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codebiogenomics/README.md

I work at Instytut Chemii Bioorganicznej Polskiej Akademii Nauk, Poznań Poland as a part of a very good team. I work as area expert and responsible for genomic analysis and software development from illumina and long read sequencing. I work using Python, R, Julia, RUST, Typescript and I provide bio-software development, algorithms, bioinformatics, machine learning as an Area Expert area for Illumina and LongRead sequencing technologies across all domains of life covering plant, bacterial, fungal and humans.

Scientific and Bio-Computing Areas of Interest: 🧬 I am specific to the genomics area such as RNA-seq, single cell genomics, and any genomics or protein language models and biological deep bio ML 🧬 and bio-software. ❌ I don't do protein structural modelling, and ML on the same. ❌ What i don't code anymore: C++ since 2021 (2010-2021), dropped DevOPS (2024).

Sequencing specifics:
2010-2021: Plant, Bacterial, Fungi 🧬 RNASeq, GenomSeq, Phylogenomics, PacBio Sequencing, Single Cell Analysis, Bio-software. 👨‍💻
2021:2023: Machine Learning, Bio-software. 👨‍💻
2024: PanGenome, Bio-software👨‍💻.
2025: Human Genomics 🧬and Bio-software, Mobile SDK 👨‍💻

🧬 I use Python, R, Julia (data analysis and web), RUST (system programming and bio-software) and Typescript and React (Web and Mobile SDK).

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  1. panscape Public

    reads to genome, pangenome graphs, summarize and analyze

    Rust 2

  2. eVaiutilities Public

    eVaiutilities for post-eVai human genomics

    Rust 1

  3. ensemblcov Public

    genomics utilities for human genomics

    Rust

  4. vcfilter Public

    population scale variant filter

    Rust 1

  5. varlinker Public

    exact point variant annotation

    Rust

  6. repgenerate Public

    repgenerate for illumina sequencing reports

    Rust

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July 2025

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