PhD Position in Bioinformatics of the Microbiome

Are you fascinated by the microbiome and its interaction with the human host? Microbiome research has flourished in the last decade, thanks in no small part to the relative ease with which large volumes of metagenomics sequencing data can be generated. Bioinformatics method development has advanced, but to this date, the human microbiome is mostly studied in terms of ‘who’s there’, followed by indicators of microbial metabolism and some specific molecular classes, such as antibiotics resistance. Long-standing biomedical knowledge says that an important part of the interaction between microbes and especially with hosts are determined by structural interactions, but this has been all but ignored. State of the art bioinformatics methods can tackle this challenge! Do you want to address this oversight with us?

In this PhD project, the objective is to develop and extend bioinformatics methods that can mine metagenomic sequencing datasets for features that are related to the physical interaction with human cells, and particularly the immune system. For this, you will make use of classical bioinformatics and machine learning approaches to detect features of interest in sequence and protein structural data. Having applied your new methods to metagenomics data, you will also test what kind of statistical considerations are important for interpreting the results.

The advertised position is under the supervision of dr. Anna Heintz-Buschart of the Biosystems Data Analysis group at the Swammerdam Institute for Life Sciences at the University of Amsterdam (UvA). The group has a broad profile in bioinformatics, multivariate statistics and modelling with a growing focus on microbiome research, for example in lively collaborations within UvA’s research priority areas Personalized Microbiome Health and System Biology Host-Microbiome Interaction and the Dutch Holomicrobiome Initiative.

What are you going to do?

You will receive training in and are expected to:

• complete a PhD thesis within the official appointment duration of four years;
• design, apply and benchmark bioinformatics algorithms, tools, and workflows to predict central aspects of host-microbiome interactions based on metagenomics sequencing data of the human microbiome;
• analyse existing and novel metagenomics datasets using your and existing methods;
• document your work in an accessible, open science manner;
• publish the findings in peer-reviewed manuscripts and as part of your PhD thesis;
• participate in the Faculty of Science PhD training program;
• be an active member of the Biosystems Data Analysis group, including by supervision of BSc or MSc students.

What do we require?

You have:

• a MSc degree in bioinformatics; or in data science, informatics, or related subjects with a strong biological or biomedical component;
• or in the life or biomedical sciences with a strong informatics component;
• hands-on experience in omics data analysis and coding skills – experience with microbiome data and machine learning are a plus;
• fluency in English, written and spoken, and the confidence to use it in scientific communication and publications;
• enthusiasm for human bioinformatics in microbiome research in a diverse team and the ability to take ownership of the research project;

Our selection will be based on your academic track record, your skills and ambition, and your enthusiasm and ideas for this research project.

Our offer

We offer a temporary contract for 38 hours a week, preferably starting on 1-12-2024, for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years). This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students.

Based on a full-time appointment (38 hours per week) the gross monthly salary will range from € 2.872 in the first year to €3.670 (scale P) in the last year. This is exclusive 8% holiday allowance and 8.3% end-of-year bonus. A favourable tax agreement, the ‘30% ruling’, may apply to non-Dutch applicants.