About

πŸ‘‹ Hi, I’m Szymon

Szymon Myrta

Bioinformatics Expert | 9+ Years | Founder of ACTN3 Bioinformatics

I transform complex genomic data into actionable insights through reproducible pipelines,
cutting-edge analysis, and AI-powered workflows.

⚑ Named after the ACTN3 β€œSpeed Gene” - symbolizing fast, efficient, high-performance bioinformatics

πŸ’Ό Professional Journey

πŸ”¬ Bioinformatician | Roche (via Avenga)

May 2017 - Present | Remote

Leading bioinformatics analysis for oncology and immunology research projects at one of the world’s largest pharmaceutical companies.

Key Achievements:

β–Έ Co-authored 6 publications in top-tier journals (iScience, Clinical Cancer Research, Cancer Immunology Research, EMBO Molecular Medicine)
β–Έ Analyzed >800 patient samples across multiple clinical trials (OAK, POPLAR, gp28363)
β–Έ Processed ~160,000 sgRNAs in genome-wide CRISPR screens
β–Έ Developed 113-gene classifier with 87-91% cross-cohort validation
β–Έ Built ML-ready datasets from scRNA-seq CRISPR perturbation screens

Technical Focus:

β–Έ NGS analysis (RNA-seq, scRNA-seq, ChIP-seq, scTCR/scBCR-seq, WGS/WES)
β–Έ CRISPR/ORF screen analysis
β–Έ Machine learning & predictive modeling
β–Έ Multi-omics data integration (TCGA, GEO, clinical trials)
β–Έ Pipeline development (Snakemake, Docker, HPC)
β–Έ R package development for internal workflows

πŸ’» LIMS Developer & Bioinformatician | Ardigen

September 2015 - April 2017 | KrakΓ³w, Poland

β–Έ Designed & maintained LIMS software (StarLIMS, JScript.NET, T-SQL)
β–Έ Developed R package supporting drug discovery workflows
β–Έ Integrated bioinformatics tools with laboratory information systems

πŸ§ͺ LIMS Developer & ISO Coordinator | Selvita

August 2014 - August 2015 | KrakΓ³w, Poland

β–Έ Led StarLIMS implementation in collaboration with Abbott
β–Έ Coordinated QA for ISO compliance during system deployment
β–Έ Bridge between IT, lab operations, and quality assurance

πŸŽ“ Visiting Student | University of Cambridge

May 2013 - September 2013 | Anne McLaren Laboratory

Project: Computational analysis of long non-coding RNAs during neural differentiation
Supervisor: Dr. Mark Kotter
Methods: R-based microarray analysis in stem cell biology

πŸ› οΈ Technical Skills

Core Bioinformatics

NGS Technologies:
βœ“ RNA-seq: limma-voom, edgeR, DESeq2, HTSeqGenie, GSNAP
βœ“ scRNA-seq: Seurat, Scanpy, UMAP, cell type annotation
βœ“ CRISPR screens: crisprVerse, MAGeCK, TMM normalization
βœ“ ChIP-seq, ATAC-seq, CUT&RUN: peak calling, motif enrichment
βœ“ scTCR/scBCR-seq: immune repertoire profiling
βœ“ WGS/WES: GATK, variant calling, COSMIC signatures
βœ“ Spatial transcriptomics: 10X Visium analysis
βœ“ Long-read sequencing: PacBio, Nanopore
βœ“ Methylation: WGBS, Infinium arrays

Analysis Methods:
βœ“ Pathway analysis: fgsea, MSigDB, IPA, Metacore GeneGO
βœ“ Differential expression: limma, edgeR, DESeq2
βœ“ Functional genomics: CRISPR/ORF screen hit calling

Machine Learning & Statistics

Unsupervised:
βœ“ Consensus NMF, hierarchical clustering, PCA/UMAP

Supervised:
βœ“ PAM, caret, feature engineering, cross-validation design

Clinical:
βœ“ Survival analysis: Cox models, Kaplan-Meier, survfit
βœ“ Statistical tests: ANOVA, t-tests, Mann-Whitney U, FDR correction

Software Development

R Package Development:
βœ“ Package structure: devtools, usethis, roxygen2
βœ“ Documentation: pkgdown websites, vignettes
βœ“ Testing: testthat, unit tests, CI/CD
βœ“ CRAN/Bioconductor submission standards

Workflow Engineering:
βœ“ Snakemake, Nextflow, Bash scripting

Reproducibility:
βœ“ RMarkdown, Quarto, literate programming

Infrastructure:
βœ“ Version control: Git, GitHub/GitLab, CI/CD
βœ“ Compute: HPC clusters, Docker, parallel processing
βœ“ Data wrangling: dplyr, data.table, FASTQ/BAM/VCF parsing

Visualization & Deployment

Static Graphics:
βœ“ ggplot2, ComplexHeatmap, volcano plots, survival curves

Interactive:
βœ“ Shiny apps, plotly, custom dashboards

Documentation:
βœ“ Quarto websites, dynamic RMarkdown, GitHub Pages

Data Sources & Integration

Public Databases:
βœ“ TCGA, GEO, EGA, SRA, cBioPortal, FoundationOne

Clinical Data:
βœ“ OAK/POPLAR trials, patient stratification

Platforms:
βœ“ Illumina (HiSeq/NovaSeq), 10X Genomics, PacBio, Affymetrix

🌍 Languages

β–Έ πŸ‡¬πŸ‡§ English: Fluent - Scientific communication, publications, international teams
β–Έ πŸ‡΅πŸ‡± Polish: Native

πŸ’‘ What Drives Me

πŸš€ Professional Interests (2025 & Beyond)

β–Έ πŸ€– AI in Bioinformatics: LLM-assisted analysis, automated QC, AI-powered variant calling
β–Έ 🧬 Multi-Modal Omics: Spatial transcriptomics, single-cell + proteomics + epigenomics integration
β–Έ πŸ§ͺ 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
β–Έ πŸ“¦ Software Development: R package development (Bioconductor standards)
β–Έ βš™οΈ Workflow Engineering: Positron IDE + Quarto, Nextflow DSL2, cloud-native pipelines
β–Έ 🎯 CRISPR & Functional Genomics: Perturb-seq, base/prime editor screens, screen validation workflows
β–Έ πŸ₯ Precision Medicine: Real-time clinical decision support, pharmacogenomics, liquid biopsy, patient-specific modeling

πŸƒ Personal Passions

β–Έ πŸ“š Continuous learning & skill development
β–Έ πŸƒ Licensed athletics referee
β–Έ πŸ’ͺ Healthy lifestyle & professional athletics training
β–Έ 🧘 Work-life balance advocacy

🀝 Let’s Work Together

I’m passionate about turning complex genomic data into discoveries that matter.

Whether you’re a biotech startup, academic lab, pharma company, or CRO, let’s discuss how I can help accelerate your research with cutting-edge bioinformatics solutions.

Connect with me:

πŸ“§ Email πŸ’Ό LinkedIn πŸ“‹ ORCID