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.
Conda recipe maintainer
Conda recipes maintainer for the following packages.