Salmonid genomics.
Genetic variation, disease resistance, robustness, and genomic data that can support breeding in Atlantic salmon and rainbow trout.
Salmonid genomics, bioinformatics and AI tools
Tim Martin Knutsen
Senior scientist at AquaGen AS, Trondheim.
My work sits where salmonid genomics and bioinformatics meet breeding decisions. I am also interested in image-based phenotyping and AI tools for coding, analysis and writing.
Research
Here are some of the topics I spend most time on:
Bioinformatics.
Reproducible analysis, data handling, automation, and workflows that are transparent enough to reuse.
Computer vision.
Image-based phenotyping and methods for extracting useful biological information from images and video.
AI tools.
LLMs, Codex, Claude Code and agents for coding, analysis, writing and technical work.
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.
Selected Publications
- 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.
Code
- Beagle imputation pipeline Snakemake workflow for chromosome-wise genotype imputation with Beagle or AlphaImpute2.
- ai-sota-tracker Small pipeline for collecting AI sources and generating structured weekly notes.
Links
- NMBU profile Interview about education, AquaGen, and applied genomics in aquaculture.
- AQUA-FAANG Exploitation Working Group Collaboration on uptake of functional annotation resources in aquaculture breeding.
- AquaGen maps lumpfish genome News coverage of the lumpfish genome resource and its applied relevance.