Waseda University
Associate Professor, Faculty of Science and Engineering[main position]
Principle Investigator, Bioinformatics Laboratory (Hamada Laboratory), Department of Electrical Engi- neering and Bioscience, Undergraduate School of Advanced Science and Engineering
Principle Investigator, Bioinformatics Laboratory (Hamada Laboratory), Department of Electrical Engi- neering and Bioscience, Graduate School of Advanced Science and Engineering
Researcher, Institute for Medical-oriented Structural Biology
AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory
(CBBD-OIL)
Invited Researcher, Team Leader, Sequence analysis algorithm team
National Institute of Advanced Industrial Science and Technology (AIST)
Visiting Researcher, Artificial Intelligence Research Center (AIRC)
Nippon Medical University
Visiting Professor
Contact Information
Address Hamada Laboratory (Bioinformatics Laboratory), Faculty of Science and Engineering, Depart- ment of Electrical Engineering and Bioscience, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
Phone +81-3-5286-3130 Email [email protected]
Web (Lab) http://www.f.waseda.jp/mhamada/
Web (Personal) https://sites.google.com/site/michiakihamada/
Education
B.S. Mathematics, Tohoku University, 2000. M.A. Mathematics, Tohoku University, 2002.
Ph.D. Bioinformatics, Tokyo Institute of Technology, 2009.
Employment
Researcher, Fuji Research Institute Corporation, Inc., 2002–2006. Consultant, Mizuho Information & research Institute, 2006–2010. Associate Professor (non-tenured), The University of Tokyo, 2010–2014.
Associate Professor (tenured), Waseda University, 2014–current (main position)
Invited Researcher, National Institute of Advanced Industrial Science and Technology (AIST), 2014– current (additional position)
Invited Professor, Nippon Medical University, 2017–current (additional position)
Academic Activities
Board member of Japanese Society of Bioinformatics (JSBi) (2014–2016)
Editorial Board of The Scientific World Journal (Computational Biology section) (2013–current) Editorial Board of Dataset Papers in Biology [Bioinformatics section] (2012–current)
Editorial Board of Frontiers in Non-Coding RNA (2011–current) Program Committee Member: IIBMP2016
Program Committee Member: WABI2017 Program Committee Member: WABI2016 Program Committee Member: BIBM2015 Program Committee Member: BIBM2014 Program Committee Member: BIBM2013 Program Committee Member: BIBM2012 Program Committee Member: BIBM2011
Publications
Journal Articles (*: corresponding author; #: joint first authors)
1. Takafumi Chishima, Junichi Iwakiri, Michiaki Hamada*, Identification of transposable elements con- tributing to tissue-specific expression of long non-coding RNAs, Genes (to appear)
2. Taikai Takeda, Michiaki Hamada*, Beyond similarity assessment: Selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm, Bioinformatics (to appear) 3. Michiaki Hamada*, In silico approaches to RNA aptamer design, Biochimie (to appear).
4. Junichi Iwakiri, Goro Terai, Michiaki Hamada, Computational prediction of lncRNA-mRNA inter- actions by integrating tissue specificity in human transcriptome, Biology Direct (2017), 12:15.
5. Tsukasa Fukunaga* and Michiaki Hamada*, RIblast: An ultrafast RNA-RNA interaction prediction system for comprehensive lncRNA interaction analysis, Bioinformatics, doi: 10.1093/bioinformat- ics/btx287.
6. Michiaki Hamada*, Yukiteru Ono, Kiyoshi Asai, Martin C. Frith*, Training alignment parameters for arbitrary sequencers with last-train, Bioinformatics 33(6), 2017, 926-928.
7. 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.
8. 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 Acid Res. (2016), 44 (W1): W302-W307. doi: 10.1093/nar/gkw337.
9. 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.
10. 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. # Joint first authors.
11. Junichi Iwakiri#, Michiaki Hamada#, Kiyoshi Asai*, Bioinformatics tools for lncRNA research, Biochim Biophys Acta (2016) Jan;1859(1):23-30. #Joint first authors
12. 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.
13. Michiaki Hamada∗, Yukiteru Ono, Ryohei Fujimaki, Kiyoshi Asai, Learning chromatin states with factorized information criteria, Bioinformatics (2015) 31 (15): 2426-2433.
14. Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada*, A semi-supervised learning approach for RNA secondary structure prediction, Computational Biology and Chemistry (2015) 57: 72–79.
15. 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
16. Edward Wijaya∗, Kana Shimizu, Kiyoshi Asai, Michiaki Hamada∗, Reference-free Prediction of Re- arrangement Breakpoint Reads, Bioinformatics (2014) 30(18):2559-67.
