Journal Papers

  1. Kyoka Higuchi, Akiko Uyeda, Lili Quan, Shogo Tanabe, Yuki Kato, Yukio Kawahara, and Rieko Muramatsu,
    Synaptotagmin 4 supports spontaneous axon sprouting after spinal cord injury,
    The Journal of Neuroscience, in press.
  2. Kotaro Miyake, Pedro Henrique Costa Cruz, Izumi Nagatomo, Yuki Kato, Daisuke Motooka, Shingo Satoh, Yuichi Adachi, Yoshito Takeda, Yukio Kawahara, and Atsushi Kumanogoh,
    A cancer-associated METTL14 mutation induces aberrant m6A modification, affecting tumor growth,
    Cell Reports, vol. 42, issue 7, 112688, Jul. 2023. [Link] [PubMed]
  3. Yanfang Xing, Taisuke Nakahama, Yuke Wu, Maal Inoue, Jung In Kim, Hiroyuki Todo, Toshiharu Shibuya, Yuki Kato, and Yukio Kawahara,
    RNA editing of AZIN1 coding sites is catalyzed by ADAR1 p150 after splicing,
    Journal of Biological Chemistry, vol. 299, issue 7, 104840, Jul. 2023. [Link] [PubMed]
  4. Reiichi Sugihara, Yuki Kato*, Tomoya Mori, and Yukio Kawahara,
    Alignment of single-cell trajectory trees with CAPITAL,
    Nature Communications, vol. 13, 5972, Oct. 2022 (*: corresponding author). [Link] [PubMed]
  5. Kengo Sato and Yuki Kato,
    Prediction of RNA secondary structure including pseudoknots for long sequences,
    Briefings in Bioinformatics, vol. 23, issue 1, bbab395, Jan. 2022. [Link] [PubMed]
  6. Maal Inoue, Taisuke Nakahama, Ryuichiro Yamasaki, Toshiharu Shibuya, Jung In Kim, Hiroyuki Todo, Yanfang Xing, Yuki Kato, Eiichi Morii, and Yukio Kawahara,
    An Aicardi-Goutieres syndrome-causative point mutation in Adar1 gene invokes multi-organ inflammation and late-onset encephalopathy in mice,
    The Journal of Immunology, vol. 207, issue 12, pp. 3016-3027, Dec. 2021. [Link] [PubMed]
  7. Akiko Uyeda, Quan Lili, Yuki Kato, Nagaaki Muramatsu, Shogo Tanabe, Kazuhisa Sakai, Noritaka Ichinohe, Yukio Kawahara, Tatsunori Suzuki, and Rieko Muramatsu,
    DDAH1 as a novel regulator of oligodendrocyte differentiation in the central nervous system remyelination,
    GLIA, vol. 69, issue 11, pp. 2591-2604, Nov. 2021. [Link] [PubMed]
  8. Taisuke Nakahama, Yuki Kato, Toshiharu Shibuya, Maal Inoue, Jung In Kim, Tuangtong Vongpipatana, Hiroyuki Todo, Yanfang Xing, and Yukio Kawahara,
    Mutations in the adenosine deaminase ADAR1 that prevent endogenous Z-RNA editing induce Aicardi-Goutieres syndrome-like encephalopathy,
    Immunity, vol. 54, issue 9, pp. 1976-1988, Sep. 2021. [Link] [PubMed]
  9. Jung In Kim, Taisuke Nakahama, Ryuichiro Yamasaki, Pedro Henrique Costa Cruz, Tuangtong Vongpipatana, Maal Inoue, Nao Kanou, Yanfang Xing, Hiroyuki Todo, Toshiharu Shibuya, Yuki Kato, and Yukio Kawahara,
    RNA editing at a limited number of sites is sufficient to prevent MDA5 activation in the mouse brain,
    PLoS Genetics, vol. 17, issue 5, e1009516, May 2021. [Link] [PubMed]
  10. Masumi Ito, Rieko Muramatsu, Yuki Kato, Bikram Sharma, Akiko Uyeda, Shogo Tanabe, Harutoshi Fujimura, Hiroyasu Kidoya, Nobuyuki Takakura, Yukio Kawahara, Masaki Takao, Hideki Mochizuki, Akiyoshi Fukamizu, and Toshihide Yamashita,
    Age-dependent decline in remyelination capacity is mediated by apelin-APJ signaling,
    Nature Aging, vol. 1, pp. 284-294, Mar. 2021. [Link]
  11. Keisuke Shimmura, Yuki Kato*, and Yukio Kawahara,
    Bivartect: accurate and memory-saving breakpoint detection by direct read comparison,
    Bioinformatics, vol. 36, issue 9, pp. 2725-2730, May 2020 (*: corresponding author). [Link] [PubMed]
  12. Tuangtong Vongpipatana, Taisuke Nakahama, Toshiharu Shibuya, Yuki Kato, and Yukio Kawahara,
    ADAR1 regulates early T cell development via MDA5-dependent and -independent pathways,
    The Journal of Immunology, vol. 204, issue 8, pp. 2156-2168, Apr. 2020. [Link] [PubMed]
  13. Pedro Henrique Costa Cruz, Yuki Kato, Taisuke Nakahama, Toshiharu Shibuya, and Yukio Kawahara,
    A comparative analysis of ADAR mutant mice reveals site-specific regulation of RNA editing,
    RNA, vol. 26, no. 4, pp. 454-469, Apr. 2020. [Link] [PubMed]
  14. Taisuke Nakahama, Yuki Kato, Jung In Kim, Tuangtong Vongpipatana, Yutaka Suzuki, Carl Walkley, and Yukio Kawahara,
    ADAR1-mediated RNA editing is required for thymic self-tolerance and prevention of autoimmunity,
    EMBO Reports, vol. 19, issue 12, e46303, Dec. 2018. [Link] [PubMed]
  15. Akino Nakasone, Rieko Muramatsu, Yuki Kato, Yukio Kawahara, and Toshihide Yamashita,
    Myotube-derived factor promotes oligodendrocyte precursor cell proliferation,
    Biochemical and Biophysical Research Communications, vol. 500, issue 3, pp. 609-613, Jun. 2018. [Link] [PubMed]
  16. Yuki Kato*, Jan Gorodkin, and Jakob Hull Havgaard*,
    Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots,
    BMC Genomics, vol. 18, 935, Dec. 2017 (*: corresponding author). [Link] [PubMed]
  17. Yuki Kato*, Tomoya Mori, Kengo Sato, Shingo Maegawa*, Hiroshi Hosokawa, and Tatsuya Akutsu,
    An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data,
    Bioinformatics, vol. 33, no. 2, pp. 202-209, Jan. 2017 (*: corresponding author). [Link] [PubMed]
  18. Michiaki Hamada, Yukiteru Ono, Hisanori Kiryu, Kengo Sato, Yuki Kato, Tsukasa Fukunaga, Ryota Mori, and Kiyoshi Asai,
    Rtools: a web server for various secondary structural analyses on single RNA sequences,
    Nucleic Acids Research, vol. 44, Web Server issue, pp. W302-W307, Jul. 2016. [Link] [PubMed]
  19. Masato Yano and Yuki Kato*,
    Using hidden Markov models to investigate G-quadruplex motifs in genomic sequences,
    BMC Genomics, vol. 15(Suppl 9), S15, Dec. 2014 (*: corresponding author). [Link] [PubMed]
    (This paper is also presented at the 13th International Conference on Bioinformatics (InCoB2014), Sydney, Australia, Aug. 2014.)
  20. Kengo Sato, Yuki Kato, Tatsuya Akutsu, Kiyoshi Asai, and Yasubumi Sakakibara,
    DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition,
    Bioinformatics, vol. 28, no. 24, pp. 3218-3224, Dec. 2012. [Link] [PubMed]
  21. Yuki Kato*, Kengo Sato, Kiyoshi Asai, and Tatsuya Akutsu,
    Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming,
    Nucleic Acids Research, vol. 40, Web Server issue, pp. W29-W34, Jul. 2012 (*: corresponding author). [Link] [PubMed]
  22. Unyanee Poolsap*, Yuki Kato*, Kengo Sato, and Tatsuya Akutsu,
    Using binding profiles to predict binding sites of target RNAs,
    Journal of Bioinformatics and Computational Biology, vol. 9, issue 6, pp. 697-713, Dec. 2011 (*: joint first and corresponding authors). [Link] [PubMed]
  23. Kengo Sato*, Yuki Kato*, Michiaki Hamada, Tatsuya Akutsu, and Kiyoshi Asai,
    IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming,
    Bioinformatics, vol. 27, no. 13, pp. i85-i93, Jul. 2011 (*: joint first and corresponding authors). [Link] [PubMed]
    (This paper is also presented at 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology (ISMB/ECCB2011), Vienna, Austria, Jul. 2011.)
  24. Yuki Kato*, Kengo Sato*, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, and Tatsuya Akutsu,
    RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming,
    Bioinformatics, vol. 26, no. 18, pp. i460-i466, Sep. 2010 (*: joint first and corresponding authors). [Link] [PubMed]
    (This paper is also presented at the 9th European Conference on Computational Biology (ECCB2010), Ghent, Belgium, Sep. 2010.)
  25. Yusuke Ishida, Yuki Kato*, Liang Zhao, Hiroshi Nagamochi, and Tatsuya Akutsu,
    Branch-and-bound algorithms for enumerating treelike chemical graphs with given path frequency using detachment-cut,
    Journal of Chemical Information and Modeling, vol. 50, no. 5, pp. 934-946, May 2010 (*: corresponding author). [Link] [PubMed]
  26. Yuki Kato*, Tatsuya Akutsu, and Hiroyuki Seki,
    Dynamic programming algorithms and grammatical modeling for protein beta-sheet prediction,
    Journal of Computational Biology, vol. 16, no. 7, pp. 945-957, Jul. 2009 (*: corresponding author). [Link] [PubMed]
  27. Yuki Kato*, Tatsuya Akutsu, and Hiroyuki Seki,
    A grammatical approach to RNA-RNA interaction prediction,
    Pattern Recognition, vol. 42, issue 4, pp. 531-538, Apr. 2009 (*: corresponding author). [Link]
  28. Unyanee Poolsap, Yuki Kato*, and Tatsuya Akutsu,
    Prediction of RNA secondary structure with pseudoknots using integer programming,
    BMC Bioinformatics, vol. 10(Suppl 1), S38, Jan. 2009 (*: corresponding author). [Link] [PubMed]
    (This paper is also published in Proc. the Seventh Asia Pacific Bioinformatics Conference (APBC2009), pp. 439-448, Beijing, China, Jan. 2009.)
  29. Hiroyuki Seki and Yuki Kato,
    On the generative power of multiple context-free grammars and macro grammars,
    IEICE Transactions on Information and Systems, vol. E91-D, no. 2, pp. 209-221, Feb. 2008.
  30. Yuki Kato*, Hiroyuki Seki, and Tadao Kasami,
    RNA pseudoknotted structure prediction using stochastic multiple context-free grammar,
    IPSJ Transactions on Bioinformatics, vol. 47, no. SIG17 (TBIO1), pp. 12-21, Nov. 2006 (*: corresponding author). [Link]
  31. Yuki Kato*, Hiroyuki Seki, and Tadao Kasami,
    On the generative power of grammars for RNA secondary structure,
    IEICE Transactions on Information and Systems, vol. E88-D, no. 1, pp. 53-64, Jan. 2005 (*: corresponding author).

