Carl Mathias Mølby Kobel, PhD
Bioinformatician in Multi-Omics Integration
Aarhus University, Denmark
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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 deep learning to identify concrete biological factors from noisy datasets. Meta-omics (microbes) often play a large role in my work, and I currently work with spatial transcriptomics.
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]
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 2025, 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
Miscellaneous
Open source contributions
Contributor to the code base of the following open source projects.
- CompareM2 - Genomes-to-report pipeline
- Snakemake - Workflow management system
- GTDB-Tk - Taxonomic classification
Conda recipe maintainer
Recipe maintainer for the following packages.