Protocol for applying a network-enabled gene discovery pipeline to non-model plant species
Dae Kwan Ko, Federica Brandizzi · 2026
Read Protocol for applying a network-enabled gene discovery pipeline to non-model plant species by Dae Kwan Ko, Federica Brandizzi (2026) in the Tower of Babel, a free online library of public-domain works preserved in clean, searchable text. No sign-up. The full text is served as a plain-text file at a predictable URL, where text is present: https://antarctic-labs.com/tower-of-babel/PMC13312126.txt.
Description
Dae Kwan Ko and Federica Brandizzi present a 2026 protocol for running the NEEDLE gene discovery pipeline in plant species that lack a model organism's resources. Finding the transcription factors that switch key genes on or off is central to understanding gene regulation, yet non-model plants have few ready tools for the job.
The protocol covers setting up the computing environment, preparing data, running the analysis, and reading the outputs. NEEDLE chains together RNA sequencing processing, co-expression network analysis, a tree-based network inference method, and promoter conservation checks to rank candidate regulators. The walkthrough uses sorghum stem development, with 11 samples, as its example. The authors note that six or more meaningful samples generally give stable networks, and that the pipeline transfers to other species with suitable data.
Catalog record
| CREATOR | Dae Kwan Ko, Federica Brandizzi |
|---|---|
| YEAR | 2026 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 169543 |
| LICENSE | https://creativecommons.org/licenses/by/4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |