Yuki Naito

Summary

Country: Japan

Publications

  1. pmc siVirus: web-based antiviral siRNA design software for highly divergent viral sequences
    Yuki Naito
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Tokyo 113 0033, Japan
    Nucleic Acids Res 34:W448-50. 2006
  2. pmc dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference
    Yuki Naito
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Nucleic Acids Res 33:W589-91. 2005
  3. pmc Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect
    Kumiko Ui-Tei
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo, Japan
    Nucleic Acids Res 36:2136-51. 2008
  4. ncbi request reprint [Designing functional siRNA sequences]
    Tomoyuki Yamada
    Graduate School of Frontier Sciences, University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa, Chiba 277 8562, Japan
    Seikagaku 77:1519-25. 2005
  5. pmc Optimal design and validation of antiviral siRNA for targeting HIV-1
    Yuki Naito
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo, 113 0033, Japan
    Retrovirology 4:80. 2007
  6. ncbi request reprint Guidelines for the selection of effective short-interfering RNA sequences for functional genomics
    Kumiko Ui-Tei
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan
    Methods Mol Biol 361:201-16. 2007
  7. pmc Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect
    Kumiko Ui-Tei
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan
    Nucleic Acids Res 36:7100-9. 2008
  8. pmc siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference
    Yuki Naito
    Department of Biophysics and Biochemistry, Graduate School of Science, School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Nucleic Acids Res 32:W124-9. 2004
  9. doi request reprint Designing functional siRNA with reduced off-target effects
    Yuki Naito
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan
    Methods Mol Biol 942:57-68. 2013
  10. pmc siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect
    Yuki Naito
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan
    BMC Bioinformatics 10:392. 2009

Collaborators

Detail Information

Publications14

  1. pmc siVirus: web-based antiviral siRNA design software for highly divergent viral sequences
    Yuki Naito
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Tokyo 113 0033, Japan
    Nucleic Acids Res 34:W448-50. 2006
    ....
  2. pmc dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference
    Yuki Naito
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Nucleic Acids Res 33:W589-91. 2005
    ....
  3. pmc Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect
    Kumiko Ui-Tei
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo, Japan
    Nucleic Acids Res 36:2136-51. 2008
    ..Thus, it may be possible to design DNA-RNA chimeras which effectively silence mammalian target genes without silencing unintended genes...
  4. ncbi request reprint [Designing functional siRNA sequences]
    Tomoyuki Yamada
    Graduate School of Frontier Sciences, University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa, Chiba 277 8562, Japan
    Seikagaku 77:1519-25. 2005
  5. pmc Optimal design and validation of antiviral siRNA for targeting HIV-1
    Yuki Naito
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo, 113 0033, Japan
    Retrovirology 4:80. 2007
    ..We present several promising antiviral siRNA candidates that effectively inhibited multiple subtypes of HIV-1 by targeting the best conserved regions in pandemic HIV-1 group M strains...
  6. ncbi request reprint Guidelines for the selection of effective short-interfering RNA sequences for functional genomics
    Kumiko Ui-Tei
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan
    Methods Mol Biol 361:201-16. 2007
    ....
  7. pmc Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect
    Kumiko Ui-Tei
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan
    Nucleic Acids Res 36:7100-9. 2008
    ..The off-target effect was more sensitive to siRNA concentration compared to intended gene silencing, which requires a near perfect sequence match between the siRNA guide strand and target mRNA...
  8. pmc siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference
    Yuki Naito
    Department of Biophysics and Biochemistry, Graduate School of Science, School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Nucleic Acids Res 32:W124-9. 2004
    ..The website accepts an arbitrary sequence as input and quickly returns siRNA candidates, providing a wide scope of applications in mammalian RNAi, including systematic functional genomics and therapeutic gene silencing...
  9. doi request reprint Designing functional siRNA with reduced off-target effects
    Yuki Naito
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan
    Methods Mol Biol 942:57-68. 2013
    ..0 Web server (http://siDirect2.RNAi.jp/). By using the default parameters, siDirect 2.0 can design at least one qualified siRNA for >94% of human mRNA sequences in the RefSeq database...
  10. pmc siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect
    Yuki Naito
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan
    BMC Bioinformatics 10:392. 2009
    ..Thus, an efficient algorithm for designing functional siRNAs with minimal off-target effect based on the mechanistic features is considered of value...
  11. pmc E-cadherin is transcriptionally activated via suppression of ZEB1 transcriptional repressor by small RNA-mediated gene silencing
    Minami Mazda
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan
    PLoS ONE 6:e28688. 2011
    ..Thus, E-cadherin could be upregulated by the suppression of ZEB1 transcriptional repressor by miRNAs in vivo...
  12. pmc Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference
    Kumiko Ui-Tei
    Department of Biophysics and Biochemistry, Graduate School of Science, School of Science, University of Tokyo, Japan
    Nucleic Acids Res 32:936-48. 2004
    ..In contrast to mammalian and chick cells, little siRNA sequence preference could be detected in Drosophila in vivo RNAi...
  13. pmc siRNA Design Software for a Target Gene-Specific RNA Interference
    Yuki Naito
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo Tokyo, Japan
    Front Genet 3:102. 2012
    ..Here we present our siRNA design software for a target-specific RNAi. In addition, we also introduce the software programs open to the public for designing functional siRNAs...
  14. doi request reprint Introduction of silencing-inducing transgene against Fgf19 does not affect expression of Tbx5 and beta3-tubulin in the developing chicken retina
    Mayumi Okamoto
    Department of Life Systems, Institute of Technology and Science, The University of Tokushima, 2 1 Minami Josanjima cho, Tokushima City 770 8506, Japan
    Dev Growth Differ 50:159-68. 2008
    ..Thus, knockdown of Fgf19 supports no obvious regulations between Fgf19 and Tbx5, or exhibits no phenotypes that perturb early retinal differentiation...