postdoctoral scientist in the area of bioinformatics of bacteria-phage interactions

Jagiellonian University
Małopolska Centre of Biotechnology
Poland Krakow
mostowylab.com/news/postdoc-mostowy-lab-embo-2020

Description

We are inviting applications for a postdoctoral scientist in the area of bioinformatics of bacteria-phage interactions. She or he will join the Microbial Genomics Group at Malopolska Centre of Biotechnology at Jagiellonian University in Kraków (mostowylab.com). The position is available from Summer 2020, with the exact start date to be agreed on, for 24 months with the possibility of extension for further 12 months and will be funded by the European Molecular Biology Organisation (embo.org).

The successful candidate will use computational approaches to study interactions between bacteriophages and bacterial surface molecules, particularly surface polysaccharides like capsules and lipopolysaccharides. These molecules are known to be highly diverse, both structurally and genetically [1], however our understanding of how they interact with phages is far from complete [2]. The project will take advantage of the rapidly growing collections of bacterial and phage genome data and combine big data genomics and genome informatics with structural biology bioinformatics to improve our understanding of bacteria-phage interactions, hence pushing the state-of-the-art of the field. The initial focus of the project will be on bacteria from the species of Klebsiella pneumoniae, but will increasingly focus on other bacterial species from the order Enterobacteriales. The long-term goal is to understand how bacteria and phages co-evolve, and the role of horizontal gene transfer in shaping their interactions. The successful candidate will work in collaboration with research groups 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). Close collaboration with experimental groups is also envisaged, depending on how the project develops. The results of the project will contribute to the fight against the problem of antibiotic resistance by helping to assess the antimicrobial potential of phages and their proteins.

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. Please note that, due to the ongoing global situation, this position will offer a possibility of working remotely.

Malopolska Centre for Biotechnology (MCB) is a flagship biotechnology institute of Southern Poland and one of the most promising biomedical institutes in Central/Eastern Europe. It is part of the Jagiellonian University and its excellence is based on three main areas: computational genomics, structural biology and plant biology. The first area, computational genomics, has recently been undergoing rapid growth, with a recent start of several groups, including Bioinformatics (dr hab. Paweł Łabaj), Microbial Genomics (dr Rafał Mostowy), Structural and Functional Genomics (dr Tomasz Kościółek) and genomics (Prof. Wojciech Branicki). MCB offers access to state-of-the-art infrastructure in both experimental and computational biology, and interactions with world-class research groups, including with the Max Planck Research Group in Structural Biology (Glatt Lab), with the Bionanoscience and Biochemistry Group (Heddle Lab), the Plant Molecular Biology Group (Yamada Lab) or the Virogenetics and Virology Group (Pyrć Lab).

References
[1] Mostowy, Rafał J., and Kathryn E. Holt. "Diversity-generating machines: genetics of bacterial sugar-coating." Trends in microbiology 26.12 (2018): 1008-1021.
[2] Nobrega, Franklin L., et al. "Targeting mechanisms of tailed bacteriophages." Nature Reviews Microbiology 16.12 (2018): 760-773.
Bionanoscience and Biochemistry Group (Heddle Lab), the Plant Molecular Biology Group (Yamada Lab) or the Virogenetics and Virology Group (Pyrć Lab).


Qualifications

The successful candidate will:
- hold a PhD in a quantitative field like biology, chemistry, physics, mathematics, computer science or similar (or is about to defend one),
- 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.

The ideal candidate will also fulfil the following requirements:
- demonstrate evidence of in-depth expertise and problem solving in at least one of the following areas: data science or machine learning, population genetics/genomics, structural biology, computational biology, microbiology, virology.
- have an active interest in the area of microbiology and phage biology,
- have a strong track record of published research and of having presented at multiple international meetings and conferences.

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 Tomasz Lab (tomaszlab.org),
- participation in collaborations and scientific meetings across the globe,
- flexible working time with an opportunity to work remotely (subject to a mutual agreement),
- a competitive salary, comparable to the highest remuneration for postdocs in the Polish National Science Centre (NCN) grants.


Start date

June 01, 2020

How to Apply

Please send me an email at rafal.mostowy@uj.edu.pl with the subject “Application for EMBO Postdoc” and:
a) a short explanation for why you would like to join my lab and how this position fits into your interests and career aspirations (max 1 page),
b) your CV including the full list of publications,
c) 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. The deadline for submitting applications is 31st of May 2020.


Contact

Dr Rafal Mostowy
rafal.mostowy@uj.edu.pl

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