Genomic Epidemiology & Pathogen Surveillance @ FISABIO — Valencia, Spain 🇪🇸

I'm a bioinformatician with 10+ years of experience in genomic data analysis and Linux/HPC administration. I work at the EPIMOL group (FISABIO) on the genomic surveillance program of the Valencian Community, where I split my time between designing reproducible pipelines, keeping shared HPC infrastructure healthy, and acting as the technical bridge between the molecular epidemiology team and IT.

I tend to identify as a problem solver — whether that means recovering a failed system at 11 pm, debugging an obscure pipeline error, or tracking down why a 10 GbE link suddenly stopped behaving. I care about solutions that are robust, reproducible, and useful for the people who actually have to run them.

• Currently working on respiratory viruses (SARS‑CoV‑2, Influenza, RSV) and antimicrobial resistance in clinical and foodborne pathogens, including Candida auris.
• Previously: WGS / WES + CNV analysis on FFPE prostate cancer samples at CNIO under a US Department of Defense contract; transcriptomics & miRNA regulatory networks at I2SysBio.
• Hands‑on experience with Nanopore (MinION / PromethION) and Illumina (MiSeq / NextSeq), plus epigenomics (modified base detection in Neisseria gonorrhoeae).
• Day‑job sysadmin for shared HPC servers (storage, GPU basecalling, NFS, Samba, networking, user management).

A complete LIMS platform for molecular epidemiology, designed and built from scratch to scale genomic surveillance across hospitals of the Valencian Community.

EPILIMS is my main ongoing project: a multi-container web application that centralises the full sample lifecycle — from reception and wet-lab tracking, to sequencing runs, to bioinformatic results across viral, bacterial and fungal pipelines.

• Multi-container architecture — Django web app, PostgreSQL database, reverse proxy, background workers, and pipeline integration, all orchestrated via Docker.
• Designed for sensitive clinical data — role-based access (lab, bioinformatics, hospital read-only), audit trail, and protection of personally identifiable patient information in compliance with GDPR / LOPDGDD.
• Built around real surveillance workflows — supports multiple pipelines per sequencing run, hybrid Illumina + Nanopore data, lineage assignment, AMR profiling, and per-hospital dashboards.
• 40+ tables, normalised schema — patients, samples, wet-lab extractions, sequencing runs, pipeline executions and results, with materialised views for fast hospital-facing reporting.

Languages

Workflow & pipelines

Web & data

AI & LLM — providers and models

Agentic development & ML

Containers, environments & HPC

Infrastructure & ops

• Sequencing — end‑to‑end Nanopore (MinION / PromethION) and Illumina (MiSeq / NextSeq) workflows, including duplex basecalling and modified base calling
• Variant analysis — germline, somatic and CNV calling, including challenging FFPE samples
• Pathogen genomics — viral lineage assignment, AMR, MLST, phylogenetics, outbreak investigation
• Epigenomics — methylation calling and modified base detection
• Pipeline engineering — Nextflow DSL2 & Snakemake, parallelization strategies, reproducible environments
• Full-stack development — Django / FastAPI web apps with PostgreSQL backends, deployed in Docker
• AI-assisted engineering — daily multi-provider LLM workflow (Claude, ChatGPT/OpenAI, Gemini, DeepSeek) and self-hosted open-weight models via Ollama (Llama, Qwen, Mistral, DeepSeek-Coder, Gemma). Hands-on prompt engineering, agentic coding with Claude Code and Cursor, custom MCP servers and integrations, and LLM-powered automation for pipeline scaffolding, code review and internal tooling. Comfortable embedding deep-learning components (neural basecallers, ML-based variant callers) into production bioinformatics pipelines.
• HPC sysadmin — SLURM, Lmod, conda/mamba, Docker / Singularity, NFS, Samba, RAID storage, networking
• Troubleshooting — pipelines, systems, networks, the occasional human

"Everything you do should be done with passion."