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Postdoctoral Fellow- Open Targets

European Molecular Biology Laboratory (EMBL)

Location: Cambridge, Hinxton
Salary: £2,752.13 monthly starting stipend after tax (Year 1 Stipend).
Hours: Full Time
Contract Type: Fixed-Term/Contract
Placed On: 10th June 2019
Closes: 19th July 2019
Job Ref: EBI01432

About the team/job

This is an exciting opportunity to work at the cutting edge of evidence generation in fast moving field of drug target identification and prioritisation. You will be embedded in a team working with cloud based technologies, integrating evidence from across EMBL-EBI and other databases to identify and prioritise drug targets.

Your role

The scientific literature is a rich source of evidence for the role of potential drug targets in disease, as well as other relationships between targets, disease, drugs, methods and so on. We are developing a robust pipeline to extract these relationships from the Open Access literature working with Europe PMC and developing machine learning and graph approaches for identifying novel and unexpected relationships.

The post will involve use of natural language processing to develop comprehensive entity recognition, testing and refinement of entity dictionaries, building a knowledge graph combining literature relationships with other evidence from the Open Targets Platform and machine learning to predict novel relationships including disease:target associations and drug repurposing opportunities.

You will

  • Participate in building an Open Targets Knowledge Graph
  • Develop machine learning approaches to identify novel associations and other opportunities, and publish these.
  • Build repertoire of training sets and gold standard for NLP for diverse entities
  • Assess and feedback on performance of Europe PMC literature entity tagging including collating user feedback
  • Contribute to implementation of graph-based approaches for the next generation Open Targets Platform

You have

  • PhD in Computer Science, Bioinformatics, Computational Biology, Data Science or related area
  • Experience in Machine Learning or Natural Language Processing in a biological context
  • Highly proficient in Python, Scala or equivalent programming language
  • Must be able to communicate analysis and results clearly to a diverse audience
  • Must be able to identify and clearly express limitations or pitfalls in potential approaches

You might also have

  • Experience in an area related to drug discovery would be an advantage
  • Experience with graphical-based approaches
  • Familiarity with cloud computing environments
  • Proficient with data analysis for instance in R

The position is embedded in the Open Targets Core Platform team. Extensive interaction with text mining and NLP experts in Europe PMC is required. Interaction with the full set of Open Targets Partners is expected.

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