literature-search

name	literature-search
description	Comprehensive literature search with automatic summarization, trend analysis, and key paper identification from PubMed and preprints. Use this skill for literature review, trend identification, key paper discovery, and staying current with research developments. Keywords: literature, pubmed, papers, search, bibliography, review
category	Literature & Intelligence
tags	["literature","pubmed","papers","search"]
version	1.0.0
author	Drug Discovery Team
dependencies	["pubmed-e-utilities","biorxiv-api"]

Literature Search Skill

Search and analyze scientific literature for drug discovery insights.

Quick Start

/pubmed EGFR resistance
/literature-search "KRAS G12C" --year 2023-2024
Find recent papers on PROTAC technology
What are the key publications on ADC toxicity?

What's Included

Feature	Description
Smart Search	Automatic query optimization and expansion
Summarization	Key findings extraction from abstracts
Trend Analysis	Publication trends over time, hot topics
Key Papers	High-impact identification by citations
Preprints	bioRxiv/arXiv integration for early access
Related Work	Citation network exploration

Data Sources

Source	Coverage	API
PubMed	35M+ citations	E-utilities
PubMed Central	9M+ full-text	E-utilities
bioRxiv	200K+ preprints	API
medRxiv	80K+ preprints	API
arXiv	2M+ preprints	API

Output Structure

# Literature Search: EGFR Resistance

## Summary
Found **847 papers** (2020-2024). Key trends: 3rd-gen TKI resistance mechanisms,
C797S mutation targeting, combination strategies, and 4th-generation TKIs.

## Publication Trend

2020: 127 papers 2021: 156 papers ↑23% 2022: 183 papers ↑17% 2023: 198 papers ↑8% 2024 (YTD): 183 papers

**Growth Rate**: +13% CAGR
**Hot Topic Alert**: C797S mutation papers up 340% (2022-2024)

## Key Papers (Top 10)

### 1. Osimertinib resistance mechanisms (Nature Medicine, 2023)
- **Citation**: 234
- **Journal Impact Factor**: 82.9
- **Key Finding**: C797S mutation accounts for 40% of 3rd-gen resistance;
  MET amplification 35%, HER2 amplification 15%
- **Authors**: Wang et al. (Memorial Sloan Kettering)

### 2. Fourth-generation EGFR TKIs (Cancer Cell, 2024)
- **Citation**: 89
- **Key Finding**: BLU-945 shows activity against C797S in xenograft models;
  clinical data promising

[... 8 more key papers ...]

## Research Themes

### Theme 1: Resistance Mechanisms (45% of papers)
| Sub-theme | Paper Count | Growth |
|-----------|-------------|--------|
| C797S mutation | 127 | +340% |
| MET amplification | 98 | +180% |
| Phenotypic transformation | 67 | +120% |

### Theme 2: Combination Strategies (25% of papers)
| Combination | Evidence Level |
|-------------|----------------|
| EGFR + MET TKI | Phase III positive |
| EGFR + Chemotherapy | Standard of care |
| EGFR + Anti-angiogenic | Mixed results |

### Theme 3: Novel Modalities (15% of papers)
| Modality | Paper Count | Status |
|----------|-------------|--------|
| 4th-gen TKI | 43 | 5 in clinic |
| Bispecific antibodies | 28 | 3 in clinic |
| ADC approaches | 34 | Early |
| PROTAC | 19 | Preclinical |

### Theme 4: Biomarker Discovery (10% of papers)
- ctDNA monitoring
- Early detection of resistance
- Patient stratification

### Theme 5: CNS Metastases (5% of papers)
- Brain penetration strategies
- Intracranial efficacy

## Top Journals

| Journal | Papers | % | Avg IF |
|---------|--------|---|--------|
| Clinical Cancer Research | 78 | 9% | 10.2 |
| J Thorac Oncol | 67 | 8% | 20.1 |
| Nat Commun | 54 | 6% | 16.6 |
| Ann Oncol | 45 | 5% | 50.5 |

## Leading Institutions

| Institution | Papers | Key Collaborators |
|-------------|--------|-------------------|
| Memorial Sloan Kettering | 67 | Dana-Farber, Mass General |
| Dana-Farber Cancer Institute | 54 | MSK, MD Anderson |
| MD Anderson | 48 | DFCI, MSK |
| AstraZeneca | 43 | Academic partners |

## Key Clinical Trials Referenced

| Trial | Phase | Finding | Citation |
|-------|-------|---------|----------|
| FLAURA2 | III | Chemo combo superior | 234 papers |
| MARIPOSA | III | Lazertinib vs osimertinib | 156 papers |
| SAVANNAH | II | MET combo resistance | 89 papers |

## Emerging Keywords (2023-2024)
| Keyword | Frequency | Growth |
|---------|-----------|--------|
| C797S | 234 | +450% |
| Fourth-generation | 189 | +380% |
| Bispecific | 156 | +220% |
| Neoantigen | 98 | +180% |
| Liquid biopsy | 87 | +150% |

## Knowledge Gaps Identified
1. Long-term resistance beyond C797S
2. Optimal combination sequencing
3. Biomarkers for patient selection
4. Quality of life endpoints

Examples

Basic Search

/pubmed EGFR resistance
/literature KRAS inhibitors
Search for ADC toxicity papers

Time-Bounded Search

/pubmed "KRAS G12C" --year 2023-2024
/literature PROTAC --since 2022-06
Papers from last 6 months on GLP-1

Focused Search

/pubmed EGFR --focus clinical
/literature "bispecific antibodies" --focus preclinical
Search reviews only on CAR-T toxicity

Comparison Search

Compare literature on 1st vs 2nd gen EGFR TKIs
/pubmem KRAS vs NRAS vs HRAS clinical data

Trend Analysis

What are the emerging trends in ADC research?
/literature trends obesity drugs --last 5years

Search Operators

Operator	Usage	Example
AND	Combine terms	EGFR AND resistance
OR	Either term	TKI OR antibody
NOT	Exclude	EGFR NOT lung
*	Wildcard	resist*
""	Phrase	"C797S mutation"
[]	MeSH terms	EGFR[MeSH]

Running Scripts

# Basic search
python scripts/pubmed_search.py "EGFR resistance" --output results.json

# With date range
python scripts/pubmed_search.py "KRAS G12C" --start 2023-01-01 --end 2024-12-31

# Include full-text
python scripts/pubmed_search.py "PROTAC" --full-text --max 50

# Trend analysis
python scripts/pubmed_search.py "ADC toxicity" --trend --years 5

# Preprints only
python/scripts/pubmed_search.py "mRNA vaccines" --preprints

Requirements

pip install requests pandas biopython

Additional Resources

• PubMed E-utilities API
• Search Strategy Guide
• Data Extraction Scripts

Best Practices

1. Start broad, then narrow: Search broad terms first
2. Use quotes for phrases: "C797S mutation" not C797S mutation
3. Check recent first: Sort by publication date for current research
4. Review high-impact: Check citation count for key papers
5. Include preprints: For cutting-edge developments

Common Pitfalls

Pitfall	Solution
Too many results	Add specific terms, date range
Too few results	Use synonyms, expand search
Missing recent	Check preprint servers
Not specific enough	Use MeSH terms
Overlap	Remove duplicates before analysis

Output Options

Format	Description
Summary (default)	Key insights, trends, top papers
Full	All papers with abstracts
BibTeX	Citation export
CSV	Data analysis ready
Markdown	Report format