I specialize in end-to-end genomic data analysis - from raw FASTQ files to publication-ready figures and clinical insights. My work bridges bioinformatics, machine learning, and precision medicine, with a focus on reproducible workflows that accelerate drug discovery and biomarker identification.

Founder & Owner | 🔗 actn3.pl | 💻 GitHub

Named after the ACTN3 "Speed Gene" - fast, efficient, high-performance bioinformatics.

ACTN3 Bioinformatics delivers genomic analysis services to biotech, pharma, and academic institutions:

• AI-powered genomic workflows (LLM-assisted analysis, automated QC, ML integration)
• Reproducible research infrastructure (Snakemake pipelines, Quarto documentation)
• Clinical trial bioinformatics (biomarker validation, patient stratification)
• Custom R package development
• Training & consulting (R/Bioconductor workshops, pipeline development)

# R/Bioconductor Ecosystem
✅ Differential Expression: limma-voom, edgeR, DESeq2
✅ Single-Cell Analysis: Seurat, Scanpy, UMAP, cell type annotation
✅ CRISPR Screens: crisprVerse, screenCounter, TMM normalization
✅ Pathway Analysis: fgsea, MSigDB, IPA, Metacore GeneGO
✅ ChIP-seq/ATAC-seq: BWA, peak calling, motif enrichment
✅ Machine Learning: caret, PAM, consensus NMF, predictive modeling
✅ Spatial Transcriptomics: 10X Visium, Xenium analysis

# R Package Development
✅ Package structure (devtools, usethis, roxygen2)
✅ Documentation (pkgdown websites, vignettes)
✅ Testing (testthat, unit tests, CI/CD)
✅ CRAN/Bioconductor submission standards

# Workflow Management
✅ Pipelines: Snakemake, Nextflow, Bash scripting
✅ Reproducibility: RMarkdown, Quarto, knitr
✅ Version Control: Git, GitHub/GitLab, CI/CD
✅ Compute: HPC clusters, Docker, parallel processing
✅ Data Handling: FASTQ/BAM/VCF parsing, dplyr, data.table

# Publication-Quality Graphics
✅ Static: ggplot2, ComplexHeatmap, UMAPs, volcano plots, survival curves etc.
✅ Interactive: Shiny apps, plotly, custom dashboards
✅ Reports: Quarto websites, dynamic RMarkdown, GitHub Pages

Reproducible Snakemake pipeline for ML-ready perturbation datasets

• Harmonized scRNA-seq data from CRISPR screens
• Balanced control/perturbation groups for unbiased ML training
• Automated QC reports with integrated visualizations

Tech: Snakemake, Python/Scanpy, Quarto, CI/CD

🔗 View Repository | 📖 Documentation

Comprehensive Quarto knowledge portal for R/Pharma 2025 workshops

• Structured documentation of tools, trends, and best practices
• Reproducible examples (Positron IDE, Shiny, Quarto workflows)
• Curated resources for pharmaceutical bioinformatics
• GitHub Pages deployment

Tech: Quarto, RMarkdown, GitHub Pages, modern R workflows

🔗 View Repository | 🌐 Live Site

Bioinformatics Role: CRISPR screen analysis (~160K sgRNAs), bulk RNA-seq (HTSeqGenie), ChIP-seq (BWA), TCGA integration
Methods: edgeR, limma-voom, TMM normalization, Cox survival models, COSMIC signatures
Impact: Identified ZFX as biomarker for immunotherapy response

Bioinformatics Role: NK cell RNA-seq (Smart-Seq V4), Differential gene expression (DGE) analysis, GSEA (fgsea) Methods: HTSeqGenie, edgeR (logCPM), limma, MSigDB (c2/c5/c7), pathway enrichment
Impact: Discovered NK cell activation mechanism in bispecific antibody therapy

Bioinformatics Role: scRNA-seq (10X Genomics, 22 clusters), bulk RNA-seq, WES
Methods: ImmGen annotation, PANTHER enrichment, UMAPs, COSMIC signatures
Impact: Multi-modal analysis revealed EGFR/ERBB-mediated immune escape

Bioinformatics Role: NMF subtype discovery (>800 patients), PAM classifier (113 genes), drug response modeling
Methods: Consensus NMF, PAM, Camera GSEA, Spearman correlations (526 compounds), survfit, Cox models
Impact: Clinical classifier for MEK inhibitor response prediction | 📊 Code

Bioinformatics Role: Microarray analysis (Affymetrix Rat Exon 1.0ST), qRT-PCR validation
Methods: RMA normalization, limma (moderated t-test), FDR correction
Impact: Identified PDE4 as therapeutic target for multiple sclerosis | 📊 Data: GSE50042

Full Publication List:

🤖 AI in Bioinformatics:
  - LLM-assisted code generation and debugging
  - AI-powered variant annotation
  - Automated literature mining for pathway enrichment

🧬 Multi-Modal Omics:
  - Spatial transcriptomics (10X Visium, Xenium)
  - Single-cell + proteomics + epigenomics integration
  - Multi-omic predictive modeling for precision medicine

🧪 Non-coding RNA:
  - lncRNA, miRNA, circRNA in cancer & development
  - Integration and correlation analysis between ncRNA and mRNA
  - Identifying ncRNA regulators of protein-coding genes
  - Regulatory network reconstruction

⚙️ Software Development:
  - R package development (Bioconductor standards)
  - Positron IDE + Quarto for literate programming
  - Nextflow DSL2 + Wave containers for cloud scalability
  - Git-based collaboration for reproducible science

🎯 CRISPR & Functional Genomics:
  - Perturb-seq analysis pipelines
  - Base editor/prime editor screen optimization
  - Screen hit validation workflows

🏥 Precision Medicine:
  - Real-time clinical decision support systems
  - Pharmacogenomics + liquid biopsy integration
  - Patient-specific therapy modeling