PhD in pangenomic graphs

Description

The Modern and Ancient Genomes Group, located at Université Laval in Québec City, Canada, is seeking one qualified candidate for a vacant PhD position in bioinformatics. In this position, you will develop algorithms and computational methods to analyze large datasets from modern and ancient sources.

Current bioinformatics algorithms and software are often ill-equipped to deal with DNA extracted from ancient sources. This ancient DNA shows high levels of fragmentation and accumulated chemical damage. Furthermore, ancient sediments often contain DNA from multiple species and often multiple individuals. Fortunately, several problems pertaining to ancient DNA can be described in a maximum-likelihood framework and computer science techniques can help us to solve such numerical problems efficiently via numerical algorithms and data structures. The Modern and Ancient Genomes Group has previously used pangenome graphs to solve several of these problems. You will work in collaboration with other partners in Europe and North America in order to develop the next generation of algorithms and software applied to DNA extraction from fossils, ancient soils and sediments.

Université Laval is one of the top research universities in Canada, recognized among the top research institutions in Canada for excellence in research, teaching, and innovation. French is the primary institutional language, but our research group works in English, and students are expected to be able to communicate effectively in English, both orally and in writing. We offer a rewarding and challenging position within a strong interdisciplinary and collegial environment. The Québec City region provides outstanding hiking opportunities in nearby Parc national de la Jacques-Cartier and Mont-Sainte-Anne.

Requirements and Conditions

Ideally, you have the following qualifications:

- Knowledge of a programming language like Python, Perl, C++ and/or Java (C/C++ is preferred).
- Ability to work in a UNIX environment, ideally in a high-performance computing environment.
- A thorough understanding of basic algorithms and data structures used in computer science.
- Knowledge of probabilities and statistics
- Firm grasp of differential calculus and linear algebra.
- Experience in bioinformatics and knowledge of metagenomics are a plus, but not needed.
- Expertise in next-generation sequencing data generation and processing is also a plus.

Ideally, you should have a Master's (or equivalent) and a B.Sc degree in computer science, quantitative biology/biochemistry or mathematics.

Your complete application must include a CV with a list of publications and a letter of motivation explaining why you are applying and explaining any gaps in your CV. The documents must be submitted no later than Jan 20th 2026 (23:59 Eastern Standard Time). Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link email here and attach all your materials in English in one PDF file.

All interested candidates, irrespective of age, gender, race, disability, religion or ethnic background, are encouraged to apply. We especially encourage women and applicants from Indigenous communities.

Application Deadline

January 20, 2026