Bioinformatics Engineer | Barcelona, Spain
I build reproducible, production-grade bioinformatics pipelines for multi-omics data, from raw NGS reads to documented, reusable analytical tools. Background in Nextflow DSL2, SLURM HPC, and multi-omics integration, with a PhD in Genetics and an MSc in Bioinformatics and Biostatistics.
- NGS Pipelines | Nextflow DSL2 · SLURM · Apptainer/Singularity · Conda
- Multi-Omics Analysis | RNA-seq · ATAC-seq · ChIP-seq · Hi-C · WES
- Data Engineering | Python ETL · API integration · count matrix production
- Statistical Methods | Differential analysis · empirical null models · FDR · ML
- Reproducibility | Containerized workflows · SOP documentation · FAIR practices
chip-nf - End-to-end ChIP-seq pipeline
Nextflow DSL2 pipeline covering the full ChIP-seq workflow: QC → alignment → peak calling → differential analysis → annotation → visualization. Per-module Conda environments, SLURM and local execution profiles. Single command to go from raw reads to annotated differential peaks and MultiQC report.
Nextflow Bowtie2 MACS2 DESeq2 HOMER deepTools SLURM Conda
PyGDC-RNA-ETL - Clinical genomics ETL pipeline
Python ETL pipeline for large-scale extraction and integration of RNA-seq data and clinical metadata from the NCI Genomic Data Commons. Parallelized batched API downloads with auto-resume, AJCC stage normalization, somatic mutation annotation, and analysis-ready output for DE and ML workflows.
Python ETL GDC API pandas clinical metadata cancer genomics
parastar - Containerized batch RNA-seq alignment
STAR + GNU Parallel pipeline packaged as an Apptainer/Singularity image (distributed via Zenodo). Single config file, no script editing, dry-run mode, skip-completed logic for resumable HPC runs. Designed for batch processing at scale.
STAR GNU Parallel Apptainer Singularity SLURM HPC
loopstrength — Hi-C chromatin loop quantification
R/Python framework for quantifying chromatin loop strength changes between conditions. Implements size- and distance-matched random controls, empirical two-sided p-values, and BH-FDR correction. Used in a Science Advances publication.
R Python Hi-C Cooler empirical null 3D genomics
| Languages | Python · R · Bash · Nextflow DSL2 · SQL |
| Workflow | Nextflow DSL2 · SLURM HPC · Apptainer/Singularity · Conda/Mamba · Git |
| NGS Tools | STAR · Bowtie2 · MACS2 · HOMER · DESeq2 · GATK · Cooler · samtools · deepTools · FastQC/MultiQC |
| Python libs | pandas · numpy · requests · matplotlib · scikit-learn |
| R libs | Tidyverse · Bioconductor · ggplot2 · Seurat |
| ML / Stats | PCA · UMAP · random forest · k-means · empirical permutation · BH-FDR |
| Databases | GEO · GDC/TCGA · Ensembl · UCSC · BioMart |
- Llorens-Giralt, P., Camilleri-Robles, C., et al. 3D genome organization in tissue regeneration involves long-range chromatin loops. Science Advances (Accepted)
- Camilleri-Robles, C., et al. (2024). Long non-coding RNAs involved in Drosophila development and regeneration. NAR Genomics and Bioinformatics
- Camilleri-Robles, C., et al. (2024). A shift in chromatin binding of phosphorylated p38 precedes transcriptional changes upon oxidative stress. FEBS Letters
Full publication list: ORCID