Martin Proks - Senior Bioinformatician

Martin Proks

Senior Bioinformatician

Copenhagen, Capital Region of Denmark

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Summary

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Senior

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Top School

Martin Proks is a Senior Bioinformatician with 11 years of experience bridging computational engineering and developmental biology, currently contributing to industry projects from Copenhagen. He holds a PhD in Developmental Biology and a strong background in software development, having built NGS pipelines (nf-core projects), GPU-accelerated causal inference tools in C++/JAX, and interpretable deep learning models for early mouse and human development. Martin combines hands-on DevOps and front-end skills—contributing Leaflet map features to the widely used nf-core website and maintaining testing/linting for nf-core/tools—with practical experience setting up HPC/GPU infrastructure and FAIR data platforms. His work spans research, production pipelines, and tooling, including converting legacy sequencing hardware into testing servers and delivering reproducible workflows for fusion detection and single-cell multimodal analysis. Colleagues rely on him for computational training and for translating complex biological questions into robust, scalable code and pipelines.

11 years of coding experience

10 years of employment as a software developer

Programming, Programming at Súkromné gymnázium Dneperská 1

Doctor of Philosophy - PhD, Developmental Biology and Embryology, Doctor of Philosophy - PhD, Developmental Biology and Embryology at Københavns Universitet - University of Copenhagen

Master of Science - MSc, Computational Biomedicine, Master of Science - MSc, Computational Biomedicine at University of Southern Denmark

Computer Science and Data Processing, Computer Science and Data Processing at Masaryk University Brno

Bachelor's degree, Software Development, Bachelor's degree, Software Development at Erhvervsakademi Aarhus | Business Academy Aarhus

English, German, Slovak, Czech

Github Skills (16)

testing10

linter10

linting10

javascript10

python10

leaflet10

nf-core10

cicd10

nextflow9

workflow-engine9

html9

css9

website-design8

github8

website-development8

Programming languages (18)

C#MDXC++JinjaCNextflowGoHTML

Github contributions (5)

nf-core/tools

Jan 2019 - May 2019

Python package with helper tools for the nf-core community.

Role in this project:

DevOps Engineer

Contributions:13 commits, 5 PRs, 31 comments in 3 months

Contributions summary:Martin's commits primarily focus on modifying linting and testing configurations within the nf-core/tools repository. They removed Singularity-related configurations, adjusted test numbers, and fixed linting issues. The commits reflect work on build and release processes, as well as code quality checks. These changes indicate a focus on maintaining and improving the tools' infrastructure and ensuring correct operation.

nf-corelinterpythonpipelinelinting

nf-core/website

Sep 2018 - Dec 2018

Code and files for the main nf-core website.

Role in this project:

Front-end Developer

Contributions:7 commits, 5 PRs, 18 comments in 3 months

Contributions summary:Martin's primary contribution involved enhancing the nf-core website's front-end capabilities by integrating a Leaflet map to display contributor locations. They added the necessary JavaScript and CSS, and implemented logic to fetch and display contributor data on the map. Further contributions refined the map implementation, corrected location parsing, and incorporated reviewer feedback. The user also updated dependencies and fixed minor styling issues.

nf-corenextflow

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