Publication

Journal papers (reviewed)

Preprints

  1. Fukunaga, Iwakiri, Ono, Hamada (submitted)
  2. Morteza et al. (submitted)
  3. Fukunaga, Hamada (invited review paper; submitted to Briefings in Functional Genomics)
  4. Anju, Hamada (submitted)
  5. Hosoda, Nishijima, Fukunaga, Hattori, Hamada (submitted)

2018

  1. Tsukasa Fukunaga*, Michiaki Hamada*, A novel method for assessing the statistical significance of RNA-RNA interactions between two long RNAs, Journal of Computational Biology (to appear)
  2. Chao Zeng*, Tsukasa Fukunaga, Michiaki Hamada*, Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data, BMC Genomics (to appear)
  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 TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (to appear)
  4. ☆Takafumi Chishima, Junichi Iwakiri, Michiaki Hamada*, Identification of transposable elements contributing to tissue-specific expression of long non-coding RNAs, Genes (to appear)

2017

  1. Taikai Takeda and Michiaki Hamada*, Beyond similarity assessment: Selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm, Bioinformatics (https://doi.org/10.1093/bioinformatics/btx643)
  2. Michiaki Hamada*, In silico approaches to RNA aptamer design, Biochimie (to appear).
  3. Junichi Iwakiri, Goro Terai, Michiaki Hamada, Computational prediction of lncRNA-mRNA interactions by integrating tissue specificity in human transcriptome, Biology Direct (2017) 12:15
  4. Tsukasa Fukunaga* and Michiaki Hamada*, RIblast: An ultrafast RNA-RNA interaction prediction system for comprehensive lncRNA interaction analysis, Bioinformatics (accepted)
  5. Michiaki Hamada*, Yukiteru Ono, Kiyoshi Asai, Martin C. Frith*, Training alignment parameters for arbitrary sequencers with last-train, Bioinformatics, 33(6), 2017, 926-928
  6. 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

  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), 44 (W1): W302-W307. 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) 17(Suppl 1):article no. 12.
  4. Junichi Iwakiri#, Michiaki Hamada#, Kiyoshi Asai*, Bioinformatics tools for lncRNA research, Biochim Biophys Acta. 2016 Jan;1859(1):23-30.

2015

  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.

2014

  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 Bionformatics (2014) 15 (5): 748-767. doi: 10.1093/bib/bbt038 First published online: June 26, 2013. [Preprint version in arXiv]

2013

  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. [Supplementary Information] [Software]

2012

  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. (I am a corresponding author of this article) (2011 Impact factor: 8.026)
  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

  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. (2011 impact factor: 5.468)
  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 (Epub 2011 May 11) . [Web Server] (2011 Impact factor: 8.026)
  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. [Pubmed] (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

  1. Michiaki Hamada*, Kengo Sato, Kiyoshi Asai, Prediction of RNA secondary structure by maximizing pseudo-expected accuracy, BMC Bioinformatics 11:586, 2010. [日本語概要] (Highly accessed paper)
  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. (First published online: September 15, 2010.) (2011 Impact factor: 8.026)
  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. [PDF] (This paper was presented at ECCB2010) (2011 impact factor: 5.468)
  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. [Abstract]
  5. Martin C Frith*, Michiaki Hamada, Paul Horton, Parameters for accurate genome alignment, BMC Bioinformatics 11:80, 2010. [PDF] [PubMed] (Highly accessed paper)

2009

  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. [PDF] [PubMed] (2011 impact factor: 5.468)
  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. [Web server] [Abstract] [PDF] (2011 Impact factor: 8.026)
  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. [Abstract] [PDF] (This paper was presented at ISMB2009) (2011 impact factor: 5.468)
  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. [Abstract][PDF][Supplementary Data] (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) [Abstract]

2008以前

  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 Research 36 (suupl 2), W75–W78, 2008. [Abstract][Full Text][PDF] (2011 Impact factor: 8.026)
  2. Michiaki Hamada*, Koji Tsuda, Taku Kudo, Taishin Kin, Kiyoshi Asai, Mining frequent stem patterns from unaligned RNA sequences, Bioinformatics 22(20):2480-2487, 2006. [Abstract] [Full Text][Print PDF] (2011 impact factor: 5.468)
  3. 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, Transactions of the Japan Society for Industrial and Applied Mathematics 14(4):267-288, 2004.[PDF]
  4. 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)

  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). [Abstract] [PDF] (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 (including book chapters)

  1. 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) [in press]
  2. 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). [分担執筆者]
  3. Michiaki Hamada, RNA secondary structure prediction from multi-aligned sequences, RNA Bioinformatics, Methods in Molecular Biology, 1269, 2015, pp 17-38 [A preprint vesion 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 in Molecular Biology Volume 1097, 2014, pp 291-301
  5. 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. [amazon]
  6. 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. [amazon]