PhD Position in Computational Biology: 3D Chromatin Organization - Role in Cancer

Research Description

Human cells contain about 2 metres of linear DNA not-randomly packed into the nucleus of a few microns diameter, and the manner in which it is wrapped plays a fundamental role in regulating genome expression. In most of the cases, it does this by putting regulatory elements and target gene promoters into physical contact. It has been estimated that the genome harbours around one million regulatory elements, but the vast majority of interactions between these elements and the corresponding regulated gene are uncharted, constituting a major missing link in understanding genome control. The recent development of Promoter Capture Hi-C (PCHi-C) method has allowed for the first time the genome-wide systematic identification of the interacting regions that are in physical contact with 31,253 human promoters (Javierre, Cell 2016). Promoter interactions are highly cell type specific and interacting regions are enriched in non-coding SNPs. This technique has enabled to connect non-coding disease variants to putative target promoters, prioritizing thousands of disease-candidate genes and implicating disease pathways.

Chromatin interactions are crucial for cellular health due to their main role in genome expression regulation and errors in these interactions could give rise to the development of a broad range of diseases including cancer. For all these reasons, we want to deeply investigate the altered promoter interactomes in cancer and their functional repercussion. This knowledge will help us to improve our knowledge of the tumour process, providing new opportunities for the development of novel treatment approaches and diagnostic strategies. In our approach, we will combine cutting-edge experimental and computational approaches for analysing spatial-temporal changes in the 3D chromatin packaging and the epigenetic profiles.

Requirements

A high level of motivation and interest.
MSc in Bioinformatics, Computational Biology or in a related field to be able to quickly acquire bioinformatics skills.
Proficiency in at least one scripting or programming language.
Proficiency in scripting environments for statistics and data analysis.
Competitive CV.
High level of collaborative and communicative skills.
Good level of English speaking and writing skills.
International mobility will be considered a major plus.

What we offer

Incorporation in two multinational and highly collaborative teams (Valencia and Javierre groups) focused on different and complementary research topics.
Enrollment in an internationally recognized PhD program.
Exciting and innovative collaborative research project in one of the most promising research topic.
Working in the mixed computational, basic and clinical research environment of the Barcelona Supercomputing Center and the Josep Carreras Leukaemia Research Institute.
Contract details will be negotiated and take into account the track record of the candidate.
Flexible start date (as soon as suitable for you).

For more information

Please also visit Valencia and Javierre group webpages:

How to apply

Interested applicants should send their CV (incl. the contact details of three referees) and a motivation letter to: alfonso.valencia@bsc.es & bmjavierre@carrerasresearch.org

Deadline for applications

We will accept applications until the position is filled but recommend to send your application before July 1^st 2018 to be included in the first evaluation round.

(Original source: PhD position call (BSC_IJC))