In the last two decades, astounding improvements in sequencing and computational capabilities have generated heaps of bacterial and archaeal genome data, leading to new insights into the biosphere's functioning and diversity. Using this information, we can aim to unlock biological principles hidden within genome sequences. An exciting avenue of research is to enquire how genomes evolve. Common patterns govern genome architecture across the tree of life, but unexplained cases exist (e.g. Tamarit et al. Genome Biol Evol 2015), and large-scale genomic analyses reveal major trends that remain to be understood. Once again, harnessing the power of big data will impact our current understanding of genome evolution, generating new observations and allowing us to test new hypotheses.

This position aims to investigate bacterial and archaeal genome organisation, studying the evolutionary mechanisms and the biological impacts of current genome architectures. A first step will involve describing and understanding novel patterns of gene localisation, and exploring bacterial and archaeal lineages with a strong emphasis on recently discovered groups. You will employ molecular evolution and comparative genomic techniques such as gene annotation, phylogenetics/phylogenomics, and a range of sequence analyses to examine large-scale genome datasets. Depending on specific opportunities and your own interests, this position may involve several additional approaches.

Pursuing a PhD in this area offers you the opportunity to gain a deep understanding on genome biology and the full scope of biological diversity. You will learn to handle large-scale genomic datasets and become an expert on state-of-the-art bioinformatics methods to analyse them, including command-line work, programming, and data visualisation. Additionally, this position will equip you with important academic skills such as teaching, effective scientific communication (written and oral), and building collaboration networks. Moreover, we want to help you learn to navigate through academic life in a way that does justice to your career ambitions but also maintains a healthy work-life balance.

We are looking for an enthusiastic new colleague with a positive, team-oriented mindset. We would also like you to have:

• A completed, or almost completed, Master's degree in biology, bioinformatics, or related discipline.
• A strong interest in evolution, genome biology, microbiology and/or bioinformatics.
• A good command of English, both oral and written.

We consider it an advantage if you bring either of the following:

• Experience in command-line or programming (e.g. bash, R, python, perl).
• Experience with sequence analysis (e.g. similarity search, alignment), comparative genomics (e.g. gene annotation, homology detection) or evolutionary analyses (phylogenetics, dN/dS).
• Demonstrable organisation and communication skills.

Please note: it has been shown that women and applicants from ethnic minority backgrounds tend to underapply for positions if they don’t feel they meet all the listed criteria. If this is how you feel, please be encouraged to apply anyway, and don’t hesitate to reach out if anything is unclear.

• Embedding within a great team of world-class scientists, where English is the main working language.
• Academic training within the Graduate School of Life Sciences.
• A supportive environment with a commitment to academic development and maintaining a healthy work-life balance.
• A full-time PhD position for 4 years.
• A full-time gross salary ranging from € 2.541 to €3.241 in scale P.
• 8% holiday bonus and 8.3% end-of-year bonus.
• A pension scheme, partially paid parental leave, and flexible employment conditions based on the Collective Labour Agreement Dutch Universities.

In addition to the employment conditions from the CAO for Dutch Universities, Utrecht University has a number of its own arrangements. These include agreements on professional development, leave arrangements and sports. We also give you the opportunity to expand your terms of employment through the Employment Conditions Selection Model. This is how we encourage you to grow.

For more information, please visit working at Utrecht University.

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The research will be performed at the Archaeal and Bacterial Evolution team headed by Dr. Daniel Tamarit. This is a new team specialised in the use of genomic analyses of bacteria and archaea to study fundamental processes in evolution. Current major lines in this group involve investigating major transitions in evolution such as the origin of eukaryotes and the diversification of other microbial lineages, the exploration of genome architecture in bacteria and archaea, and the development of related bioinformatic tools.

The team is embedded in the Theoretical Biology and Bioinformatics group (department of Biology), which uses computational biology, bioinformatics, modelling, and big data to address both fundamental and applied questions in the life sciences. A selection of ongoing research lines includes the evolution of genomes, protein complexes, systems genetics, metagenomics, host-microbe interactions, and the principles of ecology and evolution. Together with more than 35 research groups distributed over five research and educational institutes, we form the Utrecht Bioinformatics Centre that combines world-class bioinformatics research and coordinates bioinformatics education at all levels at the Utrecht Science Park.