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From Zika to wheat: Algorithms and software to help shed light into their evolution (HUBERKU18SCI)

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  • Full or part time
    Dr K Huber
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

The emergence of antibiotic-resistant bacteria (e.g. MRSA) and herbicide-resistant weeds as well as new and dangerous organisms such as the zika virus [I] poses major challenges for society ranging from public health to biodiversity protection and securing the food supply. An important stepping stone in the development of strategies to help tackle them is to understand how they have evolved. The development of powerful algorithms and software tools to describe and understand the evolution of species, populations and individuals is the main objective of the burgeoning area of phylogenetics which lies at the interface of computer science, mathematics, and molecular biology.

Firmly embedded within computer science, the PhD project is concerned with the development of cutting edge algorithms and software for phylogenetic network reconstruction (essentially rooted directed acyclic graphs) [ii] and thus is a software engineering project in nature. It combines elements from e.g. graph theory and combinatorics with the expertise of the primary supervisor (see e.g. [iii] – [v] and, more generally, the supervisor’s website www2.cmp.uea.ac.uk/~kth/Publications/publications.html) in phylogenetic network reconstruction to obtain powerful software solutions capable of dealing with big data. The successful applicant will have a good background in computer science or a related area. Biological knowledge is however not required.

Informal enquiries concerning the project are welcomed by the primary supervisor ([Email Address Removed]).

Interviews will be held w/c 22 January 2018.

For more information on the supervisor for this project, please go here: https://www.uea.ac.uk/computing/people/profile/k-huber
Type of programme: PhD
Start date of project: October 2018
Mode of study: Full time

Acceptable first degree: Computer Science, Mathematics
The standard minimum entry requirement is 2:1.

Funding Notes

This PhD project is in a Faculty of Science competition for funded studentships. These studentships are funded for 3 years and comprise home/EU fees, an annual stipend of £14,553 and £1000 per annum to support research training. Overseas applicants may apply but they are required to fund the difference between home/EU and overseas tuition fees (in 2017/18 the difference is £13,805 for the Schools of CHE ,PHA & MTH(Engineering), and £10,605 for CMP & MTH but fees are subject to an annual increase)

References

(i) Homologous recombination of Zika viruses in the Americas. J.-F. Han, T. Jiang, Q. Ye, X.-F. Li, Z.-Y. Liu, C.-F. Qin, Journal of Infection, 2016, 73(1) 87-88.

ii) ReCombinatorics: The Algorithmics of Ancestral Recombination Graphs and Explicit Phylogenetic Networks. D. Gusfield. MIT Press, 2014.

iii) Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets, K.T. Huber, L. van Iersel, V. Moulton, C. Scornavacca, T. Wu. Algorithmica. (DOI: 10.1007/s00453-015-0069-8).

iv) Reconstructing (Super)trees from data sets with missing distances: Not all is lost, G. Kettleborough, J. Dicks, I.N. Roberts, K.T. Huber. Molecular Biology and Evolution. 36(6) 1628-1642.

(v) Beyond representing orthology relation by trees, K.T. Huber, G.E. Scholz. Algorithmica, DOI 10.1007/s00453-016-0241-9


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