17. Junichi Iwakiri∗, Tomoshi Kameda, Kiyoshi Asai, Michiaki Hamada∗, Analysis of base-pairing prob- abilities of RNA molecules involved in protein-RNA interactions, Bioinformatics 29 (20): 2524-2528, 2014.
18. Michiaki Hamada∗, Fighting against uncertainty: An essential issue in bioinformatics, Briefings in Bioinformatics (2014) 15 (5): 748-767.
19. Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada∗, CentroidAlign-Web: a fast and accurate multi- ple 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).
20. Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada∗, PBSIM: PacBio reads simulator–toward accurate genome assembly, Bioinformatics, 29 (1): 119-121. 2013.
21. Michiaki Hamada∗Direct updating of an RNA base-pairing probability matrix with marginal prob- ability constraints, Journal of Computational Biology, 19(12): 1265-1276, 2012.
22. Hiroki Asida*, Kiyoshi Asai, Michiaki Hamada∗. Shape-based Alignment of Genomic Landscapes in Multi-scale Resolution, Nucleic Acids Research, 40 (14): 6435-6448, 2012.
23. Michiaki Hamada∗, Kiyoshi Asai, A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA), Journl of Computational Biology, 19(5): 532-549, May 2012. 24. 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, Bioinfor- matics 27 (22): 3085-3092, 2011.
25. 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)
26. 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.
27. Kengo Sato∗, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai, IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming, Bioinformat- ics 27(13):i85-i93, 2011.
28. Michiaki Hamada∗, Hisanori Kiryu, Wataru Iwasaki, Kiyoshi Asai, Generalized Centroid Estimators in Bioinformatics, PLoS ONE 6(2):e16450, 2011.
29. 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.
30. Michiaki Hamada∗, Kengo Sato, Kiyoshi Asai, Prediction of RNA secondary structure by maximiz- ing pseudo-expected accuracy, BMC Bioinformatics 11:586, 2010.
31. Yuki Kato∗, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, Tatsuya Akutsu, Rac- tIP: fast and accurate prediction of RNA-RNA interaction using integer programming, Bioinformatics 26(18): i460-i466, 2010.
32. 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.
33. Martin C Frith∗, Michiaki Hamada and Paul Horton, Parameters for accurate genome alignment, BMC Bioinformatics 11:80, 2010.
34. Michiaki Hamada∗, Kengo Sato, Hisanori Kiryu, Toutai Mituyama and Kiyoshi Asai, CentroidAlign: Fast and Accurate Aligner for Structured RNAs by Maximizing Expected Sum-of-Pairs Score, Bioin- formatics, 25(24): 3236–3243, 2009.
35. 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.
36. Michiaki Hamada∗, Kengo Sato, Hisanori Kiryu, Toutai Mituyama and Kiyoshi Asai, Predictions of RNA secondary structure by combining homologous sequence information, Bioinformatics, 25(12): i330–i338, 2009.
37. Michiaki Hamada∗, Hisanori Kiryu, Kengo Sato and Toutai Mituyama and Kiyoshi Asai, Predictions of RNA secondary structure using generalized centroid estimators, Bioinformatics, 25(4): 465–473, 2009.
38. Michiaki Hamada∗, Mituyama Toutai and Kiyoshi Asai, Large Scale Similarity Search for Locally Stable Secondary Structures among RNA Sequences, IPSJ transaction on Bioinformatics, 2: 36–46, 2009. 39. Kiyoshi Asai∗, Hisanori Kiryu, Michiaki Hamada, Yasuo Tabei, Kengo Sato, Hiroshi Matsui, Yasub- umi Sakakibara, Goro Terai and Totai Mituyama, Software.ncrna.org: web servers for analyses of RNA sequences, Nucleic Acids Research, 36(suupl 2), W75–W78, 2008.
40. Michiaki Hamada∗, Koji Tsuda, Taku Kudo, Taishin Kin, and Kiyoshi Asai, Mining frequent stem patterns from unaligned RNA sequences, Bioinformatics, 22(20):2480–2487, 2006.
41. Michiaki Hamada∗, Cheng Feng, Yuichiro Inagaki, Unpei Nagashima, Kazuaki Murakami and Hi- roshi Chuman, A High Performance Computing Environments for Prediction of Activity and func- tion 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. (in Japanese)
42. Michiaki Hamada∗, Remark on application of distribution function inequality for Toeplitz and Han- kel operators, Hokkaido Mathematical Journal, 32: 193-208, 2003.
Proceedings (Peer-reviewed, Full paper)
42. Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai and Yasufumi Sakakibara, A non- parametric Bayesian approach for predicting RNA secondary structures, The 9th Workshop on Al- gorithms in Bioinformatics (WABI 2009), 2009. Also in Lecture Notes in Bioinformatics (LNBI) 5724, pp. 286-297, 2009.
