IRB Barcelona is a self-standing, non-profit institution devoted to basic and applied biomedical research. It was set up in 2005 jointly by the Government of Catalonia and the University of Barcelona and is located at the Barcelona Science Park. The institute currently has more than 430 members (scientific, technical and administrative staff) from all over the world, who work across disciplines to advance research in the biomedical sciences.
Applications for the above opening should include a full C.V, university grades certificate(s), contact information of two referees, and a Motivation Letter and should be sent by e-mail to: firstname.lastname@example.org with the Reference: PREDOC/19/04
Deadline for applications: 25/08/2019
If no suitable candidate is found, the deadline will be extended.
Job offer: Will be sent to the successful candidate after the interview.
IRB Barcelona is seeking a PhD candidate to work in the Genome Data Science laboratory (https://agendas.irbbarcelona.org/ ), headed by Prof. Fran Supek. On the project entitled ‘Hypermutated tumors: insight into genome maintenance and cancer vulnerabilities provided by an extreme burden of somatic mutations —HYPER-INSIGHT’, funded from the European Research Council (ERC) under the European Union’s Horizon 2020 programme (grant agreement No 757700). We will investigate the quality control mechanisms of the human transcriptome under mutagenic conditions. We will combine high-throughput experimental and computational methods to reveal new therapeutic targets for cancer and heritable diseases.
The PhD project will deal with mechanisms of quality control of the transcriptome. In particular, we are interested in how mutations that occur in tumor cells and/or in the human germline can affect the ability to degrade the mutated mRNA, to induce ribosome frameshifting or to bypass a stop codon in the transcript.
This question will be adressed by a combination of experimental work in cancer cell lines (estimated 60% time) and computational biology (40% time). Experimentally, we will apply ‘deep mutational scanning’ techiques to systematically interogate the DNA sequence features that affect mRNA quality control. Computationally, we will analyze such data to find trends, and then search for same trends in transcriptomes of patients, in order to look for novel therapeutic avenues.
The PhD will be performed in close collaboration between the Supek lab (IRB, https://agendas.irbbarcelona.org/) and the Lehner lab (CRG); the PhD candidate will be associated with both laboratories.
Start date is flexible; fall 2019 is preferrable. Informal inquiries can be directed to the PI’s. Early applications are encouraged.
Lindeboom, Supek and Lehner (2016) Nature Genetics. “The rules and impact of nonsense-mediated mRNA decay in human cancers.”
Lindeboom, Vermeulen, Lehner and Supek (2019) under review. “The impact of nonsense-mediated mRNA decay on genetic disease, gene editing and cancer immunotherapy”
Supek et al. (2014) Cell. “Synonymous mutations frequently act as driver mutations in human cancers”
Baeza et al. (2018) Cell “Combinatorial Genetics Reveals a Scaling Law for the Effects of Mutations on Splicing”
Domingo, Diss and Lehner (2018) Nature “Pairwise and higher-order genetic interactions during the evolution of a tRNA.”
- perform excellent research according to standards set by Supek and Lehner labs
- learn experimental and computational techniques necessary to perform the research
- attend to and present at lab meetings, lab journal clubs, department seminars, and conferences
- collaborate with other members of the host lab(s) to further the advancement on the project
Must Have – Required