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BBSRC DTP Targeted PhD Studentship (Fixed Term)

From Jobs at the University of Cambridge. Published on Feb 08, 2018.

Structure function predictions of translational products from novel Open Reading Frames with Dr Sudhakaran Prabakaran, Department of Genetics

Applications are invited for a 4-year PhD studentship in the BBSRC-funded Cambridge Doctoral Training Programme (DTP), to work with Dr. Sudhakaran Prabakaran within the theme of World-Class Underpinning Bioscience.

Translation of protein and protein-like products have been observed from regions of the genome that are traditionally classified as noncoding. These regions include small Open Reading Frames (sORFs), orphan genes, De Novo genes, pseudogenes, and other yet unannotated genomic regions. The primary reason why these novel translational products have not yet been identified and systematically investigated in spite of the technological advancements in genomic and proteomics fields is because unlike translations from the canonical ORFs, translation from the noncanonical ORFs are not pervasive, they occur in specific biological conditions such as specific disease states and hence only under a systems proteogenomics framework that was developed in our lab that these novel translational products can be identified. Using this framework we have provided evidence for translation from noncanonical ORFs.

The goal of this project is to understand the biological functions of these protein-like products based on predicting structures using EV-fold, QUARK, CATHH, and other structural genomics approaches. The project involves:- 1. identifying translation products from novel ORFs from TCGA cancer datasets using the cloud interface that we have developed in the lab, 2. predicting the structures of these identified novel translational products using structural genomics algorithms such as QUARK, EV-fold, CATHH, 3. mapping specific cancer-associated variants to these regions and inferring their 'pathogenicities' using machine learning approaches and modelling their interactions with their binding partners.

The project is therefore very interdisciplinary in nature. The student will learn to perform systems proteogenomics, analyse big data in the cloud environment, and develop machine-learning tools.

All applications should be made online via the University's Applicant Portal using the Department of Genetics course code (BLGE22). Details of how to apply are on: Applicants should hold or be about to achieve a First or Upper-Second (2.i) class degree in a relevant subject. We encourage students with strong mathematical background either in engineering or physics degree.

Funding will cover the student's stipend at the current Research Council rate and University Fees for 48 months, subject to eligibility. The studentships are available to UK nationals and EU students who meet the UK residency requirements. Further information about eligibility for Research Council UK funding can be found on the BBSRC website ( Applications from ineligible candidates will not be considered.

For further information, please contact Dr Sudhakaran Prabakaran (

Please quote reference PC14748 on your application and in any correspondence about this vacancy.

The University values diversity and is committed to equality of opportunity.

The University has a responsibility to ensure that all employees are eligible to live and work in the UK.

Software Developer (Fixed Term)

From Jobs at the University of Cambridge. Published on Mar 15, 2018.

Are you passionate about open source and making user friendly client-side web applications? We're a small team comprised of five developers (six, if you join us!) and a biologist, looking for a developer to help us with BlueGenes , an open source Clojure -powered user interface for the biological data warehouse InterMine . Clojure/ ClojureScript experience is not required, so long as you have experience with JavaScript and are willing to learn Clojure.

As well as working on BlueGenes, you'll also get the chance to support some of our older Javascript and CoffeeScript based applications and plugins. Development is likely to range from data wrangling through to interface design and data visualisation. We'd like to find someone who is comfortable collaborating with others on different aspects of the same project.

Essential skills and experience: - HTML, CSS, JavaScript, some experience with Node.js - Creating client-driven applications in JavaScript (or a language that compiles to JavaScript) - Creating and maintaining tests (UI, integration, unit). - Some experience with version control. We use git. - Good communication skills, ability to work as part of a team

Desirable skills and experience: - Experience with Clojure / ClojureScript , especially re-frame and reagent . - Biology knowledge.

About InterMine - our projects:

InterMine is an open source Java-based data warehouse, integrating biological data in varied formats into a PostgreSQL database. It also includes a legacy JSP user interface and web services with client libraries in R, Python, Perl, Ruby, Java, and JavaScript. BlueGenes, the new user interface, loads its data via these web services and is in early beta release at the moment.

Most InterMines are oriented around a certain organism or range of organisms, with FlyMine and HumanMine run in-house by the core Cambridge team, with a variety of other InterMine instances run by academic institutions around the world, from the UK and France to USA and Japan.

Some of our other initiatives include: - We currently have experimental prototype implementations of a Neo4j-powered backend . - Native mobile applications for Android and iOS . - Long-term plans include expanding InterMine to become a cloud-based service with a guided user set-up wizard so non-technical users can easily analyse their data. - We have a registry of production InterMine instances around the world.

Opportunities to learn and grow: As a member of a small team, you'll have the chance to learn and extend your skills significantly. Opportunities include: - interacting with a worldwide community of open-source contributors . - mentoring students through programs such as Google Summer of Code . - user testing your applications, both in person and via video conferencing. - presenting papers, posters, and talks at technical and academic conferences.

InterMine was founded in 2002 and is based at the University of Cambridge. We offer very competitive salaries and a generous benefits package (see for the full list):

Benefits: 33 days annual holiday, 37.5 hour working week, University Pension, child care and bike to work schemes, access to the University sports facility, family friendly benefits like maternity, paternity and parental leave, flexible working and career break schemes.

Fixed-term: The funds for this post are available until 28 February 2021 in the first instance.

To apply online for this vacancy, please click on the 'Apply' button below. This will route you to the University's Web Recruitment System, where you will need to register an account (if you have not already) and log in before completing the online application form.

for further information please email:

Please quote reference PC15074 on your application and in any correspondence about this vacancy.

The University values diversity and is committed to equality of opportunity.

The University has a responsibility to ensure that all employees are eligible to live and work in the UK.