Microbiome bioinformatics research associate

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 project

Microbiome changes over time and upon perturbation: understanding the microbiome composition and function for therapeutic applications

Background
In a bit over a decade the scientists described different microbiomes and learned that the microbiome is not only necessary, as it co-evolved with us, diverse and complex, but also important to health. Changes in the composition of microbes may result in an imbalance within the ecosystem of our guts called dysbiosis, which in turn may lead or contribute to disease. We already know a wide array of microbiome-disease associations, from the quite expected ones, such as obesity or gastrointestinal problems (ulcerative colitis or Crohn’s disease), to diseases presumed far removed from the gut – type-1 diabetes, allergies, depression, anxiety, neurodegenerative disorders, cancer, and others.

With those significant health implications and vast amounts of data gathered over the years we are now in a position to turn the knowledge into action – learn to predict how the microbiome changes over time and upon perturbation. With this, we are going to learn how to change the microbiome in order to promote health or devise therapeutic strategies. Those strategies may involve probiotic interventions, dietary or lifestyle changes, not necessarily classical small-molecule drugs. This is no easy task as the microbiome is massive – 10s of trillions of microbial cells representing 100s of microbial species, harboring over 100 times more genes than the human genome. On top of that the microbiome is dynamic. Unlike our genome, which is fixed from birth, the microbiome changes from day to day, evolves with our diet, lifestyle and other life events.

Project
Our objective is to establish robust analytical pipelines for metagenomic data which would support several projects already happening within the group. With reproducible and scalable methodology in place, we will be in a position to expand our biological understanding of microbiome changes. This is a necessary step in bridging our under-development strategies for the prediction of time-series and therapeutic intervention data with functional genomics efforts to increase the accuracy and coverage of metagenomic functional annotations.

The Polish Microbiome Project (PMP) is an effort to build an infrastructure for sample acquisition, processing, sequencing and analysis on a national scale. We are already collecting 100s of samples from the Polish population and plan to expand to 1000s over the next year. This will give us an opportunity not only to validate methods developed in the Group on a novel dataset, but also establish a platform for microbiome-based biological discovery within the Polish population.

Future
As a result of this project, we are going to have an robust platform for acquisition and analysis of the microbiome data in Poland along with 1000s of fecal (and other) samples collected from the population. This will help us to better describe the regional microbiome characteristics within Poland and open up to future national and international collaborations (e.g. ongoing collaboration with the Microsetta Initiative). We will also better understand temporal and functional variability of the microbiome through an intersection with other ongoing projects. It has direct implications to our current immune-related microbiome disorders - IBD and type-1 diabetes.

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.

PLEASE NOTE: due to NCN regulations I am not allowed to hire postdocs who obtained their PhDs at the Jagiellonian University. For more information on the reason behind that or to share your opinion, please contact the agency via e-mail:: kancelaria@ncn.gov.pl

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).

The successful candidate will

The ideal candidate will

We offer

How to inquire

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

Application will be considered until the post is filled.

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.