Microbiome bioinformatics research associate

Malopolska Centre of Biotechnology, Jagiellonian University in Krakow
Poland Krakow


The Structural and Functional Genomics lab at the Małopolska Centre of Biotechnology is looking for a motivated post-doc who wants to solve real-world problems important to health to join the group. The position is available now with funding covered by the project until at least June 2023.

I have recently moved from University of California San Diego to Poland and started a group in June 2019 at the Małopolska Centre of Biotechnology, Jagiellonian University in Kraków.

# The role
Your work will be focused on bioinformatic analysis of available and newly acquired metagenomic (16S rRNA amplicon and shallow shotgun sequencing) microbiome data in order to understand how the microbiome changes. You are going to work closely with a PhD student, other Group members, who are working on the development of new machine learning-based methods for predicting microbiome function and composition, as well as with our collaborators involved in sample collection and processing.
We are also setting up the Polish Microbiome Project and starting to collect more and more data from the Polish population. We are expecting for the project to grow significantly in the coming years and you can become a vital part of it!

The role will be exclusively computational but with significant implications for experimental applications. It will involve collaborative work with high-profile international groups. The results of the project will contribute to our understanding of the function of the human gut microbiome, and to the design of precision medicine strategies (therapies and interventions) targeting the microbiome.

The position will be funded by National Science Centre SONATA 15 project.

# The group
We are a young bioinformatics group rallying around the goal of understanding how the microbiome works and how we can leverage it for health and wellbeing. Combining metagenomics, data science, machine learning, structural bioinformatics and a collaborative mindset we want to develop a multi-scale understanding of the microbiome, from genes, through structures, to functions, and therapies. We also extensively collaborate with local and international research groups and companies to grow and deliver cutting-edge, open and reproducible research which would serve the community.

# Institution
Małopolska 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 biology, structural biology and plant biology. The first area, computational biology, has recently been undergoing rapid growth, with a recent start of several groups, including Bioinformatics/Transcriptomics (Dr. Paweł Łabaj), Microbial Genomics (Dr. Rafał Mostowy), and Structural and Functional Genomics (myself). The institute will also profit from the interactions with the nearby group in Microbial Ecology and Evolution (Dr. Piotr Łukasik) and with industry (Ardigen). Microbiome is a nascent field in Central/Eastern Europe and at the moment Kraków, especially MCB with 3 groups oriented around different facets of microbiome research, are rising as the leaders in this field.

MCB offers an international and collaborative environment with access to state-of-the-art infrastructure in both experimental and computational biology. MCB hosts many world-class research groups, including the Max Planck Research Group in Structural Biology (Glatt Lab), the Bionanoscience and Biochemistry Group (Heddle Lab), the Plant Molecular Biology Group (Yamada Lab) or the Virogenetics and Virology Group (Pyrć Lab).

*Please, see tomaszlab.org/associate_sonata for more information.*


The successful candidate will:
* have a PhD degree in biology, or a quantitative field such as computer science, bioinformatics, physics or mathematics,
* have excellent written and oral communication skills in English,
* have experience in data science, metagenomics, and microbiome research,
* have a collaborative mindset,
* enjoy interdisciplinary work,
* understand the importance of communication and interactions with other group members, collaborators and Centre members.

The ideal candidate will:
* fulfill all of the expectations of the “successful candidate”,
* have some experience in machine learning (esp. deep learning methods and software, e.g. TensorFlow, Keras),
* have documented experience in metagenomic data analysis and good data science practices,
* have a track record of presenting at conferences and published research.

Start date

As soon as possible

How to Apply

Please send an email with a subject line “Sonata postdoc” to work@tomaszlab.org including:

* a cover letter including a short description of your key achievements, as well as a short explanation for why you would like to join my lab and how this position fits into your interests and career aspirations,
* CV,
* names, contact details and professional relationship status of 3 potential referees.

We are committed to equal opportunities and will not discriminate anyone on the basis of: nationality, age, sex, race, disability, religion, sexual orientation and pregnancy/maternity.

Selected applicants will be contacted within 2 weeks of applying.