---

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

Copy/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

Data Sources

Output Structure

Copy# 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

Copy**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

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

Time-Bounded Search

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

Focused Search

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

Comparison Search

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

Trend Analysis

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

Search Operators

Running Scripts

Copy# 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

Copypip 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

Output Options