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Yuki KATOPh.D.
Assistant Professor
Department of RNA Biology and Neuroscience, Graduate School of Medicine,
2-2 Yamada-oka, Suita, Osaka 565-0871, Japan
email: @rna.med.osaka-u.ac.jp
(Please click the above "y..." to me.)

Academic Activities

Membership

Program Committees and Others

  • A Vice-Chair of IPSJ Transactions on Bioinformatics (TBIO) (April 2019—)
  • (Program Committee)
  • The Editorial Committee of IPSJ JIP (Computing Group) (June 2019—May 2018)
  • The Management Committee of IPSJ SIGBIO (April 2015—March 2019)
  • The Editorial Committee of IPSJ Transactions on Bioinformatics (TBIO) (April 2015—March 2019)
  • (Program Committee)
  • The Tenth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB2013) and the Eighth IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB2013) (Program Committee)
  • (Review Editor)
  • (Program Committee)
  • (Program Committee)
  • 2009 IEEE Congress on Evolutionary Computation (CEC2009) (Special Session on Evolutionary Computation in Bioinformatics and Computational Biology) (Program Committee)

Awards

  1. 2011 IPSJ Yamashita SIG Research Award (March 2012)
  2. (December 2009)
  3. 2006 SIGBIO Best Paper Award (December 2008)
  4. 2007 IPSJ Best Paper Award (May 2008)
  5. 2006 IPSJ Digital Courier Funai Young Researcher Encouragement Award (March 2007)

Research

Bioinformatics (Computational Biology)
Particularly, the following topics have been studied:

Grants

  1. Grant-in-Aid for Scientific Research (C) (KAKENHI), Representative, #18K11526, April 2018—March 2021.
  2. Grant-in-Aid for Scientific Research (C) (KAKENHI), Representative, #15K00401, April 2015—March 2018.
  3. Grant-in-Aid for Young Scientists (B) (KAKENHI), Representative, #24700296, April 2012—March 2015.
  4. Grant-in-Aid for Young Scientists (B) (KAKENHI), Representative, #22700313, April 2010—March 2012.
  5. Grant-in-Aid for Young Scientists (Start-up) (KAKENHI), Representative, #20800023, April 2008—March 2010.
  6. Grant-in-Aid for JSPS Fellows (KAKENHI), Representative, #172830, April 2005—March 2008.

Journal Papers

10 papers as a first author, 13 papers as a corresponding author.

  1. 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, e46303, Dec. 2018.
  2. 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.
  3. 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).
  4. 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).
  5. 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. 2019.
  6. 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).
    (This paper is also presented at the 13th International Conference on Bioinformatics (InCoB2014), Sydney, Australia, Aug. 2014.)
  7. 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.
  8. 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).
  9. 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).
  10. 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).
    (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.)
  11. 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).
    (This paper is also presented at the 9th European Conference on Computational Biology (ECCB2010), Ghent, Belgium, Sep. 2010.)
  12. 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).
  13. 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).
  14. 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).
  15. 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).
    (This paper is also published in Proc. the Seventh Asia Pacific Bioinformatics Conference (APBC2009), pp. 439-448, Beijing, China, Jan. 2009.)
  16. 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.
  17. 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).
  18. 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).

Software

Several web servers and programs for solving problems in bioinformatics are available for non-commercial use.



Web Servers

  • (Updated on 2014-03-10)
  • (Updated on 2010-05-27)

Standalone Programs

  • (Updated on 2019-06-23)
  • (Released on 2017-11-16)
  • (Released on 2019-09-18)
  • (Updated on 2014-08-22)
  • (Updated on 2013-07-10)
  • (Updated on 2012-04-05)
  • (Released on 2012-01-19)

Lecture

Information on lecture is available, mostly in Japanese.

Link

International Conferences on Computational Biology

  • , Prague, Czech Republic, July 21-25, 2017
  • , Kyoto, Japan, June 28-July 2, 2019
  • , Tokyo, Japan, September 9-11, 2015
  • , Benasque, Spain, July 19-31, 2015
  • , HsinChu, Taiwan, January 21-23, 2015
  • , Tokyo, Japan, December 15-17, 2014
  • , Sydney, Australia, July 31-August 2, 2014
  • , Doubice, Czech Republic, October 2-7, 2012
  • , Vienna, Austria, July 15-19, 2011
  • , Orlando, Florida, USA, February 3-5, 2011
  • , Ghent, Belgium, September 26-29, 2010
  • , The Big Island of Hawaii, January 4-8, 2010
  • , Tuusula, Finland, June 17-18, 2006

Databases and Software for Computational Biology


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