Vacant job

The Department of Clinical Microbiology at Umeå University is seeking a PhD student in medical science with a focus on bioinformatics. We offer an international, stimulating, and collaborative research environment that supports your scientific career development.

The project aims to track differences between different species of gut bacteria in humans during early childhood. Our goal is to improve the understanding of adaptive mechanisms used by various gut bacteria with high resolution to guide the next generation of microbiota-based therapies.

Job Description

Study the development of gut microbiota composition in children

The infant gut microbiota undergoes rapid changes in both composition and at the strain level before stabilizing into a more adult-like configuration. Although these dynamics are influenced by a range of early-life exposures, the developmental trajectories of the microbiome are not yet fully mapped. In this project, the PhD student will analyze longitudinal fecal shotgun metagenomic data from 500 children followed from birth to three years of age, with the aim of investigating how environmental, clinical, and lifestyle-related factors affect the development of the microbial community structure. The PhD student will be part of the doctoral education conducted within Data Driven Life Sciences (DDLS).

Keywords: PhD position, Metagenomics, human gut microbiota, shotgun metagenomics, microbiota development, microbiome, long-read sequencing, metagenome-assembled genomes, strain-level metagenomics, high-resolution metagenomics

Those admitted to the doctoral education at the Faculty of Medicine will participate in the faculty-wide doctoral program. The doctoral education comprises 25 higher education credits and is offered in two study variants: 25 higher education credits distributed over 8 terms (total 4 years) or over 12 terms (total 6 years), starting every autumn and spring semester. More information about the education can be found on the faculty's website for doctoral education (Doctoral Education at the Faculty of Medicine - Handbook (umu.se)).

Eligibility and Qualifications

• You must have at least 240 higher education credits (HEC), of which at least 60 HEC at an advanced level, in natural sciences, life sciences, or engineering.
• You must have good ability to express yourself in speech and writing in English, be able to work both independently and in collaboration with others, and be highly motivated.

Additional Merits

• A degree in bioinformatics, computational biology, (bio)statistics, (applied) mathematics, computer science, or a related field; candidates from other fields with strong programming/coding skills (see below) are also encouraged to apply.
• Knowledge of at least one programming language, preferably Python or R.
• Experience in one or more of the following areas: large-scale sequence analysis, microbial genomics, human gut flora research (shotgun metagenomics), construction of metagenome-assembled genomes, gut flora genomes, and development of gene databases.
• Comfortable working in a diverse, inclusive, interdisciplinary, and highly collaborative environment.
• Ability to navigate UNIX file systems from the command line, work in conda environments, install and implement packages from GitHub, and submit batch jobs in clusters.

Further Information

The position (salary) is funded via SciLifeLab and the Wallenberg National Program for Data-Driven Life Science (DDLS; https://www.scilifelab.se/data-driven/), a 12-year initiative aimed at recruiting and training the next generation of data-driven life scientists. In addition to being affiliated with the Department of Clinical Microbiology at Umeå University (https://www.umu.se/institutionen-for-klinisk-mikrobiologi/), you will be linked to the national DDLS program, through which you will have access to computing resources, the national DDLS doctoral school, and other educational and networking opportunities throughout Sweden.

You will also be affiliated with the Laboratory for Molecular Infection Medicine Sweden (MIMS; https://www.mims.umu.se/); MIMS is a member of the Nordic EMBL Partnership for Molecular Medicine, which focuses on the growing area of bioscience investigating the molecular basis of diseases and exploring molecular and genetically based treatments. There will be opportunities to collaborate with experts within and outside Europe. Locally, the research group is affiliated with the Umeå Centre for Microbial Research (UCMR; https://www.umu.se/ucmr/om-ucmr/). UCMR is an interdisciplinary research center established by a consortium of researchers representing medical and molecular microbiology, molecular and structural biology, chemistry, and physics, dedicated to high-quality research and new applications in microbial pathogenesis.

Application

A complete application should include:

• A cover letter (one A4 page) highlighting your specific qualifications and motivation for the position. [e.g., how your background aligns with the research area].
• A curriculum vitae (CV), including a complete list of publications. [preprints are accepted].
• Notarized copies of degree certificates, diplomas, and transcripts.
• Names and contact details for at least two reference persons.

PhD position for 4 years, start date by agreement. Application is made electronically (via the Varbi system).

For more information about the research area, please contact

Chinmay Dwibedi [dwibedilab.org] [email protected]

Umeå University aims to offer an equal and equitable environment where open dialogue between people with different backgrounds and perspectives lays the foundation for learning, creativity, and development. We therefore welcome people with different backgrounds and experiences to apply for the current position.

To staffing and recruitment agencies and to you who are sales representatives: We kindly but firmly decline direct contact from staffing and recruitment agencies as well as sellers of additional job advertisements.