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Structure and Function of Microbial Proteins (microbiome, structural bioinformatics, protein function, genome annotation, deep learning, metagenomics)

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  • Full or part time
    Dr Tomasz Kosciolek
  • Application Deadline
    No more applications being accepted

Project Description

The human gut microbiome is a diverse and dynamic ecosystem of over 2 million unique gene families, outnumbering the human genome more than 100:1. The gut microbiome is already linked to many human diseases, ranging from inflammatory bowel disease, through diabetes, to mental health and many more. Still, even the most prevalent gut microbes can only be accurately annotated at less than 50% of gene functions. The microbiome holds a great promise for precision medicine, as it may be easily manipulated, unlike the human genome. But to be able to do it, we first must understand its functions. In this project, through the use of genomic and metagenomic data, we carry out protein structure predictions, machine learning-based function predictions and attempt to determine host-microbiome interactions. As a result, we will bridge the gap between what we already know about microbial metagenomes and their functions.

The project 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 project and salary are fully funded from a Polish Returns grant from the Polish National Agency for Academic Exchange. On top of that, the successful candidate may obtain a scholarship from the Jagiellonian University Doctoral School (

When applying, please include:
* a cover letter including a short description of your key achievements, as well as a short explanation for: (1) why you would like to join the lab and (2) how this position fits with your interests and career aspirations,
* an academic CV,
* names, contact details and professional relationship status of 2 potential referees.

more details are available at:

Funding Notes

the student will be funded by the project financed from the Polish Returns grant from the Polish National Agency for Academic Exchange.

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