General description

We are inviting applications for a postdoctoral scientist in the area of bioinformatics of bacteria-phage interactions. The successful applicant will join the Microbial Genomics Group at Malopolska Centre of Biotechnology, Jagiellonian University in Kraków (https://mostowylab.com). This is a 3 year position funded by the National Science Centre (ncn.gov.pl) OPUS grant, available from Summer/Autumn 2021, with the exact start date to be agreed.   

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 processes, 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 evolution of the phage proteome. Specifically, you will combine the pan-genome view of genetic diversity, from the microbial genomics perspective, with a structural bioinformatics perspective (secondary structure predictions), with the objective of systematically comparing the phage proteome to its domain structure and functional repertoire. You will design new computational methods for the phage biology community and apply them on large datasets consisting of hundreds of thousands of genomes of 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 (Eduardo Rocha at Institut Pasteur in Paris) 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 to find new repertoires of phage proteins with a potential antimicrobial use (so called “enzybiotics”).

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

Specific requirements

The successful candidate will:

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

  • have strong expertise in genome or protein bioinformatics,

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

  •  have excellent oral and written communication skills in English,

  • have a very good knowledge of at least one programming language (e.g., R, Python, C/C++, Java),

  • provide evidence of a high degree of intellectual independence (including experience in building and managing collaborations),

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

  • enjoy support of and interaction with other group members,

  • have published at least one publication as first-author in an international, peer-reviewed journal,

  •  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:

  • demonstrate evidence of in-depth experience in designing bioinformatics methods or pipelines (e.g., via GitHub),

  • possess in-depth expertise in phage biology and microbiology,

  • have a strong track record of published research and of having presented at multiple international meetings and conferences,

  • demonstrate evidence of intellectual independence and leadership via self-obtained funding,

  • have experience in mentorship/supervision of junior staff members and in project management.

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),

  • gross salary about 7600 PLN/month with social security and multiple benefits (e.g., subsided fitness gym membership), additional 13th salary after working a minimum of six months (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 postdoc” 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.

Application deadline:
Start date: Flexible
Location: Krakow, Poland