PhD Position in Long-Read Computational Genomics

The CHUV seeks a Junior researcher for a fixed-term role in Lausanne to develop computational pipelines for long-read genomics within an interdisciplinary medical and biological team.

This position sits at the intersection of medicine, genetics, and systems biology within a dynamic research setting. The successful candidate will join an international consortium, working both independently and as part of a collaborative, multidisciplinary team to advance genomic analysis methods.

Responsibilities

• Create, test, and maintain a full-scale analysis pipeline for long-read sequencing data.
• Process PacBio HiFi data to identify single nucleotide variants, indels, structural variations, copy number variations, and CpG methylation patterns.
• Build telomere-to-telomere de novo genome assembly workflows and help construct a reference panel specific to the studied population.
• Set up imputation methods to infer genotypes from low-coverage short-read whole-genome sequencing datasets.
• Incorporate artificial intelligence and machine learning techniques into the annotation and interpretation of genetic variants.
• Execute statistical genomics tasks, such as developing polygenic risk scores and performing genetic association studies.

Requirements

• Hold a Master’s degree or equivalent qualification in Bioinformatics, Computational Biology, Computer Science, Statistics, Genomics, Genetics, Molecular Biology, Cellular Biology, or a closely related discipline.
• Demonstrate strong programming capabilities in Python and R.
• Be proficient in using Linux operating systems and high-performance computing (HPC) clusters.
• Possess excellent written and spoken English communication skills.

Nice to have

• Prior experience analyzing sequencing data, with familiarity in long-read technologies, statistical genetics, or machine learning.
• Background in human genetics or rare disease genomics.
• Knowledge of stem cell biology, including induced pluripotent stem cell (iPSC) derivation and differentiation.
• Ability to communicate in French.

What the company offers

• Comprehensive social benefits, including 20 days of paternity leave and 4 months of maternity leave.
• Regular salary increases based on responsibilities and career progression.
• A 13th-month salary payment and 25 days of annual vacation.
• At least three days of professional training per year.
• Assistance accessing one of 500 furnished apartments for employees relocating to Switzerland from abroad.
• Social, cultural, and financial perks through the H-Oxygène association.
• Discounts on public transport passes via the mobility plan.
• Access to high-quality staff restaurants in every hospital building, providing hotel-standard catering at reduced prices.

About the company

CHUV is one of Switzerland’s five university hospitals and a leading center for clinical care, biomedical research, and academic training. The institution fosters a collaborative and multidisciplinary environment where researchers work independently while contributing to international teams.

• Work within a leading Swiss university hospital known for clinical care and biomedical research.
• Collaborate effectively in a multidisciplinary international team.
• Enjoy comprehensive social benefits and professional development opportunities.
• Access high-quality dining and housing assistance for relocating staff.