4-year BBSRC PhD funding for developing BioJavaScript Genomics Application available for UK/EU nationals

An exciting PhD training opportunity due to begin in October 2014 is available. I am looking for a candidate to join my group for a fully funded BBSRC iCASE 4 year PhD fellowship. Only UK/EU nationals are eligible to apply. The project is a partnership between the Genome Analysis Centre (TGAC, Norwich) and the Cambridge-based bioinformatics consultancy Eagle Genomics.


The aim of this PhD is to develop functionality that supports visualisation of genome data without a reference assembly within the BioJavaScript framework. Funding is available for 4 years (Doctoral Stipend ~£13,863 p.a.) and the degree will be awarded by the University of East Anglia.


Applicants with a background in computer science and with an interest in genomics are particularly encouraged to apply. If you would like to have an informal chat about this please contact me at If you know of a suitable candidate please feel free to pass on this email.


For more information about BioJS please follow links below. For more information about the PhD project itself please see text at the end of this post.



TITLE: “Integrating Visualisation of Unreferenced Genomes”

ABSTRACT: Visualisation of genomic features is an essential part of genome annotation. The standard process for annotation of genomes requires a reference sequence against which Next Generation Sequencing (NGS) transcriptomic data are aligned and assembled. There are however, cases in which a genome reference is unavailable or incomplete, as it is the case for those genomes with long stretches of repetitive sequence. These regions still have annotations that require visualisation and need to be integrated with the whole. We propose the development of a suite of computational resources for fast annotation  and  visualisation  of  unreferenced  genomic  regions. Making use of our current involvement in the development of the BioJavaScript project (BioJS), we will develop a set of visualisation components for referenced and unreferenced genomes, with the object to allow interactive annotation of crop and animal genomes.

The Genome Analysis Centre (TGAC) is a research institute focused on the application of state of the art genomics and bioinformatics to advance plant, animal and microbial research to promote a sustainable bioeconomy. TGAC is a hub for innovative bioinformatics founded on research, analysis and interpretation of multiple, complex data sets. Eagle Genomics Ltd., the UK’s leading bioinformatics cloud consultancy business, is partnering with TGAC in an exciting PhD training opportunity due to begin in October 2014. Together, these two organisations will train the successful candidate in diverse, project-enhancing skills such as data-driven knowledge discovery in bioinformatics and business consultancy. Within the project, the student will have the opportunity to develop a set of BioJS visualisation components for visualisation of unreferenced genomes and to develop new computational tools for genome/trait association, which will play a key role in developing the BioJS project. Opportunities also exist to collaborate with key project stakeholders, such as the European Bioinformatics Institute.

Applicants with a background in computer science and with an interest in genomics are particularly encouraged to apply.


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