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    Shinichi Morishita (computer scientist)

    From Wikitia - Reading time: 7 min
    Shinichi Morishita
    Born (1960-09-18) September 18, 1960 (age 64)
    Tokyo, Japan
    NationalityJapanese
    Alma materUniversity of Tokyo
    Scientific career
    FieldsComputer science Bioinformatics
    InstitutionsUniversity of Tokyo
    Doctoral advisorMasahiko Sato, Nobuo Yoneda

    Shinichi Morishita (森下 真一, September 18, 1960 - ) is a Japanese computer scientist and bioinformatician. In computer science, he is best known for proposing a widely-used heuristic algorithm for enumerating statistical association rules[1]. In the field of genetics, he made significant contributions to the construction of the first large-scale phenotypic database of yeast mutants[2], the first draft of the medaka genome[3], the confirmation of the two rounds of whole-genome duplications and dynamic genome rearrangements in early vertebrates[4], and the discovery of chromatin-associated periodicity in genetic variation downstream of transcriptional start sites[5].

    He is a professor of the Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo since 2003. He also holds a secondary appointment in the Department of Bioinformatics and Systems Biology, Faculty of Science, University of Tokyo since 2009.

    Career[edit]

    Shinichi Morishita was born and raised in Tokyo, Japan. He graduated from Kaisei High School and entered the University of Tokyo in 1979. Under the mentorship of mathematician and computer scientist Masahiko Sato and Nobuo Yoneda, he received a B.S. in 1983, a M.S. in 1985, and a Ph.D. in 1990 from Department of Information Science, Faculty of Science, University of Tokyo.

    While working at IBM Japan from 1985 to 1997, Morishita visited the Department of Computer Science, Stanford University from 1990 to 1992, where he studied recursive database query optimization[6][7][8] under the mentorship of Turing Award laureate computer scientist Jeffrey D. Ullman. Morishita moved to the Institute of Medical Science, University of Tokyo as a visiting associate professor in 1997, moved to the Department of Information Science, Faculty of Science, University of Tokyo as an associate professor in 1999, and moved to the Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo as a professor in 2003.

    Morishita developed a widely-used method of mining statistical association rules in 2000[9]. Morishita and his colleagues collaborated with biologist Yoshikazu Ohya to build the first large-scale phenotyping database of yeast mutants in 2005[10]. They reported the first draft of the medaka genome [11] and confirmed the two rounds of whole-genome duplications and dynamic genome rearrangements in early vertebrates[12] with biologist Hiroyuki Takeda in 2007. Using the medaka genome, they uncovered chromatin-associated periodicity in genetic variation downstream of transcriptional start sites with Nobel laureate biologist Andrew Fire in 2009[13].

    Since 2011, Morishita and his colleagues have used long-read sequencers to refine the medaka genome assembly in 2017 with Hiroyuki Takeda[14] and the C. elegans genome assembly in 2019 with Andrew Fire and Erich Schwarz[15]. They developed software programs to detect tandem repeats of unit strings from long reads along with computer scientist Gene Myers [16][17], discovered novel tandem repeats associated with brain disorders with medical scientist Shoji Tsuji[18][19], and constructed a database of complex tandem repeats within individual human genomes.

    References[edit]

