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Citation

When using the data obtained from the RAP-DB, kindly acknowledge the RAP project contribution
by citing the following papers:

  • Rice Annotation Project Database (RAP-DB): An integrative and interactive database for rice genomics
    Sakai, H., Lee, SS., et al., Plant & Cell Physiol., 54(2):e6 (2013)
    [PubMed] [PCP]
  • Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data
    Kawahara, Y., Bastide, M., et al., Rice, 6:4 (2013)
    [PubMed] [RICE]

Related research papers and book chapters

  • The Rice Annotation Project Database (RAP-DB): 2008 update
    Rice Annotation Project, Nucleic Acids Res., 36(Database issue), D1028-33 (2008).
    [PubMed] [NAR]
  • Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana
    Itoh, T., Tanaka, T. et al., Genome Res., 17, 175-83 (2007).
    [PubMed] [Genome Res]
  • Bioinformatics and Database of the Rice Genome
    Numa, H., Tanaka, T. and Itoh, T. in Rice Biology in the Genomics Era. (Hirano, H.-Y. et al. Ed.) Springer-Verlag, Berlin Heidelberg, pp.13-21 (2008)
    [Springer]
  • Rice Genome Annotation: Beginnings of Functional Genomics
    Itoh, T. in Rice Functional Genomics: Challenges, Progress and Prospects (Narayana M. Upadhyaya, Ed.) Springer, New York, pp. 21-30 (2007).
    [Springer]
  • Birth and death of genes promoted by transposable elements in Oryza sativa
    Sakai, H., Tanaka, T. and Itoh, T., Gene., 392, 59-63 (2007).
    [PubMed] [Gene]
  • Rate and polarity of genes fusion and fission in Oryza sativa
    Nakamura, Y., Itoh, T. and Martin W., Mol. Biol. Evol., 24, 110-121 (2006).
    [PubMed] [MBE]
  • The rice annotation project database (RAP-DB): hub for Oryza sativa ssp. japonica genome information
    Ohyanagi, H., Tanaka, T., Sakai, H., Shigemoto, Y., Yamaguchi, K., Habara, T., Fujii, Y., Antonio, BA., Nagamura, Y., Imanishi, T., Ikeo, K., Itoh, T., Gojobori, T. and Sasaki, T., Nucleic Acids Res., 34(Database issue), D741-4 (2006).
    [PubMed] [NAR]
  • The map-based sequence of the rice genome
    International Rice Genome Sequencing Project, Nature, 436, 793-800 (2005).
    [PubMed] [Nature]

Presentations

  • Rice Annotation Project Database (RAP-DB) Update 2025 - How We Maintain Up-to-Date Functional Information on Rice Genes
    Kawahara, Y., et al., Plant and Animal Genome Conference (PAG) 32, January 10-15, 2025
    [PDF]
  • Rice Annotation Project Database (RAP-DB) Update 2024
    Kawahara, Y., et al., Plant and Animal Genome Conference (PAG) 31, January 12-17, 2024
    [PDF]
  • Literature-based curation of gene annotation, genomic variations, and transcriptomics information in RAP-DB
    Kawahara, Y., et al., The 63rd Annual Meeting of JSPP, The 18th Database Workshop, March 24, 2022, Online
    [PDF]
  • The Rice Reference Genome Revisited: Extensive Update by the PacBio Smrt Sequencing Technology
    Itoh, T., et al., Taiwan-Japan Plant Biology 2017, November 3-6, 2017, Taipei, Taiwan
    [PDF]
  • イネのオミックス情報基盤の構築
    Kawahara, Y., et al., SAT Technology Showcase 2017, January 31, 2017, Tsukuba, Japan
    [PDF (in Japanese)]
  • RAP-DB: The Rice Annotation Project Database & TENOR: Database for Comprehensive mRNA-Seq Experiments in Rice
    Kawahara, Y., et al., The 130th Meeting of the Japanese Society of Breeding, September 24-25, 2016, Tottori, Japan
    [PDF (in Japanese)]
  • TENOR: Database for Comprehensive mRNA-Seq Experiments in Rice
    Kawahara, Y., et al., The 57th Annual Meeting of the Japanese Society of Plant Physiologists, March 18-20, 2016, Morioka, Japan
    [PDF]
  • TENOR: Database for Comprehensive mRNA-Seq Experiments in Rice
    Kawahara, Y., et al., Plant and Animal Genome Conference (PAG XXIV), January 9-13, 2016, San Diego, CA, USA
    [PDF (Computer Demo)] [PDF (poster)]