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PhD Studentship in School of Computing: Machine Learning for Synthetic Biology (EPSRC Portabolomics)

Newcastle University - School of Computing

Qualification Type: PhD
Location: Newcastle upon Tyne
Funding for: UK Students
Funding amount: £14,777
Hours: Full Time
Placed On: 19th October 2018
Closes: 30th November 2018
Reference: COMP007

Value of award

100% of UK tuition fees paid and an annual stipend of £14,777 (full award).

Number of awards


Start date and duration

January 2019 for 3 years.

Application closing date

30 November 2018.


This PhD studentship is part of the Portabolomics project. The vision of Portabolomics is to bring forth a breakthrough in Synthetic Biology that will enable the development of portable biocircuits across chassis (i.e. from one bacteria species to another). This vision is akin to the Java virtual machine having enabled the reuse and portability of software across different operating systems and hardware platforms.

In this doctoral project you will focus on the challenge of devising innovative strategies to transform the vast volumes of data generated in the wet lab experiments of Portabolomics into actionable knowledge that can feed into the computational work on network analysis and verification in the project. The data generated by the project is vast and diverse: imaging data, omics data, complex and heterogeneous annotation from public and private sources. Using a combination of biological data integration, state-of-the-art machine learning, knowledge extraction and information visualisation techniques we seek to build methods to identify biomarkers and infer biological networks.

The specific topic of the studentship will be decided based on the skill set of the successful applicant, although we envision that it will require a combination of the following:
Strong machine learning background and proficiency in the state of the art data science languages (e.g. R, python)

  • Deep Learning
  • Knowledge discovery
  • Biological data integration
  • Information visualisation
  • High Performance Computing (e.g. classic HPC clusters, GPUs, Intel PHI, Big Data frameworks, Cloud resources).


Engineering and Physical Sciences Research Council (EPSRC)

Name of supervisor(s)

Dr Jaume Bacardit, School of Computing.

Eligibility Criteria

Applicants should have a first class degree, or a combination of qualifications and/or experience equivalent to that level. Ideally, students should have a BSc or MSc degree in computer science. Applicants should be strong programmers, and experience in machine learning/data mining/big data/information visualisation/biological data will be greatly valued.

Full fees will only be awarded following EPSRC eligibility rules.

How to apply

You must apply through the University’s online postgraduate application system.  To do this please ‘Create a new account’.

Only mandatory fields need to be completed.  However, you will need to include the following information:

  • insert the programme code 8050F in the programme of study section
  • select PhD Computer Science (full time) - (Computing Science)', as the programme of study
  • insert the studentship code COMP007
  • attach covering letter, CV and (if English is not your first language) a copy of English language qualifications. The covering letter must state title of studentship, quote reference COMP007 and describe how your research interests fit with the topic of research project outlined in the advertisement (maximum of two pages).

please send your covering letter and CV by e-mail to


For further details, please email Dr Jaume Bacardit.

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