    1. ↑ Wu, Xindong; Kumar, Vipin; Ross Quinlan, J.; Ghosh, Joydeep; Yang, Qiang; Motoda, Hiroshi; McLachlan, Geoffrey J.; Ng, Angus; Liu, Bing; Yu, Philip S.; Zhou, Zhi-Hua; Steinbach, Michael; Hand, David J.; Steinberg, Dan (1 January 2008). "Top 10 algorithms in data mining". Knowledge and Information Systems. 14 (1): 1–37. doi:10.1007/s10115-007-0114-2.
    2. ↑ Goymer, Patrick (February 2006). "Shaping up the genome". Nature Reviews Genetics. 7 (2): 79. doi:10.1038/nrg1792.
    3. ↑ Takeda, Hiroyuki (June 2008). "Draft genome of the medaka fish: A comprehensive resource for medaka developmental genetics and vertebrate evolutionary biology". Development, Growth & Differentiation. 50 (s1): S157-66. doi:10.1111/j.1440-169X.2008.00992.x. PMID 18430160.
    4. ↑ Sacerdot, Christine; Louis, Alexandra; Bon, Céline; Berthelot, Camille; Roest Crollius, Hugues (December 2018). "Chromosome evolution at the origin of the ancestral vertebrate genome". Genome Biology. 19 (1): 166. doi:10.1186/s13059-018-1559-1. PMC 6193309. PMID 30333059.
    5. ↑ Semple, Colin A. M.; Taylor, Martin S. (16 January 2009). "The Structure of Change". Science. 323 (5912): 347–348. doi:10.1126/science.1169408. PMID 19150834.
    6. ↑ Morishita, Shinichi (15 January 1997). "Avoiding Cartesian products for multiple joins". Journal of the ACM. 44 (1): 57–85. doi:10.1145/256292.256296.
    7. ↑ Morishita, Shinichi (1 June 1996). "An Extension of Van Gelder's Alternating Fixpoint to Magic Programs". Journal of Computer and System Sciences. 52 (3): 506–521. doi:10.1006/jcss.1996.0038.
    8. ↑ Derr, Marcia A.; Morishita, Shinichi; Phipps, Geoffrey (1 June 1993). "Design and implementation of the glue-nail database system". ACM SIGMOD Record. 22 (2): 147–156. doi:10.1145/170036.170065.
    9. ↑ Morishita, Shinichi; Sese, Jun (1 May 2000). "Transversing itemset lattices with statistical metric pruning". Proceedings of the nineteenth ACM SIGMOD-SIGACT-SIGART symposium on Principles of database systems - PODS '00. pp. 226–236. doi:10.1145/335168.335226. ISBN 1-58113-214-X.
    10. ↑ Ohya, Yoshikazu; Sese, Jun; Yukawa, Masashi; Sano, Fumi; Nakatani, Yoichiro; Saito, Taro L.; Saka, Ayaka; Fukuda, Tomoyuki; Ishihara, Satoru; Oka, Satomi; Suzuki, Genjiro; Watanabe, Machika; Hirata, Aiko; Ohtani, Miwaka; Sawai, Hiroshi; Fraysse, Nicolas; Latgé, Jean-Paul; François, Jean M.; Aebi, Markus; Tanaka, Seiji; Muramatsu, Sachiko; Araki, Hiroyuki; Sonoike, Kintake; Nogami, Satoru; Morishita, Shinichi (27 December 2005). "High-dimensional and large-scale phenotyping of yeast mutants". Proceedings of the National Academy of Sciences. 102 (52): 19015–19020. Bibcode:2005PNAS..10219015O. doi:10.1073/pnas.0509436102. PMC 1316885. PMID 16365294.
    11. ↑ Kasahara, Masahiro; Naruse, Kiyoshi; Sasaki, Shin; Nakatani, Yoichiro; Qu, Wei; Ahsan, Budrul; Yamada, Tomoyuki; Nagayasu, Yukinobu; Doi, Koichiro; Kasai, Yasuhiro; Jindo, Tomoko; Kobayashi, Daisuke; Shimada, Atsuko; Toyoda, Atsushi; Kuroki, Yoko; Fujiyama, Asao; Sasaki, Takashi; Shimizu, Atsushi; Asakawa, Shuichi; Shimizu, Nobuyoshi; Hashimoto, Shin-ichi; Yang, Jun; Lee, Yongjun; Matsushima, Kouji; Sugano, Sumio; Sakaizumi, Mitsuru; Narita, Takanori; Ohishi, Kazuko; Haga, Shinobu; Ohta, Fumiko; Nomoto, Hisayo; Nogata, Keiko; Morishita, Tomomi; Endo, Tomoko; Shin-I, Tadasu; Takeda, Hiroyuki; Morishita, Shinichi; Kohara, Yuji (June 2007). "The medaka draft genome and insights into vertebrate genome evolution". Nature. 447 (7145): 714–719. Bibcode:2007Natur.447..714K. doi:10.1038/nature05846. PMID 17554307.
    12. ↑ Nakatani, Yoichiro; Takeda, Hiroyuki; Kohara, Yuji; Morishita, Shinichi (September 2007). "Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates". Genome Research. 17 (9): 1254–1265. doi:10.1101/gr.6316407. PMID 17652425.
