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Umeå University’s Department of Clinical Microbiology is looking for a PhD student within the field of medical science with a focus on bioinformatics. We offer an international, stimulating, and collaborative research environment where your scientific career development is promoted.

The project aims to track strain wide differences within human gut bacteria species in early childhood. Our goal is to improve the understanding of adaptive mechanisms employed by different gut bacteria at a high resolution to guide next generation microbiota aided therapies.

About the position

Studying gut microbiota community development in children

The infant gut microbiota undergoes rapid compositional and strain-level changes before stabilizing toward an adult-like configuration. While these dynamics are influenced by a range of early-life exposures, the trajectories of microbiome development remain incompletely understood. In this project, the candidate will analyze longitudinal fecal shotgun data from 500 children followed from birth to three years of age to investigate how environmental, clinical and lifestyle exposures shape microbial community development. The student will be part of the Data driven Life Sciences [DDLS] PhD research school.

Keywords: PhD position, Metagenomics, human gut microbiota, shotgun metagenomics, microbiota evolution, microbiome, long read sequencing, Metagenome assembled genomes, strain level metagenomics, high resolution metagenomics
You who are admitted to doctoral studies at the Faculty of Medicine will be part of the faculty-wide doctoral education programme. The doctoral programme comprises 25 credits and is offered in two study variants: 25 credits spread over 8 terms (a total of 4 years) or over 12 terms (a total of 6 years), starting each autumn and spring semester. More information about the programme can be found on the faculty’s web page for doctoral studies (Doctoral Studies at the Faculty of Medicine - Handbook (ͯÑÕÊÓƵ)).

Eligibility and Qualifications

• You must have at least 240 higher education credits (hc), of which at least 60 hc are at an advanced level, in natural sciences, life sciences, or engineering
• Applicants must be skilled in both oral and written communication in English, able to work independently as well as in collaboration with others, and be highly motivated.

Meritorious

• 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.
• Proficient in at least one programming language, preferably Python or R.
• Experience in any of the following areas: large scale sequence analysis, microbial genomics, human gut microbiota research (shotgun metagenomics), Metagenome assembled genome construction, gut microbial genome, and gene database development.
• Comfortable working in a diverse, inclusive, interdisciplinary, and highly collaborative environment.
• Ability to navigate UNIX filesystems from the command line, working in conda environment, installation and implementation of packages from github, batch job submissions in clusters

Further details

The position is funded (Salary) via the SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS; ), 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 (/en/department-of-clinical-microbiology/), you will be affiliated with the national DDLS program, through which you will have access to computing resources, the national DDLS research school, and other training and networking opportunities throughout Sweden.

You will be further affiliated with the Laboratory for Molecular Infection Medicine Sweden (MIMS; ); MIMS is a member of the Nordic EMBL Partnership for Molecular Medicine, which is dedicated to the growing field of life sciences that investigates the molecular basis of disease and explores molecularly and genetically based treatments. There will be opportunities to collaborate with experts throughout Europe and beyond. Locally the research group is affiliated to the Umeå center for microbial research (UCMR; /ucmr/om-ucmr/) UCMR is an interdisciplinary research centre established by a consortium of scientists representing medical & molecular microbiology, molecular & structural biology, chemistry & physics, and is devoted to top quality research and novel applications in the fields of microbial pathogenesis.

Application

A complete application must include:

1. A cover letter (one A4 page), highlighting your specific qualifications and motivation for the position. [eg: how your background aligns to the research area]
2. A curriculum vitae (CV), including a full list of publications. [preprints accepted]
3. Certified copies of diplomas, certificates, and grades.
4. Names and contact details of at least 2 reference persons.

Doctoral position 4 years, starting according to agreement. The application is made electronically (via the system Varbi).

For more details on the research area, contact

Chinmay Dwibedi [dwibedilab.org]               chinmay.dwibedi@ͯÑÕÊÓƵ

We welcome your application!