Developing population genomic tools for analyzing next-generation sequencing data

Supervisors: Dr Kai Zeng, Dr Jon Slate

Key words: population genomics, next-generation sequencing, Drosophila, evolution, natural selection, bioinformatics

Summary: Following the widespread application of next-generation sequencing technologies, huge amounts of DNA polymorphism data are being rapidly generated in many different species, providing an unprecedented opportunity to address questions about evolution that would otherwise be impossible to tackle by small-scale datasets. The aim of this project is to develop cutting-edge population genomic methodology for analyzing next-generation sequencing data, and apply them to the Drosophila melanogaster (a popular model organism) polymorphism dataset recently released by the Drosophila Population Genomics Project (DPGP), which contains more than 100 D. melanogaster genomes. The project is entirely computer-based, and will involve the following tasks: (1) methodology developments, which will involve extending the parameter estimation methods that our group developed recently, and formulating new methods where necessary; (2) data processing, which will involve downloading and extracting data from the DPGP dataset and relevant databases such as FlyBase; (3) data analysis, which will involve applying the newly developed methods to the curated dataset, in order to obtain reliable estimates of parameters that govern the evolution of D. melanogaster such as mutation rates and intensity of natural selection. The project is multi-disciplinary, and the student will receive plenty of training in bioinformatics, computer programming, and statistics. Applications are encouraged from students with backgrounds in any of the following disciplines: biology, computer science, statistics, and mathematics.

For more information about how to apply, or the application process, please contact Mrs S Carter (s.a.carter@sheffield.ac.uk).

To apply now go to: http://www.sheffield.ac.uk/postgraduate/online