literature-search-copy

Metadata

Status	done
Assigned	`agent-82`
Agent identity	`3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3`
Created	2026-04-01T14:49:16.690540704+00:00
Started	2026-04-01T14:50:33.031088713+00:00
Completed	2026-04-01T14:53:57.204373196+00:00
Tags	`eval-scheduled`
Eval score	0.84
└ blocking impact	0.87
└ completeness	0.88
└ coordination overhead	0.88
└ correctness	0.82
└ downstream usability	0.82
└ efficiency	0.80
└ intent fidelity	0.86
└ style adherence	0.87

Description

Goal

Search for precedent in literature for copy-number-aware enrichment analysis, particularly in subtelomeric and repetitive genomic regions.

Search Strategy

PubMed/Google Scholar search terms: copy number enrichment, multi-copy genes, subtelomeric enrichment, repeat-aware enrichment
Focus on subtelomeric biology, tandem repeats, gene family analysis
Look for statistical methods that handle gene copy number in enrichment

Output

Relevant papers with copy-number-aware enrichment approaches
Statistical methods used in similar contexts
Best practices from subtelomeric/repeat biology field
Citations for methodology validation
Gaps in current approaches that our work could fill

Validation

At least 5 relevant papers identified
Statistical methods documented with citations
Precedent for each proposed approach assessed

## Goal
Search for precedent in literature for copy-number-aware enrichment analysis, particularly in subtelomeric and repetitive genomic regions.

## Search Strategy  
- PubMed/Google Scholar search terms: copy number enrichment, multi-copy genes, subtelomeric enrichment, repeat-aware enrichment
- Focus on subtelomeric biology, tandem repeats, gene family analysis
- Look for statistical methods that handle gene copy number in enrichment

## Output
- Relevant papers with copy-number-aware enrichment approaches
- Statistical methods used in similar contexts
- Best practices from subtelomeric/repeat biology field
- Citations for methodology validation
- Gaps in current approaches that our work could fill

## Validation
- At least 5 relevant papers identified
- Statistical methods documented with citations
- Precedent for each proposed approach assessed

Depends on

Required by

done synthesize-findings-and

Log

2026-04-01T14:50:33.031090537+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
2026-04-01T14:50:46.805661766+00:00 Starting literature search for copy-number-aware enrichment analysis precedents
2026-04-01T14:52:00.681481389+00:00 Completed initial web searches - found key papers on copy number enrichment, subtelomeric analysis, and GAT tool
2026-04-01T14:52:17.241646479+00:00 Compiling comprehensive literature review covering all required areas
2026-04-01T14:53:47.128713326+00:00 Validation complete: ✓ >15 relevant papers identified ✓ Statistical methods documented with citations ✓ Precedents assessed for all approaches ✓ Gaps and opportunities identified
2026-04-01T14:53:57.204376201+00:00 Task marked as done