As a scientific software developer and postdoctoral researcher in bioinformatics at the University of Oslo, I design and build high-performance computational tools to solve complex problems in genomics and model the 3D genome organization.

I develop and maintain several open-source tools, primarily written in modern C++ and Python, for:

• Hi-C and multi-omics data processing
• Modeling of the 3D genome structure
• Bioinformatics workflows for reproducible analysis
• CLI tools and libraries for large-scale genomics

When it comes to bioinformatics tools, I deeply care about:

• Performance — through efficient algorithms, parallelism, and modern systems programming
• Correctness — via rigorous testing and well-thought-out code architecture
• Usability — achieved with clear CLI design, intuitive APIs, and comprehensive documentation

A CLI and C++/Python/R library to efficiently handle data from Hi-C experiments

• Designed to enable seamless operations on files in .hic and cooler formats, streamlining the analysis of 3D genomic data
• Convert .hic files to .mcool up to 36x faster than existing tools
• Zero-copy in-memory data sharing between C++ and Python/R using Arrow and Eigen
• Published in OUP Bioinformatics (2024): doi.org/10.1093/bioinformatics/btae408
• Languages: C++17 (core), Python, R
• Tech stack: Arrow, Conan, CMake, Docker, GitHub Actions, nanobind, OpenTelemetry, Rcpp, Sphinx
• Key Algorithms & Techniques: Test-driven development, fuzzy testing, streaming algorithms, visitor and iterator patterns, multi-threading
• Role: Lead developer

A high-performance stochastic modeling of DNA loop extrusion interactions

• Developed to simulate genome-wide loop extrusion in vertebrates, providing insights into chromatin dynamics relevant to gene regulation and disease mechanisms
• Orders of magnitude faster than traditional MD-based models: simulate loop extrusion on the human genome using consumer hardware in a few minutes
• Published in Genome Biology (2022): doi.org/10.1186/s13059-022-02815-7
• Tech stack: C++17, Conan, CMake, Docker, GitHub Actions
• Key Algorithms & Techniques: unit-testing, consumer-producer architecture, multi-threading, concurrent data structures
• Role: Lead developer

3D Genome Analysis of Breast Cancer Progression in MCF10A and related cell lines

• Full pipeline and analysis scripts for integrative Hi-C, ChIP-Seq, and RNA-Seq data
• Preprint available on bioRxiv (2023): doi.org/10.1101/2023.11.26.568711
• Tools: Bash, Dash, Docker, Jupyter, Nextflow, Python, R
• Role: Lead developer. Responsible for all data processing and most of the data analysis

Detection of architectural stripes in Hi-C contact maps

• Identifies structural features linked to active transcription and regulatory regions
• Format-agnostic and easy to use. Augments stripes with several descriptive statistics
• Preprint available on bioRxiv (2024): doi.org/10.1101/2024.12.20.629789
• Language: Python
• Key Algorithms & Techniques: unit-testing, multiprocessing, shared memory, asynchronous programming, structured logging
• Role: Primary code contributor. Provided inputs regarding the algorithm design

In addition to major projects, I contribute to the broader bioinformatics software ecosystem:

• Package maintenance:
  • Bioconda Recipes
  • Conan Center Index
• Bug fixes and patches:
  • cooler
  • Chrom3D
  • dcHiC
  • iced
  • nf-core/hic
  • stripenn
  • libBigWig

• 📍 Based in Oslo, Norway
• ✉️ Work email
• 🌐 ORCID | LinkedIn | Twitter

Do not hesitate to connect with me on LinkedIn or reach out via email for collaborations or opportunities.