# Stanford bioRxiv MCP

> Stanford bioRxiv connects your AI agent directly to the world's leading open-access preprints for biology (bioRxiv) and health sciences (medRxiv). Use this MCP to search, track revisions, and find cutting-edge research papers months before they appear in peer-reviewed journals. It lets you explore deep scientific categories like genomics, oncology, and neuroscience by date range or author institution.

## Overview
- **Category:** education
- **Price:** Free
- **Tags:** biorxiv, medrxiv, preprints, biology, health-sciences, neuroscience, genomics

## Description

Need the absolute latest science? This MCP connects your AI agent straight into bioRxiv and medRxiv—the major repositories where researchers post preprints for biology and health sciences. Instead of waiting months for journal publication, you get access to findings the day they are shared.

It’s built for anyone who needs to know what's happening at the cutting edge of research. You can filter papers by specific disciplines—think cancer immunology or developmental biology—or track how a single manuscript changes over time by checking its full revision history. Furthermore, you don't have to guess if a preprint made it into print; the MCP tracks which preprints eventually become published in peer-reviewed journals. By connecting this functionality through Vinkius, your AI client can act as an instant research librarian, pulling together complex metadata like DOI numbers and author affiliations across massive datasets of scientific findings.

## Tools

### get_preprint
Searches both bioRxiv and medRxiv. Returns title, authors, corresponding author and institution, date, version, category, abstract, and license. DOI format: "10.1101/2024.01.15.575123".

Get preprint details by DOI

### get_preprint_versions
Preprints on bioRxiv/medRxiv can be updated multiple times. This lets you see the full revision history and understand how a manuscript has evolved.

Get all versions of a preprint to track revisions

### get_published_tracking
Shows the preprint DOI, published DOI, journal name, and publication date. Essential for understanding the preprint-to-publication pipeline.

Track which preprints have been published in journals

### get_published_version
Returns the published DOI, journal citation, and publication date. Essential for finding the final, peer-reviewed version of a preprint you have read.

Find the journal-published version of a preprint

### get_recent_biorxiv
Default is 7 days. Essential for staying at the cutting edge of biological research — preprints appear here 6-12 months before peer-reviewed publication.

Get the latest bioRxiv preprints

### get_recent_medrxiv
Covers clinical medicine, epidemiology, public health, and health systems research. Critical for monitoring emerging health research before journal publication.

Get the latest medRxiv preprints

### search_biorxiv
The bioRxiv API returns preprints in batches of 100. Use the date interval format "YYYY-MM-DD/YYYY-MM-DD" (e.g. "2024-01-01/2024-01-31"). Use cursor for pagination (0, 100, 200, etc.).

Browse bioRxiv preprints by date range

### search_by_category
bioRxiv categories include: neuroscience, genomics, bioinformatics, cell_biology, cancer_biology, immunology, microbiology, molecular_biology, biochemistry, genetics, developmental_biology, evolutionary_biology, ecology, plant_biology, physiology, pharmacology, systems_biology, biophysics, synthetic_biology. medRxiv categories: epidemiology, infectious_diseases, public_and_global_health, health_systems, cardiovascular_medicine, oncology, psychiatry, neurology.

Filter preprints by subject category

### search_by_institution
Use this to explore what institutions are producing preprints in a given time period. Each preprint includes the corresponding author and their institutional affiliation.

Browse preprints with author institution metadata

### search_cancer
Covers tumor biology, oncogenomics, cancer immunology, drug resistance, and experimental therapeutics.

Browse cancer biology preprints

### search_cell_biology
Covers cell signaling, organelle biology, cytoskeleton, cell division, stem cells, and cellular mechanisms of disease.

Browse cell biology preprints

### search_epidemiology
Covers disease surveillance, outbreak analysis, population health, health policy, and clinical epidemiology. Critical for public health monitoring.

Browse epidemiology and public health preprints

### search_genomics
Covers genome sequencing, gene regulation, epigenomics, metagenomics, and computational genomics — core disciplines in modern biology.

Browse genomics and bioinformatics preprints

### search_immunology
Covers immune system research, host-pathogen interactions, vaccine development, autoimmune diseases, and immunotherapy.

Browse immunology and microbiology preprints

### search_medrxiv
medRxiv covers clinical research, epidemiology, public health, and health policy. Use interval "YYYY-MM-DD/YYYY-MM-DD" format. Results paginated in batches of 100.

Browse medRxiv preprints by date range

### search_neuroscience
Neuroscience is one of the largest and most active categories, covering brain research, neural circuits, cognitive science, and neurological disorders.

