Bioinformatics research associate
The Structural and Functional Genomics lab at the Małopolska Centre of Biotechnology is looking for a research associate/postdoc to join the group. The position is available from October 2019 with funding covered by the project until June 2023.
I have recently moved from University of California San Diego to Poland to start a group at the Małopolska Centre of Biotechnology, Jagiellonian University in Kraków.
I am still accepting applications for this position!
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 know about microbial metagenomes and their functions.
The main objective for the role is to build and maintain a consistent and extensible computational framework and database for structural and functional annotation of microbial genomes, and metagenomes. Depending on scientific or technical interests, it will be extended to work on host-microbiome protein-protein interactions, virtual screening to find molecules inhibiting identified and experimentally confirmed interactions, or work on computational problems related to the volume and living character of the data (i.e. perpetual clustering, novelty detection, data classification and visualization).
The work will be carried out as a part of the Microbiome Immunity Project. 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, what will help us design precision medicine strategies (therapies and interventions) targeting the microbiome.
The position 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 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
- hold a Masters degree in computer science or a similar field, or hold a PhD degree in a quantitative field such as biology, bioinformatics, physics, mathematics or computer science,
- have excellent written and oral communication skills in English,
- have expertise in at least one programming language (esp. Python),
- have documented experience in test-driven software development,
- 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 a track record of presenting at conferences and published research,
- have experience in data science, structural biology, or computer-aided drug design,
- have an active interest in microbiome research.
- competitive salary commensurate with experience,
- opportunity to collaborate with world-class researchers from MCB and institutions such as University of California San Diego, Broad Institute, or New York University,
- scientific and professional mentorship,
- position 100% focused on research and development (no compulsory teaching),
- opportunity to work on an ambitious and important scientific problem with interdisciplinary applications,
- opportunity and support to participate scientific meetings across the globe,
- flexible working time.
How to inquire
Please send an email with a subject line “research associate” to email@example.com 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,
- sample code or a link to a repositiory,
- 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.