# AGENTS.md — A snapshot and pipeline for tissue-specific gene expression meta-analysis in honey bees

**Paper**: A snapshot and pipeline for tissue-specific gene expression meta-analysis in honey bees (2023)
**Area**: Entomology
**Authors**: William Cameron Jasper, Timothy A. Linksvayer, Joel Atallah, Daniel Friedman, Joanna C. Chiu, Brian R. Johnson

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## Agent Roles

### 📖 Research Agent
**Focus**: Deep analysis of A snapshot and pipeline for tissue-specific gene expression meta-analysis in honey bees
**Tasks**:
- Analyze core argument: The genetic basis of phenotypic novelty is a major unresolved question in evolutionary biology. We investigate how large-scale coding sequence change ...
- Evaluate: Shows large-scale coding sequence change underlies honey bee novel traits
- Evaluate: Provides RNA-Seq evidence for TRG enrichment in postdevelopmental novel tissues

### 🔬 Methods Agent
**Focus**: Methodological rigor and replication
**Tasks**:
- Assess and document: RNA-Seq transcriptomics
- Assess and document: Coding sequence evolutionary rate analysis
- Assess and document: Taxonomically restricted gene identification
- Assess and document: Differential gene expression analysis

### 📚 Citation Agent
**Focus**: Citation context and scholarly impact
**Tasks**:
- Track citations and impact of this entomology work
- Map connections to related works in the Friedman corpus
- Identify citing papers and downstream applications

### 🔗 Synthesis Agent
**Focus**: Cross-paper and cross-domain connections
**Tasks**:
- Connect themes: honey bees, Apis mellifera, gene expression, RNA-Seq, novel traits
- Link to related works in the docxology corpus
- Identify synergies across Active Inference, entomology, and cognitive security

### 💼 Consultant Agent
**Focus**: Practical application and knowledge transfer
**Tasks**:
- Evaluates practical applications and implementation strategies for this research
- Maps findings to industry challenges, Active Inference, and technological solutions
- Facilitates knowledge transfer to external teams and collaborators

## Extraction Log

- **Source PDF**: `2023_HoneyBeeGeneExpression.pdf`
- **PDF Status**: ✅ Available
- **Documentation Quality**: Hand-curated from direct PDF analysis

## Related Papers

See [BIBLIOGRAPHY.md](../../pages/BIBLIOGRAPHY.md) for the full publication catalog.