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Evolutionary genomics of bacteria-phage co-evolution

  • Full or part time
  • Application Deadline
    Friday, September 13, 2019
  • Funded PhD Project (Students Worldwide)
    Funded PhD Project (Students Worldwide)

Project Description

We are inviting applications for a research technician (with an option of becoming a PhD student) in the area of computational biology and genomics of bacteria-phage interactions. The successful candidate will join Dr Rafał Mostowy’s Microbial Genomics Group (https://mostowylab.com) at the Malopolska Centre of Biotechnology in Krakow. The position is available from September 2019 and funded by the Polish National Agency of Academic Exchange.

The successful candidate will work on the evolutionary genomics of bacteria-phage co-evolution. The general aim of the project is to explore the diversity and specificity of interactions between bacteriophages and opportunistic bacterial pathogens in the family of Enterobacteriaceae, with primary emphasis on Klebsiella pneumoniae. The PhD project itself will be focused on using cutting-edge bioinformatics to analyse hypervariable genomic regions in bacterial genomes and metagenomes, like capsule synthesis loci and prophages, using de novo assembly and assembly graphs, working with both Illumina and Oxford Nanopore sequencing data. The project will involve close collaboration with international groups with expertise in genome bioinformatics (Zamin Iqbal at EMBL, Sebastian Deorowicz at Silesian University of Technology), genomic epidemiology (Kat Holt at Monash University, Nick Thomson at Wellcome Trust Sanger Institute), experimental microbiology (Prof. Mark Enright at Manchester Metropolitan University) and structural biology (Sebastian Glatt at MCB). Results of the project will contribute to the fight against the problem of antibiotic resistance in Poland and Europe by helping understand importance of bacteriophages in emergence of bacterial resistance and virulence as well as by helping discover novel families of enzymes against virulent strains of Klebsiella.

The successful candidate will have an opportunity to influence the direction of the project depending on his/her profile and strengths. He or she will have the opportunity learn multiple new skills (e.g., working with Nanopore sequencing data) and develop international contacts, but will be expected to manifest an increasing degree of intellectual independence throughout the project.

The successful candidate will:
- hold a degree in a quantitative field like biology, chemistry, physics, mathematics, computer science or similar,
- have a very good knowledge of at least one programming language (e.g., R, Python, C/C++, Java),
- manifest a high degree of enthusiasm for the advertised project,
- have fluent oral and written communication skills in English,
- have good communication skills,
- enjoy support of and interaction with other group members,

The ideal candidate will also fulfil one or more of the following requirements:
- demonstrate evidence of having completed scientific projects in the area of data science, machine learning, structural biology, computational biology, microbiology or virology,
- have an active portfolio of developed software applications (e.g., an active Github repository),
- have a track record of presenting at research conferences and/or published research,
- have an active interest in the area of genomics of bacteria-phage coevolution.

We offer:
- opportunity to work on an ambitious and important scientific problem, hence contributing to the fight against antimicrobial resistance,
- opportunity to collaborate with world-class scientific leaders at the leading scientific institutions and with exciting companies in the biotechnology sector,
- a fun and interactive working environment,
- a full-time salary and a possibility of an additional PhD stipend upon a successful admission to the doctoral school at the Jagiellonian University,
- participation in collaborations and scientific meetings across the globe,
- flexible working time.

How to apply?
Please send me an email at with a short explanation for why you would like to join my lab and how this position fits into your interests and career aspirations. Please take your time to think about those questions. In the same email, please include your CV as well as names and contact details of at least 2 referees. The deadline for submitting applications is Friday, 13th of September 2019.

Funding Notes

The position is available from September 2019 and funded by the Polish National Agency of Academic Exchange.

References

1. Kathryn E. Holt, Florent Lassalle, Kelly L. Wyres, Ryan Wick, Rafał J. Mostowy. Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales. bioRxiv 709832; doi: https://doi.org/10.1101/709832
2. 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.
3. Mostowy RJ, Croucher NJ, De Maio N, et al. Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination. Mol Biol Evol. 2017;34(10):2537-2554. doi:10.1093/molbev/msx173.

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