Umeå University is one of Sweden’s largest higher education institutions with over 41,500 students and about 4,600 employees. The University offers a diversity of high-quality education and world-leading research in several fields. Notably, the groundbreaking discovery of the CRISPR-Cas9 gene-editing tool, which was awarded the Nobel Prize in Chemistry, was made here. At Umeå University, everything is close. Our cohesive campuses make it easy to meet, work together and exchange knowledge, which promotes a dynamic and open culture. The ongoing societal transformation and large green investments in northern Sweden create enormous opportunities and complex challenges. For Umeå University, conducting research about – and in the middle of – a society in transition is key. We also take pride in delivering education to enable regions to expand quickly and sustainably. In fact, the future is made here. Are you interested in learning more? Read about Umeå university as a workplace
The Faculty of Medicine, which consists of 12 departments, is responsible for biomedical research and courses in the field of nursing and health care and has an extensive research and graduate education in more than 80 subjects.
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.
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 (umu.se)).
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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
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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
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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.
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Proficient in at least one programming language, preferably Python or R.
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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.
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Comfortable working in a diverse, inclusive, interdisciplinary, and highly collaborative environment.
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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
The position is funded (Salary) via the SciLifeLab and 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/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; https://www.mims.umu.se/); 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; https://www.umu.se/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.
A complete application must include:
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A cover letter (one A4 page), highlighting your specific qualifications and motivation for the position. [eg: how your background aligns to the research area]
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A curriculum vitae (CV), including a full list of publications. [preprints accepted]
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Certified copies of diplomas, certificates, and grades.
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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] [email protected]
We welcome your application!
Umeå University strives to offer an equal environment where open dialogue between people with different backgrounds and perspectives lay the foundation for learning, creativity and development. We welcome people with different backgrounds and experiences to apply for the current employment. We kindly decline offers of recruitment and advertising help.
Anställningsform: tidsbegränsad anställning | Anställningens omfattning: heltid | Antal lediga befattningar: 1 | Sysselsättningsgrad: 100% | Ort: Umeå | Län: Västerbottens län | Land: Sweden | Referensnummer: AN 2026/562 | Kontakt: Chinmay Dwibedi , Chinmay Dwibedi , | Facklig företrädare: SACO SACO 090-7865365, SACO SACO 090-7865365, SEKO SEKO 090-7865296, SEKO SEKO 090-7865296, ST ST 090-7865431, ST ST 090-7865431, | Publicerat: 2026-04-21 | Sista ansökningsdag: 2026-06-19