Browse neuroscience preprints

## Prompt Examples

**Prompt:** 
```
Show me the latest neuroscience preprints
```

**Response:** 
```
I've retrieved the latest neuroscience preprints from bioRxiv. Recent submissions cover topics including neural circuits, brain imaging, cognitive neuroscience, and neurological disorders.
```

**Prompt:** 
```
Has preprint 10.1101/2024.01.15.575123 been published in a journal?
```

**Response:** 
```
I've checked the publication tracking for this preprint. If published, I'll show the journal DOI, citation, and publication date.
```

**Prompt:** 
```
Find the latest genomics preprints from this week
```

**Response:** 
```
I've retrieved this week's genomics preprints from bioRxiv, including recent work on single-cell sequencing, CRISPR screens, and population genetics.
```

## Capabilities

### Retrieve full paper details by DOI
Find a preprint's title, authors, abstract, and institutional affiliation using its unique Digital Object Identifier.

### Monitor manuscript revision history
Trace the evolution of an idea by retrieving every version a preprint has gone through over time.

### Track publication status
Determine if a specific preprint has been accepted and published in a formal, peer-reviewed journal.

### Browse the latest submissions
Get immediate access to the most recent papers submitted across both bioRxiv and medRxiv categories.

### Filter by scientific discipline
Narrow down results instantly using specialized subject feeds, such as genomics, epidemiology, or cell biology.

## Use Cases

### Monitoring an emerging viral outbreak
A public health researcher uses the MCP with `search_epidemiology` and `get_recent_medrxiv`. They monitor for new papers on transmission vectors, allowing them to advise policy makers before any journal publication occurs.

### Reviewing novel cancer targets
A PhD student needs the latest data. Using `search_cancer` and filtering by date range via `search_biorxiv`, they pull 50 relevant preprints, saving weeks of manual database trawling.

### Verifying scientific claims
A journalist reads a promising preprint. They immediately run `get_published_tracking` on the DOI to verify if it has been submitted or accepted by a peer-reviewed journal, adding credibility to their story.

### Comparing research approaches
A lab director wants to see who's working in his field. They use `search_by_institution` to map out which universities are currently publishing the most active preprints in molecular biology.

## Benefits

- You stop waiting for journal publishing cycles. With the `get_recent_biorxiv` and `get_recent_medrxiv` tools, you get immediate access to research findings the day they're shared.
- You don't have to piece together fragmented data points. Use `search_by_category` or `search_genomics` to instantly filter thousands of papers by a precise discipline like 'cell biology'.
- You always know if that groundbreaking paper you read is final. The MCP’s publication tracking tools let you check both the initial preprint status and use `get_published_version` to find the peer-reviewed source.
- Tracking research evolution becomes simple. Instead of guessing how a concept changed, `get_preprint_versions` shows every revision history for maximum data integrity.
- You can narrow massive datasets down by origin. Use `search_by_institution` to see what specific organizations are publishing the most cutting-edge work in a given timeframe.

## How It Works

The bottom line is you skip the manual searching through multiple websites and just ask your agent to pull the data for you.

1. Tell your agent what you need to research—for example, 'Find the latest preprints on cancer immunology from last month.'
2. The MCP executes targeted searches across bioRxiv and medRxiv using the specified filters (date range, category, etc.).
3. You get back a structured list of results containing abstracts, author details, version history, and publication tracking metadata.

## Frequently Asked Questions

**How do I find the most recent preprints using Stanford bioRxiv MCP?**
You can use `get_recent_biorxiv` for general biological updates, or if you're focused on health, run `get_recent_medrxiv`. These tools pull the absolute latest submissions across their respective platforms.

**Can I check if a preprint was published using Stanford bioRxiv MCP?**
Yes, use `get_published_tracking` with the DOI. This tool tells you if the work has been accepted into a peer-reviewed journal and provides citation details.

**What is the best way to search for cancer research preprints?**
Use the dedicated `search_cancer` tool. This focuses your search specifically on tumor biology, oncogenomics, and related areas within both bioRxiv and medRxiv.

**How do I see if a preprint was updated?**
You must run `get_preprint_versions` on the DOI. This function provides the full revision history, letting you track how authors changed their data or conclusions over time.

**Which tool should I use to find papers from a specific date range?**
For biology, run `search_biorxiv` using the 'YYYY-MM-DD/YYYY-MM-DD' interval. For health sciences, use `search_medrxiv` with the same date format.