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References

This section provides links to external publications relevant to our research field and the datasets used in our analysis.

Website Icon Publications

Key papers and articles related to rice genomics, machine learning in agriculture, and bioinformatics methods that inform our work.

Rice Genome / Genomics

  • The 3,000 rice genomes project, The 3,000 rice genomes project, GigaScience, Volume 3, Issue 1, December 2014, 2047–217X–3–7 [Link to Paper]
  • [Author(s)]. ([Year]). [Paper Title]. [Journal Name], [Volume](Issue), [Pages]. [Link to Paper]

Machine Learning / Computer Science

  • Dominic, N., Cenggoro, T.W., Budiarto, A. et al. Deep polygenic neural network for predicting and identifying yield-associated genes in Indonesian rice accessions. Sci Rep 12, 13823 (2022). [Link to Paper]
  • MacNish, T.R., Danilevicz, M.F., Bayer, P.E. et al. Application of machine learning and genomics for orphan crop improvement. Nat Commun, 16, 982 (2025). [Link to Paper]
  • [Author(s)]. ([Year]). [Paper Title]. [Journal/Conference Name], [Volume](Issue), [Pages]. [Link to Paper/Source]

Website Icon Web Links for Datasets

Links to the primary data sources utilized in this research project.

  • 3000 Rice Genomes Project (3K RGP): Sequence data available via the GigaScience GigaDB repository and SNP-Seek database. [SNP-Seek Link] [GigaDB Link]
  • 3KRG Browser: 253 TB data hosted by AWS [42basepairs Link] [AWS Link]
  • Data repository for the 3K RGP and OryzaSNP Project: hosted by IRRI. [Bulk Download Page]
  • Whole Genome Sequence Data of 3KRG: [European Nucleotide Archive]
  • [Dataset Name]: [Brief Description]. [Link to Dataset]