Pre-doctoral fellow in bioinformatics
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 big picture
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 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.
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 the start of several groups, including the Bioinformatics/Transcriptomics group (Dr. Paweł Łabaj), Microbial Genomics (Dr. Rafał Mostowy) group, and Structural and Functional Genomics group (myself). The institute will also profit from 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 the 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
- 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 learning 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.
- a competitive full-time PhD fellowship,
- the opportunity to collaborate with world-class researchers from MCB and institutions such as the University of California San Diego, the Broad Institute, and New York University,
- scientific mentorship,
- the opportunity to work on an challenging and important scientific project with interdisciplinary applications,
- the opportunity and support to participate scientific meetings across the globe,
- flexible working time.
How to inquire
Please send an email with a subject line “PhD student” to firstname.lastname@example.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 with your interests and career aspirations,
- an academic CV,
- names, contact details and professional relationship status of 2 potential referees.
Applicants will be contacted within 2 weeks of applying.
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.