Date limit
16-07-2021
Institution
Barcelona Supercomputing Center (BSC)
About BSC
The Barcelona Supercomputing Center - Centro Nacional de Supercomputación (BSC-CNS) is the leading supercomputing center in Spain. It houses MareNostrum, one of the most powerful supercomputers in Europe, and is a hosting member of the PRACE European distributed supercomputing infrastructure. The mission of BSC is to research, develop and manage information technologies in order to facilitate scientific progress. BSC combines HPC service provision and R&D into both computer and computational science (life, earth and engineering sciences) under one roof, and currently has over 700 staff from 49 countries.
Context And Mission
The Computational Biology group is looking for a Junior Researcher to work in the context of a recently-granted Plan Nacional that aims to explore the interaction between biological sex and cancer germline variants. Over the last decade we have made significant progress in understanding the role of genetics in cancer predisposition, evolution and treatment. We now have thousands of germline variants associated with different types of cancer and we have also identified a few hundred genes that, when somatically mutated, drive the growth of cancer cells.
However, there are also many open questions to which we do not have, yet, a conclusive answer, and some of the most pressing ones have to do with the role of biological sex in cancer. For example, we know that the incidence of multiple cancer types (thyroid, pancreas, brain or bladder, among many others) is significantly different in males and females, sometimes by orders of magnitude. Similarly, cancer genes have different somatic mutation rates depending on the sex of the patient. Last, but not least, many cancer drugs work differently in men than in women.
The candidate will study the role of biological sex in cancer genetics. To that end, s/he will use large cancer genetics databases to identify germline variants that predispose to cancer in different ways in men and in women.
The candidate will work under the supervision of Dr. Eduard Porta Pardo, la Caixa Junior Leader, in the Computational Biology Group of the Life Sciences Department. The Computational Biology group (http://life.bsc.es/compbio) is involved in multiple projects covering a wide range of topics including cancer genomics, tumor immunology, multilayer network modeling, epigenomics and computations systems biology. The candidate will collaborate with other members of the group, as well as from other departments at the BSC, especially Computational Genomics Group led by David Torrents, ICREA Professor.
The Researcher will work in a highly sophisticated HPC environment, will have access to state-of-the-art systems and computational infrastructures, and will establish collaborations with experts in different areas both at international and local levels.
Recent publications from our group
However, there are also many open questions to which we do not have, yet, a conclusive answer, and some of the most pressing ones have to do with the role of biological sex in cancer. For example, we know that the incidence of multiple cancer types (thyroid, pancreas, brain or bladder, among many others) is significantly different in males and females, sometimes by orders of magnitude. Similarly, cancer genes have different somatic mutation rates depending on the sex of the patient. Last, but not least, many cancer drugs work differently in men than in women.
The candidate will study the role of biological sex in cancer genetics. To that end, s/he will use large cancer genetics databases to identify germline variants that predispose to cancer in different ways in men and in women.
The candidate will work under the supervision of Dr. Eduard Porta Pardo, la Caixa Junior Leader, in the Computational Biology Group of the Life Sciences Department. The Computational Biology group (http://life.bsc.es/compbio) is involved in multiple projects covering a wide range of topics including cancer genomics, tumor immunology, multilayer network modeling, epigenomics and computations systems biology. The candidate will collaborate with other members of the group, as well as from other departments at the BSC, especially Computational Genomics Group led by David Torrents, ICREA Professor.
The Researcher will work in a highly sophisticated HPC environment, will have access to state-of-the-art systems and computational infrastructures, and will establish collaborations with experts in different areas both at international and local levels.
Recent publications from our group
- Bailey, Matthew H.*, Collin Tokheim*, Eduard Porta-Pardo*, Sohini Sengupta, Denis Bertrand, Amila Weerasinghe, Antonio Colaprico, et al. 2018. “Comprehensive Characterization of Cancer Driver Genes and Mutations.” Cell 174 (4): 1034–35.
- Ding, Li*, Matthew H. Bailey*, Eduard Porta-Pardo*, Vesteinn Thorsson, Antonio Colaprico, Denis Bertrand, David L. Gibbs, et al. 2018. “Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics.” Cell 173 (2): 305–20.e10.
- Porta-Pardo, Eduard, Alfonso Valencia, and Adam Godzik. 2020. “Understanding Oncogenicity of Cancer Driver Genes and Mutations in the Cancer Genomics Era.” FEBS Letters, April. https://doi.org/10.1002/1873-3468.13781.
- Sayaman, Rosalyn W., Mohamad Saad, Vésteinn Thorsson, Wouter Hendrickx, Jessica Roelands, Younes Mokrab, Farshad Farshidfar, et al. (incl. Porta-Pardo) Immunity. “Germline Genetic Contribution to the Immune Landscape of Cancer.” https://doi.org/10.1101/2020.01.30.926527.
Key Duties
- Curation and quality control of raw germline genotype data
- Reanalysis of publicly available data from Genome Wide Association Studies.
- Development of polygenic risk scores.
- Integration of heterogeneous data sources using advanced data mining techniques.
- Preparation and presentation of scientific articles.
Requirements
- Education
- MSc in bioinformatics or similar with a strong background in human genetics
- Essential Knowledge and Professional Experience
- Programming: Python, R, Git or similar.
- Knowledge of UNIX/Linux environment.
- Competences
- Fluency in spoken and written English, while fluency in other European languages will be also valued.
- Good communication and presentation skills.
Conditions
- The position will be located at BSC within the Life Sciences Department
- We offer a full-time contract, a good working environment, a highly stimulating environment with state-of-the-art infrastructure, flexible working hours, extensive training plan, tickets restaurant, private health insurance, fully support to the relocation procedures
- Duration: Temporary - 2 years renewable
- Salary: we offer a competitive salary commensurate with the qualifications and experience of the candidate and according to the cost of living in Barcelona
- Starting date: asap
Applications Procedure
All applications must be done through the application form (bottom of the linked page) and must include:
- A Cover Letter with a statement of interest in English, including two contacts for further references - Applications without this document will not be considered
- A full CV in English including contact details
Deadline
The vacancy will remain open until a suitable candidate has been hired. Applications will be regularly reviewed and potential candidates will be contacted.
Diversity and Equal Opportunity Employment
BSC-CNS is an equal opportunity employer committed to diversity and inclusion. We are pleased to consider all qualified applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, disability or any other basis protected by applicable state or local law.
Original source: https://www.bsc.es/join-us/job-opportunities/19621lscbre1