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mijailcampos/README.md

Hi, I'm José Mijail Campos Compeán 👋

Bioinformatics scientist in Mexico City working on microbiome metabarcoding (16S/18S rRNA), reproducible NGS pipelines and bioinformatics software. PhD candidate in Biological and Health Sciences, and founder of Bioagens, a web platform of bioinformatics tools for genomic and metagenomic research.

🔬 What I'm working on

  • MetagenApp: a reproducible 16S/18S metabarcoding pipeline (VSEARCH + Wang-style naive Bayes classifier), benchmarked against mothur and QIIME 2. Presented as a poster at ECCB 2026 (Geneva). DOI · live demo
  • Actopan microbiome: prokaryotic and eukaryotic communities in oysters (Crassostrea virginica), river water and human feces from Chachalacas, Veracruz (PhD project, manuscript in preparation).
  • Bioagens: a set of web GUIs for QIIME 2, mothur, assembly, variant calling, RNA-seq and more, running on self-hosted infrastructure.
  • Exploring deep learning on DNA sequences (embeddings + clustering for taxonomic assignment).

🛠️ Tools I use

QIIME 2 · mothur · DADA2 · VSEARCH · cutadapt · SILVA · PR2 · Python · R · Bash · Linux

📫 Find me

LinkedIn · ORCID · bioagens.com

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  1. metagenapp metagenapp Public

    Reproducible 16S/18S metabarcoding pipeline (VSEARCH + Wang-style k-mer classifier). Benchmarked against mothur and QIIME 2 — ECCB 2026.

    Python