    13. ↑ Sasaki, Shin; Mello, Cecilia C.; Shimada, Atsuko; Nakatani, Yoichiro; Hashimoto, Shin-ichi; Ogawa, Masako; Matsushima, Kouji; Gu, Sam Guoping; Kasahara, Masahiro; Ahsan, Budrul; Sasaki, Atsushi; Saito, Taro; Suzuki, Yutaka; Sugano, Sumio; Kohara, Yuji; Takeda, Hiroyuki; Fire, Andrew; Morishita, Shinichi (16 January 2009). "Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites". Science. 323 (5912): 401–404. Bibcode:2009Sci...323..401S. doi:10.1126/science.1163183. PMC 2757552. PMID 19074313.
    14. ↑ Ichikawa, Kazuki; Tomioka, Shingo; Suzuki, Yuta; Nakamura, Ryohei; Doi, Koichiro; Yoshimura, Jun; Kumagai, Masahiko; Inoue, Yusuke; Uchida, Yui; Irie, Naoki; Takeda, Hiroyuki; Morishita, Shinich (28 November 2017). "Centromere evolution and CpG methylation during vertebrate speciation". Nature Communications. 8 (1): 1833. Bibcode:2017NatCo...8.1833I. doi:10.1038/s41467-017-01982-7. PMC 5705604. PMID 29184138.
    15. ↑ Yoshimura, Jun; Ichikawa, Kazuki; Shoura, Massa J.; Artiles, Karen L.; Gabdank, Idan; Wahba, Lamia; Smith, Cheryl L.; Edgley, Mark L.; Rougvie, Ann E.; Fire, Andrew Z.; Morishita, Shinichi; Schwarz, Erich M. (June 2019). "Recompleting the Caenorhabditis elegans genome". Genome Research. 29 (6): 1009–1022. doi:10.1101/gr.244830.118. PMC 6581061. PMID 31123080.
    16. ↑ Morishita, Shinichi; Ichikawa, Kazuki; Myers, Eugene W (5 May 2021). "Finding long tandem repeats in long noisy reads". Bioinformatics. 37 (5): 612–621. doi:10.1093/bioinformatics/btaa865. PMC 8097686. PMID 33031558.
    17. ↑ Masutani, Bansho; Kawahara, Riki; Morishita, Shinichi (1 April 2023). "Decomposing mosaic tandem repeats accurately from long reads". Bioinformatics. 39 (4). doi:10.1093/bioinformatics/btad185. PMC 10118999. PMID 37039842.
    18. ↑ Ishiura, Hiroyuki; Doi, Koichiro; Mitsui, Jun; Yoshimura, Jun; Matsukawa, Miho Kawabe; Fujiyama, Asao; Toyoshima, Yasuko; Kakita, Akiyoshi; Takahashi, Hitoshi; Suzuki, Yutaka; Sugano, Sumio; Qu, Wei; Ichikawa, Kazuki; Yurino, Hideaki; Higasa, Koichiro; Shibata, Shota; Mitsue, Aki; Tanaka, Masaki; Ichikawa, Yaeko; Takahashi, Yuji; Date, Hidetoshi; Matsukawa, Takashi; Kanda, Junko; Nakamoto, Fumiko Kusunoki; Higashihara, Mana; Abe, Koji; Koike, Ryoko; Sasagawa, Mutsuo; Kuroha, Yasuko; Hasegawa, Naoya; Kanesawa, Norio; Kondo, Takayuki; Hitomi, Takefumi; Tada, Masayoshi; Takano, Hiroki; Saito, Yutaka; Sanpei, Kazuhiro; Onodera, Osamu; Nishizawa, Masatoyo; Nakamura, Masayuki; Yasuda, Takeshi; Sakiyama, Yoshio; Otsuka, Mieko; Ueki, Akira; Kaida, Ken-ichi; Shimizu, Jun; Hanajima, Ritsuko; Hayashi, Toshihiro; Terao, Yasuo; Inomata-Terada, Satomi; Hamada, Masashi; Shirota, Yuichiro; Kubota, Akatsuki; Ugawa, Yoshikazu; Koh, Kishin; Takiyama, Yoshihisa; Ohsawa-Yoshida, Natsumi; Ishiura, Shoichi; Yamasaki, Ryo; Tamaoka, Akira; Akiyama, Hiroshi; Otsuki, Taisuke; Sano, Akira; Ikeda, Akio; Goto, Jun; Morishita, Shinichi; Tsuji, Shoji (April 2018). "Expansions of intronic TTTCA and TTTTA repeats in benign adult familial myoclonic epilepsy". Nature Genetics. 50 (4): 581–590. doi:10.1038/s41588-018-0067-2. PMID 29507423.
    19. ↑ Ishiura, Hiroyuki; Shibata, Shota; Yoshimura, Jun; Suzuki, Yuta; Qu, Wei; Doi, Koichiro; Almansour, M. Asem; Kikuchi, Junko Kanda; Taira, Makiko; Mitsui, Jun; Takahashi, Yuji; Ichikawa, Yaeko; Mano, Tatsuo; Iwata, Atsushi; Harigaya, Yasuo; Matsukawa, Miho Kawabe; Matsukawa, Takashi; Tanaka, Masaki; Shirota, Yuichiro; Ohtomo, Ryo; Kowa, Hisatomo; Date, Hidetoshi; Mitsue, Aki; Hatsuta, Hiroyuki; Morimoto, Satoru; Murayama, Shigeo; Shiio, Yasushi; Saito, Yuko; Mitsutake, Akihiko; Kawai, Mizuho; Sasaki, Takuya; Sugiyama, Yusuke; Hamada, Masashi; Ohtomo, Gaku; Terao, Yasuo; Nakazato, Yoshihiko; Takeda, Akitoshi; Sakiyama, Yoshio; Umeda-Kameyama, Yumi; Shinmi, Jun; Ogata, Katsuhisa; Kohno, Yutaka; Lim, Shen-Yang; Tan, Ai Huey; Shimizu, Jun; Goto, Jun; Nishino, Ichizo; Toda, Tatsushi; Morishita, Shinichi; Tsuji, Shoji (August 2019). "Noncoding CGG repeat expansions in neuronal intranuclear inclusion disease, oculopharyngodistal myopathy and an overlapping disease". Nature Genetics. 51 (8): 1222–1232. doi:10.1038/s41588-019-0458-z. PMID 31332380.

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