PhD student in Systemic Biology

PhD student in Systematic biology
Are you interested in working with fungal genomics, with the support of competent and friendly colleagues in an international environment? Are you looking for an employer that invests in sustainable employeeship and offers safe, favourable working conditions? We welcome you to apply for a PhD position at Uppsala University.

Research in the Fungal Accessory Genome Evolution (FungAGE) lab focuses on understanding the evolution of genomes and the genetic basis of adaptation in fungi. We recently discovered that many fungi harbour massive transposable elements, named Starships, that mobilize a vast diversity of fungal genes. We have now deciphered how the Starships move within genomes, but a growing amount of evidence suggests that they are also capable of moving between genomes. The main goal of this PhD position is to explore the evolutionary dynamics of the Starship elements and the fungal host genome through comparative genomic techniques. Ideally, this will reveal trade-offs between harbouring a given Starship and growth under specific environmental conditions. Additional objectives will seek to quantify such trade-offs by growing fungal strains under laboratory conditions.

Duties
This project will primarily make use of existing comparative genomic pipelines that we have developed in the group. The development of new pipelines will also be a core part of this project. As such, familiarity with coding languages is an asset. Fungal culturing using a variety of media and conditions may also be a part of the project, therefore interest in both computational and laboratory research is desired. Analysis of results with statistical methods, such as those implemented in R will also be important. Results will be written for publication in scientific journals and presented at international conferences.

Requirements
To meet the entry requirements for doctoral studies, you must

• hold a Master’s (second-cycle) degree in Evolution Biology, Bioinformatics or a closely related area, or
• have completed at least 240 credits in higher education, with at least 60 credits at Master’s level including an independent project worth at least 15 credits, or
• have acquired substantially equivalent knowledge in some other way.

Experience with running bioinformatic tools is a necessity, which may include: working in UNIX environments, scripting in python/perl/, or working with whole genome alignments.

Strengths in organization, problem solving, communication, and collaboration are required. The applicant should have documented experience and proficiency in oral and written presentation in English.

Additional qualifications
Additional assets include experience with analyzing genomic data and microbial culturing, particularly of fungi. Experience with communication of scientific concepts within an academic setting, including forming hypotheses and conducting statistical analyses is also a plus. 

Rules governing PhD students are set out in the Higher Education Ordinance chapter 5, §§ 1-7 and in Uppsala University's rules and guidelines.

About the employment
The employment is a temporary position according to the Higher Education Ordinance chapter 5 § 7. Scope of employment 100 %. Starting date 250301 or as agreed. Placement: Uppsala

For further information about the position, please contact: Aaron Vogan, aaron.vogan@ebc.uu.se

Please submit your application by 31 January 2025, UFV-PA 2024/4334.

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