The question
Which undercharacterized genes should be prioritized for experiments on oxygen-tolerant nitrogen fixation?
Context
Nitrogenase is oxygen-sensitive, yet some cyanobacteria coordinate oxygenic photosynthesis with nitrogen fixation. The search space includes many genes with incomplete functional annotation and only a limited set of experimentally established examples.
Why the problem was difficult
- The positive reference set is small relative to the genomic search space.
- Relevant evidence is distributed across expression, protein abundance, conservation, promoter architecture, and genomic context.
- The result had to support experimental prioritization rather than stop at a model score.
Approach
- Defined the biological question and assembled literature-supported reference genes.
- Integrated nitrogen step-down transcriptomics, quantitative proteomics, promoter features, genomic context, and comparative conservation.
- Compared interpretable and nonlinear models, then examined the evidence behind high-priority candidates.
- Structured outputs as a ranked, reviewable set of hypotheses for downstream validation planning.
Outcome or resulting capability
The work produced a published, reproducible framework for prioritizing FOX gene candidates and distinguishing model evidence from experimental validation.
James' role
James led data curation, machine-learning methodology, software development, formal analysis, and the initial manuscript draft, and contributed to visualization and biological interpretation.