Joachim Johansen
Research interests
Human Microbiome and Community Ecology | Multi-omics analysis and Integration | Phageology | Bacterial Immuno-peptidomes.
I am highly interested in the application and development of computational tools to understand microbiome ecology hubs in the context of human health. During my PhD in the Rasmussen lab, my main focus is working on new approaches to explore metagenomic dark matter such as viruses and mobile genetic elements and their role in relation to known clades of gut bacteria.
Main PhD project
The human gut microbiome hosts several cellular residents including the bacterial, archeal, eukaryotic and viral kingdom that occupies various ecological niches. The bacterial kingdom is the most well studied and highly acknowledged for its imperative role in metabolic processes and immune development beneficial to the host. Yet, the bacterial infecting viruses, known as bacteriophages (phages), are suggested to outnumber bacteria, regulate their density and interactome in both healthy and diseased patients. While thousands of putative gut bacterial genomes have been discovered using next generation sequencing and computational methods, relatively few phages have been added to the pool of known gut phages, leaving a knowledge gap in understanding the bacteriophage-bacterial relationship. Hence, a major component with implications for the mutualistic relationship of gut bacteria and human host remains ‘dark-matter’ for a range of gastrointestinal disorders and in the healthy microbiome. In essence, the aim of this Ph.D project is to develop a computational framework, using established methods from Artificial Intelligence to capture and illuminate phage genomes in metagenomic sequencing data useful for understanding their role in natural environments such as the human gut.
Related github repositories
- PHAMB
- Viral analysis in Centenarians, repo
Short CV
- 2019 - present: Affiliate PhD researcher Xavier Lab at the Broad Institute of MIT and Harvard
- 2019 - present: PhD Fellow in Rasmussen Lab at the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark.
- 2019: Research Assistant in Rasmussen Lab and Brunak Lab
- 2018-2019: Bioinformatics Specialist at Clinical Microbiomics
- 2018: Graduate Student Researcher at the Xavier lab of the Infectious Disease and Microbiome Program at the Broad Institute of MIT and Harvard
- 2016-2018: MSc. Eng. Bioinformatics and Systems Biology at DTU
- 2013-2016: BSc. Eng. Human Life Science at DTU