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What happens when you put a biologist behind a keyboard?

Jacob Fredegaard Hansen

I t |

Curiosity-driven data scientist who believes the best innovations happen when you empower people to think differently about their data.

Black and white portrait of Jacob Fredegaard Hansen, Bioinformatician and Data Science Specialist in Copenhagen Jacob Fredegaard Hansen — Bioinformatician specialising in computational protein design and drug discovery

The Short Version

From molecules to models

I started in a wet lab, pipetting and staring at protein gels. Somewhere along the way, I realised the most exciting part wasn't the experiment itself — it was the data it produced. That curiosity pulled me from biochemistry into computational biomedicine, and eventually into the role I have today: helping researchers and students unlock the power of data science and AI.

What drives me

I'm driven by watching people grow. Whether it's a scout learning to lead a patrol, a clinician running their first R script, a professor discovering what AI can do for their teaching, or a student winning a Gold Medal at an international competition — that moment of transformation is what gets me out of bed.

To make those moments happen, I combine state-of-the-art data science and AI with bioinformatics tools. Together, these can spark novel innovations that wouldn't exist in either field alone.

Location

Copenhagen, Denmark

Current Role

Data Science Specialist, University of Copenhagen

Background

MSc Computational Biomedicine, SDU

Languages

Danish (Native), English (Fluent), German (Intermediate)

Where I've Been

Data Science Specialist

2025 – Present
Center for Pharmaceutical Data Science Education

Department of Drug Design & Pharmacology, University of Copenhagen

Leading cross-institutional AI workflow development and designing data science curricula across pharmaceutical programmes at UCPH and SDU. Building hands-on teaching frameworks, workshops, and strategic outreach connecting academia with industry.

Data Scientist in Computational Proteomics

2022 – 2024
Protein Research Group, University of Southern Denmark

Built and integrated a proteomic workflow into the National Health Data Science Sandbox. Created Docker-based environments on UCloud HPC with GPU-accelerated protein structure prediction. Co-founded the AI Special Interest Group and supported 60+ researchers.

Young Academy Panel Member

2024 – Present
DDSA — Danish Data Science Academy

Shaping DDSA strategy and serving as jury member in the Danish National Championship in AI (DMiAI). Helping strengthen the Danish data science ecosystem through community initiatives.

iGEM Supervisor

2023 – 2024

SDU-Denmark iGEM Team

Novo Nordisk Foundation supported

Mentored student teams in the world's largest synthetic biology competition. 2023: Gold Medal + Special Prize for Best Integrated Human Practices. 2024: Silver Medal + nomination for Best Education.

Outreach Ambassador & Teaching Assistant

2019 – 2022

University of Southern Denmark

Introduced high school students to bioinformatics through lectures and hands-on exercises. Served on the departmental Teaching Committee and supported IT infrastructure.

Freelance Photographer

Event & Concert Photography

Autodidact photographer capturing live performances and science events. Collaborations with the University of Southern Denmark and Roskilde Festival.

Education

2020 – 2022

Master of Science

Computational Biomedicine

University of Southern Denmark, Odense

Master project (60 ECTS): PWM-based Prediction of Transcription Factor Binding Sites. Worked across Functional Genomics and Data Science & Statistics, developing expertise in R, Linux, Bash, and DuckDB for large-scale data analysis.

2017 – 2020

Bachelor of Science

Biochemistry & Molecular Biology

University of Southern Denmark, Odense

Thesis on genome-wide PPARγ analysis with Prof. Susanne Mandrup. Won a Gold Medal for Conjugaid in the iGEM Competition through the SDU Talent Program (additional 30 ECTS). Chaired the department's student association.

Teaching & Mentorship

I teach to make the complex accessible. My courses blend bioinformatics, data science, and real-world biomedical data — so students don't just learn theory, they build something they can use.

MSc

Biostatistics in R I & II

Lead instructor & course designer

ANOVA, linear models, and hands-on R projects applied to omics data including RNA-seq, proteomics, and epidemiological datasets.

MSc

Protein Structure & Modeling

Co-instructor & content developer

Structural bioinformatics with AlphaFold2, AlphaFold3, ColabFold, ESMFold, and molecular visualization in VMD.

PhD

Applied Bioinformatics Workshops

Module designer & co-instructor

Computational workflows on UCloud HPC with Git-based version control. Emphasis on reproducibility and practical scripting.