Conference Papers

  1. Nobuyoshi Mizoguchi, Yuki Kato, and Hiroyuki Seki,
    A grammar-based approach to RNA pseudoknotted structure prediction for aligned sequences,
    Proc. the 1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS2011), pp. 135-140, Orlando, Florida, USA, Feb. 2011.
  2. Unyanee Poolsap*, Yuki Kato*, and Tatsuya Akutsu,
    Dynamic programming algorithms for RNA structure prediction with binding sites,
    Proc. the Fifteenth Pacific Symposium on Biocomputing (PSB2010), vol. 15, pp. 98-107, The Big Island of Hawaii, USA, Jan. 2010 (*: joint first and corresponding authors). [Link] [PubMed]
  3. Yuki Kato*, Tatsuya Akutsu, and Hiroyuki Seki,
    Prediction of protein beta-sheets: dynamic programming versus grammatical approach,
    Third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB2008), Lecture Notes in Bioinformatics, vol. 5265, pp. 66-77, Melbourne, Australia, Oct. 2008 (*: corresponding author). [Link]
  4. Yuki Kato*, Tatsuya Akutsu, and Hiroyuki Seki,
    A grammatical approach to RNA-RNA interaction prediction,
    2007 International Symposium on Computational Models for Life Sciences (CMLS'07), AIP Conference Proceedings, vol. 952, pp. 197-206, Gold Coast, Australia, Dec. 2007 (*: corresponding author).
  5. Yuki Kato*, Hiroyuki Seki, and Tadao Kasami,
    Stochastic multiple context-free grammar for RNA pseudoknot modeling,
    Proc. the 8th International Workshop on Tree Adjoining Grammar and Related Formalisms (TAG+8), pp. 57-64, Sydney, Australia, Jul. 2006 (*: corresponding author).
  6. Yuki Kato*, Hiroyuki Seki, and Tadao Kasami,
    Subclasses of tree adjoining grammar for RNA secondary structure,
    Proc. the 7th International Workshop on Tree Adjoining Grammar and Related Formalisms (TAG+7), pp. 48-55, Vancouver, Canada, May 2004 (*: corresponding author). [Link]

Preprints

  1. Reiichi Sugihara, Yuki Kato*, Tomoya Mori, and Yukio Kawahara,
    Alignment of time-course single-cell RNA-seq data with CAPITAL,
    bioRxiv, doi: https://doi.org/10.1101/859751, Nov. 2019 (*: corresponding author). [Link]
  2. Pedro Henrique Costa Cruz, Yuki Kato, Taisuke Nakahama, Toshiharu Shibuya, and Yukio Kawahara,
    A comparative analysis among ADAR mutant mice reveals site-specific regulation of RNA editing,
    bioRxiv, doi: https://doi.org/10.1101/822916, Oct. 2019. [Link]

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