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

Work Experience:
April 2016 — present: Assistant Professor at Graduate School of Medicine, Osaka University, Osaka, Japan
July 2014 — present: Part-Time Lecturer at Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
May 2014 — March 2016: Assistant Professor at Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
September 2012 — March 2013: Visiting Researcher at Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
October 2010 — April 2014: Assistant Professor at Graduate School of Information Science, Nara Institute of Science and Technology, Nara, Japan
April 2008 — September 2010: Postdoctoral Researcher at Institute for Chemical Research, Kyoto University, Kyoto, Japan
April 2007 — March 2008: Research Fellow (PD) of Japan Society for the Promotion of Science, Kyoto, Japan
April 2005 — March 2007: Research Fellow (DC1) of Japan Society for the Promotion of Science, Nara, Japan
April 2002 — March 2003: Research Assistant at Faculty of Engineering, Doshisha University, Kyoto, Japan

Education:
March 2007: Graduate School of Information Science, Nara Institute of Science and Technology, Nara, Japan, Received Doctor of Engineering, Major in Bioinformatics
March 2005: Graduate School of Information Science, Nara Institute of Science and Technology, Nara, Japan, Received Master of Engineering, Major in Computer Science
March 2002: Faculty of Engineering, Doshisha University, Kyoto, Japan, Received Bachelor of Engineering, Major in Applied Mathematics

Academic Activities

Membership

Program Committees and Others

Awards

  1. 2011 IPSJ Yamashita SIG Research Award (March 2012)
  2. 2009 Oxford Journals - Japanese Society for Bioinformatics Prize (GIW2009 Best Poster Award) (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 using computational methods:

Grants

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

Journal Papers

  1. 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]
  2. 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]
  3. 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.)
  4. 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]
  5. 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]
  6. 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 authors). [Link] [PubMed]
  7. 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 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.)
  8. 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 authors). [Link] [PubMed]
    (This paper is also presented at the 9th European Conference on Computational Biology (ECCB2010), Ghent, Belgium, Sep. 2010.)
  9. 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]
  10. 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]
  11. 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]
  12. 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.)
  13. 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.
  14. 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]
  15. 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.



Lecture

Information on lecture is available, mostly in Japanese.

Link

International Conferences on Computational Biology

Databases and Software for Computational Biology


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