Mixed

Health Data Science Sandbox

Lead on proteomics module

Docker-based proteomics environment on UCloud HPC, enabling researchers with limited programming experience to analyse clinical datasets.

Contributions

Competition

SDU-Denmark — iGEM 2024 (Silver Medal)

SDU-Denmark iGEM Team — supervised by Jacob Fredegaard Hansen

iGEM Grand Jamboree 2024 — Nominated for Best Education

Supervised the SDU iGEM team to a Silver Medal with a nomination for Best Education.

Competition

vitroFAS — iGEM 2023 (Gold Medal)

SDU-Denmark iGEM Team — supervised by Jacob Fredegaard Hansen

iGEM Grand Jamboree 2023 — Special Prize: Best Integrated Human Practices

Supervised the SDU iGEM team to a Gold Medal and multiple nominations including Best Bioremediation Project and Best Presentation.

Competition

Conjugaid — iGEM 2019 (Gold Medal)

SDU-Denmark iGEM Team — including Jacob Fredegaard Hansen

iGEM 2019 — SDU Talent Program

Won a Gold Medal as part of the SDU-Denmark team through the extracurricular SDU Talent Program (30 ECTS).

Thesis

PWM-based Prediction of Transcription Factor Binding Sites

Jacob Fredegaard Hansen

MSc Thesis, University of Southern Denmark, 2022

60 ECTS master project supervised by Asst. Prof. Jesper Grud Skat Madsen, conducted across Functional Genomics and Data Science & Statistics.

Beyond the Lab

The best ideas don't come from staring at a screen. They come from the space between disciplines, between effort and rest, between a good book and a long run.

Reading

I'm always in the middle of something — from popular science and biographies to leadership books and AI. A few favourites: Factfullnes by Hans Rosling, and Atomic Habits by James Clear.

See what I'm reading on Goodreads →

Music

Music is how I recharge. Whether it's discovering new artists, getting lost in a playlist while coding, or experiencing live concerts through a camera lens - it's a constant companion.

Running

Running taught me that small, consistent efforts compound into something remarkable. One kilometre at a time, one day at a time. The same philosophy applies to science, teaching, and building anything meaningful.

Scouting & Leadership

More than 20 years in the Danish scouting movement shaped how I think about leadership: it's about enabling others, not directing them. That principle carries into everything I do — from mentoring students to guiding organisations.

Skills & Expertise

Programming & Tools

R Python Bash Linux Git Docker DuckDB HPC / UCloud

Bioinformatics & Proteomics

Proteomics AlphaFold ColabFold ESMFold VMD Mass Spectrometry Sequence Analysis RNA-seq

Data Science & AI

Machine Learning Statistical Analysis Data Visualization LLM Workflows ChatGPT / Claude / Gemini R Markdown

Leadership & Teaching

Curriculum Design BSc/MSc/PhD Teaching Mentorship Project Management Workshop Facilitation Science Outreach Community Building

Molecular Playground

From nuclear receptors to GPCRs and transcription factors — explore the 3D structures behind my research. These are the kinds of targets I work with using AlphaFold, ColabFold, and molecular visualization tools.

PPARγ (Human)

PDB: 1PRG

Peroxisome proliferator-activated receptor gamma — a nuclear receptor and master regulator of adipogenesis and glucose metabolism. This structure shows the ligand-binding domain bound to rosiglitazone, a thiazolidinedione antidiabetic drug. Central to my BSc thesis on genome-wide PPARγ analysis.

Residues 272
Method X-ray
Resolution 2.3 Å

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Things I've Built

Proteomics Sandbox

Educational proteomics tools for biomedical researchers, deployed on UCloud HPC as part of the national Health Data Science Sandbox.

Jupyter Proteomics Docker

AlphaFold Workshop

Hands-on protein folding prediction with AlphaFold2 and MMseqs2, designed as a learning resource for students and researchers.

Jupyter AlphaFold Protein Structure

FASTA Parser

Python tool for sequence analysis and TSV output of DNA or protein sequences.

Python Bioinformatics CLI

Photo Batch Downscaler

GUI app for batch image resizing, built to streamline photography workflows.

Python GUI Photography

FTP Directory Size

Python script to calculate directory and file sizes by type on an FTP server.

Python FTP DevOps

File Organizer Tool

Shell utility for searching, copying, and unzipping files based on pattern matching.

Shell Automation Utility

Let's Talk

Whether you want to collaborate on data science education, explore AI for your research, or just swap book recommendations — I'd love to hear from you.