43. Michiaki Hamada∗, Yuichiro Inagaki, and Hiroshi Chuman, Drug Discovery Using Grid Technol- ogy, In High Performance Computing and Grid in Asia Pacific Region, Seventh International Conference (HPCAsia’04), pp. 352-356, 2004.
Books
44. 瀬々潤, 浜田道昭 著, 生命情報処理における機械学習: 多重検定と推定量設計 (Machine learning in bioinformatics), 機械学習プロフェッショナルシリーズ，講談社，2015 年
45. 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 年
46. Michiaki Hamada, RNA secondary structure prediction from multi-aligned sequences, “Methods in Molecular Biology”, 1269, 2015, pp 17-38.
47. 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" (in press, will be published in the early 2013).
48. 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 and Hiroshi Chuman, Drug Discovery Using Grid Technology, 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.
Presentations
1. Subcellular localization of lncRNAs is affected by Transposable Element (TE) derived sequences in- side lncRNAs, The Sixteenth Asia Pacific Bioinformatics Conference (APBC 2018), Yokohama, Japan, 15-17 January 2018 [poster, reviewed]
2. Clarification of human gut microbial community using Latent Dirichlet Allocation, The Sixteenth Asia Pacific Bioinformatics Conference (APBC 2018), Yokohama, Japan, 15-17 January 2018 [poster, reviewed]
3. SCAST:A cost effective diagnostic framework based on cancer associated significant transcript screen- ing, The Sixteenth Asia Pacific Bioinformatics Conference (APBC 2018), Yokohama, Japan, 15-17 January 2018 [poster, reviewed]
4. Shimpei Nishida, Shun Sakuraba, Kiyoshi Asai, Michiaki Hamada, Estimating energy parameters for RNA secondary structure predictions using both experimental and computational data, The 28th International Conference on Genome Informatics GIW/BIOINFO 2017, Seoul | Korea OCT 31 (Tue) - NOV 3 (Fri), 2017 [oral, reviewd]
5. Tsukasa Fukunaga and Michiaki Hamada. RIblast: A high-speed RNA-RNA interaction prediction system for comprehensive lncRNA interactome analysis. Computational RNA Biology Workshop 2016, 2016/10 [oral, reviewed]
6. Tsukasa Fukunaga, Michiaki Hamada. RIblast: An ultrafast RNA-RNA interaction prediction method based on seed-and-extension approach. ECCB2016, 2016/9 [poster, reviewed]
7. Michiaki Hamada, Training alignment paremters for Nanopore and PacBio sequencers, WABI2016, 2016/08 [poster, reviewed]
8. Takafumi Chishima, Michiaki Hamada, Search of the sequences common in human lncRNAs, RNA2016, Kyoto, Japan. [poster, reviewed]
9. 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, RNA2016, Kyoto, Japan. [poster, reviewed]
10. Junichi Iwakiri, Goro Terai, Michiaki Hamada, Computational prediction of lncRNA-mRNA inter- actions by integrating tissue-specificity of human transcripts, RNA2016, Kyoto, Japan. [poster, re- viewed]
11. Junichi Iwakiri, Michiaki Hamada, Kiyoshi Asai, Tomoshi Kameda, Improved accuracy in RNA- protein rigid body docking by incorporating force eld for molecular dynamics simulation into the scoring function, RNA2016, Kyoto, Japan [poster, reviewed]
12. Wataru Okada, Junichi Iwakiri, Michiaki Hamada, Investigation of evolutionarily conserved NEAT1- NEAT1 interactions, RNA2016, Kyoto, Japan. [poster, reviewed]
13. Michiaki Hamada, Comprehensive Prediction of lncRNA-RNA Interactions in Human Transcrip- tome, The Fourteenth Asia Pacific Bioinformatics Conference (APBC2016), San Francisco Bay Area, United States, Jan 11th-13th, 2016 [oral, reviewed]
14. Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada (presenter), A semi-supervised learning ap- proach for RNA secondary structure prediction, The thirteenth Asia Pacific Bioinformatics Confer- ence (APBC2015), HsinChu, Taiwan, Jan 21th-23th, 2015. [oral, reviewed]
15. Kotaro Ishii, Yusuke Kazama, Tomonari Hirano, Michiaki Hamada, Yukiteru Ono, Tomoko Abe; Pipeline for whole-genome analysis of heavy-ion-induced mutants in Arabidopsis thaliana; The 26th international conference on arabidopsis research; 2015.[poster, reviewed]
16. Kotaro Ishii, Tomonari Hirano, Yusuke Kazama, Michiaki Hamada, Yukiteru Ono, Tomoko Abe; Pipeline for whole-genome analysis of heavy-ion-induced mutants, International Symposium on Genome Science 2015; 2015/01 [poster, reviewed]
