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raonyguimaraes/README.md

Raony Guimarães

Senior Bioinformatician at M42 · Emirati Genome Programme · Abu Dhabi

I build the bioinformatics that turns a nation's genomes into clinical answers: population-scale whole-genome sequencing, Nextflow pipelines on Kubernetes, rare-disease and population genomics.

PhD in Bioinformatics (UFMG, Brazil). Previously in Dublin, Belo Horizonte, Ribeirão Preto and the Netherlands.

Projects

Project What it is
Mendel,MD Open-source web tool for annotating, filtering and diagnosing exomes and genomes from patients with Mendelian disorders. Live at mendelmd.org.
Pynnotator VEP-centric VCF annotation framework for exomes and genomes.
bioinformatics-mcp MCP server with 62 tools connecting AI agents to scanpy, Biopython, squidpy, NCBI, UniProt, Ensembl and PubMed.
vus-meta-predictor Missense pathogenicity prediction combining ESM-2 embeddings, physicochemistry and gene constraint.
fast-ngs-admix Nextflow pipeline for ancestry and admixture estimation from 23andMe files.

Selected publications

  • The Emirati Genome Program Enables Population-wide Penetrance Estimation and Novel Discovery for Inherited Retinal Disease. medRxiv, 2025.
  • Mendel,MD: A user-friendly open-source web tool for analyzing WES and WGS in the diagnosis of patients with Mendelian disorders. PLOS Computational Biology, 2017.
  • Mendel,MD: a user-friendly online program for clinical exome analysis. BMC Bioinformatics, 2015.

Elsewhere

LinkedIn · X · Biostars

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  1. mendelmd mendelmd Public

    An online tool for annotating, filtering and diagnosing patients (Exome and Genome) with Mendelian Disorders.

    Python 36 10

  2. pynnotator pynnotator Public

    This is a Genome Annotation Framework developed with the goal of annotating VCF files (Exomes or Genomes) from patients with Mendelian Disorders.

    Python 23 4

  3. fast-ngs-admix fast-ngs-admix Public

    Nextflow pipeline for estimating ancestry/admixture proportions of 23andMe files

    Nextflow 1

  4. bioinformatics-mcp bioinformatics-mcp Public

    🧬 A comprehensive MCP server for bioinformatics — 62 tools for genomics, transcriptomics, epigenetics & more. Connects AI agents to scanpy, biopython, squidpy, NCBI, UniProt, Ensembl, and PubMed.

    Python 1

  5. rrrm2-crosstissue rrrm2-crosstissue Public

    Cross-tissue single-cell RNA-seq analysis of spaceflight and aging in NASA RRRM-2 mice (spleen, bone marrow, PBMCs)

    Python

  6. vus-meta-predictor vus-meta-predictor Public

    VUS Meta-Predictor: Genomic language model-powered variant interpretation. Combines ESM-2, amino acid physicochemistry, and gene constraints for calibrated missense pathogenicity prediction (AUROC …

    Python