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Postdoctoral Fellow - Modeling Gene Essentiality in Cancer

Salary £31,503 to £39,492 (dependant on experience) plus excellent benefits

Fixed term for 3 years

The Wellcome Sanger Institute is seeking a highly motivated researcher with strong skills in computational genomics to fill a postdoctoral fellow position. The aim of the fellow is to develop a quantitative framework for predicting cancer vulnerabilities. To achieve this, the successful candidate will create generative probabilistic models that integrate the abundant data gathered in the international DepMap consortium for the available cancer cell lines, as well as apply deep neural networks and other suitable machine learning approaches to identify features to include in the model. Our collaborators in the consortium have world-leading expertise in cancer genomics to help guide model development.

The broader goal of the Cancer Dependency Map (http://depmap.org/sanger, and http://depmap.org/broad) is to identify a targetable vulnerability in every cancer cell. Ultimately, this will pave way for tumor-specific treatments. The groups involved have already characterized up to 1,000 cancer cell lines using high throughput genomic, transcriptomic, and proteomic techniques, as well as applied large scale drug panels to assess line-specific sensitivities. Work is currently ongoing to identify genes that inhibit cell growth when knocked out using CRISPR/Cas9 -- these could then be used as targets for therapies. The initiative is funded by OpenTargets (www.opentargets.org), a unique pre-competitive collaboration of companies and research institutions. As part of this effort, positions are also available for a bioinformatician to process genome-wide knock-out screen data, and a postdoctoral fellow to identify new therapeutic targets, and molecular markers of response to genetic and small molecule perturbations.

The successful candidate will perform original research in quantitative modelling of gene essentiality in cancer cell lines. The ultimate expected output is a model, that given a genome sequence and potentially additional molecular characterization, predicts the phenotypic impact of the knockout of each gene. It is important you have the ability to bridge from understanding the processes generating the observed data, to implementing computational pipelines to extract information and creating correct generative models for analysis. You are expected to make progress on your project as the first priority, while budgeting time for training in further skills, piloting new leads, and potentially collaborating on other projects. To function effectively in a multidisciplinary, collaborative setting, you have to be able to communicate well with scientists from diverse backgrounds, and be a pleasant colleague.

This position offers the opportunity to work at one of the world’s leading genomic centres at the forefront of genomic research. You will have access to Sanger's computational resources, including a 15000+ core computational cluster, the largest in life science research in Europe, and multiple petabytes of high-speed cluster file systems. Our group also has laboratory space and access to core facilities, where we generate our own data with the help of dedicated staff. This provides an exciting opportunity for you to not only analyse the data, but to be actively involved in the planning and execution of large-scale experiments.

We are part of a dynamic and collaborative environment at the Genome Campus and, although we seek someone who can work independently, you will have the opportunity to interact with researchers across Sanger, as well as our neighbours at the European Bioinformatics Institute.

This PDF post is currently being advertised alongside a Postdoctoral Fellow- Cancer Dependency Map Analytics (ref 83073) in Cancer Genomics

Job Reference
83076

Essential Skills

  • PhD in a relevant subject area (Physics, Computer Science, Engineering, Statistics, Mathematics, Computational Biology, Bioinformatics) 
  • Ability to devise novel quantitative models, use relevant mathematics-heavy literature 
  • Experience in formulating the world in statistical models and applying them to real data 
  • Full working proficiency in a scripting language (e.g. Python, R, Perl) 
  • Full working proficiency in UNIX/Linux 
  • Strong publishing record 
  • Ability to communicate ideas and results effectively 
  • Ability to work independently and organise own workload 
  • Motivation to understand how cells work 

Ideal Skills

  • Knowledge of genomics and molecular biology 
  • Previous experience with data from high throughput assays 
  • Previous experience with data from genetic screens 
  • Previous experience in creating finished software 
  • Full working proficiency in a compiled language (e.g. C, C++, D, Fortran) 
  • Previous experience with implementing–omics data analysis pipelines on a cluster 

Other information

Postdoctoral Fellows are typically in their first or second postdoctoral position as part of a period of early career research training.

Open Targets is a pioneering public-private partnership between Biogen, Celgene, EMBL-EBI, GlaxoSmithKline (GSK), Takeda, and the Wellcome Sanger Institute and is located on the Wellcome Genome Campus in Hinxton, near Cambridge, UK. Open Targets brings together expertise from six complementary institutions to systematically identify and prioritise targets from which safe and effective medicines can be developed, to help others find good targets, and to get those targets adopted into drug discovery pipelines. 

We currently focus on oncology, immunology and neurodegeneration through an R&D framework that can be applied to all aspects of human disease. We believe that evidence generated in the most human relevant systems showing which targets are causing disease will have a significant impact on the successful development of new medicines. To build a good therapeutic hypothesis we need to find not only which targets are involved, but also how we might alter complex disease mechanisms.

Our Campus: Set over 125 acres, the stunning and dynamic Wellcome Genome Campus is the biggest aggregate concentration of people in the world working on the common theme of Genomes and BioData. It brings together a diverse and exceptional scientific community, committed to delivering life-changing science with the reach, scale and imagination to pursue some of humanity’s greatest challenges.

Our Benefits: Our employees have access to a comprehensive range of benefits and facilities including:

  • Group Defined Contribution Pension Scheme and Life Assurance
  • Group Income Protection
  • Private Health Insurance
  • 25 days annual leave, increasing by one day a year to a maximum of 30
  • Family friendly environment including options for flexible and part-time working, a childcare voucher scheme, Campus Nursery and Summer holiday club
  • Two days paid Employee Volunteering Leave a year
  • Employee Discount Scheme
  • Campus Gym, tennis courts, cricket pitch and sports hall plus a range of dining facilities
  • Active Campus Sports and Social Club
  • Free Campus Bus Service

Genome Research Limited is an Equal Opportunity employer. As part of our commitment to equality, diversity and inclusion and promoting equality in careers in science, we hold an Athena SWAN Bronze Award and have an active Equality, Diversity and Inclusion programme of activity. We will consider all applicants without discrimination on grounds of disability, sexual orientation, pregnancy or maternity leave status, race or national or ethnic origin, age, religion or belief, gender identity or re-assignment, marital or civil partnership status, protected veteran status (if applicable) or any other characteristic protected by law. We are open to a range of flexible working options including part-time or full-time employment as well as flexible hours due to caring or other commitments.

Please include a covering letter and CV with your application.  Closing date for applications: 10th June 2018.

Contact leopold.parts@sanger.ac.uk for informal enquiries