Carl Mathias Kobel, PhD

I’m a bioinformatician with the perspective that microbiomes are largely undervalued, and that we should better understand the minute interactions within them. I have a big data inspired approach, enjoy tinkering with hardware, and like to build parallelizable bioinformatics pipelines to gain insights into large multi-omic microbiome datasets.

Currently open to work.

Selected works

Research paper: Kobel et al. 2025, Protozoal populations drive system-wide variation in the rumen microbiome, Nature Communications [pdf | doi]
Software paper: Kobel et al. 2025, CompareM2 is a genomes-to-report pipeline for comparing microbial genomes, OUP Bioinformatics [pdf | doi | docs | repo | bioconda]
Review paper: Kobel et al. 2024, Integrating host and microbiome biology using holo-omics, RSC Molecular Omics [pdf | doi]
PhD thesis: Kobel 2025, Rumen-Centric Assembly of the Cattle Holobiont, NMBU Library [pdf]

Activities

Presentations

Norwegian University of Life Sciences (NMBU) 2025, PhD defense “Rumen-Centric Assembly of the Cattle Holobiont” [ad | announcement | so-me]
Center for Evolutionary Hologenomics (CEH) 2024, University of Copenhagen, Center guest presentation “CompareM2 is a genomes-to-report pipeline” [so-me]
Applied Hologenomics Conference (AHC) 2024, Copenhagen DK, Presentation “Holo-omic Workflow Utilizing Network Analysis Reveals Compositional Bistability Between Rumen Microbiomes” [youtube | abstract]
Congress on Gastrointestinal Function (CGIF) 2024, Urbana-Champaign USA, Presentation “Holo-omic network analysis reveals bistability in the rumen microbiome” [abstract]
Australian Microbial Ecology Conference (AusME) 2022, Melbourne Australia, Poster and pitch “Holo-omics and host-microbiome interactions in the herbivore rumen” [abstract]
International Society of Microbial Ecology (ISME) 2022, Lausanne Switzerland, Poster “Holo-omics and host-microbiome interactions in the herbivore rumen”

Teaching

Aarhus University Hospital course in bioinformatics for MDs specializing in Microbiology 2025 | Microbial Genomes: Functional characterization and species identification
Norwegian University of Life Sciences Bin420 “Bioinformatics for Functional Meta-Omics” 2024 | Development of dry-lab course material and exercises [link]
Norwegian University of Life Sciences Bio326 “Genome sequencing; tools and analyses” 2023-2024 | Development of dry-lab course material and exercises [link]
Aarhus University Hospital course in microbiology for MDs specializing in Microbiology 2021 | Rapid long-read sequencing and characterization of clinical isolates