Skills & Competencies

Tecnical expertise and methodologies across bioinformatics, data science, and infrastructure.

Bioinformatics Core

Workflow Management

  • Nextflow DSL2: Modern, modular workflow definition language
  • Bash scripting for automation
  • HPC/Cloud agnostic pipeline design

NGS Analysis Tools

Alignment & Quantification

  • RNA-Seq: STAR, Salmon, Kallisto
  • DNA-seq: BWA-MEM, GATK
  • Long-read: Minimap2 (Nanopore/PacBio)

Quality Control & Preprocessing

  • FastQC/MultiQC: Comprehensive QC reports
  • Trimmomatic/Fastp: Adapter trimming and filtering
  • Custom downsampling workflows

Cloud & Infrastructure

Cloud Platforms

  • AWS Batch: Scalable workflow execution
  • Google Cloud Platform: Alternative deployment options
  • SLURM/HPC: High-performance computing clusters

Containerization

  • Docker for development
  • Singularity for production HPC environments
  • Immutable container best practices

Data Science & Machine Learning

Languages & Libraries

  • R: Bioconductor, ggplot2, Seurat, DESeq2
  • Python: Scikit-learn, PyTorch/TensorFlow (LSTM)

Time Series & Predictive Modeling

  • LSTM Networks: Long Short-Term Memory for clinical data
  • Cross-validation strategies for robust validation
  • Feature engineering for biomedical data

Advanced Technologies

Emerging Platforms

  • Oxford Nanopore: Long-read epigenomics analysis
  • MGI STOMICS: Spatial transcriptomics
  • NVIDIA Parabricks: GPU-accelerated genomic pipelines