I have recently moved to Poland to start a group in microbial genomics at the Malopolska Centre of Biotechnology, Jagiellonian University in Kraków (Poland). I am currently looking for a postdoc to join my group. The position is available from April 2019 for up to 46 months.
I am looking for someone with strong quantitative skills as well as expertise in bioinformatics and computational genomics. The 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. This will build on my previous work on bacterial polysaccharide capsules [1,2], and will explore different ways in which these molecules interact with bacteriophages. The core of the project will be carried out using computational approaches and next-generation sequencing to characterise (i) bacterial extracellular polysaccharides and (b) bacteriophage components which interact with those antigens. This work will be complemented by close collaborations and data sharing with international research groups with expertise in genomics of enteric bacteria (Prof. Kat Holt at Monash University and Prof. Nick Thomson at the Wellcome Trust Sanger Institute), and with groups with expertise in the microbiology of bacteria-phage interactions (Prof. Mark Enright at Manchester Metropolitan University). The results of the project will contribute to the fight against the problem of antibiotic resistance in Poland and Europe by helping discover potentially novel antimicrobial drugs.
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 to learn multiple new skills (e.g., working with Nanopore sequencing data) and develop international contacts by spending time abroad, but will be expected to manifest an increasing degree of intellectual independence throughout the project.
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 (myself), and Metagenomics (dr Tomasz Kościółek; from June 2019). The institute will also profit from the interactions with the nearby group in Microbial Ecology and Evolution (dr Piotr Łukasik; from June 2019). 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).
The successful candidate will:
hold a PhD in a quantitative field like biology, chemistry, physics, mathematics, computer science or similar (by the time of application date),
have strong expertise in genomics and next-generation sequencing bioinformatics,
have excellent written and oral communication skills in English,
have a very good knowledge of at least one programming language (e.g., R, Python, C/C++, Java),
have good 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 have in-depth expertise in one or more of the following areas:
data science, statistics and/or machine learning,
microbiology and/or phage biology,
computational structural biology,
evolutionary biology, ecology and population genetics/genomics.
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,
salary competitive with industry rates, subject to candidate’s qualifications and experience
participation in collaborations and scientific meetings across the globe,
flexible working time
How to apply?
Please send me an email at email@example.com with a short explanation for why you would like to join my lab and how this position fits into your interests and career aspirations. In the same email, please include your CV with a list of publications, as well as names and contact details of 3 referees. The deadline for submitting applications is Thursday, 21st of March 2019.
The postdoc will be involved in the project “Genomics of phage therapy: evolutionary drivers and medical implications” financed from the Polskie Powroty programme of the Polish National Academy of Academic Exchange.
 Mostowy RJ, Holt KE. Diversity-Generating Machines: Genetics of Bacterial
Sugar-Coating. Trends Microbiol. 2018 Dec;26(12):1008-1021.
 Mostowy RJ, Croucher NJ, De Maio N, Chewapreecha C, Salter SJ, Turner P,
Aanensen DM, Bentley SD, Didelot X, Fraser C. Pneumococcal Capsule Synthesis
Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by
Recombination. Mol Biol Evol. 2017 Oct 1;34(10):2537-2554.