What is MaizeCODE?




Research Team

  • Thomas Gingeras, Principal Investigator
    Cold Spring Harbor Laboratory
  • Kenneth Birnbaum, Co-PI
    New York University
  • David Jackson, Co-PI
    Cold Spring Harbor Laboratory
  • Robert Martienssen, Co-PI
    Cold Spring Harbor Laboratory
  • W. Richard McCombie, Co-PI
    Cold Spring Harbor Laboratory
  • David Micklos, Co-PI
    Cold Spring Harbor Laboratory
  • Michael Schatz, Co-PI
    Johns Hopkins University
    & Cold Spring Harbor Laboratory
  • Doreen Ware, Co-PI
    & Cold Spring Harbor Laboratory

The MaizeCODE project aims to create a comprehensive reference encyclopedia of maize (also known as corn) and teosinte genome reference sequences and active sites. Maize is one of the most economically and agriculturally important crops in the world. The MaizeCODE data will provide an important resource for breeders and plant scientists to improve crop traits such as disease resistance, drought tolerance, and yield by providing high quality genome sequences paired with diverse molecular data. Information generated by the MaizeCODE project will be made publically available via CyVerse.

Guiding Principles

  • MaizeCODE is fundamentally a discovery-based project
  • We aim to interrogate 100% of the Maize genomes.
  • We strive to be as unbiased in our interrogation methods as possible while maintaining specificity.
  • We aim to be as transparent in our methods as possible.
  • We strive to utilize (meta)data community standards and develop where needed.
  • We strive to release quality checked data in a rapid fashion, and place no restrictions on data use.
  • We strive to be responsive to and an integral part of the plant community.

Project Deliverables

  • Metadata: A collection of experimental methods and quality control and other phenotyping results.
  • Data
    • Primary Data: FASTQs
    • Secondary Data: BAMs, bigwigs
    • Tertiary Data: Element files: vcf, GFF, GTF, BED, etc...
  • Workflows
    • Powered by CyVerse
  • Portal
    • Powered by CyVerse
  • Education and Outreach
    • DNA Learning Center
    • Workshops
    • Webinars
Maize Samples






Pipelines and Metadata

Pipelines &