jobs

All open and upcoming CompMicroLab positions 💼

Open/upcoming postdoc positions

There are currently no open/upcoming postdoc positions in the CompMicroLab, but we’ll keep you posted here! 🙏



Open/upcoming PhD student positions

There are currently no open/upcoming PhD student positions in the CompMicroLab, but we’ll keep you posted here! 🙏



Open/upcoming Master’s student positions

Looking to do a microbial bioinformatics Master’s thesis project? We’ve got you covered! If you’re a Master’s student at a Swedish university, and you’re interested in one of the projects listed below, feel free to reach out to Laura for more information!

🌲 Build ALL the trees!

Benchmarking bioinformatic pipelines used in foodborne pathogen surveillance

The project: Phylogenies are important tools for foodborne pathogen surveillance; they allow us to track foodborne pathogens around the world as they move along the food supply chain. There are many ways to construct a phylogeny...but which is the best? In this project, you'll be comparing different bioinformatic pipelines for constructing phylogenies, using whole-genome sequencing (WGS) data derived from foodborne pathogens (e.g., Salmonella enterica, Listeria monocytogenes, Escherichia coli)--all with the goal of finding the pipeline(s) that reign supreme! 👑

Required educational background: Any STEM discipline 😊

Required programming skills: None (some knowledge of any programming language is beneficial, but not necessary, for this project 😊)


🍄 He’s a fun-gi

Discovering novel fungal secondary metabolites using conditional random fields

The project: Fungi use biosynthetic gene clusters (BGCs) to produce secondary metabolites, also known as natural products. These secondary metabolites allow fungi to interact with their environment and can be used for virulence, defense, quorum sensing, protection, nutrient acquisition and/or the promotion of growth...but they can also have uses/roles outside of fungal ecology (some famous examples include the immunosuppressant cyclosporin, cholesterol-reducing lovastatin, the antibiotic penicillin, the hallucinogenic prodrug psilocybin, and the mycotoxins trichothecene and aflatoxin)! In this project, you will train a conditional random field (CRF) to detect BGCs in fungal genomes...and maybe discover a novel fungal BGC in the process!

Required educational background: Any STEM discipline 😊

Required programming skills: Python


💬 Naive Bayes for naïve bae-s

Developing a text mining approach for pathogen metadata classification

The project: Pathogens in the Bacillus cereus group can cause a variety of illnesses in humans, including deadly anthrax and anthrax-like illnesses, mild-to-severe foodborne illnesses, and severe non-gastrointestinal infections. We recently developed a database of B. cereus group genomes, which can be used to improve pathogen surveillance and outbreak response efforts. In addition to genomic data, our database contains standardized, manually curated metadata denoting where, when, and how each strain was isolated...which took multiple curators a YEAR to clean up! Can you train a model to help us automate the process and help laboratories around the world detect and solve outbreaks?

Required educational background: Computer science and related disciplines with natural language processing/text mining experience.

Required programming skills: Python


⛏️ Mining for col(istin resistance)

Discovering novel antimicrobial resistance determinants using machine learning

The project: Antimicrobial resistance (AMR) is one of the biggest threats facing global public health today, and numerous genes can equip bacterial pathogens with AMR. In this project, you will train a model to detect AMR genes in bacterial genomes, with the goal of finding novel genes involved in AMR!

Required educational background: Any STEM discipline 😊

Required programming skills: Python