Carl Mathias Kobel, MSc
I’m a bioinformatician and a PhD candidate in the MEMO group at NMBU, Norway. My perspective is 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.
Looking for a postdoc position in the Copenhagen area from ~april 2025.
First-author publications/preprints
- PhD thesis: Kobel 2025, Rumen-Centric Assembly of the Cattle Holobiont, NMBU Library [pdf]
- Research paper: Kobel et al. 2024, Protozoal populations drive system-wide variation in the rumen microbiome, preprint/bioRxiv [pdf | doi]
- Software paper: Kobel et al. 2024, CompareM2 is a genomes-to-report pipeline for comparing microbial genomes, preprint/bioRxiv [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
Upcoming
- PhD defense. “The Cattle Holobiont”. Venue: Husdyrfagbygget, Norwegian University of Life Sciences, Ås, Norway. Date: 12:00, Friday, 17th of January 2025.
Previous presentations
- CEH (Center for Evolutionary Hologenomics) Center guest presentation 2024, University of Copenhagen, “CompareM2 is a genomes-to-report pipeline” [linkedin]
- AHC (Applied Hologenomics Conference) 2024, Copenhagen, DK, Presentation “Holo-omic Workflow Utilizing Network Analysis Reveals Compositional Bistability Between Rumen Microbiomes” [youtube]
- CGIF (Congress on Gastrointestinal Function) 2024, Urbana-Champaign, USA, Presentation “Holo-omic network analysis reveals bistability in the rumen microbiome”
- AusME (Australian Microbial Ecology Conference) 2022, Melbourne Australia, poster and pitch “Holo-omics and host-microbiome interactions in the herbivore rumen (#18)”.
- ISME (International Society of Microbial Ecology) 2022, Lausanne Switzerland, poster “Holo-omics and host-microbiome interactions in the herbivore rumen”.
Teaching
- NMBU Bin420 “Bioinformatics for Functional Meta-Omics” 2024 | Development of dry-lab course material and exercises [link]
- NMBU Bio326 “Genome sequencing; tools and analyses” 2023-2024 | Development of dry-lab course material and exercises [link]
- Course in Microbiology at Aarhus University Hospital 2021 for MDs specializing in Microbiology | Rapid long-read sequencing of clinical isolates.
Miscellaneous
Conda recipe maintainer
Maintaining the recipes for the following Conda packages.
(archived)Open source wizardry
Contribution to the upstream code base of:
