VACATION STUDENTSHIP IN BIOINFORMATICS
Applications are invited for a vacation studentship working on a project using a BioModelAnalyzer (BMA), which is a novel tool for the creation of abstract computer models of regulatory networks. The models created are discrete high-level description of the behaviour of a network, where every component is associated with a state (such as high-medium-low-off) and components change their state over time according to interaction rules between components. BMA enables the user to elaborate such models in a user-friendly way without requiring the user to explicitly write code. It also supports some analysis options for the models that are automatically created from dragging and dropping objects onto a canvas.
In this project the student will connect the BMA with existing work on network motifs and known network elements common in cell biology. The goal is to create BMA models of known network motifs representing a mechanistic understanding of biology as building blocks corresponding to specific behaviours.
The student will work under the supervision of Dr Ben Hall at the MRC Cancer Unit to elaborate these building blocks. It will be performed in collaboration with Dr Jasmin Fisher (Microsoft Research Cambridge and Department of Biochemistry, University of Cambridge), Dr Claus Bendtsen (Astra Zeneca Cambridge), and Dr Nir Piterman (Department of Computer Science, University of Leicester).
The papers listed below introduce models of elements such as bi-stability switches and negative feedback amplifiers. These building blocks are traditionally described by ODE models.
Tyson et al. (2003), Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signalling pathways in the cell http://www.ncbi.nlm.nih.gov/pubmed/12648679
Markevich et al. (2004), Signalling switches and bi-stability arising from multisite phosphorylation in protein kinase cascades http://www.ncbi.nlm.nih.gov/pubmed/14744999
Kholodenko et al. (2010), The Mammalian MAPK/ERK Pathway Exhibits Properties of a Negative Feedback Amplifier http://stke.sciencemag.org/content/3/153/ra90.abstract
Ahmed et al. (2014), Data‐driven modelling reconciles kinetics of ERK phosphorylation, localization, and activity states http://msb.embopress.org/content/10/1/718.long
The vacation studentship is available for between 8-12 weeks and funded by the Royal Society. Students will receive a maintenance grant (stipend) of £180 per week.
Applications should include a covering letter and a full CV.
Please email your application to: firstname.lastname@example.org by 3 June 2016.