Szymon Myrta
Bioinformatics Expert | 9+ Years | NGS & AI Workflows
Transform your genomic data into actionable insights with reproducible pipelines and cutting-edge analysis.
⚡ Powered by the ACTN3 “Speed Gene” Philosophy - Fast, Efficient, High-Performance Bioinformatics
9+
Years Experience
500+
NGS Datasets Analyzed
6
Publications
💡 What Problems Do I Solve?
🧬 Raw NGS Data Chaos
Problem: You have TBs of FASTQ files but no pipeline
Solution: End-to-end analysis from QC to DE to figures
Tools: Snakemake, Seurat, edgeR, HTSeqGenie
🤖 AI-Ready Genomic Data
Problem: Messy datasets, batch effects, imbalanced classes
Solution: Harmonized, ML-ready perturbation datasets
Tools: CRISPR normalization, feature engineering, CV design
📊 Publication-Quality Figures
Problem: Analysis done but figures look unprofessional
Solution: Heatmaps, UMAPs, survival curves ready for Nature/Cell
Tools: ggplot2, ComplexHeatmap, Quarto reports
🏥 Clinical Trial Biomarkers
Problem: Which patients respond to your drug?
Solution: Cox models, patient stratification, companion diagnostics
Tools: TCGA integration, survfit, pathway enrichment
🛠️ Core Services
NGS Analysis
▸ RNA-seq (bulk & single-cell)
▸ ChIP-seq, ATAC-seq, CUT&RUN
▸ WGS/WES variant calling
▸ scTCR/scBCR-seq repertoires
▸ CRISPR/ORF screen analysis
▸ Spatial transcriptomics (10X Visium)
▸ Long-read sequencing (PacBio, Nanopore)
▸ Methylation arrays, WGBS
Format: Quarto reports + GitHub repo
R Package Development
▸ Custom packages
▸ Package documentation (pkgdown)
▸ Unit testing (testthat)
▸ Vignettes and tutorials
Format: Documented package + GitHub repo
Pipeline Development
▸ Snakemake/Nextflow workflows
▸ Docker containerization
▸ HPC optimization
▸ CI/CD integration
▸ Automated testing
Format: Reproducible code + documentation
AI-Powered Analysis
▸ ML-ready feature extraction
▸ Multi-omics integration
▸ LLM-assisted code generation
▸ Automated QC systems
Format: Trained models + deployment scripts
Interactive Dashboards
▸ Shiny apps for data exploration
▸ Real-time QC monitoring
▸ Client-facing visualizations
▸ GitHub Pages portfolios
▸ Quarto knowledge bases
Format: Hosted app + source code
Multi-Omics Integration
▸ Transcriptomics + genomics + epigenomics
▸ Spatial transcriptomics analysis
▸ TCGA/GEO public data mining
▸ Cross-species comparisons
▸ Pathway enrichment analysis
Format: Integrated dataset + insights report
🎯 Technical Arsenal
🧬 Bioinformatics
Core: limma, edgeR, DESeq2, fgsea, ComplexHeatmap
Single-cell: Seurat, UMAPs, cell type annotation
CRISPR: crisprVerse, screenCounter, MAGeCK
ML: caret, PAM, consensus NMF, feature engineering
⚙️ Engineering
Pipelines: Snakemake, Nextflow, Bash scripting
R Packages: devtools, usethis, roxygen2, testthat
Reproducibility: Quarto, Shiny, RMarkdown
Compute: HPC clusters, parallel processing, CI/CD
Data: FASTQ/BAM/VCF parsing, dplyr, data.table
📊 Visualization
Static: ggplot2, ComplexHeatmap, volcano plots
Interactive: Shiny dashboards, plotly, custom widgets
Reports: Quarto websites, dynamic RMarkdown, GitHub Pages
🗄️ Data Sources
Public: TCGA, GEO, EGA, SRA, cBioPortal
Clinical: OAK/POPLAR trials, FoundationOne
Platforms: Illumina (HiSeq, NovaSeq), 10X Genomics, PacBio
📚 Research Impact
6
Publications in Top-Tier Journals
800+
Patient Samples Analyzed
160K
sgRNAs in CRISPR Screens
Featured Publications
🧬 Transcription factor Zfx regulates tumor immune evasion
iScience (2025)
Role: CRISPR screen analysis (160K sgRNAs), ChIP-seq, TCGA survival models
📄 Read Paper
🧬 Transcriptional subtypes in lung adenocarcinoma
Clinical Cancer Research (2021)
Role: NMF subtype discovery, 113-gene PAM classifier (87-91% accuracy)
📄 Read Paper | 💻 Code
🧬 ERBB signalling in KRAS-driven lung cancer
bioRxiv (2023)
Role: scRNA-seq analysis (10X, 22 clusters), PANTHER enrichment
📄 Read Paper