PhD position on Microbial Genome Evolution

Join us to explore microbial genome evolution across the tree of life using cutting-edge evolutionary bioinformatics. This PhD project offers hands-on experience with large-scale genomics, phylogenomics, gene annotation, and machine learning, with the goal of revealing how genome architecture shapes physiology, ecology, and evolution. Unlock hidden biological patterns while developing key computational and academic skills.

Your job
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 diversity and functioning. At our laboratory, we aim to unlock biological principles hidden within genome sequences. One outstanding knowledge gap we want to tackle is the evolution of genome architecture across the tree of life. Harnessing the power of large-scale genomic analyses and developing novel frameworks using evolutionary bioinformatics, we can now significantly advance this field, ultimately generating new observations and testing new hypotheses that will illuminate the complex interplay between genome biology, physiology, ecology and evolution.

This position aims to investigate bacterial and archaeal genome organisation, studying the evolutionary mechanisms underlying genome architecture, and their physiological consequences. 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 computational tools such as gene annotation, orthology detection, phylogenetics/phylogenomics, omics-data integration, machine learning and visualisation techniques. This project will be performed in collaboration with experts in different fields, and keeping possibilities open to follow research directions depending on obtained results and your interests.

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. We want to help you learn to navigate through academic life in a way that does justice to your career ambitions and maintains a healthy work-life balance.

We are looking for an enthusiastic new colleague with a positive, team-oriented mindset. You 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.

You will become part of a great team of world-class scientists, where English is the main working language. We have a strong commitment to maintaining a healthy work-life balance and academic development. You will receive academic training within the Graduate School of Life Sciences. Besides that, we offer

• a nurturing and inclusive environment, where we strive for everyone to feel comfortable being their authentic selves;
• a PhD position for four years;
• a working week of 38 hours and a gross monthly salary between €2,901 and €3,707 (salary scale P under the Collective Labour Agreement for Dutch Universities (CAO NU));
• 8% holiday pay and 8.3% year-end bonus;
• a pension scheme, partially paid parental leave and flexible terms of employment based on the CAO NU.

In addition to the terms of employment laid down in the CAO NU, Utrecht University has a number of schemes and facilities of its own for employees. This includes schemes facilitating professional development, leave schemes and schemes for sports and cultural activities, as well as discounts on software and other IT products. We also offer access to additional employee benefits through our Terms of Employment Options Model. In this way, we encourage our employees to continue to invest in their growth. For more information, please visit Working at Utrecht University.

A better future for everyone. This ambition motivates our scientists in executing their leading research and inspiring teaching. At Utrecht University, the various disciplines collaborate intensively towards major strategic themes. Our focus is on Dynamics of Youth, Institutions for Open Societies, Life Sciences and Pathways to Sustainability. Sharing science, shaping tomorrow.

Working at the Faculty of Science means bringing together inspiring people across disciplines and with a variety of perspectives and backgrounds. The Faculty has six departments: Biology, Pharmaceutical Sciences, Information & Computing Sciences, Physics, Chemistry and Mathematics. Together, we work on excellent research and inspiring education. We do so, driven by curiosity and supported by outstanding infrastructure. Visit us on LinkedIn and discover how you can become part of our community.

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, 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.

For more information, please contact Dr Daniel Tamarit via d.tamaritchulia@uu.nl.

Do you have a question about the application procedure? Please send an email to science.recruitment@uu.nl.

Candidates for this vacancy will be recruited by Utrecht University.