193-208, 2003. 

International conference papers (reviewed) / 国際会議論文（査読有り）

1. Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai, IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming, Proceeding of 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology (ISMB/ECCB2011) (also in Bioinformatics 27(13):i85-i93, 2011) (Acceptance rate: 19%) 

2. Yuki Kato, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, Tatsuya Akutsu, RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming, Proc. of 9th European Conference on Computational Biology (ECCB 2010) (also in Bioinformatics 26(18): i414-i419, 2010) (Acceptance rate: 36/215=17%) 

3. Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasufumi Sakakibara, A non-parametric Bayesian approach for predicting RNA secondary structures, The 9th Workshop on Algorithms in Bioinformatics (WABI 2009), 2009; Lecture Notes in Bioinformatics (LNBI) 5724, pp 286-297, 2009. [Abstract] 

4. Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai, Predictions of RNA secondary structure by combining homologous sequence information, Proc. of The 17th Annual International Conference on Intelligent Systems for Molecular Biology and 7th Annual European Conference on Computational Biology (ISMB/ECCB 2009), 2009. (also in Bioinformatics 25(12): i330-i338, 2009).  (Acceptance rate: 19%) 

5. Michiaki Hamada, Yuichiro Inagaki, Hiroshi Chuman, Drug Discovery Using Grid Technology, Proc. of High Performance Computing and Grid in Asia Pacific Region, Seventh International Conference (HPCAsia’04), pp 352-356, 2004. [Abstract]

Note: ISMB and ECCB are the 1st and 2nd rank conferences in the field of bioinformatics/computational biology, respectively.

Books / 書籍

1. 由良敬，松永浩子，細川正人，和泉自泰，村松知成，福永津嵩，浜田道昭，馬場健史，竹山春子，善光龍哉編，辻川和丈編，"第1章　最新の疾患標的分子の探索・評価技術，第4節 シングルセル/微小組織マルチオミクス解析"，実験医学増刊 Vol.42 No.2／あなたのラボから薬を生み出す　アカデミア創薬の実践，All JAPAN体制の先端技術支援を利用した創薬の最前線，羊土社，2024-01-19

2. 岩野夏樹，浜田道昭，清水秀幸編，第 12 章 発展編①：機械学習を用いた アプタマー配列の解析と創薬，実験医学別冊 Pythonで実践　生命科学データの機械学習，羊土社，2023-03-28

3. 浜田道昭，RNA情報科学・AI技術を融合したAIアプタマー創薬技術の開発，革新的AI創薬最前線（第５章，第５節），株式会社NTS  (2022)

4. 藤 博幸(編集), 岩部 直之(著), 川端 猛(著), 浜田 道昭(著), 門田 幸二(著), 須山 幹太(著), 光山 統泰(著), 黒川 顕(著), 森 宙史(著), 東 光一(著), 吉沢 明康(著), 片山 俊明(著), よくわかるバイオインフォマティクス入門（KS生命科学専門書）,  講談社 (2018)

5. 瀬々潤，浜田 道昭，生命情報処理における機械学習：多重検定と推定量設計，講談社  (2015) 

6. 日本バイオインフォマティクス学会編，バイオインフォマティクス入門，慶應大学出版会(2015). 

7. 稲垣 祐一郎, 浜田 道昭, 西下 容史. 概説 ＸＭＬ＆ライフサイエンス. Bio・IT World（第３弾）, pp 67-73, 2003.

Books / 書籍（監修）

1. バイオインフォマティクスのための生命科学入門 (バイオインフォマティクスシリーズ 1) | 福永 津嵩, 岩切 淳一 （著），浜田 道昭（監修）

2. 生物統計 (バイオインフォマティクスシリーズ 3) | 木立 尚孝（著） 浜田 道昭（監修）

3. 生物ネットワーク解析 (バイオインフォマティクスシリーズ 2) | 竹本 和広（著） 浜田 道昭（監修） 

4. システムバイオロジー (バイオインフォマティクスシリーズ 4) | 宇田 新介（著）浜田 道昭（監修）

Review papers in Japanese / 日本語解説論文

1. 大里直樹, 浜田道昭, 機械学習による遺伝子転写制御に関わる因子の探索, 月刊細胞（ニューサイエンス社）2022年11月号（特集　翻訳制御の最前線）, 62-64.

2. 浜田道昭，RNA情報科学・AI技術を融合したAIアプタマー創薬技術の開発，革新的AI創薬最前線（第５章，第５節），株式会社NTS (in press)

3. 大里直樹, 浜田道昭  実験データ解析と機械学習による転写制御因子の探索, 月刊細胞（ニューサイエンス社）2021年12月号（特集　エピトランスクリプトミクス）, 67-71.

4. 福永津嵩，浜田道昭，バイオイメージインフォマティクスにおける機械学習技術の活用, 日本画像学会誌 Vol. 56 (2017) No. 2 p. 163-167

5. 岩切淳一，浜田道昭，長鎖ノンコーディングRNAのためのバイオインフォマティクス, 生物物理, Vol. 56 (2016) No. 4 通巻326号 p. 217-220

6. 浜田道昭, 浅井潔, 期待精度最大化とバイオインフォマティクス, 応用数理 vol 21 (1), 34-39, 2011. 

7. 浜田道昭, 佐藤智之, 評価指標に適した推定量の設計方法―理論とバイオインフォマティクスにおける応用―, みずほ情報総研技法 vol.3 No. 1, 15-20, 2011.

8. 浜田道昭, 非整列RNA配列群からの頻出ステムパターンのマイニング, みずほ情報総研技報 Vol.1 No.1, 1-7, 2007.

Patents / 特許

1. (WO2013038698) SEARCH SYSTEM, SEARCH METHOD, AND PROGRAM，岩村　佳奈 IWAMURA, Kana 広川　貴次 HIROKAWA, Takatsugu 津田　宏治 TSUDA, Kouji 荒井　ひろみ ARAI, Hiromi 佐久間　淳 SAKUMA, Jun 浅井　潔 ASAI, Kiyoshi 浜田　道昭 HAMADA, Michiaki 花岡　悟一郎 HANAOKA, Goichiro 縫田　光司 NUIDA, Koji，国立研究開発法人産業技術総合研究所 、国立大学法人東京大学，出願番号 PCT/JP2012/005885，出願日 14.09.2012

2. 特開２００７－２２６７００, ＲＮＡ配列情報処理装置，出願人 国立研究開発法人産業技術総合研究所 、みずほ情報総研株式会社 、国立大学法人東京大学，発明者  津田宏治 、金大真 、浜田道昭 、浅井潔，出願番号 2006-049694，公開番号 2007-226700，出願日 2006年2月27日

学位論文：

1. Michiaki Hamada, Prediction of RNA Secondary Structures for Estimating Accurate Base-pairs（正確な塩基対推定のための2次構造予測）, 博士論文(東京工業大学), 2009. 

2. 浜田 道昭, ある種の分布関数不等式を用いたティープリッツ及びハンケル作用素の解析, 修士論文（東北大学）, 2002.