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Scientific References

Curated list of key publications, datasets, and technical resources for precision medicine bioinformatics.

Core Publications

Model Context Protocol & AI Orchestration

BioinfoMCP: Bioinformatics Workflows with Model Context Protocol

  • Citation: arXiv:2510.02139v1 (2025)
  • Link: https://arxiv.org/html/2510.02139v1
  • Summary: Pioneering work demonstrating how MCP can orchestrate complex bioinformatics workflows using natural language. Foundation for this repository's architecture.
  • Key Contributions: Server design patterns, workflow orchestration, integration strategies

Spatial Transcriptomics

Spatial Transcriptomics: Technologies, Applications, and Experimental Considerations

  • Citation: Nucleic Acids Research, Volume 53, Issue 12 (2025)
  • Link: https://academic.oup.com/nar/article/53/12/gkaf536/8174767
  • Summary: Comprehensive review of spatial transcriptomics technologies including Visium, MERFISH, and seqFISH+
  • Relevance: Technical foundation for mcp-spatialtools implementation

STAR: Ultrafast Universal RNA-seq Aligner

  • Citation: Dobin et al., Bioinformatics (2013)
  • DOI: 10.1093/bioinformatics/bts635
  • Summary: Spliced alignment algorithm for RNA-seq data
  • Implementation: Used in mcp-spatialtools.align_spatial_data()

Batch Effect Correction

ComBat: Adjusting Batch Effects in Microarray Expression Data

  • Citation: Johnson et al., Biostatistics (2007)
  • DOI: 10.1093/biostatistics/kxj037
  • Summary: Empirical Bayes method for removing batch effects while preserving biological variation
  • Implementation: Used in mcp-spatialtools.perform_batch_correction()

Multi-Omics Integration

HAllA: Hierarchical All-against-All Association Discovery

  • Citation: Rahnavard et al., PLOS Computational Biology (2017)
  • DOI: 10.1371/journal.pcbi.1005308
  • Summary: Method for discovering associations between high-dimensional datasets
  • Implementation: Core algorithm in mcp-multiomics (95% real)

Meta-Analysis with Stouffer's Method

  • Citation: Stouffer et al., "The American Soldier" (1949)
  • Summary: Combines p-values from independent tests using Z-score transformation
  • Implementation: Used in mcp-multiomics.calculate_stouffer_meta()

Public Datasets

Cancer Genomics

The Cancer Genome Atlas (TCGA) - Ovarian Cancer

  • Project: TCGA-OV
  • Link: https://portal.gdc.cancer.gov/projects/TCGA-OV
  • Data Types: WXS, RNA-seq, SNP arrays, clinical data
  • Sample Size: 600+ High-Grade Serous Ovarian Carcinoma samples
  • Relevance: Reference cohort for mcp-mocktcga server, pathway curation

TCGA Publications:

  • Integrated genomic analyses of ovarian carcinoma (Nature, 2011)
  • DOI: 10.1038/nature10166

Spatial Transcriptomics Datasets

10x Genomics Public Datasets

  • Link: https://www.10xgenomics.com/datasets
  • Platforms: Visium, Xenium, Chromium
  • Data Types: Spatial gene expression, histology images, spatial coordinates
  • Use Cases: Validation data for mcp-spatialtools, educational examples

Visium Spatial Gene Expression

  • Human breast cancer datasets
  • Mouse brain tissue datasets
  • Human ovarian cancer (if available)

Pathway & Annotation Databases

KEGG (Kyoto Encyclopedia of Genes and Genomes)

  • Link: https://www.genome.jp/kegg/
  • Pathways Used: PI3K-Akt signaling, p53 signaling, cell cycle, apoptosis
  • Implementation: 44 curated pathways in mcp-spatialtools pathway enrichment

Gene Ontology (GO)

  • Link: http://geneontology.org/
  • Categories Used: Biological Process (GO_BP), Molecular Function, Cellular Component
  • Implementation: Pathway enrichment in mcp-spatialtools

MSigDB (Molecular Signatures Database)

Genome References

GENCODE Human Genome Annotation

  • Link: https://www.gencodegenes.org/
  • Version Used: GRCh38.p14 (hg38)
  • Components: Gene annotations, transcript models, regulatory elements
  • Implementation: STAR genome index preparation, gene ID mapping

Ensembl Genome Browser

Statistical Methods

Multiple Testing Correction

Benjamini-Hochberg FDR Control

  • Citation: Benjamini & Hochberg, Journal of the Royal Statistical Society (1995)
  • DOI: 10.1111/j.2517-6161.1995.tb02031.x
  • Implementation: FDR correction in pathway enrichment, differential expression

Spatial Statistics

Moran's I Spatial Autocorrelation

  • Citation: Moran, Biometrika (1950)
  • DOI: 10.2307/2332142
  • Summary: Measures spatial autocorrelation (clustering vs random distribution)
  • Implementation: mcp-spatialtools.calculate_spatial_autocorrelation()

Non-Parametric Tests

Mann-Whitney U Test

  • Citation: Mann & Whitney, Annals of Mathematical Statistics (1947)
  • Summary: Non-parametric test for comparing two independent groups
  • Implementation: Differential expression in mcp-spatialtools

Fisher's Exact Test

  • Citation: Fisher, Journal of the Royal Statistical Society (1922)
  • Summary: Test for independence in 2×2 contingency tables
  • Implementation: Pathway enrichment (gene overlap significance)

Technical Specifications

FHIR (Fast Healthcare Interoperability Resources)

  • Link: https://hl7.org/fhir/
  • Version: R4
  • Resources Used: Patient, Condition, Observation, MedicationStatement
  • Implementation: mcp-mockepic server structure

Model Context Protocol

Clinical Resources (For Context Only)

ClinicalTrials.gov - Ovarian Cancer

  • Link: https://clinicaltrials.gov/
  • Search: "ovarian cancer" + "precision medicine"
  • Note: For educational reference only - not clinical recommendations

National Cancer Institute (NCI) - Ovarian Cancer

How to Cite

If you use any of these references in your research with this repository, please cite both the original publication and this repository:

@software{langit2026precision,
  author = {Langit, Lynn},
  title = {Precision Medicine MCP Servers: AI-Orchestrated Clinical Bioinformatics},
  year = {2026},
  url = {https://github.com/lynnlangit/precision-medicine-mcp},
  note = {PatientOne - In memory of a dear friend}
}

Last Updated: January 31, 2026
Maintained by: Lynn Langit
Contributions: Pull requests welcome to add relevant publications