Postdoc in the area of bioinformatics of bacteria-phage co-evolution

General description

We are inviting applications for a postdoctoral researcher working on the bioinformatics of co-evolution between temperate phages and the bacteria from the Klebsiella genus. The successful candidate will join the Microbial Genomics Group at Malopolska Centre of Biotechnology, Jagiellonian University in Kraków. This is a 2-year National Science Foundation (ncn.gov.pl) funded position with the possibility of extension, available from March 2023.

The successful candidate will work as part of the team, funded by the Sonata Bis NCN project, the goal of which is to predict the specificity of interactions between phage proteins and bacterial sugars during the phage infection cycle. Bacterial surface sugars are highly diverse, both structurally and genetically, and they confer an obstacle to phage infection [1]. Phages have evolved enzymes called depolymerases, located in receptor-binding proteins (RBPs), like tail fibres or tail spikes, which decompose these surface sugars and help the virus proceed with infection. The aim of the project is to test the hypothesis that we can predict interactions between phage RBPs and bacterial sugars by training bioinformatic models with experimental data. The project will be led by dr hab. Rafal Mostowy at Jagiellonian University in Krakow, and the experimental part will be conducted in collaboration with the lab of Professor Zuzanna Drulis-Kawa at University of Wroclaw.

As a postdoc in this team, you will reconcile evolutionary relationships between the genetics of bacterial surface molecules and structural proteins within prophages co-evolving with the population of bacteria from the Klebsiella pneumoniae species. RBPs of Klebsiella-infecting phages are known to be highly sugar-specific [2] and RBP-sugar interactions are a strong determinant of phage host range in K. pneumoniae [3]. It is therefore expected that many prophages found in bacterial genomes carry RBPs specific to the surface polysaccharides of the bacteria in question. However, such in silico inference of RBP-sugar specificity may be challenging due to multiple reasons (e.g., rapid evolution occurring at both capsule and prophage loci, between-phage interactions, complexity of the phage infection phenotype). To address this problem, you will work with large collections of bacterial genomes and develop phylogenetic models of co-evolution between bacteria and their mobile genetic elements. You will apply structural bioinformatics tools (like AlphaFold2) to investigate the genetic and phenotypic diversity of prophage proteins within the tail module. You will interact with other members of our rapidly growing Microbial Genomics group and the Drulis-Kawa lab and work together as a team. You will work in collaboration with other top research groups in the UK, France and Australia. Finally, your work will contribute to the fight against the problem of antibiotic resistance by helping us understand the adaptive potential of phages to bacterial pathogens and helping find potential new candidates for antimicrobial drugs (enzybiotics).  

The successful candidate will be able to influence the direction of the project depending on their profile and strengths. They will have the opportunity learn multiple new skills, particularly in the areas of genome informatics and microbiology, and develop international contacts, but will be expected to manifest an increasing degree of intellectual independence throughout the project.

References

  1. Mostowy RJ, Holt KE. Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating. Trends Microbiol. 2018;26(12):1008-1021. doi:10.1016/j.tim.2018.06.006.

  2. Pan Y-J, Lin T-L, Chen C-C, et al. Klebsiella Phage ΦK64-1 Encodes Multiple Depolymerases for Multiple Host Capsular Types. Sandri-Goldin RM, ed. Journal of Virology. 2017;91(6):e02457–16. doi:10.1128/JVI.02457-16.

  3. Majkowska-Skrobek G, Latka A, Berisio R, et al.Phage-Borne Depolymerases Decrease Klebsiella pneumoniae Resistance to Innate Defense Mechanisms. Front Microbiol. 2018;9:2517. doi:10.3389/fmicb.2018.02517. 

Specific requirements

The successful candidate will:

  • hold a PhD in a quantitative field like biology, chemistry, physics, mathematics, computer science or similar,

  • manifest a high degree of enthusiasm for the advertised project,

  • have excellent oral and written communication skills in English,

  • have strong presentation skills (ideally having presented on at least one international conference),

  • enjoy support of and interaction with other group members,

  • fulfil formal criteria of the competition as specified by the National Science Foundation (see section 2.1.1 here, in Polish)

The ideal candidate will also fulfil the following requirements:

  • have extensive experience of using a major programming language (e.g., R, Python, C/C++, Java) for data analysis purposes,

  • have experience in designing bioinformatic pipelines (e.g., via an existing GitHub repository),

  • demonstrate in-depth knowledge in at least one of the following research areas: structural biology, phage biology, microbiology, next-generation sequence data genomics, 

  • have a strong track record of published research and presenting at international conferences,

We offer:

  • opportunity to work on an ambitious and important scientific problem, hence contributing to the fight against antimicrobial resistance,

  • a competitive salary compared to other NCN-funded postdoctoral positions in Poland,

  • opportunity to collaborate with world-class scientific leaders at the leading scientific institutions,

  • a fun and interactive working environment closely linked to the bioinformatics community at Malopolska Centre of Biotechnology,

  • participation in collaborations and scientific meetings across the globe,

  • flexible working time with an opportunity to work remotely (subject to a mutual agreement),

  • social security and multiple benefits (e.g., subsided fitness gym membership), additional 13th salary after working a minimum of six months.

How to apply?

To be considered for this position, please send an email to rafal.mostowy@uj.edu.pl or aleksandra.sulma@uj.edu.pl with the subject “Post-doc Mostowy Lab Sonata Bis” and:

  1. A cover letter (max 1 page) with explicit answers to the following questions: (1) What do you know about our laboratory and why you want to join us specifically? (2) What are your long-term goals and how this position will help you achieve them? (3) What makes you stand out amongst all the candidates?

  2. Your CV including the full list of publications.

  3. Names and contact details of at least 2 referees.

The deadline for applications is 12th of February 2023.