Role of Horizontal Gene Transfer in evolution of bacteriophage genomes.

General description

We are inviting applications for a PhD student in the area of bioinformatics of bacteria-phage interactions. The successful candidate will join the Microbial Genomics Group at Malopolska Centre of Biotechnology, Jagiellonian University in Kraków (https://mostowylab.com). This is a 4-year National Science Foundation (ncn.gov.pl) funded position, available from October 2021, with the exact start date to be agreed on.

The successful candidate will work on bioinformatics and genomics of phages that infect opportunistic bacterial pathogens like Klebsiella pneumoniae and interact with their polysaccharide capsules. Bacterial polysaccharides are known to be highly diverse, both structurally and genetically, however evolutionary forces that drive that diversity are not fully understood (Mostowy & Holt 2018, Trends Microbiol). Hence, to better understand and quantify evolution of phages, we need tools that can inform us how evolutionary process, like mutation and horizontal gene transfer (HGT), shape phage diversity at different levels, from domains, to proteins, to modules and genomes.

As a successful candidate, you will work on a new generation of bioinformatic methods to study how HGT impacts bacterial genome. Specifically, you will combine state-of-the-art approaches in the field of microbial genomics (e.g., pan-genome view of microbial diversity) with those in phylogenomics (e.g., tree reconciliation methods) to reconstruct how phage diversity emerges at different levels and how it shapes evolution of bacterial genomes. You will design new bioinformatic methods for the phage biology community and apply them on large datasets consisting hundreds of thousands of genomes of both lytic and lysogenic phages. You will interact with other members of our rapidly growing group working on microbial genomics and work together as a team. You will work in collaboration with other top research groups: those with expertise in genomic epidemiology of Klebsiella pneumoniae (Kat Holt at Monash University in Australia), bacterial evolutionary genomics (Florent Lassalle at Wellcome Trust Sanger Institute) and structural bioinformatics (Stanisław Dunin-Horkawicz at University of Warsaw). 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 quantify underlying evolutionary forces that drive success or failure of phage therapy.

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

Specific requirements

The successful candidate will:

• hold a MSc in a quantitative field like biology, chemistry, physics, mathematics, computer science or similar,
• manifest a high degree of enthusiasm for the advertised project,
• have a very good knowledge of at least one programming language (e.g., R, Python, C/C++, Java),
• have excellent oral and written communication skills in English,
• have strong presentation skills (ideally having presented on at least one international conference),
• enrol in the Biomedical Sciences Doctoral School programme at the Jagiellonian University in Krakow,
• enjoy support of and interaction with other group members.

The ideal candidate will also fulfil the following requirements:

• demonstrate evidence of in-depth experience in designing bioinformatics methods or pipelines (e.g., via GitHub),
• demonstrate evidence of having led and completed scientific projects in the area of computational biology, population genetics, phylogenetics, phage biology, microbiology or similar,
• 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,
• 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),
• a gross stipend of 5000 PLN/month (around 4500 PLN net) with social security and health insurance (you can use numbeo.com to compare this salary to the estimated costs of living in Krakow).

How to apply?

1. Please send me an email at rafal.mostowy@uj.edu.pl with the subject “Application for NCN OPUS PhD” and 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.

Please note that only candidates who will have sent all of the above will be considered for the position and notified. The deadline for submitting applications is 30th of April 2021.