Médico-technique

PhD Position in Long-Read Computational Genomics

We are seeking a motivated PhD candidate to join the Santoni lab into the PakGene consortium, a large-scale rare disease genomics initiative built around a unique cohort of several thousand consanguineous Pakistani families. The successful candidate will develop and deploy the computational backbone for a state-of-the-art long-read sequencing program based on PacBio HiFi data. This is a rare opportunity to build infrastructure from the ground up on a cohort whose extensive homozygosity offers exceptional statistical power for variant discovery and disease-gene mapping.

Contexte

The Centre Hospitalier Universitaire Vaudois (CHUV) is one of the five Swiss university hospitals and a leading center for clinical care, biomedical research, and academic training. Through its close collaboration with the University of Lausanne (Faculty of Biology and Medicine) and the École Polytechnique Fédérale de Lausanne (EPFL), the CHUV offers a highly dynamic and interdisciplinary research environment at the interface of medicine, genetics, and systems biology.

Mission

• Contribute to the design, development, benchmarking, and maintenance of a comprehensive long-read sequencing analysis pipeline.
• Perform alignment and variant calling from PacBio HiFi data, including SNVs, indels, structural variants, CNVs, and CpG methylation profiling.
• Develop and implement telomere-to-telomere (T2T) de novo genome assembly workflows and contribute to the construction of a population-specific reference panel.
• Establish imputation frameworks to recover genotypes from low-coverage short-read whole-genome sequencing data.
• Integrate artificial intelligence and machine-learning approaches into variant annotation and interpretation workflows.
• Conduct statistical genomics analyses, including polygenic risk score development and genetic association studies.
• Contribute to the analysis of diverse genomic and phenotypic datasets within an international research consortium.

Profil

• Master’s degree (or equivalent) in Bioinformatics, Computational Biology, Computer Science, Statistics, Genomics, Genetics, Molecular Biology, Cellular Biology, or a related field.
• Strong programming skills in Python and R.
• Proficiency in Linux environments and high-performance computing (HPC) systems.
• Experience in sequencing data analysis; familiarity with long-read sequencing technologies, statistical genetics, or machine learning is an asset.
• Previous experience in human genetics and/or rare disease genomics is desirable.
• Experience in stem cell biology, including iPSC derivation and differentiation, is an advantage.
• Strong organizational skills, scientific rigor, and attention to detail.
• Ability to work independently while contributing effectively to a collaborative and multidisciplinary international team.
• Excellent written and spoken English; knowledge of French is an asset.

Nous offrons

To become an employee of the world-famous University Hospital Center from the Canton of Vaud is an assurance of:

• Comprehensive social benefits, including 20 days of paternity leave and 4 months of maternity leave (with the possibility of an additional month of breastfeeding leave).
• Regular salary progression aligned with responsibilities and career development.
• A 13th-month salary and 25 days of annual leave.
• Entitlement to at least three days of training per year, with access to a wide range of courses offered by the CHUV Training Center and partner training institutions of the State of Vaud.
• Easier access to one of the 500 furnished apartments available in nearby neighborhoods for employees relocating to Switzerland from abroad.
• Social, cultural, and financial benefits offered to members of the H-Oxygène association.
• Benefits available through the mobility plan, including discounts on public transport passes, promotion of Mobility car-sharing vehicles, and discounts on the purchase of electric bicycles.
• High-quality staff restaurants in every hospital building, offering hotel-standard catering at preferential rates.

Contact et envoi de candidature

Contact for information on the function : Dr Federico Santoni - Head of laboratory, per e-mail : E-Mail schreiben

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The CHUV applies the highest quality requirements as part of its recruitment process. In addition, mindful to promote workplace diversity and inclusion we strive to ensure equal treatment and avoid any discrimination. We are looking forward to receiving your application.

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