17. Takashi Matsuda, Michiaki Hamada and Kiyoshi Asai; Prediction of joint RNA secondary structure by using their homologous sequence information; GIW2014; 2014; Tokyo, Japan; Best poster award [poster, reviewed]
18. Kana Shimizu, Hiromi Arai, Koji Nuida, Michiaki Hamada, Koji Tsuda, Jun Sakuma, Takatsugu Hirokawa, Goichiro Hanaoka, Kiyoshi Asai; Privacy-preserving search for a chemical compound database; ISMB/ECCB 2013; 2013. [poster, reviewed]
19. Hiroki Ashida, Michiaki Hamada, Kiyoshi Asai; A New Approach to Elucidate Genomic Landscapes in MultiscaleResolution; 5th Asian Young Researchers Conferenceon Computational and Omics Bi- ology(AYRCOB); 2011/08 (Best poster award was given to this poster) [poster, reviewed]
20. Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Kiyoshi Asai; Centroid series: fundamental pro- grams of sequence analysis for non-coding RNAs; The 16th Annual Meeting of the RNA Society (RNA2011); 2011/06. [poster, reviewed]
21. Hironori Adachi, Akira Ishiguro, Michiaki Hamada, Eri Sakota, Kiyoshi Asai, Yoshikazu Nakamura; Antagonistic RNA Aptamer Specific to a Heterodimeric Form of Human Interleukin-17 A/F; The 16th Annual Meeting of the RNA Society (RNA2011); Jun 2011.
22. Kiyoshi Asai, Michiaki Hamada, Hisanori Kiryu; Binary Estimation Problems in Structural Informa- tion Analysis of RNA; The 16th Annual Meeting of the RNA Society (RNA2011). Jun 2011.
23. Yuki Kato, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, Tatsuya Akutsu; Rac- tIP: Fast and Accurate Prediction of RNA-RNA Interaction Using Integer Programming; The 16th Annual Meeting of the RNA Society (RNA2011). 2011/06.
24. Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai; IPknot: Fast and Accurate Prediction of RNA Secondary Structures with Pseudoknots Using Integer Programming; The 16th Annual Meeting of the RNA Society (RNA2011). 2011/06.
25. Kiyoshi Asai, Michiaki Hamada, Hisanori Kiryu, Kengo Sato, Toutai Mituyama; Software tools for RNA sequence analysis in ncrna.org; PSB2011, 2011/01.
26. Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai; Centroid series: fundamental programs of sequence analysis for non-coding RNAs; ISMB2010, 2010/07
27. Yuki Kato, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, Tatsuya Akutsu; Rac- tIP: fast and accurate prediction of RNA-RNA interaction using integer programming; ISMB2010(Poster). 28. Martin C. Frith, Michiaki Hamada, Paul Horton; How (not) to Align Genomes; The 20th International
Conference on Genome Informatics December 14-16; 2009. (poster presentaion)
29. Michiaki Hamada, Kengo Sato(*), Hisanori Kiryu, Toutai Mituyama and Kiyoshi Asai; CentroidFold: Predictions of RNA Secondary Structure for Estimating Accurate Base-pairs; The 9th Workshop on Algorithms in Bioinformatics (WABI 2009). (Poster presentation; Reviewed international conference)
30. Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama and Kiyoshi Asai; Predictions of RNA secondary structure by combining homologous sequence information; IThe 17th Annual Inter- national Conference on Intelligent Systems for Molecular Biology and 7th Annual European Con- ference on Computational Biology (ISMB/ECCB 2009). (Oral presentation; Reviewed International conference)
31. Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama and Kiyoshi Asai; CentroidFold: Predictions of RNA Secondary Structure for Estimating Accurate Base-pairs,The 17th Annual Inter- national Conference on Intelligent Systems for Molecular Biology and 7th Annual European Con- ference on Computational Biology (ISMB/ECCB 2009). (poster presentation; Reviewed international conference)
32. Michiaki Hamada, Koji Tsuda, Taku Kudo, Taishin Kin, Kiyoshi Asai; Mining Local Secondary Struc- ture Motifs from Unaligned RNA Sequences Using Graph Mining Techniques; 5th Annual Interna- tional Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB); 2007. (poster presentation)
33. Michiaki Hamada, Koji Tsuda, Taku Kudo, Taishin Kin, Kiyoshi Asai; RNAmine: Frequent Stem Pat- tern Miner from RNAs; The 17th International Conference on Genome Informatics (GIW2006).(poster presentation)
Last updated: December 28, 2017
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