PREDOCTORAL POSITION (ref. PREDOC/20/01)

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.

How to apply: 

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: irbjobs@irbbarcelona.org with the Reference: PREDOC/20/01

 

  • Deadline for applications: 10/09/2020

If no suitable candidate is found, the deadline will be extended.  

 

  • Number of positions available: 1

 

  • Selection process:

 

  • Pre-selection: Will be based on CV, motivation letter, experience, university track record (grades, awards).

 

  • Interviews: Short-listed candidates will be interviewed.

 

  • Job offer: Will be sent to the successful candidate after the interview. 
Reference: 
PREDOC/20/01
Status: 
Open Positions
Deadline: 
Thursday, September 10, 2020

IRB Barcelona is seeking a motivated PhD candidate to work on the project entitled ‘Hypermutated tumors: insight into genome maintenance and cancer vulnerabilities provided by an extreme burden of somatic mutations HYPER-INSIGHT’, funded by the European Research Council (ERC), under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 757700).

 

The PhD project will explore mutagenic mechanisms causing structural variations (rearrangements) in the human genome, and their impact on cancer and inherited disease, with translational implications.

 

In particular, we are interested in how DNA damage that occurs in tumor cells and/or in the germline cells can result in mutations: copy number changes, other structural variation (translocations, inversions), and small indels.  We are also interested in predicting whether such mutations cause disease. These questions will be addressed by large-scale computational analyses of human and/or mouse genomic data sets. 

 

We will employ machine learning methodologies to characterize mutation patterns in DNA of patients and healthy controls, and statistically associate them with disease outcomes.  We are very interested in applying deep learning approaches (such as recurrent neural networks or transformers) to analysis of rearranged DNA sequences.

 

The PhD project will be developed in the Genome Data Science lab (https://agendas.irbbarcelona.org/), under supervision of ICREA professor and EMBO young investigator Fran Supek, in collaboration with the diverse, international team of the laboratory, which consists of genomics biologists, wet-lab biologists and mathematicians at the PhD and postdoc level.

 

Start date is flexible; fall 2020 is preferable. Informal inquiries can be directed to the PI at fran.supek@irbbarcelona.org. Early applications are encouraged.

 

Relevant publications:

 

Lindeboom, Vermeulen, Lehner and Supek (2019) Nature GeneticsThe impact of nonsense-mediated mRNA decay on genetic disease, gene editing and cancer immunotherapy

Mas-Ponte and Supek (2020) Nature Genetics, in press “DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers” (text available by request)

Supek and Lehner. (2017) Cell.Clustered Mutation Signatures Reveal that Error-Prone DNA Repair Targets Mutations to Active Genes

Supek et al. (2014) Cell.Synonymous mutations frequently act as driver mutations in human cancers
 

Duties: 

perform excellent research according to the high standards of the Supek lab and the IRB Barcelona

- learn various bioinformatics and machine learning techniques required to perform the research

- present at weekly lab meetings and journal clubs, at department seminars, and conferences

- collaborate with other members of the host lab to facilitate progress on the project

 

Profile: 

Must Have – Required

 

  • Experience: MSc in the natural sciences, engineering, medicine or mathematics.

 

  • Knowledge: good level of spoken English. Beginner-to-intermediate knowledge of one programming language.

 

  • Skills: a highly motivated young researcher with enthusiasm to work on challenging, important topics in biomedical science

 

Desirable

 

  • Experience: some experience with machine learning methods esp. deep learning would be helpful, but is not necessary.  Experience with various genomics and/or epigenomics and/or transcriptomics software tools.

 

  • Knowledge: high level of spoken and written English.  Evolutionary genomics or population genomics or cancer genomics-related topics.

 

  • Skills: independent, self-learning, goal-oriented.
Remarks: 
  • Working conditions: Employed in compliance with Spanish legislation and regulations under a full-time contract. Employees receive the benefits of the Spanish Social Security system covering sickness, maternity/paternity leaves and injuries at work.

 

  • Training and Career: Training is a way of life at IRB Barcelona. PhDs have access to a wide variety of scientific activities and services and an extensive network of academic and industrial contacts, which serve to strengthen the perspectives of their research career. Furthermore, they can benefit from our Language Training Programme. PhD students receive close mentoring and work on a research project that is chosen in mutual agreement with their group leader.

 

  • International environment: Nearly 100 students (almost half non-Spanish nationals) are currently working toward their PhD theses at IRB Barcelona.