PhD Position in Long-Read Computational Genomics

ppbContexte /b /p /ppThe 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. /p ppbMission /b /p /p liContribute to the design, development, benchmarking, and maintenance of a comprehensive long-read sequencing analysis pipeline. /li liPerform alignment and variant calling from PacBio HiFi data, including SNVs, indels, structural variants, CNVs, and CpG methylation profiling. /li liDevelop and implement telomere-to-telomere (T2T) de novo genome assembly workflows and contribute to the construction of a population-specific reference panel. /li liEstablish imputation frameworks to recover genotypes from low-coverage short-read whole-genome sequencing data. /li liIntegrate artificial intelligence and machine-learning approaches into variant annotation and interpretation workflows. /li liConduct statistical genomics analyses, including polygenic risk score development and genetic association studies. /li liContribute to the analysis of diverse genomic and phenotypic datasets within an international research consortium. /li ppbProfil /b /p /p liMaster’s degree (or equivalent) in Bioinformatics, Computational Biology, Computer Science, Statistics, Genomics, Genetics, Molecular Biology, Cellular Biology, or a related field. /li liStrong programming skills in Python and R. /li liProficiency in Linux environments and high-performance computing (HPC) systems. /li liExperience in sequencing data analysis; familiarity with long-read sequencing technologies, statistical genetics, or machine learning is an asset. /li liPrevious experience in human genetics and/or rare disease genomics is desirable. /li liExperience in stem cell biology, including iPSC derivation and differentiation, is an advantage. /li liStrong organizational skills, scientific rigor, and attention to detail. /li liAbility to work independently while contributing effectively to a collaborative and multidisciplinary international team. /li liExcellent written and spoken English; knowledge of French is an asset. /li ppbNous offrons /b /p /p pbTo become an employee of the world-famous University Hospital Center from the Canton of Vaud is an assurance of: /b /p libComprehensive social benefits /b, including b20 days of paternity leave /b and b4 months of maternity leave /b (with the possibility of an additional month of breastfeeding leave). /li libRegular salary progression /b aligned with responsibilities and career development. /li liA b13th-month salary /b and b25 days of annual leave /b. /li liEntitlement to bat least three days of training per year /b, with access to a wide range of courses offered by the bCHUV Training Center /b and partner training institutions of the bState of Vaud /b. /li liEasier access to one of the b furnished apartments /b available in nearby neighborhoods for employees relocating to Switzerland from abroad. /li libSocial, cultural, and financial benefits /b offered to members of the bH-Oxygène association /b. /li liBenefits available through the bmobility plan /b, including discounts on public transport passes, promotion of bMobility /b car-sharing vehicles, and discounts on the purchase of electric bicycles. /li libHigh-quality staff restaurants /b in every hospital building, offering hotel-standard catering at preferential rates. /li