Tim Martin Knutsen

Tim Martin
Knutsen

I'm a geneticist from Ås, Norway. I like building things with code and AI, and this is where I keep them.

Portrait of Tim Martin Knutsen
Photo: via NMBU
A made-up mountain ridge. The sun and moon follow an illustrative day and night cycle in Oslo. The moon phase is approximate.

About

I work with genetic data, and I write software to make sense of it.

I worked five years as a bioengineer in a hospital laboratory, then went back to university. I took an MSc in biology and a PhD in statistical genomics at NMBU. My thesis mapped the genes behind milk fat composition in cattle.

Away from the computer I train, and I forage mushrooms around Ås. I have built a small app for each.

AI

AI has changed how I build things.

I use coding agents every day. Projects that used to stop at an idea, like a small web app or a data pipeline, now get finished. The agent writes much of the code. I decide what to build, check the results, and know the data well enough to see when something is wrong. That last part still matters most.

  • Coding agents

    Writing and reviewing code for research pipelines and small apps.

  • Language models for data

    Pulling structured data out of messy text and documents.

  • MCP servers

    Connecting language models to databases and tools, so they look things up instead of guessing.

  • Computer vision

    Measuring traits from images, so more animals can be recorded at lower cost.

  • Deep learning in genomics

    Predicting the effect of genetic variants from DNA sequence. I am a co-author on a 2025 paper on this.

  • Small apps

    Web apps for my own use, hosted on this domain. Two of them are below.

Projects

Things I have built, from GitHub and this domain. Some are apps I use myself, some are research pipelines.

  • gpt-install

    A one-minute video and written steps for installing the ChatGPT desktop app on Windows and connecting it to a server over SSH, with Codex fixing the connection when it fails.

  • soppkart

    An interactive map of likely mushroom habitat around Ås, built from public map layers. It logs my own finds and empty searches, so the model improves as I use it.

  • treningsapp

    A training-plan web app for the phone. Strength on Saturday, running on Sunday, and missed sessions move automatically.

  • wgs-align-varcall

    Slurm and GATK pipelines for whole-genome alignment and short-variant calling. One site config makes it portable across HPC clusters.

  • beagle_impute

    Chromosome-wise genotype imputation with Beagle or AlphaImpute2, run through Snakemake.

Background

  1. 2018

    PhD, Norwegian University of Life Sciences

    Centre for Integrative Genetics (CIGENE), Ås

    Genomics of bovine milk fat composition. Defended 25 May 2018, in Sigbjørn Lien's group. Supervisors Sigbjørn Lien, Hanne Gro Olsen, Matthew Peter Kent and Torfinn Nome. Done in collaboration with Geno.

  2. Earlier

    MSc in Biology, Norwegian University of Life Sciences

    Molecular genomics and evolution, with statistical genomics, population genetics, bioinformatics and programming.

  3. Earlier

    Consultant, Geno

    Led work to systematise and quality-check genetic data for important cattle traits.

  4. Earlier

    Bioengineer, Lovisenberg hospital

    Oslo

    Five years of medical laboratory analyses.

Papers

Twelve peer-reviewed articles, on the genetics of cattle, salmon, trout and lumpfish. Also available as publications.json.

Show the list
  1. 2026 Phenotypic sex determines recombination rate and distribution in sex-reversed rainbow trout (Oncorhynchus mykiss) Brekke C, Knutsen TM. Aquaculture.
  2. 2025 Sequence-based chromatin activity modeling and regulatory impact prediction of genetic variants in farmed animals using deep learning Nguyen DT, Knutsen TM, Sandve SR, Lien S, Grønvold L. NAR Genomics and Bioinformatics 7(4): lqaf139.
  3. 2025 Dissecting the genetic basis of response to salmonid alphavirus in Atlantic salmon Manousi D, Jaskula DM, …, Knutsen TM, …, Lien S. BMC Genomics 26: 657.
  4. 2024 Trans-Atlantic genomic differentiation and parallel environmental and allelic variation in lumpfish (Cyclopterus lumpus) Langille BL, Kess T, …, Knutsen TM, …, Bradbury IR. ICES Journal of Marine Science 81(6): 1025.
  5. 2023 Genetic architecture of individual meiotic crossover rate and distribution in Atlantic salmon Brekke C, Johnston SE, Knutsen TM, Berg P. Scientific Reports 13: 20481.
  6. 2023 Fine-scale environmentally associated spatial structure of lumpfish (Cyclopterus lumpus) across the Northwest Atlantic Langille BL, Kess T, …, Knutsen TM, …, Bradbury IR. Evolutionary Applications 16(9): 1619-1636.
  7. 2022 Genetic variants associated with two major bovine milk fatty acids offer opportunities to breed for altered milk fat composition Knutsen TM, Olsen HG, Ketto IA, …, Lien S. Genetics Selection Evolution 54: 35.
  8. 2022 Reference genome of lumpfish Cyclopterus lumpus Linnaeus provides evidence of male heterogametic sex determination through the AMH pathway Holborn MK, Einfeldt AL, …, Knutsen TM, …, Bradbury IR. Molecular Ecology Resources 22(4): 1427-1439.
  9. 2020 Interleukin-1 ligands and receptors in lumpfish (Cyclopterus lumpus L.): molecular characterization, phylogeny, gene expression, and transcriptome analyses Eggestøl HØ, Lunde HS, Knutsen TM, Haugland GT. Frontiers in Immunology 11: 502.
  10. 2018 Unravelling genetic variation underlying de novo-synthesis of bovine milk fatty acids Knutsen TM, Olsen HG, Tafintseva V, Svendsen M, Kohler A, Kent MP, Lien S. Scientific Reports 8: 2179.
  11. 2017 Genome-wide association mapping for milk fat composition and fine mapping of a QTL for de novo synthesis of milk fatty acids on bovine chromosome 13 Olsen HG, Knutsen TM, Kohler A, …, Lien S. Genetics Selection Evolution 49: 20.
  12. 2016 Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production Olsen HG, Knutsen TM, Lewandowska-Sabat AM, …, Lien S. Genetics Selection Evolution 48: 79.

Data

  1. 2018 Lumpfish (Cyclopterus lumpus) draft genome assembly Knutsen TM, Kirubakaran TG, Mommens M, Moen T. Figshare.

Conference

  1. 2022 Distinct spatial genomic structure of lumpfish Cyclopterus lumpus across the Northwest Atlantic Langille BL, Kess T, … Knutsen TM, … Bradbury IR. Aquaculture Canada and WAS North America, St. John's.