Master's project on spatial transcriptomics

Job description

We are searching for a graduate student to contribute to the development of the open-source software project “GSVA: Optimizing Gene Set Variation Analysis for Single-Cell Data”, funded by the Chan Zuckerberg Initiative (CZI) in the last call for Essential Open Source Software for Science. The candidate will work in the research group of Robert Castelo at the Department of Medicine and Life Sciences from the Universitat Pompeu Fabra (UPF), in the Barcelona Biomedical Research Park (PRBB), in Barcelona, Spain and in close collaboration with Justin Guinney, senior researcher at Tempus Labs, USA. With over 1,400 residents, the PRBB has a large critical mass of scientists from different institutions at the forefront of research in bioinformatics and computational biology, giving the possibility to attend seminars, conferences and soft-skills training.

GSVA is an R/Bioconductor package that facilitates pathway-centric analyses of molecular data. With more than 200,000 downloads and 5,000 citations to the paper describing it, GSVA has become a very popular open-source software. We offer a graduate student to carry out his/her master’s thesis project in the framework of adapting GSVA to analyse spatial transcriptomics data.

Specific requirements

  • BSc or higher degree in either computer science, engineering, mathematics, physics or in the life sciences with a motivation for scientific method and software development.

  • Ideally enrolled in a master’s programme in the field of bioinformatics, biostatistics, data science, mathematics or related discipline, in which a master’s project should be developed during the academic year 2023-24. Candidates not enrolled in a master’s programme may be considered if they have a strong profile in the other requirements.

  • Solid knowledge of fundamental statistics and programming, ideally with R.

  • Fluency in written and spoken English. Excellent teamwork and collaboration skills.

  • High motivation for interdisciplinary work, and particularly, for contributing to address questions of biological and clinical relevance.

Compensation and benefits

We offer a full-time two-year contract starting on the third trimester of 2023, funded by the CZI, with a gross salary of a PhD student, about 17,000 EUR/year (monthly gross salary of about 1,400EUR), including the standard health benefits of an European Union member state.

Application process

Send CV and letter of interest, including names of two referees that could send a recommendation letter to robert.castelo@upf.edu (REF: CZI_GSVA). Additional information about this job offer can be also requested to the same email address.