Pre-doctoral fellow in bioinformatics (microbiome; protein structure and funciton)

Jagiellonian University
Małopolska Centre of Biotechnology
Poland Krakow


The Structural and Functional Genomics lab at the Małopolska Centre of Biotechnology is looking for a pre-doctoral fellow to join the group. The position is available from October 2019 with funding covered by the project until December 2022.

The work will be focused on protein structure prediction, and structure-assisted protein function predictions using deep learning methods to understand the functional potential within the human gut microbiome. Your role will be to improve function predictions by testing various sources of structural information and determining the contributions the structures play in improving function predictions. Once the function predictions are optimized, we will use them to characterize genomes and metagenomes from the human gut microbiome.
The work will be carried out as a part of the Microbiome Immunity Project ( There will also be multiple opportunities to work on projects related to the human microbiome analyses, especially in type-1 diabetes, and mental health (the gut-brain axis).
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 student will be funded by the project financed from the Polish Returns grant from the Polish National Agency for Academic Exchange.


The successful candidate will:
* hold an undergraduate degree in a quantitative field like biology, chemistry, physics, mathematics, computer science or similar by the time of starting the position,
* enroll in the Doctoral School programme at the Jagiellonian University in Kraków,
* have excellent written and oral communication skills in English,
* be open to learn at least one programming language (esp. Python),
* have a collaborative mindset,
* 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 experience in either data science, statistics, machine learning, and/or metagenomics, structural bioinformatics,
* have documented experience in test-driven software development,
* have an active interest in microbiome research,
* have a track record of presenting at research conferences and/or published research.

Start date

October 01, 2019

Start date

To be determined

How to Apply

Please send an email with a subject line “PhD student” to 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 with your interests and career aspirations,
* an academic CV,
* names, contact details and professional relationship status of 2 potential referees.

Selected applicants will be contacted before the end of June.


Tomasz Kosciolek