AI tools, computer vision and applied genomics

Tim Martin Knutsen

Senior scientist at AquaGen AS, Trondheim.

My background is in genomics, but these days most of my time goes into building things: tools that lean on LLMs, image-based phenotyping, and the pipelines, dashboards, and small APIs that sit between raw data and a decision someone actually has to make. The messy part in the middle is the part I like.

Photo: AquaGen, via NMBU

What I build

Most of what I do falls into a few areas.

LLM workflows.

Using LLMs and coding agents to pull structure out of text: extraction, ingestion, and the kind of summaries I'd rather not write by hand.

Computer vision.

Image-based phenotyping: getting reliable measurements out of images and video, in a way that gives the same answer twice.

Reproducible pipelines.

Analysis workflows someone else can rerun and actually trust, from raw input all the way to the result.

Dashboards & APIs.

Small dashboards, FastAPI services, and PWAs that make the numbers easy to see and easy to check.

Selected projects

A few things I've built in the open. Side projects, really — not the full picture of what I do day to day.

ai-sota-tracker Pulls in AI sources, uses an LLM to extract what matters, and writes a structured weekly summary. SQLite, FastAPI, and a PWA front end.
stock_dashboard Pulls market and news data into one view, with GPT-assisted analysis on top.
beagle_impute A reproducible genomics workflow: chromosome-wise genotype imputation with Beagle or AlphaImpute2, wired together with Snakemake.

Selected Publications

A few below. Google Scholar has the complete, up-to-date list, and there's a machine-readable version in publications.json.

Nguyen, D. T., Knutsen, T. M., Sandve, S. R., Lien, S., and Grønvold, L. 2025. Sequence-based chromatin activity modeling and regulatory impact prediction of genetic variants in farmed animals using deep learning. NAR Genomics and Bioinformatics.
Brekke, C., Johnston, S. E., Knutsen, T. M., and Berg, P. 2023. Genetic architecture of individual meiotic crossover rate and distribution in Atlantic Salmon. Scientific Reports.
Brekke, C., and Knutsen, T. M. 2026. Phenotypic sex determines recombination rate and distribution in sex-reversed rainbow trout. Aquaculture.
Knutsen, T. M., Olsen, H. G., Ketto, I. A., Sundsaasen, K. K., Kohler, A., Tafintseva, V., Svendsen, M., Kent, M. P., and Lien, S. 2022. Genetic variants associated with two major bovine milk fatty acids offer opportunities to breed for altered milk fat composition. Genetics Selection Evolution.
Langille, B. L., Kess, T., Nugent, C. M., Messmer, A., Duffy, S. J., Knutsen, T. M., Kent, M., Boyce, D., Gregory, R. S., Gauthier, J., Fairchild, E. A., Pietrak, M., Garcia de Leaniz, C., Consuegra, S., Whittaker, B., Bentzen, P., and Bradbury, I. R. 2024. Trans-Atlantic genomic differentiation and parallel environmental and allelic variation in lumpfish. ICES Journal of Marine Science.

PhD Thesis

Genomics of bovine milk fat composition. Doctoral thesis, Norwegian University of Life Sciences, 2018. Series: PhD Thesis;2018:19.

The thesis examined mutations affecting fatty acid composition in Norwegian Red cattle milk, with emphasis on de novo synthesized fatty acids and the major milk fatty acids palmitic acid and oleic acid.