The Dwibedi research group at the Department of Clinical Microbiology and the Laboratory for Molecular Infection Medicine Sweden (MIMS; https://www.mims.umu.se/), Umeå University, Sweden, is seeking a post-doctoral fellowship candidate (2-years) in Bioinformatics: The project aims at investigating adaptive mechanisms in human gut associated microbes.
Studying the human gut microbiota at strain level
Research Topic
Our group aims to track strain wide differences within human gut bacteria species across different populations. 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.
Your role
You will be responsible for carrying out research in the Chinmay Dwibedi lab (www.dwibedilab.org) in close collaboration with local and international experts. Specifically, you will employ Bioinformatic and statistical methods to analyze human gut microbiome data from large cohorts.
Responsibilities
Develop bioinformatic pipelines to generate metagenome assembled genomes.
Evaluate differential fitness of specific strains in different populations.
Study structure and function of microbial genes across strains.
Participate and contribute to scientific group meetings.
Coordinate work with collaboration partners.
Contribute as appropriate to the publication of research findings.
Participate in training and supervision of scientists and research students.
· Comply with the University’s Equal Opportunities and Data Protection policies.
Selection criteria
Essential
· PhD in computational biology, bioinformatics, or computer science with a focus on human gut microbiome data
· Excellent written and oral English communication skills.
· Significant experience in handling large metagenome datasets (first author publication/s in the topic are required).
· Relevant experience in R and/or python programming (eg. pipeline development for metagenomic data analysis, generation of metagenome assemblies)
· Ability to work as part of a team as well as independently.
· Ability to deliver results to required standard and schedule.
· Ability to organize and prioritize own work with minimal supervision.
Desirable
Experience in microbial DNA isolation, Anaerobic bacteria culturing, Microbial single cell capture
Research environment
The Dwibedi lab is part of 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.
The successful candidate 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.
Fellowship summary
Full-time 2-year stipend (tax-free), financed by the Kempe Foundations starting between 2025 and (latest) 2026.
For questions, please contact:
Chinmay Dwibedi, Department of Clinical Microbiology, E-mail: chinmay.dwibedi@umu.se
Application
Please apply with the following documents:
1. Letter highlighting your qualification and motivation
2. CV including publication list
3. Copy of PhD certificate, and other relevant exam certificates
4. Contact information of 2 references
The complete application, marked with reference number UMU-PDF-CD-01, must be sent to chinmay.dwibedi@umu.se (state the reference number as subject) no later than February 15th, 2025.
Comments