Carl Mathias Kobel, PhD

I’m a bioinformatician in multi-omics integration seeking to distill biological interpretations of multi-modal large-scale experimental data. I use dimensionality reduction and network analysis to identify concrete biological compounds from noisy datasets. Meta-omics (microbes) often play a large role in my 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

“Spatial Imputation for Nodule Organogenesis”, Presentation at the ENSA Annual Meeting 2026, Freiburg DE
“Rumen-Centric Assembly of the Cattle Holobiont”, PhD defense at Norwegian University of Life Sciences 2026, Ås NO [ad | announcement | so-me]
“CompareM2 is a genomes-to-report pipeline”, Guest presentation at Center for Evolutionary Hologenomics, University of Copenhagen 2024, Copenhagen DK [so-me]
“Holo-omic Workflow Utilizing Network Analysis Reveals Compositional Bistability Between Rumen Microbiomes”, Presentation at Applied Hologenomics Conference 2024, Copenhagen DK [youtube | abstract]
“Holo-omic network analysis reveals bistability in the rumen microbiome”, Presentation at Congress on Gastrointestinal Function 2024, Urbana-Champaign USA [abstract]
“Holo-omics and host-microbiome interactions in the herbivore rumen”, Poster and pitch at Australian Microbial Ecology Conference 2022, Melbourne AU [abstract]
“Holo-omics and host-microbiome interactions in the herbivore rumen”, Poster at International Society of Microbial Ecology 2022, Lausanne CH

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